De novo design of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike protein

Abstract

1The emergence of SARS-CoV-2 is responsible for the pandemic of respiratory disease known as COVID-1 2 19, which emerged in the city of Wuhan, Hubei province, China in late 2019. Both vaccines and targeted 1 3 therapeutics for treatment of this disease are currently lacking. Viral entry requires binding of the viral 1 4 spike receptor binding domain (RBD) with the human angiotensin converting enzyme (ACE2). In an 1 5 3 1 (Cellex, GeneTex etc.) for the development of antibody-based tests for SARS-CoV-2 detection are 3 2 ongoing 8 . At the same time, significant progress towards the isolation and design of vaccines (mRNA-3 3 1273 vaccine © 2020 Moderna, Inc) and neutralizing antibodies 9 has been made. A computational study : bioRxiv preprint identified the structural basis for multi-epitope vaccines 10,11 whereas in another study, the glycosylation 3 5 patterns of the spike SARS-CoV-2 protein were computationally deduced 12 . In one study 13 , fully human 3 6 single domain anti-SARS-CoV-2 antibodies with sub-nanomolar affinities were identified from a phage-3 7 displayed single-domain antibody library by grafting naïve CDRs into framework regions of an identified 3 8 human germline IGHV allele using SARS-CoV-2 RBD and S1 protein as antigens. In another study 14 , a 3 9 human antibody 47D11 was identified to have cross neutralizing effect on SARS-CoV-2 by screening 4 0 through a library of SARS-Cov-1 antibodies. In two other studies, potent neutralizing antibodies were 4 1 isolated from the sera of convalescent COVID-19 patients 15,16 . To the best of our knowledge, none of 4 2 these neutralizing antibody sequences are publicly available. In another very encouraging study 17 , human 4 3 antibody CR3022 (which is neutralizing against SARS-CoV-1 18 ) has been shown to bind to SARS-CoV-2 4 4 RBD in a cryptic epitope but without a neutralizing effect for SARS-CoV-2 in vitro. Moreover, we did 4 5 not find any studies that performed guided design of high affinity antibodies against specific epitopes of 4 6 SARS-CoV-2 proteins such as targeting the spike protein and subsequently prevent its binding with 4 7 human ACE2. 8 9Motivated by these shortcomings, here we explore the de novo design of antibody variable regions For each one of the 3,234 spike poses, OptMAVEn-2.0 identified a variable region combination 9 3 composed of end-to-end joined V*, CDR3, and J* region parts that minimized the Rosetta binding energy 9 4 between the variable region and spike epitope formed by the seven residues. As part of OptMAVEn-2.0, 9 5 the combinatorial optimization problem was posed and solved as a mixed-integer linear programming 9 6 (MILP) problem using the cplex solver 26 . The solution of this problem identifies, for each one of the spike 9 7 poses, the complete design of the variable region using parts denoted as HV*, HCDR3, HJ* for the heavy 9 8 chain H and L/KV*, L/KCDR3 and L/KJ* for the light chain-L/K. Only 173 antigen-presenting poses out 9 9 of 3,234 explored, yielded non-clashing antigen-antibody complexes. These 173 poses ...

Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations

“…Different groups have computationally studied the binding of nCOV-2019 RBD with ACE2. − All these studies point to the higher binding affinity of nCOV-2019 RBD than SARS-COV RBD to ACE2. Interestingly, the role of water-mediated interactions has been pointed out to be a driving force which is shown to be similar for both SARS-COV and nCOV-2019 RBD .…”

Potential Trends for COVID-19 Fighting: An Immuno-informatics Overview

“…It is believed that these variable regions designs can be later grafted onto a human framework Fc fragment to construct a potential antibody [33]. However, both in vitro and in vivo assessments of these designs seem to be essential as they may elicit the generation of sub-neutralizing or non-neutralizing antibodies inside the body.…”

Preparation, Purification and Performance Evaluation of Polyclonal Antibody Against SARS-CoV-2 Produced in Rat

“…11,12 With this regard, many attempts are doing for developing antibody-based tests to detection of SARS-CoV-2 by companies and laboratories (e.g., GeneTex, Cellex, etc.). 13 With attention to the mentioned subjects and due to the current situation caused by the distribution and mortality of SARS-CoV-2, the goal of this study was pAb production in response to concentrated antigen. Thereafter, the performance evaluation of produced antibody was performed by SDS-PAGE, ELISA, and western blot methods.…”