ELECT++: Faster conformational search method for docking flexible molecules using molecular similarity

We have developed a program, ELECT++ (Effective LEssening of Conformations by Template molecules in C++), to speed up the conformational search for small flexible molecules using the similar property principle. We apply this principle to molecular shape and, importantly, to molecular flexibility. After molecules in a database are clustered according to flexibility and shape (FCLUST++), additional reagents are generated to screen the conformational space of molecules in each cluster (TEMPLATE++). We call these representative reagents of each cluster template reagents. Template reagents and clustered reagents produce, after reaction, template molecules and clustered molecules, respectively (tREACT++). The conformations of a template molecule are searched in the context of a macromolecular target. Acceptable conformational choices are then applied to all molecules in its cluster, thus effectively biasing conformational space to speed up conformational searches (tSEARCH++). In our incremental search method, it is necessary to calculate the root-mean-square deviations (RMSD) matrix of distances between different conformations of the same molecule to reduce the number of conformations. Instead of calculating the RMSD matrix for all molecules in a cluster, the RMSD matrix of a template molecule is chosen as a reference and applied to all the molecules in its cluster. We demonstrate that FCLUST++ clusters the primary amine reagents from the Available Chemicals Directory (ACD) successfully. The program tSEARCH++ was applied to dihydrofolate reductase with virtual molecules generated by tREACT++ using clustered primary amine reagents. The conformational search by the program tSEARCH++ was about 4.8 times faster than by SEARCH++, with an acceptable range of errors. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1834–1852, 1998     

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.     

Solution- and bound-state conformational study of N,N',N"-triacetyl chitotriose and other analogous potential inhibitors of hevamine: application of trNOESY and STD NMR spectroscopy

The solution-state conformations of N,N',N"-triacetyl chitotriose (1) and other potential chitinase inhibitors 2-4 were studied using a combination of NMR spectroscopy (NOESY) and molecular mechanics calculations. Determination solely of the global energy minimum conformation was found to be insufficient for an agreement with the NMR results. An appropriate consistency between the NMR experimental data and theoretical calculations was only reached by assessing the structures as population-weighted average conformers based on Boltzmann distributions derived from the calculated relative energies. Analogies, but also particular differences, between the synthetic compounds 2-4 and the naturally-occurring N,N',N"-triacetyl chitotriose were found. Furthermore, the conformation of compounds 1 and 2 when bound to hevamine was also studied using transferred NOESY experiments and the binding process was found to impart a level of conformational restriction on the ligands. The preferred conformation as determined for 1 in the bound state to hevamine belonged to one of the conformational families found for the compound when free in solution, although full characterisation of the bound-state conformations was impeded due to severe signal overlap. Saturation transfer difference NMR experiments were also employed to analyse the binding epitopes of the bound compounds. We thus determined that it is mainly the acetyl amido groups of the trisaccharide and the heterocyclic moiety which are in close contact with hevamine.     

Comparison of conformer distributions in the crystalline state with conformational energies calculated by ab initio techniques

Summary The conformational preferences of 12 molecular substructures in the crystalline state have been determined and compared with those predicted for relevant model compounds by ab initio molecular orbital calculations. Least-squares regression shows that there is a statistically significant correlation between the crystal-structure conformer distributions and the calculated potential-energy differences, even though the calculations relate to a gas-phase environment. Torsion angles associated with high strain energy (>1 kcal mol^-1) appear to be very unusual in crystal structures and, in general, high-energy conformers are underrepresented in crystal structures compared with a gas-phase, room-temperature Boltzmann distribution. It is concluded that crystal packing effects rarely have a strong systematic effect on molecular conformations. Therefore, the conformational distribution of a molecular substructure in a series of related crystal structures is likely to be a good guide to the corresponding gas-phase potential energy surface.     

Molecular mechanics conformational analysis of tylosin

The conformations of the 16-membered macrolide antibiotic tylosin were studied with molecular mechanics (AMBER* force field) including modelling of the effect of the solvent on the conformational preferences (GB/SA). A Monte Carlo conformational search procedure was used for finding the most probable low-energy conformations. The present study provides complementary data to recently reported analysis of the conformations of tylosin based on NMR techniques. A search for the low-energy conformations of protynolide, a 16-membered lactone containing the same aglycone as tylosin, was also carried out, and the results were compared with the observed conformation in the crystal as well as with the most probable conformations of the macrocyclic ring of tylosin. The dependence of the results on force field was also studied by utilizing the MM3 force field. Some particular conformations were computed with the semiempirical molecular orbital methods AM1 and PM3.     

Non-natural amino acids as modulating agents of the conformational space of model glycopeptides

The synthesis and conformational analysis in aqueous solution of different alpha-methyl-alpha-amino acid diamides, derived from serine, threonine, beta-hydroxycyclobutane-alpha-amino acids, and their corresponding model beta-O-glucopeptides, are reported. The study reveals that the presence of an alpha-methyl group forces the model peptides to adopt helix-like conformations. These folded conformations are especially significant for cyclobutane derivatives. Interestingly, this feature was also observed in the corresponding model glucopeptides, thus indicating that the alpha-methyl group and not the beta-O-glucosylation process largely determines the conformational preference of the backbone in these structures. On the other hand, atypical conformations of the glycosidic linkage were experimentally determined. Therefore, when a methyl group was located at the Cbeta atom with an R configuration, the glycosidic linkage was rather rigid. Nevertheless, when the S configuration was displayed, a significant degree of flexibility was observed for the glycosidic linkage, thus showing both alternate and eclipsed conformations of the psi(s) dihedral angle. In addition, some derivatives exhibited an unusual value for the phi(s) angle, which was far from a value of -60 degrees expected for a conventional beta-O-glycosidic linkage. In this sense, the different conformations exhibited by these molecules could be a useful tool in obtaining systems with conformational preferences "à la carte".     

Multistep conformational interconversion mechanism of cyclododecane. A simple and fast analysis using potential energy curves

An ab initio and Density Functional Theory (DFT) study of the conformational properties of cyclododecane was carried out. The energetically preferred equilibrium structures, their relative stability, and some of the transition state (TS) structures involved in the conformational interconversion pathways were analyzed from RHF/6‐31G(d), B3LYP/6‐31G(d,p) and B3LYP/6311++G(d,p) calculations. Aug‐cc‐pVDZ//B3LYP/6311++G(d,p) single point calculations predict that the multistep conformational interconversion mechanism requires 11.07 kcal/mol, which is in agreement with the available experimental data. These results allow us to form a concise idea about the internal intricacies of the preferred forms of cyclododecane, describing the conformations as well as the conformational interconversion processes in the conformational potential energy hypersurface. Our results indicated that performing an exhaustive analysis of the potential energy curves connecting the most representative conformations is a valid alternate tool to determine the principal conformational interconversion paths for cyclododecane. This methodology represents a satisfactory first approximation for the conformational analysis of medium‐ and large‐size flexible cyclic compounds. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition

Quantifying the density of conformations over phase space (the conformational distribution) is needed to model important macromolecular processes such as protein folding. In this work, we quantify the conformational distribution for a simple polypeptide (N-mer polyalanine) using the cumulative distribution function (CDF), which gives the probability that two randomly selected conformations are separated by less than a "conformational" distance and whose inverse gives conformation counts as a function of conformational radius. An important finding is that the conformation counts obtained by the CDF inverse depend critically on the assignment of a conformation's distance span and the ensemble (e.g., unfolded state model): varying ensemble and conformation definition (1 --> 2 A) varies the CDF-based conformation counts for Ala(50) from 10(11) to 10(69). In particular, relatively short molecular dynamics (MD) relaxation of Ala(50)'s random-walk ensemble reduces the number of conformers from 10(55) to 10(14) (using a 1 A root-mean-square-deviation radius conformation definition) pointing to potential disconnections in comparing the results from simplified models of unfolded proteins with those from all-atom MD simulations. Explicit waters are found to roughen the landscape considerably. Under some common conformation definitions, the results herein provide (i) an upper limit to the number of accessible conformations that compose unfolded states of proteins, (ii) the optimal clustering radius/conformation radius for counting conformations for a given energy and solvent model, (iii) a means of comparing various studies, and (iv) an assessment of the applicability of random search in protein folding.     

Frozen-solution conformational analysis by REDOR spectroscopy

Frozen-solution conformational analysis (FrSCA) can be performed on organic compounds using REDOR spectroscopy. REDOR measurements on frozen aqueous solutions of 13C-methyl beta-15N-aminoglucoside indicate a bimodal distribution of conformations in a 68:32 ratio, with 13C-15N distances of 4.31 and 3.55 A, respectively. The high resolution and straightforward sample preparation make FrSCA an attractive alternative to solution-based NMR methods of conformational analysis.     

Kinetics of cooperative protein folding involving two separate conformational families

The master equation that describes the kinetics of protein folding is solved numerically for a portion of Staphylococcal Protein A by a Laplace transformation. The calculations are carried out with 50 local-minimum conformations belonging to two conformational families. The master equation allows for transitions among all the 50 conformations in the evolution toward the final folded equilibrium distribution of conformations. It is concluded that the native protein folds in a fast cooperative process. The global energy minimum of a native protein can be reached after a sufficiently long folding time regardless of the initial state and the existence of a large number of local energy minima. Conformations representing non-native states of the protein can transform to the native state even if they do not belong to the native conformational family. Given a starting conformation, the protein molecule can fold to its final conformation through different paths. Finally, when the folding reaches the equilibrium distribution, the protein molecule adopts a set of conformations in which the global minimum has the largest average probability.     

Systematic evaluation of the conformational properties of aliphatic omega-methoxy methyl esters

[structure: see text] A systematic conformational study of omega-methoxy methyl esters, CH(3)O-(CH2)n-COO-CH3 with n = 3 and 4, has been performed using quantum mechanical calculations at the MP2 level. Calculations have been carried out in both gas phase and chloroform solution, a polarizable continuum solvation model being used to represent the latter. Results have been compared with those recently obtained for the analogues omega-hydroxy acids, HO-(CH2)n-COOH with n = 3 and 4. The compounds with n = 3 clearly favor coiled conformations, the population expected for extended and semiextended conformations being very low. However, for compounds with n = 4 the minimum energy extended and semiextended structures become considerably more stable. The overall results indicate that the conformational preferences of the central aliphatic segment of omega-methoxy methyl esters and omega-hydroxy acids are not influenced by the formation of intramolecular O-H...O hydrogen bonds.     

Validated ligand mapping of ACE active site

Crystal structures of angiotensin-converting enzyme (ACE) complexed with three inhibitors (lisinopril, captopril, enalapril) provided experimental data for testing the validity of a prior active site model predicting the bound conformation of the inhibitors. The ACE active site model - predicted over 18 years ago using a series of potent ACE inhibitors of diverse chemical structure - was recreated using published data and commercial software. Comparison between the predicted structures of the three inhibitors bound to the active site of ACE and those determined experimentally yielded root mean square deviation (RMSD) values of 0.43-0.81 A, among the distances defining the active site map. The bound conformations of the chemically relevant atoms were accurately deduced from the geometry of ligands, applying the assumption that the geometry of the active site groups responsible for binding and catalysis of amide hydrolysis was constrained. The mapping of bound inhibitors at the ACE active site was validated for known experimental compounds, so that the constrained conformational search methodology may be applied with confidence when no experimentally determined structure of the enzyme yet exists, but potent, diverse inhibitors are available.     

UV resonance Raman measurements of poly-L-lysine's conformational energy landscapes: dependence on perchlorate concentration and temperature

UV resonance Raman spectroscopy has been used to determine the conformational energy landscape of poly-L-lysine (PLL) in the presence of NaClO4 as a function of temperature. At 1 degree C, in the presence of 0.83 M NaClO4, PLL shows an approximately 86% alpha-helix-like content, which contains alpha-helix and pi-bulge/helix conformations. The high alpha-helix-like content of PLL occurs because of charge screening due to strong ion-pair formation between ClO4- and the lysine side chain -NH3+. As the temperature increases from 1 to 60 degrees C, the alpha-helix and pi-bulge/helix conformations melt into extended conformations (PPII and 2.51-helix). We calculate the Psi Ramachandran angle distribution of the PLL peptide bonds from the UV Raman spectra which allows us to calculate the PLL (un)folding energy landscapes along the Psi reaction coordinate. We observe a basin in the Psi angle conformational space associated with alpha-helix and pi-bulge/helix conformations and another basin for the extended PPII and 2.51-helical conformations.     

A robust force field based method for calculating conformational energies of charged drug-like molecules

The binding affinity of a drug-like molecule depends among other things on the availability of the bioactive conformation. If the bioactive conformation has a significantly higher energy than the global minimum energy conformation, then the molecule is unlikely to bind to its target. Determination of the global minimum energy conformation and calculation of conformational penalties of binding is a prerequisite for prediction of reliable binding affinities. Here, we present a simple and computationally efficient procedure to estimate the global energy minimum for a wide variety of structurally diverse molecules, including polar and charged compounds. Identifying global energy minimum conformations of such compounds with force field methods is problematic due to the exaggeration of intramolecular electrostatic interactions. We demonstrate that the global energy minimum conformations of zwitterionic compounds generated by conformational analysis with modified electrostatics are good approximations of the conformational distributions predicted by experimental data and with molecular dynamics performed in explicit solvent. Finally the method is used to calculate conformational penalties for zwitterionic GluA2 agonists and to filter false positives from a docking study.     

Application of self-organizing maps in conformational analysis of lipids.

The characteristics of lipid assemblies are important for the functions of biological membranes. This has led to an increasing utilization of molecular dynamics simulations for the elucidation of the structural features of biomembranes. We have applied the self-organizing map (SOM) to the analysis of the complex conformational data from a 1-ns molecular dynamics simulation of PLPC phospholipids in a membrane assembly. Mapping of 1.44 million molecular conformations to a two-dimensional array of neurons revealed, without human intervention, the main conformational features in hours. Both the whole molecule and the characteristics of the unsaturated fatty acid chains were analyzed. All major structural features were easily distinguished, such as the orientational variability of the headgroup, the mainly trans state dihedral angles of the sn-1 chain, and both straight and bent conformations of the unsaturated sn-2 chain. Furthermore, presentation of the trajectory of an individual lipid molecule on the map provides information on conformational dynamics. The present results suggest that the SOM method provides a powerful tool for routinely gaining rapid insight to the main molecular conformations as well as to the conformational dynamics of any simulated molecular assembly without the requirement of a priori knowledge.     

Conformational and docking studies of acyl homoserine lactones as a robust method to investigate bioactive conformations

A method aiming at investigating possible bioactive conformations of acyl homoserine lactone (AHL) quorum sensing (QS) modulators is established. The method relies on the exhaustive conformational analysis of AHLs by varying torsion angles around the amide group then on the selection of the closest conformation to those known from co-crystallized XRD data of AHL-receptor complexes. These latter are then docked as rigid ligand within the receptor binding site, leading to interactions with binding site residues which are highly consistent as compared with the data arising from XRD studies. The method is first validated using AHLs for which XRD data of their complexes with their cognate receptor are available, then extended to examples for which the binding mode is still unknown.Three compounds were used to validate the method: hexanoyl homoserine lactone (HHL) as an example of autoinducer, 3-oxo-butanoyl homoserine lactone (OBHL), as a representative model of 3-oxo-AHLs, and 4-(4-chlorophenoxy)butanoyl homoserine lactone (CPOBHL) as an example of a QS inhibitor. The conformational analysis of these three compounds to their cognate protein (TraR, SdiA, LasR and CviR) provides the data which enable the next rigid docking step. Further rigid docking of the closest conformations compared to the known bioactive ones within the binding sites allows to recover the expected binding mode with high precision (atomic RMSD < 2 Å). This “conformational analysis/torsion angle filter/rigid ligand docking” method was then used for investigating three non-natural AHL-type QS inhibitors without known co-crystallized XRD structures, namely was 2-hexenoyl homoserine lactone (HenHL), 3-oxo-4-phenylbutanoyl homoserine lactone (OPBHL) and 3-(4-bromophenyl)propanoyl homoserine lactone (BPPHL). Results provide insights into their possible binding mode by identifying specific interactions with some key residues within the receptor binding site, allowing discussion of their biological activity.     

The NMR spectra and conformations of dihydropyran derivatives—II: The conformational energies of carbomethoxy,hydroxymethyl and acetoxymethyl groups at c-6 of the 5,6-dihydro-α-pyran ring

The sum of coupling constants of proton H-6 for conformations H1 and 1H of the 6-substituted 5,6-dihydro-α-pyran derivatives have been determined with the aid of appropriate, conformationally biased compounds. With the use of these values and the PMR spectra of the title compounds, thermodynamic values of their conformational equilibria and the conformational preferences of the carbomethoxy, hydroxymethyl and acetoxymethyl groups, have been evaluated.     

Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations

This article presents a comparative analysis of two replica‐exchange simulation methods for the structure refinement of protein loop conformations, starting from low‐resolution predictions. The methods are self‐guided Langevin dynamics (SGLD) and molecular dynamics (MD) with a Nosé–Hoover thermostat. We investigated a small dataset of 8‐ and 12‐residue loops, with the shorter loops placed initially from a coarse‐grained lattice model and the longer loops from an enumeration assembly method (the Loopy program). The CHARMM22 + CMAP force field with a generalized Born implicit solvent model (molecular‐surface parameterized GBSW2) was used to explore conformational space. We also assessed two empirical scoring methods to detect nativelike conformations from decoys: the all‐atom distance‐scaled ideal‐gas reference state (DFIRE‐AA) statistical potential and the Rosetta energy function. Among the eight‐residue loop targets, SGLD out performed MD in all cases, with a median of 0.48 Å reduction in global root‐mean‐square deviation (RMSD) of the loop backbone coordinates from the native structure. Among the more challenging 12‐residue loop targets, SGLD improved the prediction accuracy over MD by a median of 1.31 Å, representing a substantial improvement. The overall median RMSD for SGLD simulations of 12‐residue loops was 0.91 Å, yielding refinement of a median 2.70 Å from initial loop placement. Results from DFIRE‐AA and the Rosetta model applied to rescoring conformations failed to improve the overall detection calculated from the CHARMM force field. We illustrate the advantage of SGLD over the MD simulation model by presenting potential‐energy landscapes for several loop predictions. Our results demonstrate that SGLD significantly outperforms traditional MD in the generation and populating of nativelike loop conformations and that the CHARMM force field performs comparably to other empirical force fields in identifying these conformations from the resulting ensembles. Published 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

LigDockCSA: protein-ligand docking using conformational space annealing

Protein–ligand docking techniques are one of the essential tools for structure‐based drug design. Two major components of a successful docking program are an efficient search method and an accurate scoring function. In this work, a new docking method called LigDockCSA is developed by using a powerful global optimization technique, conformational space annealing (CSA), and a scoring function that combines the AutoDock energy and the piecewise linear potential (PLP) torsion energy. It is shown that the CSA search method can find lower energy binding poses than the Lamarckian genetic algorithm of AutoDock. However, lower‐energy solutions CSA produced with the AutoDock energy were often less native‐like. The loophole in the AutoDock energy was fixed by adding a torsional energy term, and the CSA search on the refined energy function is shown to improve the docking performance. The performance of LigDockCSA was tested on the Astex diverse set which consists of 85 protein–ligand complexes. LigDockCSA finds the best scoring poses within 2 Å root‐mean‐square deviation (RMSD) from the native structures for 84.7% of the test cases, compared to 81.7% for AutoDock and 80.5% for GOLD. The results improve further to 89.4% by incorporating the conformational entropy. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011