Virtual high throughput screening in new lead identification

Drug discovery continues to be one of the greatest contemporary challenges and rational application of modelling approaches is the first important step to obtain lead compounds, which can be optimised further. Virtual high throughput screening (VHTS) is one of the efficient approaches to obtain lead structures for a given target. Strategic application of different screening filters like pharmacophore mapping, shape-based, ligand-based, molecular similarity etc., in combination with other drug design protocols provide invaluable insights in lead identification and optimization. Screening of large databases using these computational methods provides potential lead compounds, thus triggering a meaningful interplay between computations and experiments. In this review, we present a critical account on the relevance of molecular modelling approaches in general, lead optimization and virtual screening methods in particular for new lead identification. The importance of developing reliable scoring functions for non-bonded interactions has been highlighted, as it is an extremely important measure for the reliability of scoring function. The lead optimization and new lead design has also been illustrated with examples. The importance of employing a combination of general and target specific screening protocols has also been highlighted

Potential choline kinase inhibitors: a molecular modeling study of bis-quinolinium compounds

Choline kinase (ChoK) is reported to involve in cell signaling pathways and cell growth by regulating the intermediate, phosphocholine (PCho), which is the first step to biosynthesis a membrane phospholipid, phosphatidylcholine. The PCho levels are overexpressed due to elevated activation of the protein under carcinogenesis conditions. ChoK has thus evolved as a novel target for various cancers and a range of compounds has been reported in this course as potent ChoK inhibitors. However, not much information is known about the binding site of the inhibitors. Therefore, we ventured to unravel the possible binding site of 39 bis-quinolinium inhibitors from which the structural requirement for better protein–ligand complex was delved. Molecular docking and 3D-QSAR studies namely comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on the series. The knowledge of the active site was obtained from the site id search and molcad surface calculations of Sybyl, which was further considered for docking studies. In 3D-QSAR, the best predictions were obtained from the model where 29 compounds were considered in the training set and remaining 10 in the test set. The best CoMFA statistics were obtained with r<SUP>2</SUP> of 0.99 and q<SUP>2</SUP> of 0.81 while, CoMSIA was resulted with r<SUP>2</SUP> of 0.98 and q<SUP>2</SUP> of 0.77. A comparative analysis was done with the resulted 3D-QSAR maps and the docked poses by overlaying the maps on the active site residues. Since, there is no reported ligand co-crystallized structure of ChoK the present study provides valuable clues on the binding conformation of the ligand and its interactions with the active site

Understanding the structural requirements of triarylethane analogues towards PDE-IV inhibitors: A molecular modeling study†

68-76A three-dimensional quantitative structure activity relationship study has been performed on a series of 44 triarylethanes to determine the structural requirements for phosphodicsterase-IV (PDE-IV) enzyme inhibition. Considering the stereochemistry of the data set molecules and the varied types of alignments available, a total of seven models are presented. While most models were optimized to yield satisfactory r2 and q2 values, the best model was obtained with 29 molecules including all the R conformation with r2 0.996, q<span style="mso-bidi-font-style: italic">2 0.510 and r2 pred 0.744. A complementary molecular docking analysis is carried out considering the 29 stereochemically characterized set of molecules. The CoMFA maps and the docking studies were used to understand the structural requirements for the PDE-IV inhibition. These studies are expected to provide useful insights into the roles of various substitution patterns on the triarylethane skeleton and also help to design more potent compounds

Characterization of calcium and magnesium binding domains of human 5-lipoxygenase

Two calcium binding sites, separated by about 9.3 Å, present in the loops that connect the β-sheets of N-terminal domain contain the ligating residues F14, A15, G16, D79, and D18, D19, L76, respectively. Magnesium is found to bind in regions, which are marginally different owing to the disparity in the ionic radii of Ca<SUP>2+</SUP> and Mg<SUP>2+</SUP>. The entropy analysis on the loops of 5-lipoxygenase, implementing the wormlike chain model, explains that the N-terminal β-barrel is well suited to accommodate calcium binding sites. The large buried side chain area of W102 (compared to W13 and W75) and comparatively smaller fraction of side chain exposed to polar atoms corroborate the calcium induced higher affinity to phosphatidylcholine (PC). However, W80 lying in close proximity of the calcium binding sites is expected to have considerable PC affinity but negligible calcium induced effect on PC binding

2D and 3D quantitative structure-activity relationship studies on a series of bis-pyridinium compounds as choline kinase inhibitors

Two-dimensional (2D) and three-dimensional (3D) quantitative structure activity relationship (QSAR) studies have been carried out on a series of 55 bis-pyridinium compounds to find out the structural requirements of choline kinase (ChoK) inhibitors. The best predictions were obtained from the model where 44 compounds were considered in the training set and the remaining 11 in the test set. The heuristic and BMLR methods resulted with r2 and q2 values of 0.86, 0.83 and 0.87, 0.84 respectively. The obtained Fisher and S2 values for both the methods are 49.02 and 54.05, 0.053 and 0.0397 respectively. The best model for 3D-QSAR has been obtained with r2=0.97, q2 = 0.58 and r2pred=0.68 when CoMFA fields were used. The r2 of 0.85, q2 of 0.55 and r2pred=0.66 have been observed when CoMSIA fields were used. The results that are obtained from 2D and 3D-QSAR studies may provide useful insights into the roles of various substitution patterns on the bis-pyridinium skeleton and may also help to design more potent compounds

Axial ligand effect on the rate constant of aromatic hydroxylation by iron(IV)-Oxo complexes mimicking cytochrome P450 enzymes

The cytochromes P450 are important iron-heme based monoxygenases that catalyze a range of different oxygen atom transfer reactions in nature. One of the key bioprocesses catalyzed by these enzymes is the aromatic hydroxylation of unactivated arenes. To gain insight into axial ligand effects and, in particular, how it affects aromatic hydroxylation processes by P450 model complexes, we studied the effects of the axial ligand on spectroscopic parameters (trans-influence) as well as on aromatic hydroxylation kinetics (trans-effect) using a range of [FeIV(O)(Por+•)X] oxidants with X = SH–, Cl–, F–, OH–, acetonitrile, GlyGlyCys–, CH3COO–, and CF3COO–. These systems give red-shifted Fe–O vibrations that are dependent on the strength of the axial ligand. Despite structural changes, however, the electron affinities of these oxidants are very close in energy, but sharp differences in pKa values are found. The aromatic hydroxylation of the para-position of ethylbenzene was tested with these oxidants, and they all show two-state-reactivity patterns although the initial low-spin C–O bond formation barrier is rate determining. We show, for the first time, that the rate determining barrier for aromatic hydroxylation is proportional to the strength of the O–H bond in the corresponding iron(IV)–hydroxo complex, i.e., BDEOH, hence this thermochemical property of the oxidant drives the reaction and represents the axial ligand effect. We have rationalized our observed barrier heights for these axially ligated systems using thermochemical cycles and a valence bond curve crossing diagram to explain the origins of the rate constants

Structural and conformational changes concomitant with the E1–E2 transition in H<SUP>+</SUP>K<SUP>+</SUP>-ATPase: a comparative protein modeling study

Comparative modeling studies on conserved regions of the gastric H+K+-ATPase reveal that the E1–E2 conformational transition induces significant tertiary structural changes while conserving the secondary structure. The residues 516–530 of the cytoplasmic domain and TM10 within the transmembrane (TM) regions undergo maximum tertiary structural changes. The luminal regions exhibit comparatively lesser tertiary structural deviations. Residues 249–304 show maximum secondary structural deviation in the conformational transition. The Cys-815 and Cys-323 residues involved in inhibitor binding are found to have smaller buried side chain areas in the E1 conformation compared to E2. Retention of activity correlates well with the buried side chain area when selected amino acid residues in TM6 are mutated using modeling techniques with bulkier amino acid residues. Conformational specificity for ion binding is corroborated with the fraction of side chains exposed to polar atoms of the residues E345, D826, V340, A341, V343, and E822

Effect of the axial ligand on substrate sulfoxidation mediated by iron (IV)–oxo porphyrin cation radical oxidants

Cytochromes P 450 catalyze a range of different oxygen-transfer processes including aliphatic and aromatic hydroxylation, epoxidation, and sulfoxidation reactions. Herein, we have investigated substrate sulfoxidation mediated by models of P 450 enzymes as well as by biomimetic oxidants using density functional-theory methods and we have rationalized the sulfoxidation reaction barriers and rate constants. We carried out two sets of calculations: first, we calculated the sulfoxidation by an iron(IV)–oxo porphyrin cation radical oxidant [Fe<SUP>IV</SUP>=O(Por<SUP>+.</SUP>)SH] that mimics the active site of cytochrome P 450 enzymes with a range of different substrates, and second, we studied one substrate (dimethyl sulfide) with a selection of different iron(IV)–oxo porphyrin cation radical oxidants [Fe<SUP>IV</SUP>=O(Por<SUP>+.</SUP>)L] with varying axial ligands L. The study presented herein shows that the barrier height for substrate sulfoxidation correlates linearly with the ionization potential of the substrate, thus reflecting the electron-transfer processes in the rate-determining step of the reaction. Furthermore, the axial ligand of the oxidant influences the pK<SUB>a</SUB> value of the iron(IV)–oxo group, and, as a consequence, the bond dissociation energy (BDE<SUB>OH</SUB>) value correlates with the barrier height for the reverse sulfoxidation reaction. These studies have generalized substrate-sulfoxidation reactions and have shown how they fundamentally compare with substrate hydroxylation and epoxidation reactions