From Implicit to Explicit: An Interaction-Reorganization Approach to Molecular Solvation Energy.

Accurate calculation of solvation energies has long fascinated researchers, but complex interactions within bulk water molecules pose significant challenges. Currently, molecular solvation energy calculations are mostly based on implicit solvent approximations in which the solvent molecules are treated as continuum dielectric media. However, the implicit solvent approach is not ideal because it lacks certain real solvation effects, such as that of the first solvation shell, etc.

Development and experimental validation of computational methods for human antibody affinity enhancement.

High affinity is crucial for the efficacy and specificity of antibody. Due to involving high-throughput screens, biological experiments for antibody affinity maturation are time-consuming and have a low success rate. Precise computational-assisted antibody design promises to accelerate this process, but there is still a lack of effective computational methods capable of pinpointing beneficial mutations within the complementarity-determining region (CDR) of antibodies.

Targeting mechanism for SARS-CoV-2 : interaction and key groups of TMPRSS2 toward four potential drugs.

The global dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seriously endangered human health. The number of confirmed cases is still increasing; however, treatment options are limited. Transmembrane protease serine 2 (TMPRSS2), as a key protease that primes the binding of SARS-CoV-2 spike protein and angiotensin-converting enzyme 2 (ACE2), has become an attractive target and received widespread attention.

Inhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 M by large-scale molecular dynamic simulations combined with accurate binding free energy calculations.

Coronavirus disease 2019 (COVID-19), which is caused by a new coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is spreading around the world. However, a universally effective treatment regimen has not been developed to date. The main protease (M), a key enzyme of SARS-CoV-2, plays a crucial role in the replication and transcription of this virus in cells and has become the ideal target for rational antiviral drug design.

Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/Bcl-2 binding to Bad/Bax.

The anti-apoptotic proteins B-cell lymphoma-extra large (Bcl-xL) and B-cell lymphoma/leukemia-2 (Bcl-2) are members of the Bcl-2 protein family, and they play important roles in regulating apoptosis and cell cycle retardation. However, the binding mechanisms of Bcl-xL/Bcl-2 with their associated agonists, including Bcl-2-associated death promoter (Bad) and Bcl-2-associated X protein (Bax), are not well understood. In the present study, the recently developed interaction entropy approach was employed for the calculation of entropic contribution, and the computational alanine scanning method was used to identify the hot spot in the protein-protein interactions between Bcl-xL/Bcl-2 and Bad/Bax.

An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein-ligand binding affinity.

The molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method is constantly used to calculate the binding free energy of protein-ligand complexes, and has been shown to effectively balance computational cost against accuracy. The relative binding affinities obtained by the MM/PBSA approach are acceptable, while it usually overestimates the absolute binding free energy. This paper proposes four free energy estimators based on the MM/PBSA for enthalpy change combined with interaction entropy (IE) for entropy change using different weights for individual energy terms.

Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin-biotin binding.

Molecular dynamics (MD) simulations were performed employing the polarized protein-specific charge (PPC) to explore the origin of the cooperativity in streptavidin-biotin systems (wild type, two single mutations and one double-mutation). The results of the experiment found that the existence of cooperativity is mainly the result of the entropic effect. In this study, the entropic contribution to the binding free energy was calculated using the recently developed interaction entropy (IE) method, and computational results are in excellent agreement with the experimental observations and are further verified by the calculation of the thermodynamic integration.

Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor.

Quantitative characterization of binding affinity in protein-ligand and residue-ligand is critical for understanding binding mechanisms of protein-ligand and predicting hot-spot residues. In this paper, binding free energies between two HIV (HIV-1 and HIV-2) proteases and four inhibitors are calculated by molecular mechanics/generalized Born surface area (MM/GBSA) combined with the newly developed interaction entropy (IE) approach. The internal dielectric constant is set on the basis of different types of amino acids.

Improving the performance of the MM/PBSA and MM/GBSA methods in recognizing the native structure of the Bcl-2 family using the interaction entropy method.

In the research and development of new drugs, theoretical and computational studies play an increasingly important role in discriminating native and decoy structures by their binding free energies. Predicting the binding free energy using the molecular mechanics/Poisson-Boltzmann (Generalized Born) surface area (MM/PB(GB)SA) methods to identify the native structure as the lowest-energy conformation is more theoretically rigorous than most scoring functions, but the main challenge of this method is the calculation of the entropic contribution. In this study, we add the entropic contribution to the MM/PBSA and two MM/GBSA (GBHCT and GBOBC1) models using the interaction entropy (IE) method.

Binding Mechanism of Thrombin-Ligand Systems Investigated by a Polarized Protein-Specific Charge Force Field and Interaction Entropy Method.

In this study, 2 groups of 10 modified ligand systems with modified P3 and P2 side chains are used to study the binding mechanism with thrombin. Experimental results show that the binding affinity is enhanced by complex ligand side chains. The binding free energy obtained from the polarized protein-specific charge (PPC) force field combined with the newly developed interaction entropy (IE) method is consistent with the experimental values with a high correlation coefficient.

Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy.

As a promising drug target in the treatment of lung cancer, anaplastic lymphoma kinase (ALK) and its mutations have been studied widely through the development of multiple generations of inhibitors. Experiments have found that compared with the wild-type, the L1198F and C1156Y/L1198F mutations resulted in resistance to 5P8 inhibitors, and the C1156Y mutation resulted in resistance to VGH inhibitors. In this study, the newly developed interaction entropy (IE) method combined with the polarized protein-specific charge (PPC) force field was utilized to explore the origin of the resistance mechanism of the ALK mutant system.

Metal-Templated Design: Enantioselective Hydrogen-Bond-Driven Catalysis Requiring Only Parts-per-Million Catalyst Loading.

Based on a metal-templated approach using a rigid and globular structural scaffold in the form of a bis-cyclometalated octahedral iridium complex, an exceptionally active hydrogen-bond-mediated asymmetric catalyst was developed and its mode of action investigated by crystallography, NMR, computation, kinetic experiments, comparison with a rhodium congener, and reactions in the presence of competing H-bond donors and acceptors. Relying exclusively on weak forces, the enantioselective conjugate reduction of nitroalkenes can be executed at catalyst loadings as low as 0.004 mol% (40 ppm), representing turnover numbers of up to 20 250.