Synthesis and anti-proliferative activity of a novel 1,2,3-triazole tethered chalcone acetamide derivatives.

A new series of 1,2,3-triazole tethered chalcone acetamide derivatives (7a-c &8a-r) have been synthesized in excellent yields and their structures were determined by analytical and spectral (FT-IR, 1H NMR, 13C NMR & HRMS) studies. The newly synthesized derivatives were evaluated for their cytotoxic activity against four human cancer cell lines, such as HeLa (Human cervical cancer), A549 (Human alveolar adenocarcinoma), MCF-7 (Human breast adenocarcinoma) and SKNSH (Human brain cancer). Among them, compound 7c exhibited good anti-proliferation activity with HeLa (IC50 7.41 + 0.8 µM), SKNSH (IC50 8.68 + 1.1 µM), MCF-7 (IC50 9.76 + 1.3 µM) and MDA-MB-231, while compounds 7a and 7b showed promising anti-proliferation against above four human cancer cell lines with IC50 7.95-11.62 µM, respectively, compared with the standard drug Doxorubicin. We explored the probable key active site and binding mode interactions in HDAC8 (PDB ID:3SFH) and EHMT2 (PDB ID:3K5K) proteins. The docking results are complementary to the experimental observations.

Uncovering Structural and Molecular Dynamics of ESAT-6:ß2M Interaction: Asp53 of Human ß2-Microglobulin Is Critical for the ESAT-6:ß2M Complexation.

ESAT-6 is a small secreted protein of Mycobacterium tuberculosis involved in the ESAT-6 secretion system (ESX-1)-mediated virulence and pathogenesis. The protein interacts with ß2M, causing downregulation of MHC class I Ag presentation, which could be one of the mechanisms by which it favors increased survival of the bacilli inside the host. In an earlier study, we have shown that the C-terminal region of ESAT-6 is crucial for its interaction with ß2M. However, the interface of ß2M involved in interaction with ESAT-6 and detailed physicochemical changes associated with ESAT-6:ß2M complexation are not fully defined. In this study, using computational and site-directed mutagenesis studies, we demonstrate the presence of strong noncovalent hydrophobic interactions between ESAT-6 and ß2M in addition to the vital hydrogen bonding between the aspartate residue (Asp53) of ß2M and methionine (Met93) of ESAT-6. Docking-based high-throughput virtual screening followed by 16-point screening on microscale thermophoresis resulted in the identification of two potent inhibitors (SM09 and SM15) that mask the critical Met93 residue of ESAT-6 that is required for ESAT-6:ß2M interaction and could rescue cell surface expression of ß2M and HLA in human macrophages as well as MHC class I Ag presentation suppressed by ESAT-6 in peritoneal macrophages isolated from C57BL/6 mice. Both SM09 and SM15 significantly inhibited intracellular survival of M. tuberculosis in human macrophages. Further, we characterized the physicochemical properties involved in the ESAT-6:ß2M complexation, which may help in understanding host-pathogen interactions.

Recent Advances in the Development of Pharmaceutical Agents for Metabolic Disorders: A Computational Perspective.

BACKGROUND: Metabolic disorders comprise a set of different disorders varying from epidemic diseases such as diabetes mellitus to inborn metabolic orphan diseases such as phenylketonuria. Despite considerable evidence showing the importance of the computational methods in discovery and development of new pharmaceuticals, there are no systematic reviews outlining how they are utilized in the field of metabolic disorders. This review aims to discuss the necessity of the development of web-based tools and databases by integration of available information for solving Big Data problems in network pharmacology of metabolic disorders. METHODS: We undertook a structured search of bibliographic databases for peer-reviewed research literature using a focused review question and inclusion/exclusion criteria. The quality of retrieved papers was appraised using standard tools. RESULTS: The alterations in metabolic pathways cause various cardiovascular, hematological, neurological, gastrointestinal, immune disorders and cancer. In this regard, informatics, Big Data and modeling techniques aid in the design of novel therapeutic agents for metabolic diseases by addressing various Big Data problems in the network polypharmacology (drugs/pharmaceutical agents, proteins, genes, diseases, bioassays, ADMET and metabolic pathways), identification of privileged scaffolds, developing new diagnostic biomarkers, understanding the pathophysiology of disease and progress in personalized medicine. CONCLUSION: The recent advances of developing pharmaceutical agents for various metabolic disorders by considering their pathogenesis, mechanisms of action, therapeutic and adverse effects have been summarized. We have highlighted the role of computational techniques, drug repurposing, and network-based polypharmacological approaches in the identification of new/existing medicines with improved drug-likeness properties for the rare metabolic disorders.

Novel benzothiazine-piperazine derivatives by peptide-coupling as potential anti-proliferative agents.

In an attempt to develop potential and selective anti-proliferative agents, a series of novel benzothiazine-piperazine derivatives 8a-i and 10a-g were synthesized by coupling of 2H-1,4-benzothiazin-3(4H)-one with various amines 7a-i and 9a-g in excellent yields and evaluated for their in vitro anti-proliferative activity against four cancer cell lines, HeLa (cervical), MIAPACA (pancreatic), MDA-MB-231 (breast) and IMR32 (neuroblastoma). In vitro inhibitory activity indicated that compounds 8a, 8d, 8g, 10a, 10b, 10e, 10f were found to be good anti-proliferative agents. Among them the derivatives 8g, 10e and 10f were found to be the most active members exhibiting remarkable growth inhibitory activity. Molecular docking was undertaken to investigate the probable binding mode and key active site interactions in HDAC8 and EHMT2 proteins. The docking results are complementary to the experimental results.

Modeling the permeability of drug-like molecules through the cell wall of Mycobacterium tuberculosis: an analogue based approach.

The emergence of drug resistant strains of Mycobacterium Tuberculosis (Mtb) accentuates the urgent need for the development of novel antitubercular drugs. The major causes of drug resistance are genetic mutations, the influx-efflux transporter system, and the complex cell wall system of Mtb, which can function as permeability barriers. The driving force for permeability of small molecules through a biological system depends on various physicochemical factors. To understand the permeability of small molecules and subsequent cell inhibition, we have developed predictive QSAR models based on reported enzyme-based (IC50) and cell-based (MIC) Mtb inhibitory data. The compounds that are highly active in enzyme-based assays and have significant variation in cell-based assays are assumed to possess the required permeability through the Mtb cell wall. The obtained models suggest the importance of molecular connectivity, lipophilicity (log P, size, shape), electrotopology (relative atomic mass, polarizability, electronegativity, ionization potential, atomic charges, van der Waals volume, hybridization, hydrogen bond acceptors/donors, number of fused rings) and functional groups (hydroxyl groups, primary and secondary amines) of a molecule in determining both its inhibitory potency and Mtb cell permeability. The models were validated with known Mtb inhibitors (9804) collected from the ChEMBL database, Mtb drugs (27) and clinical candidates (5). Further, these validated models were used to screen and prioritize a large database of compounds, including Zinc (152 128), Asinex (435 215), DrugBank (6531) and antimicrobial compounds (1324). The results obtained from 2D-QSAR analysis could improve our understanding towards Mtb cell permeability, which may aid in the rational design of novel potent molecules for tuberculosis (TB).

Design and synthesis of 3-(3-((9H-carbazol-4-yl)oxy)-2-hydroxypropyl)-2-phenylquinazolin-4(3H)-one derivatives to induce ACE inhibitory activity.

In an attempt to develop a new class of cardiovascular drugs, a series of novel carbazolyloxy phenylquinazoline derivatives 9a-g have been synthesized and evaluated as angiotensin converting enzyme (ACE) inhibitors. Most of these compounds exhibited activity as significant ACE inhibitors and three compounds (9b, 9c & 9e) showed maximum inhibitory potency in enzyme based assays. To render support to the experimental results, a series of quinazolinone derivatives were docked into active site of ACE and identified the probable binding modes compared to Lisinopril. Also we have identified common pharmacophore hypothesis (AAADDRR) among the best docked conformers of most potent compounds in a series of compounds. The most potent 9b, 9c, 9e compounds shared common active site with the Lisinopril binding site and retained the key active site residue interactions. The obtained results from pharmacological and molecular modeling studies can be utilized for further optimization of identified hits for selective inhibition of ACE.

Luotonin-A based quinazolinones cause apoptosis and senescence via HDAC inhibition and activation of tumor suppressor proteins in HeLa cells.

A series of novel quinazolinone hybrids were synthesized by employing click chemistry and evaluated for anti-proliferative activities against MCF-7, HeLa and K562 cell lines. Among these cell lines, HeLa cells were found to respond effectively to these quinazolinone hybrids with IC50 values ranging from 5.94 to 16.45 µM. Some of the hybrids (4q, 4r, 4e, 4k, 4t, 4w) with promising anti-cancer activity were further investigated for their effects on the cell cycle distribution. FACS analysis revealed the G1 cell cycle arrest nature of these hybrids. Further to assess the senescence inducing ability of these compounds, a senescence associated ß-gal assay was performed. The senescence inducing nature of these compounds was supported by the effect of hybrid (4q) on p16 promoter activity, the marker for senescence. Moreover, cells treated with most effective compound (4q) show up-regulation of p53, p21 and down-regulation of HDAC-1, HDAC-2, HDAC-5 and EZH2 mRNA levels. Docking results suggest that, the triazole nitrogen showed Zn(+2) mediated interactions with the histidine residue of HDACs.

Novel hydrazine derivatives as selective DPP-IV inhibitors: findings from virtual screening and validation through molecular dynamics simulations.

The present study demonstrates and validates the discovery of two novel hydrazine derivatives as selective dipeptidyl peptidase-IV (DPP-IV) inhibitors. Virtual screening (VS) of publicly available databases was performed using virtual screening workflow (VSW) of Schrödinger software against DPP-IV and the most promising hits were selected. Selectivity was further assessed by docking the hits against homology modeled structures of DPP8 and DPP9. Two novel hydrazine derivatives were selected for further studies based on their selectivity threshold. To assess their correct binding modes and stability of their complexes with enzyme, molecular dynamic (MD) simulation studies were performed against the DPP-IV protein and the results revealed that they had a better binding affinity towards DPP-IV as compared to DPP 8 and DPP 9. The binding poses were further validated by docking these ligands with different softwares (Glide and Gold). The proposed binding modes of hydrazines were found to be similar to sitagliptine and alogliptine. Thus, the study reveals the potential of hydrazine derivatives as highly selective DPP-IV inhibitors.

Dipeptidyl peptidase IV inhibitors: a new paradigm in type 2 diabetes treatment.

Dipeptidyl peptidase IV (DPP4) is a promising target for the treatment of chronic metabolic type 2 diabetes mellitus (T2D). DPP4 is a highly specific serine protease involved in the regulation and cleavage of two incretin hormones, glucagon-like peptide (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP). These incretin hormones are released by the gastrointestinal tract in response to ingestion of food and stimulate insulin secretion and thereby regulate glucose homeostasis with a low risk of hypoglycemia and glucagon secretion. Currently different chemical classes of DPP4 inhibitors are in last-stage of clinical trials and few of them such as sitagliptin, vildagliptin, saxagliptin alogliptin and linagliptin have already been successfully released into market. These drugs have been approved as either monotherapy or combination therapy with other oral hypoglycemic agents such as metformin, pioglitazone, sulfonylurea, glyburide and glibenclamide for the treatment of T2D. Though several clinical trial compounds were discontinued because of severe adverse toxic effects that are associated with other prolyldipeptidases include DPP8 and DPP9. The current review provides an overview of DPP4 and its inhibitors with emphasis on the structure, expression, activity, selectivity and pharmacokinetics information. This review further dwells upon the issues relating to the rational design and development of selective DPP4 inhibitors for the treatment of T2D.

Pyrid-2-yl and 2-CyanoPhenyl fused heterocyclic compounds as human P2X3 inhibitors: a combined approach based on homology modelling, docking and QSAR analysis.

P2X receptors are hetero-oligomeric proteins that function as membrane ion channels and are gated by extracellular ATP. The hP2X[Formula: see text] subunit is a constituent of the channels on a subset of sensory neurons involved in pain signaling, where ATP released by damaged and inflamed tissue can initiate action potentials. Hence, the inhibition of ATP-activated P2X3 receptor is an exciting approach for the treatment of inflammatory and neuropathic pain. Recently, the crystal structures of zebrafish P2X4 (zP2X4) were obtained in closed, apo state (PDB ID: 3I5D) and ATP-bound, open state (PDB ID: 4DW1). These structures were used to develop a homology model of human P2X3 (hP2X3 in order to identify through docking studies, the binding modes of known P2X3 inhibitors and their key active site interactions, along with a pharmacophore-based 3D-QSAR model for a series of 136 Pyrid-2-yl and 2-CyanoPhenyl fused heterocyclic compounds. These 3D-QSAR models have been developed with different combinations of training and test set divisions obtained by random separation, Jarvis-Patrick clustering, K-means clustering and sphere exclusion methods. The best predictive 3D-QSAR model resulted in training set R2 of 0.75, internal test set Q2 of 0.74, Pearson-R value of 0.87 and root mean square error of 0.37. The information generated by the pharmacophore model and docking analyses using the homology model provides valuable clues to design novel potent hP2X3 inhibitors.

Toward a general predictive QSAR model for gamma-secretase inhibitors.

Gamma secretase (GS) is an appealing drug target for Alzheimer disease and cancer because of its central role in the processing of amyloid precursor protein and the notch family of proteins. In the absence of three-dimensional structure of GS, there is an urgent need for new methods for the prediction and screening of GS inhibitors, for facilitating discovery of novel GS inhibitors. The present study reports QSAR studies on diverse chemical classes comprising 233 compounds collected from the ChEMBL database. Herein, continuous [PLS regression and neural-network (NN)] and categorical QSAR models (NN and linear discriminant analysis) were developed to obtain pertinent descriptors responsible for variation of GS inhibitor potency. Also, SAR within various chemical classes of compounds is analyzed with respect to important QSAR descriptors, which revealed the significance of electronegative substitutions on aryl rings (PEOE3) in determining variation of GS inhibitor potency. Furthermore, substitution of acyclic amines with N-substituted cyclic amines appears to be favorable for enhancing GS inhibitor potency by increasing the values of sssN_Cnt and number of aliphatic rings. The models developed are statistically significant and improve our understanding of compounds contributing toward GS inhibitor potency and aid in the rational design of novel potent GS inhibitors.