Computation of 3D queries for ROCS based virtual screens

Rapid overlay of chemical structures (ROCS) is a method that aligns molecules based on shape and/or chemical similarity. It is often used in 3D ligand-based virtual screening. Given a query consisting of a single conformation of an active molecule ROCS can generate highly enriched hit lists. Typically the chosen query conformation is a minimum energy structure. Can better enrichment be obtained using conformations other than the minimum energy structure? To answer this question a methodology has been developed called CORAL (COnformational analysis, Rocs ALignment). For a given set of molecule conformations it computes optimized conformations for ROCS screening. It does so by clustering all conformations of a chosen molecule set using pairwise ROCS combo scores. The best representative conformation is that which has the highest average overlap with the rest of the conformations in the cluster. It is these best representative conformations that are then used for virtual screening. CORAL was tested by performing virtual screening experiments with the 40 DUD (Directory of Useful Decoys) data sets. Both CORAL and minimum energy queries were used. The recognition capability of each query was quantified as the area under the ROC curve (AUC). Results show that the CORAL AUC values are on average larger than the minimum energy AUC values. This demonstrates that one can indeed obtain better ROCS enrichments with conformations other than the minimum energy structure. As a result, CORAL analysis can be a valuable first step in virtual screening workflows using ROCS.     

Semi-rigid analogues of the calcium antagonist verapamil: A molecular modelling study

Summary In this work the rigid-analogue approach has been used to obtain information on the active conformation(s) of the calcium antagonist verapamil. A series of semi-rigid analogues of verapamil were synthesized and their biological activities evaluated on guinea-pig heart and aorta. These molecules were analysed by means of molecular modelling techniques.On the basis of the pharmacological profile and conformational analysis of these compounds, two different models for negative inotropic and negative chronotropic activity are proposed. The two actions seem to be due to conformations of the molecules which differ in the orientation of their phenylethylamino groups.     

Torsion angle preference and energetics of small-molecule ligands bound to proteins

Small organic molecules can assume conformations in the protein-bound state that are significantly different from those in solution. We have analyzed the conformations of 21 common torsion motifs of small molecules extracted from crystal structures of protein-ligand complexes and compared them with their torsion potentials calculated by an ab initio DFT method. We find a good correlation between the potential energy of the torsion motifs and their conformational distribution in the protein-bound state: The most probable conformations of the torsion motifs agree well with the calculated global energy minima, and the lowest torsion-energy state becomes increasingly dominant as the torsion barrier height increases. The torsion motifs can be divided into 3 groups based on torsion barrier heights: high (>4 kcal/mol), medium (2-4 kcal/mol), and low (<2 kcal/mol). The calculated torsion energy profiles are predictive for the most preferred bound conformation for the high and medium barrier groups, the latter group common in druglike molecules. In the high-barrier group of druglike ligands, >95% of conformational torsions occur in the energy region <4 kcal/mol. The conformations of the torsion motifs in the protein-bound state can be modeled by a Boltzmann distribution with a temperature factor much higher than room temperature. This high-temperature factor, derived by fitting the theoretical model to the experimentally observed conformation occurrence of torsions, can be interpreted as the perturbation that proteins inflict on the conformation of the bound ligand. Using this model, it is calculated that the average strain energy of a torsion motif in ligands bound to proteins is approximately 0.6 kcal/mol, a result which can be related to the lower binding efficiency of larger ligands with more rotatable bonds. The above results indicate that torsion potentials play an important role in dictating ligand conformations in both the free and the bound states.     

Conformational sensitivity of polyether macrocycles to electrostatic potential: Partial atomic charges,molecular mechanics,and conformational prediction

Molecular recognition (whether by enzymes, the immune system, or chelating ligands) depends critically on molecular conformation. Molecular mechanics predicts energetically favorable molecular conformations by locating low energy conformations using an empirical fit of molecular potential energy as a function of internal coordinates. Molecular mechanics analysis of 18-crown-6 demonstrates that the nonbonded term (primarily the electrostatic part) is the largest contributor to the conformational energy. Nevertheless, common methods of treating the electrostatic interaction for 18-crown-6 yield inconsistent values for conformational energies partly because partial charges assigned to each atom can change with conformation due to through-space inductive effects which are not considered in most molecular mechanics programs. Similar findings from several other groups are reviewed to support our conclusions. We argue for care and caution in predicting conformational preferences of molecules with two or more highly polar atoms. We also discuss the desirability of using an empirical method of partial charge determination such as the charge equilibration algorithm of Rappé and Goddard (or a suitable generalization which includes polarization) as a method of including these effects in molecular mechanics and molecular dynamics calculations.     

Design, synthesis, and biological evaluation of diminutive forms of (+)-spongistatin 1: lessons learned

The design, synthesis, and biological evaluation of two diminutive forms of (+)-spongistatin 1, in conjunction with the development of a potentially general design strategy to simplify highly flexible macrocyclic molecules while maintaining biological activity, have been achieved. Examination of the solution conformations of (+)-spongistatin 1 revealed a common conformational preference along the western perimeter comprising the ABEF rings. Exploiting the hypothesis that the small-molecule recognition/binding domains are likely to comprise the conformationally less mobile portions of a ligand led to the design of analogues, incorporating tethers (blue) in place of the CD and the ABCD components of the (+)-spongistatin 1 macrolide, such that the conformation of the retained (+)-spongistatin 1 skeleton would mimic the assigned solution conformations of the natural product. The observed nanomolar cytotoxicity and microtubule destabilizing activity of the ABEF analogue provide support for both the assigned solution conformation of (+)-spongistatin 1 and the validity of the design strategy.     

Conformational study of the structure of free 18-crown-6

A conformational search was performed for 18-crown-6 using the CONLEX method at the MM3 level. To have a more accurate energy order of the predicted conformations, the predicted conformations were geometry optimized at the HF/STO-3G level and the 198 lowest energy conformations, according to the HF/STO-3G energy order, were geometry optimized at the HF/6-31+G level. In addition, the 47 nonredundant lowest energy conformations, according to the MP2/6-31+G energy order at the HF/6-31+G optimized geometry, hereafter the MP2/6-31+G//HF/6-31+G energy order, were geometry optimized at the B3LYP/6-31+G level. According to the MP2/6-31+G//B3LYP/6-31+G energy order, three conformations had energies lower than the experimentally known Ci conformation of 18c6. At the MP2/6-31+G//B3LYP/6-31+G level, the S6 lowest energy conformation is more stable by 1.96 kcal/mol than this Ci conformation. This was confirmed by results at the MP2/6-31+G level with an energy difference of 1.84 kcal/mol. Comparison between the structure of the S6 conformation of 18c6 and the S4 lowest energy conformation of 12-crown-4, as well as other important conformations of both molecules, is made. It is concluded that the correlation energy is necessary to have an accurate energy order of the predicted conformations. A rationalization of the conformational energy order in terms of the hydrogen bonding and conformational dihedral angles is given. It is also suggested that to have a better energy order of the predicted conformations at the MM3 level, better empirical force fields corresponding to the hydrogen bond interactions are needed.     

Interplay among folding, sequence, and lipophilicity in the antibacterial and hemolytic activities of alpha/beta-peptides

Host-defense peptides inhibit bacterial growth but manifest relatively little toxicity toward eukaryotic cells. Many host-defense peptides adopt alpha-helical conformations in which cationic side chains and lipophilic side chains are segregated to distinct regions of the molecular surface ("globally amphiphilic helices"). Several efforts have been made to develop unnatural oligomers that mimic the selective antibacterial activity of host-defense peptides; these efforts have focused on the creation of molecules that are globally amphiphilic in the preferred conformation. One such endeavor, from our laboratories, focused on helix-forming alpha/beta-peptides, i.e., oligomers containing a 1:1 pattern of alpha- and beta-amino acid residues in the backbone [Schmitt, M. A.; Weisblum, B.; Gellman, S. H. J. Am. Chem. Soc. 2004, 126, 6848-6849]. We found, unexpectedly, that the most favorable biological activity profile was displayed by a "scrambled" sequence, which was designed not to be able to form a globally amphiphilic helix. Here we report new data, involving an expanded set of alpha/beta-peptides, from experiments designed to elucidate the origins of this surprising result. In addition, we evaluate the susceptibility of alpha/beta-peptides to proteolytic degradation. Our results support the hypothesis that the ability to adopt a globally amphiphilic helical conformation is not a prerequisite for selective antibacterial activity. This conclusion represents a significant advance in our understanding of the relationship among molecular composition, conformation, and biological activity. Our results should therefore influence the design of other unnatural oligomers intended to function as antibacterial agents.     

Conformational Analysis of Planar Enol Rotamers of 2,4-Pentanedione: an Ab Initio Study

All conformations among different planar enol conformers (rotamers) of 2,4-pentanedione were studied by means of the Hartree-Fock method using the STO-3G** basis set. The calculations were carried out with the Gaussian-98 program. For each conformation, stationary points with the highest energy on the energy curve were found graphically. Several conformations have low energy barriers and correspond to rotations around single bonds. They describe the spatial motion of only one (in most cases, hydrogen) atom or a small molecular fragment. All low energy barriers are in the interval 13-59 kJ·mol^-1. As would be expected, the lowest energy barrier is exhibited by the conformation that leads to the formation of an enol rotamer having an intramolecular H-bond (so-called -shaped form). On the other hand, conformations in which rotation around a bond leads to a break of the intramolecular hydrogen bond have the highest energy barriers. Conformations in which rotation occurs around the double bond have high energy barriers. The influence of the solvents CHCl₃ and CH₃CN on the intramolecular H-bond has also been studied by means of IPCM at the HF/6-31G** level.     

On the implications of the structure of 3′-azido-3′-deoxythymidine and related compounds to antiviral activity

We report structure–activity relation studies on 3′-azido-3′-deoxythymidine (AZT) and the implications to the biological activity of this class of compounds. The adiabatic potential surface (APS ) of the title compound has been examined with the LCAO –MO –SCF method within the AMI approximation. This study has shown at least 13 minima, all separated by small energy differences and barriers. We have found that the equilibrium favors the anti,gg conformations, in variance to previous studies that predicted the syn,gg conformers to be the most stable forms. The most stable conformation (A) is favored by about 0.5 kcal/mol. However, calculations simulating a bulk-water environment suggest that the three lowest energy conformations (A, B, and C) become almost degenerate in solution. We suggest that the crystallographic conformation (L), characterized by a high dipole moment, and analogous to C, undergoes a strong stabilization upon rotation of the 3′-azido group and that these two conformers, C and L, are the only ones in which the hydroxyl proton is free of steric hindrance. This last point has some relevance from the biological point of view since it is generally accepted that this site must be phosphorylated in order for AZT to achieve its therapeutic effects. The above results suggest that, once in solution, conformer L isomerizes to C, which is the bioactive form of AZT. © 1992 John Wiley & Sons, Inc.     

Conformational energy downward driver (CEDD): Characterization and calibration of the method

Summary A method has been developed that allows one to drive a molecule to conformations of lowest energy given the starting conformation, the identity of the rotatable bonds and the step size. This method has proved useful in our hands in the drug design arena where it is frequently more important to get low-energy conformers of a molecule that match some other (e.g. pharmacophoric or enzyme pocket) requirements than to exhaustively enumerate all possible low-energy conformations for each of the molecules to be studied. The method has been shown to work in the test cases studied to date. Furthermore, so far it has been shown to be sufficiently fast to be used for molecules containing up to 70 rotatable bonds.     

The "nearest single neighbor" method-finding families of conformations within a sample

A simple method for self-organization of conformation samples into families is presented. According to this method, any large sample of molecular conformations may be reorganized according to the nearest single root-mean-square displacement (rmsd) neighbor, starting at any chosen "seed" conformation. Following such reordering, conformational families may be determined by a novel process that maximizes family sizes while minimizing family mixing. This process eliminates much of the arbitrariness that was inherent in most of the related methods of conformation clustering. We demonstrate the construction of rmsd matrices and discuss the convergence criteria for the sample size as well as criteria for determining the cutoff value for the definition of families in each sample. The method is invariant to changes of the "seed" conformation. After applying this method, families of conformations may be more easily recognized in graphic matrices. The method has been applied to the analysis of the conformational space of two cyclic peptides. It is also shown that the "organized" conformational space, at least in those specific examples, has an energy topology that reminds of energy basins. The method is general and applicable to molecules of any type.     

Powerful simulated-annealing algorithm locates global minimum of protein-folding potentials from multiple starting conformations

Protein-folding potentials, designed with the explicit goal that the global energy minimum correspond to crystallographically observed conformations of protein molecules, may offer great promise toward calculating native protein structures. Achieving this promise, however, depends on finding an effective means of dealing with the multiple-minimum problem inherent in such potentials. In this study, a protein-folding-potential test system has been developed that exhibits the properties of general protein-folding potentials yet has a unique well-defined global energy minimum corresponding to the crystallographically determined conformation of the test molecule. A simulated-annealing algorithm is developed that locates the global minimum of this potential in four of eight test runs from random starting conformations. Exploration of the energy-conformation surface of the potential indicates that it contains the numerous local minima typical of protein-folding potentials and that the global minimum is not easily located by conventional minimization procedures. When the annealing algorithm is applied to a previously developed actual folding potential to analyze the conformation of avian pancreatic polypeptide, a new conformer is located that is lower in energy than any conformer located in previous studies using a variety of minimization techniques.     

The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

One of the main challenges for protein redesign is the efficient evaluation of a combinatorial number of candidate structures. The modeling of protein flexibility, typically by using a rotamer library of commonly-observed low-energy side-chain conformations, further increases the complexity of the redesign problem. A dominant algorithm for protein redesign is dead-end elimination (DEE), which prunes the majority of candidate conformations by eliminating rigid rotamers that provably are not part of the global minimum energy conformation (GMEC). The identified GMEC consists of rigid rotamers (i.e., rotamers that have not been energy-minimized) and is thus referred to as the rigid-GMEC. As a postprocessing step, the conformations that survive DEE may be energy-minimized. When energy minimization is performed after pruning with DEE, the combined protein design process becomes heuristic, and is no longer provably accurate: a conformation that is pruned using rigid-rotamer energies may subsequently minimize to a lower energy than the rigid-GMEC. That is, the rigid-GMEC and the conformation with the lowest energy among all energy-minimized conformations (the minimized-GMEC) are likely to be different. While the traditional DEE algorithm succeeds in not pruning rotamers that are part of the rigid-GMEC, it makes no guarantees regarding the identification of the minimized-GMEC. In this paper we derive a novel, provable, and efficient DEE-like algorithm, called minimized-DEE (MinDEE), that guarantees that rotamers belonging to the minimized-GMEC will not be pruned, while still pruning a combinatorial number of conformations. We show that MinDEE is useful not only in identifying the minimized-GMEC, but also as a filter in an ensemble-based scoring and search algorithm for protein redesign that exploits energy-minimized conformations. We compare our results both to our previous computational predictions of protein designs and to biological activity assays of predicted protein mutants. Our provable and efficient minimized-DEE algorithm is applicable in protein redesign, protein-ligand binding prediction, and computer-aided drug design.     

Are isolated nucleic acid bases really planar? A Car-Parrinello molecular dynamics study

Car-Parrinello molecular dynamics simulations of the flexibility of isolated DNA bases have been carried out. The comparison of lowest ring out-of-plane vibrations calculated by using MP2/cc-pvdz and BLYP/PW methods reveals that the DFT method with the plane wave basis set reasonably reproduces out-of-plane deformability of the pyrimidine ring in nucleic acid bases and could be used for reliable modeling of conformational flexibility of nucleobases. The conformational phase space of pyrimidine rings in thymine, cytosine, guanine, and adenine has been investigated by using the ab initio Car-Parrinello molecular dynamics method. It is demonstrated that all nucleic acid bases are highly flexible molecules and possess a nonplanar effective conformation of the pyrimidine ring despite the fact that the planar geometry corresponds to a minimum on the potential energy surface. The population of the planar geometry of the pyrimidine ring does not exceed 30%. Among the nonplanar conformations of the pyrimidine rings, the boat-like and half-chair conformations are the most populated.     

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.     

Systematic drug receptor mapping: A new approach to the analysis of conformational energy calculations of flexible molecules with application to dopaminergic and adrenergic agonists

The computer program PRODIS is used to find low energy conformations of flexible molecules by searching the potential energy surface(s) of one or more torsion angles via rigid rotation. The n-dimensional grid of energy versus torsion angles is then converted to a Boltzman probability distribution, with the probability being represented not as a function of torsion angle, but rather a distance between two atoms. These atoms are chosen by comparison with a known, active analogue in which certain atoms have previously been determined as requirements for drug activity. PRODIS produces a list of low energy conformations, their corresponding interatomic distances and the Boltzman probability for each distance ±0.125, as well as the total probability for each conformation. The user also specifies a target interatomic distance and range (usually derived from a more rigid analogue) for which PRODIS lists all conformations and their Boltzman probability that meet this distance.     

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

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

Conformational preferences in alkylbenzenes and aryl-alkylamines: A comparative study using CAMSEQ,MM2 and molecular dynamics methods

Conformational preferences in a series of alkylbenzenes and protonated and neutral aryl-alkylamines of biological interest have been examined. First, a general picture was obtained for the 25 compounds in the series by means of the CAMSEQ empirical potential software system. This provided solution as well as vacuum data. A low-energy “folded” conformation (alkyl chain coiled toward aromatic ring) was observed in every case. The presence of an amino nitrogen atom in the alkyl chain did not significantly influence conformational preference. Secondly, a group of 14 compounds, representative of the subgroupings within the main series, was selected and the previously established (CAMSEQ) folded and extended minimum positions were further examined by means of a modified MM2 program. Energy differences between conformers were also calculated, and the presence of a stable folded form was confirmed. A feature common to many of the folded conformations is the positioning over the ring of a hydrogen atom from the terminal group of the chain. The MM2 folded/extended energy differences were in some cases smaller than those determined by CAMSEQ, with the “extended” form in many cases being about 1 or 2 kcal/mol more stable. Thirdly, three representative compounds from the series were examined by means of a molecular dynamics program which permitted the sampling of conformational space throughout the transition from extended to folded forms. This method gave energy differences between folded and extended conformations which agreed with the corresponding MM2 differences.