SARS-COV-2 M^pro conformational changes induced by covalently bound ligands

Abstract

SARS-CoV-2’s main protease (M pro ) interaction with ligands has been explored with a myriad of crystal structures, most of the monomers. Nonetheless, M pro is known to be active as a dimer but the relevance of the dimerization in the ligand-induced conformational changes has not been fully elucidated. We systematically simulated different M pro -ligand complexes aiming to study their conformational changes and interactions, through molecular dynamics (MD). We focused on covalently bound ligands (N1 and N3, ∼9 μs per system both monomers and dimers) and compared these trajectories against the apostructure. Our results suggest that the monomeric simulations led to an unrealistically flexible active site. In contrast, the M pro dimer displayed a stable oxyanion-loop conformation along the trajectory. Also, ligand interactions with residues His41, Gly143, His163, Glu166 and Gln189 are postulated to impact the ligands' inhibitory activity significantly. In dimeric simulations, especially Gly143 and His163 have increased interaction frequencies. In conclusion, long-timescale MD is a more suitable tool for exploring in silico the activity of bioactive compounds that potentially inhibit the dimeric form of SARS-CoV-2 M pro . Communicated by Ramaswamy H. Sarma

Key dimer interface residues impact the catalytic activity of 3CLpro, the main protease of SARS-CoV-2

“…Consistent with these findings, in a previous study, the Q299A and Q299N mutants of SARS-CoV 3CLpro exhibited reductions of k cat of ∼45-fold and ∼19-fold, respectively, while S139A exhibited no reduction of activity or dimerization compared with WT ( 46 ). Molecular dynamics simulations of ligand complexes of SARS-CoV-2 3CLpro suggest that a water-mediated interaction between S139 of one monomer and Q299 of the other monomer links dimerization with appropriate active site conformation, as S139 is also part of the oxyanion hole ( 50 ).…”

Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure–Activity Relationships, Antiviral Activity, and X-ray Structure Determination

“…This collection contains over 10,000 compounds that target a nucleophilic cysteine residue in a variety of kinases. Starting from the M pro 3D structure, 40 we employed a pipeline combining docking with short molecular dynamics (MD) simulations of 200 ns to yield 15 selected hit molecules, which were subsequently tested for their SARS-CoV-2 M pro inhibitory activity (Supporting information, Table S1 ).…”

In Silico Drug Repositioning to Target the SARS-CoV-2 Main Protease as Covalent Inhibitors Employing a Combined Structure-Based Virtual Screening Strategy of Pharmacophore Models and Covalent Docking

“…The binding site of M pro consists of a conserved catalytic dyad that is represented by His41 and Cys145, playing an important role in other residues such as Phe140, Leu141 Asn142, Gly143, Ser144, Cys145, Met165, Glu166, Gln189 and Thr190, which promote complementary interactions favoring the molecular recognition of ligands. Previously, these types of interactions had been identified by structure-based methods including X-ray diffraction [ 32 ], molecular dynamics simulations [ 33 ], and pharmacophoric modeling [ 34 , 35 , 36 , 37 , 38 ], suggesting a high reliability of the design of our pharmacophoric map focused on the search for covalent inhibitors.…”