Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di-mannose deoxy analogs with P51G-m4-Cyanovirin-N

Complexes of two Cyanovirin-N (CVN) mutants, m4-CVN and P51G-m4-CVN, with deoxy di-mannose analogs were employed as models to generate conformational ensembles using explicit water Molecular Dynamics (MD) simulations in solution and in crystal environment. The results were utilized for evaluation of binding free energies with the molecular mechanics Poisson-Boltzmann (or Generalized Born) surface area, MM/PB(GB)SA, methods. The calculations provided the ranking of deoxy di-mannose ligands affinity in agreement with available qualitative experimental evidences. This confirms the importance of the hydrogen-bond network between di-mannose 3'- and 4'-hydroxyl groups and the protein binding site B(M) as a basis of the CVN activity as an effective HIV fusion inhibitor. Comparison of binding free energies averaged over snapshots from the solution and crystal simulations showed high promises in the use of the crystal matrix for acceleration of the conformational ensemble generation, the most time consuming step in MM/PB(GB)SA approach. Correlation between energy values based on solution versus crystal ensembles is 0.95 for both MM/PBSA and MM/GBSA methods.     

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

We study how the results of molecular dynamics (MD) simulations are affected by various choices during the setup, e.g., the starting velocities, the solvation, the location of protons, the conformation of His, Asn, and Gln residues, the protonation and titration of His residues, and the treatment of alternative conformations. We estimate the binding affinity of ligands to four proteins calculated with the MM/GBSA method (molecular mechanics combined with a generalized Born and surface area solvation energy). For avidin and T4 lysozyme, all variations gave similar results within 2 kJ/mol. For factor Xa, differences in the solvation or in the selection of alternative conformations gave results that are significantly different from those of the other approaches by 4-6 kJ/mol, whereas for galectin-3, changes in the conformations, rotations, and protonation gave results that differed by 10 kJ/mol, but only if residues close to the binding site were modified. This shows that the results of MM/GBSA calculations are reasonably reproducible even if the MD simulations are set up with different software. Moreover, we show that the sampling of phase space can be enhanced by solvating the systems with different equilibrated water boxes, in addition to the common use of different starting velocities. If different conformations are available in the crystal structure, they should also be employed to enhance the sampling. Protonation, ionization, and conformations of Asn, Gln, and His may also be used to enhance sampling, but great effort should be spent to obtain as reliable predictions as possible close to the active site.     

Molecular dynamics simulations of PNIPAM‐co‐PEGMA copolymer hydrophilic to hydrophobic transition in NaCl solution

Classical molecular dynamics simulations were carried out to investigate the hydrophilic to hydrophobic transition of PNIPAM‐co‐PEGMA close to its lower critical solution temperature (LCST) in 1 M NaCl solution. PNIPAM‐co‐PEGMA is a copolymer of poly(N‐isopropylacrylamide) (PNIPAM) and poly(ethylene glycol) methacrylate (PEGMA). The copolymer consists of 38 monomer units of NIPAM with two PEGMA chains attached to the PNIAPM backbone. The PNIPAM‐co‐PEGMA was observed to go through the hydrophilic?hydrophobic conformational change for simulations at temperature slightly above its LCST. Na⁺ ions were found to bind strongly and directly with amide O, even more strongly with the O atoms on PEGAMS chains, whereas Cl^? ions only exhibit weak interaction with the polymer. Significantly a novel caged stable metal‐organic complex involving a Na⁺ ion coordinated by six O atoms from the copolymer was observed after the PNIPAM‐co‐PEGMA copolymer went through conformational transition to form a hydrophobic folded structure. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

分子动力学模拟研究康里新(Conessine)对MexB的抑制机理

通过分子动力学模拟结合自由能MM/PBSA方法,确定了康里新与MexB的结合位点与关键氨基酸.通过对康里新与内膜转运蛋白MexB的疏水作用和氢键的分析,发现康里新的结合口袋是一个"疏水陷阱",MexB中的"疏水陷阱"抑制了MexB蠕动外排作用.     

The Jahn-Teller effect of the Cr(2+) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulations

The hydration structure of Cr(2+) has been studied using molecular dynamics (MD) simulations including three-body corrections and combined ab initio quantum mechanical/molecular mechanical (QM/MM) MD simulations at the Hartree-Fock level. The structural properties are determined in terms of radial distribution functions, coordination numbers, and several angle distributions. The mean residence time was evaluated for describing ligand exchange processes in the second hydration shell. The Jahn-Teller distorted octahedral [Cr(H(2)O)(6)](2+) complex was pronounced in the QM/MM MD simulation. The first-shell distances of Cr(2+) are in the range of 1.9-2.8 A, which are slightly larger than those observed in the cases of Cu(2+) and Ti(3+). No first-shell water exchange occurred during the simulation time of 35 ps. Several water-exchange processes were observed in the second hydration shell with a mean residence time of 7.3 ps.     

Molecular dynamics simulations of LiCl association and NaCl association in water by means of ABEEM/MM

Constrained molecular dynamics simulations have been used to investigate the LiCl and NaCl ionic association in water in terms of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM). The simulations make use of the seven-site fluctuating charge and flexible ABEEM-7P water model, based on which an ion-water interaction potential has been constructed. The mean force and the potential of mean force for LiCl and NaCl in water, the charge distributions, as well as the structural and dynamical properties of contact ion pair dissociation have been investigated. The results are reasonable and informative. For LiCl ion pair in water, the solvent-separated ion pair configurations are more stable than contact ion pair configurations. The calculated PMF for NaCl in water indicates that contact ion pair and solvent-separated ion pair configurations are of comparable stability.     

Quantum mechanical/molecular mechanical simulations of the Tl(III) ion in water

Classical molecular dynamics (MD) and combined quantum mechanical/molecular mechanical (QM/MM) MD simulations have been performed to investigate the structural and dynamical properties of the Tl(III) ion in water. A six-coordinate hydration structure with a maximum probability of the Tl-O distance at 2.21 A was observed, which is in good agreement with X-ray data. The librational and vibrational spectra of water molecules in the first hydration shell are blue-shifted compared with those of pure liquid water, and the Tl-O stretching force constant was evaluated as 148 Nm(-1). Both structural and dynamical properties show a distortion of the first solvation shell structure. The second shell ligands' mean residence time was determined as 12.8 ps. The Tl(III) ion can be classified as "structure forming" ion; the calculated hydration energy of -986 +/- 9 kcal mol agrees well with the experimental value of -986 kcal mol.     

Rational design of InhA inhibitors in the class of diphenyl ether derivatives as potential anti-tubercular agents using molecular dynamics simulations

A series of diphenyl ether derivatives were developed and showed promising potency for inhibiting InhA, an essential enoyl acyl carrier protein reductase involved in mycolic acid biosynthesis, leading to the lysis of Mycobacterium tuberculosis. To understand the structural basis of diphenyl ether derivatives for designing more potent inhibitors, molecular dynamics (MD) simulations were performed. Based on the obtained results, the dynamic behaviour in terms of flexibility, binding free energy, binding energy decomposition, conformation, and the inhibitor–enzyme interaction of diphenyl ether inhibitors were elucidated. Phe149, Tyr158, Met161, Met199, Val203 and NAD+ are the key residues for binding of diphenyl ether inhibitors in the InhA binding pocket. Our results could provide the structural concept to design new diphenyl ether inhibitors with better enzyme inhibitory activity against M. tuberculosis InhA. The present work facilitates the design of new and potentially more effective anti-tuberculosis agents.     

Importance of the catalytic effect of the substrate in the functionality of lubricant additives: the case of molybdenum dithiocarbamates

Molybdenum dithiocarbamates (MoDTCs) are lubricant additives very efficient in reducing the friction of steel, and they are used in a number of industrial applications. The functionality of these additives is ruled by the chemical interactions occurring at the buried sliding interface, which are of key importance for the improvement of the lubrication performance. Yet, these tribochemical processes are very difficult to monitor in real time. Ab initio molecular dynamics simulations are the ideal tool to shed light on such a complicated reactivity. In this work, we perform ab initio simulations, both in static and tribological conditions, to understand the effect of surface oxidation on the tribochemical reactivity of MoDTC, and we find that when the surfaces are covered by oxygen, the first dissociative steps of the additives are significantly hindered. Our preliminary tribological tests on oxidized steel discs support these results. Bare metallic surfaces are necessary for a stable adsorption of the additives, their quick decomposition, and the formation of a durable MoS₂ tribolayer. This work demonstrates the importance of the catalytic role of the substrate and confirms the full capability of the computational protocol in the pursuit of materials and compounds more efficient in reducing friction.     

An averaged solvent electrostatic potential from molecular dynamics study of the anomeric equilibrium of D-xylose in aqueous solution

We applied the free-energy perturbation method together with the averaged solvent electrostatic potential from molecular dynamics (ASEP/MD) method to study the anomeric equilibrium of d-xylose in aqueous solution. The level of calculation, 6-311G++(2d,2p) basis set and density functional theory, permits one to explain the main characteristics of the anomeric equilibrium of d-xylopyranose: in vacuo, the anomeric effect predominates and the form is the stabler. In water, solvation leads to the form being the stabler. A comparison between the performances of the ASEP/MD and polarizable continuum models is also presented.Contribution to the Jacopo Tomasi Honorary Issue     

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

An integrated Feynman path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method has been used to investigate the kinetic isotope effects (KIEs) in the proton transfer reaction between nitroethane and acetate ion in water. In the present study, both nuclear and electronic quantum effects are explicitly treated for the reacting system. The nuclear quantum effects are represented by bisection sampling centroid path integral simulations, while the potential energy surface is described by a combined quantum mechanical and molecular mechanical (QM/MM) potential. The accuracy essential for computing KIEs is achieved by a FEP technique that transforms the mass of a light isotope into a heavy one, which is equivalent to the perturbation of the coordinates for the path integral quasiparticle in the bisection sampling scheme. The PI-FEP/UM method is applied to the proton abstraction of nitroethane by acetate ion in water through molecular dynamics simulations. The rule of the geometric mean and the Swain-Schaad exponents for various isotopic substitutions at the primary and secondary sites have been examined. The computed total deuterium KIEs are in accord with experiments. It is found that the mixed isotopic Swain-Schaad exponents are very close to the semiclassical limits, suggesting that tunneling effects do not significantly affect this property for the reaction between nitroethane and acetate ion in aqueous solution.     

Theoretical analysis of the kinetic isotope effect on carboxylation in RubisCO

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) fixes atmospheric carbon dioxide into bioavailable sugar molecules. It is also well known that a kinetic isotope effect (KIE; CO₂ carbon atoms) accompanies the carboxylation process. To describe the reaction and the KIE α, two different types of molecular dynamics (MD) simulations (ab initio MD and classical MD) have been performed with an Own N-layered Integrated molecular Orbitals and molecular Mechanics (ONIOM)-hybrid model. A channel structure for CO₂ transport has been observed during the MD simulation in RubisCO, and assuming the reaction path from the inlet to the product through the coordinate complex with Mg²⁺, simulations have been performed on several molecular configuration models fixing several distances between CO₂ and ribulose-1,5-bisphosphate along the channel. Free energy analysis and diffusion coefficient analysis have been evaluated for different phases of the process. It is confirmed that the isotopic fractionation effect for CO₂ containing either ¹³C or ¹²C would appear through the transiting path in the channel structure identified in RubisCO. The estimated isotope fractionation constant was quite close to the experimental value.     

Systematic profiling of chemotherapeutic drug response to EGFR gatekeeper mutation in non-small cell lung cancer

The epidermal growth factor receptor (EGFR) targeted therapy has been established as a routine strategy for treating non-small cell lung cancer (NSCLC). However, the gatekeeper mutation T790M in EGFR active site can confer generic resistance to tyrosine kinase inhibitors (TKIs), largely limiting the clinical applications of chemotherapeutic drugs in NSCLC. Here, a combined method of computational analysis and growth inhibition assay was described to systematically investigate the molecular response profile of wild-type–sparing and mutant-resistant inhibitors to the EGFR T790M mutation. The profile is highly consistent with previous clinical observations; three first-line chemotherapeutic drugs Gefitinib, Erlotinib and Lapatinib are established with acquired resistance upon the mutation. In addition, it was found that the alkaloid compound K252a, a Staurosporine analog isolated from Nocardiopisis sp., can selectively target the EGFR T790M mutant over wild-type kinase (23-fold selectivity), suggesting that the compound is good lead candidate for development of T790M mutant-selective inhibitors. Structural analysis revealed that the mutation-resulting Met790 residue does not induce steric hindrance to the EGFR T790M–K252a complex system, while a number of hydrophobic forces, van der Waals contacts and S⋯π interactions are observed between the aromatic rings of K252a and the sulfhydryl group of Met790, contributing considerable stabilization energy to the system.     

Toward a new approach for determination of solute's charge distribution to analyze interatomic electrostatic interactions in quantum mechanical/molecular mechanical simulations

We present an alternative approach to determine "density-dependent property"-derived charges for molecules in the condensed phase. In the case of a solution, it is essential to take into consideration the electron polarization of molecules in the active site of this system. The solute and solvent molecules in this site have to be described by a quantum mechanical technique and the others are allowed to be treated by a molecular mechanical method (QM/MM scheme). For calculations based on this scheme, using the forces and interaction energy as density-dependent property our charges from interaction energy and forces (CHIEF) approach can provide the atom-centered charges on the solute atoms. These charges reproduce well the electrostatic potentials around the solvent molecules and present properly the picture of the electron density of the QM subsystem in the solution system. Thus, the CHIEF charges can be considered as the atomic charges under the conditions of the QM/MM simulation, and then enable one to analyze electrostatic interactions between atoms in the QM and MM regions. This approach would give a view of the QM nuclei and electrons different from the conventional methods.     

On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations

During the past years, the use of combined quantum-classical, QM/MM, methods for the study of complex biomolecular processes, such as enzymatic reactions and photocycles, has increased considerably. The quality of the results obtained from QM/MM calculations is largely dependent on five aspects to be considered when setting up a molecular model: the QM Hamiltonian, the MM Hamiltonian or force field, the boundary and coupling between the QM and MM regions, the size of the QM region and the boundary condition for the MM region. In this study, we systematically investigate the influence of a variation of the molecular mechanics force field and the size of the QM region in QM/MM MD simulations on properties of the photoactive part of the blue light photoreceptor protein AppA. For comparison, we additionally performed classical MD simulations and studied the effect of a variation of the type of spatial boundary condition. The classical boundary conditions and the force field used in a QM/MM MD simulation are shown to have non-neglegible effects upon the structural and energetic properties of the protein which makes it advisable to minimize computational artifacts in QM/MM MD simulations by application of periodic boundary conditions and a thermodynamically calibrated force field. A comparison of the structural and energetic properties of MD simulations starting from two alternative, different X-ray structures for the blue light utilizing flavin protein in its dark state indicates a slight preference of the two force fields used for the so-called Anderson structure over the Jung structure.     

Molecular insight into the T798M gatekeeper mutation-caused acquired resistance to tyrosine kinase inhibitors in ErbB2-positive breast cancer

Human epidermal growth factor receptor 2 (ErbB2) is an attractive therapeutic target for metastatic breast cancer. The kinase has been clinically observed to harbor a gatekeeper mutation T798M in its active site, which causes acquired resistance to the first-line targeted breast cancer therapy with small-molecule tyrosine kinase inhibitors. Previously, several theories have been proposed to explain the molecular mechanism of gatekeeper mutation-caused drug resistance, such as blocking of inhibitor binding and increasing of ATP affinity. In the current study, the direct binding of three wild type-selective inhibitors (Lapatinib, AEE788 and TAK-285) and two wild type-sparing inhibitors (Staurosporine and Bosutinib) to the wild-type ErbB2 and its T798M mutant are investigated in detail by using rigorous computational analysis and binding affinity assay. Substitution of the polar threonine with a bulky methionine at residue 798 can impair and improve the direct binding affinity of wild type-selective and wild type-sparing inhibitors, respectively. Hindrance effect is responsible for the affinity decrease of wild type-selective inhibitors, while additional nonbonded interactions contribute to the affinity increase of wild type-sparing inhibitors, thus conferring selectivity to the inhibitors for mutant over wild type. The binding affinity of Staurosporine and Bosutinib to ErbB2 kinase domain is improved by 11.9-fold and 2.1-fold upon T798M mutation, respectively. Structural analysis reveals that a nonbonded network of S–π contact interactions (for Staurosporine) or an S-involving halogen bond (for Bosutinib) forms with the sulfide group of mutant Met798 residue.     

Binding free energy of several sterols to the N-terminal domain of Niemann-Pick C1-like 1 protein due to mutation: Molecular dynamics study

The membrane protein Niemann-Pick type C1-like 1 (NPC1L1) plays a central role in the absorption of cholesterol in the small intestine. Other sterols, notably vitamin E and vitamin K1 also utilize NPC1L1 as a membrane transporter even though other absorption paths exist. Many NPC1L1 mutations causing the disease due to poor transport of cholesterol are known. It is not clear at this moment if the same mutation can lead to reduced transport behavior with these vitamins. In this study, we have obtained the binding free energies of these two sterols using molecular dynamics simulation and compared these values with the cholesterol-binding free energy. The N-terminal domain (NTD) of the wild as well as the disease-causing two mutations, T61M and L110F, are used for this purpose. The result indicates that the mutations show reduced binding affinity compared to the wild except for the vitamin K1 in the T61M mutant, which has increased binding free energy. Also, we found the similarity of the key amino acids responsible for the change of free energy by mutation between T61M and L110F. At the same time, non-negligible differences exist also.     

Molecular dynamics simulation as a complement to diffraction in the study of disorder in crystals

Summary It is not uncommon that a crystal structure contains a minority component which does not share the overall space-group of the remainder of the structure, but has a lower (or no) effective space-group symmetry. A conventional diffraction treatment will inevitably be made within the space-group of the majority of the system, and will therefore result in an average structure also with this symmetry. We here indicate the value of molecular dynamics (MD) simulation within a supercell of the structure as a complementary tool in providing information concerning the local structure for the minority component. Such information, though illusive, is often the most interesting and the physically most significant aspect of the structure. It can also be crucial information for the testing of new theory, and in the design of new materials. The approach is illustrated for the case of the Na⁺ ion distribution in Na⁺ '-alumina, and for the experimentally more inaccessible mixed-ion system Na⁺/Ba²⁺ '-alumina.On leave of absence from Departamento de Fisica, Universidad Autonoma Metropolitana, Unidad Iztapalapa, Mexico D.F., Mexico.     

Understanding of the drug resistance mechanism of hepatitis C virus NS3/4A to paritaprevir due to D168N/Y mutations: A molecular dynamics simulation perspective

Hepatitis C virus (HCV) NS3/4A protease is an attractive target for the development of antiviral therapy. However, the evolution of antiviral drug resistance is a major problem for treatment of HCV infected patients. Understanding of drug-resistance mechanisms at molecular level is therefore very important for the guidance of further design of antiviral drugs with high efficiency and specificity. Paritaprevir is a potent inhibitor against HCV NS3/4A protease genotype 1a. Unfortunately, this compound is highly susceptible to the substitution at D168 in the protease. In this work, molecular dynamics simulations of paritaprevir complexed with wild-type (WT) and two mutated strains (D168 N and D168Y) were carried out. Due to such mutations, the inhibitor-protein hydrogen bonding between them was weakened and the salt-bridge network among residues R123, R155 and D168 responsible for inhibitor binding was disrupted. Moreover, the per-residue free energy decomposition suggested that the main contributions from key residues such as Q80, V132, K136, G137 and R155 were lost in the D168 N/Y mutations. These lead to a lower binding affinity of paritaprevir for D168 N/Y variants of the HCV NS3/4A protease, consistent with the experimental data. This detailed information could be useful for further design of high potency anti-HCV NS3/4A inhibitors.