A multi-reference poly-conformational method for in silico design, optimization, and repositioning of pharmaceutical compounds illustrated for selected SARS-CoV-2 ligands

PeerJ

article

Vadim Alexandrov¹  Alexander Kirpich²  Omar Kantidze³  Yuriy Gankin³ 

[1] Liquid Algo LLC;Department of Population Health Sciences, School of Public Health, Georgia State University;Quantori

关键词: Conformers;    Multi-reference;    Poly-conformational;    SARSCOV- 2;    In silico;    Ligand-based;    Structure-based;    Virtual library;    Computational framework;    Validation;   

DOI  :  10.7717/peerj.14252

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundThis work presents a novel computational multi-reference poly-conformational algorithm for design, optimization, and repositioning of pharmaceutical compounds.MethodsThe algorithm searches for candidates by comparing similarities between conformers of the same compound and identifies target compounds, whose conformers are collectively close to the conformers of each compound in the reference set. Reference compounds may possess highly variable MoAs, which directly, and simultaneously, shape the properties of target candidate compounds.ResultsThe algorithm functionality has been case study validated in silico, by scoring ChEMBL drugs against FDA-approved reference compounds that either have the highest predicted binding affinity to our chosen SARS-CoV-2 targets or are confirmed to be inhibiting such targets in-vivo. All our top scoring ChEMBL compounds also turned out to be either high-affinity ligands to the chosen targets (as confirmed in separate studies) or show significant efficacy, in-vivo, against those selected targets. In addition to method case study validation, in silico search for new compounds within two virtual libraries from the Enamine database is presented. The library’s virtual compounds have been compared to the same set of reference drugs that we used for case study validation: Olaparib, Tadalafil, Ergotamine and Remdesivir. The large reference set of four potential SARS-CoV-2 compounds has been selected, since no drug has been identified to be 100% effective against the virus so far, possibly because each candidate drug was targeting only one, particular MoA. The goal here was to introduce a new methodology for identifying potential candidate(s) that cover multiple MoA-s presented within a set of reference compounds.

【 授权许可】

CC BY