Molecular Dynamics Simulation of Tryptophan Hydroxylase-1: Binding Modes and Free Energy Analysis to Phenylalanine Derivative Inhibitors

Serotonin is a neurotransmitter that modulates many central and peripheral functions. Tryptophan hydroxylase-1 (TPH1) is a key enzyme of serotonin synthesis. In the current study, the interaction mechanism of phenylalanine derivative TPH1 inhibitors was investigated using molecular dynamics (MD) simulations, free energy calculations, free energy decomposition analysis and computational alanine scanning. The predicted binding free energies of these complexes are consistent with the experimental data. The analysis of the individual energy terms indicates that although the van der Waals and electrostatics interaction contributions are important in distinguishing the binding affinities of these inhibitors, the electrostatic contribution plays a more crucial role in that. Moreover, it is observed that different configurations of the naphthalene substituent could form different binding patterns with protein, yet lead to similar inhibitory potency. The combination of different molecular modeling techniques is an efficient way to interpret the interaction mechanism of inhibitors and our work could provide valuable information for the TPH1 inhibitor design in the future.     

Application of free energy simulations to the binding of a transition-state-analogue inhibitor to HTV protease

Free energy simulations (slow-change method) have been usedto estimate quantitatively the ratio of the binding constantsof (S) and (R) isomers of a novel HIV protease inhibitor, JG365.As a starting geometry, we used the X-ray crystallographic structureof a complex of HTV protease and JG365 provided by A.Wlodawer.According to our results the (S) configuration, i.e. the formpreviously identified experimentally, binds considerably moretightly to the protease (G° = 2.9 kcal/mol). When the (S)inhibitor is bound, there is a very strong preference for protonationof the Aspl25 (rather than the Asp25) residue of the protease.This study is the first to apply a new method for quantitativelyassessing the precision of free energies calculated by the slow-changemethod     

A new method for predicting binding affinity in computer-aided drug design

A new semi–empirical method for calculating free energiesof binding from molecular dynamics (MD) simulations is presented.It is based on standard thermodynamic cycles and on a linearapproximation of polar and non–polar free energy contributionsfrom the corresponding MD averages. The method is tested ona set of endothiapepsin inhibitors and found to give accurateresults both for absolute as well as relative free energies.     

Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations

Computational methods, namely molecular dynamics (MD) simulations in combination with inhomogeneous fluid solvation theory (IFST) were used to retrospectively investigate various cases of ligand structure modifications that led to the displacement of binding site water molecules. Our findings are that water displacement per se is energetically unfavorable in the discussed examples, and that it is merely the fine balance between change in protein–ligand interaction energy, ligand solvation free energies, and binding site solvation free energies that determine if water displacement is favorable or not. We furthermore evaluated if we can reproduce experimental binding affinities by a computational approach combining changes in solvation free energies with changes in protein–ligand interaction energies and entropies. In two of the seven cases, this estimation led to large errors, implying that accurate predictions of relative binding free energies based on solvent thermodynamics is challenging. Nevertheless, MD simulations can provide insight regarding which water molecules can be targeted for displacement.     

Computational Studies of Difference in Binding Modes of Peptide and Non-Peptide Inhibitors to MDM2/MDMX Based on Molecular Dynamics Simulations

Inhibition of p53-MDM2/MDMX interaction is considered to be a promising strategy for anticancer drug design to activate wild-type p53 in tumors. We carry out molecular dynamics (MD) simulations to study the binding mechanisms of peptide and non-peptide inhibitors to MDM2/MDMX. The rank of binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA) method agrees with one of the experimental values. The results suggest that van der Waals energy drives two kinds of inhibitors to MDM2/MDMX. We also find that the peptide inhibitors can produce more interaction contacts with MDM2/MDMX than the non-peptide inhibitors. Binding mode predictions based on the inhibitor-residue interactions show that the π-π, CH-π and CH-CH interactions dominated by shape complimentarity, govern the binding of the inhibitors in the hydrophobic cleft of MDM2/MDMX. Our studies confirm the residue Tyr99 in MDMX can generate a steric clash with the inhibitors due to energy and structure. This finding may theoretically provide help to develop potent dual-specific or MDMX inhibitors.     

Molecular mechanics analysis of inhibitor binding to HIV-1 protease

Crystallographic structures of HIV protease with three differentpeptide-mimetic inhibitors were subjected to energy minimizationusing molecular mechanics, the minimized structures analyzedand the inhibitor binding energies calculated. Partial chargeassignment for the hydrogen bonded catalytic aspartk acids,Asp25 and -25', was in good agreement with charge calculationsusing semi-empirical molecular orbital methods. Root mean squaredeviations on minimization were small and similar for both subunitsin the protease dimer. The surface loops, which had the largestB factors, changed most on minimization; the hydrophobic coreand the inhibitor binding site showed little change. The distance-dependentdielectric of D(r) = 4r was found to be preferable to D(r) =r. Distance restraints were applied for the intermolecular hydrogenbonds to maintain the conformation of the inhibitor bindingsite. Using the dielectric of D(r) = 4r, the calculated interactionenergy of the three inhibitors with the protease ranged from–53 to –56 kcal/mol. The groups of the inhibitorswere changed to add or remove a ‘transition state analogue’hydroxyl group, and the loss in energy on the removal of thisgroup was calculated to be 0.9–1.7 kcal/mol. This wouldrepresent 19–36% of the total measured difference in bindingenergy between the inhibitors JG365 and MVT-101.     

Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations

Absolute binding free energies for three inhibitors of HIV–1proteinase were estimated from molecular dynamics simulationsby a recently reported linear approximation procedure. The resultswere in fairly good agreement with experimental binding data.Two of the inhibitors were very similar and, for comparison,their relative free energies of binding were also calculatedby free energy perturbation methods, giving virtually the sameresult Effects of cutoff radii and charge states of the proteinmodel were examined. The effects of pH on binding of one ofthe inhibitors were predicted.     

Dynophore-Based Approach in Virtual Screening: A Case of Human DNA Topoisomerase IIα

In this study, we utilized human DNA topoisomerase IIα as a model target to outline a dynophore-based approach to catalytic inhibitor design. Based on MD simulations of a known catalytic inhibitor and the native ATP ligand analog, AMP-PNP, we derived a joint dynophore model that supplements the static structure-based-pharmacophore information with a dynamic component. Subsequently, derived pharmacophore models were employed in a virtual screening campaign of a library of natural compounds. Experimental evaluation identified flavonoid compounds with promising topoisomerase IIα catalytic inhibition and binding studies confirmed interaction with the ATPase domain. We constructed a binding model through docking and extensively investigated it with molecular dynamics MD simulations, essential dynamics, and MM-GBSA free energy calculations, thus reconnecting the new results to the initial dynophore-based screening model. We not only demonstrate a new design strategy that incorporates a dynamic component of molecular recognition, but also highlight new derivates in the established flavonoid class of topoisomerase II inhibitors.     

Relative binding free energy calculations of inhibitors to two mutants (Glu46-- Ala/Gln) of ribonuclease T1 using molecular dynamics/free energy perturbation approaches

We present free energy perturbation calculations on the complexesof Glu46— Ala46 (E46A) and Glu46— Gln46 (E46Q) mutantsof ribonuclease T1 (RNaseT1) with inhibitors 2‘-guanosinemonophosphate (GMP) and 2’adenosine monophosphate (AMP)by a thermodynamic perturbation method implemented with moleculardynamics (MD). Using the available crystal structure of theRNaseT1–GMP complex, the structures of E46A-GMP and E46Q-GMPwere model built and equilibrated with MD simulations. The structuresof E46A-AMP and E46Q-AMP were obtained as a final structureof the GMP—AMP perturbation calculation respectively.The calculated difference in the free energy of binding (Gbind)was 0.31 kcal/mol for the E46A system and —1.04 kcal/molfor the E46Q system. The resultant free energies are much smallerthan the experimental and calculated value of 3 kcal/mol forthe native RNase T1, which suggests that both mutants have greaterrelative adenine affinities than native RNaseT1. EspeciallyE46Q is calculated to have a larger affinity for adenine thanguanine, as we suggested previously from the calculation onthe native RNaseT1. Thus, the molecular dynamics/free energyperturbation method may be helpful in protein engineering, directedtoward increasing or changing the substrate specificity of enzymes.     

Water Resistance of Poly(imide-siloxane) Adhesives: An IGC Surface Energetics Study

Inverse Gas Chromatography was utilized to examine the interaction of water vapor with the surfaces of a polyimide homopolymer and poly(imide-siloxane) random-block copolymers of increasing siloxane content. The studies employed 45-60 meter, thin-polymer-film mega-bore capillary columns to maximize surface area. The free energies of specific surface interaction with water and the dispersive components of the solid surface free energies were determined. An increase in the polymer siloxane content from 0-wt% to 10-wt% resulted in a decrease of approximately 4 kJ/mol in the free energy of water-specific surface interaction. A further increase in siloxane content to 30-wt% was not found to increase surface water resistance significantly. Dispersive components of the solid surface free energies of the copolymers were comparable to values reported for poly(dimethylsiloxane) homopolymer.     

Water Resistance of Poly(imide-siloxane) Adhesives: An IGC Surface Energetics Study

Inverse Gas Chromatography was utilized to examine the interaction of water vapor with the surfaces of a polyimide homopolymer and poly(imide-siloxane) random-block copolymers of increasing siloxane content. The studies employed 45-60 meter, thin-polymer-film mega-bore capillary columns to maximize surface area. The free energies of specific surface interaction with water and the dispersive components of the solid surface free energies were determined. An increase in the polymer siloxane content from 0-wt% to 10-wt% resulted in a decrease of approximately 4 kJ/mol in the free energy of water-specific surface interaction. A further increase in siloxane content to 30-wt% was not found to increase surface water resistance significantly. Dispersive components of the solid surface free energies of the copolymers were comparable to values reported for poly(dimethylsiloxane) homopolymer.     

Distribution and Energies of Grain Boundaries in Magnesia as a Function of Five Degrees of Freedom

The multiplicity of distinct grain boundary configurations in polycrystals has made it difficult to determine the relative frequency with which each configuration is adopted. As a result, the physiochemical properties of each boundary and the influence of the distribution of boundaries on macroscopic materials properties are not well understood. Using a semiautomated system, we have measured all five macroscopically observable degrees of freedom of 4.1 × 10⁶ boundary plane segments making up 5.2 × 10⁶μm² of grain boundary interface area in a magnesia polycrystal. Our observations demonstrate that not all grain boundary configurations occur with the same frequency and that the relative free energies of the different interfacial configurations influence the population distribution. Furthermore, the results indicate that relative grain boundary energies can be estimated based on the free surface energies.     

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed us to reach the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynamics trajectories. We illustrate such applications on nucleic acid duplexes, RNA hairpins, protein folding trajectories, and protein-ligand, protein-protein, and protein-nucleic acid interactions.     

A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis

We have shown that the binding free energy calculation from molecular dynamics can be adapted successfully to cysteine proteinases, such as arginine-specific gingipain (HRgpA) from Porphyromonas gingivalis. The binding free energy obtained is in good agreement with the available experimental data for eight benzamidine derivatives including urea and ether linker. The calculations showed that the electrostatic energies between HRgpA and inhibitors were important in determining the relative affinities of the inhibitors to the HRgpA, with an average binding free energy of about -5 kcal/mol. The average structures of the eight complexes suggest that benzamidine inhibitors interact with Asp387, His435, and Cys468 by hydrogen bonding and with Trp508 by hydrophilic interactions that are essential for the activities of benzamidine inhibitors. It can therefore be expected that the method provides a reliable tool for the investigation of new HRgpA inhibitors. This finding could significantly benefit the future design of HRgpA inhibitors.     

Molecular mechanics analysis of drug-resistant mutants of HIV protease

Drug-resistant mutants of HIV-1 protease limit the long-termeffectiveness of current anti-viral therapy. In order to studydrug resistance, the wild-type HIV-1 protease and the mutantsR8Q, V32I, M46I, V82A, V82I, V82F, I84V, V32I/I84V and M46I/I84Vwere modeled with the inhibitors saquinavir and indinavir usingthe program AMMP. A new screen term was introduced to reproducemore correctly the electron distribution of atoms. The atomicpartial charge was represented as a delocalized charge distributioninstead of a point charge. The calculated protease–saquinavirinteraction energies showed the highly significant correlationof 0.79 with free energy differences derived from the measuredinhibition constants for all 10 models. Three different protonationstates of indinavir were evaluated. The best indinavir modelincluded a sulfate and gave a correlation coefficient of 0.68between the calculated interaction energies and free energiesfrom inhibition constants for nine models. The exception wasR8Q with indinavir, probably due to differences in the solvationenergy. No significant correlation was found using the standardmolecular mechanics terms. The incorporation of the new screencorrection resulted in better prediction of the effects of inhibitorson resistant protease variants and has potential for selectingmore effective inhibitors for resistant virus.     

Study of specific interactions in inclusion complexes of amine-terminated PAMAM dendrimer/flavonoids by experimental and computational methods

Polyamidoamine (PAMAM) dendrimers have a multifunctional structure, able to encapsulate molecules for pharmacological applications. We evaluated the specific interaction that govern the encapsulating and affinity of one group of natural and synthetic flavonoids into the G₅-PAMAM dendrimers. The complexation and capture percent of one flavonoid series into G₅-PAMAM dendrimers, under neutral and acid pH conditions, were studied through UV–Vis spectroscopy. Additionally, only three of the flavonoids (two synthetic and one natural) were studied by high-performance liquid chromatography (HPLC) and molecular dynamic (MD) simulation, at neutral pH to calculate the affinity constants (K_d) and binding free energies (ΔG_b). From spectroscopic results, we observed that the encapsulation was much more rapid at low pH than at neutral pH, which was attributed to a greater number of cavities inside the dendrimer. The MD simulations suggested that the more compact molecular structure at neutral pH reduces the capture kinetics. Finally, the relative binding free energies calculated using MD simulations showed the same tendency as the experimental data for the three complexes. These affinities appear to be due to a complex balance of different contributions, which cannot be attributed to hydrogen bonds or charge–charge interactions alone. Nevertheless, we suggest that a protocol including UV–Vis, HPLC, and MD simulation can be a powerful predictive tool to determine the affinity of drug binding to nanocarriers.     

Discovery of Tyrosine Kinase Inhibitors by Docking into an Inactive Kinase Conformation Generated by Molecular Dynamics

Several small molecules that bind to the inactive DFG‐out conformation of tyrosine kinases (called type II inhibitors) have shown a good selectivity profile over other kinase targets. To obtain a set of DFG‐out structures, we performed an explicit solvent molecular dynamics (MD) simulation of the complex of the catalytic domain of a tyrosine kinase receptor, ephrin type‐A receptor 3 (EphA3), and a manually docked type II inhibitor. Automatic docking of four previously reported type II inhibitors was used to select a single snapshot from the MD trajectory for virtual screening. High‐throughput docking of a pharmacophore‐tailored library of 175 000 molecules resulted in about 4 million poses, which were further filtered by van der Waals efficiency and ranked according to a force‐field‐based energy function. Notably, around 20 % of the compounds with predicted binding energy smaller than ?10 kcal mol^?1 are known type II inhibitors. Moreover, a series of 5‐(piperazine‐1‐yl)isoquinoline derivatives was identified as a novel class of low‐micromolar inhibitors of EphA3 and unphosphorylated Abelson tyrosine kinase (Abl1). The in silico predicted binding mode of the new inhibitors suggested a similar affinity to the gatekeeper mutant T315I of Abl1, which was verified in vitro by using a competition binding assay. Additional evidence for the type II binding mode was obtained by two 300 ns MD simulations of the complex between N‐(3‐chloro‐4‐(difluoromethoxy)phenyl)‐2‐(4‐(8‐nitroisoquinolin‐5‐yl)piperazin‐1‐yl)acetamide and EphA3.     

Combining Molecular Docking and Molecular Dynamics to Predict the Binding Modes of Flavonoid Derivatives with the Neuraminidase of the 2009 H1N1 Influenza A Virus

Control of flavonoid derivatives inhibitors release through the inhibition of neuraminidase has been identified as a potential target for the treatment of H1N1 influenza disease. We have employed molecular dynamics simulation techniques to optimize the 2009 H1N1 influenza neuraminidase X-ray crystal structure. Molecular docking of the compounds revealed the possible binding mode. Our molecular dynamics simulations combined with the solvated interaction energies technique was applied to predict the docking models of the inhibitors in the binding pocket of the H1N1 influenza neuraminidase. In the simulations, the correlation of the predicted and experimental binding free energies of all 20 flavonoid derivatives inhibitors is satisfactory, as indicated by R(2) = 0.75.