Allosteric Hotspots in the Main Protease of SARS-CoV-2

Abstract

Inhibiting the main protease of SARS-CoV-2 is of great interest in tackling the COVID-19 pandemic caused by the virus. Most efforts have been centred on inhibiting the binding site of the enzyme. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. We further score the highest ranking sites against random sites in similar distances through statistical bootstrapping and identify four statistically significant putative allosteric sites as good candidates for alternative drug targeting.

Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface

“…Indeed, the importance of allosteric connectivity between allosteric and functional sites has been increasingly witnessed during recent years. 26,27 Several potential allosteric sites were recently discussed in order to offer allosteric drug target strategies [28][29][30] inside SARS-CoV-2 M pro . For example, Stromich et al 29 studied the scoring of putative allosteric sites and underlined a zone located in the dimerization site showing a high connectivity towards the catalytic active site.…”

“…Indeed, comparing their volume fluctuations along trajectories can tell us about a possible allosteric connectivity between them. 29,32 We show in Figure 2, a) and b) a 2D plot graphic of the distances separating the residues of the catalytic dyad for both chains A and B vs the distances between residues from the allosteric dimerization site : Arg4 chain B and Glu290 chain A since they present a robust interaction. AMOEBA trajectories show a high density of structures having both narrow catalytic and allosteric dimerization sites respectively around 4Å and 3Å as shown in Figure 2, a) and b).…”

“…26,27 Several potential allosteric sites were recently discussed in order to offer allosteric drug target strategies [28][29][30] inside SARS-CoV-2 M pro . For example, Stromich et al 29 studied the scoring of putative allosteric sites and underlined a zone located in the dimerization site showing a high connectivity towards the catalytic active site. They proposed the definition of a potential allosteric dimerization site formed by the six following residues of the interface : Arg131, Asp197, Thr199, Asp289 and Glu290 from chain A and Arg4 form chain B.…”

Prediction of allosteric sites and signaling: Insights from benchmarking datasets

“…Bond-to-bond propensity analysis has successfully predicted 19 out 20 allosteric sites for a test set of 20 proteins 57 and showcased the allostery in aspartate carbamoyltransferase (ATCase) and the main protease of the severe acute respiratory syndrome coronavirus 2. 62 , 64 It has also been built into an efficient web application, ProteinLens, for the study of allostery. 65 To further benchmark this methodology and provide comparable insights into its performance across as diverse proteins as possible, we apply it here to two recently developed large, encompassing datasets, ASBench and CASBench.…”

Prediction of allosteric sites and signalling: insights from benchmarking datasets

“…Bond-to-bond propensity analysis has successfully predicted 19 out 20 allosteric sites for a test set of 20 proteins [53] and showcased the allostery in aspartate carbamoyltransferase (ATCase) and the main protease of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [58, 59]. It has also been built into a efficient web application, ProteinLens, for the study of allostery [60].…”