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Supuran CT. A simple yet multifaceted 90 years old, evergreen enzyme: Carbonic anhydrase, its inhibition and activation. Bioorg Med Chem Lett 2023; 93:129411. [PMID: 37507055 DOI: 10.1016/j.bmcl.2023.129411] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
Advances in the carbonic anhydrase (CA, EC 4.2.1.1) research over the last three decades are presented, with an emphasis on the deciphering of the activation mechanism, the development of isoform-selective inhibitors/ activators by the tail approach and their applications in the management of obesity, hypoxic tumors, neurological conditions, and as antiinfectives.
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Affiliation(s)
- Claudiu T Supuran
- Neurofarba Department, University of Florence, Section of Pharmaceutical Sciences, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
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2
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A decade of tail-approach based design of selective as well as potent tumor associated carbonic anhydrase inhibitors. Bioorg Chem 2022; 126:105920. [DOI: 10.1016/j.bioorg.2022.105920] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/22/2022] [Accepted: 05/28/2022] [Indexed: 12/24/2022]
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Llull R, Montalbán G, Vidal I, Gomila RM, Bauzá A, Frontera A. Theoretical study of spodium bonding in the active site of three Zn-proteins and several model systems. Phys Chem Chem Phys 2021; 23:16888-16896. [PMID: 34328165 DOI: 10.1039/d1cp02150h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this manuscript, three examples retrieved from the PDB are selected to demonstrate the existence and relevance of spodium bonding (SpB) in biological systems. SpB is defined as an attractive noncovalent interaction between elements of group 12 of the periodic table acting as a Lewis acid and any atom or group of atoms acting as an electron donor. The utilization of this term (SpB) is convenient to differentiate classical coordination bonds from noncovalent interactions. In the latter, the distance between the electron rich and the spodium atoms is longer than the sum of the covalent radii but shorter than the sum of the van der Waals radii. In most Zn-dependent metalloenzymes, the spodium atom is bonded to three imidazole moieties belonging to the side chains of histidine amino-acids. Herein, in addition to the investigation of the SpB in the active site of three exemplifying enzymes, theoretical models where the Zn(ii) atom is bonded either to three imidazole or triazole ligands are used in order to investigate the strength of the SpB and its competition with hydrogen bonding. A series of Lewis bases and anions have been used as SpB acceptors combined with six SpB donors (receptors) of general formula [ZnY3X]+ (Y = imidazole and triazole and X = Cl, N3 and SCH3). In addition to the investigation of the energetic and geometric features of the complexes, the SpB interactions have been further characterized using the natural bond orbital (NBO) method, quantum theory of "atoms-in-molecules" and the noncovalent interaction plot (NCI plot).
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Affiliation(s)
- Rosa Llull
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
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Nocentini A, Angeli A, Carta F, Winum JY, Zalubovskis R, Carradori S, Capasso C, Donald WA, Supuran CT. Reconsidering anion inhibitors in the general context of drug design studies of modulators of activity of the classical enzyme carbonic anhydrase. J Enzyme Inhib Med Chem 2021; 36:561-580. [PMID: 33615947 PMCID: PMC7901698 DOI: 10.1080/14756366.2021.1882453] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Inorganic anions inhibit the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1) generally by coordinating to the active site metal ion. Cyanate was reported as a non-coordinating CA inhibitor but those erroneous results were subsequently corrected by another group. We review the anion CA inhibitors (CAIs) in the more general context of drug design studies and the discovery of a large number of inhibitor classes and inhibition mechanisms, including zinc binders (sulphonamides and isosteres, dithiocabamates and isosteres, thiols, selenols, benzoxaboroles, ninhydrins, etc.); inhibitors anchoring to the zinc-coordinated water molecule (phenols, polyamines, sulfocoumarins, thioxocoumarins, catechols); CAIs occluding the entrance to the active site (coumarins and derivatives, lacosamide), as well as compounds that bind outside the active site. All these new chemotypes integrated with a general procedure for obtaining isoform-selective compounds (the tail approach) has resulted, through the guidance of rigorous X-ray crystallography experiments, in the development of highly selective CAIs for all human CA isoforms with many pharmacological applications.
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Affiliation(s)
- Alessio Nocentini
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
| | - Andrea Angeli
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
| | - Fabrizio Carta
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
| | | | - Raivis Zalubovskis
- Latvian Institute of Organic Synthesis, Riga, Latvia.,Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Riga, Latvia
| | - Simone Carradori
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Clemente Capasso
- Institute of Biosciences and Bioresources, National Research Council, Napoli, Italy
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Claudiu T Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
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Andring JT, Fouch M, Akocak S, Angeli A, Supuran CT, Ilies MA, McKenna R. Structural Basis of Nanomolar Inhibition of Tumor-Associated Carbonic Anhydrase IX: X-Ray Crystallographic and Inhibition Study of Lipophilic Inhibitors with Acetazolamide Backbone. J Med Chem 2020; 63:13064-13075. [PMID: 33085484 DOI: 10.1021/acs.jmedchem.0c01390] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This study provides a structure-activity relationship study of a series of lipophilic carbonic anhydrase (CA) inhibitors with an acetazolamide backbone. The inhibitors were tested against the tumor-expressed CA isozyme IX (CA IX), and the cytosolic CA I, CA II, and membrane-bound CA IV. The study identified several low nanomolar potent inhibitors against CA IX, with lipophilicities spanning two log units. Very potent pan-inhibitors with nanomolar potency against CA IX and sub-nanomolar potency against CA II and CA IV, and with potency against CA I one order of magnitude better than the parent acetazolamide 1 were also identified in this study, together with compounds that displayed selectivity against membrane-bound CA IV. A comprehensive X-ray crystallographic study (12 crystal structures), involving both CA II and a soluble CA IX mimetic (CA IX-mimic), revealed the structural basis of this particular inhibition profile and laid the foundation for further developments toward more potent and selective inhibitors for the tumor-expressed CA IX.
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Affiliation(s)
- Jacob T Andring
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Mallorie Fouch
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Suleyman Akocak
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Andrea Angeli
- NEUROFARBA Department, Pharmaceutical Sciences Section, Universita degli Studi di Firenze, Polo Scientifico, Via Ugo Schiff no. 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Pharmaceutical Sciences Section, Universita degli Studi di Firenze, Polo Scientifico, Via Ugo Schiff no. 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Marc A Ilies
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
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Angeli A, Carta F, Nocentini A, Winum JY, Zalubovskis R, Akdemir A, Onnis V, Eldehna WM, Capasso C, Simone GD, Monti SM, Carradori S, Donald WA, Dedhar S, Supuran CT. Carbonic Anhydrase Inhibitors Targeting Metabolism and Tumor Microenvironment. Metabolites 2020; 10:metabo10100412. [PMID: 33066524 PMCID: PMC7602163 DOI: 10.3390/metabo10100412] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/24/2022] Open
Abstract
The tumor microenvironment is crucial for the growth of cancer cells, triggering particular biochemical and physiological changes, which frequently influence the outcome of anticancer therapies. The biochemical rationale behind many of these phenomena resides in the activation of transcription factors such as hypoxia-inducible factor 1 and 2 (HIF-1/2). In turn, the HIF pathway activates a number of genes including those involved in glucose metabolism, angiogenesis, and pH regulation. Several carbonic anhydrase (CA, EC 4.2.1.1) isoforms, such as CA IX and XII, actively participate in these processes and were validated as antitumor/antimetastatic drug targets. Here, we review the field of CA inhibitors (CAIs), which selectively inhibit the cancer-associated CA isoforms. Particular focus was on the identification of lead compounds and various inhibitor classes, and the measurement of CA inhibitory on-/off-target effects. In addition, the preclinical data that resulted in the identification of SLC-0111, a sulfonamide in Phase Ib/II clinical trials for the treatment of hypoxic, advanced solid tumors, are detailed.
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Affiliation(s)
- Andrea Angeli
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (F.C.); (A.N.)
| | - Fabrizio Carta
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (F.C.); (A.N.)
| | - Alessio Nocentini
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (F.C.); (A.N.)
| | - Jean-Yves Winum
- IBMM, Univ. Montpellier, CNRS, ENSCM, 34296 Montpellier, France;
| | - Raivis Zalubovskis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia, Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, 3/7 Paula Valdena Str., 1048 Riga, Latvia;
| | - Atilla Akdemir
- Computer-aided Drug Discovery Laboratory, Department of Pharmacology, Faculty of Pharmacy, Bezmialem Vakif University, Fatih, Istanbul 34093, Turkey;
| | - Valentina Onnis
- Department of Life and Environmental Sciences, Unit of Pharmaceutical, Pharmacological and Nutraceutical Sciences, University of Cagliari, University Campus, S.P. n° 8, Km 0.700, I-09042 Monserrato, Cagliari, Italy;
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Kafrelsheikh University, Kafrelsheikh 33516, Egypt;
| | - Clemente Capasso
- Institute of Biosciences and Bioresources—National Research Council, via Pietro Castellino 111, 80131 Napoli, Italy;
| | - Giuseppina De Simone
- Institute of Biostructures and Bioimages—National Research Council, 80131 Napoli, Italy; (G.D.S.); (S.M.M.)
| | - Simona Maria Monti
- Institute of Biostructures and Bioimages—National Research Council, 80131 Napoli, Italy; (G.D.S.); (S.M.M.)
| | - Simone Carradori
- Department of Pharmacy, “G. d’Annunzio” University of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy;
| | - William A. Donald
- School of Chemistry, University of New South Wales, 1466 Sydney, Australia;
| | - Shoukat Dedhar
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver Vancouver, BC V5Z 1L3, Canada;
| | - Claudiu T. Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (F.C.); (A.N.)
- Correspondence:
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Akocak S, Güzel-Akdemir Ö, Kishore Kumar Sanku R, Russom SS, Iorga BI, Supuran CT, Ilies MA. Pyridinium derivatives of 3-aminobenzenesulfonamide are nanomolar-potent inhibitors of tumor-expressed carbonic anhydrase isozymes CA IX and CA XII. Bioorg Chem 2020; 103:104204. [PMID: 32891000 DOI: 10.1016/j.bioorg.2020.104204] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/26/2022]
Abstract
Building on the conclusions of previous inhibition studies with pyridinium-benzenesulfonamides from our team and on the X-ray crystal structure of the lead compound identified, a series of 24 pyridinium derivatives of 3-aminobenzenesulfonamide was synthesized and investigated for carbonic anhydrase inhibition. The new pyridinium-sulfonamides were evaluated as inhibitors of four human carbonic anhydrase (CA, EC 4.2.1.1) isoforms, namely CA I, CA II (cytosolic), CA IX and XII (transmembrane, tumor-associated forms). Excellent inhibitory activity in the nanomolar range was observed against CA IX with most of these sulfonamides, and against CA XII (nanomolar/sub-nanomolar) with some of the new compounds. These sulfonamides were generally potent inhibitors of CA II and CA I too. Docking studies revealed a preference of these compounds to bind the P1 hydrophobic site of CAs, supporting the observed inhibition profile. The salt-like nature of these positively charged sulfonamides can further focus the inhibitory ability on membrane-bound CA IX and CA XII and could efficiently decrease the viability of three human carcinomas under hypoxic conditions where these isozymes are over-expressed, thus recommending the new compounds as potential diagnostic tools or therapeutic agents.
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Affiliation(s)
- Suleyman Akocak
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N Broad Street, Philadelphia PA-19140, United States
| | - Özlen Güzel-Akdemir
- NEUROFARBA Department, Università degli Studi di Firenze, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy; Istanbul University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 34116 Beyazıt, Istanbul, Turkey
| | - Rajesh Kishore Kumar Sanku
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N Broad Street, Philadelphia PA-19140, United States
| | - Samson S Russom
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N Broad Street, Philadelphia PA-19140, United States
| | - Bogdan I Iorga
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles (ICSN), 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Claudiu T Supuran
- NEUROFARBA Department, Università degli Studi di Firenze, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy.
| | - Marc A Ilies
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N Broad Street, Philadelphia PA-19140, United States.
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Sağlık BN, Osmaniye D, Çevik UA, Levent S, Çavuşoğlu BK, Büyükemir O, Nezir D, Karaduman AB, Özkay Y, Koparal AS, Beydemir Ş, Kaplancıklı ZA. Synthesis, characterization and carbonic anhydrase I and II inhibitory evaluation of new sulfonamide derivatives bearing dithiocarbamate. Eur J Med Chem 2020; 198:112392. [PMID: 32388113 DOI: 10.1016/j.ejmech.2020.112392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/16/2020] [Accepted: 04/25/2020] [Indexed: 12/11/2022]
Abstract
In this study, novel dithiocarbamate-sulfonamide derivatives (3a-3k) were synthesized to investigate their inhibitory activity on purified human carbonic anhydrase (hCA) I and II. The IC50 and Ki values of the compounds were calculated to compare their inhibition profiles on hCA I and II isoenzymes. Acetazolamide was used as the standard inhibitor in the enzyme inhibition assay. Compounds 3a, 3e, 3g, 3h, 3j and 3k showed notable inhibitory effects against hCA I and II. Among these compounds, compound 3h was found to be the most active derivate against both the hCA I and II enzymes with Ki values of 0.032 ± 0.001 μM and 0.013 ± 0.0005 μM, respectively. The cytotoxicity of compounds 3a, 3e, 3g, 3h, 3j and 3k toward NIH/3T3 (mouse embryonic fibroblast cell line) was observed and the compounds were found to be non-cytotoxic. Furthermore, molecular docking studies were performed to investigate the interaction types between compound 3h and the hCA I and II enzymes. As a result of this study a novel and potent class of CA inhibitors with good activity potential were identified.
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Affiliation(s)
- Begüm Nurpelin Sağlık
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey; Doping and Narcotic Compounds Analysis Laboratory, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey.
| | - Derya Osmaniye
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey; Doping and Narcotic Compounds Analysis Laboratory, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Ulviye Acar Çevik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey; Doping and Narcotic Compounds Analysis Laboratory, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Serkan Levent
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey; Doping and Narcotic Compounds Analysis Laboratory, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Betül Kaya Çavuşoğlu
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Zonguldak Bülent Ecevit University, 67600 Zonguldak, Turkey
| | - Oya Büyükemir
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Deniz Nezir
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Abdullah Burak Karaduman
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Yusuf Özkay
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey; Doping and Narcotic Compounds Analysis Laboratory, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | | | - Şükrü Beydemir
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Zafer Asım Kaplancıklı
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
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Supuran CT. Exploring the multiple binding modes of inhibitors to carbonic anhydrases for novel drug discovery. Expert Opin Drug Discov 2020; 15:671-686. [PMID: 32208982 DOI: 10.1080/17460441.2020.1743676] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION The spacious active site cavity of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1) shows a great versatility for a variety of binding modes for modulators of activity, inhibitors, and activators, some of which are clinically used drugs. AREAS COVERED There are at least four well-documented CA inhibition mechanisms and the same number of binding modes for CA inhibitors (CAIs), one of which superposes with the binding of activators (CAAs). They include (i) coordination to the catalytic metal ion; (ii) anchoring to the water molecule coordinated to the metal ion; (iii) occlusion of the active site entrance; and (iv) binding outside the active site. A large number of chemical classes of CAIs show these binding modes explored in detail by kinetic, crystallographic, and other techniques. The tail approach was applied to all of them and allowed many classes of highly isoform-selective inhibitors. This is the subject of our review. EXPERT OPINION All active site regions of CAs accommodate inhibitors to bind, which is reflected in very different inhibition profiles for such compounds and the possibility to design drugs with effective action and new applications, such as for the management of hypoxic tumors, neuropathic pain, cerebral ischemia, arthritis, and degenerative disorders.
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Affiliation(s)
- Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence , Florence, Italy
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10
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Sağlık BN, Çevik UA, Osmaniye D, Levent S, Çavuşoğlu BK, Demir Y, Ilgın S, Özkay Y, Koparal AS, Beydemir Ş, Kaplancıklı ZA. Synthesis, molecular docking analysis and carbonic anhydrase I-II inhibitory evaluation of new sulfonamide derivatives. Bioorg Chem 2019; 91:103153. [DOI: 10.1016/j.bioorg.2019.103153] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 05/23/2019] [Accepted: 07/24/2019] [Indexed: 11/16/2022]
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
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Lomelino CL, Andring JT, McKenna R. Crystallography and Its Impact on Carbonic Anhydrase Research. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2018; 2018:9419521. [PMID: 30302289 PMCID: PMC6158936 DOI: 10.1155/2018/9419521] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
X-ray and neutron crystallography are powerful techniques utilized to study the structures of biomolecules. Visualization of enzymes in complex with substrate/product and the capture of intermediate states can be related to activity to facilitate understanding of the catalytic mechanism. Subsequent analysis of small molecule binding within the enzyme active site provides insight into mechanisms of inhibition, supporting the design of novel inhibitors using a structure-guided approach. The first X-ray crystal structures were determined for small, ubiquitous enzymes such as carbonic anhydrase (CA). CAs are a family of zinc metalloenzymes that catalyze the hydration of CO2, producing HCO3 - and a proton. The CA structure and ping-pong mechanism have been extensively studied and are well understood. Though the function of CA plays an important role in a variety of physiological functions, CA has also been associated with diseases such as glaucoma, edema, epilepsy, obesity, and cancer and is therefore recognized as a drug target. In this review, a brief history of crystallography and its impact on CA research is discussed.
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Affiliation(s)
- Carrie L. Lomelino
- University of Florida College of Medicine, Department of Biochemistry and Molecular Biology, Gainesville, FL 32610, USA
| | - Jacob T. Andring
- University of Florida College of Medicine, Department of Biochemistry and Molecular Biology, Gainesville, FL 32610, USA
| | - Robert McKenna
- University of Florida College of Medicine, Department of Biochemistry and Molecular Biology, Gainesville, FL 32610, USA
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Carta F, Birkmann A, Pfaff T, Buschmann H, Schwab W, Zimmermann H, Maresca A, Supuran CT. Lead Development of Thiazolylsulfonamides with Carbonic Anhydrase Inhibitory Action. J Med Chem 2017; 60:3154-3164. [DOI: 10.1021/acs.jmedchem.7b00183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Fabrizio Carta
- Sezione
di Scienze Farmaceutiche e Nutraceutiche, NEUROFARBA, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Alexander Birkmann
- AiCuris Anti-Infective Cures GmbH, Friedrich-Ebert-Strasse 475, 42117 Wuppertal, Germany
| | - Tamara Pfaff
- AiCuris Anti-Infective Cures GmbH, Friedrich-Ebert-Strasse 475, 42117 Wuppertal, Germany
| | - Helmut Buschmann
- AiCuris Anti-Infective Cures GmbH, Friedrich-Ebert-Strasse 475, 42117 Wuppertal, Germany
| | - Wilfried Schwab
- AiCuris Anti-Infective Cures GmbH, Friedrich-Ebert-Strasse 475, 42117 Wuppertal, Germany
| | - Holger Zimmermann
- AiCuris Anti-Infective Cures GmbH, Friedrich-Ebert-Strasse 475, 42117 Wuppertal, Germany
| | - Alfonso Maresca
- Sezione
di Scienze Farmaceutiche e Nutraceutiche, NEUROFARBA, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T. Supuran
- Sezione
di Scienze Farmaceutiche e Nutraceutiche, NEUROFARBA, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
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5-Substituted-benzylsulfanyl-thiophene-2-sulfonamides with effective carbonic anhydrase inhibitory activity: Solution and crystallographic investigations. Bioorg Med Chem 2017; 25:857-863. [DOI: 10.1016/j.bmc.2016.11.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 11/23/2016] [Indexed: 11/18/2022]
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15
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Abdel Gawad NM, Amin NH, Elsaadi MT, Mohamed FMM, Angeli A, De Luca V, Capasso C, Supuran CT. Synthesis of 4-(thiazol-2-ylamino)-benzenesulfonamides with carbonic anhydrase I, II and IX inhibitory activity and cytotoxic effects against breast cancer cell lines. Bioorg Med Chem 2016; 24:3043-3051. [PMID: 27234893 DOI: 10.1016/j.bmc.2016.05.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/04/2016] [Accepted: 05/11/2016] [Indexed: 10/21/2022]
Abstract
A series of 4-(thiazol-2-ylamino)-benzenesulfonamides was synthesized and screened for their carbonic anhydrase (CA, EC 4.2.1.1) inhibitory and cytotoxic activity on human breast cancer cell line MCF-7. Human (h) CA isoforms I, II and IX were included in the study. The new sulfonamides showed excellent inhibition of all three isoforms, with KIs in the range of 0.84-702nM against hCA I, of 0.41-288nM against hCA II and of 5.6-29.2 against the tumor-associated hCA IX, a validated anti-tumor target, with a sulfonamide (SLC-0111) in Phase I clinical trials for the treatment of hypoxic, metastatic solid tumors overexpressing CA IX. The new compounds showed micromolar inhibition of growth efficacy against breast cancer MCF-7 cell lines.
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Affiliation(s)
- Nagwa M Abdel Gawad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Noha H Amin
- Department of Medicinal Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt.
| | - Mohammed T Elsaadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Fatma M M Mohamed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Andrea Angeli
- Università degli Studi di Firenze, Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Viviana De Luca
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
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16
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Mishra CB, Kumari S, Angeli A, Monti SM, Buonanno M, Prakash A, Tiwari M, Supuran CT. Design, synthesis and biological evaluation of N-(5-methyl-isoxazol-3-yl/1,3,4-thiadiazol-2-yl)-4-(3-substitutedphenylureido) benzenesulfonamides as human carbonic anhydrase isoenzymes I, II, VII and XII inhibitors. J Enzyme Inhib Med Chem 2016; 31:174-179. [PMID: 27314170 DOI: 10.1080/14756366.2016.1197221] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022] Open
Abstract
A series of N-(5-methyl-isoxazol-3-yl/1,3,4-thiadiazol-2-yl)-4-(3-substitutedphenylureido) benzenesulfonamide derivatives has been designed, synthesized and screened for their in vitro human carbonic anhydrase (hCA; EC 4.2.1.1) inhibition potential. These newly synthesized sulfonamide compounds were assessed against isoforms hCA I, II, VII and XII, with acetazolamide (AAZ) as a reference compound. The majority of these compounds were found quite weak inhibitor against all tested isoforms. Compound 15 showed a modest inhibition potency against hCA I (Ki = 73.7 μM) and hCA VII (Ki = 85.8 μM). Compounds 19 and 25 exhibited hCA II inhibition with Ki values of 96.0 μM and 87.8 μM, respectively. The results of the present study suggest that, although the synthesized derivatives have weak inhibitory potential towards all investigated isoforms, some of them may serve as lead molecules for the further development of selective inhibitors incorporating secondary sulfonamide functionalities, a class of inhibitors for which the inhibition mechanism is poorly understood.
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Affiliation(s)
- Chandra Bhushan Mishra
- a Bio-Organic Chemistry Laboratory, Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi , Delhi , India
| | - Shikha Kumari
- a Bio-Organic Chemistry Laboratory, Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi , Delhi , India
| | - Andrea Angeli
- b Dipartimento Neurofarba, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche , Florence , Italy
| | - Simona Maria Monti
- c Istituto di Biostrutture e Bioimmagini (IBB) CNR , via Mezzocannone , Naples , Italy , and
| | - Martina Buonanno
- c Istituto di Biostrutture e Bioimmagini (IBB) CNR , via Mezzocannone , Naples , Italy , and
| | - Amresh Prakash
- d School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi , India
| | - Manisha Tiwari
- a Bio-Organic Chemistry Laboratory, Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi , Delhi , India
| | - Claudiu T Supuran
- b Dipartimento Neurofarba, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche , Florence , Italy
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17
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Lomelino CL, Mahon BP, McKenna R, Carta F, Supuran CT. Kinetic and X-ray crystallographic investigations on carbonic anhydrase isoforms I, II, IX and XII of a thioureido analog of SLC-0111. Bioorg Med Chem 2016; 24:976-81. [PMID: 26810836 DOI: 10.1016/j.bmc.2016.01.019] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 01/09/2016] [Indexed: 10/22/2022]
Abstract
SLC-0111 (4-(4-fluorophenylureido)-benzenesulfonamide) is the first carbonic anhydrase (CA, EC 4.2.1.1) IX inhibitor to reach phase I clinical trials as an antitumor/antimetastatic agent. Here we report a kinetic and X-ray crystallographic study of a congener of SLC-0111 which incorporates a thioureido instead of ureido linker between the two aromatic rings as inhibitor of four physiologically relevant CA isoforms. Similar to SLC-0111, the thioureido derivative was a weak hCA I and II inhibitor and a potent one against hCA IX and XII. X-ray crystallography of its adduct with hCA II and comparison of the structure with that of other five hCA II-sulfonamide adducts belonging to the SLC-0111 series, afforded us to understand the particular inhibition profile of the new sulfonamide. Similar to SLC-0111, the thioureido sulfonamide primarily interacted with the hydrophobic side of the hCA II active site, with the tail participating in van der Waals interactions with Phe131 and Pro202, in addition to the coordination of the deprotonated sulfonamide to the active site metal ion. On the contrary, the tail of other sulfonamides belonging to the SLC-0111 series (2-isopropyl-phenyl; 3-nitrophenyl) were orientated towards the hydrophilic half of the active site, which was correlated with orders of magnitude better inhibitory activity against hCA II, and a loss of selectivity for the inhibition of the tumor-associated CAs.
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Affiliation(s)
- Carrie L Lomelino
- University of Florida College of Medicine, Department of Biochemistry and Molecular Biology, Gainesville, FL, USA
| | - Brian P Mahon
- University of Florida College of Medicine, Department of Biochemistry and Molecular Biology, Gainesville, FL, USA
| | - Robert McKenna
- University of Florida College of Medicine, Department of Biochemistry and Molecular Biology, Gainesville, FL, USA.
| | - Fabrizio Carta
- Dipartimento di Chimica Ugo Schiff, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Firenze), Italy; Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Claudiu T Supuran
- Dipartimento di Chimica Ugo Schiff, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Firenze), Italy; Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy.
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18
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Gaspari R, Rechlin C, Heine A, Bottegoni G, Rocchia W, Schwarz D, Bomke J, Gerber HD, Klebe G, Cavalli A. Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies. J Med Chem 2016; 59:4245-56. [PMID: 26700575 DOI: 10.1021/acs.jmedchem.5b01643] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The binding of sulfonamides to human carbonic anhydrase II (hCAII) is a complex and long-debated example of protein-ligand recognition and interaction. In this study, we investigate the para-substituted n-alkyl and hydroxyethylene-benzenesulfonamides, providing a complete reconstruction of their binding pathway to hCAII by means of large-scale molecular dynamics simulations, density functional calculations, surface plasmon resonance (SPR) measurements, and X-ray crystallography experiments. Our analysis shows that the protein-ligand association rate (kon) dramatically increases with the ligand's hydrophobicity, pointing to the existence of a prebinding stage largely stabilized by a favorable packing of the ligand's apolar moieties with the hCAII "hydrophobic wall". The characterization of the binding pathway allows an unprecedented understanding of the structure-kinetic relationship in hCAII/benzenesulfonamide complexes, depicting a paradigmatic scenario for the multistep binding process in protein-ligand systems.
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Affiliation(s)
- Roberto Gaspari
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , 16163 Genova, Italy
| | - Chris Rechlin
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Giovanni Bottegoni
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , 16163 Genova, Italy
| | - Walter Rocchia
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , 16163 Genova, Italy
| | - Daniel Schwarz
- Small Molecule Platform/MIB, Merck KGaA, Merck Serono Research , Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Jörg Bomke
- Small Molecule Platform/MIB, Merck KGaA, Merck Serono Research , Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Hans-Dieter Gerber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Andrea Cavalli
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , 16163 Genova, Italy.,Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
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19
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Fluorescent sulfonamide carbonic anhydrase inhibitors incorporating 1,2,3-triazole moieties: Kinetic and X-ray crystallographic studies. Bioorg Med Chem 2016; 24:104-12. [DOI: 10.1016/j.bmc.2015.11.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 11/21/2015] [Accepted: 11/24/2015] [Indexed: 12/19/2022]
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20
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Ferraroni M, Carta F, Scozzafava A, Supuran CT. Thioxocoumarins Show an Alternative Carbonic Anhydrase Inhibition Mechanism Compared to Coumarins. J Med Chem 2015; 59:462-73. [DOI: 10.1021/acs.jmedchem.5b01720] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Marta Ferraroni
- Polo
Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
| | - Fabrizio Carta
- Polo
Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
| | - Andrea Scozzafava
- Polo
Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
| | - Claudiu T. Supuran
- Polo
Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
- NEUROFARBA
Dept., Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy
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21
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Capasso C, Supuran CT. Bacterial, fungal and protozoan carbonic anhydrases as drug targets. Expert Opin Ther Targets 2015; 19:1689-704. [PMID: 26235676 DOI: 10.1517/14728222.2015.1067685] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The carbonic anhydrases (CAs, EC 4.2.1.1), a group of ubiquitously expressed metalloenzymes, are involved in numerous physiological and pathological processes, as well as in the growth and virulence of pathogens belonging to bacteria, fungi and protozoa. AREAS COVERED CAs belonging to at least four genetic families, the α-, β-, γ- and η-CAs, were discovered and characterized in many pathogens: i) Bacteria encode enzymes from one or more such families, which were investigated as potential drug targets. Inhibition of bacterial CAs by sulfonamides/phenol derivatives lead to inhibition of growth of the pathogen for Helicobacter pylori, Mycobacterium tuberculosis, Brucella suis; ii) Fungi encode for α- and β-CAs, and inhibitors of the sulfonamide, thiol or dithiocarbamate type inhibited the growth of some of them (Malassezia globosa, Candida albicans, Crytpococcus neoformans, etc) in vivo; and iii) Protozoa encode α-, β- or η-CAs. Sulfonamide, thiols and hydroxamates effectively killed such parasites (Trypanosoma cruzi, Leishmania donovani chagasi, Plasmodium falciparum) in vivo. EXPERT OPINION None of the microorganism CAs is validated as drug targets as yet, but the inhibitors designed against many such enzymes showed interesting in vitro/in vivo results. By interfering with the activity of CAs from microorganisms, both pH homeostasis as well as crucial biosynthetic reactions are impaired, which lead to significant antiinfective effects, not yet exploited for obtaining pharmacological agents. As resistance to the clinically used antiinfectives is a serious healthcare problem worldwide, inhibition of parasite CAs may constitute an alternative approach for obtaining such agents with novel mechanisms of action.
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Affiliation(s)
- Clemente Capasso
- a 1 CNR, Institute of Biosciences and Bioresorces (IBBR) , via P. Castellino, 111, 80131, Napoli, Italy
| | - Claudiu T Supuran
- b 2 University of Florence, Neurofarba Department, Section of Pharmaceutical Chemistry , Via U. Schiff 6, 5019 Sesto Fiorentino, Firenze, Italy
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22
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Congiu C, Onnis V, Deplano A, Balboni G, Dedeoglu N, Supuran CT. Synthesis of sulfonamides incorporating piperazinyl-ureido moieties and their carbonic anhydrase I, II, IX and XII inhibitory activity. Bioorg Med Chem Lett 2015; 25:3850-3. [PMID: 26233435 DOI: 10.1016/j.bmcl.2015.07.060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/17/2015] [Accepted: 07/18/2015] [Indexed: 01/15/2023]
Abstract
By using SLC-0111 (4-fluorophenylureido-benzenesulfonamide), a sulfonamide carbonic anhydrase (CA, EC 4.2.1.1) inhibitor in Phase I clinical trials as an antitumor agent as lead molecule, a series of benzenesulfonamide derivatives incorporating ureido moieties was synthesized. The new compounds contain a 4-N-substituted piperazine fragment in which the ureido linker has been included, and were tested as inhibitors of the cytosolic human (h) hCA I and II isoforms, as well as the transmembrane, tumor-associated enzymes hCA IX and XII. Depending on the substitution pattern at the piperazine ring, low nanomolar inhibitors were detected against all four isoforms, making the new class of sulfonamides of interest for various pharmacologic applications.
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Affiliation(s)
- Cenzo Congiu
- Department of Life and Environmental Sciences, Unit of Pharmaceutical, Pharmacological and Nutraceutical Sciences, University of Cagliari, Via Ospedale 72, Cagliari I-09124, Italy.
| | - Valentina Onnis
- Department of Life and Environmental Sciences, Unit of Pharmaceutical, Pharmacological and Nutraceutical Sciences, University of Cagliari, Via Ospedale 72, Cagliari I-09124, Italy
| | - Alessandro Deplano
- Department of Life and Environmental Sciences, Unit of Pharmaceutical, Pharmacological and Nutraceutical Sciences, University of Cagliari, Via Ospedale 72, Cagliari I-09124, Italy
| | - Gianfranco Balboni
- Department of Life and Environmental Sciences, Unit of Pharmaceutical, Pharmacological and Nutraceutical Sciences, University of Cagliari, Via Ospedale 72, Cagliari I-09124, Italy
| | - Nurcan Dedeoglu
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
| | - 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; Università degli Studi di Firenze, NEUROFARBA Department, Section of Pharmaceutical and Nutraceutical Chemistry, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy.
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23
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De Luca V, Vullo D, Del Prete S, Carginale V, Scozzafava A, Osman SM, AlOthman Z, Supuran CT, Capasso C. Cloning, characterization and anion inhibition studies of a new γ-carbonic anhydrase from the Antarctic bacterium Pseudoalteromonas haloplanktis. Bioorg Med Chem 2015; 23:4405-4409. [PMID: 26145820 DOI: 10.1016/j.bmc.2015.06.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
A new γ-class carbonic anhydrase (CA, EC 4.2.1.1) was cloned, purified and characterized from the Antarctic bacterium Pseudoalteromonas haloplanktis, PhaCAγ. The enzyme has a medium-low catalytic activity for the physiologic reaction of CO2 hydration to bicarbonate and protons, with a kcat of 1.4×10(5)s(-1) and a kcat/Km of 1.9×10(6)M(-1)s(-1). An anion inhibition study of PhaCAγ with inorganic anions and small molecule inhibitors is also reported. Many anions present in sea water, such as chloride, fluoride, sulfate, iodide, but also others such as azide, perchlorate and tetrafluoroborate did not inhibit this enzyme. Pseudohalides such as cyanate, thiocyanate, cyanide, selenocyanide, and also bicarbonate, nitrate, nitrite and many complex inorganic anions showed inhibition in the millimolar range (KI in the range of 1.7-9.3mM). The best PhaCAγ inhibitors detected in this study were diethyldithiocarbamate (KI of 0.96 mM) as well as sulfamide, sulfamate, phenylboronic acid and phenylarsonic acid (KI in the range of 82-91 μM). Since γ-CAs are poorly understood at this moment, being present in carboxysomes and thus involved in photosynthesis, this study may be relevant for a better understanding of these processes in Antarctic bacteria/cyanobacteria.
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Affiliation(s)
- Viviana De Luca
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Daniela Vullo
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Sonia Del Prete
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy; Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Vincenzo Carginale
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Andrea Scozzafava
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Sameh M Osman
- Department of Chemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Zeid AlOthman
- Department of Chemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy; Università degli Studi di Firenze, Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy.
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Bozdag M, Carta F, Vullo D, Akdemir A, Isik S, Lanzi C, Scozzafava A, Masini E, Supuran CT. Synthesis of a new series of dithiocarbamates with effective human carbonic anhydrase inhibitory activity and antiglaucoma action. Bioorg Med Chem 2015; 23:2368-76. [DOI: 10.1016/j.bmc.2015.03.068] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 12/13/2022]
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25
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Vullo D, De Luca V, Del Prete S, Carginale V, Scozzafava A, Capasso C, Supuran CT. Sulfonamide inhibition studies of the γ-carbonic anhydrase from the Antarctic cyanobacterium Nostoc commune. Bioorg Med Chem 2015; 23:1728-34. [PMID: 25773015 DOI: 10.1016/j.bmc.2015.02.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 02/11/2015] [Accepted: 02/24/2015] [Indexed: 02/09/2023]
Abstract
A carbonic anhydrase (CA, EC 4.2.1.1) belonging to the γ-class has been cloned, purified and characterized from the Antarctic cyanobacterium Nostoc commune. The enzyme showed a good catalytic activity for the physiologic reaction (hydration of carbon dioxide to bicarbonate and a proton) with the following kinetic parameters, kcat of 9.5×10(5)s(-1) and kcat/KM of 8.3×10(7)M(-1)s(-1), being the γ-CA with the highest catalytic activity described so far. A range of aromatic/heterocyclic sulfonamides and one sulfamate were investigated as inhibitors of the new enzyme, denominated here NcoCA. The best NcoCA inhibitors were some sulfonylated sulfanilamide derivatives possessing elongated molecules, aminobenzolamide, acetazolamide, benzolamide, dorzolamide, brinzolamide and topiramate, which showed inhibition constants in the range of 40.3-92.3nM. As 1,5-bisphosphate carboxylase/oxygenase (RubisCO) and γ-CAs are closely associated in carboxysomes of cyanobacteria for enhancing the affinity of RubisCO for CO2 and the efficiency of photosynthesis, investigation of this new enzyme and its affinity for modulators of its activity may bring new insights in these crucial processes.
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Affiliation(s)
- Daniela Vullo
- Università degliStudi di Firenze, Dipartimento Di Chimica, Laboratorio di ChimicaBioinorganica, Polo Scientifico, Via della Lastruccia3, 50019 Sesto Fiorentino, Florence, Italy
| | - Viviana De Luca
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Sonia Del Prete
- Università degliStudi di Firenze, Dipartimento Di Chimica, Laboratorio di ChimicaBioinorganica, Polo Scientifico, Via della Lastruccia3, 50019 Sesto Fiorentino, Florence, Italy; Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Vincenzo Carginale
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Andrea Scozzafava
- Università degliStudi di Firenze, Dipartimento Di Chimica, Laboratorio di ChimicaBioinorganica, Polo Scientifico, Via della Lastruccia3, 50019 Sesto Fiorentino, Florence, Italy
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy.
| | - Claudiu T Supuran
- Università degliStudi di Firenze, Dipartimento Di Chimica, Laboratorio di ChimicaBioinorganica, Polo Scientifico, Via della Lastruccia3, 50019 Sesto Fiorentino, Florence, Italy; Università degliStudi di Firenze, DipartimentoNeurofarba, Sezione di ScienzeFarmaceutiche, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
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Haider S, Alam MS, Hamid H. 1,3,4-Thiadiazoles: A potent multi targeted pharmacological scaffold. Eur J Med Chem 2015; 92:156-77. [DOI: 10.1016/j.ejmech.2014.12.035] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 12/15/2014] [Accepted: 12/20/2014] [Indexed: 11/30/2022]
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Carta F, Di Cesare Mannelli L, Pinard M, Ghelardini C, Scozzafava A, McKenna R, Supuran CT. A class of sulfonamide carbonic anhydrase inhibitors with neuropathic pain modulating effects. Bioorg Med Chem 2015; 23:1828-40. [PMID: 25766630 DOI: 10.1016/j.bmc.2015.02.027] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/10/2015] [Accepted: 02/16/2015] [Indexed: 12/21/2022]
Abstract
A series of benzene sulfonamide carbonic anhydrase (CA, EC 4.2.1.1) inhibitors which incorporate lipophilic 4-alkoxy- and 4-aryloxy moieties, together with several derivatives of ethoxzolamide and sulfanilamide are reported. These derivatives were investigated as inhibitors of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1) of which multiple isoforms are known, and some appear to be involved in pain. These sulfonamides showed modest inhibition against the cytosolic isoform CA I, but were generally effective, low nanomolar CA II, VII, IX and XII inhibitors. X-ray crystallographic data for the adduct of several such sulfonamides with CA II allowed us to rationalize the good inhibition data. In a mice model of neuropathic pain induced by oxaliplatin, one of the strong CA II/VII inhibitors reported here induced a long lasting pain relieving effect, a fact never observed earlier. This is the first report of rationally designed sulfonamide CA inhibitors with pain effective modulating effects.
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Affiliation(s)
- Fabrizio Carta
- Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Lorenzo Di Cesare Mannelli
- Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Farmacologia, Viale G. Pieraccini 6, 50139 Florence, Italy
| | - Melissa Pinard
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA
| | - Carla Ghelardini
- Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Farmacologia, Viale G. Pieraccini 6, 50139 Florence, Italy
| | - Andrea Scozzafava
- Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy; Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
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De Luca V, Del Prete S, Carginale V, Vullo D, Supuran CT, Capasso C. A failed tentative to design a super carbonic anhydrase having the biochemical properties of the most thermostable CA (SspCA) and the fastest (SazCA) enzymes. J Enzyme Inhib Med Chem 2015; 30:989-94. [DOI: 10.3109/14756366.2014.1002403] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Viviana De Luca
- Istituto di Bioscienze e Biorisorse , CNR, Napoli, Italy and
| | - Sonia Del Prete
- Istituto di Bioscienze e Biorisorse , CNR, Napoli, Italy and
- DipartimentoNeurofarba, Università degliStudi di Firenze, Sezione di ScienzeFarmaceutiche, and Laboratorio di ChimicaBioinorganica, Polo Scientifico, Sesto Fiorentino, Florence, Italy
| | | | - Daniela Vullo
- DipartimentoNeurofarba, Università degliStudi di Firenze, Sezione di ScienzeFarmaceutiche, and Laboratorio di ChimicaBioinorganica, Polo Scientifico, Sesto Fiorentino, Florence, Italy
| | - Claudiu T. Supuran
- DipartimentoNeurofarba, Università degliStudi di Firenze, Sezione di ScienzeFarmaceutiche, and Laboratorio di ChimicaBioinorganica, Polo Scientifico, Sesto Fiorentino, Florence, Italy
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Del Prete S, De Luca V, Supuran CT, Capasso C. Protonography, a technique applicable for the analysis of η-carbonic anhydrase activity. J Enzyme Inhib Med Chem 2015; 30:920-4. [PMID: 25676328 DOI: 10.3109/14756366.2014.990963] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Protonography, a sodium dodecyl sulfate - polyacrylamide gel electrophoresis (SDS-PAGE) technique derived from zymography was recently reported by our group to be an effective, cheap and reproducible technique for evidencing catalytically active α-carbonic anhydrase (CA, EC 4.2.1.1) isoforms, such as the bovine red blood cell isoform bCA or the bacterial enzyme from Vibrio cholerae, VchCA. CA activity was also observed on the protonogram of a cellular extract of Escherichia coli, evidencing the presence of one or more β-class such enzymes. Here we show that protonography can also be applied to the recently discovered η-CA family using the Plasmodium falciparum enzyme PfCA as an example. The protonogram of PfCA clearly showed catalytically active η-CA with a specific band at 22.0 kDa, which was quite distinct from the band of the red blood cell bovine enzyme bCA, which was observed at 28.8 kDa. The different migration pattern of α- and η-CAs might be a useful tool to detect Plasmodium falciparum in infected human red blood cells by an easy, routine inexpensive technique.
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Affiliation(s)
- Sonia Del Prete
- a CNR - Istituto di Bioscienze e Biorisorse , Napoli , Italy and.,b Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, and Laboratorio di Chimica Bioinorganica, Polo Scientifico , Università Degli Studi di Firenze , Florence , Italy
| | - Viviana De Luca
- a CNR - Istituto di Bioscienze e Biorisorse , Napoli , Italy and
| | - Claudiu T Supuran
- b Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, and Laboratorio di Chimica Bioinorganica, Polo Scientifico , Università Degli Studi di Firenze , Florence , Italy
| | - Clemente Capasso
- a CNR - Istituto di Bioscienze e Biorisorse , Napoli , Italy and
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30
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Bozdag M, Pinard M, Carta F, Masini E, Scozzafava A, McKenna R, Supuran CT. A class of 4-sulfamoylphenyl-ω-aminoalkyl ethers with effective carbonic anhydrase inhibitory action and antiglaucoma effects. J Med Chem 2014; 57:9673-86. [PMID: 25358036 PMCID: PMC4255726 DOI: 10.1021/jm501497m] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
We
report a series of 4-sulfamoylphenyl-ω-aminoalkyl ethers
as carbonic anhydrase (CA, EC 4.2.1.1) inhibitors. The structure–activity
relationship was drawn for the inhibition of four physiologically
relevant isoforms: hCA I, II, IX, and XII. Many of these compounds
were highly effective, low nanomolar inhibitors of all CA isoforms,
whereas several isoform-selective were also identified. X-ray crystal
structures of two new sulfonamides bound to the physiologically dominant
CA II isoform showed the tails of these derivatives bound within the
hydrophobic half of the enzyme active site through van der Waals contacts
with Val135, Leu198, Leu204, Trp209, Pro201, and Pro202 amino acids.
One of the highly water-soluble compound (as trifluoroacetate salt)
showed effective IOP lowering properties in an animal model of glaucoma.
Several fluorescent sulfonamides incorporating either the fluorescein-thiourea
(7a–c) or tetramethylrhodamine-thiourea
(9a,b) moieties were also obtained and showed
interesting CA inhibitory properties for the tumor-associated isoforms
CA IX and XII.
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Affiliation(s)
- Murat Bozdag
- Polo Scientifico, Neurofarba Department and Laboratorio di Chimica Bioinorganica, Rm 188, Università degli Studi di Firenze , Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
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31
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Abdel-Aziz AAM, El-Azab AS, Ceruso M, Supuran CT. Carbonic anhydrase inhibitory activity of sulfonamides and carboxylic acids incorporating cyclic imide scaffolds. Bioorg Med Chem Lett 2014; 24:5185-9. [DOI: 10.1016/j.bmcl.2014.09.076] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 12/15/2022]
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Bozdag M, Ferraroni M, Carta F, Vullo D, Lucarini L, Orlandini E, Rossello A, Nuti E, Scozzafava A, Masini E, Supuran CT. Structural Insights on Carbonic Anhydrase Inhibitory Action, Isoform Selectivity, and Potency of Sulfonamides and Coumarins Incorporating Arylsulfonylureido Groups. J Med Chem 2014; 57:9152-67. [DOI: 10.1021/jm501314c] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Murat Bozdag
- Laboratorio di Chimica
Bioinorganica, Polo Scientifico, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Marta Ferraroni
- Laboratorio di Chimica
Bioinorganica, Polo Scientifico, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Fabrizio Carta
- Laboratorio di Chimica
Bioinorganica, Polo Scientifico, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Daniela Vullo
- Laboratorio di Chimica
Bioinorganica, Polo Scientifico, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Laura Lucarini
- Sezione di Farmacologia, Dipartimento di Neuroscienze,
Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), Università degli Studi di Firenze, Viale Pieraccini 6, 50139 Florence, Italy
| | | | - Armando Rossello
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno,
6, 56126 Pisa, Italy
| | - Elisa Nuti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno,
6, 56126 Pisa, Italy
| | - Andrea Scozzafava
- Laboratorio di Chimica
Bioinorganica, Polo Scientifico, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Emanuela Masini
- Sezione di Farmacologia, Dipartimento di Neuroscienze,
Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), Università degli Studi di Firenze, Viale Pieraccini 6, 50139 Florence, Italy
| | - Claudiu T. Supuran
- Laboratorio di Chimica
Bioinorganica, Polo Scientifico, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
- Sezione di Scienze Farmaceutiche, Dipartimento
di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino
(NEUROFARBA), Università degli Studi di Firenze, Via Ugo Schiff
6, 50019 Sesto Fiorentino, Florence, Italy
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33
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Pala N, Micheletto L, Sechi M, Aggarwal M, Carta F, McKenna R, Supuran CT. Carbonic Anhydrase Inhibition with Benzenesulfonamides and Tetrafluorobenzenesulfonamides Obtained via Click Chemistry. ACS Med Chem Lett 2014; 5:927-30. [PMID: 25147616 DOI: 10.1021/ml500196t] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/07/2014] [Indexed: 01/23/2023] Open
Abstract
A series of novel benzene- and 2,3,5,6-tetrafluorobenzenesulfonamide was synthesized by using a click chemistry approach starting from azido-substituted sulfonamides and alkynes, incorporating aryl, alkyl, cycloalkyl, and amino-/hydroxy-/halogenoalkyl moieties. The new compounds were medium potency inhibitors of the cytosolic carbonic anhydrase (CA, EC 4.2.1.1) isoforms I and II and low nanomolar/subnanomolar inhibitors of the tumor-associated hCA IX and XII isoforms. The X-ray crystal structure of two such sulfonamides in adduct with hCA II allowed us to understand the factors governing inhibitory power.
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Affiliation(s)
- Nicolino Pala
- Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna
2, 07100 Sassari, Italy
| | - Laura Micheletto
- Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna
2, 07100 Sassari, Italy
| | - Mario Sechi
- Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna
2, 07100 Sassari, Italy
| | - Mayank Aggarwal
- Department of Biochemistry and Molecular
Biology, College of Medicine, University of Florida, Box 100245, Gainesville, Florida 32610, United States
| | - Fabrizio Carta
- Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Rm 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Firenze), Italy
| | - Robert McKenna
- Department of Biochemistry and Molecular
Biology, College of Medicine, University of Florida, Box 100245, Gainesville, Florida 32610, United States
| | - Claudiu T. Supuran
- Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Rm 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Firenze), Italy
- Neurofarba Dept., Università degli Studi di Firenze, Via U. Schiff 6, 50019 Sesto Fiorentino (Firenze), Italy
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Capasso C, Supuran CT. An overview of the alpha-, beta- and gamma-carbonic anhydrases from Bacteria: can bacterial carbonic anhydrases shed new light on evolution of bacteria? J Enzyme Inhib Med Chem 2014; 30:325-32. [PMID: 24766661 DOI: 10.3109/14756366.2014.910202] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Carbonic anhydrases (CAs, EC 4.2.1.1) are metalloenzymes which catalyze a simple but physiologically crucial reaction in all life Domains, the carbon dioxide hydration to bicarbonate and protons: CO2 + H2O ⇔ HCO3(-)+ H(+). These enzymes are involved in many physiologic processes, such as photosynthesis, respiration, CO2 transport, as well as metabolism of xenobiotics. Five different, genetically distinct CA families are known to date: the α-, β-, γ-, δ- and ζ-CAs. α-, β- and δ-CAs use Zn(II) ions at the active site, the γ-CAs are probably Fe(II) enzymes (but they are active also with bound Zn(II) or Co(II) ions), whereas the ζ-class uses Cd(II) or Zn(II) to perform the physiologic reaction catalysis. Bacteria encode for enzymes belonging to the α-, β-, and γ-CA classes. They contain zinc ion (Zn(2+)) in their active site, coordinated by three histidine residues and a water molecule/hydroxide ion (in the α and γ) or by two cysteine and one histidine residues (in the β class), with the fourth ligand being a water molecule/hydroxide ion. Here we propose that bacterial CAs can be used as markers for understanding the evolution and genetic variability of the Gram-positive and Gram-negative bacteria. We addressed several questions such as: (1) why are α-CAs present only in the genome of Gram-negative bacteria; (2) why are α-CAs not present in all Gram-negative bacteria; (3) why do Bacteria show an intricate pattern of CA gene expression; (4) what are the physiologic roles of such diverse CAs in these prokaryotes. We proposed possible answers to the previous questions. Moreover, we speculated on the evolution of the CA classes (α, β and γ) identified in the Gram-negative and -positive bacteria. Our main hypothesis is that from the ancestral Ur-CA, the γ-class arose first, followed by the β-class; the α-class CAs came last it is found only in the Gram-negative bacteria.
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35
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Combining the tail and the ring approaches for obtaining potent and isoform-selective carbonic anhydrase inhibitors: Solution and X-ray crystallographic studies. Bioorg Med Chem 2014; 22:334-40. [DOI: 10.1016/j.bmc.2013.11.016] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/07/2013] [Accepted: 11/11/2013] [Indexed: 11/22/2022]
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36
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Salen and tetrahydrosalen derivatives act as effective inhibitors of the tumor-associated carbonic anhydrase XII—A new scaffold for designing isoform-selective inhibitors. Bioorg Med Chem Lett 2013; 23:6759-63. [DOI: 10.1016/j.bmcl.2013.10.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 10/15/2013] [Accepted: 10/16/2013] [Indexed: 11/22/2022]
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37
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Güzel-Akdemir O, Biswas S, Lastra K, McKenna R, Supuran CT. Structural study of the location of the phenyl tail of benzene sulfonamides and the effect on human carbonic anhydrase inhibition. Bioorg Med Chem 2013; 21:6674-80. [PMID: 24012377 DOI: 10.1016/j.bmc.2013.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
The crystal structure of 4-phenylacetamidomethyl-benzenesulfonamide (4ITP) bound to human carbonic anhydrase (hCA, EC 4.2.1.1) II is reported. 4ITP is a medium potency hCA I and II inhibitor (KIs of 54-75nM), a strong mitochondrial CA VA/VB inhibitor (KIs of 8.3-8.6nM) and a weak transmembrane CA inhibitor (KIs of 136-212nM against hCA IX and XII). This elongated compound binds in an extended conformation to hCA II, with its tail lying towards the hydrophobic half of the active site whereas the sulfonamide moiety coordinates the zinc ion. The present structure was compared to that of structurally related aromatic sulfonamides, such as 4-phenylacetamido-benzene-sulfonamide (3OYS), 4-(2-mercaptophenylacetamido)-benzene-sulfonamide (2HD6) and 4-(3-nitrophenyl)-ureido-benzenesulfonamide (3N2P). Homology models of the hCA I, VA, VB, IX and XII structures were build which afforded an understanding of the amino acids involved in the binding of these compounds to these isoforms. The main conclusion of the study is that the orientation of the tail moiety and the presence of flexible linkers as well polar groups in it, strongly influence the potency and the selectivity of the sulfonamides for the inhibition of cytosolic, mitochondrial or transmembrane CA isoforms.
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Affiliation(s)
- Ozlen Güzel-Akdemir
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Istanbul University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 34116 Beyazit, Istanbul, Turkey
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38
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Biswas S, McKenna R, Supuran CT. Effect of incorporating a thiophene tail in the scaffold of acetazolamide on the inhibition of human carbonic anhydrase isoforms I, II, IX and XII. Bioorg Med Chem Lett 2013; 23:5646-9. [DOI: 10.1016/j.bmcl.2013.08.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/05/2013] [Accepted: 08/05/2013] [Indexed: 02/06/2023]
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39
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Inhibition of tumor-associated human carbonic anhydrase isozymes IX and XII by a new class of substituted-phenylacetamido aromatic sulfonamides. Bioorg Med Chem 2013; 21:5228-32. [DOI: 10.1016/j.bmc.2013.06.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/14/2013] [Accepted: 06/12/2013] [Indexed: 11/19/2022]
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40
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Del Prete S, De Luca V, Vullo D, Scozzafava A, Carginale V, Supuran CT, Capasso C. Biochemical characterization of the γ-carbonic anhydrase from the oral pathogen Porphyromonas gingivalis, PgiCA. J Enzyme Inhib Med Chem 2013; 29:532-7. [PMID: 23914926 DOI: 10.3109/14756366.2013.822371] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Carbonic anhydrases (CAs, EC 4.2.1.1) catalyze a simple but physiologically relevant reaction in all life kingdoms, carbon dioxide hydration to bicarbonate and protons. CAs are present in many pathogenic species and are involved in the bicarbonate metabolism/biosynthetic reactions involving this ion. Ubiquity of these enzymes suggests a pivotal role in microbial virulence and pathogenicity. Porphyromonas gingivalis is an anaerobic bacterium, which colonizes the oral cavity, being involved in the pathogenesis of periodontitis, an inflammatory disease leading to tooth loss. Recently, we reported an anion inhibitory study on the γ-CA (denominated PgiCA) identified in the genome of this Gram-negative bacterium. In this paper we continue our research on PgiCA, and describe the biochemical characterization of the recombinant protein, its thermal stability, the oligomeric state and the enzyme kinetics. PgiCA is a polypeptide chain formed of 192 amino acids and displays an identity of 30-33% when compared with the prototypical γ-CAs, CAM or CAMH (from Methanosarcina thermophila) or CcmM (from Thermosynechococcus elongatus). A subunit molecular mass of 21 kDa was estimated by SDS-PAGE, while HPLC size exclusion chromatography under native conditions gave an estimated molecular mass of 65 kDa suggesting that the recombinant enzyme self-associate in a homotrimer, as all other γ-CAs studied so far. Enzyme kinetic analysis showed that PgiCA is 62 times more effective as a catalyst compared to CAM, the only other γ-CA characterized in detail kinetically. All these features represent an interesting attractive for the drug design of inhibitors/activators of this new enzyme.
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41
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Durdagi S, Scozzafava G, Vullo D, Sahin H, Kolayli S, Supuran CT. Inhibition of mammalian carbonic anhydrases I-XIV with grayanotoxin III: solution and in silico studies. J Enzyme Inhib Med Chem 2013; 29:469-75. [DOI: 10.3109/14756366.2013.804072] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Serdar Durdagi
- University of Calgary, Institute for Biocomplexity and Informatics
Calgary, ABCanada
- Bahcesehir University, Faculty of Medicine, Department of Biophysics
IstanbulTurkey
| | - Gabriele Scozzafava
- University of Florence, Dipartimento di Economia, Ingegneria, Scienze e Tecnologie Agrarie e Forestali
FlorenceItaly
| | - Daniela Vullo
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, Sesto Fiorentino
FlorenceItaly
| | - Hüseyin Sahin
- Department of Chemistry, Faculty of Sciences, Karadeniz Technical University
TrabzonTurkey
| | - Sevgi Kolayli
- Department of Chemistry, Faculty of Sciences, Karadeniz Technical University
TrabzonTurkey
| | - Claudiu T. Supuran
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, Sesto Fiorentino
FlorenceItaly
- University of Florence, Neurofarba Department, Sezione di Scienze Farmaceutiche
Via Ugo Schiff 6, 50019 Sesto Fiorentino, FlorenceItaly
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42
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Wang L, Yang C, Lu W, Liu L, Gao R, Liao S, Zhao Z, Zhu L, Xu Y, Li H, Huang J, Zhu W. Discovery of new potent inhibitors for carbonic anhydrase IX by structure-based virtual screening. Bioorg Med Chem Lett 2013; 23:3496-9. [DOI: 10.1016/j.bmcl.2013.04.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 04/17/2013] [Accepted: 04/19/2013] [Indexed: 11/25/2022]
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43
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De Simone G, Alterio V, Supuran CT. Exploiting the hydrophobic and hydrophilic binding sites for designing carbonic anhydrase inhibitors. Expert Opin Drug Discov 2013; 8:793-810. [DOI: 10.1517/17460441.2013.795145] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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44
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Biswas S, Carta F, Scozzafava A, McKenna R, Supuran CT. Structural effect of phenyl ring compared to thiadiazole based adamantyl-sulfonamides on carbonic anhydrase inhibition. Bioorg Med Chem 2013; 21:2314-2318. [DOI: 10.1016/j.bmc.2013.02.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 02/06/2013] [Indexed: 10/27/2022]
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45
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Carta F, Vullo D, Maresca A, Scozzafava A, Supuran CT. Mono-/dihydroxybenzoic acid esters and phenol pyridinium derivatives as inhibitors of the mammalian carbonic anhydrase isoforms I, II, VII, IX, XII and XIV. Bioorg Med Chem 2013; 21:1564-9. [DOI: 10.1016/j.bmc.2012.05.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 01/14/2023]
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Li Y, Geng J, Liu Y, Yu S, Zhao G. Thiadiazole-a Promising Structure in Medicinal Chemistry. ChemMedChem 2012. [DOI: 10.1002/cmdc.201200355] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Marini AM, Maresca A, Aggarwal M, Orlandini E, Nencetti S, Da Settimo F, Salerno S, Simorini F, La Motta C, Taliani S, Nuti E, Scozzafava A, McKenna R, Rossello A, Supuran CT. Tricyclic sulfonamides incorporating benzothiopyrano[4,3-c]pyrazole and pyridothiopyrano[4,3-c]pyrazole effectively inhibit α- and β-carbonic anhydrase: X-ray crystallography and solution investigations on 15 isoforms. J Med Chem 2012; 55:9619-29. [PMID: 23067387 DOI: 10.1021/jm300878g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Carbonic anhydrases (CAs, EC 4.2.1.1) are ubiquitous isozymes involved in crucial physiological and pathological events, representing the targets of inhibitors with several therapeutic applications. In this connection, we report a new class of carbonic anhydrase inhibitors, based on the thiopyrano-fused pyrazole scaffold to which a pendant 4-sulfamoylphenyl moiety was attached. The new sulfonamides 3a-e were designed as constrained analogues of celecoxib and valdecoxib. The most interesting feature of sulfonamides 3 was their predominantly strong inhibition of human (h) CA I and II, as well as those of the mycobacterial β-class enzymes (Rv1284, Rv3273, and Rv3588c), whereas their inhibitory action against hCA III, IV, VA, VB, VI, VII, IX, XII, XIII, and XIV was found to be at least 2 orders of magnitude lower. X-ray crystallography and structural superposition studies made it possible to explain the very distinct inhibition profile of the tricyclic sulfonamides, different from those of celecoxib and valdecoxib.
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Affiliation(s)
- Anna M Marini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy.
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Winum JY, Maresca A, Carta F, Scozzafava A, Supuran CT. Polypharmacology of sulfonamides: pazopanib, a multitargeted receptor tyrosine kinase inhibitor in clinical use, potently inhibits several mammalian carbonic anhydrases. Chem Commun (Camb) 2012; 48:8177-9. [PMID: 22733110 DOI: 10.1039/c2cc33415a] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pazopanib, a new, multi-targeted tyrosine kinase inhibitor (TKI) used clinically for the treatment of several types of tumors, incorporates a primary sulfonamide moiety normally associated with the inhibition of the metallo enzyme carbonic anhydrase (CA, EC 4.2.1.1). Here we show that pazopanib and related sulfonamides such as indisulam, acetazolamide or ureido-substituted peptidomimetic benzenesulfonamides are low nanomolar inhibitors of many of the fifteen human isoforms hCA I-XIV. These data indicate that in addition to the TK inhibitory action, pazopanib may exert antitumor/antimetastatic effects also due to the potent inhibition of the tumor-associated, hypoxia-inducible enzymes CA IX and XII.
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Affiliation(s)
- Jean-Yves Winum
- Institut des Biomolécules Max Mousseron, 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
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Turkoglu S, Maresca A, Alper M, Kockar F, Işık S, Sinan S, Ozensoy O, Arslan O, Supuran CT. Mutation of active site residues Asn67 to Ile, Gln92 to Val and Leu204 to Ser in human carbonic anhydrase II: Influences on the catalytic activity and affinity for inhibitors. Bioorg Med Chem 2012; 20:2208-13. [DOI: 10.1016/j.bmc.2012.02.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/06/2012] [Accepted: 02/08/2012] [Indexed: 11/15/2022]
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Can D, Spingler B, Schmutz P, Mendes F, Raposinho P, Fernandes C, Carta F, Innocenti A, Santos I, Supuran CT, Alberto R. [(Cp-R)M(CO)3] (M=Re or 99mTc) Arylsulfonamide, Arylsulfamide, and Arylsulfamate Conjugates for Selective Targeting of Human Carbonic Anhydrase IX. Angew Chem Int Ed Engl 2012; 51:3354-7. [DOI: 10.1002/anie.201107333] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 01/24/2012] [Indexed: 12/11/2022]
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