A new inactive conformation of SARS-CoV-2 main protease

Abstract

The SARS-CoV-2 main protease (Mpro) has a pivotal role in mediating viral genome replication and transcription of the coronavirus, making it a promising target for drugs against the COVID-19 pandemic. Here, a crystal structure is presented in which Mpro adopts an inactive state that has never been observed before, called new-inactive. It is shown that the oxyanion loop, which is involved in substrate recognition and enzymatic activity, adopts a new catalytically incompetent conformation and that many of the key interactions of the active conformation of the enzyme around the active site are lost. Solvation/desolvation energetic contributions play an important role in the transition from the inactive to the active state, with Phe140 moving from an exposed to a buried environment and Asn142 moving from a buried environment to an exposed environment. In new-inactive Mpro a new cavity is present near the S2′ subsite, and the N-terminal and C-terminal tails, as well as the dimeric interface, are perturbed, with partial destabilization of the dimeric assembly. This novel conformation is relevant both for comprehension of the mechanism of action of Mpro within the catalytic cycle and for the successful structure-based drug design of antiviral drugs.

In-silico investigation of phenolic compounds from leaves of Phillyrea angustifolia L. as a potential inhibitor against the SARS-CoV-2 main protease (Mpro PDB ID:5R83) using a virtual screening method

“…In summary, for 5R83-Luteolin-7-O-glucoside, 5R83-Demethyloleoeuropein, and 5R83-Oleuropein aglycone, many hydrogen bonds were established between Thr24, Thr26, Asn142, Gly143, Ser144, Glu189, and the binding pocket- 2 of M pro were observed, indicating that these amino acid residues interact strongly with the ligands in all possible directions. Similarly, with several studies, we found His41 and Cys145 (catalytic dyad) strongly interact with both Demethyloleoeuropein and Oleuropein aglycon [37] , [38] , [39] , [40] . Additionally, for 5R83-Luteolin-7-O-glucoside 5R83-Demethyloleoeuropein and 5R83-Oleuropein aglycone water bridges were existed in parallel along with hydrogen bonding in the majority of residues ( Figure 8 ).…”

From the Wuhan-Hu-1 strain to the XD and XE variants: is targeting the SARS-CoV-2 spike protein still a pharmaceutically relevant option against COVID-19?

“…Its catalytic activity revolves around the processing of two overlapping polyproteins, namely pp1a and pp1ab, which leads to the formation of 16 mature non-structural proteins (NSPs) 75 . Composed of 306 amino acids, the SARS-CoV-2 M pro shares 96% sequence identity and a highly conserved three-dimensional structure with the SARS-CoV M pro (0.53 Å R.M.SD between PDB entries 6Y2E and 2BX4) 76 , 77 . Although a dynamic equilibrium between a monomeric and a dimeric form exists, only the dimer is responsible for the protease’s enzymatic activity 78 , 79 .…”

“…The catalytic site is a shallow, solvent-exposed cavity that is formed by several sub-pockets that are responsible for the recognition of various residues composing the substrate peptide sequences 76 , 80 . Concerning this, particularly important is the conserved sequence Gln↓-Ser, where Gln↓- indicates the glutamine residue that precedes the cleavage site 81 .…”

“…As can be seen in Figure 7 , this mutated residue is located outside the substrate-binding site, specifically in a turn that precedes the sequence leading to the oxyanion loop (residues 138–145), which is a vital part of the catalytic machinery that is responsible for the processing of substrate peptides 76 . Although the position of such mutation could suggest a possible destabilisation of the catalytic site related to an alteration of the enzymatic activity of the protease, a visual inspection of the surroundings of residue 132 suggests that this mutation should not affect in any way the stability of the three-dimensional structure of the protease, thereby not harming its ability to correctly process the substrate.…”

Bat coronaviruses related to SARS-CoV-2: what about their 3CL proteases (MPro)?

“…To date, several studies have contributed to thoroughly characterising the nature of the shallow and solvent-exposed catalytic site of the SARS-CoV-2 28 , which has proven to be readily investigable with both time-dependent and time-independent structure based-approaches such as molecular docking 29 and molecular dynamics 30 , leading to the development of compounds with affinities in the low nanomolar range 31 , 32 .…”