[Show abstract][Hide abstract] ABSTRACT: The unimolecular G-quadruplex structures of d(GGGTGGGTGGGTGGGT) (G1) and d(GTGGTGGGTGGGTGGGT) (G2) are known as the potent nanomolar HIV-1 integrase inhibitors, thus investigating the 3D structures of the two sequences is significant for structure-based rational anti-HIV drug design. In this research, based on the experimental data of circular dichroism (CD) spectropolarimetry and electrospray ionization mass spectrometry (ESI-MS), the initial models of G1 and G2 were constructed by molecular modeling method. The modeling structures of G1 and G2 are intramolecular parallel-stranded quadruplex conformation with three guanine tetrads. Particularly, the structure of G2 possesses a T loop residue between the first and the second G residues that are the component of two adjacent same-stranded G-tetrad planes. This structure proposed by us has a very novel geometry and is different from all reported G-quadruplexes. The extended (35 ns) molecular dynamic (MD) simulations for the models indicate that the G-quadruplexes maintain their structures very well in aqueous solution whether the existence of K(+) or NH (4) (+) in the central channel. Furthermore, we perform 500 ns MD simulations for the models in the gas phase. The results show that all the ion-G-quadruplex complexes are maintained during the whole simulations, despite the large magnitude of phosphate-phosphate repulsions. The gas phase MD simulations provide a good explanation to ESI-MS experiments. Our 3D structures for G1 and G2 will assist in understanding geometric formalism of G-quadruplex folding and may be helpful as a platform for rational anti-HIV drug design.
Journal of Molecular Modeling 10/2009; 16(4):645-57. · 1.98 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The 3D structure of a novel epoxide hydrolase from Aspergillus niger SQ-6 (sqEH) was constructed by using homology modeling and molecular dynamics simulations. Based on the 3D model, Asp191, His369 and Glu343 were predicted as catalytic triad. The putative active pocket is a hydrophobic environment and is rich in some important non-polar residues (Pro318, Trp282, Pro319, Pro317 and Phe242). Using three sets of epoxide inhibitors for docking study, the interaction energies of sqEH with each inhibitor are consistent with their inhibitory effects in previous experiments. Moreover, a critical water molecule which closes to the His369 was identified to be an ideal position for the hydrolysis step of the reaction. Two tyrosine residues (Tyr249 and Tyr312) are able to form hydrogen bonds with the epoxide oxygen atom to maintain the initial binding and positioning of the substrate in the active pocket. These docked complex models can well interpret the substrate specificity of sqEH, which could be relevant for the structural-based design of specific epoxide inhibitors.
Journal of Molecular Modeling 03/2009; 15(9):1125-32. · 1.98 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: N-carbamyl-d-amino acid amidohydrolasecatalyzes the hydrolysis of N-carbamyl-d-amino acids to d-amino acids, ammonia and the carbon dioxide. The docking studies validate that d-NCAase possesses of preference for d-enantiomers, predict that Gly194 and Arg174 may take part in the catalytic mechanism, and Glu136 is essential to maintain the stable conformation for catalysis. The initial step of the acylation reaction catalyzed by d-NCAase has been studied by density functional calculations. It was furthermore demonstrated that Lys126, His143, and Asn196 decrease the reaction barrier, while Asn172 raise the barrier. The structural and mechanistic insights obtained from computational study should be valuable for the mechanisms of cysteine proteases.
Chemical Physics Letters 01/2009; 472:107-112. · 2.15 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The 3D structure of the amidase from Rhodococcus erythropolis (EC 184.108.40.206) built by homology-based modeling is presented. Propionamide and acetamide are docked to the amidase. The reaction models were used to characterize the explicit enzymatic reaction. The calculated free energy barrier at B3LYP/6-31G* level of Model A (Ser194 + propionamide) is 19.72 kcal mol(-1) in gas (6.47 kcal mol(-1) in solution), and of Model B (Ser194 + Gly193 + propionamide) is 18.71 kcal mol(-1) in gas (4.57 kcal mol(-1) in solution). The docking results reveal that propionamide binds more strongly than acetamide due to the ethyl moiety of propionamide, which makes the carboxyl oxygen center of the substrate slightly more negative, making formation of the positively charged tetrahedral intermediate slightly easier. The quantum mechanics results demonstrate that Ser194 is essential for the acyl-intermediate, and Gly193 plays a secondary role in stabilizing acyl-intermediate formation as the NH groups of Ser194 and Gly193 form hydrogen bonds with the carbonyl oxygen of propionamide. The new structural and mechanistic insights gained from this computational study should be useful in elucidating the detailed structures and mechanisms of amidase and other homologous members of the amidase signature family.
Journal of Molecular Modeling 01/2009; 15(5):481-7. · 1.98 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This article describes an in vitro investigation of the inhibition of cytochrome P450 (P450) 2C9 by a series of flavonoids made up of flavones (flavone, 6-hydroxyflavone, 7-hydroxyflavone, chrysin, baicalein, apigenin, luteolin, scutellarein, and wogonin) and flavonols (galangin, fisetin, kaempferol, morin, and quercetin). With the exception of flavone, all flavonoids were shown to inhibit CYP2C9-mediated diclofenac 4'-hydroxylation in the CYP2C9 RECO system, with K(i) value <or= 2.2 microM. In terms of the mechanism of inhibition, 6-hydroxyflavone was found to be a noncompetitive inhibitor of CYP2C9, whereas the other flavonoids were competitive inhibitors. Computer docking simulation and constructed mutants substituted at residue 100 of CYP2C9.1 indicate that the noncompetitive binding site of 6-hydroxyflavone lies beside Phe100, similar to the reported allosteric binding site of warfarin. The other flavonoids exert competitive inhibition through interaction with the substrate binding site of CYP2C9 accessed by flurbiprofen. These results suggest flavonoids can participate in interactions with drugs that act as substrates for CYP2C9 and provide a possible molecular basis for understanding cooperativity in human P450-mediated drug-drug interactions.
Drug metabolism and disposition: the biological fate of chemicals 12/2008; 37(3):629-34. · 3.74 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To better understand the ligand-binding mechanism of protein Pir7b, important part in detoxification of a pathogen-derived compound against Pyricularia oryzae, a 3D structure model of protein Pir7b was constructed based on the structure of the template SABP2. Three substrates were docking to this protein, two of them were proved to be active, and some critical residues are identified, which had not been confirmed by the experiments. His87 and Leu17 considered as 'oxyanion hole' contribute to initiating the Ser86 nucleophilic attack. Gln187 and Asp139 can form hydrogen bonds with the anilid group to maintain the active binding orientation with the substrates. The docking model can well interpret the specificity of protein Pir7b towards the anilid moiety of the substrates and provide valuable structure information about the ligand binding to protein Pir7b.
Journal of Molecular Modeling 08/2008; 14(7):559-69. · 1.98 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: With homology modeling techniques, a 3D structure model of CYP2C19 was built and refined with molecular mechanics and molecular dynamics simulations. The refined model was assessed to be reasonable by Profile-3D and PROCHECK programs. With the aid of the automatic molecular docking, one substrate and two inhibitors were docked to CYP2C19 by InsightII/Affinity program. The docking results, which are in well agreement with the reported results, demonstrate that the refined model of CYP2C19 is reliable. Then, with the refined model of CYP2C19 and the crystal structure of CYP2C9, the metabolisms of them for gliclazide in two different metabolic pathways were studied and the results show that both enzymes have more favorable interaction energies and stronger affinity with gliclazide in methylhydroxylation pathway than in 6beta-hydroxylation pathway. It is exciting that substrate inhibition phenomenon can be found in metabolisms of CYP2C9 and CYP2C19 for gliclazide in two metabolic pathways. Gliclazide can change the conformation of the active sites and decrease obviously the affinities between gliclazide in the active site and enzymes when it is docked in the second active sites in CYP2C9 and CYP2C19. These results are in well agreement with the kinetic experimental results.
European Journal of Medicinal Chemistry 06/2008; 44(2):854-61. · 3.43 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Human photoreceptor retinol dehydrogenase (hRDH8) catalyzes the reduction of all-trans-retinal to all-trans-retinol with NADPH as a rate-limiting step in the visual cycle. Based on the docking results of the substrate to the 3D structure of hRDH8 which is generated by homology modeling method, three quantum chemical calculation models with different sizes were used to investigate the catalytic reaction mechanism of hRDH8 with the aid of density functional theory. The calculations indicate that hRDH8 employs a general acid/base mechanism that a proton is transferred to the keto oxygen of the substrate after the pro-S hydride of NADPH transfer to keto carbon of the substrate. The H-transfer order is converse to that in the proposed mechanism of 17ß-hydroxysteroid dehydrogenase 1, which is highly related to the hRDH8 sequence. Tyr155 always provides the proton to the keto oxygen of the substrate whether unprotonated Lys159 is considered or not in the calculation models. However, protonated Lys159 changes the initial mechanism and replaces Tyr155 to provide the proton to the keto oxygen of the substrate. Moreover, protonated Lys159 can also decrease very effectively the Gibbs free energy barrier to make the reaction indeed energetically feasible. The role of Lys159 in hRDH8 is different from that in 17ß-hydroxysteroid dehydrogenase 1. The solvent effect calculations indicate that the reaction is more feasible energetically in the protein electrostatic environment than in the gas phase.
Journal of Theoretical and Computational Chemistry 01/2008; 07(04). · 0.52 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: With the aid of the automatic molecular docking, the affinity of CYP2C9 and CYP2D6 for imrecoxib was studied by InsightII/Affinity program. The results indicate that CYP2C9–imrecoxib complex has higher stability and stronger affinity because CYP2C9 has more favorable interaction energy (-62.72 kcal/mol) and higher Ludi score (610) with imrecoxib than CYP2D6 (-50.22 kcal/mol and 551) and this is consistent with the results of the kinetic experiments by Li et al. By analyzing the theoretical results combined with the experimental ones, we suggest that the affinity difference is caused by the difference of the structure between CYP2C9 and CYP2D6, and the most important residues for enzyme–substrate complexes, such as Phe476, Asn204, Phe100, Leu366 and Arg108 of CYP2C9 and Phe120, Glu216, and Phe483 of CYP2D6 were also identified.
Journal of Theoretical and Computational Chemistry 01/2007; 06(03). · 0.52 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Aurora-C is a key member of a closely related subgroup of serine/threonine kinase that plays an important role in the completion of essential mitotic events. By means of the homology modeling and the known structure of aurora-B, the 3D structure of aurora-C sourced human sapiens is modeled and then refined by using molecular mechanics (MM) optimization and molecular dynamics (MD) simulation. The final refined model is further assessed by Profile-3D and PROCHECK, which shows that this model is reliable. And then, the inhibitors H-89 and H-8 are docked to aurora-C. The docking study shows that Ala149 and Lys134 are important in inhibition as they form hydrogen bonds and have strong nonbonding interaction with H-89. We also suggest that Ile133, His130, and Ile148 are three important residues in binding as they have strong nonbonding interaction with H-89. The high affinity of H-89 compared with H-8 is explained by the much larger value of van der Waals energy with the enzyme. Our results will be helpful for further experimental investigations.
[Show abstract][Hide abstract] ABSTRACT: With the aid of the automated molecular docking, the inhibition effect of 20(S)-Protopanaxadiol (PPD) and Ginsenoside Rh2 for CYP2C9 and CYP3A4, respectively, were studied by InsightII/Affinity program and the docking complexes were analyzed by InsightII/Ludi program. The results indicate that PPD is a competitive inhibitor for CYP2C9 but a poor inhibitor for CYP3A4, Rh2 is a noncompetitive inhibitor for CYP3A4, but a poor inhibitor for CYP2C9. Hydrophobic PPD is stabilized in the center of the substrate-binding regions of CYP2C9 by hydrogen bond and has strong interactions with heme and the key residues in active site which play important role for binding the substrate. Theoretical Ki value was calculated to be 26.7μM by using Ludi score 457 of CYP2C9–PPD complex. As hydrophilic Rh2 is away from the substrate-binding regions of CYP3A4, it has very weak interactions with the key residues in the active site. But the docking of Rh2 makes the conformation of CYP3A4 to change, including the position of a key residue Ser119 that leads to a decrease in catalytic activity. Theoretical Ki value is 102.8μM by using Ludi score 398 of CYP3A4–Rh2 complex. The theoretical results are in well agreement with the experimental results.
[Show abstract][Hide abstract] ABSTRACT: The D structure of the AmiF formamidase of Helicobacter pylori (denoted as AmiF(fhp)) is built by homology modeling. The docking studies show that AmiF(fhp) has restricted substrate specificity, as it only hydrolyzes formamide. In order to reveal the reaction mechanism and the catalytic role for Cys166, Lys133 and Asp168 in AmiF(fhp), three quantum mechanics' models are constructed based on the D structure of AmiF(fhp) and the reaction paths are obtained at B3LYP 6-31+G∗ level. The calculated results show that (1) the reaction of Cys166–formamide anion in the enzyme active proceeds via a transition state without the intervention of tetrahedral intermediate; (2) the positive charge on Lys133 polarizes the formamide in the TS region to redistribute the electron and thence decreases the free energy barrier; (3) the active site residue of Asp168 increases the free energy barrier as the negative charge will affect the electron distribution.
[Show abstract][Hide abstract] ABSTRACT: In order to understand the mechanisms of substrate specificity and the interaction between bergaptol and bergaptol O-methyltransferase (BMT), a 3D model of BMT is generated based on the crystal structure of caffeic acid 3-O-methyltransferase (COMT EC 220.127.116.11, PDB code 1KYZ) by using the InsightII/Homology module. With the aid of the molecular mechanics and molecular dynamics methods, the final refined model is obtained and its reliability is further assessed by PROCHECK and ProSa2003. With this model, a flexible docking study is performed and the results indicate that BMT has narrow substrate specificity. Although the homology between both proteins is higher than 65% and all amino acids surrounding the binding site, except four residues, are similar in their sequences, the two proteins exhibit different substrate preferences. The differences in substrate specificity can be explained on the basis of the structures of the protein and the substrate. Our results indicate that His259 may be the catalytic base for the reaction, and Glu320, Glu287 bracket the catalytic His259. Especially, Glu320 forms a weak hydrogen bond with His259 and promotes transfer of an H ion.