Chirag N. Patel

Pharmacophore-based virtual screening of catechol-o-methyltransferase (COMT) inhibitors to combat Alzheimer’s disease

Alzheimer’s disease (AD) is one of the most significant neurodegenerative disorders and its symptoms mostly appear in aged people. Catechol-o-methyltransferase (COMT) is one of the known target enzymes responsible for AD. With the use of 23 known inhibitors of COMT, a query has been generated and validated by screening against the database of 1500 decoys to obtain the GH score and enrichment value. The crucial features of the known inhibitors were evaluated by the online ZINC Pharmer to identify new leads from a ZINC database. Five hundred hits were retrieved from ZINC Pharmer and by ADMET (absorption, distribution, metabolism, excretion, and toxicity) filtering by using FAF-Drug-3 and 36 molecules were considered for molecular docking. From the COMT inhibitors, opicapone, fenoldopam, and quercetin were selected, while ZINC63625100_413 ZINC39411941_412, ZINC63234426_254, ZINC63637968_451, and ZINC64019452_303 were chosen for the molecular dynamics simulation analysis having high binding affinity and structural recognition. This study identified the potential COMT inhibitors through pharmacophore-based inhibitor screening leading to a more complete understanding of molecular-level interactions.

Microwave-Assisted ZrSiO2 Catalysed Synthesis, Characterization and Computational Study of Novel Spiro[Indole-Thiazolidines] Derivatives as Anti-tubercular Agents

In the current investigation, we prepared a series of novel spiro[indole-thiazolidines] derivatives (5a–5h) from 5-substituted isatin derivatives and thioglycolic acid (TGA) with ZrSiO2 as an efficient catalyst under microwave irradiation. The significant merits of this protocol have some significant merits such as simplicity in operation, simple, efficient workup, good practical yields of product and the employment of recyclable catalyst. All the new synthesized scaffold has been well characterized by various spectroscopic methods and elemental analysis. All the spiro scaffolds were subjected to in vitro anti-mycobacterial activity against the Mycobacterium tuberculosis (H37Rv) strain. We have carried out molecular docking study of our synthesized compounds. We also calculated theoretically ADME–Tox parameters for synthesized compounds.

Antiproliferative Efficacy of Kaempferol on Cultured Daudi Cells: An In Silico and In Vitro Study

There is always a constant need to develop alternative or synergistic anticancer drugs with minimal side effects. One important strategy to develop effective anticancer agents is to investigate potent derived compounds from natural sources. The present study was designed to determine antiproliferative activity of Kaempferol using in silico as well as in vitro study. Docking was performed using human GCN5 (hGCN5) protein involved with cell cycle, apoptosis, and glucose metabolism. Cell viability and cytotoxicity on Daudi cells were evaluated by trypan blue and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays in a dose and time dependent manner, respectively. The compound inhibited the proliferation and growth of the Daudi cells, through induced cell death. The pure compound proved lead inhibitors of cell proliferation, thus manifesting significant antiproliferative activity. The docking results revealed that Kaempferol exhibited binding interaction to hGCN5 protein. Further, molecular dynamics using the dock pose of hGCN5-Kaempferol complex were performed to understand the basic structural unit which lead to inefficiency in binding and, therefore, pronounced instability and its possible consequences of reduced binding affinity. The data obtained in this study indicates that Kaempferol is a promising compound leading to inhibition of Daudi cell growth and proliferation.

Dual in vitro and in silico analysis of thiacalix[4]arene dinaphthalene sulfonate for the sensing of 4-nitrotoluene and 2,3-dinitrotoluene

A new fluorescent thiacalix[4]arene dinaphthalene sulfonate (TCDNS) was synthesized by a reaction of thiacalix[4]arene with naphthalene sulfonyl chloride. TCDNS was characterized by 1H-NMR, 13C-NMR, and ESI-MS spectrometric analyses. The selectivity of fluoroionophore was analyzed for 4-nitrotoluene (4-NT) and 2,3-dinitrotoluene (2,3-DNT) among various nitroaromatic compounds (NACs) using the spectrofluorimetric technique. 4-NT and 2,3-DNT behave as the strong emission quenchers for TCDNS. The information about the complexation of TCDNS with 4-NT and 2,3-DNT was revealed by ESI-MS and 1H NMR analysis. A standard addition method was used for the detection of 4-NT and 2,3-DNT in a water sample. The complex formation in the cases of TCDNS⊃4-NT and TCDNS⊃2,3-DNT has been demonstrated by molecular docking and dynamics simulation techniques.

Molecular Dynamics-Assisted Pharmacophore Modeling of Caspase-3-Isatin Sulfonamide Complex: Recognizing Essential Intermolecular Contacts and Features of Sulfonamide Inhibitor Class for Caspase-3 Binding

The identification of isatin sulfonamide as a potent small molecule inhibitor of caspase-3 had fuelled the synthesis and characterization of the numerous sulfonamide class of inhibitors to optimize for potency. Recent works that relied on the ligand-based approaches have successfully shown the regions of optimizations for sulfonamide scaffold. We present here molecular dynamics-based pharmacophore modeling of caspase-3-isatin sulfonamide crystal structure, to elucidate the essential non-covalent contacts and its associated pharmacophore features necessary to ensure caspase-3 optimal binding. We performed 20ns long dynamics of this crystal structure to extract global conformation states and converted into structure-based pharmacophore hypotheses which were rigorously validated using an exclusive focussed library of experimental actives and inactives of sulfonamide class by Receiver Operating Characteristic (ROC) statistic. Eighteen structure-based pharmacophore hypotheses with better sensitivity and specificity measures (>0.6) were chosen which collectively showed the role of pocket residues viz. Cys163 (S1 sub-site; required for covalent and H bonding with Michael acceptor of inhibitors), His121 (S1; π stack with bicyclic isatin moiety), Gly122 (S1; H bond with carbonyl oxygen) and Tyr204 (S2; π stack with phenyl group of the isatin sulfonamide molecule) as stringent binding entities for enabling caspase-3 optimal binding. The introduction of spatial pharmacophore site points obtained from dynamics-based pharmacophore models in a virtual screening strategy will be helpful to screen and optimize molecules belonging to sulfonamide class of caspase-3 inhibitors.

Selectivity for La 3+ ion by synthesized 4-((5-methylfuran-2-yl)methylene)hydrazono)methyl)phenol receptor and its spectral analysis

The functionalized molecules with specific molecular sites appear to be a promising approach for detection of cation in UV-visible and fluorescence spectroscopy. The synthesized receptor 4-((5-methylfuran-2-yl)methylene)hydrazono)methyl)phenol MFMHMP was found selective for La3+ among Ag+, K+, Na+, Be2+, Mg2+, Ca2+, Eu3+, Al3+, La3+, Zr4+, Th4+, UO22+, Fe3+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+ and Hg2+ metal ions used as their nitrates by UV-visible spectroscopy and fluorescence spectroscopy. The binding nature of MFMHMP with La3+ ion was analyzed by UV-visible, fluorescence, IR, mass spectroscopy and cyclic voltammetric studies. The stoichiometry was established to be 1:1 by Benesi-Hildebrand, mole-ratio method and method of continuous variation (Jobs method) with good association affinity K = 6.245 × 104 M-1. Computational studies and Density functional theory (DFT) calculation gives the proof of electron transfer during excitation and emission. Binding energy of complex through Density Function Theory -62.387 kcal/mol has also indication of strong binding. The electron transfer energy of Higher occupied molecular orbital (HOMO) to Lower unoccupied molecular orbital (LUMO) is about 4.662 eV for MFMHMP+La3+ Complex. Among that all transitions HOMO → LUMO + 8 and HOMO → LUMO + 9 play a key role for the blue shift transition during complexation.

Targeting epidermal growth factor receptors inhibition in non-small-cell lung cancer: a computational approach

ABSTRACT Epidermal growth factor receptors (EGFRs) are transmembrane receptors present on cell membranes, play an important role in controlling cell growth, apoptosis and other cellular functions. They have an extracellular binding moiety, a transmembrane component and an intracellular tyrosine kinase unit. Mutations of EGFRs can lead to continual or abnormal activation of the receptors causing unregulated cell division, causing cancer such as non-small-cell lung cancer (NSCLC). Hence, the objective is to recognise the potential drug targets through generating pharmacophoric pattern, identifying and building suitable ligands and docking studies with dynamics applications. The pharmacophore of these compounds explains about physicochemical properties required for designing new compounds which provides the design to develop desired targeted drug therapy. The simulation uncovers changes in the width of the essential channel to the active site, extensive to concede substrates. This study concludes the interaction of EGFRs with its inhibitors through computational modelling which can be important initial steps toward the development of novel pharmaceuticals in the fight against NSCLC.