Conformer Generation Research Articles

Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations

In continuation of our studies to evaluate the ability of various conformer generators to produce bioactive conformations, we present the extension of our work on the analysis of Catalyst's conformational subsampling algorithm in a comparative evaluation with OpenEye's currently updated tool Omega 2.0. Our study is based on an enhanced test set of 778 drug molecules and pharmacologically relevant compounds extracted from the Protein Data Bank (PDB). We elaborated protocols for two common conformer generation use cases and applied them to both programs: (i) high-throughput settings for processing large databases and (ii) high-quality settings for binding site exploration or lead structure refinement. While Catalyst is faster in the first case, Omega 2.0 better reproduces the bound ligand conformations from the PDB in less time for the latter case.

EXTENDED CONFORMAL GROUP AND DSR VELOCITIES ON THE PHYSICAL SURFACE

The relation between conformal generators and Magueijo–Smolin Doubly Special Relativity term, is achieved. Through a dimensional reduction procedure, it is demonstrated that a massless relativistic particle living in a d-dimensional space, is isomorphic to the one living in a d+2 space with pure Lorentz invariance and to a particle living in a AdS d+1 space. To accomplish these identifications, the conformal group is extended and a nonlinear algebra is obtained. Finally, because the relation between momenta and velocities is known through the dimensional reduction procedure, the problem of position space dynamics is solved.

Activation of T cells by carbamazepine and carbamazepine metabolites

T-cell-mediated hypersensitivity is a rare but serious manifestation of drug therapy. To explore the mechanisms of drug presentation to T cells and the possibility that generation of metabolite-specific T cells may provoke cross-sensitization between drugs. A lymphocyte transformation test was performed on 13 hypersensitive patients with carbamazepine, oxcarbazepine, and carbamazepine metabolites. Serial dilution experiments were performed to generate drug (metabolite)-specific T-cell clones to explore the structural basis of the T-cell response and mechanisms of antigen presentation. 3-Dimensional energy-minimized structures were generated by using computer modeling. The role of drug metabolism was analyzed with 1-aminobenzotriazole. Lymphocytes and T-cell clones proliferated with carbamazepine, oxcarbazepine, and some (carbamazepine 10,11 epoxide, 10-hydroxy carbamazepine) but not all stable carbamazepine metabolites. Structure activity studies using 29 carbamazepine (metabolite)-specific T-cell clones revealed 4 patterns of drug recognition, which could be explained by generation of preferred 3-dimensional structural conformations. T cells were stimulated by carbamazepine (metabolites) bound directly to MHC in the absence of processing. The activation threshold for T-cell proliferation varied between 5 minutes and 4 hours. 1-Aminobenzotriazole, which inhibits cytochrome P450 activity, did not prevent carbamazepine-related T-cell proliferation. Substitution of the terminal amine residue of carbamazepine with a methyl group diminished T-cell proliferation. These data show that carbamazepine and certain stable carbamazepine metabolites stimulate T cells rapidly via a direct interaction with MHC and specific T-cell receptors. Some patients with a history of carbamazepine hypersensitivity possess T cells that cross-react with oxcarbazepine, providing a rationale for cross-sensitivity between the 2 drugs.

Light-cone formulation of conformal field theory adapted to AdS/CFT correspondence

Light-cone formulation of conformal field theory in space–time of arbitrary dimension is developed. Conformal fundamental and shadow fields with arbitrary conformal dimension and arbitrary spin are studied. Representation of conformal algebra generators on space of conformal fundamental and shadow fields in terms of spin operators which enter in light-cone gauge formulation of field dynamics in AdS space is found. As an example of application of light-cone formalism we discuss AdS/CFT correspondence for massive arbitrary spin AdS fields and corresponding boundary CFT fields at the level of two point function.

Phase transitions of semiflexible hard-sphere chain liquids

We present a density-functional theory for describing liquid-crystalline phase transitions in a fluid of semiflexible hard-sphere chain molecules based on the Onsager second-virial approximation for the free energy. Key ingredients of this theory are the generation of semiflexible chain conformations and calculation of the pair excluded volume and excluded area using a single-chain Monte Carlo enumeration method. First, we investigate the isotropic-nematic phase transition. Next, the theory is extended to account for a smectic-A phase by a bifurcation analysis around the nematic solution. The perturbation is calculated using a lowest-order Fourier series representation.

Permuting input for more effective sampling of 3D conformer space

SMILES strings and other classic 2D structural formats offer a convenient way to represent molecules as a simplistic connection table, with the inherent advantages of ease of handling and storage. In the context of virtual screening, chemical databases to be screened are often initially represented by canonicalised SMILES strings that can be filtered and pre-processed in a number of ways, resulting in molecules that occupy similar regions of chemical space to active compounds of a therapeutic target. A wide variety of software exists to convert molecules into SMILES format, namely, Mol2smi (Daylight Inc.), MOE (Chemical Computing Group) and Babel (Openeye Scientific Software). Depending on the algorithm employed, the atoms of a SMILES string defining a molecule can be ordered differently. Upon conversion to 3D coordinates they result in the production of ostensibly the same molecule. In this work we show how different permutations of a SMILES string can affect conformer generation, affecting reliability and repeatability of the results. Furthermore, we propose a novel procedure for the generation of conformers, taking advantage of the permutation of the input strings--both SMILES and other 2D formats, leading to more effective sampling of conformation space in output, and also implementing fingerprint and principal component analyses step to post process and visualise the results.

Enhancing Specificity and Sensitivity of Pharmacophore-Based Virtual Screening by Incorporating Chemical and Shape Features−A Case Study of HIV Protease Inhibitors

Virtual screening (VS), if applied appropriately, could significantly shorten the hit identification and hit-to-lead processes in drug discovery. Recently, the version of VS that is based upon similarity to a pharmacophore has received increased attention. This is due to two major factors: first, the public availability of the ZINC1 conformational database has provided a large selection pool with high-quality and purchasable small molecules; second, new technology has enabled a more accurate and flexible definition of pharmacophore models coupled with an efficient search speed. The major goal of this study was to achieve improved specificity and sensitivity of pharmacophore-based VS by optimizing the variables used to generate conformations of small molecules and those used to construct pharmacophore models from known inhibitors or from inhibitor-protein complex structures. By using human immunodeficiency virus protease and its inhibitors (PIs) as a case study, the impact of the key variables, including the selection of chemical features, involvement of excluded volumes (EV), the tolerance radius of excluded volumes, energy windows, and the maximum number of conformers in conformation generation, was explored. Protein flexibility was simulated by adjusting the sizes of EV. Our best pharmacophore model, combining both chemical features and excluded volumes, was able to correctly identify 60 out of 75 structurally diverse known PIs, while misclassifying only 5 out of 75 similar compounds that are not inhibitors. To evaluate the specificity of the model, 1193 oral drugs on the market were screened, and 25 original hits were identified, including 5 out of 6 known PI drugs.

Yucca: An Efficient Algorithm for Small-Molecule Docking

In this paper, we present a new algorithm, which is based on an efficient heuristic for local search, for rigid protein-small-molecule docking. We tested our algorithm, called Yucca, on the recent 100-complex benchmark, using the conformer generator OMEGA to generate a set of low-energy conformers. The results showed that Yucca is competitive both in terms of algorithm efficiency and docking accuracy.

Considerations in Compound Database Preparation“Hidden” Impact on Virtual Screening Results

Structure-based virtual screening (SBVS) utilizing docking algorithms has become an essential tool in the drug discovery process, and significant progress has been made in successfully applying the technique to a wide range of receptor targets. In silico validation of virtual screening protocols before application to a receptor target using a corporate or commercially available compound collection is key to establishing a successful process. Ultimately, retrieval of a set of active compounds from a database of inactives is required, and the metric of enrichment (E) is habitually used to discern the quality of separation of the two. Numerous reports have addressed the performance of docking algorithms with regard to the quality of binding mode prediction and the issue of postprocessing "hit lists" of docked ligands. However, the impact of ligand database preprocessing has yet to be examined in the context of virtual screening and prioritization of compounds for biological evaluation. We provide an insight into the implications of cheminformatic preprocessing of a validation database of compounds where multiple protonated, tautomeric, stereochemical, and conformational states have been enumerated. Several commonly used methods for the generation of ligand conformations and conformational ensembles are examined, paired with an exhaustive rigid-body algorithm for the docking of different "multimeric" compound representations to the ligand binding site of the human estrogen receptor alpha. Chemgauss, a shapegaussian scoring function with intrinsic chemical knowledge, was combined with PLP as a consensus-scoring scheme to rank output from the docking protocol and enrichment rates calculated for each screen. The overheads of CPU consumption and the effect on relative database size (disk requirement) for each of the protocols employed are considered. Assessment of these parameters indicates that SBVS enrichments are highly dependent on the initial cheminformatic treatment(s) used in database construction. The interplay of SMILES representations, stereochemical information, protonation state enumeration, and ligand conformation ensembles are critical in achieving optimum enrichment rates in such screening.

Strong Fibers and Films of Microbial Polyesters

Poly[(R)-3-hydroxybutyrate] (P(3HB)) and its copolymers are accumulated by a wide variety of microorganisms as intracellular carbon and energy material, and are extensively studied as biodegradable and biocompatible thermoplastics. However, these microbial polyesters have not been recognized as practical because of their stiffness and brittleness. Recently, by new drawing techniques, we succeeded in obtaining strong fibers and films from microbial polyesters, produced by both wild-type and recombinant bacteria. The improvement in mechanical properties of the fibers and films is due not only to the orientation of molecular chains, but also to the generation of a zigzag conformation and network structure, formed by fibrillar and lamellar crystals. The structure of strong fibers with a tensile strength over 1.0 GPa was analyzed by micro-beam X-ray diffraction with synchrotron radiation. The strong fibers and films were completely degraded in natural, river freshwater or by extracellular polyhydroxybutyrate depolymerases. In this feature article, the processing, mechanical properties, highly ordered structure and biodegradability of strong fibers and films produced from microbial polyesters are presented.

The AGAAAAGA Palindrome in PrP Is Required to Generate a Productive PrPSc-PrPC Complex That Leads to Prion Propagation

The molecular hallmark of prion disease is the conversion of normal prion protein (PrPC) to an insoluble, proteinase K-resistant, pathogenic isoform (PrPSc). Once generated, PrPSc propagates by complexing with, and transferring its pathogenic conformation onto, PrPC. Defining the specific nature of this PrPSc-PrPC interaction is critical to understanding prion genesis. To begin to approach this question, we employed a prion-infected neuroblastoma cell line (ScN2a) combined with a heterologous yeast expression system to independently model PrPSc generation and propagation. We additionally applied fluorescence resonance energy transfer analysis to the latter to specifically study PrP-PrP interactions. In this report we focus on an N-terminal hydrophobic palindrome of PrP (112-AGAAAAGA-119) thought to feature intimately in prion generation via an unclear mechanism. We found that, in contrast to wild type (wt) PrP, PrP lacking the palindrome (PrPDelta112-119) neither converted to PrPSc when expressed in ScN2a cells nor generated proteinase K-resistant PrP when expressed in yeast. Furthermore, PrPDelta112-119 was a dominant-negative inhibitor of wtPrP in ScN2a cells. Both wtPrP and PrPDelta112-119 were highly insoluble when expressed in yeast and produced distinct cytosolic aggregates when expressed as fluorescent fusion proteins (PrP::YFP). Although self-aggregation was evident, fluorescence resonance energy transfer studies in live yeast co-expressing PrPSc-like protein and PrPDelta112-119 indicated altered interaction properties. These results suggest that the palindrome is required, not only for the attainment of the PrPSc conformation but also to facilitate the proper association of PrPSc with PrPC to effect prion propagation.

Exploring 3D-QSAR of thiazole and thiadiazole derivatives as potent and selective human adenosine A3 receptor antagonists+

Binding affinity data [Bioorg Med Chem (2004) 12:613-623] of thiazole and thiadiazole derivatives (n = 30) for the human adenosine A3 receptor subtype have been subjected to 3D-QSAR (Quantitative structure-activity relationships) analyses by molecular shape analysis (MSA) and molecular field analysis (MFA) techniques using Cerius2 Version 4.8. In the case of the MSA, the major steps were (1) generation of conformers and energy minimization; (2) hypothesizing an active conformer (global minimum of the most active compound); (3) selecting a candidate shape-reference compound (based on the active conformation); (4) performing pairwise molecular superimposition using the maximum common subgroup (MCSG) method; (5) measuring molecular shape commonality using MSA descriptors; (6) determining other molecular features by calculating spatial, electronic and conformational parameters; (7) selection of conformers; (8) generation of QSAR equations by genetic function algorithm (GFA) or stepwise regression. The best 3D-QSAR equation (MSA) obtained from GFA technique shows 70.0% predicted variance (leave-one-out) and 77.7% explained variance. This equation shows the importance of Jurs descriptors (atomic charge weighted positive surface area, relative negative charge and relative positive charge surface area), partial moment of inertia, energy of the most stable conformer and the ratio of common overlap steric volume to volume of individual molecules. In the case of stepwise regression, the best relation showed 46.1% predicted variance and 72.3% explained variance. In the case of MFA, the major steps were (1) generating conformers and energy minimization; (2) matching atoms using a maximum common substructure (MCS) search and aligning molecules using the default options; (3) setting MFA preferences (rectangular grid with 2 A step size, charges by the Gasteiger algorithm, H+ and CH3 as probes); (4) creating the field; (5) analysis by the Genetic partial least squares (G/PLS) method. The equation obtained was of excellent statistical quality: 96.1% explained variance and 71.6% predicted variance. Statistically reliable 3D-QSAR models obtained from this study suggest that these techniques could be useful to design potent A3 receptor antagonists.

Alkylcobalt carbonyls. Part XIV. Generation of chiral conformations by centers of chirality in organocobalt complexes

R1OC(O)CH2Co(CO)3PR23 complexes (3), (R1 = S-EtOC(O)CH(CH3), R2 = Ph, a; R1 = (1S,2R,5S)-2-isopropyl-5-methylcyclohexyl, R2 = Ph, b; R1 = (1R,2S,5R)-2-isopropyl-5-methylcyclohexyl, R2 = Ph, c; R1 = isopropyl, R23 = Ph2{(1S,2S,5R)-2-isopropyl-5-methylcyclohexyl}, d) were prepared and characterized by analyses including IR, 1H-, 13C{1H}-, and 31P{1H} NMR spectra as well as by X-ray diffraction structure determination. Principles of self-organization of chiral conformations were deduced from the structural data.Key words: alkylcobalt carbonyls, cooperative phenomena, intramolecular, chirality, conformations.

Comparative Analysis of Protein‐Bound Ligand Conformations with Respect to Catalyst′s Conformational Space Subsampling Algorithms.

We examined the quality of Catalyst's conformational model generation algorithm via a large scale study based on the crystal structures of a sample of 510 pharmaceutically relevant protein−ligand complexes extracted from the Protein Data Bank (PDB). Our results show that the tested algorithms implemented within Catalyst are able to produce high quality conformers, which in most of the cases are well suited for in silico drug research. Catalyst-specific settings were analyzed, such as the method used for the conformational model generation (FAST vs BEST) and the maximum number of generated conformers. By setting these options for higher fitting quality, the average RMS values describing the similarity of experimental and simulated conformers were improved from an RMS of 1.06 with max. 50 FAST generated conformers to an RMS of 0.93 with max. 255 BEST generated conformers, which represents an improvement by 12%. Each method provides best fitting conformers with an RMS value < 1.50 in more than 80% of all cas...

Analysis of the Contribution of Reverse Transcriptase and Integrase Proteins to Retroviral RNA Dimer Conformation

All retroviruses contain two copies of genomic RNA that are linked noncovalently. The dimeric RNA of human immunodeficiency virus type 1 (HIV-1) undergoes rearrangement during virion maturation, whereby the dimeric RNA genome assumes a more stable conformation. Previously, we have shown that the packaging of the HIV-1 polymerase (Pol) proteins reverse transcriptase (RT) and integrase (IN) is essential for the generation of the mature RNA dimer conformation. Analysis of HIV-1 mutants that are defective in processing of Pol showed that these mutant virions contained altered dimeric RNA conformation, indicating that the mature RNA dimer conformation in HIV-1 requires the correct proteolytic processing of Pol. The HIV-1 Pol proteins are multimeric in their mature enzymatically active forms; RT forms a heterodimer, and IN appears to form a homotetramer. Using RT and IN multimerization defective mutants, we have found that dimeric RNA from these mutant virions has the same stability and conformation as wild-type RNA dimers, showing that the mature enzymatically active RT and IN proteins are dispensable for the generation of mature RNA dimer conformation. This also indicated that formation of the mature RNA dimer structure occurs prior to RT or IN maturation. We have also investigated the requirement of Pol for RNA dimerization in both Mason-Pfizer monkey virus (M-PMV) and Moloney murine leukemia virus (MoMuLV) and found that in contrast to HIV-1, Pol is dispensable for RNA dimer maturation in M-PMV and MoMuLV, demonstrating that the requirement of Pol in retroviral RNA dimer maturation is not conserved among all retroviruses.

CONFORMAL GENERATORS AND DOUBLY SPECIAL RELATIVITY THEORIES

In this paper, the relation between the modified Lorenz boosts, proposed in the doubly relativity theories and a linear combination of Conformal Group generators in R1,d-1 is investigated. The introduction of a new generator is proposed in order to deform the Conformal Group to achieve the connection conjectured. The new generator is obtained through a formal dimensional reduction from a free massless particle living in a R2,d space. Due to this treatment it is possible to say that even DSR theories modify light-cone structure in R1,d-1, it could remains, in some cases, untouched in R2,d.

Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms

We examined the quality of Catalyst's conformational model generation algorithm via a large scale study based on the crystal structures of a sample of 510 pharmaceutically relevant protein-ligand complexes extracted from the Protein Data Bank (PDB). Our results show that the tested algorithms implemented within Catalyst are able to produce high quality conformers, which in most of the cases are well suited for in silico drug research. Catalyst-specific settings were analyzed, such as the method used for the conformational model generation (FAST vs BEST) and the maximum number of generated conformers. By setting these options for higher fitting quality, the average RMS values describing the similarity of experimental and simulated conformers were improved from an RMS of 1.06 with max. 50 FAST generated conformers to an RMS of 0.93 with max. 255 BEST generated conformers, which represents an improvement by 12%. Each method provides best fitting conformers with an RMS value<1.50 in more than 80% of all cases. We analyzed the computing time/quality ratio of various conformational model generation settings and examined ligands in high energy conformations. Furthermore, properties of the same ligands in various proteins were investigated, and the fitting qualities of experimental conformations from the PDB and the Cambridge Structural Database (CSD) were compared. One of the most important conclusions of former studies, the fact that bioactive conformers often have energy high above that of global minima, was confirmed.

Targacept Active Conformation Search: A New Method for Predicting the Conformation of a Ligand Bound to Its Protein Target

Targacept active conformation search (TACS) is a novel variation of well-established three-dimensional quantitative structure--activity relationship methodologies that seeks to determine probable conformation(s) of ligands bound to their protein targets. A combination of affinity or activity data and energetically accessible conformational ensembles, each conformer described by three-dimensional (3-D) sensitive descriptors, forms the basis of the TACS data model. Recursive pruning is used to reduce the size of both the conformational ensemble and the descriptor space until the TACS data model contains just enough information to determine probable conformation(s) of ligands bound to their protein targets. The TACS algorithm is comprised of five components: (1) conformational ensemble generation, (2) 3-D sensitive descriptor calculation, (3) ensemble descriptor preprocessing, (4) model generation, and (5) prediction of bound conformation(s). Significantly, this method precludes the need for subjective or objective molecular alignment. We report the application of this technique to five benchmark protein-ligand couples where the conformation of a bound ligand has been previously established using X-ray crystallography: 9-cis-retinoic (1) and 9-trans-retinoic acid (2), both agonists for the retinoic acid receptor gamma, compounds KH1060 (3) and MC1288 (4), which bind to the vitamin D3 receptor, and R04 (5), an inhibitor bound to human rhinovirus 14 thermolysin. The binding conformations predicted by TACS were compared to the crystallographic structures extracted from their respective binding sites using root-mean-squared deviation (rmsd) criteria. Three of the conformations found using TACS were within crystallographic error. 9-cis-Retinoic acid, 9-trans-retinoic acid, and MC1288, when superimposed on their crystallographic structures, gave rmsd values of 0.22, 0.17, and 0.34 A, respectively. The rmsd values for KH1060 (1.54 A) and R04 (1.01 A) were larger but still reasonable.

Development of an Importance Sampling Single Chain Mean Field Theory for Polymer Adsorption onto a Flat Wall

In this work we have introduced an importance sampling methodology in the framework of the single chain mean field theory (SCMF), to describe the adsorption of moderately long polymers onto solid surfaces. Since the method is based on the generation of self-avoiding chain conformations, excluded volume correlations along the chain backbone are maintained, leading to the proper scaling behavior in the properties depending on one-chain statistics, unlike the self-consistent field theories based on ideal (Markovian) chains. The formulation presented is general and is expected to be very useful for future applications. Because of its mean field nature, the methodology does not require large computer capabilities. As an application of the methodology given here, we present novel results on the profiles of the end-monomer distributions for two chain lengths and different bulk concentrations.

The transfer matrix method for lattice proteins—an application with cooperative interactions

The transfer matrix method for generating lattice conformations of proteins is explained and applied to lattice proteins having high-level cooperativity to represent hydrophobic interactions. The main advantage of the method is the extremely efficient attrition-free generation and enumeration of compact conformations. We review the application of the method for the generation and complete, exact enumeration of all conformation for linear and cyclic chains in 2D on the square lattice and in 3D on the cubic lattice. We show for compact conformations that the growth of the chain in a piecewise way, cross-section by cross-section, is much more efficient than the traditional linear chain growth. We discuss an extension of the method by including information about the amino acid sequence. We develop a Zimm–Bragg [J Chem Phys 31 (1959) 476–85]-like theory of hydrophobic cluster formation by using the transfer matrix method. We show that the transfer matrix approach to the generation and averaging over chain conformations can be formulated as an algebraic problem. We show also how the transfer matrix method can be extended to off-lattice proteins.