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1.
Struct Chem ; : 1-15, 2022 Jun 02.
Article in English | MEDLINE | ID: covidwho-1942564

ABSTRACT

Coronavirus disease 2019 (COVID-19) has become a major challenge affecting almost every corner of the world, with more than five million deaths worldwide. Despite several efforts, no drug or vaccine has shown the potential to check the ever-mutating SARS-COV-2. The emergence of novel variants is a major concern increasing the need for the discovery of novel therapeutics for the management of this pandemic. Out of several potential drug targets such as S protein, human ACE2, TMPRSS2 (transmembrane protease serine 2), 3CLpro, RdRp, and PLpro (papain-like protease), RNA-dependent RNA polymerase (RdRP) is a vital enzyme for viral RNA replication in the mammalian host cell and is one of the legitimate targets for the development of therapeutics against this disease. In this study, we have performed structure-based virtual screening to identify potential hit compounds against RdRp using molecular docking of a commercially available small molecule library of structurally diverse and drug-like molecules. Since non-optimal ADME properties create hurdles in the clinical development of drugs, we performed detailed in silico ADMET prediction to facilitate the selection of compounds for further studies. The results from the ADMET study indicated that most of the hit compounds had optimal properties. Moreover, to explore the conformational dynamics of protein-ligand interaction, we have performed an atomistic molecular dynamics simulation which indicated a stable interaction throughout the simulation period. We believe that the current findings may assist in the discovery of drug candidates against SARS-CoV-2.

2.
Advances in Protein Molecular and Structural Biology Methods ; : 405-437, 2022.
Article in English | Scopus | ID: covidwho-1859219

ABSTRACT

Structure-based drug discovery (SBDD) utilizes the three-dimensional (3D) structure of a target protein to identify the lead compounds. This medium is then considered a viable solution based on its availability and correlation with a particular disease. In the case of pandemics like COVID 19, shortening drug development time can save millions of people worldwide;for such a task, classical drug discovery methods will take a long time. Hence, researchers worldwide actively incorporated machine learning (ML) into the drug discovery process, particularly in SBDD, to minimize the lead optimization time. ML uses statistical methods to make a computer perform tasks, take a critical decision, and automate this entire process without being explicitly programmed. With this, the computer can discover new insights about data and unknown patterns crucial to decide the therapeutic use of lead compounds as drugs. The use of ML in the drug discovery field is not new, and it spans an ample research space. By integrating artificial intelligence with ML techniques, viable targets can be found using data clustering, regression, and classification from vast omics databases and sources. In this chapter, we will discuss the methods and applications of ML in SBDD. © 2022 Elsevier Inc. All rights reserved.

3.
Pharmaceuticals (Basel) ; 14(9)2021 Sep 03.
Article in English | MEDLINE | ID: covidwho-1390721

ABSTRACT

The unprecedented pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is threatening global health. SARS-CoV-2 has caused severe disease with significant mortality since December 2019. The enzyme chymotrypsin-like protease (3CLpro) or main protease (Mpro) of the virus is considered to be a promising drug target due to its crucial role in viral replication and its genomic dissimilarity to human proteases. In this study, we implemented a structure-based virtual screening (VS) protocol in search of compounds that could inhibit the viral Mpro. A library of >eight hundred compounds was screened by molecular docking into multiple structures of Mpro, and the result was analyzed by consensus strategy. Those compounds that were ranked mutually in the 'Top-100' position in at least 50% of the structures were selected and their analogous binding modes predicted simultaneously in all the structures were considered as bioactive poses. Subsequently, based on the predicted physiological and pharmacokinetic behavior and interaction analysis, eleven compounds were identified as 'Hits' against SARS-CoV-2 Mpro. Those eleven compounds, along with the apo form of Mpro and one reference inhibitor (X77), were subjected to molecular dynamic simulation to explore the ligand-induced structural and dynamic behavior of Mpro. The MM-GBSA calculations reflect that eight out of eleven compounds specifically possess high to good binding affinities for Mpro. This study provides valuable insights to design more potent and selective inhibitors of SARS-CoV-2 Mpro.

4.
J Biomol Struct Dyn ; 40(8): 3609-3625, 2022 05.
Article in English | MEDLINE | ID: covidwho-939480

ABSTRACT

COVID-19 pandemic has created a healthcare crisis across the world and has put human life under life-threatening circumstances. The recent discovery of the crystallized structure of the main protease (Mpro) from SARS-CoV-2 has provided an opportunity for utilizing computational tools as an effective method for drug discovery. Targeting viral replication has remained an effective strategy for drug development. Mpro of SARS-COV-2 is the key protein in viral replication as it is involved in the processing of polyproteins to various structural and nonstructural proteins. Thus, Mpro represents a key target for the inhibition of viral replication specifically for SARS-CoV-2. We have used a virtual screening strategy by targeting Mpro against a library of commercially available compounds to identify potential inhibitors. After initial identification of hits by molecular docking-based virtual screening further MM/GBSA, predictive ADME analysis, and molecular dynamics simulation were performed. The virtual screening resulted in the identification of twenty-five top scoring structurally diverse hits that have free energy of binding (ΔG) values in the range of -26-06 (for compound AO-854/10413043) to -59.81 Kcal/mol (for compound 329/06315047). Moreover, the top-scoring hits have favorable AMDE properties as calculated using in silico algorithms. Additionally, the molecular dynamics simulation revealed the stable nature of protein-ligand interaction and provided information about the amino acid residues involved in binding. Overall, this study led to the identification of potential SARS-CoV-2 Mpro hit compounds with favorable pharmacokinetic properties. We believe that the outcome of this study can help to develop novel Mpro inhibitors to tackle this pandemic.Communicated by Ramaswamy H. Sarma.


Subject(s)
COVID-19 , Molecular Dynamics Simulation , COVID-19/drug therapy , Coronavirus 3C Proteases , Humans , Molecular Docking Simulation , Pandemics , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , SARS-CoV-2
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