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Afza N, Fatma S, Ghous F, Shukla S, Rai S, Srivastava K, Bishnoi A. An Efficient Multicomponent Synthesis, Characterization, SAR, In-silico ADME prediction and Molecular docking Studies of 2-Amino-7-(substituted-phenyl)-3-cyano-4-phenyl-4,5,6,7-tetrahydropyrano[2,3-b] pyrrole-5-carboxylic acid Derivatives and Their in-vitro Antimicrobial Activity. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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2
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Kinetics, mechanism and density functional theory calculations on base hydrolysis of α-amino acid esters catalyzed by [Pd(AEMP)(H2O)2]2+ (AEMP = 2-(2-aminoethyl)-1-methylpyrrolidine). REACTION KINETICS MECHANISMS AND CATALYSIS 2020. [DOI: 10.1007/s11144-020-01734-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Devi P, Fatma S, Shukla S, Kumar R, Singh V, Bishnoi A. Synthesis, spectroscopic investigation, molecular docking and DFT studies of novel (2Z,4Z)-2,4-bis(4-chlorobenzylidene)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid (BCOPCA). Heliyon 2018; 4:e01009. [PMID: 30582037 PMCID: PMC6299111 DOI: 10.1016/j.heliyon.2018.e01009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/16/2018] [Accepted: 11/30/2018] [Indexed: 11/29/2022] Open
Abstract
The synthesized compound (2Z,4Z)-2,4-bis(4-chlorobenzylidene)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid (BCOPCA) was characterised by Ultraviolet, FT-Infra Red, 1H, 13C Nuclear Magnetic Resonance and mass spectroscopy. The compound was further subjected to quantum chemical calculations at the level of density functional theory (DFT) using 6-31G (d,p) basis sets method with B3LYP and CAM-B3LYP hybrid functionals. The intramolecular interactions, polarizability, hyperpolarizability and nonlinear optical properties of the title compound were also incorporated in the study. The total first static hyperpolarizability (β0 = 19.477 × 10−30 and 16.924 × 10−30 esu) value was also computed and indicated the title molecule as an interesting forthcoming NLO material. The other thermodynamic properties (entropy, heat capacity and zero vibrational energy) were also discussed. The study also includes NBO computations, complete vibrational assignments, Mulliken charges, UV–Visible spectral analysis and HOMO–LUMO energies. The regions of low and high electron density were obtained from MESP and ESP maps. The calculated parameters for BCOPCA using aforementioned functions are harmonious with the experimental findings. The in-vitro antimicrobial activity and molecular docking studies of BCOPCA were also done and showed a good correlation.
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Affiliation(s)
- Poornima Devi
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
| | - Shaheen Fatma
- Department of Chemistry, Shri Ramswaroop Memorial University, Lucknow Dewa Road, Barabanki 225003, India
| | - Shraddha Shukla
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
| | - Roop Kumar
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
| | - Vineeta Singh
- Department of Biotechnology, Institute of Engineering and Technology, Lucknow 226021, India
| | - Abha Bishnoi
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
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Synthesis, spectroscopic and DFT studies of novel 4-(morpholinomethyl)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.12.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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5
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MOHAJER S, BAHARFAR R. Diastereoselective synthesis of novel 2,5-dioxopyrrolidine derivatives via biocatalytic domino reactions. Turk J Chem 2017. [DOI: 10.3906/kim-1612-45] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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6
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Synthesis and antibacterial activity of new N-substituted 7-amino-4-methyl-2H-chromen-2-ones. RESEARCH ON CHEMICAL INTERMEDIATES 2016. [DOI: 10.1007/s11164-016-2510-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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7
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Rad-Moghadam K, Esmaeili AA, Ghalandarabad SA, Hoseininejad F, Fallah-Rasoulinejad SA, Kiani S. Synthesis of Novel 1-(Benzo[ d]thiazol-2-yl)-1 H-pyrrol-2(5 H)-ones. J Heterocycl Chem 2014. [DOI: 10.1002/jhet.1885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
| | - Abbas Ali Esmaeili
- Chemistry Department; University of Birjand; Birjand P.O. Box 97175/615 Iran
- Chemistry Department; Ferdowsi University of Mashhad; Mashhad Iran
| | | | | | | | - Samaneh Kiani
- Chemistry Department; University of Guilan; Rasht P.O. Box 41335-19141 Iran
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Toledo Warshaviak D, Golan G, Borrelli KW, Zhu K, Kalid O. Structure-based virtual screening approach for discovery of covalently bound ligands. J Chem Inf Model 2014; 54:1941-50. [PMID: 24932913 DOI: 10.1021/ci500175r] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We present a fast and effective covalent docking approach suitable for large-scale virtual screening (VS). We applied this method to four targets (HCV NS3 protease, Cathepsin K, EGFR, and XPO1) with known crystal structures and known covalent inhibitors. We implemented a customized "VS mode" of the Schrödinger Covalent Docking algorithm (CovDock), which we refer to as CovDock-VS. Known actives and target-specific sets of decoys were docked to selected X-ray structures, and poses were filtered based on noncovalent protein-ligand interactions known to be important for activity. We were able to retrieve 71%, 72%, and 77% of the known actives for Cathepsin K, HCV NS3 protease, and EGFR within 5% of the decoy library, respectively. With the more challenging XPO1 target, where no specific interactions with the protein could be used for postprocessing of the docking results, we were able to retrieve 95% of the actives within 30% of the decoy library and achieved an early enrichment factor (EF1%) of 33. The poses of the known actives bound to existing crystal structures of 4 targets were predicted with an average RMSD of 1.9 Å. To the best of our knowledge, CovDock-VS is the first fully automated tool for efficient virtual screening of covalent inhibitors. Importantly, CovDock-VS can handle multiple chemical reactions within the same library, only requiring a generic SMARTS-based predefinition of the reaction. CovDock-VS provides a fast and accurate way of differentiating actives from decoys without significantly deteriorating the accuracy of the predicted poses for covalent protein-ligand complexes. Therefore, we propose CovDock-VS as an efficient structure-based virtual screening method for discovery of novel and diverse covalent ligands.
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Hu Y, Li CY, Wang XM, Yang YH, Zhu HL. 1,3,4-Thiadiazole: synthesis, reactions, and applications in medicinal, agricultural, and materials chemistry. Chem Rev 2014; 114:5572-610. [PMID: 24716666 DOI: 10.1021/cr400131u] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yang Hu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing 210093, People's Republic of China
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Traube T, Shokhen M, Albeck A. Application of EMBM to Structure-Based Design of Warheads for Protease Inhibitors. Mol Inform 2014; 33:36-42. [PMID: 27485197 DOI: 10.1002/minf.201300099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/27/2013] [Indexed: 11/06/2022]
Abstract
Most CADD tools handle non-covalent enzyme inhibitors, despite the growing interest of the pharma industry in covalent inhibitors. We have recently introduced an enzyme mechanism-based method, EMBM, as a computational tool for binding trend analysis and prediction of chemical sites (CS) of reversible covalent enzyme inhibitors. In the current study we demonstrate the utility of EMBM to structure-based applications. In this mode, the energy of the enzyme-inhibitor covalent bond is accounted for by the W1 and W2 covalent descriptors we have developed, whereas the non-covalent interactions between the inhibitor CS and the enzyme active site can be estimated directly on the 3D structure of the enzyme-inhibitor complex.
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Affiliation(s)
- Tamar Traube
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel tel.: 972-3-5318862, fax: 972-3-7384053
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel tel.: 972-3-5318862, fax: 972-3-7384053.
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel tel.: 972-3-5318862, fax: 972-3-7384053.
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Thomson JE, Kyle AF, Ling KB, Smith SR, Slawin AM, Smith AD. Applications of NHC-mediated O- to C-carboxyl transfer: synthesis of (±)-N-benzyl-coerulescine and (±)-horsfiline. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.03.047] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
A convergent synthesis of alpha-ketoamide inhibitors of Pin1 is described. An alpha-hydroxyorthothioester derivative of Ser was reacted directly with an amine synthon. The reaction was catalyzed by HgO and HgCl(2) to form alpha-hydroxyamide. Thus, hydrolysis and coupling were combined in one step with 80% yield. Two diastereomers of a phospho-Ser-Pro alpha-ketoamide analogue were synthesized. The IC(50) values of 100 and 200 microM were surprisingly weak for Pin1 peptidyl prolyl isomerase.
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Affiliation(s)
- Guoyan G Xu
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
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Investigation of ketone warheads as alternatives to the nitrile for preparation of potent and selective cathepsin K inhibitors. Bioorg Med Chem Lett 2009; 19:675-9. [DOI: 10.1016/j.bmcl.2008.12.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 12/09/2008] [Accepted: 12/10/2008] [Indexed: 11/20/2022]
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Lecaille F, Brömme D, Lalmanach G. Biochemical properties and regulation of cathepsin K activity. Biochimie 2007; 90:208-26. [PMID: 17935853 DOI: 10.1016/j.biochi.2007.08.011] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 08/24/2007] [Indexed: 02/02/2023]
Abstract
Cysteine cathepsins (11 in humans) are mostly located in the acidic compartments of cells. They have been known for decades to be involved in intracellular protein degradation as housekeeping proteases. However, the discovery of new cathepsins, including cathepsins K, V and F, has provided strong evidence that they also participate in specific biological events. This review focuses on the current knowledge of cathepsin K, the major bone cysteine protease, which is a drug target of clinical interest. Nevertheless, we will not discuss recent developments in cathepsin K inhibitor design since they have been extensively detailed elsewhere. We will cover features of cathepsin K structure, cellular and tissue distribution, substrate specificity, and regulation (pH, propeptide, glycosaminoglycans, oxidants), and its putative roles in physiological or pathophysiological processes. Finally, we will review the kinetic data of its inhibition by natural endogenous inhibitors (stefin B, cystatin C, H- and L-kininogens).
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Affiliation(s)
- Fabien Lecaille
- INSERM, U618, Protéases et Vectorisation Pulmonaires, Equipe Protéases et Pathologies Pulmonaires, Faculté de Médecine, Université François Rabelais, 10 Boulevard Tonnellé, F-37032 Tours Cedex, France.
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McConnell O, Bach A, Balibar C, Byrne N, Cai Y, Carter G, Chlenov M, Di L, Fan K, Goljer I, He Y, Herold D, Kagan M, Kerns E, Koehn F, Kraml C, Marathias V, Marquez B, McDonald L, Nogle L, Petucci C, Schlingmann G, Tawa G, Tischler M, Williamson RT, Sutherland A, Watts W, Young M, Zhang MY, Zhang Y, Zhou D, Ho D. Enantiomeric separation and determination of absolute stereochemistry of asymmetric molecules in drug discovery—Building chiral technology toolboxes. Chirality 2007; 19:658-82. [PMID: 17390370 DOI: 10.1002/chir.20399] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The application of Chiral Technology, or the (extensive) use of techniques or tools for the determination of absolute stereochemistry and the enantiomeric or chiral separation of racemic small molecule potential lead compounds, has been critical to successfully discovering and developing chiral drugs in the pharmaceutical industry. This has been due to the rapid increase over the past 10-15 years in potential drug candidates containing one or more asymmetric centers. Based on the experiences of one pharmaceutical company, a summary of the establishment of a Chiral Technology toolbox, including the implementation of known tools as well as the design, development, and implementation of new Chiral Technology tools, is provided.
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Affiliation(s)
- Oliver McConnell
- Wyeth Research, Chemical and Screening Sciences, Collegeville, PA 19426, USA.
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