Molecular Mechanics Energy Minimization Research Articles

Quantum Biochemistry and MM-PBSA Description of the ZIKV NS2B-NS3 Protease: Insights into the Binding Interactions beyond the Catalytic Triad Pocket.

The Zika virus protease NS2B-NS3 has a binding site formed with the participation of a H51-D75-S135 triad presenting two forms, active and inactive. Studies suggest that the inactive conformation is a good target for the design of inhibitors. In this paper, we evaluated the co-crystallized structures of the protease with the inhibitors benzoic acid (5YOD) and benzimidazole-1-ylmethanol (5H4I). We applied a protocol consisting of two steps: first, classical molecular mechanics energy minimization followed by classical molecular dynamics were performed, obtaining stabilized molecular geometries; second, the optimized/relaxed geometries were used in quantum biochemistry and molecular mechanics/Poisson–Boltzmann surface area (MM-PBSA) calculations to estimate the ligand interactions with each amino acid residue of the binding pocket. We show that the quantum-level results identified essential residues for the stabilization of the 5YOD and 5H4I complexes after classical energy minimization, matching previously published experimental data. The same success, however, was not observed for the MM-PBSA simulations. The application of quantum biochemistry methods seems to be more promising for the design of novel inhibitors acting on NS2B-NS3.

Применение метода Тагучи для изучения структуры пептидного лиганда в составе сложного комплекса

Taguchi method was used to optimize peptide ligand structure using the H-2/TCR complex (PDB ID 2Z31). This approach greatly reduces the number of experiments that are required to analyze the contribution of various amino acid residues for each position into ligand molecule. Taguchi matrix was used to design a set of peptide ligands for molecular docking and molecular mechanics energy minimization. This approach allowed creating a new peptide structure with lower molecular mechanics energy than native peptide and demonstrates the applicability of the Taguchi method for peptide ligand optimization.

Molecular Modeling Investigation of Folic Acid Conjugation to MDM2 Inhibitors for Enhanced Cellular Uptake and Target Binding.

The activation of tumor suppressor p53 protein through inhibition of its interaction with the oncogenic Murine Double Minute 2 (MDM2) protein presents a novel therapeutic strategy against cancer. Accordingly, several small-molecule inhibitors have been developed that mimic three hydrophobic groups of p53 involved in p53-MDM2 binding and thus block the p53-binding pocket on MDM2. Interestingly, presence of a fourth, solvent-exposed hydrophilic moiety in these MDM2 inhibitors is shown to enhance their binding to MDM2 by protecting the inhibitor-MDM2 binding interface from surrounding solvent. In this context, we hypothesized that vitamin folic acid (FA) may prove to be suitable as the hydrophilic cover for enhancing activity of present MDM2 inhibitors. The proposed conjugation of FA to MDM2 inhibitors may also lead to their enhanced and selective uptake by cancer cells, owing to significantly higher expression of the FA receptors on cancer cells compared to normal cells. Therefore, based on our novel hypothesis we designed FA-conjugated MDM2 inhibitors and investigated their binding with MDM2 protein as well as the FA receptor. Specifically, a molecular modeling approach combining flexible receptor docking and molecular mechanics energy minimization calculations revealed highly favorable interactions of FA-conjugated MDM2 inhibitors with both MDM2 protein and the FA receptor as compared to native crystal ligands. Furthermore, these binding interactions were found to be stable using 50,000 ps molecular dynamics simulations. In summary, the newly-designed molecules of this kind, with better MDM2 target binding and enhanced cellular uptake potential, may prove highly useful against cancer and thus warrant further experimental investigations.

Multiscale Modeling Techniques Based on Molecular Structure and Elastic Properties

Based on the principle of using atomistic force field, and the use of ultra-flexible multi-scale modeling techniques to predict the polycarbonate and polyimide polymer molecular structure and the elastic properties of the system. The model combines molecular modeling and nonlinear continuum mechanics basic principles, to simulate and predict the behavior of the material properties of the polymer molecular structure. For the polymer structure and properties, using a plurality of force field simulation to predict the contrast, and binding experiments measured polymer performance value, using static and dynamic molecular simulation technology for molecular mechanics energy minimization to solve.

Stabilization of Silicon Islands in Silicoaluminophosphates by Proton Redistribution

The relative stabilities of different proton distributions around a five-atom silicon island in silicoaluminophosphate-34 (SAPO-34) have been investigated by periodic molecular mechanics (MM) energy minimization calculations, and the MM calculations were validated using density functional theory (DFT). SAPO-34 has chabazite topology with only one symmetrically independent tetrahedral site (T-site) and four unique oxygen sites. The preferred position of the proton at isolated acid sites has been the subject of both experimental and computational studies. In previous computational studies of silicon islands, it was assumed that the protons, necessary to keep the silicon island neutral, would occupy the same positions as those preferred for solitary silicon atoms. We have studied all 108 possible proton distributions around a five-atom silicon island in SAPO-34. The results indicate that the proton placement is critical for stability, as the limit deviation in our data set is as high as 90 kJ/mol. Careful an...

In silico inspired design and synthesis of a novel tubulin-binding anti-cancer drug: folate conjugated noscapine (Targetin)

Our screen for tubulin-binding small molecules that do not depolymerize bulk cellular microtubules, but based upon structural features of well known microtubule-depolymerizing colchicine and podophyllotoxin, revealed tubulin binding anti-cancer property of noscapine (Ye et al. in Proc Natl Acad Sci USA 95:2280-2286, 1998). Guided by molecular modelling calculations and structure-activity relationships we conjugated at C9 of noscapine, a folate group-a ligand for cellular folate receptor alpha (FRα). FRα is over-expressed on some solid tumours such as ovarian epithelial cancers. Molecular docking experiments predicted that a folate conjugated noscapine (Targetin) accommodated well inside the binding cavity (docking score -11.295kcal/mol) at the interface between α- and β-tubulin. The bulky folate moiety of Targetin is extended toward lumen of microtubules. The binding free energy (ΔG (bind)) computed based on molecular mechanics energy minimization was -221.01kcal/mol that revealed favourable interaction of Targetin with the receptor. Chemical synthesis, tubulin-binding experiments, and anti-cancer activity in vitro corroborate fully well with the molecular modelling experiments. Targetin binds tubulin with a dissociation constant (K (d) value) of 149±3.0μM and decreases the transition frequencies between growth and shortening phases of microtubule assembly dynamics at concentrations that do not alter the total polymer mass. Cancer cells in general were more sensitive to Targetin compared with the founding compound noscapine (IC(50) in the range of 15-40μM). Quite strikingly, ovarian cancer cells (SKOV3 and A2780), known to overexpress FRα, were much more sensitive to targetin (IC(50) in the range of 0.3-1.5μM).

SYNTHESIS OF VARIOUS DITHIOCARBAMATE ESTERS THROUGH REGIOSELECTIVE THIOLATION OF 2-AMINOTHIAZOLE

Dithiocarbamates are of significant importance as pesticides, vulcanizing agents and pharmaceuticals. In search of efficient regioselective strategy, the various dithiocarbamate esters were synthesized by regioselective thiolation at endo-cyclic nitrogen of 2- aminothiazole. The treatment of Boc-protected 2-aminothiazole with carbon disulphide and alkyl halide in the presence of potassium hydroxide in DMF afforded Boc-dithiocarbamate esters (3a-h). The removal of protecting group with TFA provided corresponding dithiocarbamate esters (4a-h). The formation of regioselective product was confirmed by spectral and molecular mechanical MM2 force field and PM3 approximation MOPAC energy minimization data. The strategy provides an important methodology for regioselective thiolation.

An Amber Force Field for S-Nitrosoethanethiol That Is Transferable to S-Nitrosocysteine

Protein S-nitrosation is common in cells under nitrosative stress. In order to model proteins with S-nitrosocysteine (CysSNO) residues, we first developed an Amber force field for S-nitrosoethanethiol (EtSNO) and then transferred it to CysSNO. Partial atomic charges for EtSNO and CysSNO were obtained by a restrained electrostatic potential approach to be compatible with the Amber-99 force field. The force field parameters for bonds and angles in EtSNO were obtained from a generalized Amber force field (GAFF) by running the Antechamber module of the Amber software package. The GAFF parameters for the CC-SN and CS-NO dihedrals were not accurate and thus determined anew. The CC-SN and CS-NO torsional energy profiles of EtSNO were calculated quantum mechanically at the level of B3LYP/cc-pVTZ//HF/6-31 G * . Torsional force constants were obtained by fitting the theoretical torsional energies with those obtained from molecular mechanics energy minimization. These parameters for EtSNO reproduced, to a reasonable accuracy, the corresponding torsional energy profiles of the capped tripeptide ACE-CysSNO-NLVIE as well as their structures obtained from quantum mechanical geometry optimization. A molecular dynamics simulation of myoglobin with a CysSNO residue produced a well-behaved trajectory demonstrating that the parameters may be used in modeling other S-nitrosated proteins.

Force Field Parameters for 3-Nitrotyrosine and 6-Nitrotryptophan

Nitration of tyrosine and tryptophan residues is common in cells under nitrative stress. However, physiological consequences of protein nitration are not well characterized on a molecular level due to limited availability of the 3D structures of nitrated proteins. Molecular dynamics (MD) simulation can be an alternative tool to probe the structural perturbations induced by nitration. In this study we developed molecular mechanics parameters for 3-nitrotyrosine (NIY) and 6-nitrotryptophan (NIW) that are compatible with the AMBER-99 force field. Partial atomic charges were derived by using a multi-conformational restrained electrostatic potential (RESP) methodology that included the geometry optimized structures of both <TEX>$\alpha$</TEX>- and <TEX>$\beta$</TEX>-conformers of a capped tripeptide ACE-NIY-NME or ACE-NIW-NME. Force constants for bonds and angles were adopted from the generalized AMBER force field. Torsional force constants for the proper dihedral C-C-N-O and improper dihedral C-O-N-O of the nitro group in NIY were determined by fitting the torsional energy profiles obtained from quantum mechanical (QM) geometry optimization with those from molecular mechanical (MM) energy minimization. Force field parameters obtained for NIY were transferable to NIW so that they reproduced the QM torsional energy profiles of ACE-NIW-NME accurately. Moreover, the QM optimized structures of the tripeptides containing NIY and NIW were almost identical to the corresponding structures obtained from MM energy minimization, attesting the validity of the current parameter set. Molecular dynamics simulations of thioredoxin nitrated at the single tyrosine and tryptophan yielded well-behaved trajectories suggesting that the parameters are suitable for molecular dynamics simulations of a nitrated protein.

Design, synthesis, and biological evaluation of resveratrol analogues as aromatase and quinone reductase 2 inhibitors for chemoprevention of cancer

A series of new resveratrol analogues were designed and synthesized and their inhibitory activities against aromatase were evaluated. The crystal structure of human aromatase (PDB 3eqm) was used to rationalize the mechanism of action of the aromatase inhibitor 32 (IC50 0.59μM) through docking, molecular mechanics energy minimization, and computer graphics molecular modeling, and the information was utilized to design several very potent inhibitors, including compounds 82 (IC50 70nM) and 84 (IC50 36nM). The aromatase inhibitory activities of these compounds are much more potent than that for the lead compound resveratrol, which has an IC50 of 80μM. In addition to aromatase inhibitory activity, compounds 32 and 44 also displayed potent QR2 inhibitory activity (IC50 1.7μM and 0.27μM, respectively) and the high-resolution X-ray structures of QR2 in complex with these two compounds provide insight into their mechanism of QR2 inhibition. The aromatase and quinone reductase inhibitors resulting from these studies have potential value in the treatment and prevention of cancer.

Molecular Modeling of Crystalline Alkylthiophene Oligomers and Polymers

We present the results of a thorough molecular modeling study of several alkylthiophene-based oligomers and polymers. In particular, we consider two polymers whose limit-ordered crystal structures have been recently reported by our group, on the basis of powder X-ray data analysis: poly(3-(S)-2-methylbutylthiophene) (P3MBT) and form I' of poly(3-butylthiophene) (P3BT). We first describe the development of a series general purpose force fields for the simulation of these and related systems. The force fields incorporate the results of ab initio calculations of the bond torsion energies of selected oligomers and differ in the set of atomic charges used to represent the electrostatic interactions. We then present the results of an extensive validation of these force fields, by means of molecular mechanics (MM) energy minimizations and molecular dynamics (MD) simulations of the crystal structures of these oligomers and polymers. While our "best" force field does not outperform the others on each of the investigated systems, it provides a balanced description of their overall structure and energetics. Finally, our MM minimizations and MD simulations confirm that the reported crystal structures of P3MBT and P3BT are stable and correspond to well-defined energetic minima. The room-temperature MD simulations reveal a certain degree of side-chain disorder, even in our virtually defect-free polymer crystal models.

Force field parameters for S-nitrosocysteine and molecular dynamics simulations of S-nitrosated thioredoxin

Estimation of structural perturbation induced by S-nitrosation is important to understand the mode of cellular signal transduction mediated by nitric oxide. Crystal structures of S-nitrosated proteins have been solved only for a few cases, however, so that molecular dynamics simulation may provide an alternative tool for probing structural perturbation. In this study AMBER-99 force field parameters for S-nitrosocysteine were developed and applied to molecular dynamics simulations of S-nitrosated thioredoxin. Geometry optimization at the level of HF/6-31G∗ was followed by a restrained electrostatic potential charge-fitting to obtain the atomic charges of S-nitrosocysteine. Force constants for bonds and angles were obtained from generalized AMBER force field. Torsional force constants for CC–SN and CS–NO were determined by fitting the torsional profiles obtained from geometry optimization with those from molecular mechanical energy minimization. Finally molecular dynamics simulations were performed with theses parameters on oxidized and reduced thioredoxin with and without S-nitrosocysteine. In all cases the root-mean-square deviations of α-carbons yielded well-behaved trajectories. The CC–SH dihedral angle which fluctuated severely during the simulation became quiet upon S-nitrosation. In conclusion the force field parameters developed in this study for S-nitrosocysteine appear to be suitable for molecular dynamics simulations of S-nitrosated proteins.

Loop modeling: Sampling, filtering, and scoring

We describe a fast and accurate protocol, LoopBuilder, for the prediction of loop conformations in proteins. The procedure includes extensive sampling of backbone conformations, side chain addition, the use of a statistical potential to select a subset of these conformations, and, finally, an energy minimization and ranking with an all-atom force field. We find that the Direct Tweak algorithm used in the previously developed LOOPY program is successful in generating an ensemble of conformations that on average are closer to the native conformation than those generated by other methods. An important feature of Direct Tweak is that it checks for interactions between the loop and the rest of the protein during the loop closure process. DFIRE is found to be a particularly effective statistical potential that can bias conformation space toward conformations that are close to the native structure. Its application as a filter prior to a full molecular mechanics energy minimization both improves prediction accuracy and offers a significant savings in computer time. Final scoring is based on the OPLS/SBG-NP force field implemented in the PLOP program. The approach is also shown to be quite successful in predicting loop conformations for cases where the native side chain conformations are assumed to be unknown, suggesting that it will prove effective in real homology modeling applications. Proteins 2008. © 2007 Wiley-Liss, Inc.

Regioselective synthesis of diazaspiro[4.4]nona‐ and tetrazaspiro[4.5]deca‐2,9‐diene‐6‐one derivatives

Abstractmagnified imageSeveral 1,2‐diazaspiro[4,4]nona‐2,8‐diene‐6‐one derivatives were synthesised via cycloaddition of nitrilimides to 3‐aryliden‐2(3H)‐furanone derivatives. The formed products react with hydrazine hydrate to give the corresponding pyrazolecarbohydrazide derivatives which undergo intramolecure cyclization upon treatment with HCl/AcOH mixture to affored 1,2,7,8‐tetrazaspiro[4.5]deca‐2,9‐diene‐6‐one derivatives. Molecular mechanics energy minimization techniques and related structural parameters for compound 8‐(4‐methylphenyl)‐1,3,4‐triphenyl‐7‐oxa‐1,2‐diazaspiro[4.4]nona‐2,8‐diene‐6‐one 5a are reported.

Definition by Functional and Structural Analysis of Two Malonyl-CoA Sites in Carnitine Palmitoyltransferase 1A

Carnitine palmitoyltransferase 1 (CPT1) catalyzes the conversion of palmitoyl-CoA to palmitoylcarnitine in the presence of l-carnitine, thus facilitating the entry of fatty acids to mitochondria, in a process that is physiologically inhibited by malonyl-CoA. To examine the mechanism of CPT1 liver isoform (CPT1A) inhibition by malonyl-CoA, we constructed an in silico model of both its NH2- and COOH-terminal domains. Two malonyl-CoA binding sites were found. One of these, the "CoA site" or "A site," is involved in the interactions between NH2- and COOH-terminal domains and shares the acyl-CoA hemitunnel. The other, the "opposite-to-CoA site" or "O site," is on the opposite side of the enzyme, in the catalytic channel. The two sites share the carnitine-binding locus. To prevent the interaction between NH2- and COOH-terminal regions, we produced CPT1A E26K and K561E mutants. A double mutant E26K/K561E (swap), which was expected to conserve the interaction, was also produced. Inhibition assays showed a 12-fold decrease in the sensitivity (IC50) toward malonyl-CoA for CPT1A E26K and K561E single mutants, whereas swap mutant reverts to wild-type IC50 value. We conclude that structural interaction between both domains is critical for enzyme sensitivity to malonyl-CoA inhibition at the "A site." The location of the "O site" for malonyl-CoA binding was supported by inhibition assays of expressed R243T mutant. The model is also sustained by kinetic experiments that indicated linear mixed type malonyl-CoA inhibition for carnitine. Malonyl-CoA alters the affinity of carnitine, and there appears to be an exponential inverse relation between carnitine Km and malonyl-CoA IC50.

Underpotential Deposition of Thallium, Lead, and Cadmium at Silver Electrodes Modified with Self-Assembled Monolayers of (3-Mercaptopropyl)trimethoxysilane

Investigation of the underpotential deposition (UPD) of three metals-Tl, Pb, and Cd-on Ag surfaces modified with self-assembled monolayers (SAMs) of (3-mercaptopropyl)trimethoxysilane (3MPT) is reported. On the basis of the observation of negative potential shifts for their UPD processes, Tl and Pb undergo UPD directly on the underlying Ag surface by insertion between the Ag-S bond. This process is proposed to occur by penetration of the 3MPT monolayer by hydrated metal ions through spaces in six-membered siloxane rings that form at the terminus of the 3MPT layer after hydrolysis and condensation. In contrast, Cd does not undergo similarly facile UPD at 3MPT-modified Ag electrodes due to a hydrated ion size too large to fit through these openings. The voltammetric evidence that suggests that the hydrated metal cation size, as described by the Stokes diameter, is the primary determinant of Ag electrode accessibility for UPD through the cross-linked 3MPT layer is further supported by molecular mechanics energy minimization computations of six-membered siloxane rings on each of the three low-index faces of Ag. Finally, the 3MPT monolayer is shown to be exceptionally stable to repeated UPD/stripping cycles of Tl and Pb in contrast to SAMs of similar thickness formed from normal alkanethiols.

A Karplus equation for 3JHCCN in amino sugar derivatives

The 1H– 15N coupling constants of a suite of organic-soluble amino sugar derivatives have been measured by one-dimensional and two-dimensional 1H/ 15N heteronuclear single quantum, multiple bond correlation (HSQMBC), and the values so obtained are compared with those measured by analysis of 1H spectra of 15N-labeled amino sugar derivatives. A number of bicyclic amino sugar models have been studied, including methyl 2- (and 3-)amino-4,6- O-benzylidene-2- (and 3-)deoxy-α- d-hexopyranosides in chair or skew conformations, and methyl 2,6-anhydro-3-deoxy-3-phthalimido-α- d-mannopyranoside in a locked, almost classical boat conformation. The magnitudes of the vicinal 1H– 15N coupling constants 3 J HCCN have been correlated with 1H/ 15N dihedral angles φ computed for the favored conformations by molecular dynamics with molecular mechanics energy minimization. Non-linear regression of the coupling constants on the dihedral angles has yielded a Karplus equation: 3 J HCCN = 3.1 cos 2 φ − 0.6 cos φ + 0.4. The coefficients of the terms in this equation have been compared with those reported for 15 other pairs of nuclei, and the coefficient of the important cos 2 φ term found to be numerically smallest for 3 J HCCN.

Nonlinear multiscale modeling of polymer materials

In this study, a hyperelastic multiscale modeling technique is used to predict elastic properties of polycarbonate and polyimide polymer systems using a set of widely accepted atomistic force fields. The model incorporates molecular simulations and a nonlinear, continuum mechanics-based, constitutive formulation that incorporates the behavior of the polymer materials as predicted from molecular simulations. The predicted properties of the polymers using multiple force fields are compared to experimentally measured values. Both static and dynamic molecular simulations are performed using molecular mechanics energy minimizations and molecular dynamics simulation techniques, respectively. The results of this study indicate that static molecular simulation is a useful tool to predict the bulk-level nonlinear mechanical behavior of polymers for finite deformations. It is found that the AMBER force field yields the most accurate predicted mechanical and physical properties of the modeled polymer systems compared to the other force fields used in this study.

LGA-Dock/EM-Dock — Exploring Lamarckian genetic algorithms and energy-based local search for ligand–receptor docking

We report the development of LGA-Dock and EM-Dock, two SVL-based docking programs for flexible ligand – rigid receptor docking applications. LGA-Dock is comprised of a stochastic population generator, a docking routine based on a Lamarckian genetic algorithm, and a local search function based on molecular mechanics (MM) energy minimization. Subsequent modifications of LGA-Dock to address performance issues produced EM-Dock, which proved to be as accurate and much faster than its predecessor despite the deletion of the genetic algorithm component. The basic performance of LGA-Dock and EM-Dock, compared with AutoDock and MOE™ 2004.03 docking routines is presented.Key words: docking, Lamarckian genetic algorithm, molecular mechanics, simulated annealing, tabu search, local search.

Three-dimensional models of histamine H 3 receptor antagonist complexes and their pharmacophore

Molecular modeling was used to analyze the binding mode and activities of histamine H 3 receptor antagonists. A model of the H 3 receptor was constructed through homology modeling methods based on the crystal structure of bovine rhodopsin. Known H 3 antagonists were interactively docked into the putative antagonist binding pocket and the resultant model was subjected to molecular mechanics energy minimization and molecular dynamics simulations which included a continuum model of the lipid bilayer and intra- and extracellular aqueous environments surrounding the transmembrane helices. The transmemebrane helices stayed well embedded in the dielectric slab representing the lipid bilayer and the intra- and extracellular loops remain situated in the aqueous solvent region of the model during molecular dynamics simulations of up to 200 ps in duration. A pharmacophore model was calculated by mapping the features common to three active compounds three-dimensionally in space. The 3D pharmacophore model complements our atomistic receptor/ligand modeling. The H 3 antagonist pharmacophore consists of two protonation sites (i.e. basic centers) connected by a central aromatic ring or hydrophobic region. These two basic sites can simultaneously interact with Asp 114 (3.32) in helix III and a Glu 206 (5.46) in helix V which are believed to be the key residues that histamine interacts with to stabilize the receptor in the active state. The interaction with Glu 206 is consistent with the enhanced activity resulting from the additional basic site. In addition to these two salt bridging interactions, the central region of these antagonists contains a lipophilic group, usually an aromatic ring, that is found to interact with several nearby hydrophobic side chains. The picture of antagonist binding provided by these models is consistent with earlier pharmacophore models for H 3 antagonists with some exceptions.