Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble

Representing the 3D structures of ligands in virtual screenings via multi-conformer ensembles can be computationally intensive, especially for compounds with a large number of rotatable bonds. Thus, reducing the size of multi-conformer databases and the number of query conformers, while simultaneously reproducing the bioactive conformer with good accuracy, is of crucial interest. While clustering and RMSD filtering methods are employed in existing conformer generators, the novelty of this work is the inclusion of a clustering scheme (NMRCLUST) that does not require a user-defined cut-off value. This algorithm simultaneously optimizes the number and the average spread of the clusters. Here we describe and test four inter-dependent approaches for selecting computer-generated conformers, namely: OMEGA, NMRCLUST, RMS filtering and averaged-RMS filtering. The bioactive conformations of 65 selected ligands were extracted from the corresponding protein:ligand complexes from the Protein Data Bank, including eight ligands that adopted dissimilar bound conformations within different receptors. We show that NMRCLUST can be employed to further filter OMEGA-generated conformers while maintaining biological relevance of the ensemble. It was observed that NMRCLUST (containing on average 10 times fewer conformers per compound) performed nearly as well as OMEGA, and both outperformed RMS filtering and averaged-RMS filtering in terms of identifying the bioactive conformations with excellent and good matches (0.5 < RMSD < 1.0 Å). Furthermore, we propose thresholds for OMEGA root-mean square filtering depending on the number of rotors in a compound: 0.8, 1.0 and 1.4 for structures with low (1–4), medium (5–9) and high (10–15) numbers of rotatable bonds, respectively. The protocol employed is general and can be applied to reduce the number of conformers in multi-conformer compound collections and alleviate the complexity of downstream data processing in virtual screening experiments.     

Novel inhibitor discovery through virtual screening against multiple protein conformations generated via ligand-directed modeling: a maternal embryonic leucine zipper kinase example

Kinase targets have been demonstrated to undergo major conformational reorganization upon ligand binding. Such protein conformational plasticity remains a significant challenge in structure-based virtual screening methodology and may be approximated by screening against an ensemble of diverse protein conformations. Maternal embryonic leucine zipper kinase (MELK), a member of serine-threonine kinase family, has been recently found to be involved in the tumerogenic state of glioblastoma, breast, ovarian, and colon cancers. We therefore modeled several conformers of MELK utilizing the available chemogenomic and crystallographic data of homologous kinases. We carried out docking pose prediction and virtual screening enrichment studies with these conformers. The performances of the ensembles were evaluated by their ability to reproduce known inhibitor bioactive conformations and to efficiently recover known active compounds early in the virtual screen when seeded with decoy sets. A few of the individual MELK conformers performed satisfactorily in reproducing the native protein-ligand pharmacophoric interactions up to 50% of the cases. By selecting an ensemble of a few representative conformational states, most of the known inhibitor binding poses could be rationalized. For example, a four conformer ensemble is able to recover 95% of the studied actives, especially with imperfect scoring function(s). The virtual screening enrichment varied considerably among different MELK conformers. Enrichment appears to improve by selection of a proper protein conformation. For example, several holo and unliganded active conformations are better to accommodate diverse chemotypes than ATP-bound conformer. These results prove that using an ensemble of diverse conformations could give a better performance. Applying this approach, we were able to screen a commercially available library of half a million compounds against three conformers to discover three novel inhibitors of MELK, one from each template. Among the three compounds validated via experimental enzyme inhibition assays, one is relatively potent (15; K(d) = 0.37 μM), one moderately active (12; K(d) = 3.2 μM), and one weak but very selective (9; K(d) = 18 μM). These novel hits may be utilized to assist in the development of small molecule therapeutic agents useful in diseases caused by deregulated MELK, and perhaps more importantly, the approach demonstrates the advantages of choosing an appropriate ensemble of a few conformers in pursuing compound potency, selectivity, and novel chemotypes over using single target conformation for structure-based drug design in general.     

Relationship among ligand conformations in solution, in the solid state, and at the Hsp90 binding site: geldanamycin and radicicol

The unknown effects of a receptor's environment on a ligand's conformation presents a difficult challenge in predicting feasible bioactive conformations, particularly if the receptor is ill-defined. The primary hypothesis of this work is that a structure's conformational ensemble in solution presents viable candidates for protein binding. The experimental solution profile can be achieved with the NAMFIS (NMR analysis of molecular flexibility in solution) method, which deconvolutes the average NMR spectrum of small flexible molecules into individual contributing conformations with varying populations. Geldanamycin and radicicol are structurally different macrocycles determined by X-ray crystallography to bind to a common site on the cellular chaperone heat shock protein 90 (Hsp90). Without benefit of a receptor structure, NAMFIS has identified the bioactive conformers of geldanamycin and radicicol in CDCl3 solution with populations of 4% and 21%, respectively. Conversely, docking the set of NAMFIS conformers into the unliganded proteins with GLIDE followed by MM-GBSA scoring reproduces the experimental crystallographic binding poses.     

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.     

Compare-Conformer: a program for the rapid comparison of molecular conformers based on interatomic distances and torsion angles.

A computer program for comparison of the conformations of a number of related molecular structures is described. The comparisons are performed on either interatomic distances or torsion angles. The comparisons are accomplished on ordered pairs of distances or torsion angles, and the distance comparisons can be performed in a manner that allows permutation of the distance pairs being compared. The algorithm utilizes bit-string Boolean operations that allow the comparisons to be performed rapidly. The program should be useful for computer-assisted molecular modeling studies in which the viable conformers of bioactive analogues are compared in order to locate those conformers that place key substituents in the same spatial orientation.     

Two distinct conformers of the cyclic heptapeptide phakellistatin 2 isolated from the fijian marine sponge stylotellaaurantium

The isolation, structure determination, and solution conformation of two conformers of the cyclic heptapeptide phakellistatin 2 (cyclo-[Phe1-cis-Pro2-Ile3-Ile4-cis-Pro5-Tyr6-cis-Pro7]) isolated from the Fijian marine sponge Stylotella aurantium are reported. The conformers can be isolated separately by HPLC and are stable in methanol solution over a period of weeks as determined by NMR. Their NMR spectra and mass spectral fragmentation patterns differ significantly. Their solution conformations were determined by NOE-restrained molecular dynamics calculations and indicated that the two conformers had different folds, hydrogen bonding patterns, and solvent accessible surfaces. These factors may contribute to the independent stability of the two conformers, and may explain the variable biological activity previously reported for phakellistatin 2.     

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.     

Theoretical conformational analysis of unsaturated phospines and phosphinechalcogenides

A theoretical conformational analysis was performed for vinylphosphine CH₂=CHPH₂ and three vinylphosphinechalcogenides CH₂=CHPXH₂ (X = O, S, Se). According to the quantum-chemical calculations on the level of the second order perturbation theory MP2/6-311G** the prevailing conformations, their molar ratios, and relative energies were established for each compound. The analysis of the angular distribution of the probability density for the population of the rotational conformations calculated proceeding from the potential curves of the internal rotation made it possible to establish that each compound from this series existed as a mixture of two conformers, planar s-cis and twice degenerate orthogonal. The conformers transform into each other through the corresponding transition states whose nature was established as a result of the harmonic vibration analysis carried out in every case.     

Intramolecular hydrogen bond in 3‐imino‐propenylamine isomers: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energy of 18 conformers of 3‐imino‐propenyl‐amine were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set. The atom in molecules or AIM theory of Bader, which is based on the topological properties of the electron density (ρ), was used additionally and the natural bond orbital (NBO) analysis was also carried out. Furthermore calculations for all possible conformations of 3‐imino‐propenyl‐amin in water solution were also carried out at B3LYP/6‐311++G** and MP2/6‐311++G** levels of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the imine–amine conformers of this compound are more stable than the other conformers. B3LYP method predicts the IMA‐1 as global minimum. This stability is mainly due to the formation of a strong N? H···N intramolecular hydrogen bond, which is assisted by π‐electrons resonance, and this π‐electrons are established by NH2 functional group. Hydrogen bond energies for all conformers of 3‐imino‐propenyl‐amine were obtained from the related rotamers methods. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Molecular‐Dynamics and NMR Investigation of the Property Space of the Zwitterionic Antihistamine Cetirizine

The zwitterionic antihistamine cetirizine and its parent drug hydroxyzine as reference compound were examined for their 3D structures and dynamics. After attributing, by NMR spectroscopy, the two basic pK_a values, the most common conformations for each electrical species were determined by molecular‐dynamics simulations and confirmed by NMR measurements. For cetirizine, the results demonstrate that the zwitterion, which is the predominant species at physiological pH, exists as folded conformers able to partly mask polar groups. Extended and folded conformers of similar energy were also found for neutral hydroxyzine, whereas its monocationic species displayed folded conformers stabilized by intramolecular H‐bonds. These findings are in full agreement with previous results on the lipophilicity behavior of cetirizine in isotropic solvent systems and, taken together, could explain the favorable pharmacokinetic properties of the drug.     

Total assignment of the (1)H- and (13)C-NMR spectra for TZT-1027 and related compounds

The total assignment of the (1)H- and (13)C-NMR spectra for TZT-1027 was carried out using various NMR methods (1D, 2D NMR). It was found that TZT-1027 exists in two different conformations resulting from the cis-trans isomerization of the amide bond at N-11 and C-12 in DMSO-d(6). The (1)H- and (13)C-NMR spectra of compound 1 and 2 comprised of the partial structure of TZT-1027 were also assigned to be TZT-1027. These assignments showed that compound 1 is in good agreement with TZT-1027 with regard to formation of the conformers.     

Conformational analysis of some dimethylheptanes with the aid of normal coordinate calculations

Infrared spectra were obtained for the series of 2,X-dimethylheptanes (X = 2,3,4,5,6) and were interpreted with the aid of normal coordinate calculations. 2,2-DMH exists as two conformers, with the C_s conformer being the only one present in the crystalline solid. 2,3-DMH exists in at least three conformations, all of C₁ symmetry. Ambiguities in spectral data indicate that more conformations are present. Two C₁ conformations of 2,4-DMH were shown to be present, but an unassigned band may indicate the presence of a third conformer. The presence of at least four conformers, all of C₁ symmetry, was shown to be necessary to explain the spectrum of 2,5-DMH. Finally, 2,6-DMH was shown to exist as three conformers, of symmetries C_s, C₂, and C₁. Vibrational assignments were made for all the probable conformers of all five compounds.     

Geometric accuracy of three-dimensional molecular overlays

This study examines the dependence of molecular alignment accuracy on a variety of factors including the choice of molecular template, alignment method, conformational flexibility, and type of protein target. We used eight test systems for which X-ray data on 145 ligand-protein complexes were available. The use of X-ray structures allowed an unambiguous assignment of bioactive overlays for each compound set. The alignment accuracy depended on multiple factors and ranged from 6% for flexible overlays to 73% for X-ray rigid overlays, when the conformation of the template ligand came from X-ray structures. The dependence of the overlay accuracy on the choice of templates and molecules to be aligned was found to be the most significant factor in six and seven of the eight ligand-protein complex data sets, respectively. While finding little preference for the overlay method, we observed that the introduction of molecule flexibility resulted in a decrease of overlay accuracy in 50% of the cases. We derived rules to maximize the accuracy of alignment, leading to a more than 2-fold improvement in accuracy (from 19% to 48%). The rules also allowed the identification of compounds with a low (<5%) chance to be correctly aligned. Last, the accuracy of the alignment derived without any utilization of X-ray conformers varied from <1% for the human immunodeficiency virus data set to 53% for the trypsin data set. We found that the accuracy was directly proportional to the product of the overlay accuracy from the templates in their bioactive conformations and the chance of obtaining the correct bioactive conformation of the templates. This study generates a much needed benchmark for the expectations of molecular alignment accuracy and shows appropriate usages and best practices to maximize hypothesis generation success.     

Conformational analysis of TMC114, a novel HIV-1 protease inhibitor

TMC114, a potent novel HIV-1 protease inhibitor, remains active against a broad spectrum of mutant viruses. In order to bind to a variety of mutants, the compound needs to make strong, preferably backbone, interactions and have enough conformational flexibility to adapt to the changing geometry of the active site. The conformational analysis of TMC114 in the gas phase yielded 43 conformers in which five types of intramolecular H-bond interactions could be observed. All 43 conformers were subject to both rigid and flexible ligand docking in the wild-type and a triple mutant (L63P/V82T/I84V) of HIV-1 protease. The largest binding energy was calculated for the conformations that are close to the conformation observed in the X-ray complexes of TMC114 and HIV-1 protease.     

Conformation‐Specific Circular Dichroism Spectroscopy of Cold,Isolated Chiral Molecules

The CD spectroscopy of a chiral compound in solution yields an average CD value derived from all of the conformations of a chiral molecule. By contrast, CD spectroscopy of cold chiral molecules in the gas phase distinguishes specific conformers of a chiral molecule, but the weak CD effect has limited the practical application of this technique. Reported herein is the first resonant two‐photon ionization CD spectra of ephedrines in a supersonic jet using circularly polarized laser pulses, which were generated by synchronizing the oscillation of the photoelastic modulator with the laser firing. The spectra exhibited well‐resolved CD bands which were specific for the conformations and vibrational modes of each enantiomer. The CD signs and magnitudes of the jet‐cooled chiral molecules were very sensitive to their conformations and thus offered crucial information for determining the three‐dimensional structures of chiral species, as conducted in combination with quantum chemical calculations.     

Conformation‐Specific Circular Dichroism Spectroscopy of Cold,Isolated Chiral Molecules

The CD spectroscopy of a chiral compound in solution yields an average CD value derived from all of the conformations of a chiral molecule. By contrast, CD spectroscopy of cold chiral molecules in the gas phase distinguishes specific conformers of a chiral molecule, but the weak CD effect has limited the practical application of this technique. Reported herein is the first resonant two‐photon ionization CD spectra of ephedrines in a supersonic jet using circularly polarized laser pulses, which were generated by synchronizing the oscillation of the photoelastic modulator with the laser firing. The spectra exhibited well‐resolved CD bands which were specific for the conformations and vibrational modes of each enantiomer. The CD signs and magnitudes of the jet‐cooled chiral molecules were very sensitive to their conformations and thus offered crucial information for determining the three‐dimensional structures of chiral species, as conducted in combination with quantum chemical calculations.