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Modeling of SARS-CoV-2 Virus Proteins: Implications on Its Proteome

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Homology Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2627))

Abstract

COronaVIrus Disease 19 (COVID-19) is a severe acute respiratory syndrome (SARS) caused by a group of beta coronaviruses, SARS-CoV-2. The SARS-CoV-2 virus is similar to previous SARS- and MERS-causing strains and has infected nearly six hundred and fifty million people all over the globe, while the death toll has crossed the six million mark (as of December, 2022). In this chapter, we look at how computational modeling approaches of the viral proteins could help us understand the various processes in the viral life cycle inside the host, an understanding of which might provide key insights in mitigating this and future threats. This understanding helps us identify key targets for the purpose of drug discovery and vaccine development.

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Abbreviations

3CL-pro:

3C-like protease

Ace2:

Angiotensin-converting enzyme II

Arg:

Arginine

BLAST:

Basic Local Alignment Search Tool

BST-2:

Bone marrow stromal antigen type 2

CDK:

Cyclin-dependent kinase

CHARMM:

Chemistry at Harvard Macromolecular Mechanics

COVID-19:

Coronavirus Disease 19

Cryo-EM:

Cryo-electron microscopy

CTD:

C terminal domain

E:

Envelope protein

ERGIC:

Endoplasmic reticulum–Golgi intermediate compartment

EVD:

Extreme value distribution

GROMOS:

GROningen MOlecular Simulation

IFN:

Interferon

Leu:

Leucine

Lys:

Lysine

M:

Membrane protein

MD:

Molecular dynamics

MERS:

Middle East Respiratory Syndrome

N:

Nucleocapsid protein

NiRAN:

NidovirusRdRp-associated nucleotidyl transferase

NLS:

Nuclear localization signal

NMR:

Nuclear Magnetic resonance

NRP:

Neuropilin

Nsps:

Nonstructural proteins

NTD:

N terminal domain

ORF:

Open reading frame

PBM:

PDZ-binding motif

PD:

Peptidase domain

Phe:

Phenylalanine

Pro:

Proline

PTM:

Post-translational modification

RBD:

Receptor binding domain

RBM:

Receptor binding motif

RdRp:

RNA-dependent RNA polymerase

RMSD:

Root mean square deviation

S:

Spike protein

SARS:

Severe acute respiratory syndrome

Ser:

Serine

SVM:

Support vector machine

TBM:

Template-based modeling

V-ATPase:

Vacuolar-H+ ATPase

VSR:

Viral suppressor of RNAi

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Acknowledgments

We thank Victor Hannothiaux, Paul Etheimer, Leo Janin and Sophie Ameloot for proof-reading the manuscript for language and technical details. This work was supported by MedInsights SAS (SIRET: 91842274200018; SIREN: 918422742; www.medinsights.fr), Paris. We did not receive any funding for writing this book chapter from any sources.

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  1. Hochschule für Technik und Wirtschaft (HTW) Berlin, Berlin, Germany

    Manish Sarkar

  2. MedInsights, Veuilly la Poterie, France

    Soham Saha

  3. MedInsights SAS, Paris, France

    Manish Sarkar & Soham Saha

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    Sławomir Filipek

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Sarkar, M., Saha, S. (2023). Modeling of SARS-CoV-2 Virus Proteins: Implications on Its Proteome. In: Filipek, S. (eds) Homology Modeling. Methods in Molecular Biology, vol 2627. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2974-1_15

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