key: cord-0973339-2jrichn5
authors: Manikyam, Hemanth K.; Joshi, Sunil K.
title: Computational methods to develop potential neutralizing antibody Fab region against SARS-CoV-2 as therapeutic and diagnostic tool
date: 2020-05-04
journal: bioRxiv
DOI: 10.1101/2020.05.02.071506
sha: 4cf7e54e6432ff180901519db3b11dca0a461cd1
doc_id: 973339
cord_uid: 2jrichn5

SARS-CoV-2, a global pandemic originated from Wuhan city of China in the month of December 2019. There is an urgency to identify potential antibodies to neutralize the virus and also as a diagnostic tool candidate. At present palliative treatments using existing antiviral drugs are under trails to treat SARS-CoV-2.Whole Genome sequence of Wuhan market sample of SARS-CoV-2 was obtained from NCBI Gene ID MN908947.3.Spike protein sequence PDB ID 6VSB obtained from RCSB database. Spike protein sequence had shown top V gene match with IGLV1-44*01, IGLV1-47*02 and has VL type chain. Whole Genome sequence had shown top V gene match with IGHV1-38-4*01 and has VH type chain. VD chain had shown link to allele HLA-A0206 80%, HLA-A0217 80%, HLA-A2301 75%, HLA-A0203 75%, HLA-A0202 70% and HLA-A0201 55% of binding levels. Some conserved regions of spike protein had shown strong binding affinity with HLA-A-0*201, HLA-A24, HLA-B-5701 and HLA-B-5703 alpha chains. Synthetic Fab construct BCR type antibody IgG (CR5840) had shown Polyspecific binding activity with spike glycoprotein when compared with available Anti-SARS antibody CR3022.Thus we propose CR5840 Fab constructed antibody as potential neutralizing antibody for SARS-CoV-2. Based on germline analysis we also propose cytotoxic T lymphocyte epitope peptide selective system as effective tool for the development of SARS-CoV-2 vaccine.

The SARS-CoV-2 causing COVID-19 pandemic threatened global public health and Polyclonal antibodies from SARS-CoV-2-infected patients been used to treat SARS-CoV-2 infection, but no SARS-CoV-2-specific neutralizing mAbs or Fabs have been reported.

Researchers around globe are working hard to identify monoclonal antibodies or their functional fragments Fabs as prophylactic, therapeutic and diagnostic agents against COVID-19 caused by SARS-CoV-2. Since SARS-CoV-2 closely related to SARS-Co-V-2 the conserved residues with epitopes may similar structural and functional properties. Hence there are chances of utilising mAbs or it active fragments Fabs against COVID-19 for neutralizing or cross neutralizing activity which to be proved through proper clinical studies.

As it takes time to identify proper mAbs against SARS-CoV-2, we suggest application of computational methods to predict the mAbs based on structural confirmations submitted like SARS-CoV-2 spike proteins. Once specific mAbs or Fab regions are predicted and their sequence been obtained, Phage display technology can be used to synthesize Fab fragments or Monoclonal antibody technology can be used to produce mAbs as a therapeutic and diagnostic agents against COVID-19.

IgBLAST was developed by NCBI for analysis of variable domain sequences of immunoglobulin 1, 4, 5. IMGT is a platform to access sequence, genome and structure Immunogenetics data based on gene ontology. After immunoglobulin germline prediction we compare the V-J and V-D-J junction sequence with the extremities of the corresponding "V, J and D "germline" genes (see IMGT Repertoire > Alignments of alleles). 8, 9 Binding Site and Ligand Prediction:

ProBis a computer based tool to predict binding site and corresponding Ligands for submitted protein structure. Spike protein sequence PDB ID 6VSB was obtained from RCSB database and submitted to ProBis to predict specific Ligands. 6, 10

I-TASSER is a computational approach to predict protein structure and function. It is an most accurate protein structure and function prediction algorithm. 11, 12 After IMGT and ProBis analysis predicted V-D-J and Fab Ligands were obtained and submitted to I-TASSER for best functional model of ligand which can be obtained as PDB file.

Predicted protein ligand sequences from ProBis algorithm obtained from RCSB and 

Sequences producing significant alignments with germline gene and top gene alignment 

From epitope and germline data based on spike protein sequence, ProBis ligand prediction tools generated antibodies that are specific to spike glycoprotein. From the sequence of specific antibodies obtained, we generated synthetic IgG hybrid antibody Fab sequence. LYRA and I- 

There is an urgent necessary to address potential therapeutics for global pandemic created by SARS-CoV-2 infection. Viral antigens go through human innate immune system during initial or latent periods of incubation period and generate neutralizing antibodies against the antigens. Viral genome carries the coding for viral antigens which can be used to predict neutralizing human antibodies using different genomic and Highthroughput screening tools.

Here used IgBLAST, I-TASSER and Molbiol tools to predict and design the neutralizing 

I-TASSER: a unified platform for automated protein structure and function prediction

IMGT® and 30 years of Immunoinformatics Insight in

Domain Structure and Function

IgBLAST: an immunoglobulin variable domain sequence analysis tool

ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment

I-TASSER: a unified platform for automated protein structure and function prediction

The I-TASSER Suite: Protein structure and function prediction

PROCHECK -a program to check the stereochemical quality of protein structures

LYRA, a webserver for lymphocyte receptor structural modeling

FRODOCK 2.0: Fast Protein-Protein docking server

pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring