1
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Zhang M, Huang ZY, Su Y, Chen FF, Chen Q, Xu JH, Zheng GW. Engineering a norcoclaurine synthase for one-step synthesis of (S)-1-aryl-tetrahydroisoquinolines. BIORESOUR BIOPROCESS 2023; 10:15. [PMID: 38647611 PMCID: PMC10992437 DOI: 10.1186/s40643-023-00637-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/12/2023] [Indexed: 03/05/2023] Open
Abstract
Tetrahydroisoquinoline alkaloids (THIQAs) are ubiquitous compounds with important pharmaceutical and biological activity. Their key N-heterocyclic structural motifs are synthesised via Pictet-Spengler (P-S) reaction by norcoclaurine synthases (NCS) in plants. The synthesis of 1-aryl-tetrahydroisoquinoline alkaloids has attracted increasing attention due to their antitumor and antivirus activities. Herein, the L68T/M97V mutant of NCS from Thalictrum flavum with improved activity was developed by semi-rational design. This mutant not only showed higher catalytic performance (> 96% conversion) toward benzaldehyde and dopamine over the wild-type enzyme, but also catalysed the P-S reaction of the bulky substrate 4-biphenylaldehyde and dopamine with high conversion (> 99%) for the effective synthesis of 1-aryl-THIQA. In terms of stereoselectivity, all products synthesised by the L68T/M97V mutant showed high optical purity (92-99% enantiomeric excess).
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Affiliation(s)
- Man Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Zheng-Yu Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Ying Su
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Fei-Fei Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Gao-Wei Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, College of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
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2
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Tinivella A, Nwachukwu JC, Angeli A, Foschi F, Benatti AL, Pinzi L, Izard T, Ferraroni M, Erumbi R, Christodoulou MS, Passarella D, Supuran CT, Nettles KW, Rastelli G. Design, synthesis, biological evaluation and crystal structure determination of dual modulators of carbonic anhydrases and estrogen receptors. Eur J Med Chem 2023; 246:115011. [PMID: 36516582 DOI: 10.1016/j.ejmech.2022.115011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Multi-target compounds have become increasingly important for the development of safer and more effective drug candidates. In this work, we devised a combined ligand-based and structure-based multi-target repurposing strategy and applied it to a series of hexahydrocyclopenta[c]quinoline compounds synthesized previously. The in silico analyses identified human Carbonic Anhydrases (hCA) and Estrogen Receptors (ER) as top scoring candidates for dual modulation. hCA isoforms IX and XII, and ER subtypes ER⍺ and/or ERβ are co-expressed in various cancer cell types, including breast and prostate cancer cells. ER⍺ is the primary target of anti-estrogen therapy in breast cancer, and the hCA IX isoform is a therapeutic target in triple-negative breast cancer. ER⍺-mediated transcriptional programs and hCA activity in cancer cells promote favorable microenvironments for cell proliferation. Interestingly, several lines of evidence indicate that the combined modulation of these two targets may provide significant therapeutic benefits. Moving from these first results, two additional hexahydrocyclopenta[c]quinoline derivatives bearing a sulfonamide zinc binding group (hCA) and a phenolic hydroxyl (ER) pharmacophoric group placed at the appropriate locations were designed and synthesized. Interestingly, these compounds were able to directly modulate the activities of both hCA and ER targets. In cell-based assays, they inhibited proliferation of breast and prostate cancer cells with micromolar potency and cell type-selective efficacy. The compounds inhibited hCA activity with nanomolar potency and isoform-selectivity. In transactivation assays, they reduced estrogen-driven ER activity with micro-molar potency. Finally, crystal structures of the synthesized ligands in complex with the two targets revealed that the compounds bind directly to the hCA active site, as well as to the ER ligand-binding domain, providing structural explanation to the observed activity and a rationale for optimization of their dual activity. To the best of our knowledge, this work describes the design, synthesis and biological characterization of the first dual modulators of hCA and ER, laying the ground for the structure-based optimization of their multi-target activity.
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Affiliation(s)
- Annachiara Tinivella
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy; Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, Italy
| | - Jerome C Nwachukwu
- Department of Integrative Structural and Computational Biology, University of Florida Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Andrea Angeli
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Francesca Foschi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy; Department of Chemistry, University of Milano, Via Golgi 19, 20133, Milano, Italy
| | - Anna Laura Benatti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Tina Izard
- Department of Integrative Structural and Computational Biology, University of Florida Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Marta Ferraroni
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019, Sesto Fiorentino, Florence, Italy
| | - Rangarajan Erumbi
- Department of Integrative Structural and Computational Biology, University of Florida Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Michael S Christodoulou
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy; Department of Chemistry, University of Milano, Via Golgi 19, 20133, Milano, Italy
| | - Daniele Passarella
- Department of Chemistry, University of Milano, Via Golgi 19, 20133, Milano, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Kendall W Nettles
- Department of Integrative Structural and Computational Biology, University of Florida Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.
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3
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Oladipo SD, Akinpelu OI, Omondi B. Ligand-Guided Investigation of a Series of Formamidine-Based Thiuram Disulfides as Potential Dual-Inhibitors of COX-1and COX-2. Chem Biodivers 2023; 20:e202200875. [PMID: 36515971 DOI: 10.1002/cbdv.202200875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
A series of thiuram disulfides 1-6 which had been previously synthesized and characterized,[1] were studied for their potential therapeutic properties. Target-fishing analyses through HitPick and SwissTarget prediction identified COX1 and COX2, which are essential biomolecules in cancer-related inflammations, as the possible targets for compounds 1 and 4 among all the compounds tested. These two proteins have enjoyed interest as targets for treating some neoplastic cancer types such as breast, colorectal, skin, pancreatic, haematological and head cancers. The inhibitory potency of 1 and 4 as lead anticancer drug candidates with dual-target ability against COX1 and COX2 was examined through molecular docking, molecular dynamics simulation and post-MD analyses such as binding energy calculation, RMSD, RMSF, and RoG. The two compounds had better docking scores and binding energies than the known inhibitors of COX1 and COX2. Insights from the RMSD, RMSF, and RoG suggested that both 1 and 4 showed observable influence on the structural stability of these targets throughout the simulation. The reported observations of the effects of 1 and 4 on the structures of COX1 and COX2 indicate their probable inhibitory properties against these target proteins and their potential as lead anticancer drug candidates.
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Affiliation(s)
- Segun D Oladipo
- School of Chemistry and Physics, Westville Campus, University of Kwazulu-Natal, Private Bag X54001, Durban, 4000, South Africa.,Department of Chemical Sciences, Olabisi Onabanjo University, P.M.B 2002, Ago-Iwoye, Nigeria
| | - Olayinka I Akinpelu
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural Science, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Bernard Omondi
- School of Chemistry and Physics, Westville Campus, University of Kwazulu-Natal, Private Bag X54001, Durban, 4000, South Africa
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4
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Gantner ME, Prada Gori DN, Llanos MA, Talevi A, Angeli A, Vullo D, Supuran CT, Gavernet L. Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening. J Chem Inf Model 2022; 62:4760-4770. [PMID: 36126250 DOI: 10.1021/acs.jcim.2c00910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human carbonic anhydrase VII (hCA VII) constitutes a promising molecular target for the treatment of epileptic seizures and other central nervous system disorders due to its almost exclusive expression in neurons. Achieving isoform selectivity is one of the main challenges for the discovery of new hCA inhibitors, since nonspecific inhibition may lead to tolerance and side effects. In the present work, we report the development of a molecular docking protocol based on AutoDock4Zn for the search of new hCA VII inhibitors by virtual screening. The docking protocol was applied to the screening of two sets of compounds: a ZINC15 subset of sulfur-containing structures and an in-house library consisting of synthetic and commercial candidates (including approved drugs). Five compounds were selected from the first screening campaign and three from the second one, and they were tested in vitro against the enzyme. Among the eight selected structures, four showed Ki values in the low nanomolar range. These confirmed hits include three approved drugs: meloxicam, piroxicam, and nitrofurantoin, which also showed good selectivity for hCA VII versus hCA II.
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Affiliation(s)
- Melisa E Gantner
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata (UNLP), 47&115, La Plata B1900ADU, Buenos Aires, Argentina
| | - Denis N Prada Gori
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata (UNLP), 47&115, La Plata B1900ADU, Buenos Aires, Argentina
| | - Manuel A Llanos
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata (UNLP), 47&115, La Plata B1900ADU, Buenos Aires, Argentina
| | - Alan Talevi
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata (UNLP), 47&115, La Plata B1900ADU, Buenos Aires, Argentina
| | - Andrea Angeli
- Neurofarba Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Florence, Italy
| | - Daniela Vullo
- Dipartimento di Chimica Ugo Schiff, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T Supuran
- Neurofarba Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Florence, Italy
| | - Luciana Gavernet
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata (UNLP), 47&115, La Plata B1900ADU, Buenos Aires, Argentina
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5
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Ewies EF, Sabry E, Bekheit MS, Fouad MA, Vullo D, Supuran CT. Click chemistry-based synthesis of new benzenesulfonamide derivatives bearing triazole ring as selective carbonic anhydrase II inhibitors. Drug Dev Res 2022; 83:1281-1291. [PMID: 35706360 DOI: 10.1002/ddr.21957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/22/2022] [Accepted: 05/24/2022] [Indexed: 12/11/2022]
Abstract
A series of 1,2,3-triazol-1-ylbenzenesulfonamide derivatives was designed, synthesized and their ability to inhibit several carbonic anhydrase isoforms was evaluated. The basis of our design is to hybridize the benzenesulfonamide moiety widely used as a zinc-binding group, a triazole ring as spacer with a tail of different substituted aryl moieties. The synthesis of these compounds was achieved using Cu(I)-mediated click chemistry between the azide containing the benzenesulfonamide pharmacophore and various aryl acetylenes or 1,6-heptadiyne through copper-catalyzed [3+2] cycloaddition reaction. The ability the new derivatives to inhibit four human carbonic anhydrase isoforms hCA I, II, IX, and XII was evaluated. All the compounds exhibited good potency and high selectivity towards isoforms hCA I and II more than isoforms hCA IX and XII, especially for the derivatives 3c and 3j that displayed Ki of 2.8 and 3.8 nM against hCA II and a high hCA II selectivity ratio ranging from 77.6 to 3571.4 over other isoforms. All the compounds were docked in the active site of the downloaded hCA II active site and their binding pattern confirmed their significant activity by interacting of the sulfonamide moiety with zinc ion in the active site, in addition to its hydrogen bond interaction with Thr199 and Thr200. All the above-mentioned findings pointed out towards the promising activity of the synthesized series that can be presented as a new scaffold to be further optimized as selective antiglaucoma drugs.
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Affiliation(s)
- Ewies F Ewies
- Organometallic and Organometalloid Chemistry Department, National Research Centre, Giza, Egypt
| | - Eman Sabry
- Pesticide Chemistry Department, National Research Centre, Giza, Egypt
| | - Mohamed S Bekheit
- Pesticide Chemistry Department, National Research Centre, Giza, Egypt
| | - Marwa A Fouad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Pharmaceutical Chemistry Department, School of Pharmacy, NewGiza University, Cairo, Egypt
| | - Daniela Vullo
- NEUROFARBA Department, Section of Pharmaceutical and Nutraceutical Chemistry, University of Florence, Florence, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Section of Pharmaceutical and Nutraceutical Chemistry, University of Florence, Florence, Italy
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6
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Mancuso F, Angeli A, De Luca V, Bucolo F, De Luca L, Capasso C, Supuran CT, Gitto R. Synthesis and biological evaluation of sulfonamide-based compounds as inhibitors of carbonic anhydrase from Vibrio cholerae. Arch Pharm (Weinheim) 2022; 355:e2200070. [PMID: 35739618 DOI: 10.1002/ardp.202200070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/06/2022]
Abstract
This study reports our continued efforts to identify inhibitors capable of targeting carbonic anhydrases (CAs) expressed in bacteria. Based on previously identified chemotypes, we designed and synthesized new analogs that were screened toward the α, β, and γ classes encoded in Vibrio cholerae (Vch). The Ki values measured in the stopped-flow hydrase assay revealed that very simple structural modifications might induce a relevant impact on the inhibitory effects as well as the selectivity profile over ubiquitous human isozymes (hCA I/II). Unfortunately, the best active VchCA inhibitors demonstrated a dramatic loss of hCA II selectivity when compared to previously reported compounds. Among the new series of sulfonamides, several molecules proved to be about sevenfold more potent against VchCAγ than the reference compound acetazolamide, thus furnishing new insights for further development of inhibitors targeting CAs expressed in bacteria.
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Affiliation(s)
| | - Andrea Angeli
- NEUROFARBA Department, University of Florence, Florence, Italy
| | - Viviana De Luca
- Institute of Biosciences and Bioresources, National Research Council (CNR), Naples, Italy
| | - Federica Bucolo
- CHIBIOFARAM Department, University of Messina, Messina, Italy
| | - Laura De Luca
- CHIBIOFARAM Department, University of Messina, Messina, Italy
| | - Clemente Capasso
- Institute of Biosciences and Bioresources, National Research Council (CNR), Naples, Italy
| | | | - Rosaria Gitto
- CHIBIOFARAM Department, University of Messina, Messina, Italy
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7
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Mancuso F, De Luca L, Bucolo F, Vrabel M, Angeli A, Capasso C, Supuran CT, Gitto R. 4-Sulfamoylphenylalkylamides as Inhibitors of Carbonic Anhydrases Expressed in Vibrio cholerae. ChemMedChem 2021; 16:3787-3794. [PMID: 34592052 PMCID: PMC9298201 DOI: 10.1002/cmdc.202100510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 11/21/2022]
Abstract
A current issue of antimicrobial therapy is the resistance to treatment with worldwide consequences. Thus, the identification of innovative targets is an intriguing challenge in the drug and development process aimed at newer antimicrobial agents. The state-of-art of anticholera therapy might comprise the reduction of the expression of cholera toxin, which could be reached through the inhibition of carbonic anhydrases expressed in Vibrio cholerae (VchCAα, VchCAβ, and VchCAγ). Therefore, we focused our interest on the exploitation of sulfonamides as VchCA inhibitors. We planned to design and synthesize new benzenesulfonamides based on our knowledge of the VchCA catalytic site. The synthesized compounds were tested thus collecting useful SAR information. From our investigation, we identified new potent VchCA inhibitors, some of them displayed high affinity toward VchCAγ class, for which few inhibitors are currently reported in literature. The best interesting VchCAγ inhibitor (S)-N-(1-oxo-1-((4-sulfamoylbenzyl)amino)propan-2-yl)furan-2-carboxamide (40) resulted more active and selective inhibitor when compared with acetazolamide (AAZ) as well as previously reported VchCA inhibitors.
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Affiliation(s)
- Francesca Mancuso
- CHIBIOFARAM DepartmentUniversity of MessinaViale Stagno D'Alcontres98166MessinaItaly
| | - Laura De Luca
- CHIBIOFARAM DepartmentUniversity of MessinaViale Stagno D'Alcontres98166MessinaItaly
| | - Federica Bucolo
- CHIBIOFARAM DepartmentUniversity of MessinaViale Stagno D'Alcontres98166MessinaItaly
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry (IOCB)Czech Academy of SciencesFlemingovo nám. 216000PragueCzech Republic
| | - Andrea Angeli
- NEUROFARBA DepartmentUniversity of FlorenceVia U. Schiff 650019FlorenceItaly
| | - Clemente Capasso
- Institute of Biosciences and BioresourcesCNRVia Castellino 11180131NapoliItaly
| | - Claudiu T. Supuran
- NEUROFARBA DepartmentUniversity of FlorenceVia U. Schiff 650019FlorenceItaly
| | - Rosaria Gitto
- CHIBIOFARAM DepartmentUniversity of MessinaViale Stagno D'Alcontres98166MessinaItaly
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8
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Sbravati D, Bonardi A, Bua S, Angeli A, Ferraroni M, Nocentini A, Casnati A, Gratteri P, Sansone F, Supuran CT. Calixarenes Incorporating Sulfonamide Moieties: Versatile Ligands for Carbonic Anhydrases Inhibition. Chemistry 2021; 28:e202103527. [PMID: 34882858 DOI: 10.1002/chem.202103527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 11/10/2022]
Abstract
Carbonic anhydrases (CAs) continue to represent a relevant pharmaceutical target. The need of selective inhibitors and the involvement of these metalloenzymes in many multifaceted diseases boost the search for new ligands able to distinguish among the different CA isoforms, and for multifunctional systems simultaneously able to inhibit CAs and to interfere with other pathological events by interacting with additional targets. In this work, we successfully explored the possibility of preparing new CAs ligands by combining calixarenes with benzensulfonamide units. Inhibition tests towards three human CA isoforms evidenced, for some of the ligands, Ki values in the nanomolar range and promising selectivity. X-ray and molecular modeling studies provided information on the mode of binding of these calixarene derivatives. Thanks to the encouraging results and the structural features typical of the calixarene scaffold, it is then possible to plan for the future the design of multifunctional inhibitors for this class of widely spread enzymes.
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Affiliation(s)
- Davide Sbravati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Alessandro Bonardi
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy.,Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Silvia Bua
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Andrea Angeli
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Marta Ferraroni
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy
| | - Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy.,Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Alessandro Casnati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Paola Gratteri
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy.,Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Francesco Sansone
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
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9
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Weber JK, Morrone JA, Bagchi S, Pabon JDE, Kang SG, Zhang L, Cornell WD. Simplified, interpretable graph convolutional neural networks for small molecule activity prediction. J Comput Aided Mol Des 2021; 36:391-404. [PMID: 34817762 PMCID: PMC9325818 DOI: 10.1007/s10822-021-00421-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/24/2021] [Indexed: 12/11/2022]
Abstract
We here present a streamlined, explainable graph convolutional neural network (gCNN) architecture for small molecule activity prediction. We first conduct a hyperparameter optimization across nearly 800 protein targets that produces a simplified gCNN QSAR architecture, and we observe that such a model can yield performance improvements over both standard gCNN and RF methods on difficult-to-classify test sets. Additionally, we discuss how reductions in convolutional layer dimensions potentially speak to the “anatomical” needs of gCNNs with respect to radial coarse graining of molecular substructure. We augment this simplified architecture with saliency map technology that highlights molecular substructures relevant to activity, and we perform saliency analysis on nearly 100 data-rich protein targets. We show that resultant substructural clusters are useful visualization tools for understanding substructure-activity relationships. We go on to highlight connections between our models’ saliency predictions and observations made in the medicinal chemistry literature, focusing on four case studies of past lead finding and lead optimization campaigns.
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Affiliation(s)
- Jeffrey K Weber
- IBM Thomas J Watson Research Center, Yorktown Heights, NY, USA
| | | | - Sugato Bagchi
- IBM Thomas J Watson Research Center, Yorktown Heights, NY, USA
| | | | - Seung-Gu Kang
- IBM Thomas J Watson Research Center, Yorktown Heights, NY, USA
| | - Leili Zhang
- IBM Thomas J Watson Research Center, Yorktown Heights, NY, USA
| | - Wendy D Cornell
- IBM Thomas J Watson Research Center, Yorktown Heights, NY, USA.
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10
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Synthesis, Crystal Structure, Inhibitory Activity and Molecular Docking of Coumarins/Sulfonamides Containing Triazolyl Pyridine Moiety as Potent Selective Carbonic Anhydrase IX and XII Inhibitors. CRYSTALS 2021. [DOI: 10.3390/cryst11091076] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, two classes of Carbonic Anhydrase (CA) inhibitors, sulfonamide and coumarin derivatives linked to pyta moiety (2a-b) and their corresponding rhenium complexes (3a-b), were designed. These compounds were synthesized and fully characterized by classical analytical methods and X-ray diffraction. All the synthesized compounds were evaluated for their inhibitory activity against the hCA isoforms I, II, IX and XII. They exhibited high inhibitory activities in the range of nanomolar for both hCA IX and hCA XII isoforms. The sulfonamide compound 2a showed the strongest inhibition against the tumour-associated hCA IX isoform with a Ki of 11.7 nM. The tumour-associated isoforms hCA IX and hCA XII were selectively inhibited by all the coumarin derivatives, with inhibition constants ranging from 12.7 nM (2b) to 44.5 nM (3b), while the hCA I and II isoforms were slightly inhibited (in the micromolar range), as expected. In terms of selectivity, compared to previously published rhenium complex-based CA inhibitors, complex 3b showed one of the highest selectivities against hCA IX and hCA XII compared to the off-target isoforms hCA I and hCA II, making it a potential anti-cancer drug candidate. Molecular docking calculations were performed to investigate the inhibition profiles of the investigated compounds at the tumour-associated hCA IX active site and to rationalize our results.
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11
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Mancuso F, Di Fiore A, De Luca L, Angeli A, De Simone G, Supuran CT, Gitto R. Design, synthesis and biochemical evaluation of novel carbonic anhydrase inhibitors triggered by structural knowledge on hCA VII. Bioorg Med Chem 2021; 44:116279. [PMID: 34216985 DOI: 10.1016/j.bmc.2021.116279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
To tackle the challenge of isoform selectivity, we explored the entrance of the cavity for selected druggable human Carbonic Anhydrases (hCAs). Based on X-ray crystallographic studies on the 4-(4-(2-chlorobenzoyl)piperazine-1-carbonyl)benzenesulfonamide in complex with the brain expressed hCA VII (PDB code: 7NC4), a series of 4-(4(hetero)aroylpiperazine-1-carbonyl)benzene-1-sulfonamides has been developed. To evaluate their capability to fit the hCA VII catalytic cavity, the newer benzenesulfonamides were preliminary investigated by means of docking simulations. Then, this series of thirteen benzenesulfonamides was synthesized and tested against selected druggable hCAs. Among them, the 4-(4-(furan-2-carbonyl)piperazine-1-carbonyl)benzenesulfonamide showed remarkable affinity towards hCA VII (Ki: 4.3 nM) and good selectivity over the physiologically widespread hCA I when compared to Topiramate (TPM).
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Affiliation(s)
- Francesca Mancuso
- Dipartimento CHIBIOFARAM, Università degli Studi di Messina, Viale Palatucci, Polo Didattico SS. Annunziata, 98168 Messina, Italy.
| | - Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Laura De Luca
- Dipartimento CHIBIOFARAM, Università degli Studi di Messina, Viale Palatucci, Polo Didattico SS. Annunziata, 98168 Messina, Italy
| | - Andrea Angeli
- Dipartimento NEUROFARBA, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Giuseppina De Simone
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Claudiu T Supuran
- Dipartimento NEUROFARBA, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Rosaria Gitto
- Dipartimento CHIBIOFARAM, Università degli Studi di Messina, Viale Palatucci, Polo Didattico SS. Annunziata, 98168 Messina, Italy
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12
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Angeli A, Pinteala M, Maier SS, Toti A, Di Cesare Mannelli L, Ghelardini C, Selleri S, Carta F, Supuran CT. Tellurides bearing benzensulfonamide as carbonic anhydrase inhibitors with potent antitumor activity. Bioorg Med Chem Lett 2021; 45:128147. [PMID: 34052322 DOI: 10.1016/j.bmcl.2021.128147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/16/2021] [Accepted: 05/22/2021] [Indexed: 12/19/2022]
Abstract
We evaluated in vitro a series of telluride containing compounds bearing the benzenesulfonamide group, as effective inhibitors of the physiologically relevant human (h) expressed Carbonic Anhydrase (CA; EC 4.2.1.1) enzymes I, II, IV VII and IX. The potent effects of such compounds against the tumor-associated hCA IX being low nanomolar inhibitors (KI 2.2 to 2.9 nM) and with good selectivity over the ubiquitous hCA II, gave the possibility to evaluate their lethal effect in vitro against a breast cancer cell line (MDA-MB-231). Among the series, both compounds 3a and 3g induced significant toxic effects against tumor cells after 48 h incubation. Under normoxic condition 3a showed high efficacy killing over 94% of tumor cells at 1 µM, and derivative 3g reached the tumor cell viability under the 5% at 10 µM. In hypoxic condition, these two compounds showed less effective although retained excellent cancer cell killer. These unusual features make them interesting lead compounds acting as antitumor agents also in tumor types not dependent from hCA IX overexpression.
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Affiliation(s)
- Andrea Angeli
- University of Florence, NEUROFARBA Dept, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy; Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, "Petru Poni" Institute of Macromolecular Chemistry, 700487 Iasi, Romania.
| | - Mariana Pinteala
- Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, "Petru Poni" Institute of Macromolecular Chemistry, 700487 Iasi, Romania
| | - Stelian S Maier
- Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, "Petru Poni" Institute of Macromolecular Chemistry, 700487 Iasi, Romania; Polymers Research Center, "Gheorghe Asachi" Technical University of Iasi, 700487 Iasi, Romania
| | - Alessandra Toti
- NEUROFARBA Department, Section of Pharmacology and Toxicology, Università degli Studi di Firenze, Viale Pieraccini 6, 50139, Florence, Italy
| | - Lorenzo Di Cesare Mannelli
- NEUROFARBA Department, Section of Pharmacology and Toxicology, Università degli Studi di Firenze, Viale Pieraccini 6, 50139, Florence, Italy
| | - Carla Ghelardini
- NEUROFARBA Department, Section of Pharmacology and Toxicology, Università degli Studi di Firenze, Viale Pieraccini 6, 50139, Florence, Italy
| | - Silvia Selleri
- University of Florence, NEUROFARBA Dept, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Fabrizio Carta
- University of Florence, NEUROFARBA Dept, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Claudiu T Supuran
- University of Florence, NEUROFARBA Dept, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy
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13
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Angeli A, Kartsev V, Petrou A, Pinteala M, Brovarets V, Slyvchuk S, Pilyo S, Geronikaki A, Supuran CT. Chromene-Containing Aromatic Sulfonamides with Carbonic Anhydrase Inhibitory Properties. Int J Mol Sci 2021; 22:ijms22105082. [PMID: 34064890 PMCID: PMC8150913 DOI: 10.3390/ijms22105082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 11/23/2022] Open
Abstract
Carbonic anhydrases (CAs, EC 4.2.1.1) catalyze the essential reaction of CO2 hydration in all living organisms, being actively involved in the regulation of a plethora of patho/physiological conditions. A series of chromene-based sulfonamides were synthesized and tested as possible CA inhibitors. Their inhibitory activity was assessed against the cytosolic human isoforms hCA I, hCA II and the transmembrane hCA IX and XII. Several of the investigated derivatives showed interesting inhibition activity towards the tumor associate isoforms hCA IX and hCA XII. Furthermore, computational procedures were used to investigate the binding mode of this class of compounds, within the active site of hCA IX.
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Affiliation(s)
- Andrea Angeli
- Neuro Farba Department, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy;
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Aleea Grigore Ghica-Voda, No. 41A, 700487 Iasi, Romania;
- Correspondence: (A.A.); (A.G.)
| | - Victor Kartsev
- InterBioScreen, Chernogolovka 142432, Moscow Region, Russia;
| | - Anthi Petrou
- Department of Pharmacy, School of Health, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Mariana Pinteala
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Aleea Grigore Ghica-Voda, No. 41A, 700487 Iasi, Romania;
| | - Volodymyr Brovarets
- Department of Chemistry of Bioactive Nitrogen-Containing Heterocyclic Bases, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine 1, Murmanska St, 02094 Kyiv, Ukraine; (V.B.); (S.S.); (S.P.)
| | - Sergii Slyvchuk
- Department of Chemistry of Bioactive Nitrogen-Containing Heterocyclic Bases, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine 1, Murmanska St, 02094 Kyiv, Ukraine; (V.B.); (S.S.); (S.P.)
| | - Stepan Pilyo
- Department of Chemistry of Bioactive Nitrogen-Containing Heterocyclic Bases, V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine 1, Murmanska St, 02094 Kyiv, Ukraine; (V.B.); (S.S.); (S.P.)
| | - Athina Geronikaki
- Department of Pharmacy, School of Health, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
- Correspondence: (A.A.); (A.G.)
| | - Claudiu T. Supuran
- Neuro Farba Department, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy;
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14
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Guglielmi P, Rotondi G, Secci D, Angeli A, Chimenti P, Nocentini A, Bonardi A, Gratteri P, Carradori S, Supuran CT. Novel insights on saccharin- and acesulfame-based carbonic anhydrase inhibitors: design, synthesis, modelling investigations and biological activity evaluation. J Enzyme Inhib Med Chem 2021; 35:1891-1905. [PMID: 33003975 PMCID: PMC7580763 DOI: 10.1080/14756366.2020.1828401] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A large library of saccharin and acesulfame derivatives has been synthesised and evaluated against four isoforms of human carbonic anhydrase, the two off-targets hCA I/II and the tumour related isoforms hCA IX/XII. Different strategies of scaffold modification have been attempted on both saccharin as well as acesulfame core leading to the obtainment of 60 compounds. Some of them exhibited inhibitory activity in the nanomolar range, albeit some of the performed changes led to either micromolar activity or to its absence, against hCA IX/XII. Molecular modelling studies focused the attention on the binding mode of these compounds to the enzyme. The proposed inhibition mechanism is the anchoring to zinc-bound water molecule. Docking studies along with molecular dynamics also underlined the importance of the compounds flexibility (e.g. achieved through the insertion of methylene group) which favoured potent and selective hCA inhibition.
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Affiliation(s)
- Paolo Guglielmi
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, Rome, Italy
| | - Giulia Rotondi
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, Rome, Italy
| | - Daniela Secci
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, Rome, Italy
| | - Andrea Angeli
- Neurofarba Department, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Sesto Fiorentino, Italy.,Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, "Petru Poni" Institute of Macromolecular Chemistry, Iasi, Romania
| | - Paola Chimenti
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, Rome, Italy
| | - Alessio Nocentini
- Neurofarba Department, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Sesto Fiorentino, Italy.,Neurofarba Department, Section of Pharmaceutical and Nutraceutical Sciences, Laboratory of Molecular Modeling Cheminformatics & QSAR University of Florence, Sesto Fiorentino Italy
| | - Alessandro Bonardi
- Neurofarba Department, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Sesto Fiorentino, Italy.,Neurofarba Department, Section of Pharmaceutical and Nutraceutical Sciences, Laboratory of Molecular Modeling Cheminformatics & QSAR University of Florence, Sesto Fiorentino Italy
| | - Paola Gratteri
- Neurofarba Department, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Sesto Fiorentino, Italy.,Neurofarba Department, Section of Pharmaceutical and Nutraceutical Sciences, Laboratory of Molecular Modeling Cheminformatics & QSAR University of Florence, Sesto Fiorentino Italy
| | - Simone Carradori
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Claudiu T Supuran
- Neurofarba Department, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Sesto Fiorentino, Italy
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15
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Salerno S, Amendola G, Angeli A, Baglini E, Barresi E, Marini AM, Ravichandran R, Viviano M, Castellano S, Novellino E, Da Settimo F, Supuran CT, Cosconati S, Taliani S. Inhibition studies on carbonic anhydrase isoforms I, II, IV and IX with N-arylsubstituted secondary sulfonamides featuring a bicyclic tetrahydroindazole scaffold. Eur J Med Chem 2021; 220:113490. [PMID: 33975138 DOI: 10.1016/j.ejmech.2021.113490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/24/2021] [Accepted: 04/17/2021] [Indexed: 12/15/2022]
Abstract
Carbonic Anhydrases (CAs) are pharmaceutically relevant targets for the treatment of several disease conditions. The ubiquitous localization of these enzymes and the high homology shared by the different isoforms represent substantial impediments for the discovery of potential drugs devoid of off-target side effects. As a consequence, substantial efforts are still needed to allow for the full realization of the pharmacological potential of CA modulators. In this contribution, starting from our previous studies, we describe the synthesis of a set of new bicyclic tetrahydroindazoles featuring a secondary sulfonamide. Biological evaluation of the inhibitory activity against the hCA I, II, IV, and IX isoforms allowed drawing a structure-activity relationship profile that was rationalized through theoretical studies. This allowed dissecting the new molecules into the single portions influencing the zinc chelation properties and the selectivity profile thereby offering a new platform for the discovery of new isotype selective CA inhibitors.
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Affiliation(s)
| | - Giorgio Amendola
- DiSTABiF, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Andrea Angeli
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino (Florence), Italy
| | - Emma Baglini
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | | | | | | | - Monica Viviano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano (SA), Italy
| | - Sabrina Castellano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano (SA), Italy
| | - Ettore Novellino
- Department of Pharmacy, University Federico II of Naples, Naples, Italy
| | | | - Claudiu T Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino (Florence), Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi Vanvitelli, Caserta, Italy.
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16
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Kotzé TJ, Duffy S, Avery VM, Jordaan A, Warner DF, Loots L, Smith GS, Chellan P. Synthesis and antimicrobial study of organoiridium amido-sulfadoxine complexes. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.120175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Mancuso F, De Luca L, Angeli A, Del Prete S, Capasso C, Supuran CT, Gitto R. Synthesis, computational studies and assessment of in vitro inhibitory activity of umbelliferon-based compounds against tumour-associated carbonic anhydrase isoforms IX and XII. J Enzyme Inhib Med Chem 2021; 35:1442-1449. [PMID: 32614678 PMCID: PMC7717710 DOI: 10.1080/14756366.2020.1786821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Coumarins are widely diffused secondary metabolites possessing a plethora of biological activities. It has been established that coumarins represent a peculiar class of human carbonic anhydrase (hCA) inhibitors having a distinct mechanism of action involving a non-classical binding with amino acid residues paving the entrance of hCA catalytic site. Herein, we report the synthesis of a small series of new coumarin derivatives 7-11, 15, 17 prepared via classical Pechmann condensation starting from resorcinol derivatives and suitable β-ketoesters. The evaluation of inhibitory activity revealed that these compounds possessed nanomolar affinity and high selectivity towards tumour-associated hCA IX and XII over cytosolic hCA I and hCA II isoforms. To investigate the binding mode of these new coumarin-inspired inhibitors, the most active compounds 10 and 17 were docked within hCA XII catalytic cleft.
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Affiliation(s)
- Francesca Mancuso
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Messina, Italy
| | - Laura De Luca
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Messina, Italy
| | - Andrea Angeli
- Dipartimento NEUROFARBA, Università di Firenze, Sesto Fiorentino, Italy
| | | | | | - Claudiu T Supuran
- Dipartimento NEUROFARBA, Università di Firenze, Sesto Fiorentino, Italy
| | - Rosaria Gitto
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Messina, Italy
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18
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Sahasrabuddhe A, Oakley D, Chen K, McCarter JD. Development of a High-Throughput Affinity Mass Spectrometry (AMS) Platform Using Laser Diode Thermal Desorption Ionization Coupled to Mass Spectrometry (LDTD-MS). SLAS DISCOVERY 2020; 26:230-241. [PMID: 33334237 DOI: 10.1177/2472555220979596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Affinity selection mass spectrometry (MS) or, simply, affinity mass spectrometry (AMS) is a label-free technology that has been used to identify high-affinity ligands of target proteins of interest by screening against small-molecule compound libraries and identifying molecules that are enriched in the presence of the target protein. We have previously applied Agilent Technology's (Santa Clara, CA) RapidFire solid-phase extraction (SPE)-based high-throughput MS technology to screen small-molecule libraries using AMS. However, SPE-based technologies rely on fluidics for desalting and separation prior to mass analysis with attendant high solvent consumption, relatively high sample volume requirements, risk of sample carryover, and frequent maintenance. To address these challenges, we have established an AMS platform using a laser diode thermal desorption-atmospheric pressure chemical ionization (LDTD-APCI) ionization source (Phytronix, Quebec, Canada) coupled with a SCIEX 5600+ TripleTOF MS (Framingham, MA). We also validated a data-independent acquisition (DIA) Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) method for the robust detection and analysis of small-molecule affinity hits. An informatics platform developed in-house has resulted in a streamlined data analysis workflow for high-throughput AMS screening campaigns and reduced data processing time without compromising data quality. Finally, 68,000 compounds were screened in a single plate and affinity selected hits were confirmed in an orthogonal enzyme activity assay.
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Affiliation(s)
| | - Dylan Oakley
- Research Automation Technologies, Thousand Oaks, CA, USA
| | - Kui Chen
- Discovery Technologies, Thousand Oaks, CA, USA
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19
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Mancuso F, De Luca L, Angeli A, Berrino E, Del Prete S, Capasso C, Supuran CT, Gitto R. In Silico-Guided Identification of New Potent Inhibitors of Carbonic Anhydrases Expressed in Vibrio cholerae. ACS Med Chem Lett 2020; 11:2294-2299. [PMID: 33214843 DOI: 10.1021/acsmedchemlett.0c00417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/01/2020] [Indexed: 01/01/2023] Open
Abstract
Carbonic anhydrases from Vibrio cholerae (VchCAs) play a significant role in bacterial pathophysiological processes. Therefore, their inhibition leads to a reduction of gene expression virulence and bacterial growth impairment. Herein, we report the first ligand-based pharmacophore model as a computational tool to study selective inhibitors of the β-class of VchCA. By a virtual screening on a collection of sulfonamides, we retrieved 9 compounds that were synthesized and evaluated for their inhibitory effects against VchCAβ as well as α- and γ-classes of VchCAs and selectivity over human ubiquitous isoforms hCA I and II. Notably, all tested compounds were active inhibitors of VchCAs. The N-(4-sulfamoylbenzyl)-[1,1'-biphenyl]-4-carboxamide (20e) stood out as the most exciting inhibitor toward the β-class (K i = 95.6 nM), also showing a low affinity against the tested human isoforms. By applying docking procedures, we described the binding mode of the inhibitor 20e within the catalytic cavity of the modeled open conformation of VchCAβ.
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Affiliation(s)
- Francesca Mancuso
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci 13, I-98168 Messina, Italy
| | - Laura De Luca
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci 13, I-98168 Messina, Italy
| | - Andrea Angeli
- Dipartimento NEUROFARBA, Università di Firenze, Via Ugo Schiff, I-50019 Sesto Fiorentino, Italy
| | - Emanuela Berrino
- Dipartimento NEUROFARBA, Università di Firenze, Via Ugo Schiff, I-50019 Sesto Fiorentino, Italy
| | - Sonia Del Prete
- Istituto di Bioscienze e Biorisorse - CNR, Via Pietro Castellino 111 - I-80131 Napoli, Italy
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse - CNR, Via Pietro Castellino 111 - I-80131 Napoli, Italy
| | - Claudiu T. Supuran
- Dipartimento NEUROFARBA, Università di Firenze, Via Ugo Schiff, I-50019 Sesto Fiorentino, Italy
| | - Rosaria Gitto
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci 13, I-98168 Messina, Italy
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20
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Mishra CB, Tiwari M, Supuran CT. Progress in the development of human carbonic anhydrase inhibitors and their pharmacological applications: Where are we today? Med Res Rev 2020; 40:2485-2565. [PMID: 32691504 DOI: 10.1002/med.21713] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/14/2020] [Accepted: 07/03/2020] [Indexed: 12/21/2022]
Abstract
Carbonic anhydrases (CAs, EC 4.2.1.1) are widely distributed metalloenzymes in both prokaryotes and eukaryotes. They efficiently catalyze the reversible hydration of carbon dioxide to bicarbonate and H+ ions and play a crucial role in regulating many physiological processes. CAs are well-studied drug target for various disorders such as glaucoma, epilepsy, sleep apnea, and high altitude sickness. In the past decades, a large category of diverse families of CA inhibitors (CAIs) have been developed and many of them showed effective inhibition toward specific isoforms, and effectiveness in pathological conditions in preclinical and clinical settings. The discovery of isoform-selective CAIs in the last decade led to diminished side effects associated with off-target isoforms inhibition. The many new classes of such compounds will be discussed in the review, together with strategies for their development. Pharmacological advances of the newly emerged CAIs in diseases not usually associated with CA inhibition (neuropathic pain, arthritis, cerebral ischemia, and cancer) will also be discussed.
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Affiliation(s)
- Chandra B Mishra
- Department of Bioorganic Chemistry, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.,Department of Pharmaceutical Chemistry, College of Pharmacy, Sookmyung Women's University, Seoul, South Korea
| | - Manisha Tiwari
- Department of Bioorganic Chemistry, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Florence, Italy
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21
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Mancuso F, Di Fiore A, De Luca L, Angeli A, Monti SM, De Simone G, Supuran CT, Gitto R. Looking toward the Rim of the Active Site Cavity of Druggable Human Carbonic Anhydrase Isoforms. ACS Med Chem Lett 2020; 11:1000-1005. [PMID: 32435417 DOI: 10.1021/acsmedchemlett.0c00062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/04/2020] [Indexed: 11/28/2022] Open
Abstract
We report the synthesis and biochemical evaluation of a series of substituted 4-(4-aroylpiperazine-1-carbonyl)benzenesulfonamides (5a-s) developed as inhibitors of druggable carbonic anhydrase (CA) isoforms, as tools for the identification of new therapeutics. X-ray crystallography confirmed that this class of benzenesulfonamides binds CAs through the canonical anchoring of the benzenesulfonamide moiety to the metal ion and a tail-mediated recognition of the middle/top area of the active site cavity. Compound 5e (R = 2-Cl) demonstrated relevant selectivity toward brain-expressed hCA VII. The best balancing in binding affinity and selectivity toward tumor-expressed hCA IX/hCA XII over ubiquitous hCA I/hCA II was found for inhibitor 5o (R = 3-NO2). Notably 5b (R = 2-F) proved to be the most efficacious inhibitor of hCA XII for which computational studies elucidated the CA recognition process.
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Affiliation(s)
- Francesca Mancuso
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci, Polo Didattico SS. Annunziata, 98168 Messina, Italy
| | - Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini—CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Laura De Luca
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci, Polo Didattico SS. Annunziata, 98168 Messina, Italy
| | - Andrea Angeli
- Dipartimento NEUROFARBA, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Simona M. Monti
- Istituto di Biostrutture e Bioimmagini—CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Giuseppina De Simone
- Istituto di Biostrutture e Bioimmagini—CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Claudiu T. Supuran
- Dipartimento NEUROFARBA, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Rosaria Gitto
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci, Polo Didattico SS. Annunziata, 98168 Messina, Italy
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22
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Sulfamoyl Heteroarylcarboxylic Acids as Promising Metallo-β-Lactamase Inhibitors for Controlling Bacterial Carbapenem Resistance. mBio 2020; 11:mBio.03144-19. [PMID: 32184250 PMCID: PMC7078479 DOI: 10.1128/mbio.03144-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Carbapenem antibiotics are the last resort for control of severe infectious diseases, bloodstream infections, and pneumonia caused by Gram-negative bacteria, including Enterobacteriaceae. However, carbapenem-resistant Enterobacteriaceae (CRE) strains have spread globally and are a critical concern in clinical settings because CRE infections are recognized as a leading cause of increased mortality among hospitalized patients. Most CRE produce certain kinds of serine carbapenemases (e.g., KPC- and GES-type β-lactamases) or metallo-β-lactamases (MBLs), which can hydrolyze carbapenems. Although effective MBL inhibitors are expected to restore carbapenem efficacy against MBL-producing CRE, no MBL inhibitor is currently clinically available. Here, we synthesized 2,5-diethyl-1-methyl-4-sulfamoylpyrrole-3-carboxylic acid (SPC), which is a potent inhibitor of MBLs. SPC is a remarkable lead compound for clinically useful MBL inhibitors and can potentially provide a considerable benefit to patients receiving treatment for lethal infectious diseases caused by MBL-producing CRE. Production of metallo-β-lactamases (MBLs), which hydrolyze carbapenems, is a cause of carbapenem resistance in Enterobacteriaceae. Development of effective inhibitors for MBLs is one approach to restore carbapenem efficacy in carbapenem-resistant Enterobacteriaceae (CRE). We report here that sulfamoyl heteroarylcarboxylic acids (SHCs) can competitively inhibit the globally spreading and clinically relevant MBLs (i.e., IMP-, NDM-, and VIM-type MBLs) at nanomolar to micromolar orders of magnitude. Addition of SHCs restored meropenem efficacy against 17/19 IMP-type and 7/14 NDM-type MBL-producing Enterobacteriaceae to satisfactory clinical levels. SHCs were also effective against IMP-type MBL-producing Acinetobacter spp. and engineered Escherichia coli strains overproducing individual minor MBLs (i.e., TMB-2, SPM-1, DIM-1, SIM-1, and KHM-1). However, SHCs were less effective against MBL-producing Pseudomonas aeruginosa. Combination therapy with meropenem and SHCs successfully cured mice infected with IMP-1-producing E. coli and dually NDM-1/VIM-1-producing Klebsiella pneumoniae clinical isolates. X-ray crystallographic analyses revealed the inhibition mode of SHCs against MBLs; the sulfamoyl group of SHCs coordinated to two zinc ions, and the carboxylate group coordinated to one zinc ion and bound to positively charged amino acids Lys224/Arg228 conserved in MBLs. Preclinical testing revealed that the SHCs showed low toxicity in cell lines and mice and high stability in human liver microsomes. Our results indicate that SHCs are promising lead compounds for inhibitors of MBLs to combat MBL-producing CRE.
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23
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Gitto R, De Luca L, Mancuso F, Del Prete S, Vullo D, Supuran CT, Capasso C. Seeking new approach for therapeutic treatment of cholera disease via inhibition of bacterial carbonic anhydrases: experimental and theoretical studies for sixteen benzenesulfonamide derivatives. J Enzyme Inhib Med Chem 2019; 34:1186-1192. [PMID: 31282228 PMCID: PMC6691843 DOI: 10.1080/14756366.2019.1618292] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 01/22/2023] Open
Abstract
A series of sixteen benzenesulfonamide derivatives has been synthesised and tested as inhibitors of Vibrio cholerae carbonic anhydrase (CA) enzymes, belonging to α-CA, β-CA, and γ-CA classes (VchCAα, VchCAβ, and VchCAγ). The determined Ki values were compared to those of selected human CA isoforms (hCA I and hCA II). Structure-affinity relationship analysis highlighted that all tested compounds proved to be active inhibitors of VchCAα at nanomolar concentration. The VchCAβ activity was lower to respect inhibitory efficacy toward VchCAα, whereas, these benzenesulfonamide derivatives failed to inhibit VchCAγ. Interestingly, compound 7e combined the best activity toward VchCAα and VchCAβ. In order to obtain a model for binding mode of our inhibitors toward bacterial CAs, we carried out docking simulations by using the available crystal structures of VchCAβ.
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Affiliation(s)
- Rosaria Gitto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (CHIBIOFARAM), University of Messina, Messina, Italy
| | - Laura De Luca
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (CHIBIOFARAM), University of Messina, Messina, Italy
| | - Francesca Mancuso
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (CHIBIOFARAM), University of Messina, Messina, Italy
| | - Sonia Del Prete
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources- CNR, Napoli, Italy
| | - Daniela Vullo
- NUROFARBA Department, University of Florence, Sesto Fiorentino, Italy
| | | | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources- CNR, Napoli, Italy
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24
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Langella E, Alterio V, D’Ambrosio K, Cadoni R, Winum JY, Supuran CT, Monti SM, De Simone G, Di Fiore A. Exploring benzoxaborole derivatives as carbonic anhydrase inhibitors: a structural and computational analysis reveals their conformational variability as a tool to increase enzyme selectivity. J Enzyme Inhib Med Chem 2019; 34:1498-1505. [PMID: 31423863 PMCID: PMC6713116 DOI: 10.1080/14756366.2019.1653291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 12/22/2022] Open
Abstract
Recent studies identified the benzoxaborole moiety as a new zinc-binding group able to interact with carbonic anhydrase (CA) active site. Here, we report a structural analysis of benzoxaboroles containing urea/thiourea groups, showing that these molecules are very versatile since they can bind the enzyme assuming different binding conformations and coordination geometries of the catalytic zinc ion. In addition, theoretical calculations of binding free energy were performed highlighting the key role of specific residues for protein-inhibitor recognition. Overall, these data are very useful for the development of new inhibitors with higher selectivity and efficacy for various CAs.
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Affiliation(s)
- Emma Langella
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Vincenzo Alterio
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Katia D’Ambrosio
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Roberta Cadoni
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS, ENSCM, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier, Montpellier, France
- Dipartimento di Chimica e Farmacia, Università Degli Studi di Sassari, Sassari, Italy
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS, ENSCM, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier, Montpellier, France
| | - Claudiu T. Supuran
- Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università Degli Studi di Firenze, Florence, Italy
| | - Simona Maria Monti
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Giuseppina De Simone
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Naples, Italy
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25
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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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26
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Lisnyansky M, Yariv E, Segal O, Marom M, Loewenstein A, Ben-Tal N, Giladi M, Haitin Y. Metal Coordination Is Crucial for Geranylgeranyl Diphosphate Synthase–Bisphosphonate Interactions: A Crystallographic and Computational Analysis. Mol Pharmacol 2019; 96:580-588. [DOI: 10.1124/mol.119.117499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022] Open
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27
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Ielo L, Deri B, Germanò MP, Vittorio S, Mirabile S, Gitto R, Rapisarda A, Ronsisvalle S, Floris S, Pazy Y, Fais A, Fishman A, De Luca L. Exploiting the 1-(4-fluorobenzyl)piperazine fragment for the development of novel tyrosinase inhibitors as anti-melanogenic agents: Design, synthesis, structural insights and biological profile. Eur J Med Chem 2019; 178:380-389. [PMID: 31202126 DOI: 10.1016/j.ejmech.2019.06.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 12/22/2022]
Abstract
The development of Tyrosinase inhibitors (TYRIs) could represent an efficacious strategy for pharmacological intervention on skin pathologies related to aberrant production of melanin. Based on in silico studies we designed and tested a library of twenty-four compounds bearing the 4-(4-fluorobenzyl)piperazin-1-yl]-fragment. As result, we identified several compounds with excellent inhibit effects at low micromolar concentration against TYR from Agaricus bisporus (TyM). Among them, compound 25 (IC50 = 0.96 μM) proved to be ∼20-fold more potent than the reference compound kojic acid (IC50 = 17.76 μM) having wide applications in the cosmetics and pharmaceutical industries. The mode of interaction of active inhibitor 25 was deciphered by means of crystallography as well as molecular docking and these results were consistent with kinetic experiments. Moreover, the identified compound 25 exhibited no considerable cytotoxicity and showed anti-melanogenic effects on B16F10 melanoma cells. Therefore, a combination of computational and biochemical approaches could represent a rational guidelines for further structural modification of this class of compounds as future anti-melanogenic agents.
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Affiliation(s)
- Laura Ielo
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, Polo Universitario SS. Annunziata, University of Messina, Viale Palatucci 13, I-98168, Messina, Italy
| | - Batel Deri
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Maria Paola Germanò
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, Polo Universitario SS. Annunziata, University of Messina, Viale Palatucci 13, I-98168, Messina, Italy
| | - Serena Vittorio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, Polo Universitario SS. Annunziata, University of Messina, Viale Palatucci 13, I-98168, Messina, Italy
| | - Salvatore Mirabile
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, Polo Universitario SS. Annunziata, University of Messina, Viale Palatucci 13, I-98168, Messina, Italy
| | - Rosaria Gitto
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, Polo Universitario SS. Annunziata, University of Messina, Viale Palatucci 13, I-98168, Messina, Italy
| | - Antonio Rapisarda
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, Polo Universitario SS. Annunziata, University of Messina, Viale Palatucci 13, I-98168, Messina, Italy
| | - Simone Ronsisvalle
- Department of Drug Science, Medicinal Chemistry Section University of Catania, Catania, Italy
| | - Sonia Floris
- Department of Life and Environment Sciences, University of Cagliari, I-09042, Monserrato, Cagliari, Italy
| | - Yael Pazy
- Technion Center for Structural Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Antonella Fais
- Department of Life and Environment Sciences, University of Cagliari, I-09042, Monserrato, Cagliari, Italy
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Laura De Luca
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, Polo Universitario SS. Annunziata, University of Messina, Viale Palatucci 13, I-98168, Messina, Italy.
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28
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Buemi MR, Di Fiore A, De Luca L, Angeli A, Mancuso F, Ferro S, Monti SM, Buonanno M, Russo E, De Sarro G, De Simone G, Supuran CT, Gitto R. Exploring structural properties of potent human carbonic anhydrase inhibitors bearing a 4-(cycloalkylamino-1-carbonyl)benzenesulfonamide moiety. Eur J Med Chem 2019; 163:443-452. [PMID: 30530195 DOI: 10.1016/j.ejmech.2018.11.073] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/13/2018] [Accepted: 11/29/2018] [Indexed: 10/27/2022]
Abstract
Guided by the crystal structure of 4-(3,4-dihydroquinolin-1(2H)-ylcarbonyl)benzenesulfonamide 3 in complex with hCA II (PDB code 4Z0Q), a novel series of cycloalkylamino-1-carbonylbenzenesulfonamides was designed and synthesized. Thus, we replaced the quinoline ring with an azepine/piperidine/piperazine nucleus and introduced further modifications on cycloalkylamine nucleus by means the installation of hydrophobic/hydrophilic functionalities able to establish additional contacts in the middle area of the enzyme cavity. Among the synthesized compounds, the derivatives 7a, 7b, 8b exhibited a remarkable inhibition for hCA II and the brain-expressed hCA VII in subnanomolar range. The binding of these molecules to the target enzymes was characterized by means of a crystallographic analysis, providing a clear snapshot of the most important interactions established by this class of inhibitors into the hCA II and hCA VII catalytic site. Notably, our results showed that the benzylpiperazine tail of compound 8b is oriented both in hCA II and in hCA VII toward a poorly explored region of the active site. These features should be further investigated for the design of new isoform selective CA inhibitors.
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Affiliation(s)
- Maria Rosa Buemi
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci, Polo didattico SS, Annunziata, 98168, Messina, Italy
| | - Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Laura De Luca
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci, Polo didattico SS, Annunziata, 98168, Messina, Italy
| | - Andrea Angeli
- Dipartimento NEUROFARBA, Università di Firenze, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Francesca Mancuso
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci, Polo didattico SS, Annunziata, 98168, Messina, Italy
| | - Stefania Ferro
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci, Polo didattico SS, Annunziata, 98168, Messina, Italy
| | - Simona Maria Monti
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Martina Buonanno
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Emilio Russo
- Pharmacology Chair, Dept. of Science of Health School of Medicine, University of Catanzaro, Campus Universitario "Salvatore Venuta", Viale Europa - Loc. Germaneto, 88100, Catanzaro, Italy
| | - Giovanbattista De Sarro
- Pharmacology Chair, Dept. of Science of Health School of Medicine, University of Catanzaro, Campus Universitario "Salvatore Venuta", Viale Europa - Loc. Germaneto, 88100, Catanzaro, Italy
| | - Giuseppina De Simone
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Claudiu T Supuran
- Dipartimento NEUROFARBA, Università di Firenze, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Rosaria Gitto
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci, Polo didattico SS, Annunziata, 98168, Messina, Italy.
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29
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Identification of influenza PA-Nter endonuclease inhibitors using pharmacophore- and docking-based virtual screening. Bioorg Med Chem 2018; 26:4544-4550. [DOI: 10.1016/j.bmc.2018.07.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 01/15/2023]
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30
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31
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Angeli A, Tanini D, Capperucci A, Supuran CT. First evaluation of organotellurium derivatives as carbonic anhydrase I, II, IV, VII and IX inhibitors. Bioorg Chem 2018; 76:268-272. [DOI: 10.1016/j.bioorg.2017.12.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/29/2017] [Accepted: 12/03/2017] [Indexed: 11/25/2022]
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32
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Jayaram V, Sridhar T, Sharma GVM, Berrée F, Carboni B. Synthesis of Polysubstituted Isoquinolines and Related Fused Pyridines from Alkenyl Boronic Esters via a Copper-Catalyzed Azidation/Aza-Wittig Condensation Sequence. J Org Chem 2018; 83:843-853. [DOI: 10.1021/acs.joc.7b02831] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Vankudoth Jayaram
- Organic
and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500 007, India
| | - Tailor Sridhar
- Organic
and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500 007, India
| | - Gangavaram V. M. Sharma
- Organic
and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500 007, India
| | - Fabienne Berrée
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) - UMR 6226, F-35000 Rennes, France
| | - Bertrand Carboni
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) - UMR 6226, F-35000 Rennes, France
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33
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De Luca L, Mancuso F, Ferro S, Buemi MR, Angeli A, Del Prete S, Capasso C, Supuran CT, Gitto R. Inhibitory effects and structural insights for a novel series of coumarin-based compounds that selectively target human CA IX and CA XII carbonic anhydrases. Eur J Med Chem 2018; 143:276-282. [DOI: 10.1016/j.ejmech.2017.11.061] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/13/2017] [Accepted: 11/22/2017] [Indexed: 12/22/2022]
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34
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Alterio V, Esposito D, Monti SM, Supuran CT, De Simone G. Crystal structure of the human carbonic anhydrase II adduct with 1-(4-sulfamoylphenyl-ethyl)-2,4,6-triphenylpyridinium perchlorate, a membrane-impermeant, isoform selective inhibitor. J Enzyme Inhib Med Chem 2017; 33:151-157. [PMID: 29199489 PMCID: PMC7011996 DOI: 10.1080/14756366.2017.1405263] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pyridinium containing sulfonamides have been largely investigated as carbonic anhydrase inhibitors (CAIs), showing interesting selectivity features. Nevertheless, only few structural studies are so far available on adducts that these compounds form with diverse CA isoforms. In this paper, we report the structural characterization of the adduct that a triphenylpyridinium derivative forms with hCA II, showing that the substitution of the pyridinium ring plays a key role in determining the conformation of the inhibitor in the active site and consequently the binding affinity to the enzyme. These findings open new perspectives on the basic structural requirements for designing sulfonamide CAIs with a selective inhibition profile.
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Affiliation(s)
| | - Davide Esposito
- a Istituto di Biostrutture e Bioimagini-CNR , Naples , Italy
| | | | - Claudiu T Supuran
- b Neurofarba Department, Section of Pharmaceutical and Nutraceutical Sciences , Università degli Studi di Firenze , Sesto Fiorentino, Florence , Italy
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35
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Angeli A, Tanini D, Capperucci A, Supuran CT. Synthesis of Novel Selenides Bearing Benzenesulfonamide Moieties as Carbonic Anhydrase I, II, IV, VII, and IX Inhibitors. ACS Med Chem Lett 2017; 8:1213-1217. [PMID: 29259736 DOI: 10.1021/acsmedchemlett.7b00387] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 11/07/2017] [Indexed: 12/11/2022] Open
Abstract
A series of novel selenides bearing benzenesulfonamide moieties was synthesized and investigated for the inhibition of five human (h) isoforms of zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1), hCA I, II, IV, VII, and IX. These enzymes are involved in a variety of diseases, including glaucoma, retinitis pigmentosa, epilepsy, arthritis, and tumors. The investigated compounds showed potent inhibitory action against hCA II, VII, and IX, in the low nanomolar range, thus making them of interest for the development of isoform-selective inhibitors and as candidates for biomedical applications.
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Affiliation(s)
- Andrea Angeli
- Department of University of Florence, NEUROFARBA Dept.,
Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Damiano Tanini
- Department of University of Florence, Department of
Chemistry “Ugo Schiff″, Via della Lastruccia 13, I-50019 Sesto Fiorentino, Italy
| | - Antonella Capperucci
- Department of University of Florence, Department of
Chemistry “Ugo Schiff″, Via della Lastruccia 13, I-50019 Sesto Fiorentino, Italy
| | - Claudiu T. Supuran
- Department of University of Florence, NEUROFARBA Dept.,
Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy
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36
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Kalinin S, Kopylov S, Tuccinardi T, Sapegin A, Dar’in D, Angeli A, Supuran CT, Krasavin M. Lucky Switcheroo: Dramatic Potency and Selectivity Improvement of Imidazoline Inhibitors of Human Carbonic Anhydrase VII. ACS Med Chem Lett 2017; 8:1105-1109. [PMID: 29057059 DOI: 10.1021/acsmedchemlett.7b00300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/15/2017] [Indexed: 02/07/2023] Open
Abstract
A substantial improvement of potency and selectivity of imidazoline-based inhibitors of hCA VII (a promising target for the treatment of seizures and neuropathic pain) was achieved by simply switching the position of the benzenesulfonamide moiety from N1 (as in the earlier reported series) to C2. Selectivity indices vs the off-target isoforms (hCA I, I, I and IV) greater than 100 were reached, which is exceedingly rare for hCA VII inhibitors. The drastic profile improvement of the new series has been rationalized by an additional hydrogen bonding with the nonconserved Q69 residue in the active site of hCA VII (absent in the other three isoforms studied), which also results in a favorable accommodation of the inhibitor's lipophilic periphery in the nearby hydrophobic pocket. The robustness of the docking simulations was tested and confirmed by molecular dynamics simulations.
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Affiliation(s)
- Stanislav Kalinin
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Stanislav Kopylov
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Alexander Sapegin
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Dmitry Dar’in
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Andrea Angeli
- Neurofarba
Department, Universita degli Studi di Firenze, 50121 Florence, Italy
| | - Claudiu T. Supuran
- Neurofarba
Department, Universita degli Studi di Firenze, 50121 Florence, Italy
| | - Mikhail Krasavin
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation
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37
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Improved molecular recognition of Carbonic Anhydrase IX by polypeptide conjugation to acetazolamide. Bioorg Med Chem 2017; 25:5838-5848. [DOI: 10.1016/j.bmc.2017.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/10/2017] [Accepted: 09/13/2017] [Indexed: 02/04/2023]
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