High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling

Abstract

We provide a new unsupervised adaptive sampling strategy capable of producing microsecondtimescale molecular dynamics (MD) simulations using many-body polarizable force fields (PFF) on modern supercomputers. The global exploration problem is decomposed into a set of separate MD trajectories that can be restarted within an iterative/selective process to achieve sufficient phase-space sampling within large biosystems, while accurate statistical properties can be obtained through debiasing. With this pleasingly parallel setup, the Tinker-HP package can be powered by an arbitrary large number of GPUs (Graphics Processing Unit) cards available on pre-exascale supercomputers, reducing to days explorations that would have taken years. We applied the approach to the urgent problem of the modeling of the SARS–CoV–2 Main protease (Mpro) dimer. A 15.14 microsecond high-resolution all-atom simulation (AMOEBA PFF) of its apo state is provided and compared to other available long-timescale non-PFF data. Noticeable differences are found between clustering analysis of the simulations, the AMOEBA adaptive results exhibiting a richer conformational space. Overall, our high-resolution AMOEBA structural analysis captures key experimental observations concerning the stability of the oxyanion hole, a marker of activity through the stability of different stacking and salt bridge interactions. A dissymmetry is found between the enzyme protomers that exhibit different volumes. One of them appears fully inactive while the other is "activable", exhibiting some partial activity features. This activity evaluation can be further traced back to the large flexibility of the C terminal domain, fully captured by AMOEBA but not seen in X-rays due to insufficient electron densities related to the domain high mobility. The C–terminal region of the fully inactive protomer is shown to oscillate between several states, one of them interacting with the other protomer active site, therefore potentially modulating down its activity. Overall, these results reinforce the experimental hypothesis of a full inactivation of the apo state and clearly capture the asymmetric nature of protomers. Additional analysis show that the cavities volumes of the active and distal sites are found to be larger in the most active protomer with AMOEBA. To a larger extend, the PFF finds significantly larger cavities than those obtained with classical, non-polarizable simulations. The consequences on druggability are discussed as additional potential druggable cryptic pockets are found. All data produced within this research are fully accessible to the community for further analysis.

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

“…Clearly, our results show a collapse of the dimer interface at pH values lower than physiological as a consequence of the successive protonations of histidine residues (His172 then His163). 9,18,19 Among the observed interactions (see Table 1, SI), Arg4 -Glu290 and Gly11 -Glu14 H-bond interactions have the highest probability density of all over DES-AMBER, AMBER and AMOEBA trajectories at physiological pH. Yet, these interactions are not detected at lower pH which is consistent with experimental studies reporting that low pH is responsible for the loss of the dimer interface.…”

“…Yet, these interactions are not detected at lower pH which is consistent with experimental studies reporting that low pH is responsible for the loss of the dimer interface. 20,21 It is important to note here that protonation of His172 at lower pH has recently been shown 9,17,19 to be the source of a partial collapse in the catalytic site as well.…”

“…The detected special forms of H-bond and other interactions, at physiological pH, are highlighted in Figure 1, c). It is important to note that when successive histidine protonations occur, His172 and His163 switch from neutral histidines at pH=7.4 to positively charged at pH=6 and below, changing the nature of some of their interactions with other residues and water (for example moving from H-bonds to salt-bridges in some cases 9,23 ). Although pH lowering will affect also other residues that are not all considered in our computations, 19 this physico-chemical change in the nature of the Histidines interactions is central to the weakening of the interface stability, forcing it to redistribute its H-bond network into a different and less structured configuration.…”

“…2,8 Recently, we provided extensive simulations on M pro 9 using the AMOEBA polarizable force field (PFF) [10][11][12] and a new highly parallel GPUs-accelerated 13,14 unsupervised adaptive sampling strategy. 9 These multi-microsecond simulations and their associated conformational spaces were compared to available non-PFF long-timescale simulation data from D. E. Shaw Research (DESRES) 15 and RIKEN Center for Biosystems Dynamics Research. 16 It was found 9 that AMOEBA results were closely correlated with experimental data, highlighting the observed strong flexibility of M pro .…”

“…9 These multi-microsecond simulations and their associated conformational spaces were compared to available non-PFF long-timescale simulation data from D. E. Shaw Research (DESRES) 15 and RIKEN Center for Biosystems Dynamics Research. 16 It was found 9 that AMOEBA results were closely correlated with experimental data, highlighting the observed strong flexibility of M pro . 17 However, important differences in structural dynamics were observed compared to non-PFFs in key areas of the protease.…”