1
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Synthesis, Molecular Docking, and Bioactivity Study of Novel Hybrid Benzimidazole Urea Derivatives: A Promising α-Amylase and α-Glucosidase Inhibitor Candidate with Antioxidant Activity. Pharmaceutics 2023; 15:pharmaceutics15020457. [PMID: 36839780 PMCID: PMC9963656 DOI: 10.3390/pharmaceutics15020457] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
A novel series of benzimidazole ureas 3a-h were elaborated using 2-(1H-benzoimidazol-2-yl) aniline 1 and the appropriate isocyanates 2a-h. The antioxidant and possible antidiabetic activities of the target benzimidazole-ureas 3a-h were evaluated. Almost all compounds 3a-h displayed strong to moderate antioxidant activities. When tested using the three antioxidant techniques, TAC, FRAP, and MCA, compounds 3b and 3c exhibited marked activity. The most active antioxidant compound in this family was compound 3g, which had excellent activity using four different methods: TAC, FRAP, DPPH-SA, and MCA. In vitro antidiabetic assays against α-amylase and α-glucosidase enzymes revealed that the majority of the compounds tested had good to moderate activity. The most favorable results were obtained with compounds 3c, 3e, and 3g, and analysis revealed that compounds 3c (IC50 = 18.65 ± 0.23 μM), 3e (IC50 = 20.7 ± 0.06 μM), and 3g (IC50 = 22.33 ± 0.12 μM) had good α-amylase inhibitory potential comparable to standard acarbose (IC50 = 14.21 ± 0.06 μM). Furthermore, the inhibitory effect of 3c (IC50 = 17.47 ± 0.03 μM), 3e (IC50 = 21.97 ± 0.19 μM), and 3g (IC50 = 23.01 ± 0.12 μM) on α-glucosidase was also comparable to acarbose (IC50 = 15.41 ± 0.32 μM). According to in silico molecular docking studies, compounds 3a-h had considerable affinity for the active sites of human lysosomal acid α-glucosidase (HLAG) and pancreatic α-amylase (HPA), indicating that the majority of the examined compounds had potential anti-hyperglycemic action.
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2
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Shi J, Zhao M, Li K, Zhao Y, Li W, Peng Y, Zheng J. Metabolic Activation and Cytotoxicity of Fungicide Carbendazim Mediated by CYP1A2. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4092-4101. [PMID: 35316061 DOI: 10.1021/acs.jafc.1c08144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Carbendazim (CBZ) is a broad-spectrum fungicide widely used in many nations for foliar spray as well as seed and soil treatment. The resulting contamination and environmental pollution have been drawing public attention. In particular, CBZ was reported to cause liver damage in rats and zebrafish, and the mechanisms of its toxicity have not been clarified. The purposes of this study were to investigate the metabolic activation of CBZ and to determine a possible role of the reactive metabolites in CBZ-induced liver injury reported. One oxidative metabolite (M1), one glutathione conjugate (M2), and one N-acetyl cysteine conjugate (M3) were detected in human and rat liver microsomal incubations fortified with glutathione or N-acetyl cysteine after exposure to CBZ. CYP1A2 was the major enzyme responsible for the metabolic activation of CBZ. Biliary M2 and urinary M3 were detected in rats treated with CBZ. CBZ-derived protein adduction was found in cultured rat primary hepatocytes treated with CBZ. The increase of administration concentration intensified not only the cytotoxicity but also protein adduction induced by CBZ, suggesting a correlation of the cytotoxicity with the observed protein modification. The findings facilitate the understanding of the mechanisms of toxic action of CBZ.
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Affiliation(s)
- Junzu Shi
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P. R. China
| | - Min Zhao
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P. R. China
| | - Kaixuan Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P. R. China
| | - Yanjia Zhao
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P. R. China
| | - Wei Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P. R. China
| | - Ying Peng
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P. R. China
| | - Jiang Zheng
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P. R. China
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou 550025, P. R. China
- Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550025, P. R. China
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3
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Urokinase plasminogen activator as an anti-metastasis target: inhibitor design principles, recent amiloride derivatives, and issues with human/mouse species selectivity. Biophys Rev 2022; 14:277-301. [PMID: 35340592 PMCID: PMC8921380 DOI: 10.1007/s12551-021-00921-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/18/2021] [Indexed: 01/09/2023] Open
Abstract
The urokinase plasminogen activator (uPA) is a widely studied anticancer drug target with multiple classes of inhibitors reported to date. Many of these inhibitors contain amidine or guanidine groups, while others lacking these groups show improved oral bioavailability. Most of the X-ray co-crystal structures of small molecule uPA inhibitors show a key salt bridge with the side chain carboxylate of Asp189 in the S1 pocket of uPA. This review summarises the different classes of uPA inhibitors, their binding interactions and experimentally measured inhibitory potencies and highlights species selectivity issues with attention to recently described 6-substituted amiloride and 5‑N,N-(hexamethylene)amiloride (HMA) derivatives.
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4
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Nawaz S, Asghar F, Patujo J, Fatima S, Murtaza B, Munir S, Naz M, Badshah A, Butler IS. New ferrocene-integrated multifunctional guanidine surfactants: synthesis, spectroscopic elucidation, DNA interaction studies, and DFT calculations. NEW J CHEM 2022. [DOI: 10.1039/d1nj03424c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Investigation of three new ferrocene appended guanidines as potential surfactants, antioxidants and DNA binders with DFT measurements.
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Affiliation(s)
- Sameen Nawaz
- Department of Chemistry, Quaid-i-Azam University, Islamabad (45320), Pakistan
| | - Faiza Asghar
- Department of Chemistry, University of Wah, Quaid Avenue, Wah (47040), Pakistan
| | - Jahangeer Patujo
- Department of Chemistry, Quaid-i-Azam University, Islamabad (45320), Pakistan
| | - Saira Fatima
- Department of Chemistry, Quaid-i-Azam University, Islamabad (45320), Pakistan
| | - Babar Murtaza
- Physiologie de la Nutrition & Toxicologie, U1231 INSERM/Université de Bourgogne-Franche Comté (UBFC)/Agro-Sup, 21000 Dijon, France
| | - Shamsa Munir
- School of Applied Sciences & Humanities (NUSASH), NUTECH, Islamabad, Pakistan
| | - Mehwish Naz
- Department of Chemistry, Quaid-i-Azam University, Islamabad (45320), Pakistan
| | - Amin Badshah
- Department of Chemistry, Quaid-i-Azam University, Islamabad (45320), Pakistan
| | - Ian S. Butler
- Department of Chemistry, McGill University, Montreal, QC H3A 2K6, Canada
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5
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Privat C, Granadino-Roldán JM, Bonet J, Santos Tomas M, Perez JJ, Rubio-Martinez J. Fragment dissolved molecular dynamics: a systematic and efficient method to locate binding sites. Phys Chem Chem Phys 2021; 23:3123-3134. [PMID: 33491698 DOI: 10.1039/d0cp05471b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diverse computational methods to support fragment-based drug discovery (FBDD) are available in the literature. Despite their demonstrated efficacy in supporting FBDD campaigns, they exhibit some drawbacks such as protein denaturation or ligand aggregation that have not yet been clearly overcome in the framework of biomolecular simulations. In the present work, we discuss a systematic semi-automatic novel computational procedure, designed to surpass these difficulties. The method, named fragment dissolved Molecular Dynamics (fdMD), utilizes simulation boxes of solvated small fragments, adding a repulsive Lennard-Jones potential term to avoid aggregation, which can be easily used to solvate the targets of interest. This method has the advantage of solvating the target with a low number of ligands, thus preventing the denaturation of the target, while simultaneously generating a database of ligand-solvated boxes that can be used in further studies. A number of scripts are made available to analyze the results and obtain the descriptors proposed as a means to trustfully discard spurious binding sites. To test our method, four test cases of different complexity have been solvated with ligand boxes and four molecular dynamics runs of 200 ns length have been run for each system, which have been extended up to 1 μs when needed. The reported results point out that the selected number of replicas are enough to identify the correct binding sites irrespective of the initial structure, even in the case of proteins having several close binding sites for the same ligand. We also propose a set of descriptors to analyze the results, among which the average MMGBSA and the average KDEEP energies have emerged as the most robust ones.
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Affiliation(s)
- Cristian Privat
- Departament de Ciència dels Materials i Química Física, Universitat de Barcelona (UB) and the Institut de Quimica Teorica i Computacional (IQTCUB), Martí i Franqués 1, 08028 Barcelona, Spain.
| | - José M Granadino-Roldán
- Departamento de Química Física y Analítica, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus "Las Lagunillas" s/n, 23071, Jaén, Spain
| | - Jordi Bonet
- Departament de Ciència dels Materials i Química Física, Universitat de Barcelona (UB) and the Institut de Quimica Teorica i Computacional (IQTCUB), Martí i Franqués 1, 08028 Barcelona, Spain.
| | - Maria Santos Tomas
- Department of Architecture Technology, Universitat Politecnica de Catalunya, Av. Diagonal 649, 08028 Barcelona, Spain
| | - Juan J Perez
- Deparment of Chemical Engineering, Universitat Politecnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain
| | - Jaime Rubio-Martinez
- Departament de Ciència dels Materials i Química Física, Universitat de Barcelona (UB) and the Institut de Quimica Teorica i Computacional (IQTCUB), Martí i Franqués 1, 08028 Barcelona, Spain.
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6
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Aroua LM. Novel Mixed Complexes Derived from Benzoimidazolphenylethanamine and
4-(Benzoimidazol-2-yl)aniline: Synthesis, Characterization, Antibacterial
Evaluation and Theoretical Prediction of Toxicity. ACTA ACUST UNITED AC 2020. [DOI: 10.14233/ajchem.2020.22472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Benzoimidazolphenylethanamine (BPE) has been synthesized using condensation reaction from
o-phenyldiamine and L-phenylalanine. Some metal complexes have been synthesized from
4-(benzoimidazol-2-yl)aniline, benzoimidazolylphenylethanamine and cadmium(II), tin(II), copper(II)
and nickel(II) metal in a molar ratio (1:1:1). All new metal complexes were characterized by
spectroscopic data of FTIR, UV-visible electronic absorption, X-ray powder diffraction and thermal
analysis. Spectra analysis of the mixed metal complexes showed the coordination of ligands to the
metal ions via nitrogen atoms. The XRD powder showed that metal complexes have a monoclinic
system. The preliminary tested in vitro antibacterial activities of Sn(II) complex was assayed against
four bacterial isolates namely Micrococcus luteus, Staphylococcus aureus as Gram-positive,
Pseudomonas aerugmosa and Escherichia coli.
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Affiliation(s)
- Lotfi M. Aroua
- 1Department of Chemistry, College of Science, Qassim University, Campus University, King Abdulaziz Road, P.O.Box: 6644, Buraydah, Qassim, Kingdom of Saudi Arabia 2Laboratory of Organic Structural Chemistry & Macromolecules, Department of Chemistry, Faculty of Sciences of Tunis, Tunis El-Manar University, El Manar I 2092, Tunis, Tunisia
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7
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Solis-Calero C, Zanatta G, Pessoa CDÓ, Carvalho HF, Freire VN. Explaining urokinase type plasminogen activator inhibition by amino-5-hydroxybenzimidazole and two naphthamidine-based compounds through quantum biochemistry. Phys Chem Chem Phys 2018; 20:22818-22830. [DOI: 10.1039/c8cp04315a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Urokinase plasminogen activator (uPA) is a biomarker and therapeutic target for several cancer types whose inhibition has been shown to slow tumor growth and metastasis.
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Affiliation(s)
- Christian Solis-Calero
- Department of Structural and Functional Biology
- State University of Campinas
- 13083-863 Campinas
- Brazil
| | - Geancarlo Zanatta
- Department of Physics
- Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
| | - Claudia do Ó Pessoa
- Department of Physiology and Pharmacology
- Federal University of Ceará
- 60430-270 Fortaleza
- Brazil
| | - Hernandes F. Carvalho
- Department of Structural and Functional Biology
- State University of Campinas
- 13083-863 Campinas
- Brazil
| | - Valder N. Freire
- Department of Physics
- Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
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8
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Hubbard RE. The Role of Fragment-based Discovery in Lead Finding. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch01] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Hall DR, Kozakov D, Whitty A, Vajda S. Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery. Trends Pharmacol Sci 2015; 36:724-736. [PMID: 26538314 DOI: 10.1016/j.tips.2015.08.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/01/2023]
Abstract
Analysis of binding energy hot spots at protein surfaces can provide crucial insights into the prospects for successful application of fragment-based drug discovery (FBDD), and whether a fragment hit can be advanced into a high-affinity, drug-like ligand. The key factor is the strength of the top ranking hot spot, and how well a given fragment complements it. We show that published data are sufficient to provide a sophisticated and quantitative understanding of how hot spots derive from a protein 3D structure, and how their strength, number, and spatial arrangement govern the potential for a surface site to bind to fragment-sized and larger ligands. This improved understanding provides important guidance for the effective application of FBDD in drug discovery.
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Affiliation(s)
- David R Hall
- Acpharis Inc., 160 North Mill Street, Holliston, MA 01746, USA
| | - Dima Kozakov
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA, 02215, USA.
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA; Department of Chemistry, Boston University, Boston, MA, 02215, USA.
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10
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Rauf MK, Gul R, Rashid Z, Badshah A, Tahir MN, Shahid M, Khan A. Synthesis, characterization, DNA binding and in vitro antimicrobial studies of a novel tetra-substituted N-isopropyl-N-(4-ferrocenylphenyl)-N'-(2,6-diethylphenyl)-N″-benzoylguanidine: crystallographic structure and quantum chemical computations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:1099-1106. [PMID: 25459507 DOI: 10.1016/j.saa.2014.09.134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/26/2014] [Accepted: 09/30/2014] [Indexed: 06/04/2023]
Abstract
A novel tetra-substituted guanidine, N-isopropyl-N-(4-ferrocenylphenyl)-N'-(2,6-diethylphenyl)-N″-benzoylguanidine (1), [(CH3)2CH)(C5H5FeC5H4C6H4)NC(NHCOC6H5)(NHC6H3(CH2CH3)2] has been synthesized and characterized by elemental analysis, FT-IR, multinuclear ((1)H, (13)C) NMR spectroscopy, single crystal X-rays diffraction analysis and density functional theory based quantum chemical calculations. The torsion angles indicating that the guanidine moiety and carbonyl group are almost co-planar, due to the pseudo hexagonal ring formed by intramolecular N-H⋯O hydrogen bonds. The DNA interaction studies performed by cyclic voltammetry and UV-visible spectroscopy are in close agreement with the binding constants (K) 1.4×10(4) and 1.2×10(4) respectively. The shift in peak potential, current and absorption maxima of the studied ferrocenyl guanidine in the presence of DNA discovered that CV coupled with UV-vis spectroscopy could provide an opportunity to elaborate DNA interaction mechanism, a prerequisite for the design of new drug like agents and understanding the molecular basis of their action. The synthesized compound (1) has also been screened for their antibacterial and antifungal.
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Affiliation(s)
| | - Rukhsana Gul
- Department of Chemistry, Quaid-I-Azam University, Islamabad 45320, Pakistan; Department of Chemistry, Gomal University, Dera Ismail Khan, Pakistan
| | - Zahid Rashid
- Department of Chemistry, Quaid-I-Azam University, Islamabad 45320, Pakistan
| | - Amin Badshah
- Department of Chemistry, Quaid-I-Azam University, Islamabad 45320, Pakistan.
| | | | - Muhammad Shahid
- Department of Chemistry, Quaid-I-Azam University, Islamabad 45320, Pakistan
| | - Azim Khan
- Department of Chemistry, Gomal University, Dera Ismail Khan, Pakistan
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11
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Application of molecular modeling to urokinase inhibitors development. BIOMED RESEARCH INTERNATIONAL 2014; 2014:625176. [PMID: 24967388 PMCID: PMC4055159 DOI: 10.1155/2014/625176] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/22/2014] [Indexed: 01/01/2023]
Abstract
Urokinase-type plasminogen activator (uPA) plays an important role in the regulation of diverse physiologic and pathologic processes. Experimental research has shown that elevated uPA expression is associated with cancer progression, metastasis, and shortened survival in patients, whereas suppression of proteolytic activity of uPA leads to evident decrease of metastasis. Therefore, uPA has been considered as a promising molecular target for development of anticancer drugs. The present study sets out to develop the new selective uPA inhibitors using computer-aided structural based drug design methods. Investigation involves the following stages: computer modeling of the protein active site, development and validation of computer molecular modeling methods: docking (SOL program), postprocessing (DISCORE program), direct generalized docking (FLM program), and the application of the quantum chemical calculations (MOPAC package), search of uPA inhibitors among molecules from databases of ready-made compounds to find new uPA inhibitors, and design of new chemical structures and their optimization and experimental examination. On the basis of known uPA inhibitors and modeling results, 18 new compounds have been designed, calculated using programs mentioned above, synthesized, and tested in vitro. Eight of them display inhibitory activity and two of them display activity about 10 μM.
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12
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Tran MQ, Ermolenko L, Retailleau P, Nguyen TB, Al-Mourabit A. Reaction of Quinones and Guanidine Derivatives: Simple Access to Bis-2-aminobenzimidazole Moiety of Benzosceptrin and Other Benzazole Motifs. Org Lett 2014; 16:920-3. [DOI: 10.1021/ol403672p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Minh Quan Tran
- Centre de Recherche de Gif-sur-Yvette, Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Ludmila Ermolenko
- Centre de Recherche de Gif-sur-Yvette, Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Pascal Retailleau
- Centre de Recherche de Gif-sur-Yvette, Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Thanh Binh Nguyen
- Centre de Recherche de Gif-sur-Yvette, Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Ali Al-Mourabit
- Centre de Recherche de Gif-sur-Yvette, Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
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13
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Jeyalakshmi K, Selvakumaran N, Bhuvanesh NSP, Sreekanth A, Karvembu R. DNA/protein binding and cytotoxicity studies of copper(ii) complexes containing N,N′,N′′-trisubstituted guanidine ligands. RSC Adv 2014. [DOI: 10.1039/c4ra01459f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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14
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Goudreau N, Lemke CT, Faucher AM, Grand-Maître C, Goulet S, Lacoste JE, Rancourt J, Malenfant E, Mercier JF, Titolo S, Mason SW. Novel inhibitor binding site discovery on HIV-1 capsid N-terminal domain by NMR and X-ray crystallography. ACS Chem Biol 2013; 8:1074-82. [PMID: 23496828 DOI: 10.1021/cb400075f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The HIV-1 capsid (CA) protein, a domain of Gag, which participates in formation of both the mature and immature capsid, represents a potential target for anti-viral drug development. Characterization of hits obtained via high-throughput screening of an in vitro capsid assembly assay led to multiple compounds having this potential. We previously presented the characterization of two inhibitor series that bind the N-terminal domain of the capsid (CA(NTD)), at a site located at the bottom of its helical bundle, often referred to as the CAP-1 binding site. In this work we characterize a novel series of benzimidazole hits. Initial optimization of this series led to compounds with improved in vitro assembly and anti-viral activity. Using NMR spectroscopy we found that this series binds to a unique site on CA(NTD), located at the apex of the helical bundle, well removed from previously characterized binding sites for CA inhibitors. 2D (1)H-(15)N HSQC and (19)F NMR showed that binding of the benzimidazoles to this distinct site does not affect the binding of either cyclophilin A (CypA) to the CypA-binding loop or a benzodiazepine-based CA assembly inhibitor to the CAP-1 site. Unfortunately, while compounds of this series achieved promising in vitro assembly and anti-viral effects, they also were found to be quite sensitive to a number of naturally occurring CA(NTD) polymorphisms observed among clinical isolates. Despite the negative impact of this finding for drug development, the discovery of multiple inhibitor binding sites on CA(NTD) shows that capsid assembly is much more complex than previously realized.
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Affiliation(s)
- Nathalie Goudreau
- Departments of †Chemistry and ‡Biological Sciences, Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5
| | - Christopher T. Lemke
- Departments of †Chemistry and ‡Biological Sciences, Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5
| | - Anne-Marie Faucher
- Departments of †Chemistry and ‡Biological Sciences, Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5
| | - Chantal Grand-Maître
- Departments of †Chemistry and ‡Biological Sciences, Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5
| | - Sylvie Goulet
- Departments of †Chemistry and ‡Biological Sciences, Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5
| | - Jean-Eric Lacoste
- Departments of †Chemistry and ‡Biological Sciences, Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5
| | - Jean Rancourt
- Departments of †Chemistry and ‡Biological Sciences, Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5
| | - Eric Malenfant
- Departments of †Chemistry and ‡Biological Sciences, Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5
| | - Jean-François Mercier
- Departments of †Chemistry and ‡Biological Sciences, Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5
| | - Steve Titolo
- Departments of †Chemistry and ‡Biological Sciences, Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5
| | - Stephen W. Mason
- Departments of †Chemistry and ‡Biological Sciences, Boehringer Ingelheim (Canada) Ltd, Research & Development, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5
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15
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16
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Omar MA, Shaker YM, Galal SA, Ali MM, Kerwin SM, Li J, Tokuda H, Ramadan RA, El Diwani HI. Synthesis and docking studies of novel antitumor benzimidazoles. Bioorg Med Chem 2012; 20:6989-7001. [PMID: 23123017 DOI: 10.1016/j.bmc.2012.10.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 10/11/2012] [Indexed: 11/27/2022]
Abstract
In this work, the benzimidazole-pyrrole conjugates 6a-h and benzimidazole-tetracycles conjugates 12-14 were prepared. The cytotoxicity of the compounds 3, 4a-h, 6a-h, 8, 10 and 12-14 was tested against lung cancer cell line A549. Compound 6b exhibited higher activity than the bis-benzoxazole natural product (UK-1), the standard. The tested 4g,h, 6a-h, 10 and 12-14 exhibited remarkable cytotoxicity activity against breast cancer cell line MCF-7 with higher activity than tamoxifen. Furthermore, compound 4h was found to be also more potent than doxurubicin. The antitumor promotion activity of synthesized compounds 4g,h, 6a-h, 10 and 12-14 has been estimated by studying their possible inhibitory effects on EBV-EA activation induced by 12-O-tetradecanoylphorbol-13-acetate (TPA). Among the studied compounds, the inhibitory activities of compounds 8, 13 and 14 demonstrated strong inhibitory effects on the Epstein-Barr virus early antigen (EBV-EA) activation without showing any cytotoxicity on the Raji cells and their effects being stronger than that of a representative control, oleanolic acid. Moreover, the molecular docking of the new compounds into plasminogen activator (uPA) receptor has been in correlation with the antitumor activity. All synthesized compounds 3, 4a-h, 6a-h, 8, 10 and 12-14 were docked into same groove of the binding site of the native co-crystalized (4-iodobenzo[b]thiophene-2-carboxamidine) ligand (PDB code:1c5x) for activity explaination. Compounds 4h, 6b and 13, giving the best docking results, were further studied to estimate their effect on the level of uPA using AssayMax human urokinase (uPA) ELISA kit. In case of A549 cell line, compound 6 exhibited similar activity to MMC, and for MCF-7 cell line, compound 4h exhibited similar activity to doxorubicin, in inhibiting the expression of uPA.
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Affiliation(s)
- Mohamed A Omar
- Chemistry of Natural and Microbial Products Department, National Research Center, Dokki, 12311 Cairo, Egypt
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17
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Karle M, Knecht W, Xue Y. Discovery of benzothiazole guanidines as novel inhibitors of thrombin and trypsin IV. Bioorg Med Chem Lett 2012; 22:4839-43. [DOI: 10.1016/j.bmcl.2012.05.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/10/2012] [Accepted: 05/10/2012] [Indexed: 12/19/2022]
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18
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Pharmacological evaluation of benzimidazole derivatives with potential antiviral and antitumor activity. RESEARCH ON CHEMICAL INTERMEDIATES 2012. [DOI: 10.1007/s11164-012-0569-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Synthesis, structural characterization and in vitro biological screening of some homoleptic copper(II) complexes with substituted guanidines. Eur J Med Chem 2012; 48:26-35. [DOI: 10.1016/j.ejmech.2011.11.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 11/14/2011] [Accepted: 11/15/2011] [Indexed: 11/19/2022]
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20
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Hall DR, Ngan CH, Zerbe BS, Kozakov D, Vajda S. Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery. J Chem Inf Model 2011; 52:199-209. [PMID: 22145575 DOI: 10.1021/ci200468p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Fragment-based drug design (FBDD) starts with finding fragment-sized compounds that are highly ligand efficient and can serve as a core moiety for developing high-affinity leads. Although the core-bound structure of a protein facilitates the construction of leads, effective design is far from straightforward. We show that protein mapping, a computational method developed to find binding hot spots and implemented as the FTMap server, provides information that complements the fragment screening results and can drive the evolution of core fragments into larger leads with a minimal loss or, in some cases, even a gain in ligand efficiency. The method places small molecular probes, the size of organic solvents, on a dense grid around the protein and identifies the hot spots as consensus clusters formed by clusters of several probes. The hot spots are ranked based on the number of probe clusters, which predicts the binding propensity of the subsites and hence their importance for drug design. Accordingly, with a single exception the main hot spot identified by FTMap binds the core compound found by fragment screening. The most useful information is provided by the neighboring secondary hot spots, indicating the regions where the core can be extended to increase its affinity. To quantify this information, we calculate the density of probes from mapping, which describes the binding propensity at each point, and show that the change in the correlation between a ligand position and the probe density upon extending or repositioning the core moiety predicts the expected change in ligand efficiency.
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Affiliation(s)
- David R Hall
- Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA
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21
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Hit clustering can improve virtual fragment screening: CDK2 and PARP1 case studies. J Mol Model 2011; 18:2553-66. [DOI: 10.1007/s00894-011-1280-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 10/12/2011] [Indexed: 11/25/2022]
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22
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Gohda K, Teno N, Wanaka K, Tsuda Y. Predicting subsite interactions of plasmin with substrates and inhibitors through computational docking analysis. J Enzyme Inhib Med Chem 2011; 27:571-7. [DOI: 10.3109/14756366.2011.603129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Keigo Gohda
- Computer-Aided Molecular Modeling Research Center, Kansai (CAMM-Kansai),
Kobe, Japan
| | - Naoki Teno
- Faculty of Pharmaceutical Science, Hiroshima International University,
Kure, Japan
| | - Keiko Wanaka
- Kobe Research Projects on Thrombosis and Haemostasis,
Kobe, Japan
| | - Yuko Tsuda
- Faculty of Pharmaceutical Sciences, Kobe Gakuin University,
Kobe, Japan
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23
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Haider MK, Bertrand HO, Hubbard RE. Predicting fragment binding poses using a combined MCSS MM-GBSA approach. J Chem Inf Model 2011; 51:1092-105. [PMID: 21528911 DOI: 10.1021/ci100469n] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Improved methods are required to predict the position and orientation (pose) of binding to the target protein of low molecular weight compounds identified in fragment screening campaigns. This is particularly important to guide initial chemistry to generate structure-activity relationships for the cases where a high resolution structure cannot be obtained. We have assessed the benefit of an implicit solvent method for assessment of fragment binding poses generated by the Multiple Copy Simultaneous Search (MCSS) method in CHARMm. Additionally, the effect of using multiple receptor structures for a flexible receptor is investigated. The original MCSS performance -50% of fragment positions accurately predicted and scored - was increased up to 67% by scoring MCSS energy minima with a Molecular Mechanics Generalized Born approach with molecular volume integration and Surface Area model (MM-GBSA). The same increase in performance (but occasionally for different targets) was observed when using the docking program GOLD followed by MM-GBSA rescoring. The combined results from both methods resulted in a higher success rate emphasizing that a comparison of different docking methods can increase the correct identification of binding poses. For a receptor where multiple structures are available, Hsp90, the average performance on randomly adding receptor structures was also investigated. The results suggest that predictions using these docking methods can be used with some confidence to guide chemical optimization, if the structure of the target either remains relatively fixed on ligand binding, or if a number of crystal structures are available with diverse ligands bound and there is information on the positions of key water molecules in the binding site.
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Affiliation(s)
- Muhammad K Haider
- York Structural Biology Laboratory, University of York , Heslington, York YO10 5DD, U.K
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24
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Wang K, Herdtweck E, Dömling A. One-pot synthesis of 2-amino-indole-3-carboxamide and analogous. ACS COMBINATORIAL SCIENCE 2011; 13:140-6. [PMID: 21395342 DOI: 10.1021/co100040z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An efficient one-pot, two-step solution-phase synthetic method was developed to synthesize twenty-three 2-amino-indole-3-carboxamides (3) from 2-halonitrobenzene (1) or heterocyclic analogous and cyanoacetamides (2). In this sequence, first, intermediate 2-cyano-2-(2-nitrophenyl)acetamide (4) was generated under basic condition via S(NAr) reaction; after direct addition of hydrochloric acid solution, FeCl(3), and Zn powder, indole 3 was generated via reduction/cyclization process.
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Affiliation(s)
- Kan Wang
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Eberhardt Herdtweck
- Lehrstuhl für Anorganische Chemie, Technische Universität München, Garching bei München, Germany
| | - Alexander Dömling
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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25
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Galal SA, Abdelsamie AS, Rodriguez ML, Kerwin SM, El Diwani HI. Synthesis and studying the antitumor activity of novel 5-(2-methylbenzimidazol-5-yl)-1,3,4-oxadiazole-2(3H)-thiones. ACTA ACUST UNITED AC 2010. [DOI: 10.5155/eurjchem.1.2.67-72.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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26
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Garza JA, Ilangovan U, Hinck AP, Barnes LD. Kinetic, dynamic, ligand binding properties, and structural models of a dual-substrate specific nudix hydrolase from Schizosaccharomyces pombe. Biochemistry 2009; 48:6224-39. [PMID: 19462967 DOI: 10.1021/bi802266g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Schizosaccharomyces pombe Aps1 is a nudix hydrolase that catalyzes the hydrolysis of both diadenosine 5',5'''-P(1),P(n)-oligophosphates and diphosphoinositol polyphosphates in vitro. Nudix hydrolases act upon a wide variety of substrates, despite having a common 23 amino acid catalytic motif; hence, the residues responsible for substrate specificity are considered to reside outside the common catalytic nudix motif. The specific residues involved in binding each substrate of S. pombe Aps1 are unknown. In this study, we have conducted mutational and kinetic studies in combination with structural homology modeling and NMR spectroscopic analyses to identify potential residues involved in binding each class of substrates. This study demonstrates several major findings with regard to Aps1. First, the determination of the kinetic parameters of K(m) and k(cat) indicated that the initial 31 residues of Aps1 are not involved in substrate binding or catalysis with respect to Ap(6)A. Second, NMR spectroscopic analyses revealed the secondary structure and three dynamic backbone regions, one of which corresponds to a large insert in Aps1 as compared to other putative fungal orthologues. Third, two structural models of Aps1Delta2-19, based on the crystal structures of human DIPP1 and T. thermophilus Ndx1, were generated using homology modeling. The structural models were in excellent agreement with the NMR-derived secondary structure of Aps1Delta2-19. Fourth, NMR chemical shift mapping in conjunction with structural homology models indicated several residues outside the catalytic nudix motif that are involved in specific binding of diphosphoinositol polyphosphate or diadenosine oligophosphate ligands.
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Affiliation(s)
- John A Garza
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA
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27
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Skinner AL, Laurence JS. High-field solution NMR spectroscopy as a tool for assessing protein interactions with small molecule ligands. J Pharm Sci 2009; 97:4670-95. [PMID: 18351634 DOI: 10.1002/jps.21378] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The ability of a small molecule to bind and modify the activity of a protein target at a specific site greatly impacts the success of drugs in the pharmaceutical industry. One of the most important tools for evaluating these interactions has been high-field solution nuclear magnetic resonance (NMR) because of its unique ability to examine even weak protein-drug interactions at high resolution. NMR can be used to evaluate the structural, thermodynamic and kinetic aspects of a binding reaction. The basis of NMR screening experiments is that binding causes a perturbation in the physical properties of both molecules. Unique properties of small and macromolecules allow selective detection of either the protein target or ligand, even in a mixture of compounds. This review outlines current methodologies for assessing protein-ligand interactions from the perspectives of the protein target and ligand and delineates the fundamental principles for understanding NMR approaches in drug research. Advances in instrumentation, pulse sequences, isotopic labeling strategies, and the development of competition experiments support the study of higher molecular weight protein targets, facilitate higher-throughput and expand the range of binding affinities that can be evaluated, enhancing the utility of NMR for identifying and characterizing potential therapeutics to druggable protein targets.
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Affiliation(s)
- Andria L Skinner
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, USA
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28
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Nestler HP. Organizing bioactive compound discovery in target families. Methods Mol Biol 2009; 575:1-19. [PMID: 19727609 DOI: 10.1007/978-1-60761-274-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The sequencing of genomes gave access to the complete set of building blocks for organisms of various species. A plethora of "-omics"-technologies has been developed to investigate the dynamic interactions of the building blocks in order to understand the functioning of living organisms. This has given rise to the clustering of proteins into target families based on the phylogenetic and structural similarities. In this chapter we will discuss how the concept of target families enables to investigate and modulate biochemical function in the quest to chart Chemical and Biological Spaces.
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Affiliation(s)
- H Peter Nestler
- Sanofi-Aventis Combinatorial Technologies Center, Tucson, AZ, USA
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29
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Frederickson M, Callaghan O, Chessari G, Congreve M, Cowan SR, Matthews JE, McMenamin R, Smith DM, Vinković M, Wallis NG. Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator. J Med Chem 2007; 51:183-6. [DOI: 10.1021/jm701359z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martyn Frederickson
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Owen Callaghan
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Gianni Chessari
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Miles Congreve
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Suzanna R. Cowan
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Julia E. Matthews
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Rachel McMenamin
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Donna-Michelle Smith
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Mladen Vinković
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Nicola G. Wallis
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
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30
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Joossens J, Ali OM, El-Sayed I, Surpateanu G, Van der Veken P, Lambeir AM, Setyono-Han B, Foekens JA, Schneider A, Schmalix W, Haemers A, Augustyns K. Small, potent, and selective diaryl phosphonate inhibitors for urokinase-type plasminogen activator with in vivo antimetastatic properties. J Med Chem 2007; 50:6638-46. [PMID: 18052026 DOI: 10.1021/jm700962j] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A set of small nonpeptidic diaryl phosphonate inhibitors was prepared. Some of these inhibitors show potent and highly selective irreversible uPA inhibition. The biochemical and modeling data prove that the combination of a benzylguanidine moiety with a diaryl phosphonate ester results in optimized molecules for derivatizing the serine alcohol in the uPA active site. Selected compounds show significant antimetastatic effects in the BN-472 rat mammary carcinoma model. We report in this paper a preclinical proof of concept that selective, irreversible uPA inhibitors could be valuable in antimetastatic therapy.
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Affiliation(s)
- Jurgen Joossens
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
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31
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Hirayama A, Shirota O, Nomura M, Nagadoi A, Nishimura Y. A protein recycling system for nuclear magnetic resonance-based screening of drug candidates. Anal Biochem 2006; 353:99-107. [PMID: 16626618 DOI: 10.1016/j.ab.2006.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2005] [Revised: 03/11/2006] [Accepted: 03/13/2006] [Indexed: 11/29/2022]
Abstract
A sample-treating system for nuclear magnetic resonance (NMR)-based interaction screening between drug candidates (small molecules) and a protein of interest was developed by applying high-performance liquid chromatography (HPLC) technology. The system prepares a test solution by mixing a (15)N-labeled protein solution and a solution of each candidate compound, loads it to a flow cell-type NMR probe, and recycles the protein after the data acquisition. The system was designed to behave differently according to the information obtained in NMR measurements. In a test operation with a 100-compound library, the system could single out known interacting substances properly. Recovery values of the protein and one representative compound were 75 and 71%, respectively, and the recovered protein was found intact as intended.
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Affiliation(s)
- Aya Hirayama
- Shiseido Material Science Research Center, Tsuzuki-ku, Yokohama, Kanagawa, Japan
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32
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Bai G, Cui Y, Yang Y, Ye C, Liu M. A competitive low-affinity binding model for determining the mutual and specific sites of two ligands on protein. J Pharm Biomed Anal 2005; 38:588-93. [PMID: 15967285 DOI: 10.1016/j.jpba.2004.12.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2004] [Revised: 11/27/2004] [Accepted: 12/13/2004] [Indexed: 11/29/2022]
Abstract
A competitive low-affinity binding model was proposed for determining the number of mutual (overlapped) and specific binding sites of two ligands (A, B) on a protein (P). To use the model, one needs to carry out a titration experiment by adding either ligand A or B into a three-component system (A-B-P), and to monitor the spectroscopic parameter changes. Fitting the titration curve to the proposed model, one can get the mutual and specific binding sites of the two ligands on the protein. The model was examined by using human serum albumin (HSA) as a receptor and tolmetin (TOL) and salicylic acid (SAL) as ligands. Proton longitudinal relaxation rates (R1) were measured on a 500-MHz NMR spectrometer during the titration and used to derive the mutual binding sites. It was found that among the binding sites of 32+/-4 for SAL and 28+/-2 for TOL on HSA, there were 17+/-5 mutual sites for the two ligands. This result indicates that, although HSA has large binding capacities for most ligands, there are still a reasonable amount of the low-affinity binding sites that are structure selective.
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Affiliation(s)
- Guoyun Bai
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
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33
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Abstract
The advent of large-scale NMR-based screening has enabled new strategies for the design of novel, potent inhibitors of therapeutic targets. In particular, fragment-based strategies, in which molecular portions of the final high-affinity ligand are experimentally identified prior to chemical synthesis, have found widespread utility. This chapter will discuss some of the practical considerations for identifying and utilizing these fragment leads in drug design, with special emphasis on some of the lessons learned from more than a decade of industry experience.
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34
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Barber CG, Dickinson RP, Fish PV. Selective urokinase-type plasminogen activator (uPA) inhibitors. Part 3: 1-isoquinolinylguanidines. Bioorg Med Chem Lett 2005; 14:3227-30. [PMID: 15149680 DOI: 10.1016/j.bmcl.2004.03.094] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Revised: 03/17/2004] [Accepted: 03/30/2004] [Indexed: 11/19/2022]
Abstract
A series of 1-isoquinolinylguanidines are shown to be potent inhibitors of uPA with selectivity over tPA and plasmin. Potency is enhanced by the presence of a 4-halo and a 7-aryl substituent, particularly when substituted by a 3-carboxylic acid group. Compound 13j (UK-356,202) combines excellent potency and selectivity, and has been selected as a candidate for clinical evaluation.
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Affiliation(s)
- Christopher G Barber
- Department of Discovery Chemistry, Pfizer Global Research and Development, Sandwich, Kent CT13 9NJ, UK.
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35
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Lepre CA, Moore JM, Peng JW. Theory and applications of NMR-based screening in pharmaceutical research. Chem Rev 2004; 104:3641-76. [PMID: 15303832 DOI: 10.1021/cr030409h] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher A Lepre
- Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139-4242, USA
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36
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Affiliation(s)
- David C Rees
- Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, UK.
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37
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Bhongade BA, Gadad AK. 3D-QSAR CoMFA/CoMSIA studies on Urokinase plasminogen activator (uPA) inhibitors: a strategic design in novel anticancer agents. Bioorg Med Chem 2004; 12:2797-805. [PMID: 15110861 DOI: 10.1016/j.bmc.2004.02.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Revised: 02/16/2004] [Accepted: 02/17/2004] [Indexed: 12/01/2022]
Abstract
Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) was performed on a series of indole/benzoimidazole-5-carboxamidines as urokinase plasminogen activator (uPA) inhibitors. The ligand molecular superimposition on template structure was performed by atom/shape-based RMS fit, multifit, and RMSD fit methods. The removal of two outliers from the initial training set of 30 molecules improved the predictivity of the models. The statistically significant model was established from 28 molecules, which were validated by evaluation of test set of nine compounds. The atom-based RMS alignment yielded best predictive CoMFA model (r2(cv) = 0.611, r2(cnv) = 0.778, F value = 43.825, r2(bs) = 0.842, r2(pred) = 0.616 with two components) while the CoMSIA model yielded (r2(cv) = 0.499, r2(cnv) = 0.976, F value=96.36, r2(bs) = 0.993, r2(pred) = 0.694 with eight components). The contour maps obtained from 3D-QSAR studies were appraised for the activity trends of the molecules analyzed. The results indicate that the steric, electrostatic, and hydrogen bond donor/acceptor substituents play significant role in uPA activity and selectivity of these compounds. The data generated from the present study can be used as putative pharmacophore in the design of novel, potent, and selective urokinase plasminogen activator inhibitors as cancer therapeutics.
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Affiliation(s)
- B A Bhongade
- Department of Medicinal Chemistry, College of Pharmacy, J. N. Medical College, Belgaum 590010, Karnataka, India
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38
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Abstract
De novo design programs such as LEGEND, LUDI, and LeapFrog can identify novel structures that are predicted to fit the active site of a target protein. However, in the conventional de novo design strategy, the output structures obtained from the programs can be problematic with regard to synthetic accessibility and binding affinity prediction. Thus it has been practically difficult to obtain novel lead compounds that are appropriate for medicinal chemists through the de novo design strategy. Since the late 1990s, several new strategies for lead identification have been reported and the successful examples have been disclosed. One of the strategies is validation of small fragments, which can be substructures of de novo ligands, by using NMR, X-ray, or MS spectra. Another method is prioritization of output structures obtained from de novo design programs by chemical accessibility. This review describes these new strategies with practical applications and future perspectives of de novo design.
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Affiliation(s)
- Teruki Honma
- Banyu Tsukuba Research Institute in Collaboration With Merck Research Laboratories, Okubo-3, Tsukuba 300-2611, Ibaraki, Japan.
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39
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Kuhn P, Wilson K, Patch MG, Stevens RC. The genesis of high-throughput structure-based drug discovery using protein crystallography. Curr Opin Chem Biol 2002; 6:704-10. [PMID: 12413557 DOI: 10.1016/s1367-5931(02)00361-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Over the past 12 years, drugs have been developed using structure-based drug design relying upon traditional crystallographic methods. Established successes, such as the drugs designed against HIV-1 protease and neuraminidase, demonstrate the utility of a structure-based approach in the drug-discovery process. However, the approach has historically lacked throughput and reliability capabilities; these bottlenecks are being overcome by breakthroughs in high-throughput structural biology. Recent technological innovations such as submicroliter high-throughput crystallization, high-performance synchrotron beamlines and rapid binding-site analysis of de novo targets using virtual ligand screening and small molecule co-crystallization have resulted in a significant advance in structure-based drug discovery.
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Affiliation(s)
- Peter Kuhn
- Stanford Synchrotron Radiation Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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Murray CW, Verdonk ML. The consequences of translational and rotational entropy lost by small molecules on binding to proteins. J Comput Aided Mol Des 2002; 16:741-53. [PMID: 12650591 DOI: 10.1023/a:1022446720849] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
When a small molecule binds to a protein, it loses a significant amount of rigid body translational and rotational entropy. Estimates of the associated energy barrier vary widely in the literature yet accurate estimates are important in the interpretation of results from fragment-based drug discovery techniques. This paper describes an analysis that allows the estimation of the rigid body entropy barrier from the increase in binding affinities that results when two fragments of known affinity and known binding mode are joined together. The paper reviews the relatively rare number of examples where good quality data is available. From the analysis of this data, we estimate that the barrier to binding, due to the loss of rigid-body entropy, is 15-20 kJ/mol, i.e. around 3 orders of magnitude in affinity at 298 K. This large barrier explains why it is comparatively rare to observe multiple fragments binding to non-overlapping adjacent sites in enzymes. The barrier is also consistent with medicinal chemistry experience where small changes in the critical binding regions of ligands are often poorly tolerated by enzymes.
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Affiliation(s)
- Christopher W Murray
- Astex Technology Ltd, 250 Cambridge Science Park, Milton Road, Cambridge, CB4 0WE, UK.
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Rudolph MJ, Illig CR, Subasinghe NL, Wilson KJ, Hoffman JB, Randle T, Green D, Molloy CJ, Soll RM, Lewandowski F, Zhang M, Bone R, Spurlino JC, Deckman IC, Manthey C, Sharp C, Maguire D, Grasberger BL, DesJarlais RL, Zhou Z. Design and synthesis of 4,5-disubstituted-thiophene-2-amidines as potent urokinase inhibitors. Bioorg Med Chem Lett 2002; 12:491-5. [PMID: 11814826 DOI: 10.1016/s0960-894x(01)00787-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A study of the S1 binding of lead 5-methylthiothiophene amidine 3, an inhibitor of urokinase-type plasminogen activator, was undertaken by the introduction of a variety of substituents at the thiophene 5-position. The 5-alkyl substituted and unsubstituted thiophenes were prepared using organolithium chemistry. Heteroatom substituents were introduced at the 5-position using a novel displacement reaction of 5-methylsulfonylthiophenes and the corresponding oxygen or sulfur anions. Small alkyl group substitution at the 5-position provided inhibitors equipotent with but possessing improved solubility.
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Affiliation(s)
- M Jonathan Rudolph
- 3-Dimensional Pharmaceuticals Inc., 665 Stockton Drive, Exton, PA 19341, USA.
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Katz BA, Sprengeler PA, Luong C, Verner E, Elrod K, Kirtley M, Janc J, Spencer JR, Breitenbucher JG, Hui H, McGee D, Allen D, Martelli A, Mackman RL. Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets. CHEMISTRY & BIOLOGY 2001; 8:1107-21. [PMID: 11731301 DOI: 10.1016/s1074-5521(01)00084-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
BACKGROUND Involved or implicated in a wide spectrum of diseases, trypsin-like serine proteases comprise well studied drug targets and anti-targets that can be subdivided into two major classes. In one class there is a serine at position 190 at the S1 site, as in urokinase type plasminogen activator (urokinase or uPA) and factor VIIa, and in the other there is an alanine at 190, as in tissue type plasminogen activator (tPA) and factor Xa. A hydrogen bond unique to Ser190 protease-arylamidine complexes between O gamma(Ser190) and the inhibitor amidine confers an intrinsic preference for such inhibitors toward Ser190 proteases over Ala190 counterparts. RESULTS Based on the structural differences between the S1 sites of Ser190 and Ala190 protease-arylamidine complexes, we amplified the selectivity of amidine inhibitors toward uPA and against tPA, by factors as high as 220-fold, by incorporating a halo group ortho to the amidine of a lead inhibitor scaffold. Comparison of K(i) values of such halo-substituted and parent inhibitors toward a panel of Ser190 and Ala190 proteases demonstrates pronounced selectivity of the halo analogs for Ser190 proteases over Ala190 counterparts. Crystal structures of Ser190 proteases, uPA and trypsin, and of an Ala190 counterpart, thrombin, bound by a set of ortho (halo, amidino) aryl inhibitors and of non-halo parents reveal the structural basis of the exquisite selectivity and validate the design principle. CONCLUSIONS Remarkable selectivity enhancements of exceptionally small inhibitors are achieved toward the uPA target over the highly similar tPA anti-target through a single atom substitution on an otherwise relatively non-selective scaffold. Overall selectivities for uPA over tPA as high as 980-fold at physiological pH were realized. The increase in selectivity results from the displacement of a single bound water molecule common to the S1 site of both the uPA target and the tPA anti-target because of the ensuing deficit in hydrogen bonding of the arylamidine inhibitor when bound in the Ala190 protease anti-target.
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Affiliation(s)
- B A Katz
- Axys Pharmaceutical Corporation, 385 Oyster Point Boulevard, South San Francisco, CA 94080, USA.
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