Rajesh Singh

Development of 3D-pharmacophore model followed by successive virtual screening, molecular docking and ADME studies for the design of potent CCR2 antagonists for inflammation-driven diseases

In order to elucidate the essential structural features for CC chemokine receptor 2 (CCR2) antagonism, 3D-pharmacophore hypotheses were built based on a set of known compounds from the literature. The hypotheses were developed with the aid of HypoGen module within Discovery Studio 2.5 program. Multiple validation approaches provided the confidence in utilising the predictive pharmacophore models developed in this study. The most predictive pharmacophore model (Hypo1) was found to be statistically significant along with its ability to predict activities of the known CCR2 antagonists in the training and test set with high correlation coefficient. The best model was then used as a 3D search query in the virtual screening of chemical databases including ChemDiv and MiniMaybridge. Lipinskis rule of five and molecular docking studies were applied to the screened hits for retrieving potential lead compounds. Eight hits showed better in silico CCR2-binding affinities than the reported CCR2 antagonists, along with good absorption, distribution, metabolism and excretion profiles. The current 3D-quantitative structure–activity relationship (QSAR) pharmacophore modelling and molecular docking studies attempt to elucidate QSAR for CCR2 antagonism and identify novel potent CCR2 antagonist scaffolds.

Synthesis in vitro/in vivo evaluation and in silico physicochemical study of prodrug approach for brain targeting of alkylating agent

Every year, there are more than two lakhs of population affected with CNS tumor. Nitrogen mustard class of alkylating drugs, used clinically against various types of tumor, is too polar to cross the BBB. The redox chemical drug delivery prodrug approach is one of the most interesting procedures for delivering drugs in a sustained and specific manner to the CNS. The objective of the present study is to investigate the redox drug delivery system for the delivery of bis(2-chloroethyl)amine (nor mustard) as alkylating cytotoxic agent to the brain. Various redox derivatives of CDS-M (4a–d) were synthesized incorporating different alkyl/aryl moieties at ring nitrogen and subjected to in silico physicochemical parameters determination required for CNS activity through computational, online, and QikProp 3.2 software. The results of stability study, in vitro chemical (silver nitrate), and biological oxidation studies in human blood, rat blood, and brain homogenate for all CDS-M (4a–d) have been promising and suggest that brain targeting could be possible with more stable CDS-M (4d). The in vivo study showed that CDS-M (4d) was able to cross the BBB at detectable concentrations, and in vitro NBP alkylating activity of its quaternary salt (3d) was comparable to the known drug chlorambucil among all the synthesized derivatives.

Design, synthesis and evaluation of aminobenzophenone derivatives containing nitrogen mustard moiety as potential central nervous system antitumor agent

A series of novel substituted aminobenzophenone derivatives containing nitrogen mustard moiety (5a–f) were synthesized and characterized on the basis of their IR, 1H NMR, 13C NMR, CHN, and mass spectral data. All the compounds when evaluated for chemical 4-(4-nitrobenzyl) pyridine alkylating activity proved to be active alkylating agents. All the synthesized compounds were subjected to physicochemical parameters determination required for central nervous system (CNS) activity through computational, online software, and QikProp 3.2. The log P values and other in silico ADME physicochemical descriptors analyzed lay between the ranges those are required for good BBB penetration. The in vitro antiproliferative activity against human cancer cell lines viz. A 549 (lung), COLO 205 (colon), U 87 (glioblastoma), and IMR-32 (neuroblastoma) was investigated. Most of the test compounds showed potent antitumor activity, especially compound (5f) which displayed the highest activity against CNS cancer cell line comparable to that of chlorambucil and docetaxel. The preliminary structure–activity relationship (SAR) revealed that 5-chloroaminobenzophenone-mustard series (5a–c) exhibited better antitumor activity than 5-nitroaminobenzophenone-mustard series (5d–f).

6-hydroxy-3,5,7,4′-tetramethoxyflavone 6-rhamnoside from roots of Pterocarpus marsupium

Abstract A new flavonol glycoside was isolated from roots of Pterocarpus marsupium . Its structure was determined as 6-hydroxy-3,5,7,4′-tetramethoxyflavone 6- O -rhamnopyranoside by spectral data and chemical degradation.

Structure prediction and molecular dynamics simulations of a G-protein coupled receptor: human CCR2 receptor.

CC chemokine receptor type-2 (CCR2) is a member of G-protein coupled receptors superfamily, expressed on the cell surface of monocytes and macrophages. It binds to the monocyte chemoattractant protein-1, a CC chemokine, produced at the sites of inflammation and infection. A homology model of human CCR2 receptor based on the recently available C-X-C chemokine recepor-4 crystal structure has been reported. Ligand information was used as an essential element in the homology modeling process. Six known CCR2 antagonists were docked into the model using simple and induced fit docking procedure. Docked complexes were then subjected to visual inspection to check their suitability to explain the experimental data obtained from site directed mutagenesis and structure-activity relationship studies. The homology model was refined, validated, and assessed for its performance in docking-based virtual screening on a set of CCR2 antagonists and decoys. The docked complexes of CCR2 with the known antagonists, TAK779, a dual CCR2/CCR5 antagonist, and Teijin-comp1, a CCR2 specific antagonist were subjected to molecular dynamics (MD) simulations, which further validated the binding modes of these antagonists. B-factor analysis of 20u2009ns MD simulations demonstrated that Cys190 is helpful in providing structural rigidity to the extracellular loop (EL2). Residues important for CCR2 antagonism were recognized using free energy decomposition studies. The acidic residue Glu291 from TM7, a conserved residue in chemokine receptors, is favorable for the binding of Teijin-comp1 with CCR2 by ΔG of −11.4u2009kcal/mol. Its contribution arises more from the side chains than the backbone atoms. In addition, Tyr193 from EL2 contributes −0.9u2009kcal/mol towards the binding of the CCR2 specific antagonist with the receptor. Here, the homology modeling and subsequent molecular modeling studies proved successful in probing the structure of human CCR2 chemokine receptor for the structure-based virtual screening and predicting the binding modes of CCR2 antagonists.

Binding site characterization of G protein-coupled receptor by alanine-scanning mutagenesis using molecular dynamics and binding free energy approach: application to C-C chemokine receptor-2 (CCR2)

The C-C chemokine receptor 2 (CCR2) was proved as a multidrug target in many diseases like diabetes, inflammation and AIDS, but rational drug design on this target is still lagging behind as the information on the exact binding site and the crystal structure is not yet available. Therefore, for a successful structure-based drug design, an accurate receptor model in ligand-bound state is necessary. In this study, binding-site residues of CCR2 was determined using in silico alanine scanning mutagenesis and the interactions between TAK-779 and the developed homology model of CCR2. Molecular dynamic simulation and Molecular Mechanics-Generalized Born Solvent Area method was applied to calculate binding free energy difference between the template and mutated protein. Upon mutating 29 amino acids of template protein and comparison of binding free energy with wild type, six residues were identified as putative hot spots of CCR2.

Synergistic application of target structure-based alignment and 3D-QSAR study of protein tyrosine phosphatase 1B (PTP1B) inhibitors

Protein tyrosine phosphatase 1B (PTP1B) has been demonstrated to play a key role in the negative signaling pathway of insulin. Potent and orally active PTP1B inhibitors are considered to be promising pharmacological agents for the treatment of type 2 diabetes and resistance to weight gain. CoMFA studies were performed on a set of PTP1B inhibitors, which are known to bind simultaneously to the active site as well as a sub-binding site. An alignment, based on eight different crystal structure complexes of PTP1B was carried out to study the synergistic application of the alignment on CoMFA. The CoMFA model with statistical parameters

QSAR study of 2,4-disubstituted phenoxyacetic acid derivatives as a CRTh2 receptor antagonists

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