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Zhou C, Kang D, Xu Y, Zhang L, Zha X. Identification of Novel Selective Lysine-Specific Demethylase 1 (LSD1) Inhibitors Using a Pharmacophore-Based Virtual Screening Combined with Docking. Chem Biol Drug Des 2014; 85:659-71. [DOI: 10.1111/cbdd.12461] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/01/2014] [Accepted: 10/15/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Chen Zhou
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 China
| | - Di Kang
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 China
| | - Yungen Xu
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 China
| | - Luyong Zhang
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
| | - Xiaoming Zha
- State Key Laboratory of Natural Medicines; China Pharmaceutical University; Nanjing 210009 China
- Jiangsu Center for Drug Screening; China Pharmaceutical University; Nanjing 210009 China
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Agostino M, Gandhi NS, Mancera RL. Development and application of site mapping methods for the design of glycosaminoglycans. Glycobiology 2014; 24:840-51. [DOI: 10.1093/glycob/cwu045] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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3
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de Candia M, Fiorella F, Lopopolo G, Carotti A, Romano MR, Lograno MD, Martel S, Carrupt PA, Belviso BD, Caliandro R, Altomare C. Synthesis and biological evaluation of direct thrombin inhibitors bearing 4-(piperidin-1-yl)pyridine at the P1 position with potent anticoagulant activity. J Med Chem 2013; 56:8696-711. [PMID: 24102612 DOI: 10.1021/jm401169a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The design and synthesis of a new class of nonpeptide direct thrombin inhibitors, built on the structure of 1-(pyridin-4-yl)piperidine-4-carboxamide, are described. Starting from a strongly basic 1-amidinopiperidine derivative (6) showing poor thrombin (fIIa) and factor Xa (fXa) inhibition activities, anti-fIIa activity and artificial membrane permeability were considerably improved by optimizing the basic P1 and the X-substituted phenyl P4 binding moieties. Structure-activity relationship studies, usefully complemented with molecular modeling results, led us to identify compound 13b, which showed excellent fIIa inhibition (Ki = 6 nM), weak anti-Xa activity (Ki = 5.64 μM), and remarkable selectivity over other serine proteases (e.g., trypsin). Compound 13b showed in vitro anticoagulant activity in the low micromolar range and significant membrane permeability. In mice (ex vivo), 13b demonstrated anticoagulant effects at 2 h after oral dosing (100 mg·kg(-1)), with a significant 43% prolongation of the activated partial thromboplastin time (aPTT), over controls (P < 0.05).
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Affiliation(s)
- Modesto de Candia
- Dipartimento di Farmacia-Scienze del Farmaco, University of Bari "Aldo Moro" , Via E. Orabona 4, 70125 Bari, Italy
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4
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Resisting resistant Mycobacterium tuberculosis naturally: Mechanistic insights into the inhibition of the parasite’s sole signal peptidase Leader peptidase B. Biochem Biophys Res Commun 2013; 433:552-7. [DOI: 10.1016/j.bbrc.2013.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 03/11/2013] [Indexed: 11/16/2022]
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Liu L, Li C, Cochran S, Feder D, Guddat LW, Ferro V. A focused sulfated glycoconjugate Ugi library for probing heparan sulfate-binding angiogenic growth factors. Bioorg Med Chem Lett 2012; 22:6190-4. [DOI: 10.1016/j.bmcl.2012.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 07/23/2012] [Accepted: 08/01/2012] [Indexed: 11/30/2022]
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6
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Grover A, Katiyar SP, Singh SK, Dubey VK, Sundar D. A leishmaniasis study: structure-based screening and molecular dynamics mechanistic analysis for discovering potent inhibitors of spermidine synthase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1476-83. [PMID: 22684087 DOI: 10.1016/j.bbapap.2012.05.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 05/18/2012] [Accepted: 05/31/2012] [Indexed: 11/16/2022]
Abstract
Protozoa Leishmania donovani (Ld) is the main cause of the endemic disease leishmaniasis. Spermidine synthase (SS), an important enzyme in the synthetic pathway of polyamines in Ld, is an essential element for the survival of this protozoan. Targeting SS may provide an important aid for the development of drugs against Ld. However, absence of tertiary structure of spermidine synthase of Leishmania donovani (LSS) limits the possibilities of structure based drug designing. Presence of the same enzyme in the host itself further challenges the drug development process. We modeled the tertiary structure of LSS using homology modeling approach making use of homologous X-ray crystallographic structure of spermidine synthase of Trypanosoma cruzi (TSS) (2.5Å resolution). The modeled structure was stabilized using Molecular Dynamics simulations. Based on active site structural differences between LSS and human spermidine synthase (HSS), we screened a large dataset of compounds against modeled protein using Glide virtual screen docking and selected two best inhibitors based on their docking scores (-10.04 and -13.11 respectively) with LSS and having least/no binding with the human enzyme. Finally Molecular Dynamics simulations were used to assess the dynamic stability of the ligand bound structures and to elaborate on the binding modes. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction.
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Affiliation(s)
- Abhinav Grover
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi 110016, India
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Liu L, Li C, Cochran S, Jimmink S, Ferro V. Synthesis of a Heparan Sulfate Mimetic Library Targeting FGF and VEGF via Click Chemistry on a Monosaccharide Template. ChemMedChem 2012; 7:1267-75. [DOI: 10.1002/cmdc.201200151] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 04/26/2012] [Indexed: 11/07/2022]
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8
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Pauly GT, Loktionova NA, Fang Q, Vankayala SL, Guida WC, Pegg AE. Substitution of aminomethyl at the meta-position enhances the inactivation of O6-alkylguanine-DNA alkyltransferase by O6-benzylguanine. J Med Chem 2009; 51:7144-53. [PMID: 18973327 DOI: 10.1021/jm800675p] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
O(6)-Benzylguanine is an irreversible inactivator of O(6)-alkylguanine-DNA alkyltransferase currently in clinical trials to overcome alkyltransferase-mediated resistance to certain cancer chemotherapeutic alkylating agents. In order to produce more soluble alkyltransferase inhibitors, we have synthesized three aminomethyl-substituted O(6)-benzylguanines and the three methyl analogs and found that the substitution of aminomethyl at the meta-position greatly enhances inactivation of alkyltransferase, whereas para-substitution has little effect and ortho-substitution virtually eliminates activity. Molecular modeling of their interactions with alkyltransferase provided a molecular explanation for these results. The square of the correlation coefficient (R(2)) obtained between E-model scores (obtained from GLIDE XP/QPLD docking calculations) vs log(ED(50)) values via a linear regression analysis was 0.96. The models indicate that the ortho-substitution causes a steric clash interfering with binding, whereas the meta-aminomethyl substitution allows an interaction of the amino group to generate an additional hydrogen bond with the protein.
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Affiliation(s)
- Gary T Pauly
- Laboratory of Comparative Carcinogenesis, National Cancer Institute at Frederick, P.O. Box B, Building 538, Frederick, Maryland 21702, USA
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Welch KT, Turner TA, Preast CE. Rational design of novel glycomimetics: Inhibitors of concanavalin A. Bioorg Med Chem Lett 2008; 18:6573-5. [DOI: 10.1016/j.bmcl.2008.09.095] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 09/24/2008] [Accepted: 09/26/2008] [Indexed: 11/30/2022]
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Gandhi NS, Mancera RL. The Structure of Glycosaminoglycans and their Interactions with Proteins. Chem Biol Drug Des 2008; 72:455-82. [DOI: 10.1111/j.1747-0285.2008.00741.x] [Citation(s) in RCA: 703] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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11
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A surface plasmon resonance-based solution affinity assay for heparan sulfate-binding proteins. Glycoconj J 2008; 26:577-87. [DOI: 10.1007/s10719-008-9210-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 10/05/2008] [Accepted: 10/27/2008] [Indexed: 12/15/2022]
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12
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Talele TT, McLaughlin ML. Molecular docking/dynamics studies of Aurora A kinase inhibitors. J Mol Graph Model 2008; 26:1213-22. [DOI: 10.1016/j.jmgm.2007.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 11/03/2007] [Accepted: 11/03/2007] [Indexed: 12/11/2022]
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13
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Kaushik-Basu N, Bopda-Waffo A, Talele TT, Basu A, Costa PRR, da Silva AJM, Sarafianos SG, Noël F. Identification and characterization of coumestans as novel HCV NS5B polymerase inhibitors. Nucleic Acids Res 2008; 36:1482-96. [PMID: 18203743 PMCID: PMC2275130 DOI: 10.1093/nar/gkm1178] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 12/22/2007] [Accepted: 12/26/2007] [Indexed: 12/31/2022] Open
Abstract
The hepatitis C virus (HCV) NS5B is essential for viral RNA replication and is therefore a prime target for development of HCV replication inhibitors. Here, we report the identification of a new class of HCV NS5B inhibitors belonging to the coumestan family of phytoestrogens. Based on the in vitro NS5B RNA-dependent RNA polymerase (RdRp) inhibition in the low micromolar range by wedelolactone, a naturally occurring coumestan, we evaluated the anti-NS5B activity of four synthetic coumestan analogues bearing different patterns of substitutions in their A and D rings, and observed a good structure-activity correlation. Kinetic characterization of coumestans revealed a noncompetitive mode of inhibition with respect to nucleoside triphosphate (rNTP) substrate and a mixed mode of inhibition towards the nucleic acid template, with a major competitive component. The modified order of addition experiments with coumestans and nucleic acid substrates affected the potencies of the coumestan inhibitors. Coumestan interference at the step of NS5B-RNA binary complex formation was confirmed by cross-linking experiments. Molecular docking of coumestans within the allosteric site of NS5B yielded significant correlation between their calculated binding energies and IC(50) values. Coumestans thus add to the diversifying pool of anti-NS5B agents and provide a novel scaffold for structural refinement and development of potent NS5B inhibitors.
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Affiliation(s)
- Neerja Kaushik-Basu
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA.
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Enyedy IJ, Egan WJ. Can we use docking and scoring for hit-to-lead optimization? J Comput Aided Mol Des 2008; 22:161-8. [PMID: 18183356 DOI: 10.1007/s10822-007-9165-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2007] [Accepted: 12/18/2007] [Indexed: 10/22/2022]
Abstract
Docking and scoring is currently one of the tools used for hit finding and hit-to-lead optimization when structural information about the target is known. Docking scores have been found useful for optimizing ligand binding to reproduce experimentally observed binding modes. The question is, can docking and scoring be used reliably for hit-to-lead optimization? To illustrate the challenges of scoring for hit-to-lead optimization, the relationship of docking scores with experimentally determined IC(50) values measured in-house were tested. The influences of the particular target, crystal structure, and the precision of the scoring function on the ability to differentiate between actives and inactives were analyzed by calculating the area under the curve of receiver operator characteristic curves for docking scores. It was found that for the test sets considered, MW and sometimes ClogP were as useful as GlideScores and no significant difference was observed between SP and XP scores for differentiating between actives and inactives. Interpretation by an expert is still required to successfully utilize docking and scoring in hit-to-lead optimization.
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Affiliation(s)
- Istvan J Enyedy
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
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Liu L, Bytheway I, Karoli T, Fairweather JK, Cochran S, Li C, Ferro V. Design, synthesis, FGF-1 binding, and molecular modeling studies of conformationally flexible heparin mimetic disaccharides. Bioorg Med Chem Lett 2008; 18:344-9. [DOI: 10.1016/j.bmcl.2007.10.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 10/19/2007] [Accepted: 10/20/2007] [Indexed: 11/15/2022]
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Taldone T, Zito SW, Talele TT. Inhibition of dipeptidyl peptidase-IV (DPP-IV) by atorvastatin. Bioorg Med Chem Lett 2008; 18:479-84. [DOI: 10.1016/j.bmcl.2007.11.107] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Revised: 11/26/2007] [Accepted: 11/27/2007] [Indexed: 11/28/2022]
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Patel PD, Patel MR, Kaushik-Basu N, Talele TT. 3D QSAR and molecular docking studies of benzimidazole derivatives as hepatitis C virus NS5B polymerase inhibitors. J Chem Inf Model 2007; 48:42-55. [PMID: 18076152 DOI: 10.1021/ci700266z] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The urgent need for novel HCV antiviral agents has provided an impetus for understanding the structural requisites of NS5B polymerase inhibitors at the molecular level. Toward this objective, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of 67 HCV NS5B polymerase inhibitors were performed using two methods. First, ligand-based 3D QSAR studies were performed based on the lowest energy conformations employing the atom fit alignment method. Second, receptor-based 3D QSAR models were derived from the predicted binding conformations obtained by docking all NS5B inhibitors at the allosteric binding site of NS5B (PDB ID: 2dxs). Results generated from the ligand-based model were found superior (r2cv values of 0.630 for CoMFA and 0.668 for CoMSIA) to those obtained by the receptor-based model (r2cv values of 0.536 and 0.561 for CoMFA and CoMSIA, respectively). The predictive ability of the models was validated using a structurally diversified test set of 22 compounds that had not been included in a preliminary training set of 45 compounds. The predictive r2 values for the ligand-based CoMFA and CoMSIA models were 0.734 and 0.800, respectively, while the corresponding predictive r2 values for the receptor-based CoMFA and CoMSIA models were 0.538 and 0.639, respectively. The greater potency of the tryptophan derivatives over that of the tyrosine derivatives was interpreted based on CoMFA steric and electrostatic contour maps. The CoMSIA results revealed that for a NS5B inhibitor to have appreciable inhibitory activity it requires hydrogen bond donor and acceptor groups at the 5-position of the indole ring and an R substituent at the chiral carbon, respectively. Interpretation of the CoMFA and CoMSIA contour maps in context of the topology of the allosteric binding site of NS5B provided insight into NS5B-inhibitor interactions. Taken together, the present 3D QSAR models were found to accurately predict the HCV NS5B polymerase inhibitory activity of structurally diverse test set compounds and to yield reliable clues for further optimization of the benzimidazole derivatives in the data set.
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Affiliation(s)
- Pallav D Patel
- Department of Pharmaceutical Sciences, College of Pharmacy and Allied Health Professions, St. John's University, Jamaica, New York 11439, USA
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Cochran S, Li CP, Bytheway I. An Experimental and Molecular-Modeling Study of the Binding of Linked Sulfated Tetracyclitols to FGF-1 and FGF-2. Chembiochem 2005; 6:1882-90. [PMID: 16175541 DOI: 10.1002/cbic.200500089] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The experimental binding affinities of a series of linked sulfated tetracyclitols [Cyc2N-R-NCyc2, where Cyc = C6H6(OSO3Na)3 and R = (CH2)n (n = 2-10), p-xylyl or (C2H4)2-Ncyc] for the fibroblast growth factors FGF-1 and FGF-2 have been measured by using a surface plasmon resonance assay. The KD values range from 7.0 nM to 1.1 microM for the alkyl-linked ligands. The binding affinity is independent of the flexibility of the linker, as replacement of the alkyl linker with a rigid p-xylyl group did not affect the KD. Calculations suggest that binding modes for the p-xylyl-linked ligand are similar to those calculated for the flexible alkyl-linked tetracyclitols. The possible formation of cross-linked FGF:cyclitol complexes was examined by determining KD values at increasing protein concentrations. No changes in KD were observed; this suggesting that only 1:1 complexes are formed under these assay conditions. Monte Carlo multiple-minima calculations of low-energy conformers of the FGF-bound ligands showed that all of the sulfated tetracyclitol ligands can bind effectively in the heparan sulfate-binding sites of FGF-1 and FGF-2. Binding affinities of these complexes were estimated by the Linear Interaction Energy (LIE) method to within a root-mean-square deviation of 1 kcal mol(-1) of the observed values. The effect of incorporating cations to balance the overall charge of the complexes during the LIE calculations was also explored.
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Affiliation(s)
- Siska Cochran
- Drug Design Group, Progen Industries Ltd. P.O. Box 28, Richlands BC, Queensland 4077, Australia
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