Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.

Screening already approved drugs for activity against a novel pathogen can be an important part of global rapid-response strategies in pandemics. Such high-throughput repurposing screens have already identified several existing drugs with potential to combat SARS-CoV-2. However, moving these hits forward for possible development into drugs specifically against this pathogen requires unambiguous identification of their corresponding targets, something the high-throughput screens are not typically designed to reveal. We present here a new computational inverse-docking protocol that uses all-atom protein structures and a combination of docking methods to rank-order targets for each of several existing drugs for which a plurality of recent high-throughput screens detected anti-SARS-CoV-2 activity. We demonstrate validation of this method with known drug-target pairs, including both non-antiviral and antiviral compounds. We subjected 152 distinct drugs potentially suitable for repurposing to the inverse docking procedure. The most common preferential targets were the human enzymes TMPRSS2 and PIKfyve, followed by the viral enzymes Helicase and PLpro. All compounds that selected TMPRSS2 are known serine protease inhibitors, and those that selected PIKfyve are known tyrosine kinase inhibitors. Detailed structural analysis of the docking poses revealed important insights into why these selections arose, and could potentially lead to more rational design of new drugs against these targets.

Effect of Intercalated Water on Potassium Ion Transport through Kv1.2 Channels Studied via On-the-Fly Free-Energy Parametrization.

We introduce a two-dimensional version of the method called on-the-fly free energy parametrization (OTFP) to reconstruct free-energy surfaces using Molecular Dynamics simulations, which we name OTFP-2D. We first test the new method by reconstructing the well-known dihedral angles free energy surface of solvated alanine dipeptide. Then, we use it to investigate the process of K+ ions translocation inside the Kv1.2 channel. By comparing a series of two-dimensional free energy surfaces for ion movement calculated with different conditions on the intercalated water molecules, we first recapitulate the widely accepted knock-on mechanism for ion translocation and then confirm that permeation occurs with water molecules alternated among the ions, in accordance with the latest experimental findings. From a methodological standpoint, our new OTFP-2D algorithm demonstrates the excellent sampling acceleration of temperature-accelerated molecular dynamics and the ability to efficiently compute 2D free-energy surfaces. It will therefore be useful in large variety complex biomacromolecular simulations.

Polymorphism at 129 dictates metastable conformations of the human prion protein N-terminal ß-sheet.

We study the thermodynamic stability of the native state of the human prion protein using a new free-energy method, replica-exchange on-the-fly parameterization. This method is designed to overcome hidden-variable sampling limitations to yield nearly error-free free-energy profiles along a conformational coordinate. We confirm that all four (M129V, D178N) polymorphs have a ground-state conformation with three intact ß-sheet hydrogen bonds. Additionally, they are observed to have distinct metastabilities determined by the side-chain at position 129. We rationalize these findings with reference to the prion "strain" hypothesis, which links the variety of transmissible spongiform encephalopathy phenotypes to conformationally distinct infectious prion forms and classifies distinct phenotypes of sporadic Creutzfeldt-Jakob disease based solely on the 129 polymorphism. Because such metastable structures are not easily observed in structural experiments, our approach could potentially provide new insights into the conformational origins of prion diseases and other pathologies arising from protein misfolding and aggregation.

Free energy and hidden barriers of the ß-sheet structure of prion protein.

On-the-fly free-energy parametrization is a new collective variable biasing approach akin to metadynamics with one important distinction: rather than acquiring an accelerated distribution via a history-dependent bias potential, sampling on this distribution is achieved from the beginning of the simulation using temperature-accelerated molecular dynamics. In the present work, we compare the performance of both approaches to compute the free-energy profile along a scalar collective variable measuring the H-bond registry of the ß-sheet structure of the mouse Prion protein. Both methods agree on the location of the free-energy minimum, but free-energy profiles from well-tempered metadynamics are subject to a much higher degree of statistical noise due to hidden barriers. The sensitivity of metadynamics to hidden barriers is shown to be a consequence of the history dependence of the bias potential, and we detail the nature of these barriers for the prion ß-sheet. In contrast, on-the-fly parametrization is much less sensitive to these barriers and thus displays improved convergence behavior relative to that of metadynamics. While hidden barriers are a frequent and central issue in free-energy methods, on-the-fly free-energy parametrization appears to be a robust and preferable method to confront this issue.

Time Recovery for a Complex Process Using Accelerated Dynamics.

The hyperdynamics method (HD) developed by Voter (J. Chem. Phys. 1996, 106, 4665) sets the theoretical basis to construct an accelerated simulation scheme that holds the time scale information. Since HD is based on transition state theory, pseudoequilibrium conditions (PEC) must be satisfied before any system in a trapped state may be accelerated. As the system evolves, many trapped states may appear, and the PEC must be assumed in each one to accelerate the escape. However, since the system evolution is a priori unknown, the PEC cannot be permanently assumed to be true. Furthermore, the different parameters of the bias function used may need drastic recalibration during this evolution. To overcome these problems, we present a general scheme to switch between HD and conventional molecular dynamics (MD) in an automatic fashion during the simulation. To decide when HD should start and finish, criteria based on the energetic properties of the system are introduced. On the other hand, a very simple bias function is proposed, leading to a straightforward on-the-fly set up of the required parameters. A way to measure the quality of the simulation is suggested. The efficiency of the present hybrid HD-MD method is tested for a two-dimensional model potential and for the coalescence process of two nanoparticles. In spite of the important complexity of the latter system (165 degrees of freedoms), some relevant mechanistic properties were recovered within the present method.

Anchoring sites to the STM tip can explain multiple peaks in single molecule conductance histograms.

Accelerated molecular dynamics and quantum conductance calculations are employed to shed light onto the electrochemical properties of the Au|1,8-octanedithiol|Au junction. Widely different contact geometries with varying degrees of roughness are examined. Strikingly, the two extreme situations considered in this work, tip-tip and tip-perfect surface junctions, give almost indistinguishable conductances. This result contrasts the usual notion that different S-Au bonding geometries combined with molecular torsions provide the explanation for the experimentally observed sets (low, medium, high) of conductance peaks. In this work, we provide an alternative explanation for the occurrence of these sets in terms of the specific anchoring sites of the molecule to the tip, which in turn determines the interaction of a portion of the carbon chain with the tip.

Configurational Behavior and Conductance of Alkanedithiol Molecular Wires from Accelerated Dynamics Simulations.

An accelerated dynamics scheme is employed to sample the configurational space of a system consisting of an alkanedithiol molecule confined to the gap between a metal tip and a perfect metal surface. With this information and by means of nonequilibrium green functions techniques (NEGF), conductance calculations are performed. The present results show that even for this system, which is one of the most simple conceivable because of the perfectness of the surface, a complex behavior appears due to the occurrence of an unexpected tip-molecule-surface arrangement, where the insertion of one of the molecular ends into the tip-surface gap generates configurations with strongly enhanced conductance. Estimates are also made for the time required to generate the molecular junction, indicating that it should depend on the tip-surface distance, thus opening the way to new experiments in this direction.