Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly growing infectious disease, widely spread with high mortality rates. Since the release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discovery, which also requires knowledge of the 3D structure of the proteome. Where there are no experimentally solved structures, our group has created 3D models with coverage of 97.5% and characterized them using state-of-the-art computational approaches. Models of protomers and oligomers, together with predictions of substrate and allosteric binding sites, protein-ligand docking, SARS-CoV-2 protein interactions with human proteins, impacts of mutations, and mapped solved experimental structures are freely available for download. These are implemented in SARS CoV-2 3D, a comprehensive and user-friendly database, available at https://sars3d.com/. This provides essential information for drug discovery, both to evaluate targets and design new potential therapeutics.
Highlights
The severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) was first detected in late 2019 in Wuhan (Hubei, China)
SARS-CoV-2 3D database, a comprehensive resource for the SARS-CoV-2 proteome, is based on 3D structures, using either experimentally solved structures or through comparative computational modelling based on structures of close homologues
Since the SARS-CoV-2 proteome is relatively small with 25 gene products, we have extended the methodology, used to construct our previously published databases such as Mabellini, and Chopin, to include models of transmembrane proteins, multi-domain proteins, and homo- and heterooligomers manually as well as using our recently developed software ProtCHOIR that is designed to build homo-oligomeric assemblies
Summary
The severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) was first detected in late 2019 in Wuhan (Hubei, China). Since it has spread dramatically, infecting over 40 million people, with over 1 million deaths reported to date and causing major health and economic challenges globally [1]. The virus belongs to the coronavirus family that includes SARS-CoV-1 and MERS-CoV, and is characterized by a positive-sense singlestranded RNA genome. SARS-CoV-2 has approximately 79% sequence similarity to SARS-CoV-1 and 50% similarity to MERSCoV [2]. The involvement of bats in transmission to humans is still not clear, the sequence similarity of human SARS-CoV-2 to that of the bat coronavirus RaTG13 is ∼96% [3]. High genetic variability and recombination are believed to enable widespread adaptive evolution of SARS-CoV-2 in humans around the world [4, 5]
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