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Cyrus Chothia – In Memoriam

November 27, 2019 by The Antibody Society

Post contributed by: Prof. Andrew C.R. Martin, Professor of Bioinformatics and Computational Biology; SMB Graduate Tutor
Institute of Structural and Molecular Biology, University College London

Cyrus Chothia, FRS, (19 February 1942 – 26 November 2019), was an emeritus scientist at the Medical Research Council Laboratory of Molecular Biology (LMB) in Cambridge, UK where he was a fellow of Wolfson College. He studied at Durham University, followed by an MSc at Birkbeck College, University of London, a small college but famed for its involvement in the development of structural biology and x-ray crystallography, being the home of such luminaries as J.D. Bernal, Aaron Klug and Rosalind Franklin. This was followed by a PhD at University College London supervised by Peter Pauling, son of Linus Pauling. Cyrus was one of the founding fathers of structural bioinformatics and made a particular contribution in the antibody field. Amongst others, he worked with Nobel prize winner, Michael Levitt, Joel Janin, Alexey Murzin, Tim Hubbard and Anna Tramontano, but he is perhaps best known for his work with Arthur Lesk. His PhD students included a number of people who have gone on to make major contributions in bioinformatics, such as Alex Bateman, Steve Brenner, Mark Gerstein, Julian Gough, Sarah Teichmann, and Bissan Al-Lazikani.

Back in the early 1970s, Wu and Kabat had demonstrated the presence of hypervariable sequence regions in antibody variable domains that they suggested would form structural loops or complementarity-determining regions (CDRs) that come together in 3D to form the binding site. This was confirmed when Poljak solved the first antibody crystal structure, and it was assumed that the CDRs would also be extremely variable in structure. I first met Cyrus in the late 1980s when I was doing my DPhil in Oxford on modelling antibody combining sites with Anthony Rees. By that time, around eight structures of antibodies, or Bence Jones light chain dimers, were available and Cyrus, together with Arthur Lesk, compared these. They found that, with the exception of the third CDR of the heavy chain (CDR-H3), the structures of the remaining CDRs were remarkably conserved. Further they proposed that the presence of certain ‘key residues’ – either within the CDRs, or packing against them – would define the conformation [PMID: 3090684, 3681981, 2687698]. To be frank, Tony and I didn’t really believe it. After all, there were potentially billions of antibody sequences and they had looked at fewer than 10. Cyrus and Arthur came to visit us in Oxford, and I remember sitting in The Eagle and Child with them discussing these ideas. Cyrus was always modest and completely accepted that they may be wrong, but of course they turned out to be largely correct. As more structures became available, the rules evolved with the importance of other positions being recognized [PMID: 2118959], but the principle was completely upheld. When we published a paper on key residues in 1986, I spoke to him about one of the outliers that appeared not to follow the rules. His view (which was almost certainly correct!) was that the crystal structure was wrong. More recent analysis by ourselves and others has suggested that the rules aren’t always as precise as might once have been thought and the requirements for framework mutations outside the key residues in order to achieve good binding in antibody humanization supports the view that the precise conformation is influenced by other residues and the detail of the environment around the CDRs.

Cyrus introduced a definition of the ‘structural loops’ in antibodies. These are frequently referred to as the ‘Chothia CDRs’, a term that he did not like as, in his view, the CDRs were the sequence-variable regions defined by Wu and Kabat, while his definition related to regions that were structurally variable and he would not presume to redefine what had been done by Wu and Kabat. In fact, his definitions changed over his various papers as more structural information became available. He also introduced the Chothia numbering scheme for antibodies, which was based on Kabat numbering but corrected the insertion sites in CDR-L1 and CDR-H1 to be structurally correct. Unfortunately in 1989, they made an error such that the insertions in CDR-L1 were placed after residue L31 rather than L30. As another example of his humility and modesty, I happened to referee a paper of theirs in 1997 and recognized this error. He guessed that I was the referee, contacted me, and immediately accepted the correction.

While I have focussed on his work on antibodies, he was widely known for his work in many areas of understanding protein structure. He was elected as a Fellow of the Royal Society (FRS) in 2000, for having “shown how the amino sequences of proteins determine their structure, function and evolution”. To name just a few of his contributions, he developed the SCOP classification of protein structure with Alexey Murzin [PMID: 7723011] and the SUPERFAMILY database with Julian Gough. He studied multi-domain proteins [PMID: 15093836], protein packing [PMID: 10388571] and was involved in functional annotation of more than 60,000 cDNAs from the mouse transcriptome [PMID: 12466851]. As well as his work on the conformation of the CDRs, he examined the packing of VH and VL domains in antibodies [PMID: 4093982] and examined the evolution of immunoglobulin domains in general [PMID: 7175935]. With Bissan Al-Lazikani, he published his final paper on canonical classes of antibody CDRs [PMID: 9367782], but then extended this into T-cell alpha-beta receptors [PMID: 10656805].

Cyrus made enormous contributions to our understanding of protein evolution in general as well as of the structure of antibodies. He will be hugely missed by the scientific community, and by me personally. His science and the many well-known scientists who did their PhDs with him or were influenced by him, are a huge and lasting legacy.

Filed Under: Bioinformatics Tagged With: bioinformatics, Cyrus Chothia

“Antibodies to Watch in 2020” at PEGS Europe

November 25, 2019 by The Antibody Society

Over the past decade, the ‘Antibodies to Watch’ article series has documented the results of the global biopharmaceutical industry’s efforts to bring innovative antibody therapeutics to patients in need. Dr. Janice Reichert, Executive Director of The Antibody Society, offered a preview of the 2020 version on Wednesday November 20, 2019 during the ‘Developing Successful Antibody Products’ session at PEGS Europe.

‘Antibodies to watch in 2020’ includes updates on recent and anticipated events relevant to antibody therapeutics in clinical development. Data for antibody therapeutics that were first approved in either the US or EU during 2019, as well as several products first approved in Russia or India, were provided. Antibody therapeutics undergoing regulatory review by the Food and Drug Administration or the European Medicines Agency as of November 2019 were also discussed. Brief summaries of antibody therapeutics in late-stage clinical study that may progress to regulatory review in late 2019 or 2020, based on public disclosures by the sponsoring companies, were included. In concluding, Dr. Reichert noted that the late-stage clinical pipeline is robust, and she anticipated that more antibody therapeutics will be in late-stage studies in 2020 than any year previously documented. Remarkably, compared to 2010, the number of antibody therapeutics currently in late-stage studies has nearly tripled (to 75 antibody therapeutics).

The ‘Antibodies to watch in 2020′ presentation can be downloaded here.

The Antibody Society was very pleased to see so many of our corporate sponsors in attendance at PEGS Europe!

Ablexis / AlivaMab
Aldevron
Antibody Solutions

Bio-Techne
Geneious Biologics
ImmunoPrecise

Trianni
Twist Bioscience

Filed Under: Antibody therapeutic, Clinical pipeline, European Medicines Agency, Food and Drug Administration, Uncategorized Tagged With: Antibodies to watch, antibody therapeutics, approved antibodies

Crizanlizumab-tmca (Adakveo) approved by FDA

November 17, 2019 by Janice Reichert

On November 15, 2019, the U.S. Food and Drug Administration approved crizanlizumab-tmca (Adakveo) as a treatment to reduce the frequency of vaso-occlusive crisis (VOC), which occurs when blood circulation is obstructed by sickled red blood cells, for patients age 16 years and older. Crizanlizumab is a humanized antibody directed against P-selectin, which contributes to the pathogenesis of sickle cell disease, including vaso-occlusive events and hemolytic anemia. Crizanlizumab was granted Orphan Drug designation in the US and European Union for the treatment of VOC in patients with sickle cell disease, as well as FDA’s Breakthrough Therapy designation for prevention of VOCs in patients of all genotypes with sickle cell disease. A marketing application for crizanlizumab is undergoing review by the European Medicines Agency.

FDA’s approval was based on Phase 2 results from the SUSTAIN study (NCT01895361), which demonstrated that crizanlizumab provided significant benefit over placebo, such as:  1) the percentage of crizanlizumab-treated patients (5 mg/kg) who did not experience any vaso-occlusive crisis (VOC) was higher compared to those treated with placebo (36% vs 17%, P=0.010); 2) 45% reduction in the median annual rate of VOCs leading to health care visits in patients with or without hydroxyurea therapy compared to placebo (1.63 vs 2.98, P=0.010); 3) 42% reduction in median annual rate of days hospitalized versus placebo (4.00 vs 6.87 P=0.45), and 4) A three-fold longer median time to first VOC vs placebo (4.07 vs 1.38 months, P< 0.001). [1, 2]

1. Novartis. FDA accepts file and accelerates review of Novartis sickle cell disease medicine crizanlizumab (SEG101). July 16, 2019 press release.

2. Kutlar A, Kanter J, Liles DK, Alvarez OA, Cançado RD, Friedrisch JR, Knight-Madden JM, Bruederle A, Shi M, Zhu Z, et al. Effect of crizanlizumab on pain crises in subgroups of patients with sickle cell disease: A SUSTAIN study analysis. Am J Hematol. Am J Hematol. 2019 Jan;94(1):55-61. doi: 10.1002/ajh.25308.

Interested in more information about US- or EU- approved antibody therapeutics? The Antibody Society maintains a comprehensive table of approved mAb therapeutics and those in regulatory review in the EU or US in the Web Resources section of our website. 

Filed Under: Antibody therapeutic, Approvals, Food and Drug Administration Tagged With: antibody therapeutics, crizanlizumab, Food and Drug Administration

Save the date for the next AIRR Community Meeting!

November 9, 2019 by jpburckert

We are excited to announce that AIRR Community Meeting V “Exploring New Frontiers” will be held in La Jolla, CA from December 8-12, 2020.

Meetings and presentations will take place at Scripps Research and the Hilton La Jolla Torrey Pines.

See AIRR C Meeting V Program at a Glance.

Filed Under: AIRR Community, New articles, Uncategorized Tagged With: Adaptive Immune Receptor Repertoire Community, Meetings

“Building Scientific Communities – Lessons Learned with AIRR”

November 1, 2019 by jpburckert

AIRR-C Executive Sub-committee member Christian Busse gave a talk at the deRSE2019 (Konferenz für ForschungssoftwareentwicklerInnen in Deutschland – Conference for software engineers in Germany) on building scientific communities using the AIRR-C as an example.

Check out his talk here: https://doi.org/10.5446/42486.

Filed Under: AIRR Community, New articles Tagged With: Adaptive Immune Receptor Repertoire Community, Meetings, Presentations

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