TY  - JOUR
AU  - Hernández González, Jorge E.
AU  - Eberle, Raphael J.
AU  - Willbold, Dieter
AU  - Coronado, Mônika A.
TI  - A Computer-Aided Approach for the Discovery of D-Peptides as Inhibitors of SARS-CoV-2 Main Protease
JO  - Frontiers in molecular biosciences
VL  - 8
SN  - 2296-889X
CY  - Lausanne
PB  - Frontiers
M1  - FZJ-2022-03004
SP  - 816166
PY  - 2022
AB  - The SARS-CoV-2 main protease, also known as 3-chymotrypsin-like protease (3CLpro), is a cysteine protease responsible for the cleavage of viral polyproteins pp1a and pp1ab, at least, at eleven conserved sites, which leads to the formation of mature nonstructural proteins essential for the replication of the virus. Due to its essential role, numerous studies have been conducted so far, which have confirmed 3CLpro as an attractive drug target to combat Covid-19 and have reported a vast number of inhibitors and their co-crystal structures. Despite all the ongoing efforts, D-peptides, which possess key advantages over L-peptides as therapeutic agents, have not been explored as potential drug candidates against 3CLpro. The current work fills this gap by reporting an in silico approach for the discovery of D-peptides capable of inhibiting 3CLpro that involves structure-based virtual screening (SBVS) of an in-house library of D-tripeptides and D-tetrapeptides into the protease active site and subsequent rescoring steps, including Molecular Mechanics Generalized-Born Surface Area (MM-GBSA) free energy calculations and molecular dynamics (MD) simulations. In vitro enzymatic assays conducted for the four top-scoring D-tetrapeptides at 20 μM showed that all of them caused 55-85% inhibition of 3CLpro activity, thus highlighting the suitability of the devised approach. Overall, our results present a promising computational strategy to identify D-peptides capable of inhibiting 3CLpro, with broader application in problems involving protein inhibition.
LB  - PUB:(DE-HGF)16
C6  - 35187076
UR  - <Go to ISI:>//WOS:000759912700001
DO  - DOI:10.3389/fmolb.2021.816166
UR  - https://juser.fz-juelich.de/record/909091
ER  -