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Oseltamivir and Severe Influenza - A Need for Complementary Drug Therapeutics

Tue, 22 Jul 2025 16:34:39 GMT

Oseltamivir (Tamiflu) is an antiviral medication used to treat influenza (flu) . It works by blocking neuraminidase on the surface of influenza viruses, preventing the virus from leaving infected cells and spreading to new cells, thereby inhibiting the influenza virus's ability to spread within the body. Oseltamivir is most effective when started within 48 hours of symptom onset. It can reduce the duration and severity of influenza symptoms, and it may also reduce the risk of lower respiratory tract complications.

Current WHO guidelines recommend against the use of oseltamivir for patients with non-severe (uncomplicated) influenza , but conditionally recommend the use of oseltamivir for patients with severe (complicated) influenza , including infection with novel influenza A viruses associated with high mortality, or unknown risk of severe disease . In the UK, NICE and UKHSA guidelines do not indicate use of oseltamivir in people who were previously healthy, unless the person is at significant risk of developing serious complications from influenza. Older adults, pregnant women, people who are immunosuppressed and those with certain chronic health conditions fall into this latter category. In the US oseltamivir treatment is recommended for all patients hospitalized with severe influenza regardless of illness duration, with its use in uncomplicated influenza left to clinical judgement .

In the case of severe influenza, a 2021 observational study reported that early (within 48 h) oseltamivir treatment was associated with improved survival rates in critically ill patients with influenza pneumonia , and may decrease ICU length of stay and mechanical ventilation duration. However, a 2024 systematic review and network meta-analysis of 73 trials involving 34,332 participants, concluded that oseltamivir had little or no effect on mortality and admission to hospital, likely had no important effect on time to alleviation of symptoms, and likely increased adverse events related to treatments. Although the validity of the analysis has been questioned , the findings have informed WHO guidelines.

A recent 2025 study retrospective cohort study using target trial emulation of 11 073 patients hospitalized for severe influenza found that patients treated with oseltamivir were less likely to die in hospital, more likely to be discharged alive earlier, less likely to be transferred to the ICU, and less likely to be readmitted to hospital after discharge. The absolute risk reduction for mortality was −1.8%, so the effect was small but clinically significant in terms of benefit in severe influenza.

Whilst clinical guidelines recommend the use of oseltamivir in patients hospitalised with severe influenza, the studies above indicate that the effects on mortality are modest. As a result, there is still a need for therapeutic interventions that can decrease mortality and reduce the duration of hospitalisation. The p38MAPK inhibitor POLB001 has great potential to do this, particularly as it does not affect the antiviral activity of oseltamivir, so it can be given to patients concurrently.

Biologic Therapies In COPD Exacerbations

Wed, 09 Jul 2025 16:03:58 GMT

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COPD exacerbations are periods where patients with COPD experience worsened symptoms , characterised by sudden increases in breathlessness and cough, and changes in sputum production (amount, colour, and/or thickness). Respiratory infections (caused by viruses or bacteria), environmental pollutants, smoking, or even changes in weather, can trigger exacerbations in COPD patients. Smoking cessation, vaccination, and management of other health conditions can help reduce the frequency and severity of exacerbations.

Recognizing the early signs of exacerbations, so that medical attention can be sought promptly, is key to the effective management of exacerbations and preventing complications. Treatment of exacerbations can range from the use of bronchodilators, corticosteroids and antibiotics, to oxygen therapy, and even mechanical ventilation in hospital.

Although type 1, neutrophilic inflammation of the lungs is a prominent feature of COPD, with increased neutrophil levels correlating with lung function decline and disease progression , between 20% and 40% of COPD patients exhibit a prominent type 2, eosinophilic inflammation in their lungs, which is considered a distinct phenotype within COPD that increases exacerbation risk. As a result, biologics which target type 2 inflammation are now emerging as a new class of therapies for COPD exacerbations.

Dupilumab , a fully human monoclonal antibody, which blocks the shared receptor component for interleukin-4 and interleukin-13 (key drivers of type 2 inflammation), has recently been approved by the US Food and Drug Administration(FDA) for use in treating patients with uncontrolled COPD and an eosinophilic phenotype. In clinical trials, COPD patients with type 2 inflammation (as indicated by elevated blood eosinophil counts), who received dupilumab had fewer exacerbations, better lung function and quality of life, and less severe respiratory symptoms than those who received placebo.

More recently, a phase 3 randomised trial found that the humanised monoclonal antibody mepolizumab reduced COPD exacerbations by targeting the cytokine interleukin 5 (IL-5) , which plays a central role in eosinophilic inflammation. Patients with COPD, a history of exacerbations, and a high eosinophil blood count received monthly injections of either mepolizumab or a placebo, in addition to continued background treatment with triple inhaled therapy. Treatment with mepolizumab led to a lower annualized rate of moderate, or severe exacerbations, when added to background triple inhaled therapy . The FDA has now approved mepolizumab as the first once-monthly biologic for COPD with eosinophilic phenotype.

COPD is a complex disease with various inflammatory pathways , so the use of biologic therapies to target specific inflammatory pathways in COPD patients is a significant advancement in disease treatment . Biologics offer a new way to target specific types of inflammation, potentially improving lung function and reducing exacerbations in certain COPD patients, and are typically used as an add-on treatment to existing therapies like inhaled corticosteroids, long-acting bronchodilators, and other medications . The therapeutic goals of biologics remain the same as with other treatments for COPD: restoration of normal inflammatory response; and alteration of disease progression. The best biologic for a specific patient will depend on their individual characteristics and the type of inflammation driving their COPD. Ongoing research is exploring the potential of various biologics for COPD , including those targeting other inflammatory pathways.

Phage Therapy Safety

Mon, 09 Jun 2025 16:27:40 GMT

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Animal studies in sheep and mice , as well as evidence from trials in humans and case studies of compassionate clinical use, indicate that phage therapy is efficacious, safe , and non-toxic . A 2022 systematic review of clinical data obtained from phage therapy clinical trials, safety trials, and case studies between 2000 and 2021 for difficult to treat bacterial infections in several medical disciplines, concluded that phage therapy given via different routes of administration is well tolerated and safe with a low incidence of side effects. Unfortunately, heterogeneity between different clinical studies precluded a meta-analysis of the data, highlighting the need for high quality clinical trials to improve knowledge on long-term patient and disease outcomes.

The use of purified phage to treat superficial bacterial infections appears to be efficacious safe, and side effect free, even when delivered by invasive routes of administration (e.g. intravenous and intra-articular ), or used in immunocompromised patients. Some would argue that phage therapy appears to have a better safety profile than antibiotics , and has a minimal impact on commensal flora , thus reducing the likelihood of opportunistic infections. Consistent with our natural exposure to phages, there are no reports of allergic responses to phages, potentially making them suitable alternatives for patients with antibiotic hypersensitivity.

Because phages can kill bacterial cells quickly , release of endotoxins from lysed bacterial cells in severe infections is a potential safety concern. However, it has been demonstrated that phage lysis releases less endotoxin than beta-lactam antibiotics.

Another potential issue with phage therapy is that phage cocktails might have effects on non-targeted bacteria and so affect the human microbiome. However, phage therapy does not appear to have an adverse effect on gut microbiota and has less of an effect on gut diversity than antibiotics, having a beneficial effect on gut health.

Studies have suggested that bacteriophages can interact with eukaryotic cells, significantly influencing the functions of tissues, organs, and systems of mammals, including humans.

In addition, there are concerns regarding the long-term impact of phages on the human immune system. In terms of effects on innate immunity , phages appear to induce anti-inflammatory responses. In terms of effects on the adaptive immune response , phages can be immunogenic, but are not very effective at inducing a specific immune response. With regards to phages inducing anaphylaxis , no cases have been reported. Autoimmune responses to phage therapy are a possibility, however, their immunomodulatory role, particularly in curbing inflammation means that phage therapy is being explored for the treatment of autoimmune liver diseases .

Although the indications are that phage therapy is safe, with few adverse effects, current research on phage safety monitoring lacks sufficient and consistent data for regulatory purposes, which would require a standardized phage safety assessment to ensure a robust evaluation of the safety profile of phage therapy. Although the Australian STAMP protocol is not a randomised clinical trial, it does provide a framework for the collection of higher quality efficacy and safety data than individual case studies.

Phage Therapy in the UK and Other Countries

Sun, 08 Jun 2025 09:46:47 GMT

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In this second article about phage therapy, I will be focussing on its use in different countries, with special emphasis on the UK.

Phage Therapy in the UK

In the UK, phages are classed as a biological medicine and none are licensed for clinical use. As a result, phage therapy is applied on a compassionate use basis as an unlicensed medicinal product (a “ special ”). Phages imported for use as an unlicensed medicine in the UK do not need to be manufactured according to Good Manufacturing Practice ( GMP ), however, the Medicines and Healthcare products Regulatory Agency ( MHRA ) must be notified at least 28 days prior to importation, and doses imported are limited to a small number. Paradoxically, phages manufactured in the UK must be produced to GMP, including phage for use in clinical trials. As a result, the current clinical provision of phage therapy in the UK is ad hoc and relies heavily upon networking with international sources of phages , including organisations such as Phage Directory , who help connect clinicians who want phages for clinical use, with groups who have appropriate phages. The MHRA recently published a document on the regulatory considerations for therapeutic use of bacteriophages in the UK.

According to Phage-UK there have been 24 clinical trials involving phage therapy since 2020.

Phage Therapy in Other Countries

Globally, different countries have different regulatory frameworks for the clinical use of phage therapy.

Eastern European countries have over 100 years of phage therapy experience. Russia and Ukraine allow open use and commercialisation of phage products. Phages are a standard medical application in Georgia . In Poland , specialised institutes have supplied personalised phage products to physicians since 2005.

In the European Union (EU) , phage therapy is not approved as a standard medicinal product for human use. Like the UK, It is primarily used in compassionate use cases, clinical trials, or for individual experimental therapy attempts. Although a European Medicines Agency (EMA) guideline exists for veterinary bacteriophage medicinal products , there is currently no corresponding regulatory guidance for human use of such products in the EU. The EMA opened a public consultation on a concept paper on the development and manufacture guidelines for human bacteriophage medicinal products tailored to phage therapy on 23 ^rd December 2023, which ended on 31 ^st March 2024. In the meantime, a regulatory roadmap for phage therapy under EU pharmaceutical legislation has been published .

Belgium has implemented a phage therapy framework focusing on magistral phage preparations that allows patients to actively seek access to personalized phage therapy. In the magistral approach , individual phages are prepared according to a phage monograph (a standardized document that provides detailed information about a specific bacteriophage, its properties, and its potential use in phage therapy), and reference laboratories provide quality control (QC) testing. Clinicians prescribe phage cocktail preparations for use in specific patients, which are then prepared by pharmacists. Based on the Belgian model, a general chapter on phage therapy medicinal products was published in 2024 by the European Pharmacopeia .

In Australia , all clinicians and researchers within the Phage Australia network have adopted the Standardised Treatment and Monitoring Protocol for Adults and Paediatric Patients ( STAMP ). STAMP is a clinical protocol for administering and monitoring phage therapy, rather than the phage product. As a result, STAMP looks at the process, not the product and means that different patients can be treated with different phages at different sites of infection, but the treatment protocol is standardised. The STAMP protocol has been approved by Australia's national ethics committee and endorsed by Australia's national infectious disease physician society, as well as its paediatric arm.

In the US , phage therapy is not yet an FDA licensed treatment. However, it available under a special programme called the “ expanded access eIND system ” . For patients who have exhausted standard-of-care therapy, an application is submitted to the FDA by the treating physician, where a patient meets a list of criteria. UC San Diego's IPATH is the first dedicated phage therapy centre in North America. They focus on treating patients with life-threatening multi-drug resistant infections through the FDA's compassionate use program. IPATH also works to advance phage therapy into clinical trials and provides guidance to physicians worldwide on phage therapy protocols. The PhagesDB database details over 25,000 new phages identified by the SEA-PHAGES programme at the University of Pittsburgh. One particular phage from this collection, called Muddy, has been used therapeutically in a cystic fibrosis patient infected with a multi-drug resistant strain of Mycobacterium abscessus. Creative Biolabs is developing libraries of characterised phages, as sell as platforms for identifying and then producing phages to GMP standard for formulation and delivery.

Israel focusses on compassionate use of phage therapy, with the Israeli Phage Therapy Center conducting all of the steps required, from phage isolation and characterization to treatments for non-resolving bacterial infections.

In India , phage therapy is offered as compassionate Phage Therapy regulated by the Declaration of Helsinki and coordinated by the Central Drugs Standard Control Organization. Vitalis Phage Therapy has created a framework for patients to access phage therapy in India.

In China , there are two routes to using phage therapy applications. Phage products with fixed ingredients are regulated as innovative biological products . Personalized phage therapies, on the other hand, need to go through investigator-initiated trials (IIT) and, if successful, the phage therapeutic can then be used at certain institutions.

Expanding the Use of Phage Therapy in the UK

To progress past the ad hoc use of phage therapy in the UK, the infrastructure to support the route from patient enrolment, through isolation and identification of pathogenic bacteria and therapeutic phages, to formulation, administration and monitoring of efficacy, as well as phage resistance, will need to be put in place. A key requirement for clinicians in the UK will be the ability to access phages that are efficient at killing the strain of bacteria causing an infection. A roadmap for the delivery of clinical phage therapy to the UK has been proposed, which would require: expansion of existing phage biobanks; the development of both personalised treatments for individual patients; and off-the-shelf phage cocktails that could be used to treat large numbers of patients.

Innovate UK has developed the Phage Innovation Network to help drive the use of phage based therapy in the UK and build on the expertise of the many phage experts based in the UK. To enable this, systematic libraries of a diverse array of phages that are well characterised and curated, as well as manufactured to GMP standard will be needed.

The Citizen Phage group at Exeter University , uses volunteer citizen scientists to collect samples from a wide range of environments to facilitate the laboratory identification of new phages for therapeutic use.

The UK Phage Library at the University of Leicester is aiming to develop libraries of phages which can be screened against specific bacterial strains to identify phages they are sensitive to. Unfortunately, these phages cannot be used in patients in the UK due to lack of GMP phage manufacturing capability, but they are provided for use in other countries whose regulatory frameworks permit their use.

On the commercial side, Nexabiome in Glasgow aims to provide an end-to-end service covering phage identification and isolation, to production and formulation.

Establishing a UK Phage Manufacturing Facility that can produce phage preparations for both commercial and non-commercial customers that are suitable for administering to patients would be a key requirement for widening the use of phage therapy in the UK. Towards this end, UK Phage Therapy is working with public and private partners to establish a centralised phage susceptibility testing and GMP phage production facility in the UK via the Centre for Process Innovation (CPI) . The Centre for Phage Research is also working with regulators, policymakers and other stakeholders to establish frameworks and pathways to enable public access to phage products. Whether the UK will remove the requirement for GMP manufacture of phages for Phase I clinical trials, as is the case in the US, is unclear. However, phase II/III trials would still require GMP manufacture for off-the-shelf phage products.

Phage-UK has developed a standardised protocol for the treatment and monitoring of phage therapy in UK patients suffering from cystic fibrosis and bronchiectasis , where there is no alternative treatment available. The protocol, based upon the Australian STAMP protocol, is a document that assists clinicians making a submission to their NHS Hospital Board for approval to use phage therapy on a named patient basis. Presumably, this protocol could be adapted for the treatment of UK patients with other serious infections such as urinary tract infections (UTIs), prosthetic joint infections (PJIs) and sepsis. A benefit of using such a standardised protocol would be the collection of safety and efficacy data on phage therapy that could then inform the design of subsequent clinical trials of phage therapy in the UK.

Conclusion

For most countries, compassionate use is the major pathway for patients to access phage therapy. Belgium (with the magistral approach), and Australia (with STAMP), currently lead the way in developing frameworks to facilitate patient access to phage therapy. The lack of such frameworks in other countries, including the UK, reflect the view that phage therapy is still an experimental treatment that requires more convincing clinical evidence of efficacy. In the UK, it will be interesting to see if any of the recommendations made in the March 2024 Policy Paper on the antimicrobial potential of bacteriophages, published under the Conservative government in power at the time, are followed up by the current Labour government.

Phage Therapy as an Approach to Treating Antibiotic-Resistant Infections

whittp163@gmail.com (Paul Whittaker) — Tue, 03 Jun 2025 19:45:27 GMT

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The growing global problem of antibiotic resistance , and the lack of new antibiotics being developed, has rekindled an interest in phage therapy: the use of viruses (bacteriophages) that specifically target and kill bacteria, as a treatment for antibiotic resistant infections in humans.

This article is an overview of phage therapy and is the first in a series where I will explore aspects of this technology in greater detail. Links to papers and websites that contain diagrams or graphics relevant to this article are provided at the end of this article, as are links to PubMed search results for phage therapy papers, reviews and clinical trials.

Bacteriophages

In 1986, nanotechnology pioneer K. Eric Drexler imagined a dystopia where invisible self-replicating nanobots proliferated voraciously and took over the entire planet. Spooked by Drexler’s nightmare, Prince Charles (the heir to the British throne at the time, but now King Charles III) requested that the eminent Royal Society investigate the risks that nanotechnology posed. However, the reality is that nano-scale self-replicating voracious killers have existed on earth for over 4 billion years. They can make hundreds of copies of themselves in as little as 15 minutes, and are found in vast numbers everywhere on our planet. Thankfully, they are not harmful to humans. Instead, they infect and destroy bacteria in a process perfected over the eons. Known as bacteriophages , these biological entities were discovered at the beginning of the twentieth century.

Bacteriophages (usually referred to as phages - derived from the Greek word “phagein”, meaning “to devour/eat”) are viruses composed of a nucleic acid genome encased in a phage-encoded protein capsid shell. Phages are found in three basic structural forms : icosahedral head with a tail; icosahedral head without a tail; and filamentous. They infect and kill bacteria by replicating inside bacterial cells, then breaking open ( lysing ) the infected cells before releasing large numbers of new progeny phage particles. In the laboratory, this process is visualised and monitored using plaque assays .

Phages are ubiquitous and diverse . It has been estimated that there are 10 ³¹ bacteriophages on the planet, more than every other organism on Earth, including bacteria. Phages can be isolated from sources where high numbers of bacteria occur, such as human sewage , soil , rivers , faeces , even slime in a stream . Phages are specific to individual bacterial species and strains and do not infect mammalian cells. However, because of the microbiome , the human body contains large numbers of phage particles and varieties of phages (the so called phageome ) and, as a result, phage can interact with mammalian cells.

Phages are fascinating biological entities. As an undergraduate biology student I learned of the importance of phages as key experimental tools in the development of the fields of molecular genetics and molecular biology. As a post-graduate biochemistry student I worked with phages in the lab of the late Pauline Meadow , who used them as a way of identifying lipopolysaccharide (LPS)-defective mutants of Pseudomonas aeruginosa. As a doctoral student in molecular biology working on DNA methylation in the slime mould Physarum polycephalum, and as a postdoctoral researcher working on human genome analysis, I used phage lambda cloning vectors to construct genomic DNA libraries for gene isolation (e.g. tubulin genes from the parasite Trypanosoma brucei) and for the physical mapping of human genomic DNA (e.g. the human dystrophin-encoding gene using a specially modified phage lambda vector I developed).

The Challenge of Bacterial Anti-Microbial Resistance

More widely referred to as anti-microbial resistance , or AMR , bacterial AMR (bAMR) occurs when bacteria develop the ability to defeat the antibiotics designed to kill them. This resistance can result from several different mechanisms . I n this article I am referring specifically to bAMR, and not viral, fungal, or parasitic AMR .

A systematic analysis published in 2022 estimated that there were 4.95 million deaths associated with bAMR globally in 2019. As a result, bAMR has the potential to affect each and every one of us by impacting the treatment of illnesses, surgical procedures and cancer treatment, as well as increasing rates of death. The increase in prevalence of bAMR has led to fears of future pandemics caused by drug-resistant bacteria. In the UK, the Government and the National Health Service (NHS) have both developed action plans to tackle bAMR which emphasise optimising and reducing exposure to antibiotics. Despite these measures, however, new antibiotics and alternatives to antibiotics are still needed, particularly in cases where infections are refractory to antibiotic use.

Developing new classes of antibiotics is challenging . The greater portion of recently approved antibiotics have tended to be derivatives of existing classes of drug compounds. Although pharmaceutical giant Roche recently reported the identification of a promising new class of antibiotic molecules that target carbapenem-resistant Acinetobacter baumannii (CRAB), many big pharma companies have ceased antibiotic development. As a result, small biotech companies are leading research and development efforts in this area.

Phage Therapy

Case studies in the scientific literature , and success stories described in the press and in books have highlighted the use of phage therapy to treat infections caused by antibiotic-resistant bacterial strains. However, phage therapy as a way of treating bacterial infections is not new. Phages were first used to treat bacterial infections in 1919 (the “pre-antibiotic era”), but the approach never really gained traction in the West, particularly after penicillin was discovered in 1928 and became the favoured way to treat bacterial infections in the 1940s. Despite this, phages have continued to be used in Russia , Georgia and Poland as an alternative to antibiotics since the early 20 ^th century . The excellent book “The Good Virus” by Tom Ireland, gives a vivid and detailed account of the history of phage therapy and how interest in it as an approach to treating bacterial infections has waxed and waned over the past century.

Now, because of the growing threat of bAMR, there has been a resurgence of interest in using phages to tackle antibiotic resistant infections. As some phages degrade biofilms, phage therapy also potentially provides a way to deal with the antibiotic tolerance seen in some chronic diseases resulting from biofilm production (e.g. cystic fibrosis ). Also of interest is the potential to use phage resistance as a way to steer bacteria towards an antibiotic-sensitive phenotype.

Unfortunately, in many parts of the world current regulations restrict the application of phage therapy to individual 'compassionate use ' in patients with infections where antibiotics have failed. In the UK phage therapy has been used sparingly to treat Pseudomonas and Mycobacterial infections mainly due to the lack of sustainable access to phages manufactured to good manufacturing practice ( GMP ) standard. The first successful clinical trial of phage therapy in the UK was published in 2009. Since then, phage therapy has been used in the treatment of patients with diabetic foot ulcers and cystic fibrosis .

There has often been a difference between the results of individual real world case reports of successful phage therapy and the results of larger scale studies. Therefore, high quality clinical trials of phage therapy in the treatment of a range of conditions are needed to provide a solid evidence base on the efficacy and safety of phage therapy in human patients to support wider clinical use. A retrospective observational analysis of 100 consecutive cases of personalised phage therapy carried out by a Belgian consortium using combinations of 26 bacteriophages and 6 defined bacteriophage cocktails reported clinical improvement and eradication of targeted bacteria for 77.2% and 61.3% of infections, respectively. However, eradication was 70% less when antibiotics were not used concurrently.

Recently, there have been calls for the British Government to invest in phage therapy as a way to tackle bAMR. As a first step, a report published in January 2024, following a Parliamentary Inquiry in 2023, recommended that the British Government bring together phage experts and stakeholders (scientific, clinical and regulatory) to assess what would be required to enable phage therapy to be used more widely in the National Health Service (NHS) and other UK healthcare settings. A Government response to this report which supports these recommendations and makes 18 additional recommendations across 4 themes, has now been published . The Innovate UK Phage Knowledge Transfer Network has been established to provide a forum for funders and phage researchers to discuss these matters and ways forward, including multi-party collaborations and co-investments by public and/or private funders.

Discussion

The dramatic results seen in sick people who have received phage therapy as a last ditch treatment when conventional antibiotic therapy has failed, provides a compelling narrative for its potential in the treatment of bAMR. However, the body of evidence required to convince regulatory authorities, governments and the medical establishment of phage therapy efficacy is clearly lacking at the moment. Even if that data is forthcoming, it is unlikely that phage therapy will ever replace antibiotics. More likely, phage therapy will continue to be used in a personalised way to treat infections that are resistant to standard antibiotic therapy, but in the future it is reasonable to envisage clinical scenarios where phages might be used in conjunction with antibiotics. The judicious use of phages might help protect and preserve existing antibiotics and combining the two appears to be more effective than either on their own. Phage therapy may also be useful for treating people who are allergic to antibiotics and may not have other treatment options.

It is, of course, entirely possible that phage therapy for humans never progresses past the stage it is at now. Maybe new classes of antibiotics will be discovered. Maybe other antimicrobial therapeutic modalities will be invented, or discovered. Hopefully, though, the many initiatives taking place worldwide will result in the development of a safe and clinically proven version of phage therapy that will become part of an expanded therapeutic toolkit. However, what is clear at present is that while these challenges are being tackled, phages are already being deployed in various animal and non-medical scenarios such as food safety and environmental pathogen control (e.g. aquaculture ).

As I explored the extensive literature around phage therapy , I realized that I could only scrape the surface of this subject in such a short article. But it is a fascinating field with therapeutic potential. Therefore, in later blog articles, I will discuss aspects of phage therapy; such as safety, phage production, commercialisation, and the regulatory approaches to using phage therapy in different countries round the world, including the UK, in more detail.

Links to websites and papers with relevant diagrams and graphics:

PubMed literature links:

Moving Beyond Airway Obstruction in Chronic Obstructive Pulmonary Disease

Wed, 28 May 2025 14:02:25 GMT

The importance of lung structural abnormalities

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Around 400 million people globally have chronic obstructive pulmonary disease (COPD) , making it a leading cause of disability and death . By 2050 the number is projected to approach 600 million cases. Approximately 70% of cases of COPD are a result of smoking and around 20% of smokers develop COPD . COPD is a heterogeneous disease which results from a subtle interplay between environmental factors (e.g. smoking) and genetic suceptibility factors (not clearly defined), so how COPD manifests in different patients is important to understand.

Therapeutic options for COPD are limited to mostly symptomatic treatments . There are currently no disease-modifying, or curative therapies for COPD. In addition, there is an absence of reliable biomarkers that can guide clinical decision making and enhance the precision of COPD patient classification.

Current recommendations for COPD diagnosis (e.g. GOLD ) emphasise the presence of airflow obstruction in the lung, measured using spirometry , which is not reversed after administration of a bronchodilator. However, spirometry is not particularly sensitive to structural changes such as airway wall thickening and emphysematous changes that often occur in the lung before airflow obstruction is evident and measurable.

A new COPD classification which moves beyond just using airflow obstruction and uses a multidimensional framework, has been proposed by Bhatt et al . using longitudinal tracking data from the COPDGene and CanCOLD patient cohorts.

Using a combination of major (airflow obstruction) and minor criteria (imaging and symptom based factors), this diagnostic model aims to provide a more holistic view of the disease. Airway wall thickening and emphysematous changes are visualised using computed tomographic (CT) scans. Dyspnea , reduced quality of life , and the presence of chronic bronchitis form the symptom-based criteria. To qualify for a COPD diagnosis, a patient must meet 1 major and at least 1 minor criterion or , in the absence of airflow obstruction, at least 3 of the 5 minor criteria.

Strikingly, the classification scheme does not require airflow obstruction for a diagnosis of COPD. Nor is the presence of airway obstruction alone regarded as being an automatic confirmation of a diagnosis of COPD. This is a diagnostic shift; acknowledging that patients who do not meet the threshold for airflow obstruction can still have COPD pathology and symptoms. In cases where COPD patients have co-morbidities that could explain the COPD symptoms, CT Imaging data is prioritised in the minor criteria.

This refined diagnostic model adds nuances to the complexity of COPD diagnosis. An important finding was that a larger proportion of Black individuals were newly classified as having COPD compared with White individuals, a finding consistent with other studies . However, it is unclear at this stage how well this classification will apply to COPD patients who have not been smokers.

When I worked at Novartis, I was lucky enough to be invited along to several COPDGene meetings in 2007 and 2008 when patient recruitment and phenotyping was in the early stages. At the time I was impressed by the leadership of James Crapo and Ed Silverman and the commitment of the many medical and scientific teams involved in COPDGene. Longitudinal studies such as this are a major undertaking, so it is good to see tangible outcomes that will impact the future diagnosis of COPD.

Calming the Cytokine Storm in Severe Influenza and Cancer Immunotherapy

Tue, 20 May 2025 16:50:05 GMT

Targeting p38MAPkinase

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In my April 2020 blog article I referred to work I led at hVIVO aimed at identifying immunomodulatory drug targets for the treatment of influenza-infected patients hospitalised with severe symptoms. This work resulted in two patent applications . The first, covered the use of a broad class of p38MAPK inhibitors (Immunomodulator I); the second, covered a clinically tested oral p38MAPK inhibitor (Immunomodulator II) as a treatment for patients with severe influenza triggered by a hyper-inflammatory response characterised by extended release of enhanced levels of cytokines, a phenomenon variously known as hypercytokinaemia (HC), cytokine storm (CS), or cytokine release syndrome (CRS).

The drug covered by the Immunomodulator II patent, HVO-001, was acquired by Poolbeg Pharma Plc in 2021 and renamed POLB 001. Patents have subsequently been granted in the EU, US and Japan for the Immunomodulator I application, and in the US and South Korea for the Immunomodulator II application. The Immunomodulator I and II patents are owned by Poolbeg who have continued development of POLB 001 for use in the treatment of hypercytokinaemia in patients with severe influenza. In addition, Poolbeg are also developing POLB 001 as a treatment for cancer patients who develop CRS following CAR-T cell immunotherapy .

Poolbeg's expansion of POLB 001 into the treatment of CRS in cancer immunotherapy is an interesting approach to a potentially life-threatening condition that affects a significant number of patients receiving certain bispecific antibody and CAR-T cancer immunotherapies, and for which there are no approved therapies for CRS prevention, and few approved for CRS management in patients. Monitoring patients at risk of CRS can require a week or more of hospitalisation. By attenuating cytokine release, POLB 001 has potential as a therapy for treating CRS in cancer patients undergoing immunotherapy.

Given that the presence of a hyper-inflammatory response is a key feature of severe influenza , severe COVID-19 , hemophagocytic lymphohistiocytosis (HLH and, as mentioned above, cancer immunotherapy , it is important to ask if hypercytokinaemia shares a common underlying mechanism in different disease settings? This question is particularly relevant when considering whether POLB 001 can be effective in modulating CAR-T therapy-induced CRS, as well as CS in severe influenza.

A recent paper in The Journal of the American Medical Association by Long et al . looked at how clinical patterns and outcomes in CS/CRS vary in CAR-T, COVID-19, and malignant neoplasm–associated HLH (MN-HLH). This study of 671 patients identified distinct inflammatory patterns and survival outcomes among the 3 cohorts with CS. Interestingly, cluster analysis revealed overlapping patterns between CS in COVID-19 and CRS in CAR-T, while CS in MN-HLH formed a separate cluster with the worst survival rates. T hese findings suggest that CAR-T CRS and COVID-CS share similar cytokine activation pathways, while MN-HLH operates differently.

As COVID-19 and influenza infections share many similarities and differences , the findings of the Long et al. paper do not directly indicate that POLB 001 could have utility in CAR-T therapy-induced CRS. But I think it is reasonable to be cautiously optimistic at this stage. Clearly, phase 2 clinical trials of POLB 001 in severe influenza and CAR-T CRS will be needed to provide definitive proof. I hope that Poolbeg Pharma are able to secure the necessary interest and funding to prove these concepts.

NOTE ADDED 28-May-2025: Poolbeg Pharma has been granted Orphan Drug Designation (ODD) by the US Food and Drug Administration for POLB 001, as an oral therapy to prevent CRS caused by T-cell engager bispecific antibodies. ODD is granted to treatments for rare diseases affecting fewer than 200,000 people in the US. The designation provides incentives relating to clinical trial costs, certain user fees, and up to seven years of market exclusivity following regulatory approval.

Beyond Vaccines: Tackling Severe Covid-19 Disease

whittp163@gmail.com (Paul Whittaker) — Sun, 18 Apr 2021 11:36:05 GMT

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SEVERE COVID-19 DISEASE

A round 20% of people infected with SARS-CoV-2 develop severe disease symptoms requiring hospitalisation and, in some cases, intensive care support for critical respiratory disease and/or multi-organ failure ( Fig. 1. ).

Fig. 1. COVID-19 symptomatology time course and approved drug treatments. COVID-19 symptoms become apparent around 5 days after initial virus exposure. Symptoms peak, on average, 5 days later and, for the majority (>60%) of people, COVID-19 symptoms are mild to moderate in severity. Although symptoms subside for 4 in 5 of these mild/moderate cases after another 5 days, 1 in 5 people can experience persistent symptoms for 12 weeks or more (long COVID). Twenty percent of infected individuals require hospitalisation with hypoxaemia caused by viral pneumonia. Of these hospitalised patients, 1 in 5 develop acute respiratory distress syndrome (ARDS) and/or multi-organ failure requiring intensive care. Up to 40% of critical care patients can die. Around 17% of infected people never develop any symptoms of COVID-19 at any time. So far, the only approved therapies are the anti-viral drug remdesivir and the immunomodulatory drugs dexamethasone and tocilizumab, used singly or in combination, for patients hospitalised with severe COVID-19. In randomised clinical trials remdesivir reduces time to recovery, whereas d examethasone and tocilizumab reduce mortality in hypoxaemic patients receiving oxygen support, as well as reducing time to recovery and/or mortality, particularly when used in combination. Abbreviations: p.o. – by mouth; and i.v. -intravenous

T he rollout of the AstraZeneca-Oxford and Pfizer-BioNtech SARS-CoV-2 vaccines is already having a major impact on the incidence of severe COVID-19 in the UK. Hopefully, similar effects will be seen as vaccines are rolled out in the EU and globally . However, despite the success in developing highly effective vaccines, there is still a need to develop other therapies. These include, antiviral drugs to directly target the SARS-CoV-2 virus, block virus entry/exit, or inhibit virus replication, as well as immunomodulatory drugs to prevent, or attenuate severe COVID-19. Developing these therapies is important given: vaccine hesitancy ; the proportion of people in the world who have still to be vaccinated ; and the continuing emergence of virus variants .

ANTI-VIRAL DRUGS

So far, remdesivir is the only anti-viral drug approved for treating Covid-19. Its use is limited to clinical settings ( Fig. 1. ), where it is reported to reduce time to recovery in hospitalised patients. A number of anti-viral drugs are currently being investigated for use in COVID-19. Interestingly, clinical trials of unapproved monoclonal antibody therapies in non-hospitalised adults with mild to moderate COVID-19 symptoms at high risk for progressing to severe COVID-19 have demonstrated reductions in hospitalisations and deaths. Potent, small molecule anti-viral drugs that could be given orally soon after symptom development , or after a positive RT-PCR test, to prevent hospitalisation in individuals at high risk of developing severe COVID-19, would be a valuable addition to the COVID-19 armamentarium.

IMMUNOMODULATORY DRUGS

Markers of inflammation are predictive of critical illness and mortality in COVID-19, and dysregulation of the host immune response is a key feature in individuals with severe disease, particularly those requiring critical care for COVID-19 ARDS . Analysis of data collected from COVID-19 patients already on immunomodulatory drugs for other diseases suggests that such drugs may provide protection from severe disease. In addition, a recent randomised controlled trial showed that early administration of the inhaled corticosteroid budesonide reduced the need for urgent medical care and reduced COVID-19 recovery time. Although children present with milder symptoms compared to adults, rare cases of a very severe multisystem inflammatory syndrome in children (MIS-C) have been reported . However, the hyper-inflammation observed in MIS-C differs from that seen in adults with severe COVID-19. Therefore, it may be that therapies for severe COVID-19 in adults and MIS-C may need to have different immunomodulatory profiles.

The value of immunomodulators in improving clinical outcomes in severe COVID-19 has been directly demonstrated by the RECOVERY trial. Administering the cheap and readily available corticosteroid dexamethasone to hospitalised severe COVID-19 patients with hypoxaemia ( Fig. 1. ) lowered mortality in those receiving invasive and non-invasive oxygen support, but not in non-hypoxaemic patients receiving no respiratory support. Although guidelines indicate reserving dexamethasone administration for patients requiring supplemental oxygen, a published study suggests that hypoxaemia should not be a trigger for dexamethasone usage unless the patient has been hospitalised for >72 hours. Key features in determining the timing of dexamethasone dosing are likely to be viral load and the level of inflammation in individual patients ( Fig. 2. ).

The RECOVERY trial also demonstrated that giving the more expensive humanized anti-human interleukin-6 (IL-6) receptor monoclonal antibody, tocilizumab , to patients hospitalised with severe COVID-19 ( Fig. 1. ) reduces the risk of death, shortens time until discharge, and reduces the need for mechanical ventilation. However, it is worth noting that there have been conflicting results from several randomised clinical trials of tocilizumab in COVID-19.

Importantly, the benefit s of tocilizumab are seen on top of those provided by dexamethasone . Combination treatment reduces mortality for hypoxic patients requiring non-invasive and invasive mechanical ventilation. As a result, UK and US clinical guidelines now recommend the use of tocilizumab and dexamethasone in the treatment of hypoxaemic patients with severe COVID-19 requiring ventilation, but not for patients without hypoxaemia, or with significant immunosuppression. Although the RECOVERY trial did not explore optimal timing, dose, or duration, data from a Spanish study indicates that administering tocilizumab in combination with dexamethasone at hospital admission results in better outcomes than giving it 24 hours later.

The impressive results using tocilizumab and dexamethasone currently set the standard for severe COVID-19 immunomodulatory therapies, however, there is still scope for the development of other classes of immunomodulators with different mechanisms of action and different (or superior) side effect profiles, especially given the complexity of the innate and adaptive immune responses in severe COVID-19 and cytokine and cytokine receptor pleiotropy and redundancy .

A number of potential immunomodulatory therapies for severe COVID-19 have been suggested including, anti-cytokines, non-specific immune modulators, and specific signalling pathway modulators affecting pro-inflammatory cytokine production . Existing small molecule immunomodulatory drugs, or biologics targeting specific cytokines other than IL-6, developed for autoimmune or other inflammatory diseases, are being tested for being suitable for re-purposing as therapies for severe COVID-19. Alternative immunomodulators could lead to improved clinical outcomes ( Fig. 2. ), particularly in subsets of severe COVID-19 patients who do not respond to tocilizumab and dexamethasone therapy, or have specific co-morbidities, or different inflammatory profiles. Because systemic inflammation is important in driving pulmonary and extra-pulmonary damage in severe COVID-19, immunomodulatory drugs would be expected to be beneficial in addressing this aspect of the disease.

Could immunomodulators be useful in preventing or treating long COVID ? Whether immunomodulators, potent anti-viral drugs, or a combination of the two, can have a positive impact on this post-COVID syndrome is unclear at the present time. This is because it is not known if the burden of health loss due to long COVID is a result of: long-term persistence of the virus; long term sequelae resulting from disruption of individuals’ immune and inflammatory responses; or due to something else entirely.

Fig. 2. Immunomodulatory drug treatment for severe COVID-19. The goal of immunomodulatory therapy in severe COVID-19 is to halt the patient’s journey along the severe disease trajectory and to re-direct them down the resolution trajectory instead. This reduces mortality, length of hospital stay, the need for ventilation and progression to critical illness. The degree and speed with which normal, or at least improved function, is restored will vary between different patients, depending on age and co-morbidities, but improvements will have a positive impact on clinical outcomes and healthcare resource usage and costs. In addition to the drug itself, dosage, timing, and duration of treatment are all likely to be important in terms of controlling severe COVID-19 disease progression, as well as minimising drug side effects. Administration of immunomodulatory drugs too early could negatively impact the host anti-viral response and actually encourage viral replication and spread in the respiratory tract, whereas effectively attenuating (not ablating) excess inflammation will be beneficial, as clinical studies using dexamethasone and t ocilizumab have shown. The identification of blood biomarkers that distinguish between protective and damaging inflammatory mediator levels could be used to guide the timing of dosing. It is likely that early treatment of symptomatic/virus positive high risk individuals with a potent anti-viral drug to reduce viral load, followed by immunomodulatory therapy to attenuate hyperinflammation, if required, will be the most effective therapeutic strategy.

PROGNOSTIC BIOMARKERS

Early detection of severe COVID-19 will enable prioritization of high-risk individuals for treatment, positively impacting healthcare resource usage and costs. Factors including age, comorbidities, immune response, radiographic findings, laboratory markers, and indicators of organ dysfunction may individually, or collectively, predict worse outcomes. Although the U.S. Food and Drug Administration has issued an emergency use authorization for a machine learning-based device that may be used to indicate SARS-CoV-2 infection in certain asymptomatic individuals, no biomarker tests for severe COVID-19 have been authorised. However, blood proteins ; cardiac injury markers; levels of COVID-19-neutralizing antibodies ; markers of complement activation and endothelial damage; immune signatures ; and cytokin e levels, including GM-CSF , all have potential for use as biomarkers of COVID-19 severity. Given the range of clinical, molecular and biochemical readouts and bioinformatics tools available, my feeling is that the best biomarkers will be prognostic algorithms which predict COVID-19 severity by combining these different readouts to allow personalised immunomodulatory treatment strategies that reflect the underlying multifactorial pathophysiological mechanisms in different patients.

CONCLUSIONS

Despite the success of vaccination and social distancing measures in reducing COVID-19 incidence in the UK, as of 18 ^th March 2021 there have been 127,508 COVID-19 related deaths . Globally there have been 3,009,215 deaths. These figures are still rising as the disease continues to have a major impact on human health and re-shapes social, economic and healthcare systems globally. The effects will continue to be felt for some time as SARS-CoV-2 likely becomes endemic .

Although vacc ines will continue to be the primary tool in protecting the world’s population from SARS-CoV-2 infection and COVID-19 disease, there is still a need for the development of anti-viral and immunomodulatory drugs to contain the effects of the virus in individuals who develop severe disease symptoms and require hospitalisation. The results obtained with remdesivir, dexamethasone and tocilizumab in clinical trials demonstrate the value of these therapeutics in positively impacting clinical care and disease outcomes. However, there is a lot of scope for improvement, particularly for patients who do not respond to these therapies.

In addition t o the drugs themselves, timing of drug dosing will be very important. Too early, and there is likely to be a negative effect on protective host immunity, encouraging virus replication and spread through the respiratory tract. Too late, and the ability to prevent or modify severe disease progression and limit long-term complications such as lung fibrosis and extra-pulmonary organ damage will be compromised. Blood biomarkers as well as clinical parameters will be an important tool for guiding clinical decisions on the timing and duration of drug dosing. Prognostic algorithms that combine clinical and physiological parameters, together with biochemical and immunological markers will be required, given the syndromic nature of COVID-19. For people at high risk of developing severe COVID-19, the use of data from wearable devices appears to be an effective way of monitoring high risk individuals to enable early anti-viral and immunomodulator treatment that may remove or reduce the need for hospitalisation and the need for critical care.

Clearly the benefits of reducing the need for hospitalisation, the length of hospital stay and the need for clinical intervention are enormous, particularly given the pressures that COVID-19 has placed on healthcare systems and the way it has impacted the treatment for non-COVID-19 disease. Finally, anti-viral and immunomodulatory drugs developed to treat COVID-19 could potentially be re-purposed in future pandemics resulting from different viruses.

SARS-CoV-2 Variant D614G

whittp163@gmail.com (Paul Whittaker) — Thu, 25 Mar 2021 16:53:44 GMT

Imaging by Cryo-Electron Microscopy Explains the Faster Spread of the Virus

Image Source

T he emergence of mutational variants in the SARS-CoV-2 spike (S) protein that have increased rates of transmission and/or may reduce, or abolish the effectiveness of the current vaccines is a concern. Analyses of S gene sequences in 2020 revealed a D614G substitution that was rare before March 2020, but became more common as the pandemic spread. The substitution was shown to enhance viral replication in human lung epithelial cells and primary human airway tissues by increasing the infectivity of SARS-CoV-2 virions. The D614G mutation appears on the UK, South African and Brazilian coronavirus variants .

Using the tec hnique of cryo-electron microscopy , researchers in the US imaged how substitution of the amino acid aspartate (D) at position 614 in the S protein by the amino acid glycine (G), enables faster spread of SARS-CoV-2 infection. This simple substitution of a single amino acid makes the S protein more stable when compared with the original SARS-CoV-2 virus. The result is that the virus is more infectious because more S proteins are available for binding to ACE2 receptors on the surface of airway epithelial cells.

In the origin al coronavirus, the S proteins would significantly change shape after binding to the ACE2 receptor and then fold in on themselves. This shape change enabled virus fusion with the epithelial cell membrane, facilitating endocytosis. Sometimes, however, the S proteins would prematurely change shape and fall apart before the virus could bind to ACE2. The D614G mutation stabilises the S protein by blocking the premature shape change.

Although the D614G mutation makes the S proteins bind more weakly to the ACE2 receptor, the fact that the proteins are less likely to fall apart prematurely increases the number of S proteins available for binding, rendering the virus more infectious overall.

A Year of COVID-19

whittp163@gmail.com (Paul Whittaker) — Mon, 15 Mar 2021 13:31:10 GMT

From SARS-CoV-2 to COVID-19 Pathogenesis, Vaccines and Therapeutics

Sources: JHU CSSE COVID-19 Data and Google

On 11th March 2020, the World Health Organisation declared pandemic status for COVID-19 , an infectious disease caused by the new coronavirus SARS-CoV-2 . This virus was first isolated from airway epithelial cells of patients presenting with pneumonia of unknown cause in Wuhan, China, in December 2019. Since then, there has been a concerted global effort to characterise the virus and understand the pathophysiology of COVID-19, develop vaccines and search for drug therapies . As of 10th March 2021, 111,300 COVID-19 or SARS- CoV-2 citations can be found in PubMed . That number is growing daily.

A year on, the aim of this article is to give an overview of what has been learned about the SARS-CoV-2 virus ( Fig. 1. ) and the symptomatology and pathogenesis of COVID-19 based on a review of published literature, particularly how it relates to disease severity. Specific details may change as future research expands and refines current knowledge, but hopefully this article will remain substantially accurate for the most part.

Fig. 1. SARS-CoV-2 virion particle. The coronavirus virion consists of the following structural proteins: spike glycoprotein ( S ), envelope protein ( E ), membrane glycoprotein ( M ), nucleocapsid protein ( N ) and haemagglutinin-esterase ( HE ). The positive-sense, single-stranded RNA genome ( +ssRNA ) is encapsidated by N , whereas M and E ensure its incorporation into the viral particle during the assembly process. S trimers protrude from the host-derived viral envelope and provide specificity for the cellular entry receptors ACE2 and TMPRSS2 ( F ig. 2. ).

TRANSMISSION AND INFECTION

Transmission and Detection

SARS-CoV-2 is spread predominantly through aerosols and airborne droplets produced by infected individuals coughing and sneezing. COVID-19 symptoms appear after an incubation period of 5 to 6 days, with peak symptoms occurring 2 to 5 days later. Virus can be detected during the incubation period by analysis of nasal or throat swab samples collected from infected individuals. A wide range of detection methods have now been developed to detect the presence of virus, with RT-PCR being the most widely used. Shedding of virus particles by infected individuals, particularly superspreaders , before symptom onset, contributes to the difficulty of controlling virus spread by public health interventions.

Infection

Infection leading to COVID-19 occurs when SARS-CoV-2 spike protein attaches to ACE2 ( Fig. 2. ), a cell surface protease expressed at variable levels on the surface of epithelial cells in the mouth , nose , and upper and lower airways of the lungs. After attachment to ACE2, the transmembrane protease TMPRSS2 cleaves and primes the bound spike protein to facilitate cell entry by endocytosis . Once inside the cell, the virus hijacks the host cellular machinery to replicate itself and assemble more virions. Virus particles are unpackaged and genes encoded by the viral RNA genome are translated into viral proteins by host ribosomes in the endoplasmic reticulum . Viral progeny are then assembled from the synthesised structural proteins and replicated viral RNA genome in the Golgi complex before being released from the host cell by exocytosis . One infected host cell can create up to a hundred new virions, accelerating the spread of the virus via infection of other cells in the respiratory tract.

Fig. 2. SARS-CoV-2 infection cycle. Virions bind to ACE2 on the apical surface of epithelial cells in the respiratory tract via the virus S glycoprotein ( A ). Cleavage and priming of the bound S protein by TMPRSS2 enables endocytosis of virion particles ( B ). After cell entry, uncoating of the virions releases the viral genomic RNA ( C ) which is then translated on the ribosomes of the endoplasmic reticulum ( D ) to form the proteins of the viral replication and transcription complex, as well as the viral structural proteins. Translated structural proteins transit through the Golgi complex ( E ), where interaction with N-encapsidated, newly produced genomic RNA results in the formation of mature virions ( F ) ready for secretion from infected cells by exocytosis ( G ).

COVID-19 and the Respiratory Tract

The respiratory tract is the first line of defence against inhaled virus particles. SARS-CoV-2 shows a gradient of infectivity from the upper to the lower airways, matching the distribution of ACE2 expression levels. Cytokines released by infected airway epithelial cells and resident, plus incoming, immune cells mediate the cell-cell communication required for a tightly regulated immune response. In COVID-19, the host immune response is a critical component of disease progression and severity. Dysregulation of this response is a key feature in individuals with severe COVID-19.

COVID-19 SYMPTOMATOLOGY AND SEVERITY

The symptoms ( Fig. 3. ) displayed by people infected with SARS-CoV-2 vary in type, number and severity, as well as duration ( Fig. 4. ). These range from asymptomatic carriage, to mild/moderate disease, to severe disease, characterised by atypical pneumonia , respiratory failure and acute respiratory distress syndrome ( ARDS ). The most severely affected patients tend to be older men , people from ethnic minorities and people with co-morbidities , such as obesity , diabetes and hypertension . In addition, factors such as genetics , viral load , the level of immune response and degree of lung damage will also play a part, with a predominance of different factors in different patients causing different individual clinical outcomes.

Fig. 3. COVID-19 symptoms and complications. Although fever, persistent cough and loss of taste and/or smell are the most common COVID-19 symptoms reported, some patients display a number of different symptoms. Difficulty breathing is a predominant feature of the majority of COVID-19 patients who are hospitalised. Common co-morbidities are heart disease, high blood pressure and diabetes. Although the lung is the primary site of COVID-19 pathology, complications affecting a range of extra-pulmonary organs are often seen in patients with severe disease, particularly those with co-morbidities causing endothelial cell dysfunction. Even in patients with mild/moderate disease, some patients experience long COVID, where symptoms can persist for 12 weeks or longer.

Asymptomatic COVID-19

It has been estimated that 17% of people infected with SARS-CoV-2 never develop any symptoms of COVID-19. These are not pre-symptomatic individuals who have no initial symptoms, but then go on to develop mild to moderate symptoms. These are individuals who never develop any symptoms at any time. It is not known which demographic, clinical, or immunological characteristics are responsible for the lack ofsymptomatology in these people compared with those who develop symptoms. Neither is it known the degree to which asymptomatic individuals contribute to virus transmission .

Fig. 4. COVID-19 symptomatology time course and outcomes. COVID-19 symptoms become apparent around 5 days after initial virus exposure. Symptoms peak, on average, 5 days later and, for the majority (>60%) of people, COVID-19 symptoms are mild to moderate in severity. Although symptoms subside for 4 in 5 of these mild/moderate cases after another 5 days, 1 in 5 people can experience persistent symptoms for 12 weeks or more (long COVID). Twenty percent of infected individuals require hospitalisation with breathing difficulties caused by viral pneumonia. Of these hospitalised patients, 1 in 5 develop ARDS and/or multi-organ failure requiring intensive care. Up to 40% of critical care patients can die. It has been estimated that around 17% of infected people never develop any symptoms of COVID-19 at any time.

Mild to Moderate COVID-19

The majority (> 60%) of infected individuals develop mild to moderate disease symptoms that generally resolve spontaneously after 6-10 days ( Fig. 4. ). However, around one in five of these individuals can have symptoms that persist from 4 weeks to over 12 weeks. Whether this post-COVID syndrome, generally known as long COVID , is a result of: long-term persistence of the virus; long term sequelae resulting from disruption of individuals’ immune and inflammatory responses; or due to something else entirely, is currently unknown.

Severe COVID-19

Around 20% of infected individuals require hospitalisation ( Fig. 4. ). Viral pneumonia , as evidenced by abnormal temporal lung changes on chest radiography , is the most common reason for admission, with patients displaying hypoxia due to a drop in blood oxygen levels. This leads to the majority of admitted patients suffering respiratory failure and requiring breathing support , which varies depending on individual patient need. Eighty percent of hospitalised patients are cared for in general medical wards.

Critical COVID-19

Twenty percent of hospitalised patients become critically ill and require invasive lung ventilation and support in high dependency and intensive care units ( Fig. 4. ). Sixty to eighty percent of these patients have ARDS and a hyper-inflammatory response. Unfortunately, up to 40% of critically ill COVID-19 patients die , although the death rate does vary with age . Severe COVID-19 can result in permanent damage and scarring to the lungs in survivors.

Multi-Organ COVID-19

Although the lungs are the primary site of COVID-19 pathology, COVID-19 is a multi-system disease exhibiting a range of complications resulting from damage to a number of different organ systems, including the heart , brain , kidney , liver and vasculature ( Fig. 3. ). Elevations in levels of cardiac injury biomarkers are observed in 50% of patients with severe COVID-19, with a significant proportion of patients developing venous and arterial complications . Individuals with pre-existing endothelial cell dysfunction have an increased risk of damage caused by SARS-CoV-2 infection, which also increases hypercoagulability and results in a high incidence of venous thromboembolism and pulmonary embolism . Less commonly, SARS-CoV-2 infection can cause heart muscle inflammation and heart rhythm disturbances , such as atrial fibrillation . In cases of multi-organ dysfunction, specialist clinical support to reduce multi-organ failure and mortality is required.

COVID-19 PATHOGENESIS

The upper airways

The nasal cavity is the first site of infection ( Fig. 5A. ). Here, SARS-CoV-2 infects ciliated and secretory cells which express ACE2 and TMPRSS2. The viral load in the nasopharynx and oropharynx appears to be similar between infected people who stay asymptomatic and those who become symptomatic. There is little data at the current time relating to the extent to which SARS-CoV-2 spreads further in to the airways of asymptomatic people, but what data there is suggests the virus can spread deeper into the airways in some of these individuals and it is the host response which is a key determinant of outcome, including pre-existing immunity.

Fig. 5. The human respiratory tract and COVID-19. Inhaled virus particles bind to ACE2 receptors on the surface of epithelial cells in the nasopharynx and oropharynx ( A ). Disease severity is dependent on how deep SARS-CoV-2 virions progress into the airways. Restriction of virus infection to the upper and conducting airways ( B ) results in mild/moderate symptoms seen in >60% of infected individuals. Progression of the virus to the alveoli ( C ) affects exchange of oxygen and carbon dioxide between the lungs and the blood, which leads to the breathing difficulties seen in the 20% of patients hospitalised with severe COVID-19. In the 20% of hospitalised patients who become critically ill and require intensive care, damage to the endothelial cells of the capillary net encasing each alveolus leads to acute respiratory distress syndrome (ARDS) and/or multi-organ complications resulting from systemic effects of the virus.

Image sources: A. B. C.

Virus spreads from the nasal cavity to infect ciliated cells and non-ciliated mucus secreting ( goblet ) cells lining the bronchi ( Fig. 5B. ) as the virus progresses deeper into the lungs. During this phase, a vigorous innate immune response to clear the virus is triggered and the infected individual becomes symptomatic and feels unwell. Infection of lung epithelial cells triggers cell death and inflammatory responses . Keratin 5-expressing basal cells, which are the progenitor cells for the airway epithelium and are not infected by SARS-CoV-2, are induced to differentiate directly into ciliated cells so damaged epithelium can be repaired and recover from the infection. If the capacity for basal cell differentiation is impaired (e.g. due to excessive interferon lambda production), lung epithelial cell regeneration does not take place and airway damage increases, as happens in the lungs of patients with severe COVID-19.

The Lower Airways

Infection of club (Clara ) cells located in the respiratory bronchioles in the lower airways facilitates spread of SARS-CoV-2 into the alveoli ( Fig. 5C. ), where oxygen and carbon dioxide exchange between the lungs and the blood is impaired in severe COVID-19.

Two types of epithelial cells line the alveoli ( Fig. 6A. ). Type I pneumocytes are large flat cells that are directly adjacent to the endothelial cells of the capillary network that closely encircles each alveolus ( Fig. 5C. ). Type I pneumocytes are critical for rapid exchange of oxygen and carbon dioxide between the blood and alveolar space. These cells are easily damaged in many forms of lung injury. Type II pneumocytes make and secrete pulmonary surfactant , which is required for effective gas exchange. Type II pneumocytes are also the progenitors of type I pneumocytes and are therefore important in the repair of alveolar damage. Both type I and type II pneumocytes help keep the alveoli free of fluid by contributing to active resorption of alveolar fluid and trans-epithelial ion movement . Type I and type II pneumocytes both express ACE 2.

Fig.6. Severe COVID-19 lower respiratory tract pathophysiology. The alveolus ( A ) is the lung structure where gaseous exchange with the blood takes place. Oxygen in inhaled air and carbon dioxide in the blood diffuse out of, and in to, the alveolar space, respectively, via type I pneumocytes and the endothelial cells of the surrounding pulmonary capillary network. Surfactant secreted by type II pneumocytes aids this process by reducing surface tension at the air-liquid interface in the alveolus. Resident phagocytic alveolar macrophages provide a first line of defence against inhaled pathogens and noxious particles that make it down through the airways into the alveoli. In a healthy, non-diseased lung type I and type II pneumocytes keep the alveoli free of fluid. In severe COVID-19 ( B ), gaseous exchange between the alveoli and blood is severely reduced. Damage to type I and type II cells by SARS-CoV-2 infection results in the alveolar space becoming filled with liquid containing dead cells, cell debris, proteins, invading immune cells, virus particles etc. In critical disease, extensive damage to the alveoli and endothelial cells of the surrounding capillaries, plus a hyperinflammatory response leads to ARDS and respiratory failure requiring prompt intensive care. In some patients this leads to death. Fibrotic changes resulting from disruption of the normal alveolar epithelial repair process lead to permanent structural changes to the lung micro-architecture that can have future health effects in some survivors depending on the scale and severity of these changes.

In addition to type I and II pneumocytes, there is a third cell type in the alveoli - alveolar macrophages ( Fig. 6A .). These phagocytes are the first line of defence against infectious agents and noxious particles present in the environment that make it down through the airways to the alveoli. Like type I and type II pneumocytes, alveolar macrophages express ACE2.

Alveolar Inflammation

Type II pneumocytes express the highest levels of ACE2 and TMPRSS2 proteins and are believed to be the primary targets for SARS-CoV-2 infection in the alveoli. Type I pneumocytes and alveolar macrophages are also infected by SARS CoV-2. As the virus propagates in infected cells, released viral particles infect other type II pneumocytes and adjacent type I pneumocytes allowing spread of the virus to adjacent alveoli. Infected type II pneumocytes and alveolar macrophages secrete cytokines to recruit immune cells from the blood into the alveolar space to destroy virus-infected cells and extracellular virus. Uninfected neighbouring cells amplify this response by responding to , and secreting , additional cytokines. The innate immune response provoked in the pulmonary parenchyma is characterized by the recruitment of bone-marrow-derived monocytes to the alveolar space and their differentiation into alveolar macrophages.

The immunological hyper-response associated with COVID-19 ARDS appears to be a key driver of severity and death in patients. Although this hyper-inflammation is often referred to as a “ cytokine storm ” in a large number of publications , some investigators have questioned the relevance of this term in relation to COVID-19, given the cytokine levels actually measured in patients. Alveolar macrophages have a key role in initiating and propagating this hyper-inflammatory phenotype. Infected alveolar macrophages and activated T-cells recruited from the blood form a positive feedback loop that drives persistent alveolar inflammation. Neutrophils also appear to be important in the immune response and amplifying the damage seen in the lungs of patients with COVID-19 ARDS.

Alveolar Damage

Loss of type I and type II pneumocytes due to infection and subsequent cell death results in reduced gaseous exchange in diseased portions of the lungs (Fig. 6B.). Death of pneumocytes also results in focal alveolar flooding, causing the characteristic radiographic images seen in severe COVID-19. This is a result of a combination of factors including: reduced active resorption of alveolar fluid; reduced active transport of sodium from the alveolar space into the surrounding interstitium; damage to the endothelium of adjacent capillaries causing leakage of fibrinogen and other plasma proteins into the alveolar space; and formation of fibrin exudates. The flooding impairs the ability of pulmonary surfactant produced by type II pneumocytes to adsorb to the surface of the alveoli, thus increasing surface tension , and reducing oxygen exchange. As alveoli become blocked and collapse , appositional atelectasis occurs leading to loss of secondary lobules .

In most forms of lung injury, type II pneumocytes proliferate and differentiate into type I pneumocytes leading to restoration of the alveolar epithelium. However, the diffuse alveolar damage (DAD) seen in severe COVID-19 means that this repair process is disrupted because of depletion of type II cells. Activation of alternative pathways for epithelial repair in the most severe disease is likely to be the cause of the scarring and residual disease seen in some COVID-19 survivors. As type II pneumocytes inhibit fibroblast proliferation and the expression of extracellular matrix genes in fibroblasts, loss of these cells is likely to trigger fibrosis as fibroblasts migrate into the alveolar lumen. Imbalance in the renin-angiotensin system in COVID-19 may also favour lung fibrosis. The landscape and timescale of these changes will vary as new areas of the lung get infected and the innate and acquired immune systems respond.

Perivascular Damage

A key part of COVID-19 disease progression is damage to the pulmonary endothelial cells that are adjacent to the infected and damaged alveoli ( Fig. 7 ). Analysis of lungs from patients who died of COVID-19 has highlighted several perivascular features , including: severe endothelial injury and disrupted endothelial cell membranes associated with intracellular SARS-CoV-2 virus; widespread vascular thrombosis with microangiopathy and occlusion of alveolar capillaries; and significant new vessel growth through intussusceptive angiogenesis . Changes in the pulmonary vasculature on chest computed tomography (CT) appear to be predictive of adverse clinical outcomes in COVID-19 patients.

Fig. 7. Endothelial damage and dysfunction in COVID-19 lung pathology and extra-pulmonary organ damage. Endothelial dysfunction is associated with the development of severe COVID-19 and life-threatening extra-pulmonary complications. Endothelial cells can be damaged and activated by: direct viral infection; by pathogen-associated molecular patterns ( PAMPs ) derived from SARS-CoV-2; damage-associated molecular patterns ( DAMPs ) from dead or dying endothelial and immune cells; or pro-inflammatory cytokines (e.g. interleukin 6/ IL-6 and tumour necrosis factor alpha/ TNFa ). Endothelial dysfunction and injury lead to: increased vascular permeability ; increased endothelial inflammatory response ; reduced levels of nitric oxide , causing vasoconstriction ; and impaired angiogenesis . Activated endothelial cells release cytokines that attract immune cells that bind to adhesion molecules expressed on the surface of the endothelial cells and also produce cytokines. This stimulation of the immune response leads to hyper-inflammation, which leads to further endothelial damage. Release of clotting factors ( Von Willebrand Factor , thrombin , fibrin and tissue factor ), platelet activation and NETosis of neutrophils, drives thrombus formation and increases in the levels of D-dimer . Neutrophils also amplify endothelial damage by releasing a number of proteolytic enzymes and reactive oxidant species that damage cells.

Pulmonary endothelial cells (ECs) have a key role in optimising gas exchange, controlling barrier integrity and function, and regulating pulmonary vascular tone in health and disease. They are involved in most lung diseases either as a direct participant, or as a victim of collateral damage. Importantly, endothelial cells express ACE2, so SARS-CoV-2 may alter vascular homeostasis by directly infecting endothelial cells. Analysis of patient tissue samples and organoids show that SARS-CoV-2 can infect endothelial cells, even though cultured primary endothelial cells are resistant to infection.

Alternatively, instead of direct infection by SARS-CoV-2, vascular damage in COVID-19 may be driven by hypoxia, hyper-inflammation and immune dysregulation. Platelet-neutrophil communication and activation of macrophages can induce a range of pro-inflammatory effects, including: cytokine release; the formation of neutrophil extracellular traps ( NETs ); increasing fibrin generation; and inducing microthrombus formation in the microvasculature. NETs can damage the endothelium and activate both extrinsic and intrinsic coagulation pathways and appear to have a significant role in COVID-19 disease severity.

EXTRAPULMONARY ORGAN DAMAGE

As noted earlier, in addition to lung pathology, SARS-CoV-2 infection can result in a number of extrapulmonary complications involving the haematological, cardiovascular, renal, gastrointestinal, hepatobiliary, endocrinologic, neurologic, opthalmologic and dermatologic systems ( Fig. 3 .). Potential mechanisms underlying the pathophysiology of this multi-organ injury include: direct viral infection of organs; endothelial cell damage and thromboinflammation ; immune response dysregulation; and dysregulation of the renin-angiotensin-aldosterone system (RAAS). The role that each of these mechanisms plays in extra-pulmonary organ damage in COVID-19 is unclear at the present time. However, the pathophysiology underlying the systemic effects of COVID-19 is likely to be multi-factorial, with different mechanisms predominating in different patients.

Direct Infection

The presence of ACE2 and TMPRSS2 in a range of different extra-pulmonary organs makes direct infection a plausible mechanism for multi-organ injury in COVID-19. Evidence for direct viral infection of the kidney and other organs in patients with COVID-19 and the detection of viral RNA in blood and urine samples from patients supports the idea of systemic spread of the virus. However, the mechanism(s) of extrapulmonary virus spread have yet to be elucidated.

Endothelial Cell Dysfunction

Endothelial cells have a number of physiological functions and are involved in a range of different diseases. Because they line the inside surface of blood vessels, they traverse a wide range of organ systems. Endothelial damage and endothelialitis are found in the vascular beds of a number of organs in patients with COVID-19 and this can trigger thromboinflammation leading to microthrombi deposition and microvascular dysfunction. Recent work suggests that inflammation and vascular damage may be the primary causes of neurological symptoms in COVID-19 patients. As a result, COVID-19 is increasingly being seen as an endothelial disease, with endothelial cell dysfunction ( Fig. 7. ) being the common link between many of the different complications seen in COVID-19 patients, from multi-organ damage, to blood clots and stroke. Moreover, pre-existing endothelial dysfunction is the common denominator among co-morbidities such as hypertension, diabetes, obesity, cardiovascular disease and ageing in individuals with an increased risk of severe COVID-19. Published data suggests that, at least in some COVID-19 patients, acute multi-organ thromboembolism may precede , or present disproportionately, over respiratory involvement. Organ dysfunction is also associated with excessive NET formation and vascular damage.

Immune Dysregulation

As mentioned previously, the host immune response is important in governing individual patient outcomes in COVID-19, whether that is a reduced response, or an over-enthusiastic response by the innate immune system. Markers of inflammation are predictive of critical illness and mortality in COVID-19 patients, supporting the idea that hyperinflammation is a driver of multi-organ failure in COVID-19. The positive effects of dexamethasone and IL6 receptor antagonist therapy also indicate the importance of the immune response in disease progression and severe pathology.

Renin-Angiotensin-Aldosterone System (RAAS) Dysfunction

ACE2 is a key regulator of RAAS in cardiovascular and pulmonary homeostasis . Vascular damage-induced by SARS-CoV-2, combined with pre-existing endothelial dysfunction caused by hypertension, diabetes, obesity, or age appears to be a contributory factor in COVID-19 related morbidity and mortality, including the vasculopathy and coagulopathy seen in COVID-19. Therefore, dysregulation of the RAAS offers another plausible mechanism for SARS-CoV-2 tissue damage of extra-pulmonary organs.

COVID-19 VACCINES AND THERAPEUTICS

As of 12 ^th March 2021, there have been 118,742,439 COVID-19 cases worldwide , resulting in 2,632,955 deaths. In the UK there have been 4,241,677 cases and 125,168 deaths, although the number of cases and deaths has declined markedly from the late January 2021 peak, as a result of lockdown measures and an efficient vaccination programme.

Twelve vaccines have been approved at the time of writing. Thanks to the rapid availability of the SARS-CoV-2 genome sequence and advances in vaccine technology, the speed of COVID-19 vaccine development has been remarkable, taking less than a year from genome sequence determination to the UK approvin g the Pfizer-BioNtech vaccine, quickly followed by approval of the AZ-Oxford vaccine . This was a timescale previously unimaginable using traditional vaccine development methodology.

As of 10 ^th March 2021 , 23,053,716 people, representing 34.59% of the UK population have received at least one dose of the Pfizer-BioNtech or AZ-Oxford vaccine. A smaller number, 1,351,515 people, representing 2.03% of the UK population, have been fully vaccinated after receiving two doses. The number continues to grow daily.

The roll out of SARS-CoV-2 vaccines is already having a major impact on the incidence of severe COVID-19. The emergence of new SARS-CoV-2 variants that have increased rates of transmission and/or may reduce or abolish the effectiveness of the current vaccines is a concern. However, global surveillance of virus variants by sequencing , combined with the ability to quickly develop new vaccines, will reduce this threat. As the risk of new variants is lowered if the rate of new infections (and viral replication) is reduced, equitable access to vaccines for the world’s population, particularly poorer countries, will also be very important in reducing the number of new variants in the medium to long-term.

Can SARS-CoV-2 be eradicated , or will we just have to learn to live with it? I suspect the latter is the more achievable scenario, at least in the medium term, given: the level of vaccine hesitancy that exists; the proportion of people in the world who have still to be vaccinated ; and the continuing emergence of virus variants .

The global research effort focussed on SARS-CoV-2 and COVID-19 has been unprecedented. In the time it has taken to write this article, over 8,000 new papers have been added to the 103,276 papers that existed in PubMed when I started writing! However, in contrast to the situation with vaccines, only modest progress has been made with regard to the development of anti-viral drugs to prevent SARS-CoV-2 infections, and other drugs to stop COVID-19 disease from worsening. This lack of success is not due to lack of effort , just a reflection of the scale of the problem that COVID-19 has presented to the scientific and medical worlds. In truth, drug discovery has still to reach the level of speed and refinement that vaccine technology currently has. So far, remdesivir is the only anti-viral drug approved for treating Covid-19, but its use is limited to clinical settings and, at best, it appears to be only modestly effective. Emergency use applications (EUAs) have also been issued by the US Federal Drugs Administration (FDA) for several unapproved monoclonal antibody therapies to treat mild to moderate COVID-19 in children and adults. I n terms of immunomodulators for severe COVID-19 disease , dexamethasone and tocilizumab , particularly when used together , have been shown to reduce COVID-19 mortality.

How can the world be better prepared for similar threats in the future? Preparation for the next crisis occurs needs to begin now. Pre-emptive development of effective and readily available drugs that can be quickly tested in new diseases as they arise is required, mirroring the pre-emptive strategie s that allowed the rapid development of SARS-CoV-2 vaccines. The last point notwithstanding, there will always be a lag between the outbreak of a new pandemic and the delivery of an effective vaccine, so antiviral drugs will be the primary tools that can be used to help keep populations safe during this period. There will also be a need for immunomodulatory drugs to treat severe disease in susceptible individuals and reduce mortality. In the main, I believe this can be most effectively approached using drug re-purposing strategies, rather than starting drug discovery programmes from scratch. This is an opportunity for pharmaceutical companies to work together with government agencies and academia in public-private consortia to pool resources and expertise to form a centralised library of drug compounds that can be rapidly tested in clinical trials. Furthermore, investment in identifying future primary threats and making a societal commitment to pre-emptive preparation is also needed. This will require a high degree of coordination and the involvement of scientists from fundamental researchers, to drug development experts. Given the remarkable response to the current pandemic, this is achievable . Ideally, t h e work needs to be undertaken global ly, to spread the cost and maximise expertise and resources, as well as ensure that important research on other diseases is not disadvantaged.

What about the use of viral challenge studies in the development of new anti-viral drugs and vaccines? Approval of the world’s first challenge study in the UK is a key step towards this goal. If such studies can be conducted safely on healthy volunteers they will be important in facilitating the development of new vaccines and therapeutics. However, they will not be of value in the development of drugs to target severe disease as it would clearly be unethical to deliberately trigger life threatening symptoms in volunteers. For this, standard clinical trials using patients hospitalised with severe disease will still be required, underlining the importance of having libraries of immunomodulatory drugs ready for rapid testing in such studies when a pandemic arises.

CONCLUSION

Although the scientific and medical response to the COVID-19 pandemic has been exceptional, and the progress made in understanding the disease and developing vaccines has been astounding, the social and economic cost underlines the importance of learning from the current pandemic and being better prepared for the next one. Clearly, it is not a question of if, but when, it will occur again and how well the world will be prepared for it next time…

COVID-19 Information Resources

whittp163@gmail.com (Paul Whittaker) — Mon, 04 May 2020 11:32:21 GMT

A collection of links to information sources relevant to the coronavirus pandemic. From disease and healthcare information, to drug therapies and diagnostics, as well as epidemiology and clinical trials in progress.

Association of British Pharmaceutical Industries

British Broadcasting Corporation

BBC Horizon programme investigating the scientific facts and figures behind the Coronavirus pandemic as at 9th April 2020

British Medical Association COVID-19 Guidance

Official guidance for doctors

British Medical Journal Coronavirus Hub

Support for health professionals and researchers with practical guidance, latest news, comment and research

British Society for Antimicrobial Chemotherapy

Information and the latest guidance from health bodies, academic publications and other professional societies

British Thoracic Society COVID-19 Information

Information, guidance and resources to support the respiratory community

Centers for Disease Control and Prevention

Cochrane Library COVID-19 Information

Cochrane Reviews and related content from the Cochrane Library relating to the COVID-19 pandemic

COVID-19 Diagnostics Resources

Drug Target Review

Latest news and updates relating to COVID-19 drug discovery efforts

European Respiratory Society COVID-19 Resource Centre

European Respiratory Society (ERS) and European Lung Foundation (ELF) resources on SARS-CoV-2 and COVID-19 as it is published

International Severe Acute respiratory and Emerging Infection Consortium (ISARIC) COVID-19 Resources

COVID-19 clinical research resources

Medical Research Centre for Epidemiological Analysis and Modelling of Infectious Diseases

All output from the Imperial College COVID-19 Response Team, including publicly published online reports, planning tools, scientific resources, publications and video updates

Public Health England

PHE COVID-19 dashboard

Royal College of Pathologists

Latest information available on COVID-19 relevant to the practice of pathology

Royal Society of Biology

Royal Society of Medicine

University of Oxford Centre for Evidence-Based Medicine

Rapid reviews of primary care questions relating to the coronavirus pandemic, updated regularly

US National Institutes of Health

Latest research information from NIH

Wiley Online Library

Articles related to the current COVID-19 outbreak, as well as a collection of journal articles and book chapters on coronavirus research freely available to the global scientific community

Cryo-Electron Microscopy: High Resolution Molecular Structural Biology Enters the Ice Age

Fri, 01 May 2020 11:17:04 GMT

Image Source

“ By the help of microscopes, there is nothing so small, as to escape our inquiry; hence there is a new visible world discovered to the understanding. ” Robert Hooke , 1635 - 1703.

The history of microscopes is one of ever higher magnification, enabling scientists to pry deeper and deeper into the minute details of nature invisible to the naked eye. Now microscopy is playing a key role in visualising the molecular architecture of proteins and macromolecular complexes; information which is critical to understanding biomolecular function and discovering new drugs. X-ray crystallography has been the most widely used technique for obtaining atomic level detail, but it does require a large amount of sample and the generation of crystals, which can be problematic. Nuclear magnetic resonance (NMR) does not require crystallization, but it does require large amounts of sample and isotopic enrichment and the technique has generally been restricted to small proteins, single protein domains, or small RNAs. Single-particle cryo-electron microscopy (cryo-EM) is a structural biology technique, first developed back in the 1970s, which does not require crystallization, or large amounts of sample. Using a flash-freezing process that fixes proteins in thin films of ice, cryo-EM avoids the problems of crystallization. Then, thousands of 2-D images of proteins caught in random orientations are stitched together to reveal the 3D structure. Advances in detector technology and software algorithms now mean that cryo-EM can be used for the determination of biomolecular structures at near-atomic resolution , including proteins and macromolecular assemblies “intractable” to X-ray crystallography and NMR. In an application relevant to the current COVID-19 pandemic, cryo-EM has recently been used to study the functional evolution of coronavirus spike proteins and provide a structural basis for the inhibition of coronavirus replication by Remdesivir .

Cryo-EM is now being used for a range of applications from studying eukaryotic DNA replication, to structure-based drug discovery (SBDD), as showcased during a recent ELRIG webinar on this topic, held on 2nd April 2020 entitled “From Blob-ology to Near Atomic Resolution Structures: Current Uses of Cryo-EM within Biological Research”.

While the number of protein structures being determined by cryo-EM is booming , the cost of a microscope (up to £5/$7 million), the need for custom laboratory facilities and the associated operational costs, means that many structural biologists have no access to this technology. Jason Van-Rooyen explained how The Electron Bio-Imaging Centre ( eBIC ) at Diamond in Oxfordshire provides state-of-the-art cryo-EM equipment and expertise, as well as molecular and cellular cryo-electron tomography for use by academic and industrial scientific groups . Use of the eBIC cryo-EM facility has resulted in 113 publications at the time of writing this article, ranging from the determination of cryo-EM structures of the Escherichia coli RecBCD complex to the cryo–EM structure of RagA/RagC in complex with mTORC1 . Planned, are the provision of a Dual Beam Scanning Electron Microscope (SEM) and Focused Ion Beam (FIB) system for the generation of thin lamellae of cellular samples for cryo-electron tomography, as well as electron crystallography for structure determination.

The eukaryotic genome must be accurately duplicated in an a timely manner during the S (synthesis) phase of each cell division cycle . As the genomic DNA in eukaryotic cells is packaged into nucleosome arrays , the nucleosomes need to be dismantled ahead of the advancing DNA replication fork and reassembled again once the DNA has been duplicated. A key component in this highly regulated biological process is the replisome , a large, multiprotein complex, comprising an array of DNA unwinding ( helicase ) and synthesis ( primase / polymerase ) functions, whose assembly is closely linked to cell cycle phase. Initiation of DNA replication takes place when pre-replication complexes (pre-RCs) comprising the origin recognition complex (ORC) , chromatin licensing and DNA replication factor 1 (Cdt1) and cell division cycle 6 (Cdc6) are assembled at multiple DNA replication start sites ( origins ) in the genome during G1 phase. Origins of replication are subsequently licensed by loading of the inactive mini-chromosome maintenance protein complex (MCM) DNA unwinding (helicase) motor onto DNA, which is then activated in a series of steps during S phase to form functional replisomes. It is believed that the activated MCM melts the double helix and unwinds the DNA at the replication fork, allowing the replicative polymerases to do their work.

Alessandro Costa ( The Francis Crick Institute ) described how cryo-EM is being used to understand the molecular basis of DNA engagement by the MCM and the mechanics of the helicase motor. Using purified yeast proteins in a reconstituted DNA replication system, his team have used single-particle cryo-EM to study the mechanisms of MCM helicase loading onto DNA and MCM-driven DNA melting and untwisting during origin licensing . DNA fork progression depends on the energy derived from ATP hydrolysis by the MCM motor, however, it is unclear how this is achieved. Using cryo-EM, sub-nanometre resolution structures of the CMG helicase trapped on a DNA replication fork have been determined and combined with single-molecule FRET measurements to suggest a replication fork unwinding mechanism. Further studies on the mechanism of helicase activation show that activated helicases are bound to unwound single DNA strands and pass each other within the replication origin as they translocate in opposite directions along the DNA strands in a process driven by different helicase conformational states. Three different polymerases act sequentially on the leading-strand template to establish DNA replication. Cryo-EM has been used to study the structure and dynamics of the main leading-strand polymerase bound to the CMG helicase and how polymerase binding changes both helicase structure and fork-junction engagement .

Pfizer was the first pharmaceutical company to adopt cryo-EM in-house. Due to its ability to visualize protein structures and ligand interactions , cryo-EM has been increasingly adopted by the pharmaceutical industry as a tool to facilitate structure-based and fragment-based drug discovery. Cryo-EM is one of several technologies that AstraZeneca has invested in, as they push to develop novel drug targets. The DNA damage response is one of AZ’s strategic areas within oncology and Taiana Maia de Oliveira described how single-particle cryo-EM has been used to reveal insights into the structure of the DNA damage sensor phosphatidylinositol 3-kinase related kinase (PIKK) protein family, which controls the response of cells to stress and nutrient status. In collaboration with the MRC Laboratory of Molecular Biology , and using facilities at the Cambridge Pharmaceutical Cryo-EM Consortium , AZ researchers used cryo-EM to define the world’s first protein structures for human ataxia telangiectasia mutated (ATM) and the structure of ATM in different functional states. Because of its large size (350 kDa), previous attempts to obtain a high resolution structure of ATM with other techniques proved impossible. ATM is a key trigger protein in the DNA damage repair response, involved in tumorigenesis and survival of cancer cells and, as a result, a prime therapeutic target for oncology. This structural work revealed that ATM functions as a “molecular switch”. In the asymmetric (“on”) ATM dimer state, the active site is open and can bind substrate, whereas in the symmetric (“off”) state the active site is closed and substrate binding is blocked. Both open and closed ATM molecules co-exist in the sample protein samples, explaining why catalytic activity of ATM can be seen even under basal conditions and indicating that activators and inhibitors may work by altering the equilibrium between the two dimer populations. AZ have also used cryo-EM to elucidate the mechanism of RET activation with a view to targeting this mechanism in neurodegenerative disease and diabetes.

Conclusion

Once derided as being “Blobology” because of the lack of definition in its blurry images, cryo-EM has rapidly become one of the hottest new approaches in biological research, with many calling it a “resolution revolution” . In the last few years there has been an exponential growth in the number of images being uploaded to The Electron Microscopy Data Bank , with the quality of the images rivalling those obtained using X-ray crystallography. As was demonstrated during the ELRIG webinar, cryo-EM is well-suited to providing high resolution structural information to aid both academic and industrial projects. Successful applications in small molecule drug discovery will certainly gather pace as pharma seek to exploit the power of this technology to deduce the structures of therapeutically relevant protein targets, as well as provide information on binding site and ligand interactions , to enable the study of drug-target interactions. In due course, we can expect cryo-EM to be applied to a variety of areas in the pharmaceutical industry, including vaccines, protein degradation, gene therapy, biologics, epitope mapping and antibody-antigen interactions.

Technological improvements in direct electron detection , image collection and image analysis , enabled the successes of cryo-EM, but there are still a number of methodological aspects that could be improved , including validating the accuracy of cryo-EM structures and developing data standards . Automation of many steps from sample preparation to data pre-processing will improve the efficiency and productivity of cryo-EM and, hopefully, take specimen preparation for cryo-EM from a trial and error “art” to a controlled and reproducible process making it easier to use and providing robust protocols from beginning to end. The development of graphene supports also promises improvements in the reliability of specimen preparation and image quality. There is also a drive to make cryo-EM more affordable using machines that operate at lower voltages.

Finally, for readers interested in learning more about the practicalities of cryo-EM, a good starting point is the MRC Laboratory of Molecular Biology electron microscopy webpage .

Medical Innovation

whittp163@gmail.com (Paul Whittaker) — Mon, 06 Apr 2020 14:08:10 GMT

From Patient Monitoring to Improving Surgical Procedures

Healthcare organisations such as the NHS face unrivalled challenges, from improving access and care for patients, to increasing efficiency and reducing costs. Medical and healthcare innovation is seen as having a key role in driving these improvements , particularly in the NHS . Twice a year the Royal Society of Medicine (RSM) holds a day of presentations and discussions around new ideas and developments in medicine and healthcare. The presenters range from early stage entrepreneurs, to those who are embedding innovations in a clinical setting. The variety of topics covered is always stimulating and provides an early insight into how medicine and healthcare are likely to be shaped in the future. In this article I will be reviewing the two RSM Medical Innovations summits I attended in 2019 on 6th March and 21st September .

Patient Monitoring

Patient monitoring is an essential part of clinical and disease management. It allows an assessment of the progress/regression of a disease, or the development of complications. Poor monitoring can lead to poor disease control. With all its innovations and possibilities, digital technology has the capability to capture and quantify the physical, mental and social wellbeing of patients, as well as aid in disease management.

Digital technology provides an opportunity to deliver patient triage in new ways. Using data from wireless-enabled implanted cardiac devices received via the CareLink network, Matt Cook and Roel Bogaarts ( Medtronic ) explained how the FOCUSON team monitors and triages incoming data to aid hospital clinical teams. Clinical teams receive alerts via telephone, email, or the FOCUSON Platform. As a result they are able to devote more time to patients, particularly those in need of urgent care.

The use of algorithms and software ( artificial intelligence, AI ) has great potential for helping clinicians understand complex medical data sets and help guide clinical decision making. Letizia Gionfrida ( Arthronica ) revealed how AI is being used for the assessment and management of chronic rheumatic conditions so that examinations can be performed remotely using a laptop or smartphone camera, to reduce, or eliminate, the need for face-to-face consultations. Elina Naydenova ( Feebris ) described how AI is being used to improve diagnosis in vulnerable patient groups (the young and the elderly) by analysing data from a wide range of point-of-care devices (digital stethoscopes, wearables etc.) to extract clinical information that can be used by healthcare professionals to facilitate early diagnosis.

Wearable sensors (wearables) are smart electronic devices worn next to the skin that can collect physiological and environmental data that can be used for immediate user feedback, or downstream analysis. Wearables are increasingly being used to collect and process physiological parameters for digital health information . In terms of the evaluation of human movement, sensors can be used to provide feedback to the user that they can use to modify their movements and improve their daily life. Nuala Barker ( Walk With Path ) talked about two wearables to improve patient mobility: a shoe attachment ( Path Finder ) to improve movement and gait in patients with neurodegenerative diseases such as Parkinson’s disease and; a shoe insole that provides haptic feedback to patients at risk of falls due to diseases such as peripheral neuropathy ( Path Feel ).

Patient Self Help

Patient self-care is important not only for preventing future health problems (e.g. heart disease and lung cancer), but also in managing the course of long-term conditions.

Chris Edson ( OurPath ) explained how smart technology and behavioural science are being combined to help patients replace bad habits with good ones. Nutritional advice and planning are combined with smart scales and a step tracker to facilitate behavioural change and monitor progress. The OurPath online habit change platform has now been commissioned by the NHS .

Knowledge is power, as the saying goes. Patient knowledge can improve health outcomes and enable patients to actively participate in disease control and treatment. However, the knowledge needs to be evidence-based and relevant to the patient. Seb Tucknott ( IBDrelief ) has developed an online portal to provide information and support for sufferers of inflammatory bowel disease (IBD) . IBD, which includes Crohn’s disease and ulcerative colitis, is generally managed through strong drugs and/or surgery. For millions of people worldwide, everyday life can be a struggle as sufferers deal with a range of debilitating symptoms which impact their quality of life. The IBDRelief portal is based on research Seb carried out to help him deal with the symptoms of IBD following his diagnosis in 2008 and is aimed at helping sufferers learn how to control their symptoms alongside their medical treatment, as well as connect with other sufferers and share experiences.

Mental Health

Mental health disorders are complex and challenging, as well as placing an increasing burden on healthcare globally . Digital health interventions (DHIs) , which include smartphone apps, computer‐assisted therapy and wearable technologies, have enormous potential for the treatment for mental health disorders by improving accessibility, clinical effectiveness and personalisation of mental health interventions . Data obtained by digital sensors and wearables can be used as digital biomarkers to assess the mental states of individuals, but the effectiveness has still to be proven clinically.

Individuals with autism are at increased risk of having co-occurring mental health conditions such as anxiety and depression . Many of those affected find that existing psychological and drug-based treatments for their conditions have limited impact. Based on research into the ways interoception can influence emotions and behaviour, Sarah Garfinkel ( University of Sussex ) presented an innovative approach to help people with autism who develop an anxiety disorder. This approach aims to help sufferers manage the stress they feel in response to unexpected changes, by tuning into their own heartbeat to reduce anxiety levels. This treatment, known as interoception-directed therapy , is computer based and uses a finger monitor to measure users’ heartbeats as they move through a series of tests and training exercises. A clinical trial is being conducted to understand how effective this approach can be in the short and long term. If effective, the potential is immense and there are plans to develop an app version.

Given their ubiquitous digital activity, the use of DHIs may be preferred by children and young people. Richard Andrews ( Healios ) introduced ThinkNinja , a downloadable app designed to help 11-18 year olds learn about mental health and wellbeing and develop skills to help them build resilience and stay well. Built using the principles of cognitive behavioural therapy , the user is coached by the AI-powered app and the skills of a clinical psychologist, to help them deal with a range of mental health issues. Currently, ThinkNinja is a commissioned service only, available in the UK via the NHS, schools, local authorities and charities working with young people.

Cancer

Cancer screening can save lives by finding cancers at an early stage, or even preventing them. The UK currently has three screening programmes for bowel, breast and cervical cancer.

Skin cancer is one of the most common cancers. When diagnosed and treated early, melanoma is curable. Rotimi Fadiya ( PRSM Medical ) introduced The sKan , a low-cost non-invasive handheld device for diagnosing melanoma that provides a quantitative assessment. The technology is based on research showing that cancerous cells are warmer than normal cells. The sKan’s thermistors monitor cancerous cells' heat emissions in real time, creating a heat map showing which cells recover more quickly from thermal shock, indicating the presence of melanoma. The device is still being developed with a view to clinical testing and regulatory approval.

Breast cancer is the most common type of cancer in the UK. Early stage detection with suitable treatment can reduce mortality, so there is a lot of interest in developing faster and lower cost ways of diagnosing breast cancer earlier . Francisco J Gonzalez ( Higia Technologies ) described how the Eva bra is being developed for the early detection of breast cancer. Eva uses thermal sensing and artificial intelligence to identify abnormal temperatures in the breast that can correlate to tumour growth so that users are alerted to any disturbing changes. The Eva bra is in early development. It is worth noting that thermal imaging for cancer screening is a controversial area .

Radiotherapy is generally considered the most effective cancer treatment after surgery. Proton beam therapy is a type of radiotherapy that uses a beam of high energy protons generated by a cyclotron to treat specific types of cancer (e.g. brain, head and neck cancers). Gillian Wheatfield ( Christie Hospital, Manchester ) explained how precise targeting of the proton beam reduces damage to surrounding healthy tissue and vital organs (e.g. the spinal cord). In the UK, The Christie Centre which opened in 2018, currently provides high energy proton beam therapy, with a second centre at University College London Hospital due to open in 2021.

Surgery

The convergence of surgical expertise and digital technologies via imaging, virtual and augmented reality (VR and AR), 3-D reconstruction, simulation, 3-D printing, navigation guided surgery and robotic assisted surgery techniques, promises to transform future surgical care .

Advancements in VR and AR are starting to impact surgical training. In 2014 around 13,000 medical students, professionals, and interested lay people from more than 100 countries watched an operation live via a camera on a Google Glass worn by colorectal surgeon Shafi Ahmed , while he was performing surgery to remove cancerous tissue from the liver and bowel of a 78 year old patient in London. This was the first time Google Glass had been used during an operation in the UK and demonstrated how a broadcast could reach anybody with an internet connection. In 2016, Ahmed performed surgery on a cancer patient that was streamed live online, using 360-degree virtual reality video and viewed by 55,000 people in 140 countries. Now he is leading an effort to build a fully digital hospital in Bolivia.

Robotic surgery, or robot-assisted surgery is a type of minimally invasive surgery which allows surgeons to perform complex procedures with more precision, flexibility and control than is possible using conventional techniques. Compared to open (large incision) surgery, robotic surgery is claimed to cause less trauma, minimal scarring and needs less recovery time. Mark Slack ( CMR Surgical ) described the Versius surgical robotic system which is a rival to the da Vinci system used in some hospitals in the UK. Versius, is a portable modular system of robot arms with a small footprint that can be wheeled into an operating theatre. In a typical scenario, three or more robots are used to perform a range of procedures, with one arm holding an imaging probe and the others equipped with surgical instruments. The surgeon uses gaming style controllers and a 3D display screen at a console in the theatre to perform the procedure. The underpinning innovation for the system is the robotic arm which allows seven degrees of movement . Versius has now been used for operations in the UK .

Katerina Spranger and Liya Asner explained how Oxford Heartbeat has developed computational tools to facilitate surgical planning for minimally invasive surgery. Aneurysm surgery requires precise spatial understanding of the vascular anatomy and surrounding tissue to visualise the surgical intervention and pre-define the surgical steps. By reconstructing accurate 3-D anatomy from pre-operative scan data she presented an example of how this approach can be used in planning for aneurysm endovascular stent surgery by helping surgeons choose the best stent and placement for the patient. Potentially, this could reduce waste of devices, complications and costs.

Disease

The European Union defines a disease as rare if it affects fewer than 1 in 2,000 people. Due to the limited market size and the cost, development of treatments for rare diseases continues to be challenging, despite the incentives in the Orphan Drug Acts of various countries worldwide . The defective gene underlying Duchenne’s Muscular Dystrophy (DMD) was identified in the mid-1980s , however, it took around 30 years for the first approved therapy for DMD to appear and these work only in patients with specific mutations. Josie Godfrey and Fleur Chandler explained how Duchenne UK has brought 8 pharmaceutical companies together through Project Hercules to pool data and resources to accelerate the discovery and development of new therapies for Duchenne’s Muscular Dystrophy (DMD). Initiatives similar to Project HERCULES for other rare diseases could have similar benefits for accelerating the development of new therapies.

Over 5% of the world’s population suffers from hearing loss and this figure is expected to rise to 10% by the year 2050. Krishan Ramdoo ( Tympa Health ) described a smartphone-based hearing health assessment system aimed at simplifying the clinical pathway for patients and professionals by improving the communication between GPs and ENT specialists to bridge primary and secondary care. The Tympa system combines: an otoscope for assessing ear health; earwax removal by micro-suction; a screening hearing test; the creation of a digital hearing record with integrated machine learning; and the capability for remote consultation with an ENT specialist. Tympa is currently undergoing trials with the NHS and being rolled out in the Boots Hearingcare network.

Eye diseases affecting the cornea are a major cause of blindness worldwide. Around 5 million people suffer total blindness due to corneal scarring . Corneal transplantation is the treatment of choice for loss of corneal function, however, it is limited by the supply of corneal donors. Bioprinting using bioinks is an emerging technology for the fabrication of functional tissue constructs to replace injured or diseased tissues. Che Connon (Newcastle University and Atelerix ) talked about efforts to plug the gap between supply and demand for corneas for transplant surgery by embedding live, functional corneal cells in a hydrogel to create cell-laden bioinks for 3-D bioprinting of a corneal stroma equivalent . When combined with continuous bioprocessing of stromal cells and 4-D tissue engineering using localised cell activators, bioprinting could potentially be used to ensure an unlimited supply of corneas in the future.

Drug Discovery and Development

Stem cell therapy , also known as regenerative medicine , aims to promote the repair of diseased, dysfunctional, or injured tissue using stem cells . For several decades, stem cell therapy has been used to treat people with conditions such as leukaemia and lymphoma , but its use to treat other diseases is unproven and a cause of concern for regulatory bodies . Osman Kibar explained how Samumed is developing regenerative therapies based on small molecule drugs targeting the Wnt pathway , which is one of the key signalling pathways for controlling the differentiation of adult stem cells. Dysregulation of the Wnt pathway in tissues invariably leads to disease in that tissue, so Wnt pathway modulation has potential as a therapy for degenerative diseases. Although targeting a key cell signalling pathway such as Wnt can be problematic , Samumed are developing a pipeline of treatments for a range of diseases from osteoarthritis to idiopathic pulmonary fibrosis based on drug targets upstream of Wnt receptors, rather than Wnt receptors on the cell membrane.

Clinical trials are a vital part of the drug development process. There are tens of thousands of clinical trials taking place globally, each requiring the recruitment of eligible patients for their success, but this has become an increasing challenge. Maya Zlatanova revealed how the FindMeCure Foundation is bringing clinical trials and patients closer together by educating patients about clinical trials and has developed a searchable database of clinical trials so that patients can learn what trials are available that provide access to innovative therapies. On the converse, via Trialhub , FindMeCure provides data to help clinical trial organisers with regards to country and site selection, as well as patient recruitment and engagement. So far, this free service has helped nearly 400,000 patients in their search for clinical trials.

Medical Education

Advances in medical education have long played a vital part in informing clinical practice. Given the importance of nutrition to human health and the benefits that dietary patterns can have on cardiovascular disease risk and overall mortality , there is a belief that nutrition training should be a compulsory part of medical education, as a way of tackling the increasing burden of chronic lifestyle-related disease in the UK and worldwide. There is also a growing interest in culinary medicine as a way for clinicians to engage better with their patients on lifestyle-related disease. Iain Broadley and Ally Joffee described how Nutritank , an information and innovation hub for food, nutrition and lifestyle medicine, was set up to encourage UK medical schools to increase the levels of nutrition and lifestyle education in their curricula. Nutritank is now part of the NNEdPro network and offers a number of resources for medical students and healthcare professionals.

Innovation

Innovation is critical in enabling the NHS to deliver better outcomes for patients. However, ensuring the adoption and spread of innovations can be challenging. Chris Chaney discussed the work of CW Innovation in delivering new initiatives and improvements from a smartphone app that provides advice to new parents, to work with the Chelsea and Westminster Hospital Burns Unit on the in-house production of bespoke face masks and splints, for facial scar healing. They are also working with Digital Health London to speed up the adoption of digital health innovation in the NHS.

Medical progress is dependent upon the successful translation of basic science discoveries into new medical devices, diagnostics, and therapeutics. “Technology transfer” is the process by which new innovations flow from the laboratory bench to commercial entities and then to market . Since its founding in 2000, Cleveland Clinic Innovations (CCI) , the commercialization arm of The Cleveland Clinic , has translated 3400+ inventions in health IT , medical devices , therapeutics and diagnostics , and delivery solutions into 800+ granted patents, 450+ licenses and 40+ spin-offs. Peter O’Neil revealed how CCI maintains its innovation pipeline using its INVENT (Ideas; Need; Viability; Enhancement; Negotiations; Translation) process and a team of market analysts, subject matter experts and former medical industry leaders to mine, assess, and commercialize new innovations.

Industry is increasingly looking to work with small venture capital -backed companies, or universities, to capitalise on their early research capabilities. Funding of early-stage translational research is important for the delivery of investment-worthy opportunities to the venture capital community. However, there are a limited number of investors willing to offer the sums involved. Steve Rockman chatted about how Merism Capital provide seed investment to health & education start-ups.

Design is an iterative process in which a prototype solution, selected from a variety of potential solutions to a problem, is tested and revised as needed. In patient-centred design , this process is focused on the patient and their specific needs and considers a range of other factors, such as the environment and economics of the patient’s situation. Nicole Parks and Dipanjan Chatterjee described Medtronic’s approach to patient-centred design via their Applied Innovation Lab (AIL) approach. Much of AIL’s work is focussed on experience design and solution design rather than creating prototypes of new medical devices or apps.

We will all die and we will all have to die somewhere. Of the 500,000 or so people who die each year in the UK, around half of these deaths occur in hospital . Yet 70% of people would like to die at home . Having an advance care plan is an effective way of giving people control over where they end their life and is an important part of end of life care . Ivor Williams ( The Helix Centre ), talked about how human-centred design had been used to tackle care planning for emergency hospital admissions ( ReSPECT ) and a digital platform designed to help individuals and families create an advance care plan ( Amber Care Plans ) that can be shared with family, carers and GPs.

Conclusion

The RSM Innovation meetings are always worth attending. The format of the meetings and the breadth of innovations presented make for a very interesting and stimulating day. What is clear from the 2019 meetings is that digital technology and artificial intelligence are driving healthcare innovation in a wide range of areas, from patient monitoring, to new disease treatments, to improving surgical procedures. The opportunities that are now available for individuals to use digital technology to become active participants in managing both their health and their diseases are exciting and welcome developments. The potential of using data from wearables as digital biomarkers for the assessment of the mental health status of individuals could be a powerful and much needed tool as more and more people suffer mental health issues in society. The use of patient-centred design to improve the patient experience, particularly with regards to end of life care is also welcome, as disease can often be viewed as a scientific and/or technological problem to be solved, while overlooking the “humanness” of the situation.

Unfortunately, the 20th RSM Innovation Summit scheduled for 25th April 2020 has now been cancelled because of the current corona virus pandemic, but hopefully it will go ahead later on in the year.

Targeting the Host Immune Response in Patients Hospitalised with Severe COVID-19

Wed, 01 Apr 2020 14:55:18 GMT

The COVID-19 pandemic which recently originated in China has had a significant impact on the populations , healthcare systems and economies of many countries worldwide. People who get infected appear to vary in their response to the virus , from being asymptomatic or having mild symptoms, to having severe respiratory symptoms which require hospitalisation and can even result in death. Unfortunately, the elderly and people with co-morbidities are often to be found in the latter group, although deaths of people in their twenties or teens have been recorded .

Severe responses to respiratory virus infections are often characterised by an exaggerated inflammatory response in which pro-inflammatory cytokine release from damaged lung cells attracts a variety of activated immune cells to the lungs which then cause further lung damage. This appears to also be the case for severe COVID-19 infections . Controlling this excessive immune response will be important in the control of severe disease. However, the aim would be to attenuate the response, rather than ablate it. Total ablation of inflammation would likely promote disease mortality, whereas attenuation should provide protection against the damaging effects caused by excess inflammatory responses, whilst preserving essential innate host defence activities to help clear the virus. As a result, the damaging effects of the excessive inflammatory response would be blunted, but its protective and disease pro-resolution effects would be preserved.

Currently, Clinicaltrials.gov lists 239 trials that are planned, or in recruitment, as academic and industrial groups race to develop therapies for COVID-19-induced disease. Most of these are aimed at testing vaccines or anti-viral drugs. None appear to be aimed at testing inhibitors of p38MAPK as immunomodulators for use in severe COVID-19. However, I think such inhibitors have potential and deserve consideration for testing. Several years ago, whilst working at hVIVO, I set up and ran a programme aimed at identifying immunomodulatory drug targets for the treatment of influenza-infected patients who are hospitalised with severe symptoms. The result was a drug repurposing strategy based around p38MAPK inhibitors. Full details can be found in these two submitted patent applications . For various commercial and financial (not scientific) reasons, although a clinically tested p38MAPK inhibitor was in-licensed, the concept was never tested in clinical studies. Given the similarities between severe COVID-19 and severe influenza and the desperate need for drug treatments for hospitalised patients, I do think p38MAPK inhibitor treatment is worth trialling alongside other approaches.

Please contact me if you would like to discuss further.

Note added 20-MAR-2021: The first of the patent applications referred to above ( Immunomodulator I ), EP3478322 , was granted a European patent on 30th December 2020.

Note Added 06 -MAR-2024: European, US and Japanese patents have now been granted for ( Immunomodulator I ) EP3478322 .

Note Added 02-May-2025: US and South Korean patents have been granted for the second of the two patent applications ( Immunomodulator II ) referred to above .

Knowledge Extraction Using a Knowledge Graph

whittp163@gmail.com (Paul Whittaker) — Thu, 20 Feb 2020 18:09:27 GMT

Image Source: Nickel, M et al. (2015)

In the era of the zettabyte , patterns can be identified in data and results ranked, without necessarily knowing the reasons why, as exemplified by the Google search engine . However, for the value of big data to be fully realised, knowledge needs to be extracted from that data. Knowledge extraction is the creation of knowledge from data sources that are unstructured (e.g. text, documents, images) and/or structured (e.g. RDMS - relational database management systems ). Knowledge graphs are central to this process, with the Google Knowledge Graph , the best known example. Getting to an understandable definition of a knowledge graph is not easy , although there are some good articles aimed at demystifying the subject for non-experts . However, the potential of knowledge extraction is huge, so when I received an invitation to attend the Grakn Cosmos meeting in London on 6-7th February 2020, I was intrigued to find out more about knowledge graphs and their utility, particularly for drug discovery and development, healthcare, and life sciences in general.

Grakn is a knowledge graph for artificial intelligence (AI) which uses automated reasoning to extract knowledge from diverse and complex data sets in its knowledge base . Grakl is the query language . Both Grakn and Grakl are open source and are already being enthusiastically adopted by a community of collaborators, developers and users for a range of applications in the life sciences , as well as defence and security , financial services and robotics . In this article, I will cover the applications in healthcare and biology highlighted at Grakn Cosmos.

Open access journals and datasets have become increasingly common in recent years. Now, pharma has started to embrace the concept of open innovation , at least in the earlier phases of drug discovery. Data gathered in clinical trials are critical for making informed decisions about patient care, designing new research proposals and crafting regulations. However, although vast amounts of clinical trial data are generated, only around 50% are made available for use/analysis outside of pharma. Furthermore, only a portion of clinical trials results are ever published and these tend to be biased towards positive, rather than negative trials . Sharing of clinical trial data could facilitate the development of new disease therapies and allow the generation of novel data-driven hypotheses not formulated in the original clinical studies . Therefore, there have been calls to promote data sharing and initiatives are underway to develop structured open databases of clinical trial data . Sanchita Bhattacharya ( Bakar Computational Health Sciences Institute ), talked about the benefits and challenges of sharing clinical trials data and how the open access knowledgebase ImmPort facilitates the use of systems immunology data to better understand the dynamic complexities of the immune system , as well as provide a reference data set for human immunology , via the ten thousand immunomes project . Clinical and flow cytometry data from ImmPort and the Immune Tolerance Network have been used to identify subsets of blood cells in patients with anti-neutrophil cytoplasmic antibody-associated vasculitis that predicted response to cyclophosphamide , or rituximab treatment. Finally, a new influenza vaccine knowledge base, ImmGrakn, is being built to leverage crowd-sourced clinical trial data in ImmPort. The aim of ImmGrakn is to better understand vaccination responses based on age, gender, race, medication etc.

A clinical decision support system (CDSS) is a health information technology system designed to assist clinicians and other healthcare professionals in clinical decision-making . Such systems may suggest next steps for treatments, provide medical information alerts, clinical guidelines , diagnostic support, or highlight dangerous drug-drug interactions. CDSSs have become a hot topic in artificial intelligence as medics are increasingly overwhelmed and patient consultation times continue to shorten. Alessia Basadonne ( Medas ) described SOPHIA, a text-mined knowledge graph which matches patient data to hospital diagnostic guidelines for integrated care in oncology in an Italian hospital. Natural language processing (NLP) using Apache cTAKES was used to analyse free text documents (PubMed articles, guideline text, patient demographic information and unstructured text from medical records) and medical entities were annotated as SNOMED-CT concepts , before migration into Grakn. Automated reasoning then extracts the outputs as medical information, alerts and tailored recommendations.

Healthcare is a complex system. An array of factors and multiple inter-dependencies influence outcomes. Healthcare providers produce large amounts of information as written and digital records, from the patient level (test results, vital signs etc.) to the organisational level (waiting times, outcomes, financial performance etc.). Potentially, analysis of these data can provide useful insights that could be used to improve process measures (e.g. changes to the way patient bookings are made ) and outcomes (e.g. reducing missed patient appointments ). However, the unstructured nature of much of this organisational information makes it hard to extract useful knowledge. Mining of electronic medical records is an area of increasing interest and there are now initiatives underway in a number of countries, including Portugal , the US and the UK to extract insights and knowledge from such records for the benefit of stakeholders. Vincenzo Schiano ( University of Naples ) explained how he is using Grakn for the analysis of more than 10 million data entries (medical references, prescriptions and booking data) collected since 2014 through a public healthcare booking centre in Italy. A Grakn knowledge graph of data sets lacking an entity-relationship structure parsed from legacy databases and web services has been generated with the help of KGLIB . APIs are then used to integrate and study the data using different Python modules.

Bioinformatics has been an integral part of biological research in academia and industry for several decades. In the 1990s it was driven by the need to process and analyse sequence data from The Human Genome Project and, in the 2000s, by the analysis of high dimensional omics outputs . However, without developing computer models, data is basically noise. As a result, computer modelling of biological systems is vital to maximise the use of progressively larger and complex data sets. Knowledge extraction from this data deluge is now seen as being central to understanding disease biology and enhancing drug discovery efforts. Sven Sewitz and Muhammad Alkarouri ( Eagle Genomics ) explained how they are using Grakn to model the biological domain, particularly the microbiome . The importance of the microbiome in health and disease , the human host response and therapeutic response , has focussed efforts on its therapeutic modulation . In order to understand the functional mechanisms that underlie host-microbiome interactions, data from metabolomic and metagenomic studies are being combined with host disease co-variates to identify metabolites that affect microbiome growth and function and could be targeted in the development of novel disease therapies. According to Alkarouri, experimental biologists and bioinformaticians both find Grakn and Graql easier to work with than RDF technologies (which necessitate the involvement of semantic technology experts), by reducing the object-relational impedance mismatch often encountered when RDMSs are used.

Drug discovery and development is an expensive and lengthy process with a high failure rate . For drugs that make it through to clinical trials, finding the best clinicians in a specific disease area (e.g. respiratory, oncology etc.) to work with as key opinion leaders (KOLs), principal clinical investigators (PIs), or both, is an important part of the drug development process. Because of their asymmetric influence on the opinion and medical practice of their peers, KOLs are a key lever in pharmaceutical marketing and communications strategy , helping pharma raise awareness of new drugs. Traditionally, surveys and literature searches have been the main ways of identifying KOLs. However, mining of social networks is now receiving attention as a way of identifying KOLs. Paul Agapow ( AstraZeneca ) detailed how a social graph for the identification of KOLs in the drug trial space is being built using data from social networks and the literature. By combining analysis of this graph with text analysis of social network conversation topics and links with other investigators, AZ hope to identify KOLs that can be engaged, plus clinical investigators and sites that can be recruited into clinical trials.

Conclusion

Judging by the talks at Grakn Cosmos, the ability of knowledge graphs to identify novel connections and reveal insights within massive data sets is impressive. These connections and insights would be difficult, or even impossible to make otherwise. The impact on the healthcare spectrum, from drug discovery through to clinical treatment, potentially, could be enormous. In the UK, knowledge extraction using NHS data sets could be used to identify ways to help a service which is under immense pressure to meet rising patient demand . It is still early in the game, but the development of targeted applications which result in positive outcomes that are then adopted by the NHS is a necessary first step. It will be interesting to see how the field of knowledge extraction develops in the coming years and the impact it will have on healthcare and drug discovery and development. I am optimistic that open source knowledge graphs such as Grakn/Grakl and their community of collaborators, developers and users can help catalyse such developments.

Drug Discovery - Looking Back to the Future

Tue, 04 Feb 2020 17:49:04 GMT

The reductionist target-driven approach to drug discovery, fuelled by sequencing of the human genome, omics technologies and genetic studies has not been as successful in generating new therapies as was initially hoped. Sixty percent of drugs fail in clinical trials due to lack of efficacy, because the underlying therapeutic concept is flawed. This weakness in hypothesis generation is due to gaps in understanding of the underlying human disease biology and drug target validation. So I was interested to attend the ELRIG Drug Discovery 2019 conference entitled “Looking Back to the Future”, held at the ACC in Liverpool on 5-6 November 2019 and catch up on the latest thinking and approaches to tackling these issues.

With 8 topic-specific tracks across two days, plus plenary talks, poster sessions and an exhibition featuring 100 companies showcasing their latest drug discovery aids, I was only able to attend a selection of what was on offer. So in this post, I will be concentrating on the talks I attended in sessions dealing with artificial intelligence, cellular models of disease and biomarker strategies in drug discovery. But first, I’ll start with the three plenary talks by Mene Pangalos ( AstraZeneca ), Fiona Marshall ( MSD UK Discovery Centre ) and Melanie Lee ( LifeArc ), who each gave their perspectives on the current issues faced in the discovery of new drugs and how improvements might be made.

Plenary Talks

Astra Zeneca’s 5Rs framework has already resulted in a 4-fold improvement in clinical trial success rates. In the first plenary talk of the conference, Mene Pangalos explained how AZ aim to improve on this, by rigorous drug target selection and validation using data science and artificial intelligence , as well as technologies such as CRISPR and multi-modal molecular mass spectrometry imaging . Artificial intelligence, in particular, is being leveraged across the drug discovery process in a number of areas in an attempt to make the design-make-test-analyse (DMTA) cycle more efficient and effective. AZ are also expanding the number of therapeutic modalities beyond the trinity of small molecule, antibody and peptide approaches, to include anticalin proteins , proteolysis targeting chimeras ( PROTACs ), antisense and bicyclic peptides , amongst others.

Neurodegenerative diseases such as Alzheimer’s disease (AD) have been particularly challenging for the development of new drugs. Only 2 classes of drugs are currently approved for therapeutic use in AD ( acetylcholinesterase inhibitors and NMDA receptor antagonists ). These drugs are able to lessen symptoms (e.g. memory loss and confusion), but are not disease modifying. Fiona Marshall explained how lack of progress in developing new AD therapies is largely due to poor mechanistic understanding of AD, as well as poor predictably of disease models. Drugs based on the genetics-driven amyloid hypothesis have failed to show efficacy in clinical studies , and a recent report suggests that high levels of brain amyloid alone are not sufficient to cause AD. As a result, clinical trials testing possible interventions aimed at other drug targets are currently in progress. Whether the failure of trials of anti-amyloid drugs was due to selecting the wrong drug dosages, the wrong patients, or other reasons, is unclear. However, future success will require biomarkers , neuroimaging and brain activity monitoring for testing drugs with the right mechanism of action in the right patients at the right stage of the disease.

The translation of drugs from pre-clinical to clinical testing is clearly an inefficient process that will undoubtedly benefit from well validated therapeutic opportunities. However, Melanie Lee cautioned that, in addition, future products will also need to carry richer data packages, including information on which patient sub-groups to target, as well as companion diagnostics. There will also be an emphasis on diagnosing patients earlier in their disease course, as current points of intervention tend to be late in the disease trajectory. So, in addition to targeted interventions, surveillance screening will be very important. For example, Oncimmune’s Early CDT-Lung test can detect lung cancer 4 or more years before clinical diagnosis. Future improvements in the diagnosis, treatment and outcomes for patients may also come from using crowd sourcing approaches .

Cellular Models of Disease

The lack of preclinical models that faithfully mimic key aspects of human disease biology in patients has long been an Achilles heel of the drug discovery process. The Holy Grail is to have models that are more capable of predicting clinical success and drug side effects. Organoids derived from adult stem cells, differentiated embryonic stem cells, pluripotent stem cells (iPSCs) and precision genome engineering via CRISPR, offer new opportunities for the generation of diseased and healthy cell types that mimic at least some aspects of the disease in vitro .

There is a lot of excitement about using patient-derived iPSCs to overcome the constraints of limited access to viable human tissue and poorly translatable animal models, by enabling the generation of large, reproducible quantities of biologically relevant cells from healthy and diseased individuals. Paul Andrews ( National Phenotypic Screening Centre ), reviewed how phenotypic screening by high content imaging of organoids and iPSC-derived cells is being used to marry “old style” (physiology-driven) and “new style” (target-driven) drug discovery approaches. Phenotypic screening makes no assumptions about the target and limited assumptions about the mechanism of action. The use of iPSCs in phenotypic screening will be aided by: the development of best practices for iPSC disease models ; mapping cell phenotypes to genotypes with single cell genomics ; studying how genetic variations affect cell behaviour by integrating different omics data sets from human iPSCs ; developing well characterised collections of iPSC cell lines for the research community and; developing a collection of cellular reference maps for all the cell types in the human body.

There are no effective therapies to treat Glioblastoma (GBM), which is the most common type of brain tumour. Surgery, radiotherapy and chemotherapy, even when combined, only increase survival by a year, on average. Developing clinically effective treatments has been a challenge, despite increasing genomic and genetic knowledge. Steven Pollard ( Centre for Regenerative Medicine, Edinburgh ) discussed how patient-derived models, genome editing and high content phenotypic screening are being used to accelerate drug discovery for GBM. GBM stem cells (which have molecular hallmarks of neural stem cells) and non-transformed neural stem cells have been used as patient-derived models to identify tumour-specific vulnerabilities via genetic screens, or cell-based drug discovery. In addition, the glioma cellular genetics resource is generating a toolkit of cellular reagents and data to expedite research into the biology and treatment of GBM.

Wendy Rowan outlined GSKs approach to developing fit-for-purpose cellular models, by scoring models against sets of criteria, so that the most appropriate model(s) can be selected for the research question(s) being asked. Full characterisation of cellular models with respect to how well they model healthy and diseased human tissue physiology using “due diligence checklists” is now seen by GSK as being key to improving drug discovery. For any given drug target, several cellular models may be used to progress the target from validation to candidate selection. GSK are developing cellular models based on organoids , iPSCs and even assessing organ/body-on-a-chip approaches, based on microfluidic technology.

Artificial Intelligence (AI) and Machine Learning (ML)

As mentioned earlier, AstraZeneca are incorporating AI throughout the drug discovery process. Werngard Czechtizky explained how AZ are incorporating AI into medicinal chemistry by developing algorithms for reaction/route prediction, chemical space generation and affinity/property prediction for low molecular weight compounds, in the first instance, before potentially expanding out to other therapeutic modalities. The aim of doing this is to reduce costs, time, resources and the number of compounds tested (from around 2000 compounds to less than 500) in a 2-3 year time horizon. In terms of hit to lead optimisation , ML is being used for augmented design, predicting synthesis, analytics, and automated DMTA.

The extraction of biologically meaningful signals from large diverse omic data sets for target discovery is a major challenge. Michael Barnes ( William Harvey Research Institute ) described how ML and AI are being used to support drug discovery and drug repositioning from genome wide association study data using a tensor-flow framework. Over a thousand genetic loci affecting blood pressure have been identified . These data have been used to teach a tensor-flow algorithm to identify new BP genes. In human population genetics, ML is being used to identify benign human knockouts from exome sequencing data , as potentially safer drug targets with fewer side effects. In personalised healthcare, ML is being used to develop multi-omic predictors of response to biologic therapies .

Biomarker Strategies for Drug Discovery

Oncology leads the field in the development of biomarkers for drug development and clinical testing. Development of biomarkers for other disease indications lags behind, facing challenges ranging from sample access and quality, to the resolution and sensitivity of detection technologies and the difficulties of measuring low abundance proteins in plasma. In this session, technological approaches to biomarker detection and measurement were reviewed by a range of speakers from industry and academia.

Label-free detection methods utilize molecular biophysical properties to monitor molecular presence, or molecular activity. The main advantage of label-free detection is the elimination of tags, dyes, specialized reagents, or engineered cells. This means that more direct information can be acquired about molecular events, minimising artefacts created by the use of labels. Molecular events can also be tracked in real-time, and native cells can be used for greater biological relevance. Peter O’Toole ( University of York ) reviewed how label-free microscopy, can be used to complement and enhance omic and biochemical data by providing minimal perturbations to cellular systems, as well as being quantitative and allowing prolonged live cell imaging. Ptychography (a computational method of microscopic imaging ) does not rely on the object absorbing radiation, so if visible light is used to illuminate the object then cells do not need to be stained, or labelled to create contrast. This allows the collection of cell morphological data during apoptosis and cell division, as well as the observation of the behaviour of cells at the individual level.

Understanding the distribution, metabolism and accumulation of drugs in the body is a fundamental part of drug development. Multi-modal molecular mass spectrometry imaging (MSI) allows label-free analysis of endogenous and exogenous compounds ex-vivo by imaging the surface of tissue sections taken from fresh-frozen samples. Gregory Hamm explained how AZ is using MSI to study the abundance and spatial distribution of drugs and their metabolites within biological tissue samples and is also being used for model characterisation .

Idiopathic pulmonary fibrosis (IPF) is a lung disease that results in scarring of the lungs and causes progressive and irreversible decline in lung function, with an average life expectancy of 4 years after diagnosis. Currently, only Nintedanib and Perfenidone have been approved for the treatment of IPF, despite numerous phase II and III trials in the past 25 years . This failure is due to: a lack of understanding of the disease mechanism; lack of predictability of preclinical animal models and; the lack of biomarkers to diagnose the disease and monitor response to drug therapy. Sally Price described how the development of biomarkers for IPF is a strategic focus for the Medicines Discovery Catapult , in efforts to develop novel anti-fibrotics . The MDC is working on developing new models such as organ on a chip and 3D organoid models, as well as applying a range of technologies to identify and develop biomarkers for fibrosis. Simon Cruwys ( TherapeutAix ) talked about how a fibrosis extracellular matrix biomarker panel in serum had been used to develop an ex vivo tissue model of IPF .

Amyotrophic lateral sclerosis (ALS), also known as motor neurone disease (MND), or Lou Gehrig's disease, is a clinically heterogeneous neurodegenerative disease which causes the death of neurons controlling voluntary muscles. Most sufferers eventually lose the ability to walk, use their hands, speak, swallow, and breathe. Andrea Malaspina ( Queen Mary University of London ) discussed the search for biomarkers for ALS . The development of new therapies for ALS has been limited by a poor understanding of the molecular mechanisms underlying the disease , resulting in the failure of a large number of clinical studies. Proteomic experiments in individuals with a significant difference in prognosis and survival at different time points in disease progression have identified potential biomarkers , such as neurofilaments and proteins involved in the humoral response to axonal proteins and in axonal regeneration. Natural history studies , clinical trials and a biological repository are being used as sources of tissue for biomarker identification and qualification. With regard to Parkinson’s disease , depression, loss of sense of smell and constipation are clinical features that often prelude PD symptoms . Therefore, clinical observations are being used to identify biomarkers that track these symptoms in patients for use in preventive neurology.

Although a cell’s proteome contains a lot of biologically and therapeutically useful information, proteome analysis has lagged behind genome and transcriptome analysis. This is due to the complexity of the proteomes of mammalian cells, tissues and body fluids and the wide dynamic range of protein concentrations that are encountered. The emergence of newer sophisticated mass spectrometry (MS) technology in the past decade, with higher resolution and faster scan rates, has enabled smoother and quicker identification of complex proteomes with shorter analysis periods. As a result, Ian Pike ( Proteome Sciences Plc ) explained, mass spectrometry-based proteomic platforms are being increasingly used for: therapeutic protein analysis; target identification and deconvolution; biomarker ID; analysis of target engagement; systems biology and; clinical studies. Ian presented a couple of case studies where MS had been applied to the study of pancreatic cancer and for plasma biomarker discovery in IPF .

Finishing the Biomarker session, Chantal Bazzenet ( Evotec ) talked about the portfolio of assays that Evotec have developed to aid the development of therapies for Huntington’s disease . Patients suffer uncontrolled movements, emotional problems, and loss of cognition. This progressive brain disorder is caused by aggregation of Huntingtin (HTT) protein . The wild-type protein is monomeric, but the mutated protein is aggregated and accumulates in neurons, affecting normal neuronal functioning. Evotec have developed assays to measure total and mutated Huntingtin (HTT) protein in mouse and human tissues.

Comment

Discovering new drugs is challenging and that will continue to be the case for the foreseeable future. Central to the whole drug discovery process is establishing the biological and disease relevance of a particular drug target. However, it is sobering to consider that it took over two decades after the defective genes causing cystic fibrosis (CF) and Duchenne’s muscular dystrophy (DMD) were identified, before the first FDA approved drugs ( Ivacaftor for CF and Eteplirsen for DMD ) were available to treat subsets of patients carrying specific mutations. My personal view is that target validation should called target qualification, as the drug target is not truly validated until it is shown that therapies based on the drug target hypothesis actually work in clinical trials. As I mentioned in the introduction to this post, this is not the case for 60% of pre-clinically “validated” targets...

In concert with the efforts to produce better drug targets and therapeutic hypotheses, it is clear that biomarkers for disease characterisation, early detection of disease, determining the trajectory of disease progression, patient selection for drug testing and, patient response to therapy, will be just as important for future clinical success as validated qualified drug targets. Interventions at earlier stages of the disease process are also required so that new drug therapies for common complex diseases are disease-modifying, or even curative, rather than just being symptomatic.

What is clear, is that modern drug discovery requires a multi-disciplinary approach employing a number of different technologies, from omics, to CRISPR gene editing, plus everything in between. In turn, this means that ever more complex data sets are being generated that present challenges, not just in analysis, but in interpretation and knowledge extraction. AI will certainly have a key role to play in the data science arena, as well as making the DMTA cycle more efficient and effective. However, the hypothesis-free approach that typifies the omics era of drug discovery can mean that the wrong datasets are generated and analysed, so no matter how “smart” the algorithm used for data analysis, the outputs will not be therapeutically relevant. Therefore, the focus on rigour and quality being pursued by pharma companies such as AZ in everything, from understanding the disease biology, to better target validation qualification, can only be a good thing. What the impact on clinical success rates will be is uncertain at this stage, so it really is a case of watch this space…

Artificial Intelligence and Drug Discovery

Wed, 17 Apr 2019 11:51:56 GMT

Creating new and cost-effective medicines

Image source: FierceBiotech

Intelligent augmentation by artificial intelligence (AI) is becoming more commonplace in daily life thanks to the dramatic improvements that have been made in computing power over the past decades. Clearly, building machines that can sense, reason and think like people (“ general AI ”) is likely to remain in the realms of science fiction for some time. However, most of us are now familiar with the “narrow” AI used to solve specific problems such as speech and facial recognition every time we use our smartphones.

Not surprisingly, many pharmaceutical companies are now turning to machine learning and artificial intelligence as a way to make drug discovery quicker, cheaper and more effective. This was the subject of the excellent free to attend ELRIG networking meeting “Artificial Intelligence in Drug Discovery” held at the CRUK Cambridge Institute on 20th March 2019.

The event featured three interesting presentations by speakers from Cambridge University, AstraZeneca and Benevolent AI on how this technology is being used to facilitate the discovery of new drugs.

The use of AI to mine and exploit the drug-like chemistry space for the most promising candidate molecules to synthesise and test is particularly attractive, given the vastness of this space. In the last 40 years, the discipline of chemoinformatics has created a set of computational drug design tools, (e.g. QSAR ) that have been used in the discovery of most recent medicines. In the first talk, Andreas Bender ( Centre for Molecular Informatics , Cambridge University) explained how chemical data are now being combined with biological data to generate algorithms to determine the link between chemical activity and biological effect, and answer questions such as:

· what is the biological mechanism by which a drug exerts its phenotypic effects?

· which drug compound should be synthesised to have a specific biological effect?

· which patients will respond better to a particular drug?

These algorithms use molecular structure, phenotype, protein and mode of action data as the core data sets, as well as molecular pathway, bioactivity and phenotypic response data. Algorithms developed using such data sets had been successfully used to:

· Predict the protein targets of chemical compounds from phenotypic screening experiments;

· Identify drug compounds that induce differentiation of stem cells ;

· Predict drug compounds that modulate sleep and;

· Predict and prioritise drug combinations that improve the efficacy of anti-cancer treatment .

Bender highlighted the fact that poor understanding of biological systems still meant that the “unknown unknowns outnumber the known knowns”, so more data was needed to fill in the many gaps in understanding of the biology that still exist.

Drug discovery requires the optimisation of a range of different parameters in concert. In the second talk Adam Corrigan ( AstraZeneca ) gave an overview of how AZ is incorporating AI into early drug discovery , from efficient extraction of information from cellular screening assays using image analysis, to building computational models that can be used to predict compound activity. The goals of this work are to get a better understanding of the disease biology and make the discovery process more effective, predictive and economical. AI is being incorporated in all aspects of the drug discovery process at AZ, from robotics and assays through to data analysis and interpretation, with the aim of speeding up the entire design-make-test-analyse cycle of drug compound synthesis and testing. Certainly, AZ is making a strong commitment to AI and it will be interesting to see if this investment pays off in further reducing their phase II attrition rates, which have already improved from 4% in 2010 to 19% in 2016 on the back of their 5Rs framework .

In the third talk, Andrea Taddei talked about how Benevolent AI has identified candidate drug targets for motor neurone disease (amyotrophic lateral sclerosis, ALS ) using their AI platform. ALS results in the degeneration of motor neurones in the brain and spinal cord so activities such as gripping, speaking swallowing, walking and breathing become increasingly difficult, or even impossible, as the condition progresses. Life expectancy in people with ALS is between two and five years. Although Riluzole and Edaravone have been approved for use in ALS they have a modest improvement on survival and quality of life, so there is a high unmet medical need to develop more effective therapies for ALS. The Benevolent AI platform is a cloud-based representation of over a billion known and inferred relationships between genes, disease, symptoms, diseases, proteins, tissues, species and candidate drugs. “Knowledge graphs” of genes associated with a disease, or drugs that affect the disease are produced by querying this repository and contextualise this information aiding the generation of hypotheses that can be tested experimentally. Using this approach, Taddei described how Benevolent had used their platform to identify a list of existing drug compounds that might have potential as treatments in ALS.Drugs against the five most promising targets identified were tested by the Sheffield Institute for Translational Neuroscience ( SITraN ) and one was identified as having therapeutic potential. Further testing using in vitro co-cultures of ALS patient-derived astrocytes and motor neurons, and in vivo mouse models of ALS provided further support for this lead target and it is now being developed for use in clinical trials. If Benevolent is successful in developing a new treatment for ALS based on AI approaches it will be an important milestone in proving the concept for AI-driven drug discovery.

As with all new technologies, there are enthusiastic proponents and sceptics about the impact that AI will have on drug discovery. What was clear from the talks at this meeting is that data, and lots of it, are one of the key requirements to making progress in this area. Time will tell how valuable AI will be, but if the impacts in other areas of society are any benchmark, I believe AI can make a significant impact by greatly augmenting our ability to mine biological data and extract therapeutically important insights, as well as greatly improve many of the interconnected processes that typify modern drug discovery.

Gene Editing and Drug Discovery

Fri, 05 Apr 2019 13:44:39 GMT

From Identifying Drug Targets to New Disease Therapeutics

Image source: Genetic Literacy Project

Gene editing has, on occasion, been a cause of controversy , but there is no denying that this powerful technology has numerous positive uses. The impact that CRISPR-based genome engineering is having on drug discovery was covered at the inaugural ELRIG meeting on this topic held at the Kings Centre in Oxford on 27th and 28th February 2019.

CRISPR ( C lustered R egularly I nterspaced S hort P alindromic R epeat) DNA sequences are a feature of the defence system that bacteria use to defend themselves against viruses. Snippets of the invading viral DNA are incorporated into the spacers in the CRISPR DNA sequence and act as a "photofit" reference to the DNA of the virus so that the next time the virus attacks, the bacteria remembers the virus and is able to destroy it. This is achieved by converting the viral DNA in the spacer into RNA which then attaches to the corresponding DNA piece on the attacking virus. A Cas ( C RISPR- as sociated) enzyme, produced by Cas genes located near the CRISPR sequence and attached to the RNA molecule subsequently cleaves the target DNA, rendering the virus harmless.

Image source: Lee S, et al. Journal of Cellular Biotechnology (2015)

In 2012, researchers showed that the CRISPR/Cas9 system could be used to cut any genome at any specified place. Further publications in 2013 showed that the technology could be used for precise and efficient genome editing in living human and mouse cells.

Image source: Vox

Since then, the technology has literally "gone viral", with CRISPR editing being successfully used in yeast, worms, flies, fish and monkeys. This has been paralleled by interest in scientific and commercial uses of CRISPR editing, as well as ethical concerns around using the technology to create designer babies.

The 20 year backstory to the development of CRISPR involved the work of a number of scientists in different parts of the world, so it was very appropriate that one of these pioneers, Virginijus Siksnys, from Vilnius University in Lithuania kicked off the meeting by describing his work on characterising the Cas9 nuclease, which is the variant that is most efficient at cutting human and animal DNA. This was followed by a range of talks from academic and industry scientists describing how CRISPR is impacting drug discovery from target identification and validation through to the use of CRISPR as a therapeutic modality.

By using the CRISPR/Cas9 system to activate or inhibit genes, genome wide CRISPR screens have been used to identify factors involved in cellular reprogramming (E. Metzakopian, Cambridge University), genes involved in drug resistance in BRAF mutant colon cancer (U. McDermott, AstraZeneca) and essential human genes (J. Moffatt, University of Toronto). Jon Moore (Horizon Discovery) reviewed the use of CRISPR for identifying drug targets for synthetic lethality in cancer , but stressed the importance of subsequent validation of identified hits.

One of the key reasons for failure of drugs at phase II is lack of efficacy so increasingly, companies such as Astra Zeneca, as part of their 5Rs framework , are using CRISPR as a key technology in their target discovery activities . Samantha Peel (AstraZeneca, Cambridge) described how genome wide CRISPR screens were being used to identify drug targets that regulate oncogenic protein stability and the technical challenges they had encountered, from false negatives to compensatory mechanisms.

In vitro cell culture models using cell lines and primary cells isolated directly from tissues continue to be a mainstay of drug discovery research. Because primary cells are isolated directly from tissues they retain normal cell morphology and many of the important markers and functions seen in vivo, at the expense of having a finite lifespan and limited expansion capacity. Although performing genome editing in low passage, primary human cells is notoriously difficult, Klio Maratou (GSK, Stevenage) described a workflow for efficient CRISPR editing in primary human lung fibroblasts. In vitro three-dimensional cell culture models in which embryonic and adult stem cells self-organise into organoids are becoming increasingly important tools in therapeutic research and development. Bon-Kyoung Koo (Institute of Molecular Biotechnology, Vienna) described how CRISPR gene editing had been used to correct a mutation in the cystic fibrosis transmembrane regulator (CFTR) locus by homologous recombination in cultured intestinal stem cells of cystic fibrosis patients and also the generation of biallelic conditional or reversible gene knockouts in various mammalian cell lines using the technique of CRISPR-FLIP .

Genetically modified animal models are a powerful way to study gene function and generate models of human disease. Ben Davies (Oxford University) described how maternal cell supply of Cas9 protein to zygotes results in increased CRISPR mutagenesis rates and how CRISPR gene editing had been used to generate mice containing a mutation in the gene GRIA3 that causes severe sleep-wake cycle dysregulation in two human brothers.

There is a lot of excitement about the use of CRISPR gene editing as a way to treat human disease and genetic defects and two talks reviewed progress in this area. Toni Cathomen (University of Freiburg) discussed using genome editing as an approach to treat diseases of the haematopoietic system and Matt Porteus (Stanford University) reviewed work on editing of hematopoietic stem cells , with reference to sickle cell disease where gene correction approaches are getting closer and closer to phase I/II clinical trials . Matt Porteus also talked about editing hematopoietic stem cells to phenotypically correct mucopolysaccharidosis type I . Successful translation of CRISPR-based therapeutics into the clinic will depend on identifying and minimising deleterious off-target mutations introduced during the gene editing process and Marcello Maresca (AstraZeneca, Cambridge) described an experimental strategy for defining and quantifying gene-editing nuclease off-target effects in whole organisms .

To complement the talks described above, a number of companies gave presentations on services, reagents and equipment that can be used to aid the CRISPR gene editing workflow:

Company	Product
Synthego	Arrayed CRISPR screening libraries
Horizon Discovery	CRISPR screening services
Merck	CRISPR reagents
Integrated DNA Technologies	Custom gene synthesis and novel mutant Cas proteins
Labcyte inc	Liquid handling for CRISPR workflow
Takara Bio	Human iPS-derived disease model lines for drug screening
Hamilto n	Automated liquid handling equipment
Formulatrix	Automated liquid handling equipment
Integra Biosciences	Automated pipetting devices
Solentim	High throughput single cell cloning of CRISPR-edited cell lines
Aldevron	GMP manufacturing of Cas9 protein for clinical studies

In addition to the talks there was an accompanying scientific poster session with over 20 posters from various companies and academic groups covering a range of areas from optimising CRISPR vector systems through to microfluidic systems for automated gene editing. Two of the posters were presented in short poster spotlight talks given by Anne Goeppert (AstraZeneca, Cambridge) and Barbara Mair (University of Toronto) on using CRISPR for the generation of disease models in immune cells and the use of CRISPR-on-a-chip to screen for modifiers of CD47 expression, respectively.

All in all, a well organised and attended informative meeting on the use of CRISPR for drug discovery and the first in an increasingly popular series of free to attend meetings organised by ELRIG in 2019.