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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: 26] [Impact Index Per Article: 26.0] [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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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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Mert S, Alım Z, İşgör MM, Beydemir Ş, Kasımoğulları R. The synthesis of novel pyrazole-3,4-dicarboxamides bearing 5-amino-1,3,4-thiadiazole-2-sulfonamide moiety with effective inhibitory activity against the isoforms of human cytosolic carbonic anhydrase I and II. Bioorg Chem 2016; 68:64-71. [PMID: 27454619 DOI: 10.1016/j.bioorg.2016.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/15/2016] [Accepted: 07/16/2016] [Indexed: 02/02/2023]
Abstract
A series of 1-(3-substituted-phenyl)-5-phenyl-N(3),N(4)-bis(5-sulfamoyl-1,3,4-thiadiazol-2-yl)-1H-pyrazole-3,4-dicarboxamides (4-15) were synthesized. The structures of these pyrazole-sulfonamides were confirmed by FT-IR, (1)H NMR, (13)C NMR and elemental analysis methods. Human cytosolic carbonic anhydrase (CA, EC 4.2.1.1) isozymes (hCA I and II) were purified from erythrocyte cells by affinity chromatography. The inhibitory effects of newly synthesized derivatives (4-15) were investigated in vitro on esterase activities of these isozymes. The Ki values were determined as 0.119-3.999μM for hCA I and 0.084-0.878μM for hCA II. The results showed that the compound 6 for hCA I and the compound 11 for hCA II had the highest inhibitory effect. Beside that, the compound 8 had the lowest inhibition effect on both isozymes.
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Affiliation(s)
- Samet Mert
- Department of Chemistry, Faculty of Arts and Sciences, Dumlupinar University, 43100 Kutahya, Turkey
| | - Zuhal Alım
- Department of Chemistry, Faculty of Arts and Sciences, Ahi Evran University, 40000 Kırşehir, Turkey
| | - Mehmet Mustafa İşgör
- Department of Biochemistry, Faculty of Veterinary Sciences, Mustafa Kemal University, 31000 Hatay, Turkey
| | - Şükrü Beydemir
- Department of Chemistry, Faculty of Sciences, Atatürk University, 25240 Erzurum, Turkey; Department of Chemistry, Faculty of Natural Sciences, Architecture and Engineering, Bursa Technical University, Osmangazi, 16200 Bursa, Turkey.
| | - Rahmi Kasımoğulları
- Department of Chemistry, Faculty of Arts and Sciences, Dumlupinar University, 43100 Kutahya, Turkey.
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Lomelino CL, Supuran CT, McKenna R. Non-Classical Inhibition of Carbonic Anhydrase. Int J Mol Sci 2016; 17:ijms17071150. [PMID: 27438828 PMCID: PMC4964523 DOI: 10.3390/ijms17071150] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/02/2016] [Accepted: 07/07/2016] [Indexed: 11/16/2022] Open
Abstract
Specific isoforms from the carbonic anhydrase (CA) family of zinc metalloenzymes have been associated with a variety of diseases. Isoform-specific carbonic anhydrase inhibitors (CAIs) are therefore a major focus of attention for specific disease treatments. Classical CAIs, primarily sulfonamide-based compounds and their bioisosteres, are examined as antiglaucoma, antiepileptic, antiobesity, antineuropathic pain and anticancer compounds. However, many sulfonamide compounds inhibit all CA isoforms nonspecifically, diluting drug effectiveness and causing undesired side effects due to off-target inhibition. In addition, a small but significant percentage of the general population cannot be treated with sulfonamide-based compounds due to a sulfa allergy. Therefore, CAIs must be developed that are not only isoform specific, but also non-classical, i.e. not based on sulfonamides, sulfamates, or sulfamides. This review covers the classes of non-classical CAIs and the recent advances in the development of isoform-specific inhibitors based on phenols, polyamines, coumarins and their derivatives.
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Affiliation(s)
- Carrie L Lomelino
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
| | - Claudiu T Supuran
- Neurofarba Department, University of Florence, Piazza di San Marco, Firenze 50019, Italy.
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
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Sharif HMA, Dong GY, Arshad MN, Khan IU. 4-Benzene-sulfonamido-benzoic acid. Acta Crystallogr Sect E Struct Rep Online 2009; 65:o3086. [PMID: 21578816 PMCID: PMC2972151 DOI: 10.1107/s1600536809047291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 11/09/2009] [Indexed: 11/13/2022]
Abstract
In the molecule of the title sulfonamide compound, C13H11NO4S, the dihedral angle between the planes of the benzene ring and the carboxyl substituent group is 6.7 (4)°. The two aromatic rings are inclined at 45.36 (15)° to one another. In the crystal, adjacent molecules are linked via classical intermolecular N—H⋯O and O—H⋯O, and non-classical C—H⋯O hydrogen bonds, which stabilize the crystal structure.
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Haider Z, Khan IU, Zia-Ur-Rehman M, Arshad MN. N-Benzyl-N-cyclo-hexyl-benzene-sulfonamide. Acta Crystallogr Sect E Struct Rep Online 2009; 65:o3053. [PMID: 21578785 PMCID: PMC2971833 DOI: 10.1107/s1600536809046960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 11/06/2009] [Indexed: 11/17/2022]
Abstract
In the title compound, C19H23NO2S, the cyclohexyl ring exists in a chair form. The dihedral angle between the two terminal phenyl rings is 86.70 (6)°. No significant interactions are observed except for a weak intramolecular C—H⋯O hydrogen bond.
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Carbonic anhydrase inhibitors: 2-Substituted-1,3,4-thiadiazole-5-sulfamides act as powerful and selective inhibitors of the mitochondrial isozymes VA and VB over the cytosolic and membrane-associated carbonic anhydrases I, II and IV. Bioorg Med Chem Lett 2008; 18:6332-5. [DOI: 10.1016/j.bmcl.2008.10.093] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 10/20/2008] [Accepted: 10/20/2008] [Indexed: 11/22/2022]
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Ozensoy O, Isik S, Arslan O, Arslan M, Scozzafava A, Supuran CT. Carbonic anhydrase inhibitors. Inhibition of red blood cell ostrich (Struthio camelus) carbonic anhydrase with a series of aromatic and heterocyclic sulfonamides. J Enzyme Inhib Med Chem 2008; 20:383-7. [PMID: 16206834 DOI: 10.1080/14756360500141960] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The purification of red blood cell carbonic anhydrase (CA, EC 4.2.1.1) from ostrich (scCA) blood is reported, as well as an inhibition study of this enzyme with a series of aromatic and heterocylic sulfonamides. The ostrich enzyme showed a high activity, comparable to that of the human isozyme II, with kcat, of 1.2 x 10(6) s(-1) and kcat/KM of 1.8 x 10(7) M(-1)s(-1), and an inhibition profile quite different from that of the human red blood cell cytosolic isozymes hCA I and II. scCA has generally a lower affinity for sulfonamide inhibitors as compared to hCA I and II. The only sulfonamide which behaved as a very potent inhibitor of this enzyme was ethoxzolamide (KI = 3.9 nM) whereas acetazolamide and sulfanilamide behaved as weaker inhibitors (inhibition constants in the range 303-570 nM). Several other aromatic and heterocyclic sulfonamides, mostly derivatives of sulfanilamide, homosulfanilamide, 4-aminoethylbenzenesulfonamide or 5-amino-1,3,4-thiadiazole-2-sulfonamide, showed good affinities for the ostrich enzyme, with KI values in the range 25-72 nM.
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Affiliation(s)
- Ozen Ozensoy
- Polo Scientifico, Laboratorio di Chimica Bioinorganica, Universitá degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
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Vitale RM, Pedone C, Amodeo P, Antel J, Wurl M, Scozzafava A, Supuran CT, De Simone G. Molecular modeling study for the binding of zonisamide and topiramate to the human mitochondrial carbonic anhydrase isoform VA. Bioorg Med Chem 2007; 15:4152-8. [PMID: 17420132 DOI: 10.1016/j.bmc.2007.03.070] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 03/16/2007] [Accepted: 03/23/2007] [Indexed: 11/19/2022]
Abstract
Zonisamide and topiramate are two antiepileptic drugs known to induce weight loss in epilepsy patients. These molecules were recently shown to act as carbonic anhydrase (CA) inhibitors, being presumed that the weight loss may be due to the inhibition of the mitochondrial isozymes CA VA and CA VB involved in metabolic processes, among which lipid biosynthesis. To better understand the interaction of these compounds with CAs, here, we report a homology modeling and molecular dynamics simulations study on their adducts with human carbonic anhydrase VA (hCA VA). According to our results, in both cases the inhibitor sulfamate/sulfonamide moiety participates in the canonical interactions with the catalytic zinc ion, whereas the organic scaffold establishes a large number of van der Waals and polar interactions with the active site cleft. A structural comparison of these complexes with the corresponding homologues with human carbonic anhydrase II (hCA II) provides a rationale to the different affinities measured for these drugs toward hCA VA and hCA II. In particular, our data suggest that a narrower active site cleft, together with a different hydrogen bond network arrangement of hCA VA compared to hCA II, may account for the different Kd values of zonisamide and topiramate toward these physiologically relevant hCA isoforms. These results provide useful insights for future design of more isozyme-selective hCA inhibitors with potential use as anti-obesity drugs possessing a novel mechanism of action.
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Affiliation(s)
- Rosa Maria Vitale
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134 Naples, Italy
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Nishimori I, Vullo D, Innocenti A, Scozzafava A, Mastrolorenzo A, Supuran CT. Carbonic Anhydrase Inhibitors. The Mitochondrial Isozyme VB as a New Target for Sulfonamide and Sulfamate Inhibitors. J Med Chem 2005; 48:7860-6. [PMID: 16302824 DOI: 10.1021/jm050483n] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A lately discovered carbonic anhydrase (hCA, EC 4.2.1.1), the mitochondrial hCA VB, was cloned, expressed, and purified. Kinetic parameters proved it to be 3.37 times more effective than hCA VA as a catalyst for the physiological reaction, with kcat = 9.5 x 10(5) s(-1) and kcat/K(M) = 9.8 x 10(7) M(-1) s(-1), being second only to hCA II among the 16 isoforms presently known in humans. We investigated the inhibition of hCA VB with a library of sulfonamides/sulfamates, some of which are clinically used compounds. Benzenesulfonamides were ineffective inhibitors, whereas derivatives bearing 4-amino, 4-hydrazino, 4-methyl, 4-carboxy moieties or halogenated sulfanilamides were more effective (Ki's of 1.56-4.3 microM). Among the 10 clinically used compounds, acetazolamide, benzolamide, topiramate, and indisulam showed effective inhibitory activity (Ki's of 18-62 nM). Three compounds showed better activity against hCA VB over hCA II, among which were sulpiride and ethoxzolamide, which were 2 times more effective inhibitors of the mitochondrial over the cytosolic isozyme. hCA VB is a druggable target and some of its inhibitors may lead to the development of novel antiobesity therapies.
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Affiliation(s)
- Isao Nishimori
- Department of Gastroenterology and Hepatology, Kochi Medical School, Nankoku, Kochi 783-8505, Japan
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Ozensoy O, Puccetti L, Fasolis G, Arslan O, Scozzafava A, Supuran CT. Carbonic anhydrase inhibitors: Inhibition of the tumor-associated isozymes IX and XII with a library of aromatic and heteroaromatic sulfonamides. Bioorg Med Chem Lett 2005; 15:4862-6. [PMID: 16168653 DOI: 10.1016/j.bmcl.2005.08.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 04/27/2005] [Accepted: 04/27/2005] [Indexed: 10/25/2022]
Abstract
The inhibition of the two transmembrane, tumor-associated isozymes of carbonic anhydrase (CA, EC 4.2.1.1) of human origin, hCA IX and XII, with a library of aromatic and heteroaromatic sulfonamides has been investigated. Most of them were sulfanilamide, homosulfanilamide, and 4-aminoethyl-benzenesulfonamide derivatives, to which tails that should induce diverse physico-chemical properties have been attached at the amino moiety, whereas several of these compounds were derived from metanilamide, benzene-1,3-disulfonamide or the 1,3,4-thiadiazole/thiadiazoline-2-sulfonamides. The tails were of the alkyl/aryl-carboxamido/sulfonamido-, ureido or thioureido type. Against hCA IX the investigated compounds showed inhibition constants in the range of 3-294 nM, whereas against hCA XII in the range of 1.9-348 nM, respectively. The best hCA IX inhibitors were ureas/thioureas incorporating 4-aminoethyl-benzenesulfonamide and metanilamide moieties. The best hCA XII inhibitors were 1,3,4-thiadiazole/thiadiazoline-2-sulfonamides incorporating 5-acylamido or 5-arylsulfonylamido moieties. These compounds also inhibited appreciably the cytosolic isozymes hCA I and II, but some selectivity for the transmembrane, tumor-associated isozymes was observed for some of them, which is an encouraging result for the design of novel therapies targeting hypoxic tumors, in which these carbonic anhydrases are highly overexpressed.
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Affiliation(s)
- Ozen Ozensoy
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Room 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
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Verma RP, Hansch C. An approach toward the problem of outliers in QSAR. Bioorg Med Chem 2005; 13:4597-621. [PMID: 15951183 DOI: 10.1016/j.bmc.2005.05.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 05/03/2005] [Accepted: 05/03/2005] [Indexed: 11/16/2022]
Abstract
Compounds that have unexpected biological activity and are unable to fit in a QSAR model are known as outliers. These are valuable in defining the limitations under which compounds act by a common molecular mechanism modeled by one or more descriptors, and also in defining the experimental limitations of the biological test data. Thus, the outliers should be submitted to particular attention to see if the reason for their peculiarity can be determined. Separating these outliers from the main data set and formulating another QSAR can resolve the problem. Our result shows that these outliers may be acting by a different mechanism or interacting with the receptor in different modes.
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Almajan GL, Innocenti A, Puccetti L, Manole G, Barbuceanu S, Saramet I, Scozzafava A, Supuran CT. Carbonic anhydrase inhibitors. Inhibition of the cytosolic and tumor-associated carbonic anhydrase isozymes I, II, and IX with a series of 1,3,4-thiadiazole- and 1,2,4-triazole-thiols. Bioorg Med Chem Lett 2005; 15:2347-52. [PMID: 15837323 DOI: 10.1016/j.bmcl.2005.02.088] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Revised: 02/24/2005] [Accepted: 02/28/2005] [Indexed: 11/27/2022]
Abstract
A series of heterocyclic mercaptans incorporating 1,3,4-thiadiazole- and 1,2,4-triazole rings have been prepared and assayed for the inhibition of three physiologically relevant carbonic anhydrase (CA, EC 4.2.1.1) isozymes, the cytosolic human isozymes I and II, and the transmembrane, tumor-associated hCA IX. Against hCA I the investigated thiols showed inhibition constants in the range of 97 nM to 548 microM, against hCA II in the range of 7.9-618 microM, and against hCA IX in the range of 9.3-772 microM. Thiadiazoles were generally more active than triazoles against all investigated isozymes. Generally, the best inhibitors were the simple derivative 5-amino-1,3,4-thiadiazole-2-thiol and its N-acetylated derivative, which were anyhow at least two orders of magnitude less effective inhibitors when compared to the corresponding sulfonamides, acetazolamide, and its deacetylated derivative. An exception was constituted by 5-(2-pyridylcarboxamido)-1,3,4-thiadiazole-2-thiol, which is the first hCA I-selective inhibitor ever reported, possessing an inhibition constant of 97 nM against isozyme I, and being a 105 times less effective hCA II inhibitor, and 3154 times less effective hCA IX inhibitor. Thus, the thiol moiety may lead to effective CA inhibitors targeting isozyme I, whereas it is a less effective zinc-binding function for the design of CA II and CA IX inhibitors over the sulfonamide group.
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Affiliation(s)
- Gabriela Laura Almajan
- Organic Chemistry Department, Faculty of Pharmacy, Traian Vuia Street 6, 77210 Bucharest, Romania
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De Simone G, Di Fiore A, Menchise V, Pedone C, Antel J, Casini A, Scozzafava A, Wurl M, Supuran CT. Carbonic anhydrase inhibitors. Zonisamide is an effective inhibitor of the cytosolic isozyme II and mitochondrial isozyme V: solution and X-ray crystallographic studies. Bioorg Med Chem Lett 2005; 15:2315-20. [PMID: 15837316 DOI: 10.1016/j.bmcl.2005.03.032] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Accepted: 03/01/2005] [Indexed: 11/30/2022]
Abstract
The antiepileptic drug zonisamide was considered to act as a weak inhibitor of the zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1) (with a K(I) of 4.3 microM against the cytosolic isozyme II). Here we prove that this is not true. Indeed, testing zonisamide in the classical assay conditions of the CO2 hydrase activity of hCA II, with incubation times of enzyme and inhibitor solution of 15 min, a K(I) of 10.3 microM has been obtained. However, when the incubation between enzyme and inhibitor was prolonged to 1 h, the obtained K(I) was of 35.2 nM, of the same order of magnitude as that of the clinically used sulfonamides/sulfamates acetazolamide, methazolamide, ethoxzolamide and topiramate (K(I)s in the range of 5.4-15.4 nM). The inhibition of the human mitochondrial isozyme hCA V with these compounds has been also tested by means of a dansylamide competition binding assay, which showed zonisamide and topiramate to be effective inhibitors, with K(I)s in the range of 20.6-25.4 nM. The X-ray crystal structure of the adduct of hCA II with zonisamide has also been solved at a resolution of 1.70 A, showing that the sulfonamide moiety participates in the classical interactions with the Zn(II) ion and the residues Thr199 and Glu106, whereas the benzisoxazole ring is oriented toward the hydrophobic half of the active site, establishing a large number of strong van der Waals interactions (<4.5 A) with residues Gln92, Val121, Phe131, Leu198, Thr200, Pro202.
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Affiliation(s)
- Giuseppina De Simone
- Dipartimento di Chimica Biologica-Sezione Biostrutture and Istituto di Biostrutture e Bioimmagini-CNR, University of Naples Federico II, via Mezzocannone 16, 80134 Naples, Italy.
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