Time-efficient flexible superposition of medium-sized molecules

We present an efficient algorithm for the structural alignment of medium-sized organic molecules. The algorithm has been developed for applications in 3D QSAR and in receptor modeling. The method assumes one of the molecules, the reference ligand, to be presented in the conformation that it adopts inside the receptor pocket. The second molecule, the test ligand, is considered to be flexible, and is assumed to be given in an arbitrary low-energy conformation. Ligand flexibility is modeled by decomposing the test ligand into molecular fragments, such that ring systems are completely contained in a single fragment. Conformations of fragments and torsional angles of single bonds are taken from a small finite set, which depends on the fragment and bond, respectively. The algorithm superimposes a distinguished base fragment of the test ligand onto a suitable region of the reference ligand and then attaches the remaining fragments of the test ligand in a step-by-step fashion. During this process, a scoring function is optimized that encompasses bonding terms and terms accounting for steric overlap as well as for similarity of chemical properties of both ligands. The algorithm has been implemented in the FLEXS system. To validate the quality of the produced results, we have selected a number of examples for which the mutual superposition of two ligands is experimentally given by the comparison of the binding geometries known from the crystal structures of their corresponding protein–ligand complexes. On more than two-thirds of the test examples the algorithm produces rms deviations of the predicted versus the observed conformation of the test ligand below 1.5 Å. The run time of the algorithm on a single problem instance is a few minutes on a common-day workstation. The overall goal of this research is to drastically reduce run times, while limiting the inaccuracies of the model and the computation to a tolerable level.     

Fast 3D molecular superposition and similarity search in databases of flexible molecules

We present a new method (fFLASH) for the virtual screening of compound databases that is based on explicit three-dimensional molecular superpositions. fFLASH takes the torsional flexibility of the database molecules fully into account, and can deal with an arbitrary number of conformation-dependent molecular features. The method utilizes a fragmentation-reassembly approach which allows for an efficient sampling of the conformational space. A fast clique-based pattern matching algorithm generates alignments of pairs of adjacent molecular fragments on the rigid query molecule that are subsequently reassembled to complete database molecules. Using conventional molecular features (hydrogen bond donors and acceptors, charges, and hydrophobic groups) we show that fFLASH is able to rapidly produce accurate alignments of medium-sized drug-like molecules. Experiments with a test database containing a diverse set of 1780 drug-like molecules (including all conformers) have shown that average query processing times of the order of 0.1 seconds per molecule can be achieved on a PC.     

An automated method for predicting the positions of hydrogen-bonding atoms in binding sites

Hydrogen bonds are the most specific, and therefore predictable of the intermolecular interactions involved in ligand–protein binding. Given the structure of a molecule, it is possible to estimate the positions at which complementary hydrogen-bonding atoms could be found. Crystal-survey data are used in the design of a program, HBMAP, that generates a hydrogen-bond map for any given ligand, which contains all the feasible positions at which a complementary atom could be found. On superposition of ligands, the overlapping regions of their maps represent positions of receptor atoms to which each molecule can bind. The certainty of these positions is increased by the incorporation of a larger number and diversity of molecules. In this work, superposition is achieved using the program HBMATCH, which uses simulated annealing to generate the correspondence between points from the hydrogen-bonding maps of the two molecules. Equivalent matches are distinguished on the basis of their steric similarity. The strategy is tested on a number of ligands for which ligand–protein complexes have been solved crystallographically, which allows validation of the techniques. The receptor atom positions of thermolysin are successfully predicted when the correct superposition is obtained.     

QUASI: a novel method for simultaneous superposition of multiple flexible ligands and virtual screening using partial similarity

The structure of many receptors is unknown, and only information about diverse ligands binding to them is available. A new method is presented for the superposition of such ligands, derivation of putative receptor site models and utilization of the models for screening of compound databases. In order to generate a receptor model, the similarity of all ligands is optimized simultaneously taking into account conformational flexibility and also the possibility that the ligands can bind to different regions of the site and only partially overlap. Ligand similarity is defined with respect to a receptor site model serving as a common reference frame. The receptor model is dynamic and coevolves with the ligand alignment until an optimal self-consistent superposition is achieved. When ligand conformational flexibility is permitted, different superposition models are possible and consistent with the data. Clustering of the superposition solutions is used to obtain diverse models. When the models are used to screen a database of compounds, high enrichments are obtained, comparable to those obtained in docking studies.     

Methodological developments and strategies for a fast flexible superposition of drug-size molecules

An alternative to experimental high through-put screening is the virtual screening of compound libraries on the computer. In absence of a detailed structure of the receptor protein, candidate molecules are compared with a known reference by mutually superimposing their skeletons and scoring their similarity. Since molecular shape highly depends on the adopted conformation, an efficient conformational screening is performed using a knowledge-based approach. A comprehensive torsion library has been compiled from crystal data stored in the Cambridge Structural Database. For molecular comparison a strategy is followed considering shape associated physicochemical properties in space such as steric occupancy, electrostatics, lipophilicity and potential hydrogen-bonding. Molecular shape is approximated by a set of Gaussian functions not necessarily located at the atomic positions. The superposition is performed in two steps: first by a global alignment search operating on multiple rigid conformations and then by conformationally relaxing the best scored hits of the global search. A normalized similarity scoring is used to allow for a comparison of molecules with rather different shape and size. The approach has been implemented on a cluster of parallel processors. As a case study, the search for ligands binding to the dopamine receptor is given.     

A general model of the opiate pharmacophore 1. Regions of the opiate pharmacophore responsible for nonselective affinity for the opiate receptor

By superposition of the molecules of opiate receptor ligands of various structural classes, three regions responsible for the nonselective ligand affinity were distinguished in the opiate pharmacophore. Spatial arrangement features, electronic properties, the capability of H-bonding and hydrophobic and electrostatic interactions of these regions were determined. The set of geometric parameters found can be used as a criterion for estimation of the opiate activity in simulation of new types of ligands. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1469–1475, September, 2006.     

A promising method for phosphinidene generation: complexes of phosphinidenes with N-donor ligands

1,3,2-diazaphospholenes and related compounds can formally be regarded as complexes of phosphinidenes (R-P) with 1,4-diazabutadienes. The dissociation Gibbs free energies of these "complexes" were calculated by using density functional theory (B3LYP/3-21G(*) and B3LYP/6-311+G**). The dissociation Gibbs free energies show systematic dependence on the phosphorus substituent as well as on the stability of the N-donor ligand formed as a byproduct. The thermodynamics and kinetics of the dissociations were thoroughly examined. The results allow us to conclude that novel routes of phosphinidene generation can be developed.     

A high yielding one-pot method for the preparation of salen ligands

Phenols are converted to salicylaldehydes with paraformaldehyde, MgCl₂-Et₃N in THF, and subsequently treated with (+)-(R,R)-1,2-diammoniumcyclohexane mono-(+)-tartrate salt affording the corresponding salen ligands in high yields. The reactions are conveniently carried out as a one-pot procedure.     

Structure-based ligand design for flexible proteins: Application of new F-DycoBlock

A method of structure-based ligand design – DycoBlock – has been proposed and tested by Liu et al.[1]. It was further improved by Zhu et al. and applied to design new selective inhibitors of cyclooxygenase 2 [2]. In the current work, we present a new methodology – F-DycoBlock that allows for the incorporation of receptor flexibility. During the designing procedure, both the receptor and molecular building blocks are subjected to the multiple-copy stochastic molecular dynamics (MCSMD) simulation [1], while the protein moves in the mean field of all copies. It is tested for two enzymes studied previously – cyclooxygenase 2 (COX-2) and human immunodeficiency type 1 (HIV-1) protease. To identify the applicability of F-DycoBlock, the binding protein structure was used as starting point to explore the conformational space around the bound state. This method can be easily extended to accommodate the flexibility in different degree. Four types of treatment of the receptor flexibility – all-atom restrained, backbone restrained, intramolecular hydrogen-bond restrained and active-site flexible – were tested with or without the grid approximation. Two inhibitors, SC-558 for COX-2 and L700417 for HIV-1 protease, are used in this testing study for comparison with previous results. The accuracy of recovery, binding energy, solvent accessible surface area (SASA) and positional root-mean-square (RMS) deviation are used as criteria. The results indicate that F-DycoBlock is a robust methodology for flexible drug design. It is particularly notable that the protein flexibility has been perfectly associated with each stage of drug design – search for the binding sites, dynamic assembly and optimization of candidate compounds. When all protein atoms were restrained, F-DycoBlock yielded higher accuracy of recovery than DycoBlock (100%). If backbone atoms were restrained, the same ratio of accuracy was achieved. Moreover, with the intramolecular hydrogen bonds restrained, reasonable conformational changes were observed for HIV-1 protease during the long-time MCSMD simulation and L700417 was reassembled at the active site. It makes it possible to study the receptor motion in the binding process.     

Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: Comparison of predicted and experimental conformations of inhibitors of three enzymes

Summary A computer procedure TFIT, which uses a molecular superposition force field to flexibly match test compounds to a 3D pharmacophore, was evaluated to find out whether it could reliably predict the bioactive conformations of flexible ligands. The program superposition force field optimizes the overlap of those atoms of the test ligand and template that are of similar chemical type, by applying an attractive force between atoms of the test ligand and template which are close together and of similar type (hydrogen bonding, charge, hydrophobicity). A procedure involving Monte Carlo torsion perturbations, followed by torsional energy minimization, is used to find conformations of the test ligand which cominimize the internal energy of the ligand and the superposition energy of ligand and template. The procedure was tested by applying it to a series of flexible ligands for which the bioactive conformation was known experimentally. The 15 molecules tested were inhibitors of thermolysin, HIV-1 protease or endothiapepsin for which X-ray structures of the bioactive conformation were available. For each enzyme, one of the molecules served as a template and the others, after being conformationally randomized, were fitted. The fitted conformation was then compared to the known binding geometry. The matching procedure was successful in predicting the bioactive conformations of many of the structures tested. Significant deviation from experimental results was found only for parts of molecules where it was readily apparent that the template did not contain sufficient information to accurately determine the bioactive conformation.     

Reaction of azole heterocycles with tris(dimethylamino)borane, a new method for the construction of tripodal borate-centred ligands

Reaction of 2-mercapto-1-methylimidazole (methimazole) with tris(dimethylamino)borane, B(NMe2)3, provides the tetrahedral dimethylamine adduct of tris(methimazolyl)borane, [(Me2HN)B(methimazolyl)3]. By contrast, imidazole, 2-methylimidazole, 2-chloroimidazole and benzimidazole provide the homoleptic tetra-azolyl systems H[B(azolyl)4], and the same product is obtained even when a substoichiometric quantity of the heterocyle is employed. The change in reaction outcome is correlated with the variation of basic pKa for the heterocycles. A simple acid-base reaction with elimination of HNMe2 is proposed for the reaction with the weakly basic, but more strongly acidic, methimazole. However, for the more strongly basic imidazoles, initial coordination of the heterocycle imine nitrogen to the weakly Lewis acidic boron centre in B(NMe2)3 to form the tetrahedral adduct [(azole)B(NMe2)3] is proposed. The greater availability of the NMe2 lone pairs in this species results in increased basicity and a rapid reaction with further heterocycle to provide the observed H[B(azolyl)4] products. For 2-nitroimidazole, the low basicity (and increased N-H acidity) results in the formation of [(HNMe2)B(2-nitroimidazolyl)3] on reaction with B(NMe2)3, analogous to the product formed with methimazole. Both [(HNMe2)B(methimazolyl)3] and H[B(benzimidazolyl)4] have been structurally characterised by single crystal X-ray crystallography. This chemistry has been exploited to provide a new synthesis of borate-centred tripod ligands, whereby N-methylimidazole is used to activate B(NMe2)3 to reaction with methimazole to form the new ligand [(N-methylimidazole)B(methimazolyl)3] in good yield and a complex of this ligand with Ru(II) has been structurally characterised.     

Comparison of basis set superposition error corrected perturbation theories for calculating intermolecular interaction energies

Recently, two different but conceptually similar basis set superposition error (BSSE) free second‐order perturbation theoretical schemes were developed by us that are being based on the chemical Hamiltonian approach (CHA). Using these CHA‐MP2 and CHA‐PT2 methods, a comparison is made between the a posteriori and a priori BSSE correction schemes at the correlated level. Sample calculations are presented for four hydrogen bonded complexes (HFH₃N, HFH₂O, H₂SHF, and H₂OHCl) in nine different basis sets (from 6–31G to TZV**++). The results show that the BSSE content is very significant in the interaction energy if electron correlation is accounted for, so removing the BSSE is very important. The differences of the two perturbational theories discussed are connected solely with the different one electron orbital sets used for building up the unperturbed single determinant wave function. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 274–283, 1999     

TGSA-Flex: Extending the capabilities of the Topo-Geometrical Superposition Algorithm to handle flexible molecules

In this work, an extension of the already studied Topo-Geometrical Superposition Approach (TGSA) is presented. TGSA, a general-purpose, fast, automatic, and user-intuitive three-dimensional molecular alignment procedure, was originally designed to superpose rigid molecules simply based on atomic numbers, molecular coordinates, and connectivity. The algorithm is further developed to enable handling rotations around single bonds; in this way, common structural features, which were not properly aligned due to conformational causes, can be brought together, thus improving the molecular similarity picture of the final alignment. The present procedure, implemented in Fortran 90 and named TGSA-Flex, is deeply detailed and tested over four molecular sets: amino acids, nordihydroguaiaretic acid (NDGA) derivatives, HIV-1 protease inhibitors, and 1-[2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) derivatives. TGSA-Flex performance is evaluated by means of computational time, number of superposed atoms (also comparing it with respect to the rigid approach), and index of fit between the compared structures.     

甲状腺激素受体配体化合物的定量构效关系(QSAR)研究

研究了68个TR（Thyroid Hormone Receptor,甲状腺激素受体）配体化合物的化学结构与活性的定量构效关系．采用实验室新近提出的三维原子场全息相互作用矢量,对化合物进行了结构参数化表达,采用逐步回归对变量进行筛选后,建立了定量构效关系模型．复相关系数和交互检验复相关系数R^2=0．767,Q^2=0．625（TRα）,R^2=0．734,Q^2=0．61（TRβ）．模型具有良好的稳定性和预测能力,证明了该三维原子场全息相互作用矢量在分子结构表征和生物活性预测上的适用性,并可应用于潜在和新型的TR配体化合物的设计和开发．     

In vitro anticancer activity and biologically relevant metabolization of organometallic ruthenium complexes with carbohydrate-based ligands

The synthesis and in vitro anticancer activity of dihalogenido(eta6-p-cymene)(3,5,6-bicyclophosphite-alpha-D-glucofuranoside)ruthenium(II) complexes are described. The compounds were characterized by NMR spectroscopy and ESI mass spectrometry, and the molecular structures of dichlorido-, dibromido- and diiodido(eta6-p-cymene)(3,5,6-bicyclophosphite-1,2-O-isopropylidene-alpha-D-glucofuranoside)ruthenium(II) were determined by X-ray diffraction analysis. The complexes were shown to undergo aquation of the first halido ligand in aqueous solution, followed by hydrolysis of a P--O bond of the phosphite ligand, and finally formation of dinuclear species. The hydrolysis mechanism was confirmed by DFT calculations. The aquation of the complexes was markedly suppressed in 100 mM NaCl solution, and notably only very slow hydrolysis of the P--O bond was observed. The complexes showed affinity towards albumin and transferrin and monoadduct formation with 9-ethylguanine. In vitro studies revealed that the 3,5,6-bicyclophosphite-1,2-O-cyclohexylidene-alpha-D-glucofuranoside complex is the most cytotoxic compound in human cancer cell lines (IC50 values from 30 to 300 microM depending on the cell line).     

Comparison of two implementations of the incremental construction algorithm in flexible docking of thrombin inhibitors

A set of 32 known thrombin inhibitors representing different chemical classes has been used to evaluate the performance of two implementations of incremental construction algorithms for flexible molecular docking: DOCK 4.0 and FlexX 1.5. Both docking tools are able to dock 10–35% of our test set within 2 Å of their known, bound conformations using default sampling and scoring parameters. Although flexible docking with DOCK or FlexX is not able to reconstruct all native complexes, it does offer a significant improvement over rigid body docking of single, rule-based conformations, which is still often used for docking of large databases. Docking of sets of multiple conformers of each inhibitor, obtained with a novel protocol for diverse conformer generation and selection, yielded results comparable to those obtained by flexible docking. Chemical scoring, which is an empirically modified force field scoring method implemented in DOCK 4.0, outperforms both interaction energy scoring by DOCK and the Böhm scoring function used by FlexX in rigid and flexible docking of thrombin inhibitors. Our results indicate that for reliable docking of flexible ligands the selection of anchor fragments, conformational sampling and currently available scoring methods still require improvement.     

A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor

We have developed a new docking method to consider receptor flexibility, a hybrid method of molecular dynamics and harmonic dynamics. The global motions of the whole receptor were approximately introduced into those of the receptor in the docking simulation as harmonic dynamics. On the other hand, the local flexibility of the side chains was also considered by conventional molecular dynamics. We confirmed that this new method can reproduce the fluctuations of the whole receptor by making a comparison of the directions and amplitudes of the global fluctuations. Then this method was applied to the docking of HIV-1 protease and its ligand. As a result, we observed a docking process where the ligand enters into the binding pocket well, which implies that this method is effective enough to reproduce a molecular complex formation.