Large-Scale Study of Hydration Environments through Hydration Sites

Inhibitor design for TMPRSS2: insights from computational analysis of its backbone hydrogen bonds using a simple descriptor

Transmembrane protease serine 2 (TMPRSS2) is an important drug target due to its role in the infection mechanism of coronaviruses including SARS-CoV-2. Current understanding regarding the molecular mechanisms of known inhibitors and insights required for inhibitor design are limited. This study investigates the effect of inhibitor binding on the intramolecular backbone hydrogen bonds (BHBs) of TMPRSS2 using the concept of hydrogen bond wrapping, which is the phenomenon of stabilization of a hydrogen bond in a solvent environment as a result of being surrounded by non-polar groups. A molecular descriptor which quantifies the extent of wrapping around BHBs is introduced for this. First, virtual screening for TMPRSS2 inhibitors is performed by molecular docking using the program DOCK 6 with a Generalized Born surface area (GBSA) scoring function. The docking results are then analyzed using this descriptor and its relationship to the solvent-accessible surface area term ΔGsa of the GBSA score is demonstrated with machine learning regression and principal component analysis. The effect of binding of the inhibitors camostat, nafamostat, and 4-guanidinobenzoic acid (GBA) on the wrapping of important BHBs in TMPRSS2 is also studied using molecular dynamics. For BHBs with a large increase in wrapping groups due to these inhibitors, the radial distribution function of water revealed that certain residues involved in these BHBs, like Gln438, Asp440, and Ser441, undergo preferential desolvation. The findings offer valuable insights into the mechanisms of these inhibitors and may prove useful in the design of new inhibitors.

Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding

Atomistic-level understanding of surface hydration mediating protein-protein interactions and ligand binding has been a challenge due to the dynamic nature of water molecules near the surface. We develop a computational method to evaluate the solvation free energy based on the density map of the first hydration shell constructed from all-atom molecular dynamics simulation and use it to examine the binding of two intrinsically disordered ligands to their target protein domain. One ligand is from the human protein, and the other is from the 1918 Spanish flu virus. We find that the viral ligand incurs a 6.9 kcal/mol lower desolvation penalty upon binding to the target, which is consistent with its stronger binding affinity. The difference arises from the spatially fragmented and nonuniform water density profiles of the first hydration shell. In particular, residues that are distal from the ligand-binding site contribute to a varying extent to the desolvation penalty, among which the "entropy hotspot" residues contribute significantly. Thus, ligand binding alters hydration on remote sites in addition to affecting the binding interface. The nonlocal effect disappears when the conformational motion of the protein is suppressed. The present results elucidate the interplay between protein conformational dynamics and surface hydration. Our approach of measuring the solvation free energy based on the water density of the first hydration shell is tolerant of the conformational fluctuation of protein, and we expect it to be applicable to investigating a broad range of biomolecular interfaces.

Total free energy analysis of fully hydrated proteins

The total free energy of a hydrated biomolecule and its corresponding decomposition of energy and entropy provides detailed information about regions of thermodynamic stability or instability. The free energies of four hydrated globular proteins with different net charges are calculated from a molecular dynamics simulation, with the energy coming from the system Hamiltonian and entropy using multiscale cell correlation. Water is found to be most stable around anionic residues, intermediate around cationic and polar residues, and least stable near hydrophobic residues, especially when more buried, with stability displaying moderate entropy-enthalpy compensation. Conversely, anionic residues in the proteins are energetically destabilized relative to singly solvated amino acids, while trends for other residues are less clear-cut. Almost all residues lose intraresidue entropy when in the protein, enthalpy changes are negative on average but may be positive or negative, and the resulting overall stability is moderate for some proteins and negligible for others. The free energy of water around single amino acids is found to closely match existing hydrophobicity scales. Regarding the effect of secondary structure, water is slightly more stable around loops, of intermediate stability around β strands and turns, and least stable around helices. An interesting asymmetry observed is that cationic residues stabilize a residue when bonded to its N-terminal side but destabilize it when on the C-terminal side, with a weaker reversed trend for anionic residues.

Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo

The prediction of protein-ligand binding affinities using free energy perturbation (FEP) is becoming increasingly routine in structure-based drug discovery. Most FEP packages use molecular dynamics (MD) to sample the configurations of proteins and ligands, as MD is well-suited to capturing coupled motion. However, MD can be prohibitively inefficient at sampling water molecules that are buried within binding sites, which has severely limited the domain of applicability of FEP and its prospective usage in drug discovery. In this paper, we present an advancement of FEP that augments MD with grand canonical Monte Carlo (GCMC), an enhanced sampling method, to overcome the problem of sampling water. We accomplished this without degrading computational performance. On both old and newly assembled data sets of protein-ligand complexes, we show that the use of GCMC in FEP is essential for accurate and robust predictions for ligand perturbations that disrupt buried water.

Applications of water molecules for analysis of macromolecule properties

Water molecules maintain proteins' structures, functions, stabilities and dynamics. They can occupy certain positions or pass quickly via a protein's interior. Regardless of their behaviour, water molecules can be used for the analysis of proteins' structural features and biochemical properties. Here, we present a list of several software programs that use the information provided by water molecules to: i) analyse protein structures and provide the optimal positions of water molecules for protein hydration, ii) identify high-occupancy water sites in order to analyse ligand binding modes, and iii) detect and describe tunnels and cavities. The analysis of water molecules' distribution and trajectories sheds a light on proteins' interactions with small molecules, on the dynamics of tunnels and cavities, on protein composition and also on the functionality, transportation network and location of functionally relevant residues. Finally, the correct placement of water molecules in protein crystal structures can significantly improve the reliability of molecular dynamics simulations.

On the microscopic origin of the cryoprotective effect in lysine solutions

Lysine cryoprotective properties are due to the tight bonding of the first hydration Shell to the amino acid. However this effect is only possible for concentration up to 5.4 water molecules per lysine.

Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin

This study investigates the role of hydration and its relationship to the conformational equilibrium of the host molecule β-cyclodextrin. Molecular dynamics simulations indicate that the unbound β-cyclodextrin exhibits two state behavior in explicit solvent due to the opening and closing of its cavity. In implicit solvent, these transitions are not observed, and there is one dominant conformation of β-cyclodextrin with an open cavity. Based on these observations, we investigate the hypothesis that the expulsion of thermodynamically unfavorable water molecules into the bulk plays an important role in controlling the accessibility of the closed macrostate at room temperature. We compare the results of the molecular mechanics analytical generalized Born plus nonpolar solvation approach to those obtained through grid inhomogeneous solvation theory analysis with explicit solvation to elucidate the thermodynamic forces at play. The work illustrates the use of continuum solvent models to tease out solvation effects related to the inhomogeneity and the molecular nature of water and demonstrates the key role of the thermodynamics of enclosed hydration in driving the conformational equilibrium of molecules in solution.