Theoretical study on the HIV-1 integrase–5CITEP complex based on polarized force fields

Quantifying the Molecular Polarization Response of Liquid Water Interfaces at Heterogeneously Charged Surfaces

The hydration shells of proteins mediate interactions, such as small molecule binding, that are vital to their biological function or in some cases their dysfunction. However, even when the structure of a protein is known, the properties of its hydration environment cannot be easily predicted due to the complex interplay between protein surface heterogeneity and the collective structure of water's hydrogen bonding network. This manuscript presents a theoretical study of the influence of surface charge heterogeneity on the polarization response of the liquid water interface. We focus our attention on classical point charge models of water, where the polarization response is limited to molecular reorientation. We introduce a new computational method for analyzing simulation data that is capable of quantifying water's collective polarization response and determining the effective surface charge distribution of hydrated surfaces over atomistic length scales. To illustrate the utility of this method, we present the results of molecular dynamics simulations of liquid water in contact with a heterogeneous model surface and the CheY protein.

Synthesis and evaluation of 3-hydroxy-3-phenylpropanoate ester–AZT conjugates as potential dual-action HIV-1 Integrase and Reverse Transcriptase inhibitors

Novel 3-hydroxy-3-phenylpropanoate ester-azidothymidine (AZT) conjugates have been prepared using Baylis-Hillman methodology, and their potential as dual-action HIV-1 Integrase and Reverse Transcriptase inhibitors has been explored using enzyme inhibition and computer modelling techniques; their activity and HeLa cell toxicity have been compared with those of their cinnamate ester analogues.

Understanding the basis of I50V-induced affinity decrease in HIV-1 protease via molecular dynamics simulations using polarized force field

Human immunodeficiency virus (HIV)-1 protease is one of the most promising drug target commonly utilized to combat Acquired Immune Deficiency Syndrome (AIDS). However, with the emergence of drug resistance arising from mutations, the efficiency of protease inhibitors (PIs) as a viable treatment for AIDS has been greatly reduced. I50V mutation as one of the most significant mutations occurring in HIV-1 protease will be investigated in this study. Molecular dynamics (MD) simulation was utilized to examine the effect of I50V mutation on the binding of two PIs namely indinavir and amprenavir to HIV-1 protease. Prior to the simulations conducted, the electron density distributions of the PI and each residue in HIV-1 protease are derived by combining quantum fragmentation approach molecular fractionation with conjugate caps and Poisson-Boltzmann solvation model based on polarized protein-specific charge scheme. The atomic charges of the binding complex are subsequently fitted using delta restrained electrostatic potential (delta-RESP) method to overcome the poor charge determination of buried atom. This way, both intraprotease polarization and the polarization between protease and the PI are incorporated into partial atomic charges. Through this study, the mutation-induced affinity variations were calculated and significant agreement between experiments and MD simulations conducted was observed for both HIV-1 protease-drug complexes. In addition, the mechanism governing the decrease in the binding affinity of PI in the presence of I50V mutation was also explored to provide insights pertaining to the design of the next generation of anti-HIV drugs.

Electrostatic polarization is critical for the strong binding in streptavidin-biotin system

The origin of strong affinity of biotin and its analogs binding to (strept)avidin is still the subject of an ongoing controversy. In this work, thermodynamic integration is carried out to study of the difference of binding free energies between biotin and iminobiotin to streptavidin. Three atomic charge schemes are implemented and compared. One is the traditional AMBER charge, and the other two, termed the polarized protein-specific charge, are based on a linear scaling quantum mechanical method and a continuous solvation model and have polarization effect partially or fully included. The result indicates that when nonpolarized AMBER force field is applied, the result is much underestimated. When electronic polarization is gradually included, the difference of binding affinity increases along with it. Using the linear-response approximation to eliminate the error in self-charging process, the corrected binding affinity agrees well with the experimental observation. This study is direct evidence indicating that polarization effect is critical for the strong binding in streptavidin-biotin system.

The solvated interaction energy method for scoring binding affinities

The solvated interaction energy (SIE) is an end-point, physics-based scoring function for predicting ligand-binding affinities. It supplements the force-field interaction energy with the desolvation cost of binding. Parameters such as the solute dielectric constant, Born radii, a cavity term and an overall scaling coefficient and additive constant have been previously calibrated against a training set of 99 protein-ligand complexes. We describe the application of the method to estimating binding free energies from molecular dynamics trajectories of protein-ligand binding complexes.

Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction

We carried out a prospective evaluation of the utility of the SIE (solvation interaction energy) scoring function for virtual screening and binding affinity prediction. Since experimental structures of the complexes were not provided, this was an exercise in virtual docking as well. We used our exhaustive docking program, Wilma, to provide high-quality poses that were rescored using SIE to provide binding affinity predictions. We also tested the combination of SIE with our latest solvation model, first shell of hydration (FiSH), which captures some of the discrete properties of water within a continuum model. We achieved good enrichment in virtual screening of fragments against trypsin, with an area under the curve of about 0.7 for the receiver operating characteristic curve. Moreover, the early enrichment performance was quite good with 50% of true actives recovered with a 15% false positive rate in a prospective calculation and with a 3% false positive rate in a retrospective application of SIE with FiSH. Binding affinity predictions for both trypsin and host-guest complexes were generally within 2 kcal/mol of the experimental values. However, the rank ordering of affinities differing by 2 kcal/mol or less was not well predicted. On the other hand, it was encouraging that the incorporation of a more sophisticated solvation model into SIE resulted in better discrimination of true binders from binders. This suggests that the inclusion of proper Physics in our models is a fruitful strategy for improving the reliability of our binding affinity predictions.

Polarization of intraprotein hydrogen bond is critical to thermal stability of short helix

Simulation result for protein folding/unfolding is highly dependent on the accuracy of the force field employed. Even for the simplest structure of protein such as a short helix, simulations using the existing force fields often fail to produce the correct structural/thermodynamic properties of the protein. Recent research indicated that lack of polarization is at least partially responsible for the failure to successfully fold a short helix. In this work, we develop a simple formula-based atomic charge polarization model for intraprotein (backbone) hydrogen bonding based on the existing AMBER force field to study the thermal stability of a short helix (2I9M) by replica exchange molecular dynamics simulation. By comparison of the simulation results with those obtained by employing the standard AMBER03 force field, the formula-based atomic charge polarization model gave the helix melting curve in close agreement with the NMR experiment. However, in simulations using the standard AMBER force field, the helix was thermally unstable at the temperature of the NMR experiment, with a melting temperature almost below the freezing point. The difference in observed thermal stability from these two simulations is the effect of backbone intraprotein polarization, which was included in the formula-based atomic charge polarization model. The polarization of backbone hydrogen bonding thus plays a critical role in the thermal stability of helix or more general protein structures.

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. Benchmark in the CSAR-2010 scoring exercise

Solvated interaction energy (SIE) is an end-point physics-based scoring function for predicting binding affinities from force-field nonbonded interaction terms, continuum solvation, and configurational entropy linear compensation. We tested the SIE function in the Community Structure-Activity Resource (CSAR) scoring challenge consisting of high-resolution cocrystal structures for 343 protein-ligand complexes with high-quality binding affinity data and high diversity with respect to protein targets. Particular emphasis was placed on the sensitivity of SIE predictions to the assignment of protonation and tautomeric states in the complex and the treatment of metal ions near the protein-ligand interface. These were manually curated from an originally distributed CSAR-HiQ data set version, leading to the currently distributed CSAR-NRC-HiQ version. We found that this manual curation was a critical step for accurately testing the performance of the SIE function. The standard SIE parametrization, previously calibrated on an independent data set, predicted absolute binding affinities with a mean-unsigned-error (MUE) of 2.41 kcal/mol for the CSAR-HiQ version, which improved to 1.98 kcal/mol for the upgraded CSAR-NRC-HiQ version. Half-half retraining-testing of SIE parameters on two predefined subsets of CSAR-NRC-HiQ led to only marginal further improvements to an MUE of 1.83 kcal/mol. Hence, we do not recommend altering the current default parameters of SIE at this time. For a sample of SIE outliers, additional calculations by molecular dynamics-based SIE averaging with or without incorporation of ligand strain, by MM-PB(GB)/SA methods with or without entropic estimates, or even by the linear interaction energy (LIE) formalism with an explicit solvent model, did not further improve predictions.