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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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2
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Zoppi C, Nocentini A, Supuran CT, Pratesi A, Messori L. Native mass spectrometry of human carbonic anhydrase I and its inhibitor complexes. J Biol Inorg Chem 2020; 25:979-993. [PMID: 32926233 PMCID: PMC7584553 DOI: 10.1007/s00775-020-01818-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/30/2020] [Indexed: 02/03/2023]
Abstract
Abstract Native mass spectrometry is a potent technique to study and characterize biomacromolecules in their native state. Here, we have applied this method to explore the solution chemistry of human carbonic anhydrase I (hCA I) and its interactions with four different inhibitors, namely three sulfonamide inhibitors (AAZ, MZA, SLC-0111) and the dithiocarbamate derivative of morpholine (DTC). Through high-resolution ESI-Q-TOF measurements, the native state of hCA I and the binding of the above inhibitors were characterized in the molecular detail. Native mass spectrometry was also exploited to assess the direct competition in solution among the various inhibitors in relation to their affinity constants. Additional studies were conducted on the interaction of hCA I with the metallodrug auranofin, under various solution and instrumental conditions. Auranofin is a selective reagent for solvent-accessible free cysteine residues, and its reactivity was analyzed also in the presence of CA inhibitors. Overall, our investigation reveals that native mass spectrometry represents an excellent tool to characterize the solution behavior of carbonic anhydrase. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01818-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carlotta Zoppi
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Alessio Nocentini
- Department of Neurofarba, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Claudiu T Supuran
- Department of Neurofarba, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Alessandro Pratesi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy.
| | - Luigi Messori
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy.
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3
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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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4
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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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Artier J, Holland SC, Miller NT, Zhang M, Burnap RL. Synthetic DNA system for structure-function studies of the high affinity CO2 uptake NDH-13 protein complex in cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1108-1118. [DOI: 10.1016/j.bbabio.2018.06.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 11/26/2022]
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Modak JK, Liu YC, Supuran CT, Roujeinikova A. Structure-Activity Relationship for Sulfonamide Inhibition of Helicobacter pylori α-Carbonic Anhydrase. J Med Chem 2016; 59:11098-11109. [PMID: 28002963 DOI: 10.1021/acs.jmedchem.6b01333] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
α-Carbonic anhydrase of Helicobacter pylori (HpαCA) plays an important role in the acclimation of this oncobacterium to the acidic pH of the stomach. Sulfonamide inhibitors of HpαCA possess anti-H. pylori activity. The crystal structures of complexes of HpαCA with a family of acetazolamide-related sulfonamides have been determined. Analysis of the structures revealed that the mode of sulfonamide binding correlates well with their inhibitory activities. In addition, comparisons with the corresponding inhibitor complexes of human carbonic anhydrase II (HCAII) indicated that HpαCA possesses an additional, alternative binding site for sulfonamides that is not present in HCAII. Furthermore, the hydrophobic pocket in HCAII that stabilizes the apolar moiety of sulfonamide inhibitors is replaced with a more open, hydrophilic pocket in HpαCA. Thus, our analysis identified major structural features can be exploited in the design of selective and more potent inhibitors of HpαCA that may lead to novel antimicrobials.
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Affiliation(s)
- Joyanta K Modak
- Department of Microbiology, Monash University , Clayton, Victoria 3800, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia
| | - Yu C Liu
- Department of Microbiology, Monash University , Clayton, Victoria 3800, Australia
| | - Claudiu T Supuran
- Laboratorio di Chimica Bioinorganica, Polo Scientifico, Università degli Studi di Firenze , Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy.,Neurofarba Department, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze , Via U. Schiff 6, Sesto Fiorentino, Florence 50019, Italy
| | - Anna Roujeinikova
- Department of Microbiology, Monash University , Clayton, Victoria 3800, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia.,Department of Biochemistry and Molecular Biology, Monash University , Clayton, Victoria 3800, Australia
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7
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Akocak S, Alam MR, Shabana AM, Sanku RKK, Vullo D, Thompson H, Swenson ER, Supuran CT, Ilies MA. PEGylated Bis-Sulfonamide Carbonic Anhydrase Inhibitors Can Efficiently Control the Growth of Several Carbonic Anhydrase IX-Expressing Carcinomas. J Med Chem 2016; 59:5077-88. [PMID: 27144971 DOI: 10.1021/acs.jmedchem.6b00492] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A series of aromatic/heterocyclic bis-sulfonamides were synthesized from three established aminosulfonamide carbonic anhydrase (CA, EC 4.2.1.1) inhibitor pharmacophores, coupled with either ethylene glycol oligomeric or polymeric diamines to yield bis-sulfonamides with short or long (polymeric) linkers. Testing of novel inhibitors and their precursors against a panel of membrane-bound CA isoforms, including tumor-overexpressed CA IX and XII and cytosolic isozymes, identified nanomolar-potent inhibitors against both classes and several compounds with medium isoform selectivity in a detailed structure-activity relationship study. The ability of CA inhibitors to kill tumor cells overexpressing CA IX and XII was tested under normoxic and hypoxic conditions, using 2D and 3D in vitro cellular models. The study identified a nanomolar potent PEGylated bis-sulfonamide CA inhibitor (25) able to significantly reduce the viability of colon HT-29, breast MDA-MB231, and ovarian SKOV-3 cancer cell lines, thus revealing the potential of polymer conjugates in CA inhibition and cancer treatment.
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Affiliation(s)
- Suleyman Akocak
- Department of Pharmaceutical Sciences and Molder Center for Drug Discovery Research, Temple University School of Pharmacy , 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Adiyaman University , 02040 Adiyaman, Turkey
| | - M Raqibul Alam
- Department of Pharmaceutical Sciences and Molder Center for Drug Discovery Research, Temple University School of Pharmacy , 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Ahmed M Shabana
- Department of Pharmaceutical Sciences and Molder Center for Drug Discovery Research, Temple University School of Pharmacy , 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Rajesh Kishore Kumar Sanku
- Department of Pharmaceutical Sciences and Molder Center for Drug Discovery Research, Temple University School of Pharmacy , 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Daniela Vullo
- NEUROFARBA Department, Pharmaceutical Sciences Section, Universita degli Studi di Firenze, Polo Scientifico , Via Ugo Schiff no. 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Harry Thompson
- Department of Pharmaceutical Sciences and Molder Center for Drug Discovery Research, Temple University School of Pharmacy , 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Erik R Swenson
- Medical Service, VA Puget Sound Health Care System, University of Washington , Seattle, Washington 98195, United States
| | - 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 Molder Center for Drug Discovery Research, Temple University School of Pharmacy , 3307 N Broad Street, Philadelphia, Pennsylvania 19140, United States
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Matwijczuk A, Kamiński D, Górecki A, Ludwiczuk A, Niewiadomy A, Maćkowski S, Gagoś M. Spectroscopic Studies of Dual Fluorescence in 2-((4-Fluorophenyl)amino)-5-(2,4-dihydroxybenzeno)-1,3,4-thiadiazole. J Phys Chem A 2015; 119:10791-805. [DOI: 10.1021/acs.jpca.5b06475] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Andrzej Górecki
- Department of Physical
Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology of the Jagiellonian University, 31-007 Kraków, Poland
| | - Agnieszka Ludwiczuk
- Chair and Department of Pharmacognosy with Medicinal
Plant Unit, Medical University of Lublin, 1 Chodzki Str., 20-093 Lublin, Poland
| | | | - Sebastian Maćkowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Mariusz Gagoś
- Department of Cell Biology, Institute of Biology, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
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9
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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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11
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Hu Y, Li CY, Wang XM, Yang YH, Zhu HL. 1,3,4-Thiadiazole: synthesis, reactions, and applications in medicinal, agricultural, and materials chemistry. Chem Rev 2014; 114:5572-610. [PMID: 24716666 DOI: 10.1021/cr400131u] [Citation(s) in RCA: 331] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yang Hu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing 210093, People's Republic of China
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12
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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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13
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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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14
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Alterio V, Di Fiore A, D'Ambrosio K, Supuran CT, De Simone G. Multiple binding modes of inhibitors to carbonic anhydrases: how to design specific drugs targeting 15 different isoforms? Chem Rev 2012; 112:4421-68. [PMID: 22607219 DOI: 10.1021/cr200176r] [Citation(s) in RCA: 933] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vincenzo Alterio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
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15
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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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Park H, Jung SK, Yu KR, Kim JH, Kim YS, Ko JH, Park BC, Kim SJ. Structure-Based Virtual Screening Approach to the Discovery of Novel Inhibitors of Eyes Absent 2 Phosphatase with Various Metal Chelating Moieties. Chem Biol Drug Des 2011; 78:642-50. [DOI: 10.1111/j.1747-0285.2011.01192.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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17
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The many faces of the adamantyl group in drug design. Eur J Med Chem 2011; 46:1949-63. [DOI: 10.1016/j.ejmech.2011.01.047] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/14/2011] [Accepted: 01/25/2011] [Indexed: 12/22/2022]
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18
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Durdagi S, Şentürk M, Ekinci D, Balaydın HT, Göksu S, Küfrevioğlu Öİ, Innocenti A, Scozzafava A, Supuran CT. Kinetic and docking studies of phenol-based inhibitors of carbonic anhydrase isoforms I, II, IX and XII evidence a new binding mode within the enzyme active site. Bioorg Med Chem 2011; 19:1381-9. [DOI: 10.1016/j.bmc.2011.01.016] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/06/2011] [Accepted: 01/08/2011] [Indexed: 12/27/2022]
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19
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Park H, Kim S, Kim YE, Lim SJ. A structure-based virtual screening approach toward the discovery of histone deacetylase inhibitors: identification of promising zinc-chelating groups. ChemMedChem 2010; 5:591-7. [PMID: 20157916 DOI: 10.1002/cmdc.200900500] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The inhibitors of histone deacetylases (HDACs) have drawn a great deal of attention due to their promising potential as small-molecule therapeutics for the treatment of cancer. By means of virtual screening with docking simulations under consideration of the effects of ligand solvation, we were able to identify six novel HDAC inhibitors with IC(50) values ranging from 1 to 100 muM. These newly identified inhibitors are structurally diverse and have various chelating groups for the active site zinc ion, including N-[1,3,4]thiadiazol-2-yl sulfonamide, N-thiazol-2-yl sulfonamide, and hydroxamic acid moieties. The former two groups are included in many drugs in current clinical use and have not yet been reported as HDAC inhibitors. Therefore, they can be considered as new inhibitor scaffolds for the development of anticancer drugs by structure-activity relationship studies to improve the inhibitory activities against HDACs. Interactions with the HDAC1 active site residues responsible for stabilizing these new inhibitors are addressed in detail.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 98 Kunja-dong, Kwangjin-ku, Seoul 143-747, Korea.
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Avvaru BS, Wagner JM, Maresca A, Scozzafava A, Robbins AH, Supuran CT, McKenna R. Carbonic anhydrase inhibitors. The X-ray crystal structure of human isoform II in adduct with an adamantyl analogue of acetazolamide resides in a less utilized binding pocket than most hydrophobic inhibitors. Bioorg Med Chem Lett 2010; 20:4376-81. [PMID: 20605094 DOI: 10.1016/j.bmcl.2010.06.082] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 06/11/2010] [Accepted: 06/11/2010] [Indexed: 12/01/2022]
Abstract
We investigated the inhibitory activity of several 1,3,4-thiadiazole-sulfonamides against all catalytically active CA (EC 4.2.1.1), CA I-XV. The tail derivatizing the 5-position in the 1,3,4-thiadiazole-2-sulfonamide scaffold was observed to be critical as an inhibitory determinant of these compounds. The high resolution X-ray crystal structure of hCA II in complex with 5-(1-adamantylcarboxamido)-1,3,4-thiadiazole-2-sulfonamide, showed the adamantyl moiety of the inhibitor residing in a less utilized binding pocket than that of most hydrophobic inhibitors, lined by the amino acid residues Ile91, Val121 and Phe131. This binding site may explain the diverse inhibition profiles of 5-carboxamide- and sufonamide-derivatized 1,3,4-thiadiazole-2-sulfonamides and offers a hot spot for designing isoform selective inhibitors, considering that residues 91 and 131 are highly variable among the 13 catalytically active isoforms.
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Affiliation(s)
- Balendu Sankara Avvaru
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box Gainesville, FL 32610, USA
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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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Basaran I, Sinan S, Cakir U, Bulut M, Arslan O, Ozensoy O. In vitro inhibition of cytosolic carbonic anhydrases I and II by some new dihydroxycoumarin compounds. J Enzyme Inhib Med Chem 2008; 23:32-6. [DOI: 10.1080/14756360701404100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Ismet Basaran
- Department of Chemistry, Balikesir University Science & Art Faculty, CAGIS/Kampus, 10100, Balikesir, Turkey
| | - Selma Sinan
- Department of Biology, Balikesir University Science & Art Faculty, CAGIS/Kampus, 10100, Balikesir, Turkey
| | - Umit Cakir
- Department of Chemistry, Balikesir University Science & Art Faculty, CAGIS/Kampus, 10100, Balikesir, Turkey
| | - Mustafa Bulut
- Science and Art Faculty, Department of Chemistry, Marmara University, Kadiköy, 81040, Istanbul, Turkey
| | - Oktay Arslan
- Department of Chemistry, Balikesir University Science & Art Faculty, CAGIS/Kampus, 10100, Balikesir, Turkey
| | - Ozen Ozensoy
- Department of Chemistry, Balikesir University Science & Art Faculty, CAGIS/Kampus, 10100, Balikesir, Turkey
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Krishnamurthy VM, Kaufman GK, Urbach AR, Gitlin I, Gudiksen KL, Weibel DB, Whitesides GM. Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chem Rev 2008; 108:946-1051. [PMID: 18335973 PMCID: PMC2740730 DOI: 10.1021/cr050262p] [Citation(s) in RCA: 565] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Vijay M. Krishnamurthy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George K. Kaufman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Adam R. Urbach
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Irina Gitlin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Katherine L. Gudiksen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Douglas B. Weibel
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
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Carbonic anhydrase inhibitors. Interaction of 2-N,N-dimethylamino-1,3,4-thiadiazole-5-methanesulfonamide with 12 mammalian isoforms: Kinetic and X-ray crystallographic studies. Bioorg Med Chem Lett 2008; 18:999-1005. [DOI: 10.1016/j.bmcl.2007.12.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 12/10/2007] [Accepted: 12/11/2007] [Indexed: 11/21/2022]
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Temperini C, Winum JY, Montero JL, Scozzafava A, Supuran CT. Carbonic anhydrase inhibitors: The X-ray crystal structure of the adduct of N-hydroxysulfamide with isozyme II explains why this new zinc binding function is effective in the design of potent inhibitors. Bioorg Med Chem Lett 2007; 17:2795-801. [PMID: 17346964 DOI: 10.1016/j.bmcl.2007.02.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 02/23/2007] [Accepted: 02/23/2007] [Indexed: 11/19/2022]
Abstract
N-Hydroxysulfamide is a 2000-fold more potent inhibitor of the zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1) as compared to sulfamide. It also inhibits other physiologically relevant isoforms, such as the tumor-associated CA IX and XII (K(I)s in the range of 0.865-1.34microM). In order to understand the binding of this inhibitor to the enzyme active site, the X-ray crystal structure of the human hCA II-N-hydroxysulfamide adduct was resolved. The inhibitor coordinates to the active site zinc ion by the ionized primary amino group, participating in an extended network of hydrogen bonds with amino acid residues Thr199, Thr200 and two water molecules. The additional two hydrogen bonds in which N-hydroxysulfamide bound to hCA II is involved as compared to the corresponding adduct of sulfamide may explain its higher affinity for the enzyme, also providing hints for the design of tight-binding CA inhibitors possessing an organic moiety substituting the NH group in the N-hydroxysulfamide structure.
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Affiliation(s)
- Claudia Temperini
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy.
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