Singular value decomposition of torsional angles of analogs of the dopamine reuptake inhibitor GBR 12909

Analysis of large, flexible molecules, such as the dopamine reuptake inhibitor GBR 12909 (1), is complicated by the fact that they can take on a wide range of closely related conformations. The first step in the analysis is to classify the conformers into groups. Here, Singular Value Decomposition (SVD) was used to group conformations of GBR 12909 analogs by the similarity of their nonring torsional angles. The significance of the present work, the first application of SVD to the analysis of very flexible molecules, lies in the development of a novel scaling technique for circular data and in the grouping of molecular conformations using a technique that is independent of molecular alignment. Over 700 conformers each of a piperazine (2) and piperidine (3) analog of 1 were studied. Analysis of the score and loading plots showed that the conformers of 2 separate into three large groups due to torsional angles on the naphthalene side of the molecule, whereas those of 3 separate into nine groups due to torsional angles on the bisphenyl side of the molecule. These differences are due to nitrogen inversion at the unprotonated piperazinyl nitrogen of 2, which results in a different ensemble of conformers than those of 3, where no inversion is possible at the corresponding piperidinyl carbon.     

Novel feature extraction technique for fuzzy relational clustering of a flexible dopamine reuptake inhibitor

This paper describes a novel clustering methodology for classifying over 700 conformations of a flexible analogue of GBR 12909, a dopamine reuptake inhibitor that has completed phase I clinical trials as a treatment for cocaine abuse. The major aspect of the clustering methodology includes an efficient data-conditioning scheme where a systematic feature extraction procedure based on the structural properties of the molecule was used to reduce the associated feature space. This allowed region-specific clustering that focused on individual pharmacophore elements of the molecule. For clustering of the reduced feature set, the fuzzy clustering partitional method was utilized. Due to the relational nature of the feature data, fuzzy relational clustering was employed, and it successfully detected natural groups defined by rotational minima around N(sp(3))-C(sp(3)), O(sp(3))-C(sp(3)), and C(sp(3))-C(sp(2)) bonds. The proposed clustering methodology also employed several cluster validity measures, which corroborated the partitions produced by the clustering technique and agreed with the results of hierarchical clustering using the XCluster program. Representative structures which exhibited a reasonable spread of energies and showed good spatial coverage of the conformational space were identified for use as putative bioactive conformations in a future Comparative Molecular Field Analysis of GBR 12909 analogues. The clustering methodology developed here is capable of handling other computational chemistry problems, and the feature extraction technique can be easily generalized to other molecules.     

Hierarchical clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs

Pharmacophore modeling of large, drug-like molecules, such as the dopamine reuptake inhibitor GBR 12909, is complicated by their flexibility. A comprehensive hierarchical clustering study of two GBR 12909 analogs was performed to identify representative conformers for input to three-dimensional quantitative structure–activity relationship studies of closely-related analogs. Two data sets of more than 700 conformers each produced by random search conformational analysis of a piperazine and a piperidine GBR 12909 analog were studied. Several clustering studies were carried out based on different feature sets that include the important pharmacophore elements. The distance maps, the plot of the effective number of clusters versus actual number of clusters, and the novel derived clustering statistic, percentage change in the effective number of clusters, were shown to be useful in determining the appropriate clustering level.Six clusters were chosen for each analog, each representing a different region of the torsional angle space that determines the relative orientation of the pharmacophore elements. Conformers of each cluster that are representative of these regions were identified and compared for each analog. This study illustrates the utility of using hierarchical clustering for the classification of conformers of highly flexible molecules in terms of the three-dimensional spatial orientation of key pharmacophore elements.     

Cluster analysis of molecular conformations

We describe a method for locating clusters of geometrically similar conformers in ensembles of chemical conformations. We first calculate the pairwise interconformational distance matrix in either torsional or Cartesian space and then use an agglomerative, single-link clustering method to define a hierarchy of clusterings in the same space. Especially good clusterings are distinguished by high values of the separation ratio: the ratio of the shortest intercluster distance to the characteristic threshold distance defining the clustering. We also discuss other statistics. The method has been embodied in a program called XCluster, which can display the distance matrix, the hierarchy of clusterings, and the clustering statistics in a variety of formats. XCluster can also write out the clustered conformations for subsequent or simultaneous viewing with a molecular visualization program. We demonstrate the sorts of insight that this approach affords with examples obtained from conformational search and molecular dynamics procedures. © 1994 by John Wiley & Sons, Inc.     

Poling: Promoting conformational variation

This article introduces several methods of assessing the extent to which a collection of conformations represents or covers conformational space. It also describes poling: a novel technique for promoting conformational variation that can be applied to any method of conformational analysis that locally minimizes a penalty or energy function. The function being minimized is modified to force similar conformers away from each other. The method is independent of the origin of the initial conformers and of the particular minimization method used. It is found that, with the modification of the penalty function, clustering of the resulting conformers is generally unnecessary because the conformers are forced to be dissimilar. The functional form of the poling function is presented, and the merits are discussed with reference to (1) efficacy at promoting variation and (2) perturbation of the unmodified function. Results will be presented using conformers obtained from distance geometry with and without poling. It will be shown that the addition of poling eliminates much redundancy in conformer generation and improves the coverage of the conformational space. © 1995 by John Wiley & Sons, Inc.     

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.     

The conformation of alkyl sulfoxides

Parameters for sulfoxides used in force field MM1 were modified to be incorporated into force field MM2. The conformations of ten alkyl sulfoxides were then calculated using MM2 with these new parameters. The alkyl groups used were methyl, ethyl, isopropyl, and t-butyl. It was found that of the many possible conformations for these compounds, only one or two stable conformers exist, and that the number of these conformers agrees with the number of reported S? O stretching frequencies in almost every case. No apparent correlation between the vibration frequency and the molecular structure was found.     

Conformational analysis of 14- and 16-membered unsaturated oxa, thia, and selena macrocyclic ligands

Crystallographic results retrieved from the Cambridge Structural Database (CSD) have been used to perform systematic conformational analyses of the free and metal-coordinated ligands 1,4,8,11-tetraoxa/thia/selenacyclotetradecane, 1,5,9,13-tetraoxa/thia/selenacyclohexadecane, and their derivatives. Conformational classifications established using symmetry-modified Jarvis-Patrick cluster analysis have been displayed in torsional space by principal component analysis (PCA) plots. Relative molecular mechanics energies of free macrocycles in the observed conformations are compared with the cluster populations and the effect of metal coordination investigated. While the conformations of the free macrocycles in the solid state are those with low molecular mechanics energies, substantial reorganization is required to produce tetradentate chelating conformers, particularly with S donors. With the latter, several such conformers occur, while one predominates with O donors for both macrocycles, in agreement with molecular mechanics predictions. Factors influencing the conformations adopted are discussed.     

Synthesis,lipophilicity and structure of 2,5‐disubstituted 1, 3, 5‐dithiazine derivatives

A series of 2,5‐disubstituted 1,3,5‐dithiazine derivatives were synthesized as potential analogues of the potent dopamine uptake inhibitor GBR 12909. The lipophilic character of the 1,3,5‐dithiazine derivatives were experimentally (log P) and computationally (clog P) determined. The in vitro binding affinities of the 2,5‐disubstituted 1,3,5‐dithiazine derivatives at the dopamine transporter were determined to be much less potent than the binding affinity of GBR 12909 due to steric and electronic effects inherent to the 1,3,5‐dithiazine ring system. The X‐ray crystal structure of 2‐(2‐[bis(4‐fluorophenyl)methoxy]ethyl)‐5‐(3‐phenylpropyl)‐1,3,5‐dithiazine (7) revealed that the 5‐(3‐phenylpropyl) group is in a pseudo‐axial orientation and syn to the 2‐ethoxybenzhydryl moiety.     

Intramolecular hydrogen-bonding interactions in 2-nitrosophenol and nitrosonaphthols: ab initio, density functional, and nuclear magnetic resonance theoretical study

Intramolecular hydrogen bonding (IHB) interactions and molecular structures of 2-nitrosophenol, nitrosonaphthols, and their quinone-monooxime tautomers were investigated at ab initio and density functional theory (DFT) levels. The geometry optimization of the structures studied was performed without any geometrical restrictions. Possible conformations with different types of the IHB of the tautomers were considered to understand the nature of the HB among these conformers. The effect of solvent on hydrogen bond energies, conformational equilibria, and tautomerism in aqueous solution were studied. Natural bond orbital analysis was performed to study the IHB in the gaseous phase and in aqueous medium. The NMR 1H, 13C, 15N, and 17O chemical shifts in the gaseous phase and in solution for the studied compounds were calculated using the gauge-including atomic orbitals approach implemented in the Gaussian 03 program package. The optimized geometrical parameters and 1H NMR chemical shifts are in good agreement with previous theoretical and experimental data.     

Computer simulation of the conformational behavior of cholecystokinin fragments: Conformational families of sulfated CCK8

Summary Display methods, such as principal component analysis, and clustering methods were applied to a sample of cholecystokinin, (sulfated CCK8) conformations obtained from a Monte Carlo simulation. It is shown that six families of conformations can entirely describe the sample. Each family represents a typical conformer. These theoretical models are in agreement with recent experimental results which stress the predominance of folded conformers in aqueous medium.     

Computational protocols for prediction of solute NMR relative chemical shifts. a case study of L-tryptophan in aqueous solution

In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute-solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.     

The design and synthesis of novel derivatives of the dopamine uptake inhibitors GBR 12909 and GBR 12935. High-affinity dopaminergic ligands for conjugation with highly fluorescent cadmium selenide/zinc sulfide core/shell nanocrystals

There is a growing demand for compounds with very high affinities for the dopamine transporter protein (DAT) that can be conjugated to fluorescent markers such as cadmium selenide/zinc sulfide core/shell nanocrystals. This paper describes the design and synthesis of two derivatives of the DAT antagonists GBR 12935 and GBR 12909. These compounds have a high biological affinity for DAT and may be conjugated to nanocrystals via a thiol linkage without a significant reduction in their biological activity. Such conjugates may be used in fluorescent imaging studies.     

Inherent structure versus geometric metric for state space discretization

Inherent structure (IS) and geometry‐based clustering methods are commonly used for analyzing molecular dynamics trajectories. ISs are obtained by minimizing the sampled conformations into local minima on potential/effective energy surface. The conformations that are minimized into the same energy basin belong to one cluster. We investigate the influence of the applications of these two methods of trajectory decomposition on our understanding of the thermodynamics and kinetics of alanine tetrapeptide. We find that at the microcluster level, the IS approach and root‐mean‐square deviation (RMSD)‐based clustering method give totally different results. Depending on the local features of energy landscape, the conformations with close RMSDs can be minimized into different minima, while the conformations with large RMSDs could be minimized into the same basin. However, the relaxation timescales calculated based on the transition matrices built from the microclusters are similar. The discrepancy at the microcluster level leads to different macroclusters. Although the dynamic models established through both clustering methods are validated approximately Markovian, the IS approach seems to give a meaningful state space discretization at the macrocluster level in terms of conformational features and kinetics. © 2016 Wiley Periodicals, Inc.     

Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.     

Dependence of the L-alanyl-L-alanine conformation on molecular charge determined from ab initio computations and NMR spectra

The l-alanyl-l-alanine (AA) molecule behaves differently in acidic, neutral, and basic environments. Because of its molecular flexibility and strong interaction with the aqueous environment, its behavior has to be deduced from the NMR spectra indirectly, using statistical methods and comparison with ab initio predictions of geometric and spectral parameters. In this study, chemical shifts and indirect spin-spin coupling constants of the AA cation, anion, and zwitterion were measured and compared to values obtained by density functional computations for various conformers of the dipeptide. The accuracy and sensitivity of the quantum methods to the molecular charge was also tested on the (mono)-alanine molecule. Probable AA conformers could be identified at two-dimensional potential energy surfaces and verified by the comparison of the computed parameters with measured NMR data. The results indicate that, whereas the main-chain peptide conformations of the cationic (AA+) and zwitterionic (AAZW) forms are similar, the anion (AA-) adopts also another, approximately equally populated conformer in the aqueous solution. Additionally, the NH2 group can rotate in the two main chain conformations of the anionic form AA-. According to a vibrational quantum analysis of the two-dimensional energy surfaces, higher-energy conformers might exist for all three charged AA forms but cannot be detected directly by NMR spectroscopy because of their small populations and short lifetimes. In accord with previous studies, the NMR parameters, particularly the indirect nuclear spin-spin coupling constants, often provided an excellent probe of a local conformation. Generalization to peptides and proteins, however, has to take into account the environment, molecular charge, and flexibility of the peptide chain.     

Molecular properties from conformational ensembles. 1. Dipole moments of molecules with multiple internal rotations

We present a novel method for constructing the stable conformational space of small molecules with many rotatable bonds that uses our iterative stochastic elimination (ISE) algorithm, a robust stochastic search method capable of finding ensembles of best solutions for large combinatorial problems. To validate the method, we show that ISE reproduces the best conformers found in a fully exhaustive search, as well as compare computed dipole moments to experimental values, based on molecular ensembles and their Boltzmann distributions. Results were also compared to the alternative molecular dynamics and simulated annealing methods. Our results clarify that many low energy conformations may be required to reproduce molecular properties, while single low energy conformers or ensembles of low energy conformers cannot account for the experimental properties of flexible molecules. Whereas ISE well reproduces conformations that are not separated by very large energy barriers, it has not been successful in reproducing conformations of strained molecules.     

Studies on structure and conformational stability of free canonical 2′‐deoxyribonucleosides: Approximate SCC‐DFTB and LMP2 methods

The molecular structure of free canonical 2′‐deoxyribonucleosides have been studied by applying the electron‐correlated local second‐order Møller–Plesset perturbation theory (LMP2) and self‐consistent‐charge density‐functional tight‐binding (SCC‐DFTB) methods. The variation of structural parameters for C2, C3 endo and exo conformations, and anti, syn orientation of the base unit with furanose ring have been discussed. The relative energies have been calculated for the anti and syn conformations of dT, dC, dG, and dA. Conformational analysis has been performed using the results of the LMP2 and SCC‐DFTB methods. Chemical hardness and chemical potential have been used to study the conformational stability of the conformers. The maximum hardness principle is obeyed for the furanose ring conformations and not for the nucleosides. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Conformational Transformations of Sulfur‐Containing Rings: 2‐Methyltetrahydrothiophene Gas‐Phase Structures

Stable conformations of five‐member rings with the prototype cyclopentane are well‐known to exist as twist or envelope structures and are of general interest in chemistry. Here, we report on the conformational analysis of the sulfur‐containing ring 2‐methyltetrahydrothiophene studied by a combination of molecular beam Fourier transform microwave (MB‐FTMW) spectroscopy and quantum chemistry. Two twist conformers were observed, whereby highly accurate molecular parameters could be determined. In addition, the ³⁴S‐isotopologue of the most stable conformer was assigned in natural abundances. Geometry optimizations were performed at different levels of theory and the calculated rotational constants were compared with experimental values. Two transition states optimized at the MP2/6‐311++G(d,p) level using the Berny algorithm could illustrate the intramolecular conversion between both conformers.