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Samoi TB, Banerjee S, Ghosh B, Jha T, Adhikari N. Exploring crucial structural attributes of quinolinyl methoxyphenyl sulphonyl-based hydroxamate derivatives as ADAM17 inhibitors through classification-dependent molecular modelling approaches. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:157-179. [PMID: 38346125 DOI: 10.1080/1062936x.2024.2311689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/23/2024] [Indexed: 02/15/2024]
Abstract
A Disintegrin and Metalloproteinase 17 (ADAM17), a Zn2+-dependent metalloenzyme of the adamalysin family of the metzincin superfamily, is associated with various pathophysiological conditions including rheumatoid arthritis and cancer. However, no specific inhibitors have been marketed yet for ADAM17-related disorders. In this study, 94 quinolinyl methoxyphenyl sulphonyl-based hydroxamates as ADAM17 inhibitors were subjected to classification-based molecular modelling and binding pattern analysis to identify the significant structural attributes contributing to ADAM17 inhibition. The statistically validated classification-based models identified the importance of the P1' substituents such as the quinolinyl methoxyphenyl sulphonyl group of these compounds for occupying the S1' - S3' pocket of the enzyme. The quinolinyl function of these compounds was found to explore stable binding of the P1' substituents at the S1' - S3' pocket whereas the importance of the sulphonyl and the orientation of the P1' moiety also revealed stable binding. Based on the outcomes of the current study, four novel compounds of different classes were designed as promising ADAM17 inhibitors. These findings regarding the crucial structural aspects and binding patterns of ADAM17 inhibitors will aid the design and discovery of novel and effective ADAM17 inhibitors for therapeutic advancements of related diseases.
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Affiliation(s)
- T B Samoi
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - B Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - N Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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2
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Guti S, Baidya SK, Banerjee S, Adhikari N, Jha T. A robust classification-dependent multi-molecular modelling study on some biphenyl sulphonamide based MMP-8 inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:835-861. [PMID: 34587852 DOI: 10.1080/1062936x.2021.1976831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
Matrix metalloproteinases (MMPs) are a group of zinc and calcium-dependent endopeptidases, which contribute to different physiological and biological activities via extracellular matrix (ECM) degradation. Matrix metalloproteinase-8 (MMP-8) belongs to type-II collagenases of the MMP family that has contribution in several physiological disorders such as cardiovascular diseases, joint, renal, digestive and respiratory disorders as well as in cancer. In clinical study, MMP-8 is found to be associated with periodontal disease condition. Therefore, MMP-8 specific inhibitors should be developed to target these disorders. The biphenyl sulphonamide (BPS) moiety is one of the crucial structural characteristics found in several MMP-8 inhibitors. Here, different classification-based molecular modelling methods were used to explore the structural features that lead to the activity variation of a series of MMP-8 inhibitors possessing a BPS moiety. Our current classification-based structural analysis of these BPS-derived MMP-8 inhibitors was able to identify the importance of several structural features such as the tetrahydroisoquinoline and N-Boc pyridyl groups, which have positive influences on MMP-8 inhibition. This study was also reflected the importance of the zinc-binding groups (ZBGs) like the hydroxamate and phosphonate for potent and sub-nanomolar range MMP-8 inhibition, which may benefit the development of highly potent MMP-8 inhibitors.
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Affiliation(s)
- S Guti
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S K Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - N Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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3
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Tang M, Pei G, Su D, Wang C, Feng X, Srivastava M, Chen Z, Zhao Z, Chen J. Genome-wide CRISPR screens reveal cyclin C as synthetic survival target of BRCA2. Nucleic Acids Res 2021; 49:7476-7491. [PMID: 34197614 PMCID: PMC8287926 DOI: 10.1093/nar/gkab540] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/04/2021] [Accepted: 06/23/2021] [Indexed: 01/15/2023] Open
Abstract
Poly (ADP-ribose) polymerase inhibitor (PARPi)-based therapies initially reduce tumor burden but eventually lead to acquired resistance in cancer patients with BRCA1 or BRCA2 mutation. To understand the potential PARPi resistance mechanisms, we performed whole-genome CRISPR screens to discover genetic alterations that change the gene essentiality in cells with inducible depletion of BRCA2. We identified that several RNA Polymerase II transcription Mediator complex components, especially Cyclin C (CCNC) as synthetic survival targets upon BRCA2 loss. Total mRNA sequencing demonstrated that loss of CCNC could activate the transforming growth factor (TGF)-beta signaling pathway and extracellular matrix (ECM)-receptor interaction pathway, however the inhibition of these pathways could not reverse cell survival in BRCA2 depleted CCNC-knockout cells, indicating that the activation of these pathways is not required for the resistance. Moreover, we showed that the improved survival is not due to restoration of homologous recombination repair although decreased DNA damage signaling was observed. Interestingly, loss of CCNC could restore replication fork stability in BRCA2 deficient cells, which may contribute to PARPi resistance. Taken together, our data reveal CCNC as a critical genetic determinant upon BRCA2 loss of function, which may help the development of novel therapeutic strategies that overcome PARPi resistance.
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Affiliation(s)
- Mengfan Tang
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, Unit 1052, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Importance of Biometals as Targets in Medicinal Chemistry: An Overview about the Role of Zinc (II) Chelating Agents. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10124118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Zinc (II) is an important biometal in human physiology. Moreover, in the last two decades, it was deeply studied for its involvement in several pathological states. In particular, the regulation of its concentration in synaptic clefts can be fundamental for the treatment of neurodegenerative diseases, such as Alzheimer’s disease (AD). Zinc (II) is also a constituent of metalloenzymes (i.e., matrix metalloproteinases, MMPs, and carbonic anhydrases, CAs) with catalytic function; therefore, it can be an important target for the inhibition of these proteins, frequently involved in cancer onset. This review is focused on the significance of zinc (II) chelating agents in past and future medicinal chemistry research, and on the importance of selectivity in order to revamp the possibility of their use in therapy, often hindered by possible side effects.
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Cortes-Pacheco A, Jiménez-Arellanes MA, Palacios-Can FJ, Valcarcel-Gamiño JA, Razo-Hernández RS, Juárez-Vázquez MDC, López-Torres A, Ramírez-Marroquín OA. Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors. Beilstein J Org Chem 2020; 16:1277-1287. [PMID: 32566030 PMCID: PMC7296197 DOI: 10.3762/bjoc.16.108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/25/2020] [Indexed: 12/19/2022] Open
Abstract
Bisphosphonic acids (or bisphosphonates) have been successfully used in the clinic treatment of bone diseases for over decades. Additionally, the antiinflammatory activity of these compounds has been gaining attention. In our previous work, we synthesized and in vivo evaluated the bisphosphonic esters 1 and 2, finding a moderate edema inhibition upon oral and topical administration on BALB/c mice. Thus, in this work, the bioisosteric replacement of an amide functional group for an ester afforded the new bisphosphonates 3-6, which had a moderate oral edema inhibition (25 mg/kg dose) and a significant topical antiinflammatory activity (2 mg/ear) on BALB/c mice, with 6 being the most active hit (55.9% edema inhibition), comparable to the positive control (55.5% edema inhibition) on a TPA topical model. Next, to assess the acute toxicity of the synthesized derivatives, test animals were administered with 50-100 mg/kg of 3-6, respectively, by an oral route, and after 14 days, neither lethality nor a significative weight loss were observed. Finally, a structure-activity relationship (SAR) and a molecular docking analysis of 3-6 helped us to explain the trend observed in biological tests. Considering all these aspects, we propose the inhibition of MMP-8 and MMP-9 as a possible action mechanism of the synthesized derivatives.
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Affiliation(s)
- Abimelek Cortes-Pacheco
- Instituto de Química Aplicada, Universidad del Papaloapan. Tuxtepec, 68301, Mexico
- Unidad de Investigación Médica (UIM) en Farmacología, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI (CMN-SXXI), Instituto Mexicano del Seguro Social (IMSS). Av. Cuauhtémoc 330, Col. Doctores 06720, Ciudad de México (CdMx), Mexico
| | - María Adelina Jiménez-Arellanes
- Unidad de Investigación Médica (UIM) en Farmacología, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI (CMN-SXXI), Instituto Mexicano del Seguro Social (IMSS). Av. Cuauhtémoc 330, Col. Doctores 06720, Ciudad de México (CdMx), Mexico
| | - Francisco José Palacios-Can
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos Avenida Universidad 1001, Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - José Antonio Valcarcel-Gamiño
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos Avenida Universidad 1001, Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Rodrigo Said Razo-Hernández
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos Avenida Universidad 1001, Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - María del Carmen Juárez-Vázquez
- Unidad de Investigación Médica (UIM) en Farmacología, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI (CMN-SXXI), Instituto Mexicano del Seguro Social (IMSS). Av. Cuauhtémoc 330, Col. Doctores 06720, Ciudad de México (CdMx), Mexico
| | - Adolfo López-Torres
- Instituto de Química Aplicada, Universidad del Papaloapan. Tuxtepec, 68301, Mexico
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Bone-Seeking Matrix Metalloproteinase Inhibitors for the Treatment of Skeletal Malignancy. Pharmaceuticals (Basel) 2020; 13:ph13060113. [PMID: 32492898 PMCID: PMC7344628 DOI: 10.3390/ph13060113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/29/2020] [Accepted: 05/30/2020] [Indexed: 12/21/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are a family of enzymes involved at different stages of cancer progression and metastasis. We previously identified a novel class of bisphosphonic inhibitors, selective for MMPs crucial for bone remodeling, such as MMP-2. Due to the increasing relevance of specific MMPs at various stages of tumor malignancy, we focused on improving potency towards certain isoforms. Here, we tackled MMP-9 because of its confirmed role in tumor invasion, metastasis, angiogenesis, and immuno-response, making it an ideal target for cancer therapy. Using a computational analysis, we designed and characterized potent MMP-2/MMP-9 inhibitors. This is a promising approach to develop and clinically translate inhibitors that could be used in combination with standard care therapy for the treatment of skeletal malignancies.
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7
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Virtual screening identification and chemical optimization of substituted 2-arylbenzimidazoles as new non-zinc-binding MMP-2 inhibitors. Bioorg Med Chem 2020; 28:115257. [DOI: 10.1016/j.bmc.2019.115257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 01/02/2023]
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8
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Gimeno A, Beltrán-Debón R, Mulero M, Pujadas G, Garcia-Vallvé S. Understanding the variability of the S1′ pocket to improve matrix metalloproteinase inhibitor selectivity profiles. Drug Discov Today 2020; 25:38-57. [DOI: 10.1016/j.drudis.2019.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 06/23/2019] [Accepted: 07/26/2019] [Indexed: 12/15/2022]
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9
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The Cell Killing Mechanisms of Hydroxyurea. Genes (Basel) 2016; 7:genes7110099. [PMID: 27869662 PMCID: PMC5126785 DOI: 10.3390/genes7110099] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 11/23/2022] Open
Abstract
Hydroxyurea is a well-established inhibitor of ribonucleotide reductase that has a long history of scientific interest and clinical use for the treatment of neoplastic and non-neoplastic diseases. It is currently the staple drug for the management of sickle cell anemia and chronic myeloproliferative disorders. Due to its reversible inhibitory effect on DNA replication in various organisms, hydroxyurea is also commonly used in laboratories for cell cycle synchronization or generating replication stress. However, incubation with high concentrations or prolonged treatment with low doses of hydroxyurea can result in cell death and the DNA damage generated at arrested replication forks is generally believed to be the direct cause. Recent studies in multiple model organisms have shown that oxidative stress and several other mechanisms may contribute to the majority of the cytotoxic effect of hydroxyurea. This review aims to summarize the progress in our understanding of the cell-killing mechanisms of hydroxyurea, which may provide new insights towards the improvement of chemotherapies that employ this agent.
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Tauro M, Laghezza A, Loiodice F, Piemontese L, Caradonna A, Capelli D, Montanari R, Pochetti G, Di Pizio A, Agamennone M, Campestre C, Tortorella P. Catechol-based matrix metalloproteinase inhibitors with additional antioxidative activity. J Enzyme Inhib Med Chem 2016; 31:25-37. [PMID: 27556138 DOI: 10.1080/14756366.2016.1217853] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
New catechol-containing chemical entities have been investigated as matrix metalloproteinase inhibitors as well as antioxidant molecules. The combination of the two properties could represent a useful feature due to the potential application in all the pathological processes characterized by increased proteolytic activity and radical oxygen species (ROS) production, such as inflammation and photoaging. A series of catechol-based molecules were synthesized and tested for both proteolytic and oxidative inhibitory activity, and the detailed binding mode was assessed by crystal structure determination of the complex between a catechol derivative and the matrix metalloproteinase-8. Surprisingly, X-ray structure reveals that the catechol oxygens do not coordinates the zinc atom.
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Affiliation(s)
- Marilena Tauro
- a Department of Tumor Biology , H. Lee Moffitt Cancer Center and Research Institute , Tampa , FL , USA
| | - Antonio Laghezza
- b Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi "A. Moro" di Bari , Bari , Italy
| | - Fulvio Loiodice
- b Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi "A. Moro" di Bari , Bari , Italy
| | - Luca Piemontese
- b Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi "A. Moro" di Bari , Bari , Italy
| | - Alessia Caradonna
- b Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi "A. Moro" di Bari , Bari , Italy
| | - Davide Capelli
- c Istituto di Cristallografia, CNR , Monterotondo Stazione (Roma) , Italy
| | - Roberta Montanari
- c Istituto di Cristallografia, CNR , Monterotondo Stazione (Roma) , Italy
| | - Giorgio Pochetti
- c Istituto di Cristallografia, CNR , Monterotondo Stazione (Roma) , Italy
| | - Antonella Di Pizio
- d Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem , Rehovot , Israel , and
| | | | - Cristina Campestre
- e Dipartimento di Farmacia, Università "G. d'Annunzio" Chieti , Chieti , Italy
| | - Paolo Tortorella
- b Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi "A. Moro" di Bari , Bari , Italy
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11
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Li ZC, Huang MH, Zhong WQ, Liu ZQ, Xie Y, Dai Z, Zou XY. Identification of drug–target interaction from interactome network with ‘guilt-by-association’ principle and topology features. Bioinformatics 2015; 32:1057-64. [DOI: 10.1093/bioinformatics/btv695] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/19/2015] [Indexed: 12/31/2022] Open
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12
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Investigation on the ZBG-functionality of phenyl-4-yl-acrylohydroxamic acid derivatives as histone deacetylase inhibitors. Bioorg Med Chem Lett 2015; 25:4457-60. [DOI: 10.1016/j.bmcl.2015.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/30/2022]
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13
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Palermo G, Campomanes P, Cavalli A, Rothlisberger U, De Vivo M. Anandamide Hydrolysis in FAAH Reveals a Dual Strategy for Efficient Enzyme-Assisted Amide Bond Cleavage via Nitrogen Inversion. J Phys Chem B 2014; 119:789-801. [DOI: 10.1021/jp5052276] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Giulia Palermo
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Pablo Campomanes
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
| | - Andrea Cavalli
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
| | - Marco De Vivo
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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Tauro M, Loiodice F, Ceruso M, Supuran CT, Tortorella P. Dual carbonic anhydrase/matrix metalloproteinase inhibitors incorporating bisphosphonic acid moieties targeting bone tumors. Bioorg Med Chem Lett 2014; 24:2617-20. [DOI: 10.1016/j.bmcl.2014.04.077] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/15/2014] [Accepted: 04/21/2014] [Indexed: 11/29/2022]
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Abstract
Ribonucleotide reductase (RNR) supplies cellular deoxyribonucleotide triphosphates (dNTP) pools by converting ribonucleotides to the corresponding deoxy forms using radical-based chemistry. Eukaryotic RNR comprises α and β subunits: α contains the catalytic and allosteric sites; β houses a diferric-tyrosyl radical cofactor (FeIII2-Y•) that is required to initiates nucleotide reduction in α. Cells have evolved multi-layered mechanisms to regulate RNR level and activity in order to maintain the adequate sizes and ratios of their dNTP pools to ensure high-fidelity DNA replication and repair. The central role of RNR in nucleotide metabolism also makes it a proven target of chemotherapeutics. In this review, we discuss recent progress in understanding the function and regulation of eukaryotic RNRs, with a focus on studies revealing the cellular machineries involved in RNR metallocofactor biosynthesis and its implication in RNR-targeting therapeutics.
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Tauro M, Laghezza A, Loiodice F, Agamennone M, Campestre C, Tortorella P. Arylamino methylene bisphosphonate derivatives as bone seeking matrix metalloproteinase inhibitors. Bioorg Med Chem 2013; 21:6456-65. [PMID: 24071448 DOI: 10.1016/j.bmc.2013.08.054] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/29/2013] [Accepted: 08/23/2013] [Indexed: 11/24/2022]
Abstract
The complexity of matrix metalloproteinase inhibitors (MMPIs) design derives from the difficulty in carefully addressing their inhibitory activity towards the MMP isoforms involved in many pathological conditions. In particular, specific metalloproteinases, such as MMP-2 and MMP-9, are key regulators of the 'vicious cycle' occurring between tumor metastases growth and bone remodeling. In an attempt to devise new approaches to selective inhibitor derivatives, we describe novel bisphosphonate bone seeking MMP inhibitors (BP-MMPIs), capable to be selectively targeted and to overcome undesired side effects of broad spectrum MMPIs. In vitro activity (IC50 values) for each inhibitor was determined against MMP-2, -8, -9 and -14, because of their relevant role in skeletal development and renewal. The results show that BP-MMPIs reached IC50 values of enzymatic inhibition in the low micromolar range. Computational studies, used to rationalize some trends in the observed inhibitory profiles, suggest a possible differential binding mode in MMP-2 that explains the selective inhibition of this isoform. In addition, survival assay was conducted on J774 cell line, a well known model system used to evaluate the structure-activity relationship of BPs for inhibiting bone resorption. The resulting data, confirming the specific activity of BP-MMPIs, and their additional proved propensity to bind hydroxyapatite powder in vitro, suggest a potential use of BP-MMPIs in skeletal malignancies.
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Affiliation(s)
- Marilena Tauro
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi 'Aldo Moro' di Bari, Via Orabona 4, 70126 Bari, Italy
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17
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Trillo-Muyo S, Jasilionis A, Domagalski MJ, Chruszcz M, Minor W, Kuisiene N, Arolas JL, Solà M, Gomis-Rüth FX. Ultratight crystal packing of a 10 kDa protein. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:464-70. [PMID: 23519421 PMCID: PMC4048058 DOI: 10.1107/s0907444912050135] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 12/07/2012] [Indexed: 11/10/2022]
Abstract
While small organic molecules generally crystallize forming tightly packed lattices with little solvent content, proteins form air-sensitive high-solvent-content crystals. Here, the crystallization and full structure analysis of a novel recombinant 10 kDa protein corresponding to the C-terminal domain of a putative U32 peptidase are reported. The orthorhombic crystal contained only 24.5% solvent and is therefore among the most tightly packed protein lattices ever reported.
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Affiliation(s)
- Sergio Trillo-Muyo
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Spanish Research Council CSIC, Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Spain
| | - Andrius Jasilionis
- Department of Microbiology and Biotechnology, Vilnius University, M. K. Čiurlionio 21/27, 03101 Vilnius, Lithuania
| | - Marcin J. Domagalski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908-0736, USA
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908-0736, USA
| | - Nomeda Kuisiene
- Department of Microbiology and Biotechnology, Vilnius University, M. K. Čiurlionio 21/27, 03101 Vilnius, Lithuania
| | - Joan L. Arolas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Spanish Research Council CSIC, Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Spain
| | - Maria Solà
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Spanish Research Council CSIC, Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Spain
| | - F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Spanish Research Council CSIC, Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Spain
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18
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Chakrabarti B, Bairagya HR, Mishra DK, Chatterjee PK, Mukhopadhyay BP. Insight towards the conserved water mediated recognition of catalytic and structural Zn(+2) ions in human Matrix Metalloproteinase-8 enzyme: A study by MD-simulation methods. Bioinformation 2013; 9:126-33. [PMID: 23423544 PMCID: PMC3569599 DOI: 10.6026/97320630009126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 01/10/2013] [Indexed: 11/23/2022] Open
Abstract
Human matrix metalloproteinase-8 (hMMP-8) plays a important role in the progression of colorectal cancer, metastasis, multiple sclerosis and rheumetoid arthritis. Extensive MD-simulation of the PDB and solvated structures of hMMP-8 has revealed the presence of few conserved water molecules around the catalytic and structural zinc (ZnC and ZnS) ions. The coordination of two conserved water molecules (W and WS) to ZnS and the H-bonding interaction of WS to S151 have indicated the plausible involvement of that metal ion in the catalytic process. Beside this the coupling of ZnC and ZnS metal ions (ZnC - W(H) (W(1))…..W(2) ….H(162) - ZnS) through two conserved hydrophilic centers (occupied by water molecules) may also provide some rational on the recognition of two zinc ions which were separated by ~13 Å in their X-ray structures. This unique recognition of both the Zn(+2) ions in the enzyme through conserved water molecules may be implemented/ exploited for the design of antiproteolytic agent using water mimic drug design protocol.
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Affiliation(s)
- Bornali Chakrabarti
- Department of Chemistry, National Institute of Technology, Durgapur – 713 209, W.B. India
| | - Hridoy R Bairagya
- Department of Chemistry, National Institute of Technology, Durgapur – 713 209, W.B. India
| | - Deepak Kr Mishra
- Department of Chemistry, National Institute of Technology, Durgapur – 713 209, W.B. India
| | - Pradip Kumar Chatterjee
- Thermal Engineering Department, Central Mechanical Engineering Research Institute, Durgapur – 713209,W.B, India
| | - Bishnu P Mukhopadhyay
- Department of Chemistry, National Institute of Technology, Durgapur – 713 209, W.B. India
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Kawai K, Nagata N. Metal-ligand interactions: an analysis of zinc binding groups using the Protein Data Bank. Eur J Med Chem 2012; 51:271-6. [PMID: 22405284 DOI: 10.1016/j.ejmech.2012.02.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 02/13/2012] [Accepted: 02/14/2012] [Indexed: 01/11/2023]
Abstract
In the present study, we investigated zinc binding groups (ZBGs) using the coordinates of protein-ligand complex structures obtained from the Protein Data Bank. The distance from the zinc to the nearest ligand atom was measured to determine whether the atom was part of the ZBG. The most frequently found ZBG was carboxylate, followed by sulfonamide, hydroxamate, and phosphonate/phosphate. Because it was found that few heteroatoms, such as nitrogen, oxygen, and sulfur atoms, interacted with zinc, ideal distances between the zinc and these heteroatoms were identified. Whereas carboxylates bound to the zinc via both monodentate and bidentate interactions, the hydroxamates bound dominantly in a bidentate manner. These results will aid in the design of new inhibitors with the potential to interact with zinc in the target protein.
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Affiliation(s)
- Kentaro Kawai
- Central Research Laboratories, Kaken Pharmaceutical Co., Ltd, 14, Shinomiya Minamikawara-cho, Yamashina, Kyoto 607-8042, Japan
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20
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Chibba A, Poloczek J, Little DJ, Howell PL, Nitz M. Synthesis and evaluation of inhibitors of E. coli PgaB, a polysaccharide de-N-acetylase involved in biofilm formation. Org Biomol Chem 2012; 10:7103-7. [DOI: 10.1039/c2ob26105g] [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]
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21
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Yadav MR, Murumkar PR, Zambre VP. Advances in studies on collagenase inhibitors. EXPERIENTIA SUPPLEMENTUM (2012) 2012; 103:83-135. [PMID: 22642191 DOI: 10.1007/978-3-0348-0364-9_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Matrix metalloproteinases (MMPs) play an important role in many physiological and pathological processes. Development of MMP inhibitors, in particular collagenase inhibitors, for the treatment of arthritis has been more challenging, undoubtedly. Small-molecular-weight collagenase inhibitors may be classified into several different arbitrary structural classes, depending on the catalytic zinc-binding function as well as other structural elements of the inhibitors. This chapter tries to make an attempt in providing the reader with an overall flavor of the type of scaffolds reported in the past few years along with the molecular modeling studies.
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Affiliation(s)
- Mange Ram Yadav
- Pharmacy Department, The M.S. University of Baroda, Vadodara 390 001, Gujarat, India.
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22
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Matrix metalloproteinase inhibitors as investigative tools in the pathogenesis and management of vascular disease. EXPERIENTIA SUPPLEMENTUM (2012) 2012; 103:209-79. [PMID: 22642194 DOI: 10.1007/978-3-0348-0364-9_7] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Matrix metalloproteinases (MMPs) are proteolytic enzymes that degrade various components of the extracellular matrix (ECM). MMPs could also regulate the activity of several non-ECM bioactive substrates and consequently affect different cellular functions. Members of the MMPs family include collagenases, gelatinases, stromelysins, matrilysins, membrane-type MMPs, and others. Pro-MMPs are cleaved into active MMPs, which in turn act on various substrates in the ECM and on the cell surface. MMPs play an important role in the regulation of numerous physiological processes including vascular remodeling and angiogenesis. MMPs may also be involved in vascular diseases such as hypertension, atherosclerosis, aortic aneurysm, and varicose veins. MMPs also play a role in the hemodynamic and vascular changes associated with pregnancy and preeclampsia. The role of MMPs is commonly assessed by measuring their gene expression, protein amount, and proteolytic activity using gel zymography. Because there are no specific activators of MMPs, MMP inhibitors are often used to investigate the role of MMPs in different physiologic processes and in the pathogenesis of specific diseases. MMP inhibitors include endogenous tissue inhibitors (TIMPs) and pharmacological inhibitors such as zinc chelators, doxycycline, and marimastat. MMP inhibitors have been evaluated as diagnostic and therapeutic tools in cancer, autoimmune disease, and cardiovascular disease. Although several MMP inhibitors have been synthesized and tested both experimentally and clinically, only one MMP inhibitor, i.e., doxycycline, is currently approved by the Food and Drug Administration. This is mainly due to the undesirable side effects of MMP inhibitors especially on the musculoskeletal system. While most experimental and clinical trials of MMP inhibitors have not demonstrated significant benefits, some trials still showed promising results. With the advent of new genetic and pharmacological tools, disease-specific MMP inhibitors with fewer undesirable effects are being developed and could be useful in the management of vascular disease.
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Palermo G, Branduardi D, Masetti M, Lodola A, Mor M, Piomelli D, Cavalli A, De Vivo M. Covalent inhibitors of fatty acid amide hydrolase: a rationale for the activity of piperidine and piperazine aryl ureas. J Med Chem 2011; 54:6612-23. [PMID: 21830831 DOI: 10.1021/jm2004283] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, covalent drugs have attracted great interest in the drug discovery community, with successful examples that have demonstrated their therapeutic effects. Here, we focus on the covalent inhibition of the fatty acid amide hydrolase (FAAH), which is a promising strategy in the treatment of pain and inflammation. Among the most recent and potent FAAH inhibitors (FAAHi), there are the cyclic piperidine and piperazine aryl ureas. FAAH hydrolyzes efficiently the amide bond of these compounds, forming a covalent enzyme-inhibitor adduct. To rationalize this experimental evidence, we performed an extensive computational analysis centered on piperidine-based PF750 (1) and piperazine-based JNJ1661010 (2), two potent lead compounds used to generate covalent inhibitors as clinical candidates. We found that FAAH induces a distortion of the amide bond of the piperidine and piperazine aryl ureas. Quantum mechanics/molecular mechanics ΔE(LUMO-HOMO) energies indicate that the observed enzyme-induced distortion of the amide bond favors the formation of a covalent FAAH-inhibitor adduct. These findings could help in the rational structure-based design of novel covalent FAAHi.
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Affiliation(s)
- Giulia Palermo
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , Via Morego 30, 16163 Genova, Italy
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24
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Rubino MT, Maggi D, Laghezza A, Loiodice F, Tortorella P. Identification of novel matrix metalloproteinase inhibitors by screening of phenol fragments library. Arch Pharm (Weinheim) 2011; 344:557-63. [PMID: 21695711 DOI: 10.1002/ardp.201000350] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 11/07/2022]
Abstract
In the last 20 years, a great variety of synthetic, low molecular weight MMP inhibitors (MMPIs) have been synthesized and tested, although none has reached clinical utility. Exploration of novel ZBGs and development of non-hydroxamate MMPI has become a focus in current research. It's well-known that polyphenols can produce beneficial effects on human health by their antioxidant properties as well as they have the ability to block gelatinase activity. In this work we tested a series of selected phenols as MMP inhibitors. The most interesting hit (B6) shows sub-micromolar activity against MMP-2 (IC(50) 0.59 ± 0.05 µM, LE = 1.07) and a fairly good selectivity spectrum.
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Affiliation(s)
- Maria Teresa Rubino
- Dipartimento Farmaco-Chimico, Università degli Studi "Aldo Moro", Bari, Italy
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25
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Durrant JD, de Oliveira CAF, McCammon JA. Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitors. Chem Biol Drug Des 2011; 78:191-8. [PMID: 21609408 PMCID: PMC3135671 DOI: 10.1111/j.1747-0285.2011.01148.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Matrix metalloproteinases are zinc-containing enzymes capable of degrading all components of the extracellular matrix. Owing to their role in human disease, matrix metalloproteinase have been the subject of extensive study. A bioinorganic approach was recently used to identify novel inhibitors based on a maltol zinc-binding group, but accompanying molecular-docking studies failed to explain why one of these inhibitors, AM-6, had approximately 2500-fold selectivity for MMP-3 over MMP-2. A number of studies have suggested that the matrix-metalloproteinase active site is highly flexible, leading some to speculate that differences in active-site flexibility may explain inhibitor selectivity. To extend the bioinorganic approach in a way that accounts for MMP-2 and MMP-3 dynamics, we here investigate the predicted binding modes and energies of AM-6 docked into multiple structures extracted from matrix-metalloproteinase molecular dynamics simulations. Our findings suggest that accounting for protein dynamics is essential for the accurate prediction of binding affinity and selectivity. Additionally, AM-6 and other similar inhibitors likely select for and stabilize only a subpopulation of all matrix-metalloproteinase conformations sampled by the apo protein. Consequently, when attempting to predict ligand affinity and selectivity using an ensemble of protein structures, it may be wise to disregard protein conformations that cannot accommodate the ligand.
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Affiliation(s)
- Jacob D Durrant
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, CA 92093-0365, USA.
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26
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Madala PK, Tyndall JDA, Nall T, Fairlie DP. Update 1 of: Proteases Universally Recognize Beta Strands In Their Active Sites. Chem Rev 2011; 110:PR1-31. [DOI: 10.1021/cr900368a] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Praveen K. Madala
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - Tessa Nall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - David P. Fairlie
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
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27
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Rubino MT, Agamennone M, Campestre C, Campiglia P, Cremasco V, Faccio R, Laghezza A, Loiodice F, Maggi D, Panza E, Rossello A, Tortorella P. Biphenyl sulfonylamino methyl bisphosphonic acids as inhibitors of matrix metalloproteinases and bone resorption. ChemMedChem 2011; 6:1258-68. [PMID: 21714093 DOI: 10.1002/cmdc.201000540] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Indexed: 11/09/2022]
Abstract
A number of matrix metalloproteinases (MMPs), proteins important in the balance of bone remodeling, play a critical role both in cancer metastasis and in bone matrix turnover associated with the presence of cancer cells in bone. Here, we report the synthesis and biological evaluation of a new class of MMP inhibitors characterized by a bisphosphonate function as the zinc binding group. Since the bisphosphonate group is also implicated in osteoclast inhibition and provides a preferential affinity to biological apatite, the new molecules can be regarded as bone-seeking medicinal agents. Docking experiments were performed to clarify the mode of binding of bisphosphonate inhibitors in the active site of MMP-2. The most promising of the studied bisphosphonates showed nanomolar inhibition against MMP-2 and resulted in potent inhibition of osteoclastic bone resorption in vitro.
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Affiliation(s)
- Maria Teresa Rubino
- Dipartimento Farmaco-Chimico, Università degli Studi Aldo Moro, Via Orabona 4, 70126 Bari, Italy
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28
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Krause JG, Leskiw BD, Emery ML, McGahan ME, McCourt MP, Priefer R. Synthesis of substituted N-hydroxyureas via the in situ generation of t-butoxy isocyanate. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Ferreira ÂCB, Hochman B, Furtado F, Bonatti S, Ferreira LM. Keloids: a new challenge for nutrition. Nutr Rev 2010; 68:409-17. [DOI: 10.1111/j.1753-4887.2010.00300.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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30
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Durrant JD, de Oliveira CAF, McCammon JA. Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. J Mol Recognit 2010; 23:173-82. [PMID: 19882751 DOI: 10.1002/jmr.989] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Matrix metalloproteinases (MMPs) comprise a class of flexible proteins required for normal tissue remodeling. Overexpression of MMPs is associated with a wide range of pathophysiological processes, including vascular disease, multiple sclerosis, Alzheimer's disease, and cancer. Nearly all MMP inhibitors have failed in clinical trials, in part due to lack of specificity. Due to the highly dynamic molecular motions of the MMP-2 binding pockets, the rational drug design of MMP inhibitors has been very challenging. To address these challenges, in the current study we combine computer docking with molecular dynamics (MD) simulations in order to incorporate receptor-flexibility and induced-fit effects into the drug-design process. Our strategy identifies molecular fragments predicted to target multiple MMP-2 binding pockets.
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Affiliation(s)
- Jacob D Durrant
- Biomedical Sciences Program, University of California San Diego, La Jolla, California 92093-0365, USA
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31
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To bind zinc or not to bind zinc: an examination of innovative approaches to improved metalloproteinase inhibition. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2009; 1803:72-94. [PMID: 19712708 DOI: 10.1016/j.bbamcr.2009.08.006] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 08/12/2009] [Accepted: 08/12/2009] [Indexed: 12/14/2022]
Abstract
This short review highlights some recent advances in matrix metalloproteinase inhibitor (MMPi) design and development. Three distinct approaches to improved MMP inhibition are discussed: (1) the identification and investigation of novel zinc-binding groups (ZBGs), (2) the study of non-zinc-binding MMPi, and (3) mechanism-based MMPi that form covalent adducts with the protein. Each of these strategies is discussed and their respective advantages and remaining challenges are highlighted. The studies discussed here bode well for the development of ever more selective, potent, and well-tolerated MMPi for treating several important disease pathologies.
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Pochetti G, Montanari R, Gege C, Chevrier C, Taveras AG, Mazza F. Extra binding region induced by non-zinc chelating inhibitors into the S1' subsite of matrix metalloproteinase 8 (MMP-8). J Med Chem 2009; 52:1040-9. [PMID: 19173605 DOI: 10.1021/jm801166j] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mode of binding and the activity of the first two non-zinc chelating, potent, and selective inhibitors of human neutrophil collagenase are reported. The crystal structures of the catalytic domain of MMP-8, respectively complexed with each inhibitor, reveals that both ligands are deeply inserted into the primary specificity subsite S(1)', where they induce a similar conformational change of the surrounding loop that is endowed with the main specificity determinants of MMPs. Accord to this rearrangement, both inhibitors remove the floor of the pocket formed by the Y227 side-chain, rendering available an extra binding region never explored before. The present data show that potent and more selective inhibitors can be obtained by developing ligands able to interact with the selectivity regions of the enzyme rather than with the catalytic zinc ion, which is the common feature of all MMP members.
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Affiliation(s)
- Giorgio Pochetti
- Istituto di Cristallografia-CNR, Area della Ricerca Roma 1, Via Salaria Km.29,300, I-00016 Monterotondo Stazione, Roma, Italy.
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Jacobsen FE, Lewis JA, Cohen SM. The design of inhibitors for medicinally relevant metalloproteins. ChemMedChem 2008; 2:152-71. [PMID: 17163561 DOI: 10.1002/cmdc.200600204] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A number of metalloproteins are important medicinal targets for conditions ranging from pathogenic infections to cancer. Many but not all of these metalloproteins contain a zinc(II) ion in the protein active site. Small-molecule inhibitors of these metalloproteins are designed to bind directly to the active site metal ions. In this review several metalloproteins of interest are discussed, including matrix metalloproteinases (MMPs), histone deacetylases (HDACs), anthrax lethal factor (LF), and others. Different strategies that have been employed to design effective inhibitors against these proteins are described, with an effort to highlight the strengths and drawbacks of each approach. An emphasis is placed on examining the bioinorganic chemistry of these metal active sites and how a better understanding of the coordination chemistry in these systems may lead to improved inhibitors. It is hoped that this review will help inspire medicinal, biological, and inorganic chemists to tackle this important problem by considering all aspects of metalloprotein inhibitor design.
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Affiliation(s)
- Faith E Jacobsen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
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Agrawal A, Romero-Perez D, Jacobsen JA, Villarreal FJ, Cohen SM. Zinc-binding groups modulate selective inhibition of MMPs. ChemMedChem 2008; 3:812-20. [PMID: 18181119 PMCID: PMC2836234 DOI: 10.1002/cmdc.200700290] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Indexed: 12/29/2022]
Abstract
The need for selective matrix metalloproteinase (MMP) inhibition is of interest because of the range of pathologies mediated by different MMP isoforms. The development of more selective MMP inhibitors (MMPi) may help to overcome some of the undesired side effects that have hindered the clinical success of these compounds. In an effort to devise new approaches to selective inhibitors, herein we describe several novel MMPi and show that their selectivity is dependent on the nature of the zinc-binding group (ZBG). This is in contrast to most current MMPi, which obtain isoform selectivity solely from the peptidomimetic backbone portion of the compound. In the present study, six different hydroxypyrone and hydroxypyridinone ZBGs were appended to a common biphenyl backbone and the inhibition efficiency of each inhibitor was determined in vitro (IC(50) values) against MMP-1, -2, -3, -7, -8, -9, -12, and -13. The results show that the selectivity profile of each inhibitor is different as a result of the various ZBGs. Computational modeling studies were used to explain some trends in the observed selectivity profiles. To assess the importance of the ZBG in a biological model, two of the semiselective, potent MMPi (and one control) were evaluated using an isolated perfused rat heart system. Hearts were subjected to ischemia reperfusion injury, and recovery of contractile function was examined. In this model, only one of the two MMPi showed significant and sustained heart recovery, demonstrating that the choice of ZBG can have a significant effect in a relevant pathophysiological endpoint.
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Affiliation(s)
- Arpita Agrawal
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Diego Romero-Perez
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Jennifer A. Jacobsen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Francisco J. Villarreal
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA)
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35
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Di Costanzo L, Pique ME, Christianson DW. Crystal structure of human arginase I complexed with thiosemicarbazide reveals an unusual thiocarbonyl mu-sulfide ligand in the binuclear manganese cluster. J Am Chem Soc 2007; 129:6388-9. [PMID: 17469833 PMCID: PMC2593847 DOI: 10.1021/ja071567j] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Temperini C, Innocenti A, Guerri A, Scozzafava A, Rusconi S, Supuran CT. Phosph(on)ate as a zinc-binding group in metalloenzyme inhibitors: X-ray crystal structure of the antiviral drug foscarnet complexed to human carbonic anhydrase I. Bioorg Med Chem Lett 2007; 17:2210-5. [PMID: 17314045 DOI: 10.1016/j.bmcl.2007.01.113] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Accepted: 01/22/2007] [Indexed: 10/23/2022]
Abstract
Foscarnet (phosphonoformate trisodium salt), an antiviral used for the treatment of HIV and herpes virus infections, also acts as an activator or inhibitor of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1). Interaction of the drug with 11 CA isozymes has been investigated kinetically, and the X-ray structure of its adduct with isoform I (hCA I-foscarnet complex) has been resolved. The first CA inhibitor possessing a phosphonate zinc-binding group is thus evidenced, together with the factors governing recognition of such small molecules by a metalloenzyme active site. Foscarnet is also a clear-cut example of modulator of an enzyme activity which can act either as an activator or inhibitor of a CA isozyme.
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Affiliation(s)
- Claudia Temperini
- Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Florence), Italy
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Santos MA, Marques S, Vullo D, Innocenti A, Scozzafava A, Supuran CT. Carbonic anhydrase inhibitors: Inhibition of cytosolic/tumor-associated isoforms I, II, and IX with iminodiacetic carboxylates/hydroxamates also incorporating benzenesulfonamide moieties. Bioorg Med Chem Lett 2007; 17:1538-43. [PMID: 17251018 DOI: 10.1016/j.bmcl.2006.12.107] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 12/28/2006] [Accepted: 12/31/2006] [Indexed: 11/22/2022]
Abstract
The synthesis of a new class of sulfonamide carbonic anhydrase (CA, EC 4.2.1.1) inhibitors (CAIs), also possessing carboxylate/hydroxamate moieties in their molecule, is reported. These compounds may act on dual antitumor targets, the tumor-associated CA isozymes (CA IX) and some matrix metalloproteinases (MMPs). The compounds were prepared by an original method starting from iminodiacetic acid, and assayed as inhibitors of three isozymes, hCA I, II (cytosolic), and IX (transmembrane). The new derivatives showed weak inhibitory activity against isozyme I (K(I)s in the range of 95-8300 nM), were excellent to moderate CA II inhibitors (K(I)s in the range of 8.4-65 nM), and very good and selective CA IX inhibitors (K(I)s in the range of 3.8-26 nM). The primary sulfonamide moiety is a better zinc-binding group in the design of CAIs as compared to the carboxylate/hydroxamate one, but the presence of hydroxamate functionalities in the molecule of CAIs leads to selectivity for the tumor-associated isozyme IX over the ubiquitous, cytosolic isoform II.
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Affiliation(s)
- M Amelia Santos
- Centro de Química Estrutural, Instituto Superior Técnico, Rua Rovisco Pais 1, 1049-001 Lisbon, Portugal.
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Aschi M, Besker N, Re N, Pochetti G, Coletti C, Gallina C, Mazza F. Stereoselectivity by Enantiomeric Inhibitors of Matrix Metalloproteinase-8: New Insights from Molecular Dynamics Simulations. J Med Chem 2006; 50:211-8. [PMID: 17228863 DOI: 10.1021/jm0608457] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular Dynamics simulations in aqueous solution were performed for the matrix metalloproteinase-8 (MMP-8) free catalytic domain and for its complexes with the (R)- and (S)-[1-(4'-methoxybiphenyl-4-sulfonylamino)-2-methylpropyl] phosphonate. The 144-155 loop of the enzyme undergoes a drastic decrease of mobility once complexed with both enantiomers. The two enantiomers induce a different decrease of conformational entropy upon complexation. The higher affinity of the R-enantiomer can be related to the lower loss of conformational entropy accompanying its binding. The differences in the dynamical behavior of the protein induced by the two enantiomers are discussed at molecular level and the mode of binding of the simulated complexes is compared with that previously determined by X-ray crystallography.
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Affiliation(s)
- Massimiliano Aschi
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L'Aquila, Italia.
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Mannino C, Nievo M, Machetti F, Papakyriakou A, Calderone V, Fragai M, Guarna A. Synthesis of bicyclic molecular scaffolds (BTAa): An investigation towards new selective MMP-12 inhibitors. Bioorg Med Chem 2006; 14:7392-403. [PMID: 16899369 DOI: 10.1016/j.bmc.2006.07.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Revised: 07/03/2006] [Accepted: 07/10/2006] [Indexed: 10/24/2022]
Abstract
Starting from 3-aza-6,8-dioxa-bicyclo[3.2.1]octane scaffold (BTAa) a virtual library of molecules was generated and screened in silico against the crystal structure of the Human Macrophage Metalloelastase (MMP-12). The molecules obtaining high score were synthesized and the affinity for the catalytic domain of MMP-12 was experimentally proved by NMR experiments. A BTAa scaffold 20 having a N-hydroxyurea group in position 3 and a p-phenylbenzylcarboxy amide in position 7 showed a fair inhibition potency (IC50 = 149 microM) for MMP-12 and some selectivity towards five different MMPs. These results, taken together with the X-ray structure of the adduct between MMP-12, the inhibitor 20 and the acetohydroxamic acid (AHA), suggest that bicyclic scaffold derivatives may be exploited for the design of new selective matrix metalloproteinase inhibitors (MMPIs).
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Affiliation(s)
- Claudia Mannino
- Department of Organic Chemistry U. Schiff, University of Florence, 50019 Sesto Fiorentino (FI), Italy
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Temperini C, Innocenti A, Scozzafava A, Supuran CT. N-hydroxyurea--a versatile zinc binding function in the design of metalloenzyme inhibitors. Bioorg Med Chem Lett 2006; 16:4316-20. [PMID: 16759856 DOI: 10.1016/j.bmcl.2006.05.068] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 05/17/2006] [Accepted: 05/17/2006] [Indexed: 11/17/2022]
Abstract
N-Hydroxyurea binds both to carbonic anhydrase (CA) and to matrix metalloproteinases (MMPs). X-ray crystallography showed N-hydroxyurea to bind in a bidentate mode by means of the oxygen and nitrogen atoms of the NHOH moiety to the Zn(II) ion of CA, participating in a network of hydrogen bonds with a water molecule and Thr199. A derivatized N-hydroxyurea showed low-micromolar affinity for several CAs. This simple zinc binding function may be exploited for obtaining potent metalloenzyme inhibitors, due to its versatility of binding to the metal ion present in the active site of such enzymes.
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Affiliation(s)
- Claudia Temperini
- Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Sesto Fiorentino (Firenze), Italy
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