Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors

We present a computational protocol which uses the known three-dimensional structure of a target enzyme to identify possible ligands from databases of compounds with low molecular weight. This is accomplished by first mapping the essential interactions in the binding site with the program GRID. The resulting regions of favorable interaction between target and ligand are translated into a database query, and with UNITY a flexible 3D database search is performed. The feasibility of this approach is calibrated with thrombin as the target. Our results show that the resulting hit lists are enriched with thrombin inhibitors compared to the total database.     

Analysis of the genetic algorithm method of molecular conformation determination

Many important problems in chemistry require knowledge of the 3-D conformation of a molecule. A commonly used computational approach is to search for a variety of low-energy conformations. Here, we study the behavior of the genetic algorithm (GA) method as a global search technique for finding these low-energy conformations. Our test molecule is cyclic hexaglycine. The goal of this study is to determine how to best utilize GAs to find low-energy populations of conformations given a fixed amount of CPU time. Two measures are presented that help monitor the improvement in the GA populations and their loss of diversity. Different hybrid methods that combine coarse GA global search with local gradient minimization are evaluated. We present several specific recommendations about trade-offs when choosing GA parameters such as population size, number of generations, rate of interaction between subpopulations, and combinations of GA and gradient minimization. In particular, our results illustrate why approaches that emphasize convergence of the GA can actually decrease its effectiveness as a global conformation search method. © John Wiley & Sons, Inc.     

A comparison of field-based similarity searching methods: CatShape, FBSS, and ROCS

Three field-based similarity methods are compared in retrospective virtual screening experiments. The methods are the CatShape module of CATALYST, ROCS, and an in-house program developed at the University of Sheffield called FBSS. The programs are used in both rigid and flexible searches carried out in the MDL Drug Data Report. UNITY 2D fingerprints are also used to provide a comparison with a more traditional approach to similarity searching, and similarity based on simple whole-molecule properties is used to provide a baseline for the more sophisticated searches. Overall, UNITY 2D fingerprints and ROCS with the chemical force field option gave comparable performance and were superior to the shape-only 3D methods. When the flexible methods were compared with the rigid methods, it was generally found that the flexible methods gave slightly better results than their respective rigid methods; however, the increased performance did not justify the additional computational cost required.     

异丙醇的O-H伸缩振动泛频光谱和分子构像

使用高灵敏的光腔衰荡光谱(CavityRingDownSpectroscopy)技术测出了异丙醇的O-H伸缩v=4、5振动泛频光谱,每个振动能级都有三个吸收峰,被归属为分子构像的O-H伸缩泛频吸收.给出了光腔衰荡光谱的振动泛频吸收的谱带强度公式,并求得分子不同构像在不同振动能级的O-H伸缩泛频吸收的谱带强度;同时利用局域模理论,求得分子各O-H伸缩局域模振子的机械频率(X1)、非谐性(X2)以及解离能(D).用密度泛函(DFT)B3LYP/6-31+G*理论方法优化了分子的各种可能构像,验证了分子存在反式(trans)和偏转(gauche)两种稳定构像,计算的分子的O-H伸缩频率及构像稳定性同实验结果是一致的.     

Atomic-scale determination of DNA conformational response to strained furanose: a static mode approach

An original approach of macromolecular ‘induced-fit’ flexibility, namely the static modes, is applied to shed light on some fundamental mechanisms impacting DNA conformations. We first investigate a constrained nucleic acid of the D-CNA family, in which some backbone torsional angles are conformationally restricted by a dioxaphosphorinane ring structure. We take a special interest in α,β-D-CNA, in which α and β angles are restricted to the canonical conformation. We used the static mode method to evaluate the impact of the insertion of modified nucleotides on the stability of DNA/DNA and DNA/RNA duplexes. Although our approach authorizes the design of complex excitation modes on a specific molecule, we here establish with an atomic precision how a DNA south to north transition can be optimally operated through C5′ and O5′ single excitations.     

A genetic algorithm for flexible molecular overlay and pharmacophore elucidation

Summary A genetic algorithm (GA) has been developed for the superimposition of sets of flexible molecules. Molecules are represented by a chromosome that encodes angles of rotation about flexible bonds and mappings between hydrogen-bond donor proton, acceptor lone pair and ring centre features in pairs of molecules. The molecule with the smallest number of features in the data set is used as a template, onto which the remaining molecules are fitted with the objective of maximising structural equivalences. The fitness function of the GA is a weighted combination of: (i) the number and the similarity of the features that have been overlaid in this way; (ii) the volume integral of the overlay; and (iii) the van der Waals energy of the molecular conformations defined by the torsion angles encoded in the chromosomes. The algorithm has been applied to a number of pharmacophore elucidation problems, i.e., angiotensin II receptor antagonists, Leu-enkephalin and a hybrid morphine molecule, 5-HT_1D agonists, benzodiazepine receptor ligands, 5-HT₃ antagonists, dopamine D₂ antagonists, dopamine reuptake blockers and FKBP12 ligands. The resulting pharmacophores are generated rapidly and are in good agreement with those derived from alternative means.     

π-Bond Configurations,Conformations, and Dynamic Behaviour of Benzo[c]octalene and Dibenzo[c,j]octalene

The π-bond configurations, the conformations, and the dynamic behaviour of dibenzo [c,j]octalene (2) and of benzo [c]octalene (3) have been investigated by ¹³C-NMR. spectroscopy at different temperatures. Dibenzooctalene was found to present π-bond fixation in the octalene unit as in 2b ; with this π-bond fixation the molecule is not planar and takes two different conformations which are rapidly interconverted by inversion of one cyclooctatetraene ring. Monobenzooctalene (3) also presents π-bond fixation in the octalene unit but exists as two valence isomers, 3b and 3c. Isomer 3c dominates the dynamic equilibrium. With this π-bond configuration, the molecule is chiral but undergoes several isodynamic processes, namely inversion of the cyclooctatriene and/or of the cyclooctatetraene ring. The valence isomer 3b can have two different conformations which are rapidly interconverted by inversion of one cyclooctatetraene ring. The interconversion 3c ? 3b implies the occurrence of a π-bond shift process; this process affects the ¹³C-NMR. lineshape above 50°.     

Comprehensive structural studies of 2',3'-difluorinated nucleosides: comparison of theory, solution, and solid state

The conformations of three 2',3'-difluoro uridine nucleosides were studied by X-ray crystallography, NMR spectroscopy, and ab initio calculations in an attempt to define the roles that the two vicinal fluorine atoms play in the puckering preferences of the furanose ring. Two of the compounds examined contained fluorine atoms in either the arabino or xylo dispositions at C2' and C3' of a 2',3'-dideoxyuridine system. The third compound also incorporated fluorine atoms in the xylo configuration on the furanose ring but was substituted with a 6-azauracil base in place of uracil. A battery of NMR experiments in D 2O solution was used to identify conformational preferences primarily from coupling constant and NOE data. Both (1)H and (19)F NMR data were used to ascertain the preferred sugar pucker of the furanose ring through the use of the program PSEUROT. Compound-dependent parameters used in the PSEUROT calculations were newly derived from complete sets of conformations calculated from high-level ab initio methods. The solution and theoretical data were compared to the conformations of each molecule in the solid state. It was shown that both gauche and antiperiplanar effects may be operative to maintain a pseudodiaxial arrangement of the C2' and C3' vicinal fluorine atoms. These data, along with previously reported data by us and others concerning monofluorinated nucleoside conformations, were used to propose a model of how fluorine influences different aspects of nucleoside conformations.     

ZINC--a free database of commercially available compounds for virtual screening

A critical barrier to entry into structure-based virtual screening is the lack of a suitable, easy to access database of purchasable compounds. We have therefore prepared a library of 727,842 molecules, each with 3D structure, using catalogs of compounds from vendors (the size of this library continues to grow). The molecules have been assigned biologically relevant protonation states and are annotated with properties such as molecular weight, calculated LogP, and number of rotatable bonds. Each molecule in the library contains vendor and purchasing information and is ready for docking using a number of popular docking programs. Within certain limits, the molecules are prepared in multiple protonation states and multiple tautomeric forms. In one format, multiple conformations are available for the molecules. This database is available for free download (http://zinc.docking.org) in several common file formats including SMILES, mol2, 3D SDF, and DOCK flexibase format. A Web-based query tool incorporating a molecular drawing interface enables the database to be searched and browsed and subsets to be created. Users can process their own molecules by uploading them to a server. Our hope is that this database will bring virtual screening libraries to a wide community of structural biologists and medicinal chemists.     

A fast and efficient method to generate biologically relevant conformations

Summary Mutual binding between a ligand of low molecular weight and its macromolecular receptor demands structural complementarity of both species at the recognition site. To predict binding properties of new molecules before synthesis, information about possible conformations of drug molecules at the active site is required, especially if the 3D structure of the receptor is not known. The statistical analysis of small-molecule crystal data allows one to elucidate conformational preferences of molecular fragments and accordingly to compile libraries of putative ligand conformations. A comparison of geometries adopted by corresponding fragments in ligands bound to proteins shows similar distributions in conformation space. We have developed an automatic procedure that generates different conformers of a given ligand. The entire molecule is decomposed into its individual ring and open-chain torsional fragments, each used in a variety of favorable conformations. The latter ones are produced according to the library information about conformational preferences. During this building process, an extensive energy ranking is applied. Conformers ranked as energetically favorable are subjected to an optimization in torsion angle space. During minimization, unfavorable van der Waals interactions are removed while keeping the open-chain torsion angles as close as possible to the experimentally most frequently observed values. In order to assess how well the generated conformers map conformation space, a comparison with experimental data has been performed. This comparison gives some confidence in the efficiency and completeness of this approach. For some ligands that had been structurally characterized by protein crystallography, the program was used to generate sets of some 10 to 100 conformers. Among these, geometries are found that fall convincingly close to the conformations actually adopted by these ligands at the binding site.     

Enabling the exploration of biochemical pathways

The Biochemical Pathways Wall Chart (http://www.expasy.org/tools/pathways/ref.1) has been converted into a molecule and reaction database. Major features of this database are that each molecule is represented by lists of all atoms and bonds (as connection tables), and in the reactions the reaction centre, the atoms and bonds directly involved in the bond rearrangement process, are marked. The information in the database has been enriched by a set of diverse 3D structure conformations generated by the programs CORINA and ROTATE. The web-based structure and reaction retrieval system C@ROL provides a wide range of search methods to mine this rich database. The database is accessible at http://www2.chemie.uni-erlangen.de/services/biopath/index.html and http://www.mol-net.de/databases/biopath.html .     

Enrichment of ligands for the serotonin receptor using the Shape Signatures approach

Shape Signatures, a new 3-dimensional molecular comparison method, has been adapted to rank ligands of the serotonin receptors. A set of 825 agonists and 400 antagonists together with approximately 10,000 randomly chosen compounds from the NCI database were used in this study. Both 1D and 2D Shape Signature databases were created, and enrichment studies were carried out. Results from these studies reveal that the 1D Shape Signature approach is highly efficient in separating agonists from a mixture of molecules which includes compounds randomly selected from the NCI database taken as inactives. It is also equally effective at separating agonists and antagonists from a pool of active ligands for the serotonin receptor. Parallel enrichment studies using 2D shape signatures showed high selectivity with more restricted coverage due to the high specificity of 2D signatures. The influence of conformational variation of the shape signature on enrichment was explored by docking a subset of ligands into the crystal structure of serotonin N-acetyltransferase. Enrichment studies on the resulting "docked" conformations produced only slightly improved results compared with the CORINA-generated conformations.     

Do the molecules which form discotic liquid crystals have disc-like structures? The conformation of a simple model compound, 1,2-dihydroxydiacetylbenzene, determined from the NMR spectra of samples dissolved in liquid crystalline solvents

Many discotic mesogens are molecules with a central aromatic ring with adjacent alkylcarboxylate substituents. The simplest such molecule, 1,2-dihydroxydiacetylbenzene, which is not mesogenic, is studied by NMR spectroscopy as a solute in a nematic solvent. The spectra are analysed to give sets of residual dipolar couplings, D_ij , which are then used to test models for the conformation adopted by the acetate side groups. The conformations and geometry of an isolated molecule are calculated by the ab initio MP2/6-311G method and also by the DFT approach using the B3LYP functional with the 6-311++G** basis set. The quantum chemical calculations find that the minimum energy conformer has the acetate groups rotated in opposite directions out of the ring plane, and this kind of structure is also consistent with the NMR data.     

Self-assembly of designed oligomeric siloxanes with alkyl chains into silica-based hybrid mesostructures

A novel self-assembly route to ordered silica-organic hybrids using well-defined siloxane oligomers with alkoxy functionality and covalently attached alkyl chains has been investigated. Various hybrid mesostructures were obtained by hydrolysis and polycondensation without the use of any structure-directing agents. The oligomers 1(Cn), having an alkylsilane core and three branched trimethoxysilyl groups, formed highly ordered lamellar phases when n = 14-18, while those with shorter alkyl chains formed cylindrical assemblies, slightly distorted two-dimensional (2D) hexagonal structures (n = 6-10), and a novel 2D monoclinic structure (n = 12). Furthermore, the mixtures of 1(Cn) with different chain lengths yielded well-ordered 2D hexagonal phases, possibly due to the better packing of the precursors. The hybrids consisting of cylindrical assemblies were converted to ordered porous silica with tunable pore sizes upon calcination to remove organic groups. The liquid-state 29Si NMR analysis of the hydrolysis and polycondensation processes of 1(Cn) revealed a unique intramolecular reaction yielding primarily the oligomer with a tetrasiloxane ring which is a new class of amphiphilic molecule having both self-assembling ability and high cross-linking ability. We also found that the mesostructure (lamellar or 2D hexagonal) was strictly controlled by varying the number of siloxane units per alkyl chain. These results provide a deeper understanding of the present self-assembly process that is strongly governed by the molecular packing of oligosiloxane precursors.     

The Solid-State and Solution Conformations of (+)-Chelidonine

The solid-state and solution conformations of (+)-chelidonine ( 1 ), a biologically active alkaloid, were determined by X-ray diffraction and ¹H-NMR spectroscopy, X-Ray diffraction analysis revealed a conformer with B/C ‘anti-type’ cis conjunction, a half-chair of ring B , and a twist half-chair of ring C. One H₂O molecule per one alkaloid molecule was cocrystallized and stabilized by H-bonding with OH? C(11). Analysis of the thermal behavior of the crystal showed more thermal stability in the monohydrate than the anhydrate. The NMR measurement of concentration and temperature dependences in CDCl₃ and in (CD₃)₂SO suggested that the OH group of 1 was intramolecularly H -bonded to N(5) in (CD₃)₂SO and intermolecularly H-bonded to the solvent in CDCl₃. Conformational-energy calculations by the MNDO method showed that the intramolecular H -bond was little affected by the conformational stabilization of 1 .     

Synthèse et étude conformationnelle de dioxa-1,3 aza-9 spiro[5,5]undecanes

Synthesis of the new l,3-dioxa-9-azaspiro[5.5]undecane ring, was realized by the scheme represented in Figure 2. Butyro-phenones 6 posses neuroleptic activity similar to that of halo-peridol. The pharmacological activity was reported in another publication (2). Conformational study of l,3-dioxa-9-azaspiro-[5.5]undecanes shows the existence of four conformations A, B, C and D, which are shown in Figure 4. The existence of these conformations depends on the nature of the substituents R and R' on the dioxane ring. Thus, in the compounds where R ≠ H, R' = H, the four conformations are possible with a preponderance of A and B. If R and R' are different from H only the conformation A is present in 99% concentration. Lastly, when R = R' = H, the four conformations are possible with equal population for the couple A, B and the couple C, D; the first couple predominating. The presence of a fluorophenylbutyric moiety on the piperidine nitrogen does not seem to stereochemically modify the heterocyclic group.     

Conformational analysis of a flexible oligosaccharide using residual dipolar couplings.

We present a new approach to the analysis of the conformational and the motional properties of an oligosaccharide, methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside. The approach relies on an order matrix analysis of residual dipolar couplings in the solution state. By combining a number of different types of couplings, (1)D(CH), (2)D(CH), and D(HH), an order matrix is solved for each ring of the trimannoside. The resulting order parameters indicate the internal motion at the alpha (1,3) linkage to be limited, while significant motion is suggested at the alpha (1,6) linkage. Two structures for the trimannoside were determined by aligning the order tensor principal axes obtained from two different orienting media, bicelles and phage. The very similar conformations at the alpha (1,3) linkage of these two structures confirm that the internal motion at the alpha (1,3) linkage is small and the conformation is a good representation of a single preferred structure. The different conformations at the alpha (1,6) linkage suggest that the motional amplitudes are large and the conformations must be viewed as virtual conformers. Compared with traditional NMR methods, data acquisition is easy and data analysis is straightforward.