Category Archives: Coronavirus

Beyond the Vaccine: AI’s Expanding Role in LNP mediated Drug Delivery

Lipid nanoparticles (LNPs) have evolved from a specialised drug-delivery technology into a cornerstone of modern medicine. Their success became evident during the COVID-19 pandemic, enabling the delivery of the mRNA used in the Pfizer-BioNTech and Moderna vaccines. However, their applications extend far beyond vaccination, as LNPs can also deliver siRNA, plasmid DNA and gene-editing machinery, creating opportunities to treat genetic diseases, cancer and many other conditions.

Yet a fundamental challenge remains: how do we design an LNP that delivers the right payload, to the right cells, in the right place?

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The “AI-ntibody” Competition: benchmarking in silico antibody screening/design

We recently contributed to a communication in Nature Biotechnology detailing an upcoming competition coordinated by Specifica to evaluate the relative performance of in vitro display and in silico methods at identifying target-specific antibody binders and performing downstream antibody candidate optimisation.

Following in the footsteps of tournaments such as the Critical Assessment of Structure Prediction (CASP), which have led to substantial breakthroughs in computational methods for biomolecular structure prediction, the AI-ntibody initiative seeks to establish a periodic benchmarking exercise for in silico antibody discovery/design methods. It should help to identify the most significant breakthroughs in the space and orient future methods’ development.

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What can you do with the OPIG Immunoinformatics Suite? v3.0

OPIG’s growing immunoinformatics team continues to develop and openly distribute a wide variety of databases and software packages for antibody/nanobody/T-cell receptor analysis. Below is a summary of all the latest updates (follows on from v1.0 and v2.0).

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Happy 10th Birthday, Blopig!

OPIG recently celebrated its 20th year; and on 10 January 2023 I gave a talk just a day before the 10th anniversary of BLOPIG’s first blog post. It’s worth reflecting on what’s stayed the same and what’s changed since then.

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CryoEM is now the dominant technique for solving antibody structures

Last year, the Structural Antibody Database (SAbDab) listed a record-breaking 894 new antibody structures, driven in no small part by the continued efforts of the researchers to understand SARS-CoV-2.

Fig. 1: The aggregate growth in antibody structure data (all methods) over time. Taken from http://opig.stats.ox.ac.uk/webapps/newsabdab/sabdab/stats/ on 25th May 2022.

In this blog post I wanted to highlight the major driving force behind this curve – the huge increase in cryo electron microscopy (cryoEM) data – and the implications of this for the field of structure-based antibody informatics.

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New review on BCR/antibody repertoire analysis out in MAbs!

In our latest immunoinformatics review, OPIG has teamed up with experienced antibody consultant Dr. Anthony Rees to outline the evidence for BCR/antibody repertoire convergence on common epitopes post-pathogen exposure, and all the ways we can go about detecting it from repertoire gene sequencing data. We highlight the new advances in the repertoire functional analysis field, including the role for OPIG’s latest tools for structure-aware antibody analytics: Structural Annotation of AntiBody repertoires+ (SAAB+), Paratyping, Ab-Ligity, Repertoire Structural Profiling & Structural Profiling of Antibodies to Cluster by Epitope (‘SPACE’).

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2021 likely to be a bumper year for therapeutic antibodies entering clinical trials; massive increase in new targets

Earlier this month the World Health Organisation (WHO) released Proposed International Nonproprietary Name List 125 (PL125), comprising the therapeutics entering clinical trials during the first half of 2021. We have just added this data to our Therapeutic Structural Antibody Database (Thera-SAbDab), bringing the total number of therapeutic antibodies recognised by the WHO to 711.

This is up from 651 at the end of 2020, a year which saw 89 new therapeutic antibodies introduced to the clinic. This rise of 60 in just the first half of 2021 bodes well for a record-breaking year of therapeutics entering trials.

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One of my other hats – Covid-19 Response Director for UK research and innovation

The group asked me if I would tell them a little bit about one of my other hats at our regular Tuesday meeting, and this blog is about that.

In October 2019 I was seconded part-time to UKRI as the Deputy Executive Chair of the Engineering and Physical Sciences Research council (EPSRC). What is UKRI (UK research and Innovation)? It’s a non-departmental public body that funds research and innovation. It is made up of the seven disciplinary research councils (acronyms to please Tom – AHRC, BBSRC, EPSRC, ESRC, NERC, STFC and MRC), Research England, and the UK’s innovation agency, Innovate UK.

As Deputy Executive Chair of EPSRC I was helping with UKRI strategy, learning how a spending review round works, visiting universities to talk about how they could work better with UKRI – pretty much everything I was expecting to be doing. But like everyone, my world changed in early 2020.

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The Coronavirus Antibody Database: 10 months on, 10x the data!

Back in May 2020, we released the Coronavirus Antibody Database (‘CoV-AbDab’) to capture molecular information on existing coronavirus-binding antibodies, and to track what we anticipated would be a boon of data on antibodies able to bind SARS-CoV-2. At the time, we had found around 300 relevant antibody sequences and a handful of solved crystal structures, most of which were characterised shortly after the SARS-CoV epidemic of 2003. We had no idea just how many SARS-CoV-2 binding antibody sequences would come to be released into the public domain…

10 months later (2nd March 2021), we now have tracked 2,673 coronavirus-binding antibodies, ~95% with full Fv sequence information and ~5% with solved structures. These datapoints originate from 100s of independent studies reported in either the academic literature or patent filings.

The entire contents CoV-AbDab database as of 2nd March 2021.
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