| Full text | |
| Author(s): |
Ferreira, Glaucio Monteiro
;
Pillaiyar, Thanigaimalai
;
Hirata, Mario Hiroyuki
;
Poso, Antti
;
Kronenberger, Thales
Total Authors: 5
|
| Document type: | Journal article |
| Source: | SCIENTIFIC REPORTS; v. 12, n. 1, p. 13-pg., 2022-07-08. |
| Abstract | |
SARS-CoV-2's papain-like protease (PLpro) interaction with ligands has recently been explored with a myriad of crystal structures. We used molecular dynamics (MD) simulations to study different PLpro-ligand complexes, their ligand-induced conformational changes, and interactions. We focused on inhibitors reported with known IC50 against PLpro, namely GRL-0617, XR8-89, PLP_Snyder530, and Sander's recently published compound 7 (CPD7), and compared these trajectories against the apostructure (Apo), with a total of around 60 mu s worth simulation data. We aimed to study the conformational changes using molecular dynamics simulations for the inhibitors in the PLpro. PCA analyses and the MSM models revealed distinct conformations of PLpro in the absence/presence of ligands and proposed that BL2-loop contributes to the accessibility of these inhibitors. Further, bulkier substituents closer to Tyr268 and Gln269 could improve inhibition of SARS-CoV-2 PLpro by occupying the region between BL2-groove and BL2-loop, but we also expand on the relevance of exploring multiple PLpro sub-pockets to improve inhibition. (AU) | |
| FAPESP's process: | 16/12899-6 - Genomics, epigenomics and pharmacogenomics characterization of familial hypercholesterolemia in the Brazilian population |
| Grantee: | Mario Hiroyuki Hirata |
| Support Opportunities: | Research Projects - Thematic Grants |
| FAPESP's process: | 19/24112-9 - Novel HMG-CoA reductase inhibitors development by integrating dyslipidemic patients' genetic studies and molecular modelling |
| Grantee: | Glaucio Monteiro Ferreira |
| Support Opportunities: | Scholarships abroad - Research Internship - Post-doctor |
| FAPESP's process: | 21/11205-9 - Development of new drugs based on the structure of essential proteins for cholesterol synthesis and metabolism, integrating genetic studies and molecular modeling of dyslipidemic patients |
| Grantee: | Glaucio Monteiro Ferreira |
| Support Opportunities: | Scholarships in Brazil - Post-Doctoral |