Conformer Generation Research Articles

Heterogeneous structure of poly(glycolic acid) fiber studied with differential scanning calorimeter, X-ray diffraction, solid-state NMR and molecular dynamic simulation

The heterogeneous structures of poly(glycolic acid) (PGA) fibers which have been used as bio-degradable suture were studied by differential scanning calorimeter (DSC),X-ray diffraction and 13C solid state NMR. The 13C cross polarization NMR spectra without magic angle spinning of the stretched fibers observed by changing the angle between the fiber axis and the magnetic field clearly showed the heterogeneous structures which consist of three components; well-oriented, poorly-oriented and isotropic amorphous components. The local structure, distribution of the fiber axis and fraction of each component were determined quantitatively. Change in the heterogeneous structure by changing the stretching method in the sample preparation and by changing the stretching ratio was also monitored. The X-ray diffraction data of the fibers are in good agreement with the 13C CP NMR data. Change in the heterogeneous structures correlate with change in the thermal properties observed by DSC method. The molecular dynamic simulation showed the generation of trans conformation of PGA chain and also change in the fraction of other conformations by stretching, which supports the experimental results obtained above and gives additional structural information.

How does microhydration impact on structure, spectroscopy and formation of disulfide radical anions? An ab initio investigation on dimethyldisulfide

The effect of microhydration on the one-electron uptake of a prototypical disulfide is examined at the MP2/DZP++ level of theory. After systematic generation of low-lying conformers of dimethyldisulfide–water clusters (DMDS: nH 2O, n = 1–5), either neutral or anionic, it is found that their energy ranking is governed by the increasing strength of the three hydrogen bonds involved, namely, water-neutral DMDS bonds, intra-water bonds and water–anionic DMDS bonds. Their optimal values are respectively 3.5, 4.5 and 11.4 kcal/mol. The inclusion of a limited number of water molecules has a non-negligible impact on structure and UV–Vis absorption of DMDS radical anion. Furthermore, its formation is favored by up to 1.04 eV when explicitly solvated by five water molecules.

Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size

We introduce the TrixX Conformer Generator (TCG), a novel tool for generating conformational ensembles. The tool addresses especially the requirements of large-scale computer-aided drug design applications using conformer databases. For these, the trade-off between accuracy, i.e. rmsd to biologically active conformers, and database size, i.e. the number of conformers in an ensemble, is of central interest. Based on a tree data structure representing the molecule, conformations are generated incrementally in a best-first-search build-up process employing an internal rmsd clustering. This way TCG builds conformational ensembles of low energy conformers utilizing conformational energy as a scoring function. A crucial parameter is the amount of search space to be covered in the build-up process. This parameter is determined according to an exponential function employing a user-specified quality level as base and an exponent which depends on the molecule's flexibility. The quality level allows the user to set the aforementioned trade-off while taking into account the exponentially growing number of combinations of torsion angles. Tested on a set of 778 molecules, we show that on average 20 conformers per ensemble suffice to achieve an average accuracy of 1.13 A. We observed that an improvement in accuracy goes along with an exponential rise of the number of conformations per ensemble (e.g., 100 conformations per ensemble yield an accuracy of 0.99 A). Furthermore, we show that for molecules with less than nine rotatable bonds, ensembles with an average accuracy better than 1 A can be generated with an average ensemble size of 20 conformers. However, this value deteriorates for more flexible molecules. A comparison to CATALYST and OMEGA shows that TCG achieves a comparable performance in terms of accuracy. Furthermore, it performs well with respect to the trade-off between accuracy and ensemble size.

A Self-Organizing Algorithm for Modeling Protein Loops

Protein loops, the flexible short segments connecting two stable secondary structural units in proteins, play a critical role in protein structure and function. Constructing chemically sensible conformations of protein loops that seamlessly bridge the gap between the anchor points without introducing any steric collisions remains an open challenge. A variety of algorithms have been developed to tackle the loop closure problem, ranging from inverse kinematics to knowledge-based approaches that utilize pre-existing fragments extracted from known protein structures. However, many of these approaches focus on the generation of conformations that mainly satisfy the fixed end point condition, leaving the steric constraints to be resolved in subsequent post-processing steps. In the present work, we describe a simple solution that simultaneously satisfies not only the end point and steric conditions, but also chirality and planarity constraints. Starting from random initial atomic coordinates, each individual conformation is generated independently by using a simple alternating scheme of pairwise distance adjustments of randomly chosen atoms, followed by fast geometric matching of the conformationally rigid components of the constituent amino acids. The method is conceptually simple, numerically stable and computationally efficient. Very importantly, additional constraints, such as those derived from NMR experiments, hydrogen bonds or salt bridges, can be incorporated into the algorithm in a straightforward and inexpensive way, making the method ideal for solving more complex multi-loop problems. The remarkable performance and robustness of the algorithm are demonstrated on a set of protein loops of length 4, 8, and 12 that have been used in previous studies.

Flexible Alignment of Small Molecules Using the Penalty Method

An efficient flexible alignment method using the penalty method, called FAP, is described. FAP is a pairwise alignment algorithm that matches a flexible sample to a rigid template. It is a pure atom-based 3D method that utilizes the modified SEAL similarity index combined with an energy penalty term. The penalty term, defined as the third power of the ratio of the local strain energy to its target value, enables effective control of energy increase during alignment. The alignment procedure consists of the seed conformer generation, rigid-body alignment, and flexible optimization steps. Both conformation and alignment spaces are efficiently explored by the sparse, random sampling schemes. FAP has been tested with benchmark sets of seven different classes of ligands taken from the literature. In terms of the ability to produce the bioactive overlays, FAP is comparable to, or in some cases better than, other alignment methods. FAP is accurate, objective, fully automated, and fast enough to be used as a tool for virtual screening.

Hyperglycaemia impairs antithrombin secretion: Possible contribution to the thrombotic risk of diabetes

Recent data support that diabetes might be a conformational disease. Certainly, hyperglycaemia causes a broad range of deleterious effects that might facilitate protein aggregation. We have evaluated the effects of hyperglycaemia on antithrombin, a conformationally sensitive serpin with a potent anticoagulant role. Moreover, these studies might also help to understand the thrombotic risk associated to diabetes. We incubated in vitro plasma and purified antithrombin and human hepatoma cells (HepG2) with methyl-glyoxal and glucose. Moreover, a mouse model of acute diabetes was generated with streptozotocin. Antigen, anti-FXa activity, heparin affinity and conformational features of antithrombin were analysed. Histological and intracellular features and distribution of antithrombin in HepG2 and livers of mice were also evaluated. Hyperglycaemia i n vitro induced a transition of antithrombin to a form with low heparin affinity that explained the loss of anticoagulant activity, without generation of abnormal conformers (polymers or latent antithrombin). However, these effects were not observed on circulating antithrombin from diabetic mice. In contrast, hyperglycaemia in vivo had significant effects on intracellular antithrombin, which was retained, forming microaggregates within the lumen of dilated cisterns of the endoplasmic reticulum. These effects explained the moderate type I deficiency observed in diabetic mice. Similar intracellular consequences were observed for another hepatic serpin, α1-antitrypsin. Our data further support that diabetes has conformational effects on structurally sensitive proteins. These effects on antithrombin, the main natural anticoagulant, might contribute to the hypercoagulable status of diabetic patients.

Elucidating Molecular Overlays from Pairwise Alignments Using a Genetic Algorithm

Inferring the relative bioactive poses between active molecules is a common problem in drug discovery. The use of rapid pairwise alignment algorithms in conjunction with rigid conformer libraries has become a prevalent approach to this problem. These programs can be easily used to compare two molecules or suggest alternatives to a single known active. However, it is not obvious how to combine pairwise alignments between multiple actives into an overlay that reproduces the binding mode of those actives in the target receptor. We describe a new algorithm, DIFGAPE (DIstance geometry Focused Genetic Algorithm Pose Evaluator) that, given pairwise alignments of conformers of active compounds, attempts to reproduce overlays of ligand binding modes. The software was evaluated on 13 test systems from 9 protein targets using associated ligands extracted from the PDB. Starting from 2D ligand structures with no protein information, we were able in 4 systems to approximate the crystallographically observed binding mode. For example, the prediction for a set of 11 ligands targeting FXa had 1.6 A rmsd to crystal structure coordinates. Finally, the evaluation illustrated current challenges for molecular conformer generators and pairwise alignment algorithms.

Effect of Input Differences on the Results of Docking Calculations

The sensitivity of docking calculations to the geometry of the input ligand was studied. It was found that even small changes in the ligand input conformation can lead to large differences in the geometries and scores of the resulting docked poses. The accuracy of docked poses produced from different ligand input structures-the X-ray structure, the minimized Corina structure, and structures generated from conformational searches and molecular dynamics ensembles-were also assessed. It was found that using the X-ray ligand conformation as docking input does not always produce the most accurate docked pose when compared with other sources of ligand input conformations. Furthermore, no one method of conformer generation is guaranteed to always produce the most accurate docking pose. The docking scores are also highly sensitive to the source of the input conformation, which might introduce some noise in compound ranking and in binding affinity predictions. It is concluded that for the purposes of reproducibility and optimal performance, the most prudent procedure is to use multiple input structures for docking. The implications of these results on docking validation studies are discussed.

Structure−Function Analyses of Isochorismate-Pyruvate Lyase from Pseudomonas aeruginosa Suggest Differing Catalytic Mechanisms for the Two Pericyclic Reactions of This Bifunctional Enzyme

The isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB) catalyzes two pericyclic reactions in a single active site. PchB physiologically produces salicylate and pyruvate from isochorismate for ultimate incorporation of the salicylate into the siderophore pyochelin. PchB also produces prephenate from chorismate, most likely due to structural homology to the Escherchia coli chorismate mutase. The molecular basis of catalysis among enzymatic pericyclic reactions is a matter of debate, one view holding that catalysis may be derived from electrostatic transition state stabilization and the opposing view that catalysis is derived from the generation of a reactive substrate conformation. Mutant forms of PchB were generated by site-directed mutagenesis at the site (K42) hypothesized to be key for electrostatic transition state stabilization (K42A, K42Q, K42E, and K42H). The loop containing K42 is mobile, and a mutant to slow loop dynamics was also designed (A43P). Finally, a previously characterized mutation (I87T) was also produced. Circular dichroism was used to assess the overall effect on secondary structure as a result of the mutations, and X-ray crystallographic structures are reported for K42A with salicylate and pyruvate bound and for apo-I87T. The data illustrate that the active site architecture is maintained in K42A-PchB, which indicates that differences in activity are not caused by secondary structural changes or by differences in active site loop conformation but rather by the chemical nature of this key residue. In contrast, the I87T structure demonstrates considerable mobility, suggesting that loop dynamics and conformational plasticity may be important for efficient catalysis. Finally, the mutational effects on k(cat) provide evidence that the two activities of PchB are not covariant and that a single hypothesis may not provide a sufficient explanation for catalysis.

Novel Method for the Evaluation of 3D Conformation Generators

Conformation generation is a common and key process of computer-aided drug design. The reliability of the docking simulations, pharmacophore development, and 3D-QSAR analyses depends on the accuracy of conformations of small molecules used as input information for each program. Many conformation generators have been developed with the aim of efficiently generating all the putative bound conformations that small molecules adopt when they interact with macromolecules. Conformation generators have been evaluated by whether they can reproduce the experimentally determined bioactive conformations of bound small molecules. These bioactive conformations are usually obtained from publicly available crystal structures of protein-ligand complexes. However, it is difficult to obtain 2 or more than 2 bioactive conformations of one compound because multiple complex structures of a single molecule with various macromolecules are rarely available. Present methods, therefore, simply check whether a set of generated conformations includes the corresponding bioactive conformation. The overall validity of the entire set of generated conformations against bioactive conformation space has never been checked. In this work we developed a novel method for the evaluation of conformation generators, which makes it possible to measure the performance of a conformation generator based on its ability to reproduce the overall bioactive conformation space. We also determined the optimum parameter sets for OMEGA (OpenEye) based on the coverage of bioactive conformation space and computational efficiency. Our evaluation method elucidated that increasing the number of generated conformations is not necessary to obtain better reproducibility of the overall bioactive conformation space. Our method can be applied to the evaluation of the algorithm and/or design of the conformation generator program itself.

Discovery and Characterization of a Peptide Motif That Specifically Recognizes a Non-native Conformation of Human IgG Induced by Acidic pH Conditions

In therapeutic antibody preparation, acidic pH conditions are generally used for elution from Protein A affinity column of IgG or for its viral inactivation. Exposing IgG to low pH conditions induces conformational changes, leading to its functional damage or loss, although the mechanisms have not been fully elucidated. In this study using random peptide T7 phage display libraries, we isolated a unique and novel peptide motif that specifically recognized the non-native conformer (acid conformer) of human IgG that was generated by the low pH treatment, but not the native conformer. We examined the generation conditions and biochemical properties of acid conformer using the peptide motif as an affinity ligand. The acid conformer was easily generated at acidic pH (<pH 3.0) and at moderate temperatures (20-40 degrees C). The conformer was present in a monomeric form functionally maintaining antigen or Fc receptor binding, but showed a tendency to aggregate with a long incubation time at neutral pH (>25 degrees C). The peptides isolated here could contribute to the elucidation of the mechanisms of antibody dysfunction or aggregation during acid exposure as well as storage of human IgG.

Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation

BackgroundConformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm.ResultsThe conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105–112). Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 Å to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 ± 0.18 seconds per molecule) renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1.ConclusionOn the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms other four multiple conformer generators in the case of reproducing the bioactive conformations against 329 structures. The speed advantage indicates Cyndi is a powerful alternative method for extensive conformational sampling and large-scale conformer database preparation.

Binding Estimation after Refinement, a New Automated Procedure for the Refinement and Rescoring of Docked Ligands in Virtual Screening

Binding estimation after refinement (BEAR) is a novel automated computational procedure suitable for correcting and overcoming limitations of docking procedures such as poor scoring function and the generation of unreasonable ligand conformations. BEAR makes use of molecular dynamics simulation followed by MM-PBSA and MM-GBSA binding free energy estimates as tools to refine and rescore the structures obtained from docking virtual screenings. As binding estimation after refinement relies on molecular dynamics, the entire procedure can be tailored to the needs of the end-user in terms of computational time and the desired accuracy of the results. In a validation test, binding estimation after refinement and rescoring resulted in a significant enrichment of known ligands among top scoring compounds compared with the original docking results. Binding estimation after refinement has direct and straightforward application in virtual screening for correcting both false-positive and false-negative hits, and should facilitate more reliable selection of biologically active molecules from compound databases.

Assessing the Geometric Diversity of Cytochrome P450 Ligand Conformers by Hierarchical Clustering with a Stop Criterion

An algorithm is presented, which exhibits a computed number of rigid conformers of an input small molecule, covering the geometric diversity in the conformational space, with minimal structural redundancy. The algorithm calls a conformer generator, then performs an agglomerative hierarchical clustering with the modified clustering gain as the stop criterion. The number of classes is computed without an arbitrary parameter. A representative conformer is selected in each class, and nonrepresentative conformers are discarded. For illustration, the algorithm has been applied on a database containing 70 ligands of the cytochrome CYP 3A4, showing that the structural flexibility of each ligand is indeed handled via a small number of its representative conformers. The method is valid for all small molecules.

OSIRIS, an Entirely in-House Developed Drug Discovery Informatics System

We present OSIRIS, an entirely in-house developed drug discovery informatics system. Its components cover all information handling aspects from compound synthesis via biological testing to preclinical development. Its design principles are platform and vendor independence, a consistent look and feel, and complete coverage of the drug discovery process by custom tailored applications. These include electronic laboratory notebook applications for biology and chemistry, tools for high-throughput and secondary screening evaluation, chemistry-aware data visualization, physicochemical property prediction, 3D-pharmacophore comparisons, interactive modeling, computing grid based ligand-protein docking, and more. Most applications are developed in Java and are built on top of a Java library layer that provides reusable cheminformatics functionality and GUI components such as chemical editors, structure canonicalization, substructure search, combinatorial enumeration, enhanced stereo perception, force field minimization, and conformation generation.

A new method for in-silico drug screening and similarity search using molecular dynamics maximum volume overlap (MD-MVO) method

We developed a new molecular dynamics simulation method for molecular overlapping (alignment) and ligand-based in-silico drug screening based on molecular similarity. The molecular system consists of the query compound and the other compound(s) selected from a compound library. The newly introduced intermolecular interaction between compounds is proportional to the molecular overlap instead of the van der Waals and Coulomb interactions between atoms of different molecules. This method was able to achieve both conformer generation of molecules and molecular overlapping (alignment) at the same time. After an energy minimization and following short-time MD simulation, the molecules in the system were overlapped with each other and the similarity between compounds was measured by the volume of the overlap. We applied this MD simulation method to ligand-based in-silico drug screening and found that it worked well for several targets.

VSDMIP: virtual screening data management on an integrated platform

A novel software (VSDMIP) for the virtual screening (VS) of chemical libraries integrated within a MySQL relational database is presented. Two main features make VSDMIP clearly distinguishable from other existing computational tools: (i) its database, which stores not only ligand information but also the results from every step in the VS process, and (ii) its modular and pluggable architecture, which allows customization of the VS stages (such as the programs used for conformer generation or docking), through the definition of a detailed workflow employing user-configurable XML files. VSDMIP, therefore, facilitates the storage and retrieval of VS results, easily adapts to the specific requirements of each method and tool used in the experiments, and allows the comparison of different VS methodologies. To validate the usefulness of VSDMIP as an automated tool for carrying out VS several experiments were run on six protein targets (acetylcholinesterase, cyclin-dependent kinase 2, coagulation factor Xa, estrogen receptor alpha, p38 MAP kinase, and neuraminidase) using nine binary (actives/inactive) test sets. The performance of several VS configurations was evaluated by means of enrichment factors and receiver operating characteristic plots.

Fully Automated Molecular Mechanics Based Induced Fit Protein−Ligand Docking Method

We describe a method for docking a ligand into a protein receptor while allowing flexibility of the protein binding site. The method employs a multistep procedure that begins with the generation of protein and ligand conformations. An initial placement of the ligand is then performed by computing binding site hotspots. This initial placement is followed by a protein side-chain refinement stage that models protein flexibility. The final step of the process is an energy minimization of the ligand pose in the presence of the rigid receptor. Thus the algorithm models flexibility of the protein at two stages, before and after ligand placement. We validated this method by performing docking and cross docking studies of eight protein systems for which crystal structures were available for at least two bound ligands. The resulting rmsd values of the 21 docked protein-ligand complexes showed values of 2 A or less for all but one of the systems examined. The method has two critical benefits for high throughput virtual screening studies. First, no user intervention is required in the docking once the initial binding site selection has been made in the protein. Second, the initial protein conformation generation needs to be performed only once for a given binding region. Also, the method may be customized in various ways depending on the particular scenario in which dockings are being performed. Each of the individual steps of the method is fully independent making it straightforward to explore different variants of the high level workflow to further improve accuracy and performance.

Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints

Inferring three-dimensional structural information of biomacromolecules such as proteins from limited experimental data is an important and challenging task. Nuclear Overhauser effect measurements based on nucleic magnetic resonance, disulfide linking, and electron paramagnetic resonance labeling studies can all provide useful partial distance constraint characteristic of the conformations of proteins. In this study, we describe a general approach for reconstructing conformations of biomolecules that are consistent with given distance constraints. Such constraints can be in the form of upper bounds and lower bounds of distances between residue pairs, contact maps based on specific contact distance cutoff values, or indirect distance constraints such as experimental phi-value measurement. Our approach is based on the framework of sequential Monte Carlo method, a chain growth-based method. We have developed a novel growth potential function to guide the generation of conformations that satisfy given distance constraints. This potential function incorporates not only the distance information of current residue during growth but also the distance information of future residues by introducing global distance upper bounds between residue pairs and the placement of reference points. To obtain protein conformations from indirect distance constraints in the form of experimental phi-values, we first generate properly weighted contact maps satisfying phi-value constraints, we then generate conformations from these contact maps. We show that our approach can faithfully generate conformations that satisfy the given constraints, which approach the native structures when distance constraints for all residue pairs are given.

Single- and Double-Stranded Helical Polymers: Synthesis, Structures, and Functions

Biological macromolecules, such as DNA and proteins, possess a unique and specific ordered structure, such as a right-handed double helix or a single alpha-helix. Those structures direct the sophisticated functions of these molecules in living systems. Inspired by biological helices, chemists have worked to synthesize polymers with controlled helicity, not only to mimic the biological helices but also to realize their functions. Although numerous synthetic polymers that fold into a single-handed helix have been reported, double-stranded helical polymers are almost unavailable except for a few oligomers. In addition, the exact structures of most helical polymers remain obscure. Therefore, the development of a conceptually new method for constructing double-stranded helical polymers and a reliable method for unambiguously determining the helical structures are important and urgent challenges in this area. In this Account, we describe the recent advances in the synthesis, structures, and functions of single- and double-stranded helical polymers from our group and others and provide a brief historical overview of synthetic helical polymers. We found unique macromolecules that fold into a preferred-handed helix through noncovalent bonding interactions with specific chiral guests. During the noncovalent helicity induction process, these guest molecules significantly amplified chirality in a dynamic helical polymer. During the intensive exploration of the helicity induction mechanism, we observed an unusual macromolecular helical memory in dynamic helical polymers. Furthermore, we found that rigid-rod helical poly(phenylacetylene)s and poly(phenyl isocyanide)s showing a cholesteric or smectic liquid crystal self-assemble to form two-dimensional crystals with a controlled helical conformation on solid substrates upon exposure to solvent vapors. We visualized their helical structures including the helical pitch and handedness by atomic force microscopy (AFM). We propose a modular strategy to construct complementary double helices by employing chiral amidinium-carboxylate salt bridges with m-terphenyl backbones. The double-stranded helical structures were characterized by circular dichroism in solution and X-ray diffraction of the crystals or the direct AFM observations. Serendipitously, we found that oligoresorcinols self-assemble into well-defined double helices resulting from interstrand aromatic stacking in water. These oligoresorcinols bound cyclic and linear oligosaccharides in water to form rotaxanes and hetero-double helices, respectively. The examples presented in this Account demonstrate the notable progress in the synthesis and structural determination of helical polymers including single- and double-stranded helices. Not only do we better understand the principle underlying the generation of helical conformations, but we have also used the knowledge of these unique helical structures to develop novel helical polymers with specific functions.