1
|
Xiao-Qun Z, Xian-Li M, Ariffin NS. The potential of carbonic anhydrase enzymes as a novel target for anti-cancer treatment. Eur J Pharmacol 2024; 976:176677. [PMID: 38825301 DOI: 10.1016/j.ejphar.2024.176677] [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: 12/29/2023] [Revised: 05/15/2024] [Accepted: 05/27/2024] [Indexed: 06/04/2024]
Abstract
Carbonic anhydrase (CA) is a zinc-dependent metal enzyme that maintains the pH and carbon dioxide (CO2) homeostasis in cells by catalyzing the reversible hydration and dehydration of CO2 and bicarbonate (HCO3-). In mammals, there are 16 isozymes of CA existed, namely CAI to CAXIV, but only 15 isozymes are found in humans except CAXV. Human CAs have highly conserved catalytic domains, all of which are distributed in different tissues and play important physiological roles. Changes in their functions may disrupt the typical distribution of CAs throughout human body and therefore CAs can be used as diagnostic biomarkers for many diseases. Furthermore, the expression of CAs is correlated to the progression of numerous tumors, therapeutic sensitivity and patient prognosis. In this review, we discuss thoroughly the structure of CAs, their functional activities in human physiology, dysregulations and diseases related to CAs, and different types of CA inhibitors that can reverse their dysregulation.
Collapse
Affiliation(s)
- Zhou Xiao-Qun
- Department of Pharmacology and Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Teknologi MARA, 42300, Bandar Puncak Alam, Selangor, Malaysia; Guilin Medical University, GuiLin, China
| | | | - Nur Syamimi Ariffin
- Department of Pharmacology and Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Teknologi MARA, 42300, Bandar Puncak Alam, Selangor, Malaysia.
| |
Collapse
|
2
|
Bua S, Bonardi A, Mük GR, Nocentini A, Gratteri P, Supuran CT. Benzothiadiazinone-1,1-Dioxide Carbonic Anhydrase Inhibitors Suppress the Growth of Drug-Resistant Mycobacterium tuberculosis Strains. Int J Mol Sci 2024; 25:2584. [PMID: 38473830 DOI: 10.3390/ijms25052584] [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: 01/12/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
2H-Benzo[e][1,2,4]thiadiazin-3(4H)-one 1,1-dioxide (BTD) based carbonic anhydrase (CA) inhibitors are here explored as new anti-mycobacterial agents. The chemical features of BTD derivatives meet the criteria for a potent inhibition of β-class CA isozymes. BTD derivatives show chemical features meeting the criteria for a potent inhibition of β-class CA isozymes. Specifically, three β-CAs (MtCA1, MtCA2, and MtCA3) were identified in Mycobacterium tuberculosis and their inhibition was shown to exert an antitubercular action. BTDs derivatives 2a-q effectively inhibited the mycobacterial CAs, especially MtCA2 and MtCA3, with Ki values up to a low nanomolar range (MtCA3, Ki = 15.1-2250 nM; MtCA2, Ki = 38.1-4480 nM) and with a significant selectivity ratio over the off-target human CAs I and II. A computational study was conducted to elucidate the compound structure-activity relationship. Importantly, the most potent MtCA inhibitors demonstrated efficacy in inhibiting the growth of M. tuberculosis strains resistant to both rifampicin and isoniazid-standard reference drugs for Tuberculosis treatment.
Collapse
Affiliation(s)
- Silvia Bua
- Research Institute of the University of Bucharest (ICUB), University of Bucharest, 050095 Bucharest, Romania
| | - Alessandro Bonardi
- Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSA, Neurofarba Department, University of Florence, Via U. Schiff 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Georgiana Ramona Mük
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, 050095 Bucharest, Romania
- St. Stephen's Pneumoftiziology Hospital, Șoseaua Ștefan cel Mare 11, 020122 Bucharest, Romania
| | - Alessio Nocentini
- Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSA, Neurofarba Department, University of Florence, Via U. Schiff 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Paola Gratteri
- Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSA, Neurofarba Department, University of Florence, Via U. Schiff 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Claudiu T Supuran
- Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSA, Neurofarba Department, University of Florence, Via U. Schiff 6, Sesto Fiorentino, 50019 Florence, Italy
| |
Collapse
|
3
|
Al-Matarneh CM, Pinteala M, Nicolescu A, Silion M, Mocci F, Puf R, Angeli A, Ferraroni M, Supuran CT, Zara S, Carradori S, Paoletti N, Bonardi A, Gratteri P. Synthetic Approaches to Novel Human Carbonic Anhydrase Isoform Inhibitors Based on Pyrrol-2-one Moiety. J Med Chem 2024; 67:3018-3038. [PMID: 38301036 PMCID: PMC10895679 DOI: 10.1021/acs.jmedchem.3c02190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Abstract
New dihydro-pyrrol-2-one compounds, featuring dual sulfonamide groups, were synthesized through a one-pot, three-component approach utilizing trifluoroacetic acid as a catalyst. Computational analysis using density functional theory (DFT) and condensed Fukui function explored the structure-reactivity relationship. Evaluation against human carbonic anhydrase isoforms (hCA I, II, IX, XII) revealed potent inhibition. The widely expressed cytosolic hCA I was inhibited across a range of concentrations (KI 3.9-870.9 nM). hCA II, also cytosolic, exhibited good inhibition as well. Notably, all compounds effectively inhibited tumor-associated hCA IX (KI 1.9-211.2 nM) and hCA XII (low nanomolar). Biological assessments on MCF7 cancer cells highlighted the compounds' ability, in conjunction with doxorubicin, to significantly impact tumor cell viability. These findings underscore the potential therapeutic relevance of the synthesized compounds in cancer treatment.
Collapse
Affiliation(s)
- Cristina M. Al-Matarneh
- Center
of Advanced Research in Bionanoconjugates and Biopolymers, “Petru Poni” Institute of Macromolecular
Chemistry of Romanian Academy, 41A Grigore Ghica Voda Alley, Iasi 700487, Romania
- Research
Institute of the University of Bucharest-ICUB, 90 Sos. Panduri, 050663 Bucharest, Romania
| | - Mariana Pinteala
- Center
of Advanced Research in Bionanoconjugates and Biopolymers, “Petru Poni” Institute of Macromolecular
Chemistry of Romanian Academy, 41A Grigore Ghica Voda Alley, Iasi 700487, Romania
| | - Alina Nicolescu
- NMR
Laboratory ”Petru Poni” Institute of Macromolecular
Chemistry of Romanian Academy, 41A Grigore Ghica Voda Alley, Iasi 700487, Romania
| | - Mihaela Silion
- Physics
of Polymers and Polymeric Materials Department, “Petru Poni” Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania
| | - Francesca Mocci
- Department
of Chemical and Geological Sciences, University
of Cagliari, 09124 Cagliari, Italy
| | - Razvan Puf
- Center
of Advanced Research in Bionanoconjugates and Biopolymers, “Petru Poni” Institute of Macromolecular
Chemistry of Romanian Academy, 41A Grigore Ghica Voda Alley, Iasi 700487, Romania
| | - Andrea Angeli
- Sezione di
Scienze Farmaceutiche, NeuroFarba Department, Universita degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Marta Ferraroni
- Dipartimento
di Chimica “Ugo Schiff”, University
of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence Italy
| | - Claudiu T. Supuran
- Sezione di
Scienze Farmaceutiche, NeuroFarba Department, Universita degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Susi Zara
- Department
of Pharmacy, “G. d’Annunzio”
University of Chieti-Pescara, via dei Vestini 31, 66100 Chieti, Italy
| | - Simone Carradori
- Department
of Pharmacy, “G. d’Annunzio”
University of Chieti-Pescara, via dei Vestini 31, 66100 Chieti, Italy
| | - Niccolò Paoletti
- Department
of Chemical and Geological Sciences, University
of Cagliari, 09124 Cagliari, Italy
- Sezione di
Scienze Farmaceutiche, NeuroFarba Department, Universita degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Alessandro Bonardi
- Sezione di
Scienze Farmaceutiche, NeuroFarba Department, Universita degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
- NEUROFARBA
Department, Pharmaceutical and Nutraceutical Section, Laboratory of
Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, 50019 Sesto Fiorentino, Firenze Italy
| | - Paola Gratteri
- NEUROFARBA
Department, Pharmaceutical and Nutraceutical Section, Laboratory of
Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, 50019 Sesto Fiorentino, Firenze Italy
| |
Collapse
|
4
|
Rodríguez-Salazar CA, van Tol S, Mailhot O, Gonzalez-Orozco M, Galdino GT, Warren AN, Teruel N, Behera P, Afreen KS, Zhang L, Juelich TL, Smith JK, Zylber MI, Freiberg AN, Najmanovich RJ, Giraldo MI, Rajsbaum R. Ebola virus VP35 interacts non-covalently with ubiquitin chains to promote viral replication. PLoS Biol 2024; 22:e3002544. [PMID: 38422166 PMCID: PMC10942258 DOI: 10.1371/journal.pbio.3002544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/15/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Ebolavirus (EBOV) belongs to a family of highly pathogenic viruses that cause severe hemorrhagic fever in humans. EBOV replication requires the activity of the viral polymerase complex, which includes the cofactor and Interferon antagonist VP35. We previously showed that the covalent ubiquitination of VP35 promotes virus replication by regulating interactions with the polymerase complex. In addition, VP35 can also interact non-covalently with ubiquitin (Ub); however, the function of this interaction is unknown. Here, we report that VP35 interacts with free (unanchored) K63-linked polyUb chains. Ectopic expression of Isopeptidase T (USP5), which is known to degrade unanchored polyUb chains, reduced VP35 association with Ub and correlated with diminished polymerase activity in a minigenome assay. Using computational methods, we modeled the VP35-Ub non-covalent interacting complex, identified the VP35-Ub interacting surface, and tested mutations to validate the interface. Docking simulations identified chemical compounds that can block VP35-Ub interactions leading to reduced viral polymerase activity. Treatment with the compounds reduced replication of infectious EBOV in cells and in vivo in a mouse model. In conclusion, we identified a novel role of unanchored polyUb in regulating Ebola virus polymerase function and discovered compounds that have promising anti-Ebola virus activity.
Collapse
Affiliation(s)
- Carlos A. Rodríguez-Salazar
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander von Humboldt, Armenia, Colombia
| | - Sarah van Tol
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Olivier Mailhot
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Maria Gonzalez-Orozco
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Gabriel T. Galdino
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Abbey N. Warren
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
| | - Natalia Teruel
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Padmanava Behera
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
| | - Kazi Sabrina Afreen
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
| | - Lihong Zhang
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Terry L. Juelich
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jennifer K. Smith
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - María Inés Zylber
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Alexander N. Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Rafael J. Najmanovich
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Maria I. Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Ricardo Rajsbaum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
| |
Collapse
|
5
|
Ommi O, Paoletti N, Bonardi A, Gratteri P, Bhalerao HA, Sau S, Nanduri S, Mohammed A, Kalia NP, Sonti R, Supuran CT, Yaddanapudi VM. Exploration of 3-aryl pyrazole-tethered sulfamoyl carboxamides as carbonic anhydrase inhibitors. Arch Pharm (Weinheim) 2023; 356:e2300309. [PMID: 37691073 DOI: 10.1002/ardp.202300309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023]
Abstract
Herein, we report the design and synthesis of two series of pyrazole-tethered sulfamoyl phenyl acetamides and pyrazole-tethered sulfamoyl phenyl benzamides. The synthesized compounds were investigated for inhibiting two human carbonic anhydrases, human carbonic anhydrases (hCA) I and II, and those of the bacterial pathogen Mycobacterium tuberculosis, mtCA 1-3. The results indicate that, among the synthesized compounds, pyrazoles with 4-aminobenzene sulfonamide were more selective toward hCA I and II over mtCAs, and compounds with 3-aminobenzene sulfonamide were selective toward mtCA 1-3 over hCA I, II. Compound 6g showed significant and selective inhibition toward hCA I and II, with Ki values of 0.0366 and 0.0310 µM, respectively. Compound 5g exhibited the best inhibition toward mtCA 2, with a Ki value of 0.0617 µM. Among the benzamides, compound 9b exhibited significant activity toward mtCA 2, with a Ki value of 0.0696 µM. Selectivity of these compounds was further supported by docking studies. When tested for antitubercular activity, many compounds showed moderate to good inhibition against the Mtb H37Rv strain, with minimum inhibitory concentration (MIC) values in the range of 4-128 µg/mL.
Collapse
Affiliation(s)
- Ojaswitha Ommi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, India
| | - Niccolò Paoletti
- Department NEUROFARBA, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino (Florence), Italy
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Department NEUROFARBA, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino (Florence), Italy
| | - Alessandro Bonardi
- Department NEUROFARBA, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino (Florence), Italy
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Department NEUROFARBA, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino (Florence), Italy
| | - Paola Gratteri
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Department NEUROFARBA, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino (Florence), Italy
| | - Harshada Anil Bhalerao
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, India
| | - Shashikanta Sau
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, India
| | - Srinivas Nanduri
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, India
| | - Arifuddin Mohammed
- Department of Chemistry, Directorate of Distance Education, Maulana Azad National Urdu University, Hyderabad, India
| | - Nitin Pal Kalia
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, India
| | - Rajesh Sonti
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, India
| | - Claudiu T Supuran
- Department NEUROFARBA, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino (Florence), Italy
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Department NEUROFARBA, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino (Florence), Italy
| | - Venkata Madhavi Yaddanapudi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, India
| |
Collapse
|
6
|
Begines P, Bonardi A, Nocentini A, Gratteri P, Giovannuzzi S, Ronca R, Tavani C, Luisa Massardi M, López Ó, Supuran CT. Design and synthesis of sulfonamides incorporating a biotin moiety: Carbonic anhydrase inhibitory effects, antiproliferative activity and molecular modeling studies. Bioorg Med Chem 2023; 94:117467. [PMID: 37722299 DOI: 10.1016/j.bmc.2023.117467] [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: 07/23/2023] [Revised: 09/02/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023]
Abstract
Sulfonamides constitute an important class of classical carbonic anhydrase (CA, EC 4.2.1.1) inhibitors. Herein we have accomplished the conjugation of biotin with an ample number of sulfonamide motifs with the aim of testing them in vitro as inhibitors of the human carbonic anhydrase (hCA) isoforms I and II (cytosolic isozymes), as well as hCA IX and XII (transmembrane, tumor-associated enzymes). Most of these newly synthesized compounds exhibited interesting inhibition profiles, with activities in the nanomolar range. The presence of a 4-F-C6H4 moiety, also found in SLC-0111, afforded an excellent selectivity towards the tumor-associated hypoxia-induced hCA isoform XII with an inhibition constant (KI) of 4.5 nM. The 2-naphthyl derivative was the most potent inhibitor against hCA IX (KI = 6.2 nM), 4-fold stronger than AAZ (KI = 25 nM) with very good selectivity. Some compounds were chosen for antiproliferative activity testing against a panel of 3 human tumor cell lines, one compound showing anti-proliferative activity on glioblastoma, triple-negative breast cancer, and pancreatic carcinoma cell lines.
Collapse
Affiliation(s)
- Paloma Begines
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Florence 50019, Italy; Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Apartado 1203, Seville E-41071, Spain
| | - Alessandro Bonardi
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Florence 50019, Italy; NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - Alessio Nocentini
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Florence 50019, Italy; NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - Paola Gratteri
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - Simone Giovannuzzi
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Florence 50019, Italy
| | - Roberto Ronca
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Camilla Tavani
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Maria Luisa Massardi
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Óscar López
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Apartado 1203, Seville E-41071, Spain.
| | - Claudiu T Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Florence 50019, Italy.
| |
Collapse
|
7
|
Sobati M, Abdoli M, Bonardi A, Gratteri P, Supuran CT, Žalubovskis R. Inhibition Profiles of Some Novel Sulfonamide-Incorporated α-Aminophosphonates on Human Carbonic Anhydrases. ACS Med Chem Lett 2023; 14:1067-1072. [PMID: 37583824 PMCID: PMC10424312 DOI: 10.1021/acsmedchemlett.3c00200] [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: 05/11/2023] [Accepted: 07/28/2023] [Indexed: 08/17/2023] Open
Abstract
A series of hitherto unknown sulfonamide-incorporated α-aminophosphonate derivatives were synthesized through the one-pot, two-step FeCl3-catalyzed coupling of 4-aminobenzenesulfonamide with the appropriate benzaldehydes and diethyl phosphite. The new sulfonamides inhibition studies were performed on four carbonic anhydrase isoforms, i.e., the cytosolic human (h) hCA I and II (off-targets) as well as transmembrane cancer-related hCA IX and XII (targets). Among the synthesized compounds, derivative 23 resulted in the most selective compound against both cancer-associated isoforms over the off-target hCA I (hCA I/IX = 78; hCA I/XII = 458) and hCA II (hCA II/IX = 10; hCA II/XII = 56) and the binding mode of both enantiomers R and S was investigated in silico.
Collapse
Affiliation(s)
- Marjan Sobati
- Institute
of Technology of Organic Chemistry, Faculty of Materials Science and
Applied Chemistry, Riga Technical University, Riga 1048, Latvia
| | - Morteza Abdoli
- Institute
of Technology of Organic Chemistry, Faculty of Materials Science and
Applied Chemistry, Riga Technical University, Riga 1048, Latvia
| | - Alessandro Bonardi
- Department
of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences,
Laboratory of Molecular Modeling, Cheminformatics & QSAR, Università degli Studi di Firenze, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, Università degli Studi di Firenze, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Paola Gratteri
- Department
of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences,
Laboratory of Molecular Modeling, Cheminformatics & QSAR, Università degli Studi di Firenze, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T. Supuran
- Department
of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, Università degli Studi di Firenze, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Raivis Žalubovskis
- Institute
of Technology of Organic Chemistry, Faculty of Materials Science and
Applied Chemistry, Riga Technical University, Riga 1048, Latvia
- Latvian
Institute of Organic Synthesis, Riga 1006, Latvia
| |
Collapse
|
8
|
Rodríguez-Salazar CA, van Tol S, Mailhot O, Galdino G, Teruel N, Zhang L, Warren AN, González-Orozco M, Freiberg AN, Najmanovich RJ, Giraldo MI, Rajsbaum R. Ebola Virus VP35 Interacts Non-Covalently with Ubiquitin Chains to Promote Viral Replication Creating New Therapeutic Opportunities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549057. [PMID: 37503276 PMCID: PMC10369991 DOI: 10.1101/2023.07.14.549057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Ebolavirus (EBOV) belongs to a family of highly pathogenic viruses that cause severe hemorrhagic fever in humans. EBOV replication requires the activity of the viral polymerase complex, which includes the co-factor and Interferon antagonist VP35. We previously showed that the covalent ubiquitination of VP35 promotes virus replication by regulating interactions with the polymerase complex. In addition, VP35 can also interact non-covalently with ubiquitin (Ub); however, the function of this interaction is unknown. Here, we report that VP35 interacts with free (unanchored) K63-linked polyUb chains. Ectopic expression of Isopeptidase T (USP5), which is known to degrade unanchored polyUb chains, reduced VP35 association with Ub and correlated with diminished polymerase activity in a minigenome assay. Using computational methods, we modeled the VP35-Ub non-covalent interacting complex, identified the VP35-Ub interacting surface and tested mutations to validate the interface. Docking simulations identified chemical compounds that can block VP35-Ub interactions leading to reduced viral polymerase activity that correlated with reduced replication of infectious EBOV. In conclusion, we identified a novel role of unanchored polyUb in regulating Ebola virus polymerase function and discovered compounds that have promising anti-Ebola virus activity.
Collapse
Affiliation(s)
- Carlos A. Rodríguez-Salazar
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander von Humboldt, Armenia 630003, Colombia
| | - Sarah van Tol
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Olivier Mailhot
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Gabriel Galdino
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Natalia Teruel
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Lihong Zhang
- Department of Pathology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Abbey N. Warren
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey 07103
| | - María González-Orozco
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Alexander N. Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Rafael J. Najmanovich
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - María I. Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Ricardo Rajsbaum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey 07103
| |
Collapse
|
9
|
Peerzada M, Vullo D, Paoletti N, Bonardi A, Gratteri P, Supuran CT, Azam A. Discovery of Novel Hydroxyimine-Tethered Benzenesulfonamides as Potential Human Carbonic Anhydrase IX/XII Inhibitors. ACS Med Chem Lett 2023; 14:810-819. [PMID: 37312840 PMCID: PMC10258898 DOI: 10.1021/acsmedchemlett.3c00094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/04/2023] [Indexed: 06/15/2023] Open
Abstract
To discover novel carbonic anhydrase (CA, EC 4.2.1.1) inhibitors for cancer treatment, a series of 4-{4-[(hydroxyimino)methyl]piperazin-1-yl}benzenesulfonamides were designed and synthesized using SLC-0111 as the lead molecule. The developed novel compounds 27-34 were investigated for the inhibition of human (h) isoforms hCA I, hCA II, hCA IX, and hCA XII. The hCA I was inhibited by compound 29 with a Ki value of 3.0 nM, whereas hCA II was inhibited by compound 32 with a Ki value of 4.4 nM. The tumor-associated hCA IX isoform was inhibited by compound 30 effectively with an Ki value of 43 nM, whereas the activity of another cancer-related isoform, hCA XII, was significantly inhibited by 29 and 31 with a Ki value of 5 nM. Molecular modeling showed that drug molecule 30 participates in significant hydrophobic and hydrogen bond interactions with the active site of the investigated hCAs and binds to zinc through the deprotonated sulfonamide group.
Collapse
Affiliation(s)
- Mudasir
Nabi Peerzada
- Medicinal
Chemistry and Drug Discovery Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India
| | - Daniela Vullo
- 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, Florence, Italy
| | - Niccolò Paoletti
- 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, Florence, Italy
| | - Alessandro Bonardi
- 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, Florence, Italy
| | - Paola Gratteri
- 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, Florence, Italy
| | - Claudiu T. Supuran
- 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, Florence, Italy
| | - Amir Azam
- Medicinal
Chemistry and Drug Discovery Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India
| |
Collapse
|
10
|
Abdoli M, Bonardi A, Paoletti N, Aspatwar A, Parkkila S, Gratteri P, Supuran CT, Žalubovskis R. Inhibition Studies on Human and Mycobacterial Carbonic Anhydrases with N-((4-Sulfamoylphenyl)carbamothioyl) Amides. Molecules 2023; 28:molecules28104020. [PMID: 37241761 DOI: 10.3390/molecules28104020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/25/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
A library of structurally diverse N-((4-sulfamoylphenyl)carbamothioyl) amides was synthesized by selective acylation of easily accessible 4-thioureidobenzenesulfonamide with various aliphatic, benzylic, vinylic and aromatic acyl chlorides under mild conditions. Inhibition of three α-class cytosolic human (h) carbonic anhydrases (CAs) (EC 4.2.1.1); that is, hCA I, hCA II and hCA VII and three bacterial β-CAs from Mycobacterium tuberculosis (MtCA1-MtCA3) with these sulfonamides was thereafter investigated in vitro and in silico. Many of the evaluated compounds displayed better inhibition against hCA I (KI = 13.3-87.6 nM), hCA II (KI = 5.3-384.3 nM), and hCA VII (KI = 1.1-13.5 nM) compared with acetazolamide (AAZ) as the control drug (KI values of 250, 12.5 and 2.5 nM, respectively, against hCA I, hCA II and hCA VII). The mycobacterial enzymes MtCA1 and MtCA2 were also effectively inhibited by these compounds. MtCA3 was, on the other hand, poorly inhibited by the sulfonamides reported here. The most sensitive mycobacterial enzyme to these inhibitors was MtCA2 in which 10 of the 12 evaluated compounds showed KIs (KI, the inhibitor constant) in the low nanomolar range.
Collapse
Affiliation(s)
- Morteza Abdoli
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, LV-1048 Riga, Latvia
| | - Alessandro Bonardi
- Neurofarba Department, Universitàdegli Studi di Firenze, 50019 Florence, Italy
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Neurofarba Department, Università degli Studi di Firenze, 50019 Florence, Italy
| | - Niccolò Paoletti
- Neurofarba Department, Universitàdegli Studi di Firenze, 50019 Florence, Italy
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Neurofarba Department, Università degli Studi di Firenze, 50019 Florence, Italy
| | - Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Fimlab Ltd., Tampere University Hospital, 33520 Tampere, Finland
| | - Paola Gratteri
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Neurofarba Department, Università degli Studi di Firenze, 50019 Florence, Italy
| | - Claudiu T Supuran
- Neurofarba Department, Universitàdegli Studi di Firenze, 50019 Florence, Italy
| | - Raivis Žalubovskis
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, LV-1048 Riga, Latvia
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| |
Collapse
|
11
|
Bukhdruker S, Varaksa T, Orekhov P, Grabovec I, Marin E, Kapranov I, Kovalev K, Astashkin R, Kaluzhskiy L, Ivanov A, Mishin A, Rogachev A, Gordeliy V, Gilep A, Strushkevich N, Borshchevskiy V. Structural insights into the effects of glycerol on ligand binding to cytochrome P450. Acta Crystallogr D Struct Biol 2023; 79:66-77. [PMID: 36601808 DOI: 10.1107/s2059798322011019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/16/2022] [Indexed: 01/06/2023] Open
Abstract
New antitubercular drugs are vital due to the spread of resistant strains. Carbethoxyhexyl imidazole (CHImi) inhibits cytochrome P450 CYP124, which is a steroid-metabolizing enzyme that is important for the survival of Mycobacterium tuberculosis in macrophages. The available crystal structure of the CYP124-CHImi complex reveals two glycerol molecules in the active site. A 1.15 Å resolution crystal structure of the glycerol-free CYP124-CHimi complex reported here shows multiple conformations of CHImi and the CYP124 active site which were previously restricted by glycerol. Complementary molecular dynamics simulations show coherence of the ligand and enzyme conformations. Spectrophotometric titration confirmed the influence of glycerol on CHImi binding: the affinity decreases more than tenfold in glycerol-containing buffer. In addition, it also showed that glycerol has a similar effect on other azole and triazole CYP124 ligands. Together, these data show that glycerol may compromise structural-functional studies and impede rational drug-design campaigns.
Collapse
Affiliation(s)
- Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Tatsiana Varaksa
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk 220084, Belarus
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Irina Grabovec
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk 220084, Belarus
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Ivan Kapranov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Kirill Kovalev
- EMBL Outstation Hamburg, c/o DESY, 22607 Hamburg, Germany
| | - Roman Astashkin
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
| | - Leonid Kaluzhskiy
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow 119121, Russian Federation
| | - Alexis Ivanov
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow 119121, Russian Federation
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Andrey Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Valentin Gordeliy
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
| | - Andrei Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk 220084, Belarus
| | | | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| |
Collapse
|
12
|
A family of amphiphilic dioxidovanadium(V) hydrazone complexes as potent carbonic anhydrase inhibitors along with anti-diabetic and cytotoxic activities. Biometals 2022; 35:499-517. [PMID: 35355153 DOI: 10.1007/s10534-022-00384-7] [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: 07/05/2021] [Accepted: 03/07/2022] [Indexed: 12/24/2022]
Abstract
A family of dioxidovanadium(V) complexes (1-4) of the type [Na(H2O)x]+[VVO2(HL1-4)]- (x = 4, 4.5 and 7) where HL2- represents the dianionic form of 2-hydroxybenzoylhydrazone of 2-hydroxyacetophenone (H2L1, complex 1), 2-hydroxy-5-methylacetophenone (H2L2, complex 2), 2-hydroxy-5-methoxyacetophenone (H2L3, complex 3) and 2-hydroxy-5-chloroacetophenone (H2L4, complex 4), have been synthesized and characterized by analytical and spectral methods. These complexes exhibited the potential abilities to suppress the erythrocytes carbonic anhydrase enzymatic activity in type 1 and type 2 diabetic patients (in vitro), promising antidiabetic activity against T2 diabetic mice (in vivo). They also exhibited significant cytotoxic activity against cervical cancer (SiHa) cells (in vitro) as the IC50 value of complexes 1, 2 and 4 is substantially lower than the value found for cisplatin while that of 3 is comparable and follow the order: 4 < 1 < 2 < 3 and can kill the cells by apoptosis via the generation of reactive oxygen species (ROS). The complexes are soluble both in water and octanol media and also non-toxic at working concentrations. The antidiabetic activity of these four complexes follows the order: 4 > 2 > 1 > 3 while both the carbonic anhydrase and cytotoxic activity follow the order: 4 > 1 > 2 > 3 suggesting that complex 4, containing electron withdrawing Cl atom is the most reactive while 3 with electron donating OCH3 group is the least reactive species. The molecular docking study on hCA-I and hCA-II demonstrates that complexes interact via hydrogen bonding as well as different types of π-stacking.
Collapse
|
13
|
Eldeeb AH, Abo-Ashour MF, Angeli A, Bonardi A, Lasheen DS, Elrazaz EZ, Nocentini A, Gratteri P, Abdel-Aziz HA, Supuran CT. Novel benzenesulfonamides aryl and arylsulfone conjugates adopting tail/dual tail approaches: Synthesis, carbonic anhydrase inhibitory activity and molecular modeling studies. Eur J Med Chem 2021; 221:113486. [PMID: 33965860 DOI: 10.1016/j.ejmech.2021.113486] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
New series of benzenesulfonamide and benzoic acid derivatives were designed and synthesized using tail/dual tail approach to improve potency and selectivity as carbonic anhydrase inhibitors. The synthesized compounds evaluated as CAIs against isoforms hCA I, II, IV and IX with acetazolamide (AAZ) as standard inhibitor. The benzenesulfonamide derivatives 7a-d, 8a-h, 12a-c, 13a and 15a-c showed moderate to potent inhibitory activity with selectivity toward isoform hCA II, especially, compound 13a with (Ki = 7.6 nM), while the benzoic acid analogues 12d-f, 13b and 15d-f didn't show any activity except compounds 12d,f and 15e that showed weak activity. Additionally, molecular docking was performed for compounds 7a, 8a, 8e, 12a, 13a and 15a on isoform hCA I, II to illustrate the possible interaction with the active site to justify the inhibitory activity.
Collapse
Affiliation(s)
- Assem H Eldeeb
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, 11829, Egypt
| | - Mahmoud F Abo-Ashour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, 11829, Egypt.
| | - 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
| | - 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
| | - Deena S Lasheen
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, P.O. Box 11566, Abbassia, Cairo, Egypt
| | - Eman Z Elrazaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, P.O. Box 11566, Abbassia, Cairo, Egypt
| | - 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
| | - Paola Gratteri
- 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
| | - Hatem A Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Center, Dokki, Cairo, 12622, Egypt
| | - 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.
| |
Collapse
|
14
|
Liu H, Westley J, Thayumanavan S. Excimer-monomer fluorescence changes by supramolecular disassembly for protein sensing and quantification. Chem Commun (Camb) 2021; 57:9776-9779. [PMID: 34486631 PMCID: PMC8761362 DOI: 10.1039/d1cc03944j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A protein binding-induced supramolecular dissociation strategy is developed with the ratio of monomer and excimer fluorescence as the tool for protein sensing and quantification. Due to the "lock-and-key" strategy based on specific ligand-protein binding, the probe exhibits excellent selectivity and quantification accuracy to the protein of interest. The ratiometric approach is immune to interference from extrinsic quenchers, while preserving the opportunity to be protein specific.
Collapse
Affiliation(s)
- Hongxu Liu
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003, USA.
| | - Jenna Westley
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003, USA.
| | - S Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003, USA.
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts, 01003, USA
- Center for Bioactive Delivery, The Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, 01003, USA
| |
Collapse
|
15
|
Askin S, Tahtaci H, Türkeş C, Demir Y, Ece A, Akalın Çiftçi G, Beydemir Ş. Design, synthesis, characterization, in vitro and in silico evaluation of novel imidazo[2,1-b][1,3,4]thiadiazoles as highly potent acetylcholinesterase and non-classical carbonic anhydrase inhibitors. Bioorg Chem 2021; 113:105009. [PMID: 34052739 DOI: 10.1016/j.bioorg.2021.105009] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/06/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022]
Abstract
Imidazole and thiadiazole derivatives display an extensive application in pharmaceutical chemistry, and they have been investigated as bioactive molecules for medicinal chemistry purposes. Classical carbonic anhydrase (CA) inhibitors are based on sulfonamide groups, but inhibiting all CA isoforms nonspecifically, thereby causing undesired side effects, is the main drawback of these types of inhibitors. Here we reported an investigation of novel 2,6-disubstituted imidazo[2,1-b][1,3,4]thiadiazole derivatives (9a-k, 10a, and 11a) and 2,5,6-trisubstituted imidazo[2,1-b][1,3,4]thiadiazole derivatives (12a-20a) that do not possess the zinc-binding sulfonamide group for the inhibition of human carbonic anhydrase (hCA, EC 4.2.1.1) I and II isoforms and also of acetylcholinesterase (AChE, EC 3.1.1.7). Imidazo[2,1-b][1,3,4]thiadiazoles demonstrated low nanomolar inhibitory activity against hCA I, hCA II, and AChE (KIs are in the range of 23.44-105.50 nM, 10.32-104.70 nM, and 20.52-54.06 nM, respectively). Besides, compound 9b inhibit hCA I up to 18-fold compared to acetazolamide, while compound 10a has a 5-fold selectivity towards hCA II. The synthesized compounds were also evaluated for their cytotoxic effects on the L929 mouse fibroblast cell line. Molecular docking simulations were performed to elucidate these inhibitors' potential binding modes against hCA I and II isoforms and AChE. The novel compounds reported here can represent interesting lead compounds, and the results presented here might provide further structural guidance to discover and design more potent hCA and AChE inhibitors.
Collapse
Affiliation(s)
- Sercan Askin
- Department of Chemistry, Faculty of Science, Karabük University, Karabük 78050, Turkey
| | - Hakan Tahtaci
- Department of Chemistry, Faculty of Science, Karabük University, Karabük 78050, Turkey.
| | - Cüneyt Türkeş
- Department of Biochemistry, Faculty of Pharmacy, Erzincan Binali Yıldırım University, Erzincan 24100, Turkey.
| | - Yeliz Demir
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, Ardahan 75700, Turkey
| | - Abdulilah Ece
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, Istanbul 34010, Turkey.
| | - Gülşen Akalın Çiftçi
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, Eskişehir 26470, Turkey
| | - Şükrü Beydemir
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, Eskişehir 26470, Turkey; The Rectorate of Bilecik Şeyh Edebali University, Bilecik 11230, Turkey
| |
Collapse
|
16
|
Tewari N, Joshi HC, Rautela R, Pant S. Photophysical study of dansylamide in polymeric micro-environment. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
17
|
Bonardi A, Nocentini A, Bua S, Combs J, Lomelino C, Andring J, Lucarini L, Sgambellone S, Masini E, McKenna R, Gratteri P, Supuran CT. Sulfonamide Inhibitors of Human Carbonic Anhydrases Designed through a Three-Tails Approach: Improving Ligand/Isoform Matching and Selectivity of Action. J Med Chem 2020; 63:7422-7444. [PMID: 32519851 PMCID: PMC8008423 DOI: 10.1021/acs.jmedchem.0c00733] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
The “tail
approach” has become a milestone in human
carbonic anhydrase inhibitor (hCAI) design for various therapeutics,
including antiglaucoma agents. Besides the classical hydrophobic/hydrophilic
division of hCAs active site, several subpockets have been identified
at the middle/outer active sites rim, which could be targeted to increase
the CAI isoform selectivity. This postulate is explored here by three-tailed
benzenesulfonamide CAIs (TTI) to fully exploit such amino
acid differences among hCAs. In this proof-of-concept study, an extensive
structure–activity relationship (SAR) study was carried out
with 32 such benzenesulfonamides differing in tails combination that
were assayed for hCAs I, II, IV, and XII inhibition. A structural
study was undertaken by X-ray crystallography and in silico tools to assess the ligand/target interaction mode. The most active
and selective inhibitors against isoforms implicated in glaucoma were
assessed in a rabbit model of the disease achieving an intraocular
pressure-lowering action comparable to the clinically used dorzolamide.
Collapse
Affiliation(s)
- Alessandro Bonardi
- Department NEUROFARBA - Pharmaceutical and nutraceutical section, University of Firenze, via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence Italy.,Department NEUROFARBA - Pharmaceutical and nutraceutical section; Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Firenze, via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Alessio Nocentini
- Department NEUROFARBA - Pharmaceutical and nutraceutical section, University of Firenze, via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence Italy.,Department NEUROFARBA - Pharmaceutical and nutraceutical section; Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Firenze, via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Silvia Bua
- Department NEUROFARBA - Pharmaceutical and nutraceutical section, University of Firenze, via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence Italy
| | - Jacob Combs
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, Florida 32610, United States
| | - Carrie Lomelino
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, Florida 32610, United States
| | - Jacob Andring
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, Florida 32610, United States
| | - Laura Lucarini
- Department NEUROFARBA - Pharmaceutical and nutraceutical section, University of Firenze, viale Gaetano Pieraccini 6, 50139 Firenze, Florence, Italy
| | - Silvia Sgambellone
- Department NEUROFARBA - Pharmaceutical and nutraceutical section, University of Firenze, viale Gaetano Pieraccini 6, 50139 Firenze, Florence, Italy
| | - Emanuela Masini
- Department NEUROFARBA - Pharmaceutical and nutraceutical section, University of Firenze, viale Gaetano Pieraccini 6, 50139 Firenze, Florence, Italy
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, Florida 32610, United States
| | - Paola Gratteri
- Department NEUROFARBA - Pharmaceutical and nutraceutical section, University of Firenze, via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence Italy.,Department NEUROFARBA - Pharmaceutical and nutraceutical section; Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Firenze, via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T Supuran
- Department NEUROFARBA - Pharmaceutical and nutraceutical section, University of Firenze, via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence Italy
| |
Collapse
|
18
|
Suzuki S, Ikuta M, Yoshii T, Nakamura A, Kuwata K, Tsukiji S. Golgi recruitment assay for visualizing small-molecule ligand–target engagement in cells. Chem Commun (Camb) 2020; 56:7961-7964. [DOI: 10.1039/d0cc02020f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A Golgi recruitment (G-REC) assay is developed as a new method for visualizing small-molecule ligand–target engagement in living cells.
Collapse
Affiliation(s)
- Sachio Suzuki
- Department of Nanopharmaceutical Sciences
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Masahiro Ikuta
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- PRESTO, Japan Science and Technology Agency (JST)
| | - Akinobu Nakamura
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM)
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- Department of Life Science and Applied Chemistry
| |
Collapse
|
19
|
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.
Collapse
|
20
|
Vullo D, Durante M, Di Leva FS, Cosconati S, Masini E, Scozzafava A, Novellino E, Supuran CT, Carta F. Monothiocarbamates Strongly Inhibit Carbonic Anhydrases in Vitro and Possess Intraocular Pressure Lowering Activity in an Animal Model of Glaucoma. J Med Chem 2016; 59:5857-67. [PMID: 27253845 DOI: 10.1021/acs.jmedchem.6b00462] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A series of monothiocarbamates (MTCs) were prepared from primary/secondary amines and COS as potential carbonic anhydrase (CA, EC 4.2.1.1) inhibitors, using the dithiocarbamates, the xanthates, and the trithiocarbonates as lead compounds. The MTCs effectively inhibited the pharmacologically relevant human (h) hCAs isoforms I, II, IX, and XII in vitro and showed KIs spanning between the low and medium nanomolar range. By means of a computational study, the MTC moiety binding mode on the CAs was explained. Furthermore, a selection of MTCs were evaluated in a normotensive glaucoma rabbit model for their intraocular pressure (IOP) lowering effects and showed interesting activity.
Collapse
Affiliation(s)
- Daniela Vullo
- Polo Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze , Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Mariaconcetta Durante
- Dipartimento NEUROFARBA, Sezione di Farmacologia, Università degli Studi di Firenze , Viale Pieraccini 6, 50139 Florence, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II" , Via D. Montesano 49, 80131 Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, Seconda Università di Napoli , Via Vivaldi 43, 81100 Caserta, Italy
| | - Emanuela Masini
- Dipartimento NEUROFARBA, Sezione di Farmacologia, Università degli Studi di Firenze , Viale Pieraccini 6, 50139 Florence, Italy
| | - Andrea Scozzafava
- Polo Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze , Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II" , Via D. Montesano 49, 80131 Naples, Italy
| | - Claudiu T Supuran
- Polo Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze , Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.,Dipartimento NEUROFARBA, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze , Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Fabrizio Carta
- Polo Scientifico, Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze , Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| |
Collapse
|
21
|
Qin S, Ren Y, Fu X, Shen J, Chen X, Wang Q, Bi X, Liu W, Li L, Liang G, Yang C, Shui W. Multiple ligand detection and affinity measurement by ultrafiltration and mass spectrometry analysis applied to fragment mixture screening. Anal Chim Acta 2015; 886:98-106. [PMID: 26320641 DOI: 10.1016/j.aca.2015.06.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/20/2015] [Accepted: 06/04/2015] [Indexed: 12/11/2022]
Abstract
Binding affinity of a small molecule drug candidate to a therapeutically relevant biomolecular target is regarded the first determinant of the candidate's efficacy. Although the ultrafiltration-LC/MS (UF-LC/MS) assay enables efficient ligand discovery for a specific target from a mixed pool of compounds, most previous analysis allowed for relative affinity ranking of different ligands. Moreover, the reliability of affinity measurement for multiple ligands with UF-LC/MS has hardly been strictly evaluated. In this study, we examined the accuracy of K(d) determination through UF-LC/MS by comparison with classical ITC measurement. A single-point K(d) calculation method was found to be suitable for affinity measurement of multiple ligands bound to the same target when binding competition is minimized. A second workflow based on analysis of the unbound fraction of compounds was then developed, which simplified sample preparation as well as warranted reliable ligand discovery. The new workflow implemented in a fragment mixture screen afforded rapid and sensitive detection of low-affinity ligands selectively bound to the RNA polymerase NS5B of hepatitis C virus. More importantly, ligand identification and affinity measurement for mixture-based fragment screens by UF-LC/MS were in good accordance with single ligand evaluation by conventional SPR analysis. This new approach is expected to become a valuable addition to the arsenal of high-throughput screening techniques for fragment-based drug discovery.
Collapse
Affiliation(s)
- Shanshan Qin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Yiran Ren
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Xu Fu
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Jie Shen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xin Chen
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Quan Wang
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Xin Bi
- Institute of Elemento-organic Chemistry, Nankai University, Tianjin 300071, China
| | - Wenjing Liu
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Lixin Li
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Guangxin Liang
- Institute of Elemento-organic Chemistry, Nankai University, Tianjin 300071, China
| | - Cheng Yang
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Wenqing Shui
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| |
Collapse
|
22
|
Göksu S, Naderi A, Akbaba Y, Kalın P, Akıncıoğlu A, Gülçin İ, Durdagi S, Salmas RE. Carbonic anhydrase inhibitory properties of novel benzylsulfamides using molecular modeling and experimental studies. Bioorg Chem 2014; 56:75-82. [DOI: 10.1016/j.bioorg.2014.07.009] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/19/2014] [Accepted: 07/23/2014] [Indexed: 12/15/2022]
|
23
|
Griss R, Schena A, Reymond L, Patiny L, Werner D, Tinberg CE, Baker D, Johnsson K. Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring. Nat Chem Biol 2014; 10:598-603. [DOI: 10.1038/nchembio.1554] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 05/15/2014] [Indexed: 02/05/2023]
|
24
|
Ohkanda J. Module Assembly for Designing Multivalent Mid-Sized Inhibitors of Protein-Protein Interactions. CHEM REC 2013; 13:561-75. [DOI: 10.1002/tcr.201300026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Junko Ohkanda
- Institute for Chemical Research; Kyoto University; Gokasho, Uji Kyoto 611-0011 Japan
| |
Collapse
|
25
|
Lee YM, Wang YT, Duh Y, Yuan HS, Lim C. Identification of Labile Zn Sites in Drug-Target Proteins. J Am Chem Soc 2013; 135:14028-31. [DOI: 10.1021/ja406300c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | | | | | | | - Carmay Lim
- Department of
Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| |
Collapse
|
26
|
Sahu C, Sen K, Pakhira S, Mondal B, Das AK. Binding affinity of substituted ureido-benzenesulfonamide ligands to the carbonic anhydrase receptor: a theoretical study of enzyme inhibition. J Comput Chem 2013; 34:1907-16. [PMID: 23712937 DOI: 10.1002/jcc.23335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 04/25/2013] [Accepted: 04/26/2013] [Indexed: 01/23/2023]
Abstract
The binding properties of a series of benzenesulfonamide inhibitors (4-substituted-ureido-benzenesulfonamides, UBSAs) of human carbonic anhydrase II (hCA II) enzyme with active site residues have been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) model. To account for the important docking interactions between the UBSAs ligand and hCA II enzyme, a molecular docking program AutoDock Vina is used. The molecular docking results obtained by AutoDock Vina revealed that the docked conformer has root mean square deviation value less than 1.50 Å compared to X-ray crystal structures. The inhibitory activity of UBSA ligands against hCA II is found to be in good agreement with the experimental results. The thermodynamic parameters for inhibitor binding show that hydrogen bonding, hydrophilic, and hydrophobic interactions play a major role in explaining the diverse inhibitory range of these derivatives. Additionally, natural bond orbital analysis is performed to characterize the ligand-metal charge transfer stability. The insights gained from this study have great potential to design new hCA-II inhibitor, 4-[3-(1-p-Tolyl-4-trifluoromethyl-1H-pyrazol-3-yl)-ureido]-benzenesulfonamide, which belongs to the family of UBSA inhibitors and shows similar type of inhibitor potency with hCA II. This work also reveals that a QM/MM model and molecular docking method are computationally feasible and accurate for studying substrate-protein inhibition.
Collapse
Affiliation(s)
- Chandan Sahu
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India
| | | | | | | | | |
Collapse
|
27
|
Aggarwal M, Boone CD, Kondeti B, Tu C, Silverman DN, McKenna R. Effects of cryoprotectants on the structure and thermostability of the human carbonic anhydrase II-acetazolamide complex. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:860-5. [PMID: 23633596 PMCID: PMC3640473 DOI: 10.1107/s0907444913002771] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 01/28/2013] [Indexed: 11/10/2022]
Abstract
Protein X-ray crystallography has seen a progressive shift from data collection at cool/room temperature (277-298 K) to data collection at cryotemperature (100 K) because of its ease of crystal preparation and the lessening of the detrimental effects of radiation-induced crystal damage, with 20-25%(v/v) glycerol (GOL) being the preferred choice of cryoprotectant. Here, a case study of the effects of cryoprotectants on the kinetics of carbonic anhydrase II (CA II) and its inhibition by the clinically used inhibitor acetazolamide (AZM) is presented. Comparative studies of crystal structure, kinetics, inhibition and thermostability were performed on CA II and its complex with AZM in the presence of either GOL or sucrose. These results suggest that even though the cryoprotectant GOL was previously shown to be directly bound in the active site and to interact with AZM, it affects neither the thermostability of CA II nor the binding of AZM in the crystal structure or in solution. However, addition of GOL does affect the kinetics of CA II, presumably as it displaces the water proton-transfer network in the active site.
Collapse
Affiliation(s)
- Mayank Aggarwal
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
| | - Christopher D. Boone
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
| | - Bhargav Kondeti
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
| | - Chingkuang Tu
- Department of Pharmacology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
| | - David N. Silverman
- Department of Pharmacology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, FL 32610, USA
| |
Collapse
|
28
|
Inhibition pattern of sulfamide-related compounds in binding to carbonic anhydrase isoforms I, II, VII, XII and XIV. Bioorg Med Chem 2013; 21:1410-8. [DOI: 10.1016/j.bmc.2012.10.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/26/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
|
29
|
Marini AM, Maresca A, Aggarwal M, Orlandini E, Nencetti S, Da Settimo F, Salerno S, Simorini F, La Motta C, Taliani S, Nuti E, Scozzafava A, McKenna R, Rossello A, Supuran CT. Tricyclic sulfonamides incorporating benzothiopyrano[4,3-c]pyrazole and pyridothiopyrano[4,3-c]pyrazole effectively inhibit α- and β-carbonic anhydrase: X-ray crystallography and solution investigations on 15 isoforms. J Med Chem 2012; 55:9619-29. [PMID: 23067387 DOI: 10.1021/jm300878g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Carbonic anhydrases (CAs, EC 4.2.1.1) are ubiquitous isozymes involved in crucial physiological and pathological events, representing the targets of inhibitors with several therapeutic applications. In this connection, we report a new class of carbonic anhydrase inhibitors, based on the thiopyrano-fused pyrazole scaffold to which a pendant 4-sulfamoylphenyl moiety was attached. The new sulfonamides 3a-e were designed as constrained analogues of celecoxib and valdecoxib. The most interesting feature of sulfonamides 3 was their predominantly strong inhibition of human (h) CA I and II, as well as those of the mycobacterial β-class enzymes (Rv1284, Rv3273, and Rv3588c), whereas their inhibitory action against hCA III, IV, VA, VB, VI, VII, IX, XII, XIII, and XIV was found to be at least 2 orders of magnitude lower. X-ray crystallography and structural superposition studies made it possible to explain the very distinct inhibition profile of the tricyclic sulfonamides, different from those of celecoxib and valdecoxib.
Collapse
Affiliation(s)
- Anna M Marini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
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
| | | | | | | | | |
Collapse
|
31
|
Imtaiyaz Hassan M, Shajee B, Waheed A, Ahmad F, Sly WS. Structure, function and applications of carbonic anhydrase isozymes. Bioorg Med Chem 2012; 21:1570-82. [PMID: 22607884 DOI: 10.1016/j.bmc.2012.04.044] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/02/2012] [Accepted: 04/21/2012] [Indexed: 01/16/2023]
Abstract
The carbonic anhydrases enzymes (CAs, EC 4.2.1.1) are zinc containing metalloproteins, which efficiently catalyse the reversible conversion of carbon dioxide to bicarbonate and release proton. These enzymes are essentially important for biological system and play several important physiological and patho-physiological functions. There are 16 different alpha-carbonic anhydrase isoforms studied, differing widely in their cellular localization and biophysical properties. The catalytic domains of all CAs possess a conserved tertiary structure fold, with predominately β-strands. We performed an extensive analysis of all 16 mammalian CAs for its structure and function in order to establish a structure-function relationship. CAs have been a potential therapeutic target for many diseases. Sulfonamides are considered as a strong and specific inhibitor of CA, and are being used as diuretics, anti-glaucoma, anti-epileptic, anti-ulcer agents. Currently CA inhibitors are widely used as a drug for the treatment of neurological disorders, anti-glaucoma drugs, anti-cancer, or anti-obesity agents. Here we tried to emphasize how CAs can be used for drug discovery, design and screening. Furthermore, we discussed the role of CA in carbon capture, carbon sensor and metabolon. We hope this review provide many useful information on structure, function, mechanism, and applications of CAs in various discipline.
Collapse
Affiliation(s)
- Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | | | | | | | | |
Collapse
|
32
|
Torres DA, Azagarsamy MA, Thayumanavan S. Supramolecular displacement-mediated activation of a silent fluorescence probe for label-free ligand screening. J Am Chem Soc 2012; 134:7235-7. [PMID: 22500607 DOI: 10.1021/ja301204z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We report a new approach for the rapid screening of analyte binding affinities for a target protein. We demonstrate that a molecular probe, with a pro-fluorophore substrate and ligand moieties, can be hindered from enzymatic access when bound to the target protein. When analytes displace the probe from the protein's binding pocket, a fluorescence profile is generated. This profile is used to discriminate analytes based on their relative binding affinities.
Collapse
Affiliation(s)
- Diego Amado Torres
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, USA
| | | | | |
Collapse
|
33
|
Gitto R, Damiano FM, Mader P, De Luca L, Ferro S, Supuran CT, Vullo D, Brynda J, Řezáčová P, Chimirri A. Synthesis, Structure–Activity Relationship Studies, and X-ray Crystallographic Analysis of Arylsulfonamides as Potent Carbonic Anhydrase Inhibitors. J Med Chem 2012; 55:3891-9. [DOI: 10.1021/jm300112w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rosaria Gitto
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
| | - Francesca M. Damiano
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
| | - Pavel Mader
- Department
of Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Laura De Luca
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
| | - Stefania Ferro
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
| | - Claudiu T. Supuran
- Università degli Studi
di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Università di Firenze, Italy
| | - Daniela Vullo
- Università degli Studi
di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Università di Firenze, Italy
| | - Jiří Brynda
- Department
of Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Structural Biology Team, Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Pavlína Řezáčová
- Department
of Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Structural Biology Team, Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Alba Chimirri
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
| |
Collapse
|
34
|
Schmid M, Nogueira ES, Monnard FW, Ward TR, Meuwly M. Arylsulfonamides as inhibitors for carbonic anhydrase: prediction & validation. Chem Sci 2012. [DOI: 10.1039/c1sc00628b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
35
|
Synthesis and biological profile of new 1,2,3,4-tetrahydroisoquinolines as selective carbonic anhydrase inhibitors. Bioorg Med Chem 2011; 19:7003-7. [DOI: 10.1016/j.bmc.2011.10.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 10/04/2011] [Accepted: 10/06/2011] [Indexed: 11/21/2022]
|
36
|
Pala N, Dallocchio R, Dessì A, Brancale A, Carta F, Ihm S, Maresca A, Sechi M, Supuran CT. Virtual screening-driven identification of human carbonic anhydrase inhibitors incorporating an original, new pharmacophore. Bioorg Med Chem Lett 2011; 21:2515-20. [DOI: 10.1016/j.bmcl.2011.02.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/10/2011] [Accepted: 02/12/2011] [Indexed: 11/16/2022]
|
37
|
Mader P, Brynda J, Gitto R, Agnello S, Pachl P, Supuran CT, Chimirri A, Řezáčová P. Structural Basis for the Interaction Between Carbonic Anhydrase and 1,2,3,4-tetrahydroisoquinolin-2-ylsulfonamides. J Med Chem 2011; 54:2522-6. [DOI: 10.1021/jm2000213] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pavel Mader
- Department of Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jiří Brynda
- Department of Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Structural Biology Team, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Rosaria Gitto
- Dipartimento Farmaco-Chimico, Università di Messina, Messina, Italy
| | - Stefano Agnello
- Dipartimento Farmaco-Chimico, Università di Messina, Messina, Italy
| | - Petr Pachl
- Department of Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Claudiu T. Supuran
- Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Firenze, Italy
| | - Alba Chimirri
- Dipartimento Farmaco-Chimico, Università di Messina, Messina, Italy
| | - Pavlína Řezáčová
- Department of Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Structural Biology Team, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| |
Collapse
|
38
|
Manokaran S, Banerjee J, Mallik S, Srivastava DK. Stabilization of anionic and neutral forms of a fluorophoric ligand at the active site of human carbonic anhydrase I. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1804:1965-1973. [PMID: 20620244 PMCID: PMC2930141 DOI: 10.1016/j.bbapap.2010.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 06/23/2010] [Accepted: 06/25/2010] [Indexed: 05/29/2023]
Abstract
We synthesized a fluorogenic dansylamide derivative (JB2-48), which fills the entire (15 A deep) active site pocket of human carbonic anhydrase I, and investigated the contributions of sulfonamide and hydrophobic regions of the ligand structure on the spectral, kinetic, and thermodynamic properties of the enzyme-ligand complex. The steady-state and fluorescence lifetime data revealed that the deprotonation of the sulfonamide moiety of the enzyme bound ligand increases the fluorescence emission intensity as well as the lifetime of the fluorophores. This is manifested via the electrostatic interaction between the active site resident Zn²+ cofactor and the negatively charged sulfonamide group of the ligand, and such interaction contributes to about 2.2 kcal/mol (ΔΔG°) and 0.89 kcal/mol (ΔΔG(#)) energy in stabilizing the ground and the putative transition states, respectively. We provide evidence that the anionic and neutral forms of JB2-48 are stabilized by the complementary microscopic/conformational states of the enzyme. The implication of the mechanistic studies presented herein in rationale design of carbonic anhydrase inhibitors is discussed.
Collapse
Affiliation(s)
- Sumathra Manokaran
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58105
| | - Jayati Banerjee
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105
| | - Sanku Mallik
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105
| | - D. K. Srivastava
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58105
| |
Collapse
|
39
|
Alterio V, Monti SM, Truppo E, Pedone C, Supuran CT, De Simone G. The first example of a significant active site conformational rearrangement in a carbonic anhydrase-inhibitor adduct: the carbonic anhydrase I-topiramate complex. Org Biomol Chem 2010; 8:3528-33. [PMID: 20505865 DOI: 10.1039/b926832d] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Topiramate is a widely used antiepileptic drug, which has been demonstrated to act as an efficient weight loss agent. Since several studies have pointed out that is a potent in vitro inhibitor of several Carbonic anhydrase (CA) isozymes, it has been hypothesized that its anti-obesity properties could be ascribed to the inhibition of the CAs involved in de novo lipogenesis. Consequently, the study of the interactions of with all human CA isoforms represents an important step for the rational drug design of selective CA inhibitors to be used as anti-obesity drugs. In this paper we report the crystallographic structure of the adduct that forms with hCA I, showing for the first time a profound reorganization of the CA active site upon binding of the inhibitor. Moreover, a structural comparison with hCA II- and hCA VA- adducts, previously investigated, has been performed showing that a different H-bond network together with the movement of some amino acid residues in the active site may account for the different inhibition constants of toward these three CA isozymes.
Collapse
Affiliation(s)
- Vincenzo Alterio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy
| | | | | | | | | | | |
Collapse
|
40
|
Yoshida T, Munei Y, Hitaoka S, Chuman H. Correlation analyses on binding affinity of substituted benzenesulfonamides with carbonic anhydrase using ab initio MO calculations on their complex structures. J Chem Inf Model 2010; 50:850-60. [PMID: 20415451 DOI: 10.1021/ci100068w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantitative structure-activity relationship analyses on the free energy change during complex formation between substituted benzenesulfonamides (BSAs) and bovine carbonic anhydrase II (bCA II) were performed using generilized Born/surface area (GB/SA) and ab initio fragment molecular orbital (FMO) calculations for the whole complex structures. The result shows that the overall free energy change is governed by the contribution from solvation and dissociation free energy changes accompanying by complex formation. The FMO-IFIE (interfragment interaction energy) analysis quantitatively revealed that the intrinsic interaction energy of bCA II with BSAs is mostly from interactions with amino acid residues in the active site of bCA II. The "Zn block" (Zn(2+) and three histidine residues coordinated to Zn(2+)) in the active site shows the lowest interaction energy and the greatest variance of interaction energy with BSAs through their coordination interaction. The proposed procedure was demonstrated to provide a quantitative basis for understanding a ligand-protein interaction at electronic and atomic levels.
Collapse
Affiliation(s)
- Tatsusada Yoshida
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | | | | | | |
Collapse
|
41
|
Bootorabi F, Jänis J, Smith E, Waheed A, Kukkurainen S, Hytönen V, Valjakka J, Supuran CT, Vullo D, Sly WS, Parkkila S. Analysis of a shortened form of human carbonic anhydrase VII expressed in vitro compared to the full-length enzyme. Biochimie 2010; 92:1072-80. [PMID: 20493921 DOI: 10.1016/j.biochi.2010.05.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 05/13/2010] [Indexed: 12/22/2022]
Abstract
Carbonic anhydrase (CA) enzymes are expressed in all organs of the mammalian body where they participate in important physiological functions. CA VII is a cytosolic isozyme which may be expressed as two forms according to the recent GenBank data. We designed a present study to express and characterize the human CA VII forms: full-length CA VII and short form (predicted to lack 56 residues from the N-terminus). Reverse transcriptase PCR analysis revealed mRNAs for both CA VII forms in the human brain. These different forms were expressed as recombinant proteins to investigate their biochemical properties. The full-length CA VII was used to raise a polyclonal antiserum in a rabbit, and the antiserum was then employed in western blot analyses and immunohistochemistry of mouse tissues. Data from mass spectrometry and comparative modeling showed that CA VII protein contains a single intramolecular disulfide bridge (Cys-56 to Cys-180) which is lacking in the short form. The computer model suggested distinctly different folding for the different forms. The more exposed structure and the absence of the disulfide bridge in the short form could make this protein more susceptible to degradation. In fact, this was realized in several protein purification efforts in which the short form readily degraded during the experimental procedures. From these results, we conclude that the full-length CA VII is a predominant active form in human brain and also in other tissues. In addition to the brain, CA VII is expressed in several other organs including the stomach, duodenum, colon, liver, and skeletal muscle. The distribution pattern suggests multiple functions for CA VII in different organs.
Collapse
Affiliation(s)
- Fatemeh Bootorabi
- Institute of Medical Technology, University of Tampere and Tampere University Hospital, 33014 Tampere, Finland
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Behnke CA, Le Trong I, Godden JW, Merritt EA, Teller DC, Bajorath J, Stenkamp RE. Atomic resolution studies of carbonic anhydrase II. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:616-27. [PMID: 20445237 DOI: 10.1107/s0907444910006554] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 02/19/2010] [Indexed: 11/10/2022]
Abstract
Carbonic anhydrase has been well studied structurally and functionally owing to its importance in respiration. A large number of X-ray crystallographic structures of carbonic anhydrase and its inhibitor complexes have been determined, some at atomic resolution. Structure determination of a sulfonamide-containing inhibitor complex has been carried out and the structure was refined at 0.9 A resolution with anisotropic atomic displacement parameters to an R value of 0.141. The structure is similar to those of other carbonic anhydrase complexes, with the inhibitor providing a fourth nonprotein ligand to the active-site zinc. Comparison of this structure with 13 other atomic resolution (higher than 1.25 A) isomorphous carbonic anhydrase structures provides a view of the structural similarity and variability in a series of crystal structures. At the center of the protein the structures superpose very well. The metal complexes superpose (with only two exceptions) with standard deviations of 0.01 A in some zinc-protein and zinc-ligand bond lengths. In contrast, regions of structural variability are found on the protein surface, possibly owing to flexibility and disorder in the individual structures, differences in the chemical and crystalline environments or the different approaches used by different investigators to model weak or complicated electron-density maps. These findings suggest that care must be taken in interpreting structural details on protein surfaces on the basis of individual X-ray structures, even if atomic resolution data are available.
Collapse
Affiliation(s)
- Craig A Behnke
- Department of Biochemistry, University of Washington, Box 357430, Seattle, WA 98195-7430, USA
| | | | | | | | | | | | | |
Collapse
|
43
|
Gitto R, Agnello S, Ferro S, De Luca L, Vullo D, Brynda J, Mader P, Supuran CT, Chimirri A. Identification of 3,4-Dihydroisoquinoline-2(1H)-sulfonamides as Potent Carbonic Anhydrase Inhibitors: Synthesis, Biological Evaluation, and Enzyme−Ligand X-ray Studies. J Med Chem 2010; 53:2401-8. [DOI: 10.1021/jm9014026] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Rosaria Gitto
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, I-98168 Messina, Italy
| | - Stefano Agnello
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, I-98168 Messina, Italy
| | - Stefania Ferro
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, I-98168 Messina, Italy
| | - Laura De Luca
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, I-98168 Messina, Italy
| | - Daniela Vullo
- Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Firenze, Italy
| | - Jiri Brynda
- Department of Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ-16637 Prague, Czech Republic
- Department of Structural Biology, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, CZ-16637 Prague, Czech Republic
| | - Pavel Mader
- Department of Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ-16637 Prague, Czech Republic
- Department of Structural Biology, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, CZ-16637 Prague, Czech Republic
| | - Claudiu T. Supuran
- Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Firenze, Italy
| | - Alba Chimirri
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, I-98168 Messina, Italy
| |
Collapse
|
44
|
Baranauskienė L, Hilvo M, Matulienė J, Golovenko D, Manakova E, Dudutienė V, Michailovienė V, Torresan J, Jachno J, Parkkila S, Maresca A, Supuran CT, Gražulis S, Matulis D. Inhibition and binding studies of carbonic anhydrase isozymes I, II and IX with benzimidazo[1,2-c][1,2,3]thiadiazole-7-sulphonamides. J Enzyme Inhib Med Chem 2010; 25:863-70. [DOI: 10.3109/14756360903571685] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Lina Baranauskienė
- Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Mika Hilvo
- Institute of Medical Technology, University of Tampere and Tampere University Hospital, FI-33014 Tampere, Finland
| | - Jurgita Matulienė
- Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Dmitrij Golovenko
- Laboratory of Protein – DNA Interactions, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Elena Manakova
- Laboratory of Protein – DNA Interactions, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Virginija Dudutienė
- Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Vilma Michailovienė
- Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Jolanta Torresan
- Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Jelena Jachno
- Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Seppo Parkkila
- Institute of Medical Technology, University of Tampere and Tampere University Hospital, FI-33014 Tampere, Finland
- School of Medicine, University of Tampere and Tampere University Hospital, FI-33014 Tampere, Finland
| | - Alfonso Maresca
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Room 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
| | - Claudiu T. Supuran
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Room 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
| | - Saulius Gražulis
- Laboratory of Protein – DNA Interactions, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania
| | - Daumantas Matulis
- Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania
| |
Collapse
|
45
|
Scott A, Phillips C, Alex A, Flocco M, Bent A, Randall A, O'Brien R, Damian L, Jones L. Thermodynamic Optimisation in Drug Discovery: A Case Study using Carbonic Anhydrase Inhibitors. ChemMedChem 2009; 4:1985-9. [DOI: 10.1002/cmdc.200900386] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
46
|
Sippel KH, Robbins AH, Domsic J, Genis C, Agbandje-McKenna M, McKenna R. High-resolution structure of human carbonic anhydrase II complexed with acetazolamide reveals insights into inhibitor drug design. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:992-5. [PMID: 19851004 DOI: 10.1107/s1744309109036665] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 09/10/2009] [Indexed: 11/10/2022]
Abstract
The crystal structure of human carbonic anhydrase II (CA II) complexed with the inhibitor acetazolamide (AZM) has been determined at 1.1 A resolution and refined to an R(cryst) of 11.2% and an R(free) of 14.7%. As observed in previous CA II-inhibitor complexes, AZM binds directly to the zinc and makes several key interactions with active-site residues. The high-resolution data also showed a glycerol molecule adjacent to the AZM in the active site and two additional AZMs that are adventitiously bound on the surface of the enzyme. The co-binding of AZM and glycerol in the active site demonstrate that given an appropriate ring orientation and substituents, an isozyme-specific CA inhibitor may be developed.
Collapse
Affiliation(s)
- Katherine H Sippel
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | | | | | | | | | | |
Collapse
|
47
|
Tsukiji S, Miyagawa M, Takaoka Y, Tamura T, Hamachi I. Ligand-directed tosyl chemistry for protein labeling in vivo. Nat Chem Biol 2009; 5:341-3. [DOI: 10.1038/nchembio.157] [Citation(s) in RCA: 277] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 02/26/2009] [Indexed: 12/18/2022]
|
48
|
Miyazaki I, Simizu S, Ishida K, Osada H. On-Chip Fragment-Based Approach for Discovery of High-Affinity Bivalent Inhibitors. Chembiochem 2009; 10:838-43. [DOI: 10.1002/cbic.200800704] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
49
|
Chambers JM, Hill PA, Aaron JA, Han Z, Christianson DW, Kuzma NN, Dmochowski IJ. Cryptophane xenon-129 nuclear magnetic resonance biosensors targeting human carbonic anhydrase. J Am Chem Soc 2009; 131:563-9. [PMID: 19140795 PMCID: PMC2629400 DOI: 10.1021/ja806092w] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
(129)Xe NMR biosensors are promising agents for early disease detection, especially when their interactions with target biomolecules can perturb (129)Xe chemical shifts well beyond the typical field inhomogeneity of clinical MRI. We introduce human carbonic anhydrase (CA) as a single-binding-site enzyme for studying xenon biosensor-protein interactions. A xenon-binding cryptophane was substituted with linkers of varying lengths to p-benzenesulfonamide to yield nondiastereomeric biosensors with a single (129)Xe NMR resonance. X-ray crystallography confirmed binding of the eight-bond-linked biosensor containing a single xenon atom in the CAII active site. Biosensor dissociation constants (K(d) = 20-110 nM) were determined by isothermal titration calorimetry (ITC) for isozymes CA I and II. The biosensor-CA complexes yielded "bound" hyperpolarized (129)Xe NMR resonances of narrow line width that were shifted by 3.0-7.5 ppm downfield, signifying much larger shifts than seen previously. Moreover, isozyme-specific chemical shifts clearly differentiated CA I and II, despite their similar structures. Thus, xenon biosensors may provide a powerful strategy for diagnosing human diseases characterized by the upregulation of specific CA isozymes and other protein biomarkers.
Collapse
Affiliation(s)
- Jennifer M. Chambers
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - P. Aru Hill
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - Julie A. Aaron
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - Zhaohui Han
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - David W. Christianson
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - Nicholas N. Kuzma
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - Ivan J. Dmochowski
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| |
Collapse
|
50
|
Bjelić S, Jelesarov I. A survey of the year 2007 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:289-312. [PMID: 18729242 DOI: 10.1002/jmr.909] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Elucidation of the energetic principles of binding affinity and specificity is a central task in many branches of current sciences: biology, medicine, pharmacology, chemistry, material sciences, etc. In biomedical research, integral approaches combining structural information with in-solution biophysical data have proved to be a powerful way toward understanding the physical basis of vital cellular phenomena. Isothermal titration calorimetry (ITC) is a valuable experimental tool facilitating quantification of the thermodynamic parameters that characterize recognition processes involving biomacromolecules. The method provides access to all relevant thermodynamic information by performing a few experiments. In particular, ITC experiments allow to by-pass tedious and (rarely precise) procedures aimed at determining the changes in enthalpy and entropy upon binding by van't Hoff analysis. Notwithstanding limitations, ITC has now the reputation of being the "gold standard" and ITC data are widely used to validate theoretical predictions of thermodynamic parameters, as well as to benchmark the results of novel binding assays. In this paper, we discuss several publications from 2007 reporting ITC results. The focus is on applications in biologically oriented fields. We do not intend a comprehensive coverage of all newly accumulated information. Rather, we emphasize work which has captured our attention with originality and far-reaching analysis, or else has provided ideas for expanding the potential of the method.
Collapse
Affiliation(s)
- Sasa Bjelić
- Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, Zürich, Switzerland
| | | |
Collapse
|