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Chen G, Fan M, Liu Y, Sun B, Liu M, Wu J, Li N, Guo M. Advances in MS Based Strategies for Probing Ligand-Target Interactions: Focus on Soft Ionization Mass Spectrometric Techniques. Front Chem 2019; 7:703. [PMID: 31709232 PMCID: PMC6819514 DOI: 10.3389/fchem.2019.00703] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
The non-covalent interactions between small drug molecules and disease-related proteins (ligand-target interactions) mediate various pharmacological processes in the treatment of different diseases. The development of the analytical methods to assess those interactions, including binding sites, binding energies, stoichiometry and association-dissociation constants, could assist in clarifying the mechanisms of action, precise treatment of targeted diseases as well as the targeted drug discovery. For the last decades, mass spectrometry (MS) has been recognized as a powerful tool to study the non-covalent interactions of the ligand-target complexes with the characteristics of high sensitivity, high-resolution, and high-throughput. Soft ionization mass spectrometry, especially the electrospray mass spectrometry (ESI-MS) and matrix assisted laser desorption ionization mass spectrometry (MALDI-MS), could achieve the complete transformation of the target analytes into the gas phase, and subsequent detection of the small drug molecules and disease-related protein complexes, and has exerted great advantages for studying the drug ligands-protein targets interactions, even in case of identifying active components as drug ligands from crude extracts of medicinal plants. Despite of other analytical techniques for this purpose, such as the NMR and X-ray crystallography, this review highlights the principles, research hotspots and recent applications of the soft ionization mass spectrometry and its hyphenated techniques, including hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (CX-MS), and ion mobility spectrometry mass spectrometry (IMS-MS), in the study of the non-covalent interactions between small drug molecules and disease-related proteins.
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Affiliation(s)
- Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Minxia Fan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Ye Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Center for Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Meixian Liu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Jianlin Wu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Na Li
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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Khan RA. Natural products chemistry: The emerging trends and prospective goals. Saudi Pharm J 2018; 26:739-753. [PMID: 29991919 PMCID: PMC6036106 DOI: 10.1016/j.jsps.2018.02.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/05/2018] [Indexed: 01/01/2023] Open
Abstract
The role and contributions of natural products chemistry in advancements of the physical and biological sciences, its interdisciplinary domains, and emerging of new avenues by providing novel applications, constructive inputs, thrust, comprehensive understanding, broad perspective, and a new vision for future is outlined. The developmental prospects in bio-medical, health, nutrition, and other interrelated sciences along with some of the emerging trends in the subject area are also discussed as part of the current review of the basic and core developments, innovation in techniques, advances in methodology, and possible applications with their effects on the sciences in general and natural products chemistry in particular. The overview of the progress and ongoing developments in broader areas of the natural products chemistry discipline, its role and concurrent economic and scientific implications, contemporary objectives, future prospects as well as impending goals are also outlined. A look at the natural products chemistry in providing scientific progress in various disciplines is deliberated upon.
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Affiliation(s)
- Riaz A. Khan
- Department of Medicinal Chemistry, Qassim University, Qassim 51452, Saudi Arabia
- Manav Rachna International University, National Capital Region, Faridabad, HR 121 004, India
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Baratte B, Serive B, Bach S. [Screening marine resources to find novel chemical inhibitors of disease-relevant protein kinases]. Med Sci (Paris) 2015; 31:538-45. [PMID: 26059305 DOI: 10.1051/medsci/20153105016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Since the early 1970's, investigators at Station Biologique de Roscoff (SBR), France, have been using marine organisms as models to describe molecular pathways conserved through evolution in mammalian cells (e.g. the cyclin-dependent kinases involved in the control of the cell division cycle). Some kinases are misregulated in various human pathologies, including cancers. Using a specialized screening approach, chemical libraries were analysed, using on-site facilities at Roscoff, in order to identify small chemical inhibitors of protein kinases. Eight chemical scaffolds produced by marine organisms were characterized as candidate drugs by our screening facility, some of which are being considered as chemical tools to pinpoint specific cellular functions of the targeted kinases. In this review, we describe our existing screening facilities and we discuss new perspectives related to marine bioprospecting.
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Affiliation(s)
- Blandine Baratte
- CNRS/UPMC USR3151, plate-forme de criblage KISSf (kinase inhibitor specialized screening facility), station biologique de Roscoff, place Georges Teissier, CS 90074, 29688 Roscoff Cedex, France
| | - Benoît Serive
- CNRS/UPMC USR3151, plate-forme de criblage KISSf (kinase inhibitor specialized screening facility), station biologique de Roscoff, place Georges Teissier, CS 90074, 29688 Roscoff Cedex, France
| | - Stéphane Bach
- CNRS/UPMC USR3151, plate-forme de criblage KISSf (kinase inhibitor specialized screening facility), station biologique de Roscoff, place Georges Teissier, CS 90074, 29688 Roscoff Cedex, France
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Abdelrahim MYM, Tanc M, Winum JY, Supuran CT, Barboiu M. Dominant behaviours in the expression of human carbonic anhydrase hCA I activity. Chem Commun (Camb) 2014; 50:8043-6. [DOI: 10.1039/c4cc03289f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic deconvolution ofDCLsof inhibitors (CAIs) and activators (CAAs) of hCA I show that the inhibitory effects dominate over the activating ones.
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Affiliation(s)
- M. Yahia M. Abdelrahim
- Adaptative Supramolecular Nanosystems Group
- Institut Européen des Membranes
- ENSCM/UMII/UMR-CNRS 5635
- 34095 Montpellier, Cedex 5, France
| | - Muhammet Tanc
- Università degli Studi di Firenze
- Polo Scientifico, Laboratorio di Chimica Bioinorganica
- 50019 Sesto Fiorentino (Florence), Italy
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS
- Ecole Nationale Supérieure de Chimie de Montpellier
- 34296 Montpellier Cedex, France
| | - Claudiu T. Supuran
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS
- Ecole Nationale Supérieure de Chimie de Montpellier
- 34296 Montpellier Cedex, France
| | - Mihail Barboiu
- Adaptative Supramolecular Nanosystems Group
- Institut Européen des Membranes
- ENSCM/UMII/UMR-CNRS 5635
- 34095 Montpellier, Cedex 5, France
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5
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Baron PS, Neve JE, Camp D, Suraweera L, Lam A, Lai J, Jovanovic L, Nelson C, Davis RA. Design, synthesis and spectroscopic characterisation of a focused library based on the polyandrocarpamine natural product scaffold. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:358-63. [PMID: 23609961 DOI: 10.1002/mrc.3958] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 05/15/2023]
Abstract
A focused library based on the marine natural products polyandrocarpamines A (1) and B (2) has been designed and synthesised using parallel solution-phase chemistry. In silico physicochemical property calculations were performed on synthetic candidates in order to optimise the library for drug discovery and chemical biology. A library of ten 2-aminoimidazolone products (3-12) was prepared by coupling glycocyamidine and a variety of aldehydes using a one-step stereoselective aldol condensation reaction under microwave conditions. All analogues were characterised by NMR, UV, IR and MS. The library was evaluated for cytotoxicity towards the prostate cancer cell lines, LNCaP, PC-3 and 22Rv1.
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Affiliation(s)
- Paul S Baron
- Eskitis Institute, Griffith University, Brisbane, Queensland 4111, Australia
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6
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Natural product coumarins that inhibit human carbonic anhydrases. Bioorg Med Chem 2013; 21:1539-43. [DOI: 10.1016/j.bmc.2012.07.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/13/2012] [Accepted: 07/13/2012] [Indexed: 11/19/2022]
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Abstract
Native state mass spectrometry (MS) has been recognised as a rapid, sensitive, and high throughput method to directly investigate protein-ligand interactions for some time, however there are few examples reporting this approach as a screening method to identify relevant protein–fragment interactions in fragment-based drug discovery (FBDD). In this paper an overview of native state MS will be presented, highlighting the attractive properties of this method within the context of fragment screening applications. A summary of published examples using MS for fragment screening will be described and reflection on the outlook for the future adoption and implementation of native state MS as a complementary fragment screening method will be presented.
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Miller BL. DCC in the development of nucleic acid targeted and nucleic acid inspired structures. Top Curr Chem (Cham) 2012; 322:107-37. [PMID: 21769715 DOI: 10.1007/128_2011_200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Nucleic acids were one of the first biological targets explored with DCC, and research into the application has continued to yield novel and useful structures for sequence- and structure-selective recognition of oligonucleotides. This chapter reviews major developments in DNA- and RNA-targeted DCC, including methods under development for the conversion of DCC-derived lead compounds into probe molecules suitable for studies in vitro and in vivo. Innovative applications of DCC for the discovery of new materials based on nucleic acids and new methods for the modification of nucleic acid structure and function are also discussed.
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Affiliation(s)
- Benjamin L Miller
- Department of Dermatology, University of Rochester Medical Center, Rochester, NY 14642, USA.
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Cannell RJP, Sarker SD, Nahar L. Follow-up of natural products isolation. Methods Mol Biol 2012; 864:473-514. [PMID: 22367909 DOI: 10.1007/978-1-61779-624-1_19] [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: 05/31/2023]
Abstract
Follow-up of natural products isolation refers to re-isolation of compound(s) of interest in larger amounts for further pharmacological testing, conclusive structure elucidation, structure modifications to synthesize analogs for structure-activity relationships (SAR) studies, preformulation and formulation studies or clinical trials. In addition to conventional synthetic chemistry approaches, several other methodologies can be applied for following-up natural products isolation. This chapter outlines, with specific examples, various strategies and methods involved in follow-up of natural products isolation.
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Affiliation(s)
- Richard J P Cannell
- Department of Pharmacy, School of Applied Sciences, University of Wolverhampton, Wolverhampton, WV11LY, UK
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Lopez M, Vu H, Wang CK, Wolf MG, Groenhof G, Innocenti A, Supuran CT, Poulsen SA. Promiscuity of carbonic anhydrase II. Unexpected ester hydrolysis of carbohydrate-based sulfamate inhibitors. J Am Chem Soc 2011; 133:18452-62. [PMID: 21958118 DOI: 10.1021/ja207855c] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbonic anhydrases (CAs) are enzymes whose endogenous reaction is the reversible hydration of CO(2) to give HCO(3)(-) and a proton. CA are also known to exhibit weak and promiscuous esterase activity toward activated esters. Here, we report a series of findings obtained with a set of CA inhibitors that showed quite unexpectedly that the compounds were both inhibitors of CO(2) hydration and substrates for the esterase activity of CA. The compounds comprised a monosaccharide core with the C-6 primary hydroxyl group derivatized as a sulfamate (for CA recognition). The remaining four sugar hydroxyl groups were acylated. Using protein X-ray crystallography, the crystal structures of human CA II in complex with four of the sulfamate inhibitors were obtained. As expected, the four structures displayed the canonical CA protein-sulfamate interactions. Unexpectedly, a free hydroxyl group was observed at the anomeric center (C-1) rather than the parent C-1 acyl group. In addition, this hydroxyl group is observed axial to the carbohydrate ring while in the parent structure it is equatorial. A mechanism is proposed that accounts for this inversion of stereochemistry. For three of the inhibitors, the acyl groups at C-2 or at C-2 and C-3 were also absent with hydroxyl groups observed in their place and retention of stereochemistry. With the use of electrospray ionization-Fourier transform ion cyclotron resonance-mass spectrometry (ESI-FTICR-MS), we observed directly the sequential loss of all four acyl groups from one of the carbohydrate-based sulfamates. For this compound, the inhibitor and substrate binding mode were further analyzed using free energy calculations. These calculations suggested that the parent compound binds almost exclusively as a substrate. To conclude, we have demonstrated that acylated carbohydrate-based sulfamates are simultaneously inhibitor and substrate of human CA II. Our results suggest that, initially, the substrate binding mode dominates, but following hydrolysis, the ligand can also bind as a pure inhibitor thereby competing with the substrate binding mode.
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Affiliation(s)
- Marie Lopez
- Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan, Queensland 4111, Australia
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11
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Yuliana ND, Khatib A, Choi YH, Verpoorte R. Metabolomics for bioactivity assessment of natural products. Phytother Res 2011; 25:157-69. [PMID: 20658470 DOI: 10.1002/ptr.3258] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Natural products historically have been a rich source of lead molecules in drug discovery, based on their capability to create unique and diverse chemical structures. However, it is also true that the vast number of metabolites typically present in natural products and their huge dynamic range results in the loss of many possibly bioactive natural compounds, becoming an inextricable obstacle for drug development. Recently, new strategies which favour a holistic approach as opposed to the traditional reductionist methods used previously, have been introduced with the purpose of overcoming the bottlenecks in natural product research. This approach is based on the application of new technologies, including metabolomics, for example. Metabolomics allows a systematic study of a complex mixture such as a phytochemical preparation, which can be linked to observations obtained through biological testing systems without the need for isolating active principles. This may put drug discovery from natural products back in the limelight again. In this review paper, the description of some examples of successful metabolomics applications in several important fields related to drug discovery from natural sources aims at raising the potential of metabolomics in reducing the gap between natural products (NP) and modern drug discovery demand.
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Affiliation(s)
- Nancy Dewi Yuliana
- Division of Pharmacognosy, Section of Metabolomics, Institute of Biology, Leiden University, Leiden, The Netherlands
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12
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Davis RA, Hofmann A, Osman A, Hall RA, Mühlschlegel FA, Vullo D, Innocenti A, Supuran CT, Poulsen SA. Natural Product-Based Phenols as Novel Probes for Mycobacterial and Fungal Carbonic Anhydrases. J Med Chem 2011; 54:1682-92. [DOI: 10.1021/jm1013242] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Rohan A. Davis
- Eskitis Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Andreas Hofmann
- Eskitis Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Asiah Osman
- Eskitis Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Rebecca A. Hall
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Fritz A. Mühlschlegel
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
- Clinical Microbiology Service, East Kent Hospitals University NHS Foundation Trust, Ashford, Kent, TN24 0LZ, United Kingdom
| | - Daniela Vullo
- Laboratorio di Chimica Bioinorganica, Rm. 188, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Alessio Innocenti
- Laboratorio di Chimica Bioinorganica, Rm. 188, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T. Supuran
- Laboratorio di Chimica Bioinorganica, Rm. 188, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Sally-Ann Poulsen
- Eskitis Institute, Griffith University, Nathan, Queensland 4111, Australia
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Barboiu M. Multistate and Phase Change Selection in Constitutional Multivalent Systems. CONSTITUTIONAL DYNAMIC CHEMISTRY 2011; 322:33-53. [DOI: 10.1007/128_2011_196] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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Wei Y, Wesson PJ, Kourkine I, Grzybowski BA. Measurement of Protein−Ligand Binding Constants from Reaction-Diffusion Concentration Profiles. Anal Chem 2010; 82:8780-4. [DOI: 10.1021/ac102055a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yanhu Wei
- Department of Chemical and Biological Engineering and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Paul J. Wesson
- Department of Chemical and Biological Engineering and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Igor Kourkine
- Department of Chemical and Biological Engineering and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Bartosz A. Grzybowski
- Department of Chemical and Biological Engineering and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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Davis RA, Healy PC. N-Benzyl-2-(3-chloro-4-hy-droxy-phen-yl)acetamide. Acta Crystallogr Sect E Struct Rep Online 2010; 66:o2521. [PMID: 21587515 PMCID: PMC2983291 DOI: 10.1107/s1600536810035397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 09/02/2010] [Indexed: 11/26/2022]
Abstract
The title compound, C(15)H(14)ClNO(2), was synthesized as part of a project to generate a combinatorial library based on the fungal natural product 2-(3-chloro-4-hy-droxy-phen-yl)acetamide. It crystallizes as non-planar discrete mol-ecules [the peripheral 3-chloro-4-hy-droxy-phenyl and benzyl groups are twisted out of the plane of the central acetamide group, with N-C-C-C and C-C-C-C torsion angles of -58.8 (3) and 65.0 (2)°, respectively] linked by inter-molecular N-H⋯O and O-H⋯O hydrogen bonds.
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Affiliation(s)
- Rohan A. Davis
- Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan, Brisbane 4111, Australia
| | - Peter C. Healy
- School of Biomolecular and Physical Sciences, Griffith University, Nathan, Brisbane 4111, Australia
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Davis RA, Innocenti A, Poulsen SA, Supuran CT. Carbonic anhydrase inhibitors. Identification of selective inhibitors of the human mitochondrial isozymes VA and VB over the cytosolic isozymes I and II from a natural product-based phenolic library. Bioorg Med Chem 2010; 18:14-8. [DOI: 10.1016/j.bmc.2009.11.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 10/29/2009] [Accepted: 11/07/2009] [Indexed: 12/21/2022]
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17
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Nasr G, Petit E, Supuran CT, Winum JY, Barboiu M. Carbonic anhydrase II-induced selection of inhibitors from a dynamic combinatorial library of Schiff’s bases. Bioorg Med Chem Lett 2009; 19:6014-7. [PMID: 19796939 DOI: 10.1016/j.bmcl.2009.09.047] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 09/14/2009] [Accepted: 09/14/2009] [Indexed: 10/20/2022]
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18
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Nasr G, Petit E, Vullo D, Winum JY, Supuran CT, Barboiu M. Carbonic Anhydrase-Encoded Dynamic Constitutional Libraries: Toward the Discovery of Isozyme-Specific Inhibitors. J Med Chem 2009; 52:4853-9. [PMID: 19580287 DOI: 10.1021/jm900449v] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gihane Nasr
- Adaptative Supramolecular Nanosystems Group, Institut Européen des Membranes, ENSCM/UMII/UMR-CNRS 5635, Place Eugène Bataillon, CC 047, 34095 Montpellier, Cedex 5, France
| | - Eddy Petit
- Adaptative Supramolecular Nanosystems Group, Institut Européen des Membranes, ENSCM/UMII/UMR-CNRS 5635, Place Eugène Bataillon, CC 047, 34095 Montpellier, Cedex 5, France
| | - Daniela Vullo
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS-UM1-UM2, Bâtiment de Recherche Max Mousseron, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l’Ecole Normale, 34296 Montpellier Cedex, France
| | - Claudiu T. Supuran
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
| | - Mihail Barboiu
- Adaptative Supramolecular Nanosystems Group, Institut Européen des Membranes, ENSCM/UMII/UMR-CNRS 5635, Place Eugène Bataillon, CC 047, 34095 Montpellier, Cedex 5, France
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Davis RA, Baron PS, Neve JE, Cullinane C. A microwave-assisted stereoselective synthesis of polyandrocarpamines A and B. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2008.12.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Koehn FE. High impact technologies for natural products screening. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2007; 65:175, 177-210. [PMID: 18084916 DOI: 10.1007/978-3-7643-8117-2_5] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural products have historically been a rich source of lead molecules in drug discovery. However, natural products have been de-emphasized as high throughput screening resources in the recent past, in part because of difficulties in obtaining high quality natural products screening libraries, or in applying modern screening assays to these libraries. In addition, natural products programs based on screening of extract libraries, bioassay-guided isolation, structure elucidation and subsequent production scale-up are challenged to meet the rapid cycle times that are characteristic of the modern HTS approach. Fortunately, new technologies in mass spectrometry, NMR and other spectroscopic techniques can greatly facilitate the first components of the process - namely the efficient creation of high-quality natural products libraries, bimolecular target or cell-based screening, and early hit characterization. The success of any high throughput screening campaign is dependent on the quality of the chemical library. The construction and maintenance of a high quality natural products library, whether based on microbial, plant, marine or other sources is a costly endeavor. The library itself may be composed of samples that are themselves mixtures - such as crude extracts, semi-pure mixtures or single purified natural products. Each of these library designs carries with it distinctive advantages and disadvantages. Crude extract libraries have lower resource requirements for sample preparation, but high requirements for identification of the bioactive constituents. Pre-fractionated libraries can be an effective strategy to alleviate interferences encountered with crude libraries, and may shorten the time needed to identify the active principle. Purified natural product libraries require substantial resources for preparation, but offer the advantage that the hit detection process is reduced to that of synthetic single component libraries. Whether the natural products library consists of crude or partially fractionated mixtures, the library contents should be profiled to identify the known components present - a process known as dereplication. The use of mass spectrometry and HPLC-mass spectrometry together with spectral databases is a powerful tool in the chemometric profiling of bio-sources for natural product production. High throughput, high sensitivity flow NMR is an emerging tool in this area as well. Whether by cell based or biomolecular target based assays, screening of natural product extract libraries continues to furnish novel lead molecules for further drug development, despite challenges in the analysis and prioritization of natural products hits. Spectroscopic techniques are now being used to directly screen natural product and synthetic libraries. Mass spectrometry in the form of methods such as ESI-ICRFTMS, and FACS-MS as well as NMR methods such as SAR by NMR and STD-NMR have been utilized to effectively screen molecular libraries. Overall, emerging advances in mass spectrometry, NMR and other technologies are making it possible to overcome the challenges encountered in screening natural products libraries in today's drug discovery environment. As we apply these technologies and develop them even further, we can look forward to increased impact of natural products in the HTS based drug discovery.
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Affiliation(s)
- Frank E Koehn
- Natural Products Discovery Research - Chemical and Screening Sciences, Wyeth Research, Pearl River, NY 10965, USA.
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Temperini C, Winum JY, Montero JL, Scozzafava A, Supuran CT. Carbonic anhydrase inhibitors: The X-ray crystal structure of the adduct of N-hydroxysulfamide with isozyme II explains why this new zinc binding function is effective in the design of potent inhibitors. Bioorg Med Chem Lett 2007; 17:2795-801. [PMID: 17346964 DOI: 10.1016/j.bmcl.2007.02.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 02/23/2007] [Accepted: 02/23/2007] [Indexed: 11/19/2022]
Abstract
N-Hydroxysulfamide is a 2000-fold more potent inhibitor of the zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1) as compared to sulfamide. It also inhibits other physiologically relevant isoforms, such as the tumor-associated CA IX and XII (K(I)s in the range of 0.865-1.34microM). In order to understand the binding of this inhibitor to the enzyme active site, the X-ray crystal structure of the human hCA II-N-hydroxysulfamide adduct was resolved. The inhibitor coordinates to the active site zinc ion by the ionized primary amino group, participating in an extended network of hydrogen bonds with amino acid residues Thr199, Thr200 and two water molecules. The additional two hydrogen bonds in which N-hydroxysulfamide bound to hCA II is involved as compared to the corresponding adduct of sulfamide may explain its higher affinity for the enzyme, also providing hints for the design of tight-binding CA inhibitors possessing an organic moiety substituting the NH group in the N-hydroxysulfamide structure.
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Affiliation(s)
- Claudia Temperini
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy.
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Davis RA, Pierens GK, Parsons PG. Synthesis and spectroscopic characterisation of a combinatorial library based on the fungal natural product 3-chloro-4-hydroxyphenylacetamide. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45:442-5. [PMID: 17372964 DOI: 10.1002/mrc.1984] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Parallel solution-phase chemistry has yielded a series of secondary amide analogues of the fungal natural product 3-chloro-4-hydroxyphenylacetamide. 3-Chloro-4-hydroxyphenylacetic acid was coupled to a variety of primary amines using 1-ethyl-3-(3'-dimethylamino- propyl)-carbodiimide hydrochloride. The desired products were obtained in good yield and high purity following rapid silica purification. All analogues were spectroscopically characterised using NMR, UV, IR and MS data. One compound displayed moderate cytotoxicity against the human melanoma and prostate cell lines, MM96L and DU145.
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Affiliation(s)
- Rohan A Davis
- Natural Product Discovery, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, QLD 4111, Australia.
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Scozzafava A, Mastrolorenzo A, Supuran CT. Carbonic anhydrase inhibitors and activators and their use in therapy. Expert Opin Ther Pat 2006. [DOI: 10.1517/13543776.16.12.1627] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Poulsen SA. Direct screening of a dynamic combinatorial library using mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1074-1080. [PMID: 16735129 DOI: 10.1016/j.jasms.2006.03.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Revised: 03/30/2006] [Accepted: 03/31/2006] [Indexed: 05/09/2023]
Abstract
A dynamic combinatorial library (DCL) screening approach is described that permits direct identification of the effective (from ineffective) combination of building blocks in the equilibrating DCL. The approach uses Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) together with sustained off-resonance irradiation collision activated dissociation (SORI-CAD) to detect noncovalent protein-DCL ligand complexes under native conditions. It was shown that in a single, rapid experiment one could concurrently identify all the ligands of interest from the DCL against a background of inactive DCL ligands while still in the presence of the target protein. This result has demonstrated that mass spectrometry may provide a fast preliminary screening approach to identify DCL candidates for later verification with more traditional but time-consuming analysis. The MS/MS enables DCL mixtures to be effectively deconvoluted without the need for either chromatography, synthesis of DCL sub-libraries, conversion of the DCL to a static library, or disruption of the protein-ligand complexes before analysis--all typically necessary for the current screening method for DCLs.
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Affiliation(s)
- Sally-Ann Poulsen
- Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan, Brisbane, 4111, Queensland, Australia.
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Poulsen SA, Bornaghi LF. Fragment-based drug discovery of carbonic anhydrase II inhibitors by dynamic combinatorial chemistry utilizing alkene cross metathesis. Bioorg Med Chem 2006; 14:3275-84. [PMID: 16431113 DOI: 10.1016/j.bmc.2005.12.054] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Revised: 12/20/2005] [Accepted: 12/20/2005] [Indexed: 10/25/2022]
Abstract
A fragment-based drug discovery approach to the synthesis and identification of small molecule inhibitors of bovine carbonic anhydrase II (bCA II) is described. The classical bCA II recognition fragment is an aromatic sulfonamide (ArSO2NH2) moiety. This fragment was incorporated into a scaffold building block, which was subsequently derivatized by dynamic combinatorial chemistry utilizing alkene cross metathesis as the reversible reaction. Screening against bCA II was then carried out and the results allowed determination of the relative bCA II binding affinities of the cross metathesis products that contained the ArSO2NH2 fragment. A bCA II competitive binding assay validated these results with a representative number of pure compounds. The results for screening, without prior isolation of the active constituent, were in full agreement with those obtained for equilibrium dissociation constants (K(i)'s) of pure compounds. Some of these compounds exhibited K(i)'s in the low nanomolar range. Heterogeneous catalysis was shown to be very effective in this drug discovery application of dynamic combinatorial chemistry.
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Affiliation(s)
- Sally-Ann Poulsen
- Chemical Biology Group, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan Campus, Brisbane 4111, Australia.
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