A method and program for mass quantum chemical calculations of protein—ligand docking complexes

A new fast computational method for mass calculations of docking complexes by the AM1/PM3 semiempirical methods is proposed. The computation time is shortened by at least an order of magnitude compared to alternative schemes of quantum chemical calculations. The root-mean-square deviation of the AM1 calculated energies of formation of complexes from the results obtained by conventional diagonalization procedure is at most 0.4 kcal mol⁻¹. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 418–420, February, 2008.     

Molecular modeling study of the differential ligand–receptor interaction at the μ, δ and κ opioid receptors

3D models of the opioid receptors , and were constructed using BUNDLE, an in-house program to build de novo models of G-protein coupled receptors at the atomic level. Once the three opioid receptors were constructed and before any energy refinement, models were assessed for their compatibility with the results available from point-site mutations carried out on these receptors. In a subsequent step, three selective antagonists to each of three receptors (naltrindole, naltrexone and nor-binaltorphamine) were docked onto each of the three receptors and subsequently energy minimized. The nine resulting complexes were checked for their ability to explain known results of structure-activity studies. Once the models were validated, analysis of the distances between different residues of the receptors and the ligands were computed. This analysis permitted us to identify key residues tentatively involved in direct interaction with the ligand.     

New pyranosyl cembranoid diterpenes from Sarcophyton trocheliophorum

During our continual searching programme for novel bioactive metabolites from Sarcophyton trocheliophorum, collected from Red Sea, we describe herein the isolation and structural elucidation of further two new pyrane-based cembranoid diterpenes: 9-hydroxy-7,8-dehydro-sarcotrocheliol (1) and 8,9-expoy-sarcotrocheliol acetate (2), along with the well-known sarcotrocheliol acetate (3), (+)-sarcophine (4), (+)-sarcophytoxide (5) and (-)-sarcophytoxide (6). The chemical structures of compounds 1 and 2 were determined on the basis of 1D and 2D NMR (¹H, ¹³C, ¹H–¹H COSY, HMQC, HMBC and NOE), mass spectra (ESI and HR-ESIMS) and by comparison with related structures. The antimicrobial activities of the reported compounds 1–6 were investigated. According to the molecular docking study of compounds 1–6 using 3D structure of α,β tubulin in complex with taxol (PDB code 1JFF) and epothilone A (PDB code 1TVK), sarcophine (4) displayed the highest affinity towards both crystal structures, followed by 5 and 6, meanwhile pyrane-based cembranoid diterpenes (1–3) showed less affinity.     

A molecular docking model of SARS-CoV S1 protein in complex with its receptor, human ACE2

The exact residues within severe acute respiratory syndrome coronavirus (SARS-CoV) S1 protein and its receptor, human ACE2, involved in their interaction still remain largely undetermined. Identification of exact amino acid residues that are crucial for the interaction of S1 with ACE2 could provide working hypotheses for experimental studies and might be helpful for the development of antiviral inhibitor. In this paper, a molecular docking model of SARS-CoV S1 protein in complex with human ACE2 was constructed. The interacting residue pairs within this complex model and their contact types were also identified. Our model, supported by significant biochemical evidence, suggested receptor-binding residues were concentrated in two segments of S1 protein. In contrast, the interfacial residues in ACE2, though close to each other in tertiary structure, were found to be widely scattered in the primary sequence. In particular, the S1 residue ARG453 and ACE2 residue LYS341 might be the key residues in the complex formation.     

Reverse-docking as a computational tool for the study of asymmetric organocatalysis

A novel methodology for 'reverse-docking' a cationic peptide-based organocatalyst to a rigid anionic transition state (TS) model for the conjugate addition of azide to alpha,beta-unsaturated carbonyl substrates is described. The resulting docking poses serve as simplified TS models for enantioselective catalysis. Molecular mechanics-based scoring and ranking of the docking poses, followed by clustering and structural analysis, reveal a clear energetic preference for docking to the S-enantiomeric azidation TS model, in agreement with experiment. Clear energetic trends emerged from docking the catalyst to both enantiomers of all six azidation TS models of this study. Structural analysis of the most favorable pose suggests a mechanism for enantioselective catalysis that is consistent with principles of molecular recognition, catalysis, and experimental data.     

Objective comparison of concentration profiles in solids by means of mathematical statistics

To compare concentration profiles in solids in an objective manner, a multi-dimensional generalization of the comparison of two means by Student'st-test is proposed. The approach is based on piecewise modelling the profiles using rougha priori information, estimating the model parameters and their covariance matrix and comparing the estimated parameters by use of multidimensional test variables. The piecewise modelling is treated in the most important cases in such a way that the partial functions are straight lines or cubic polynoms (splines) with continuity at all knots in each case. It enables us to compare whole profiles as well as the most relevant parts of them. Two ways of estimating the covariance matrix as a generalization of the variance estimation are discussed. The approach is useful for any kind of line profiles if rough information on the profile type is available. As an example SIMS depth-profiles of aluminum obtained from thin-layer systems after different technological heat treatments are considered. These profiles are modeled by three straight lines.     

Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

Agonist–PPARγ interactions: Molecular modeling study with docking approach

Docking simulation of 18 agonists with the ligand binding pocket (LBP) of PPARγ has been performed. The binding conformations and binding affinities of these agonists were obtained by use of the flexible docking protocol FlexX. Test compound calculations indicated that FlexX can reproduce the binding conformation of the crystal structure (root mean square deviation = 1.43 Å); moreover, the predicted binding affinities correlate well with the activities of these agonists. The interaction model and pharmacophore of PPARγ agonists were derived and the difference in biologic activities of these agonists can be well explained. The PPARγ agonists must have both polar head and the hydrophobic tail, which form hydrogen bonds and hydrophobic contacts with hydrophilic and hydrophobic regions of the LBP of PPARγ, respectively. In addition, a suitable linker is also necessary. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 405–410, 2003     

Multiple binding modes of the camptothecin family to DNA oligomers

The binding constants of camptothecin, topotecan and its lactone ring-opened carboxylate derivative to DNA octamers were measured by UV and NMR spectroscopy. The self-association of topotecan (TPT) was also measured. The carboxylate form of TPT binds in the same way as the lactone, but more weakly. Titration of TPT into d(GCGATCGC)2 shows a preferred location stacked onto the terminal G1 base. However, the intermolecular NOEs cannot be reconciled with a single conformation of the complex, and suggest a model of a limited number of conformations in fast exchange. MD calculations on four pairs of starting structures with TPT stacked onto the G1-C8 base pair in different orientations were therefore performed. The use of selected experimental "docking" restraints yielded ten MD trajectories covering a wide conformational space. From a combination of calculated free energies, NOEs and chemical shifts, some of the structures produced could be eliminated, and it is concluded that the data are consistent with two major families of conformations in fast exchange. One of these is the conformation found in a crystal of a TPT/DNA/topoisomerase I ternary complex [Proc. Natl. Acad. Sci. USA 2002, 99, 15 387-15 392].     

Effect of the ionic strength of salts on retention and overloading behavior of ionizable compounds in reversed-phase liquid chromatography I. XTerra-C18

The influence of the salt concentration (potassium chloride) on the retention and overloading behavior of the propranolol cation (R'-NH2+ -R) on an XTerra-C18 column, in a methanol:water solution, was investigated. The adsorption isotherm data were first determined by frontal analysis (FA) for a mobile phase without salt (25% methanol, v/v). It was shown that the adsorption energy distribution calculated from these raw adsorption data is bimodal and that the isotherm model that best accounts for these data is the bi-Moreau model. Assuming that the addition of a salt into the mobile phase changes the numerical values of the parameters of the isotherm model, not its mathematical form, we used the inverse method (IM) of chromatography to determine the isotherm with seven salt concentrations in the mobile phase (40% methanol, v/v; 0, 0.002, 0.005, 0.01, 0.05, 0.1 and 0.2 M). The saturation capacities of the model increase, q(s,1) by a factor two and q(s,2) by a factor four, with increasing salt concentration in the range studied while the adsorption constant b1 increases four times and b2 decreases four times. Adsorbate-adsorbate interactions vanish in the presence of salt, consistent with results obtained previously on a C18-Kromasil column. Finally, besides the ionic strength of the solution, the size, valence, and nature of the salt ions affect the thermodynamic as well as the mass transfer kinetics of the adsorption mechanism of propranolol on the XTerra column.