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Sanyal S, Amin SA, Banerjee P, Gayen S, Jha T. A review of MMP-2 structures and binding mode analysis of its inhibitors to strategize structure-based drug design. Bioorg Med Chem 2022; 74:117044. [DOI: 10.1016/j.bmc.2022.117044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 12/13/2022]
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Baidya SK, Banerjee S, Adhikari N, Jha T. Selective Inhibitors of Medium-Size S1' Pocket Matrix Metalloproteinases: A Stepping Stone of Future Drug Discovery. J Med Chem 2022; 65:10709-10754. [PMID: 35969157 DOI: 10.1021/acs.jmedchem.1c01855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Among various matrix metalloproteinases (MMPs), MMPs having medium-size S1' pockets are established as promising biomolecular targets for executing crucial roles in cancer, cardiovascular diseases, and neurodegenerative diseases. However, no such MMP inhibitors (MMPIs) are available to date as drug candidates despite a lot of continuous research work for more than three decades. Due to a high degree of structural resemblance among these MMPs, designing selective MMPIs is quite challenging. However, the variability and uniqueness of the S1' pockets of these MMPs make them promising targets for designing selective MMPIs. In this perspective, the overall structural aspects of medium-size S1' pocket MMPs including the unique binding patterns of enzyme-inhibitor interactions have been discussed in detail to acquire knowledge regarding selective inhibitor designing. This overall knowledge will surely be a curtain raiser for the designing of selective MMPIs as drug candidates in the future.
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Affiliation(s)
- Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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Das S, Amin SA, Jha T. Inhibitors of gelatinases (MMP-2 and MMP-9) for the management of hematological malignancies. Eur J Med Chem 2021; 223:113623. [PMID: 34157437 DOI: 10.1016/j.ejmech.2021.113623] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/18/2021] [Accepted: 06/03/2021] [Indexed: 12/30/2022]
Abstract
Matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9) are collectively known as gelatinases whereas MMP-2 is gelatinase-A and MMP-9 is termed as gelatinase-B. Gelatinases and other matrix metalloproteinases (MMPs) have long been associated with solid tumor invasion, metastasis and angiogenesis. However, there is paucity of data available regarding the role of gelatinases in hematological malignancies. Recent studies have shown that gelatinases activities or functions are correlated with hematological malignancies. Strategies for designing more specific gelatinase inhibitors like catalytic (CAT) domain inhibitors and hemopexin (PEX) domain inhibitors as well as signaling pathway based or gelatinase expression inhibitors had been reported against hematologic malignant cells. Several substrate based non-selective to non-substrate based relatively selective synthetic matrix metalloproteinase inhibitors (MMPIs) had been developed. Few MMPIs had reached in clinical trials during the period of 1990s-2000s. Unfortunately the anti-tumor and anti-metastatic efficacies of these MMPIs were not justified with patients having several advanced stage solid tumor cancers in any substantial number of clinical trials. Till date not a single MMPI passed phase III clinical trials designed for advanced metastatic cancers due to adverse events as well as lack of ability to show uniformity in disease prolongation. With the best of our knowledge no clinical trial study has been reported with small molecule synthetic inhibitors against hematological malignancies. This review looks at the outcome of clinical trials of MMPIs for advanced stage solid tumors. This can therefore, act as a learning experience for future development of successful gelatinase inhibitors for the management of hematological malignancies.
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Affiliation(s)
- Sanjib Das
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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Wang Y, Bartlett MJ, Denard CA, Hartwig JF, Zhao H. Combining Rh-Catalyzed Diazocoupling and Enzymatic Reduction To Efficiently Synthesize Enantioenriched 2-Substituted Succinate Derivatives. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00254] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Yajie Wang
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Mark J. Bartlett
- Department
of Chemistry, University of California-Berkeley, Berkeley, California 94720, United States
| | - Carl A. Denard
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - John F. Hartwig
- Department
of Chemistry, University of California-Berkeley, Berkeley, California 94720, United States
| | - Huimin Zhao
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Departments
of Chemistry, Biochemistry, and Bioengineering, Carl R. Woese Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Song J, Peng P, Chang J, Liu MM, Yu JM, Zhou L, Sun X. Selective non-zinc binding MMP-2 inhibitors: Novel benzamide Ilomastat analogs with anti-tumor metastasis. Bioorg Med Chem Lett 2016; 26:2174-8. [PMID: 27038494 DOI: 10.1016/j.bmcl.2016.03.064] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/14/2016] [Accepted: 03/16/2016] [Indexed: 12/31/2022]
Abstract
Novel Ilomastat analogs with substituted benzamide groups, instead of hydroxamic acid groups, were designed, synthesized and evaluated against MMP-2 and MMP-9. Among these analogs, the most potent compound 10a exhibited potent inhibitory activity against MMP-2 with IC50 value of 0.19 nM, which is 5 times more potent than that of Ilomastat (IC50=0.94 nM). Importantly, 10a exhibited more than 8300 fold selectivity for MMP-2 versus MMP-9 (IC50=1.58 μM). Molecular docking studies showed that 10a bond to the catalytic active pocket of MMP-2 by a non-zinc-chelating mechanism which was different from that of Ilomastat. Furthermore, the invasion assay showed that 10a was effective in reducing HEY cells invasion at 84.6% in 50 μM concentration. For 10a, the pharmacokinetic properties had been improved and especially the more desirable t1/2z was achieved compared with these of the lead compound Ilomastat.
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Affiliation(s)
- Jiao Song
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Peng Peng
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Jun Chang
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Ming-Ming Liu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Jian-Ming Yu
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.
| | - Xun Sun
- Department of Natural Products Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China; Shanghai Key Lab of Clinical Geriatric Medicine, 221 West Yanan Road, Shanghai 200040, China.
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Bourguet E, Brazhnik K, Sukhanova A, Moroy G, Brassart-Pasco S, Martin AP, Villena I, Bellon G, Sapi J, Nabiev I. Design, Synthesis, and Use of MMP-2 Inhibitor-Conjugated Quantum Dots in Functional Biochemical Assays. Bioconjug Chem 2016; 27:1067-81. [DOI: 10.1021/acs.bioconjchem.6b00065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Erika Bourguet
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, SFR Cap-Santé, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Kristina Brazhnik
- Laboratoire de Recherche en Nanosciences, LRN - EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe shosse, 115409 Moscow, Russian Federation
| | - Alyona Sukhanova
- Laboratoire de Recherche en Nanosciences, LRN - EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe shosse, 115409 Moscow, Russian Federation
| | - Gautier Moroy
- Molécules Thérapeutiques In Silico, INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité, 35 rue Hélène Brion, 75013 Paris, France
| | - Sylvie Brassart-Pasco
- Laboratoire de Biochimie et de Biologie moléculaire, MEDyC, UMR CNRS/URCA 7369, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Anne-Pascaline Martin
- Laboratoire de Biochimie et de Biologie moléculaire, MEDyC, UMR CNRS/URCA 7369, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratoire de Parasitologie-Mycologie, EA3800, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51100 Reims, France
| | - Isabelle Villena
- Laboratoire de Parasitologie-Mycologie, EA3800, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51100 Reims, France
| | - Georges Bellon
- Laboratoire de Biochimie et de Biologie moléculaire, MEDyC, UMR CNRS/URCA 7369, SFR Cap-Santé, UFR de Médecine, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Janos Sapi
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, SFR Cap-Santé, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
| | - Igor Nabiev
- Laboratoire de Recherche en Nanosciences, LRN - EA4682, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51100 Reims, France
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe shosse, 115409 Moscow, Russian Federation
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Marković D, Barboux C, Salle de Chou Y, Bettach J, Grougnet R, Deguin B. Centrifugal partition chromatography: an efficient tool to access highly polar and unstable synthetic compounds on a large scale. RSC Adv 2014. [DOI: 10.1039/c4ra12141d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Bernasconi M, Müller MA, Pfaltz A. Asymmetric Hydrogenation of Maleic Acid Diesters and Anhydrides. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Bernasconi M, Müller MA, Pfaltz A. Asymmetric Hydrogenation of Maleic Acid Diesters and Anhydrides. Angew Chem Int Ed Engl 2014; 53:5385-8. [DOI: 10.1002/anie.201402034] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 11/10/2022]
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Hydroxamic Acids as Matrix Metalloproteinase Inhibitors. MATRIX METALLOPROTEINASE INHIBITORS 2012; 103:137-76. [DOI: 10.1007/978-3-0348-0364-9_5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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Zhong H, Wees MA, Faure TD, Carrillo C, Arbiser J, Bowen JP. The impact of ionization States of matrix metalloproteinase inhibitors on docking-based inhibitor design. ACS Med Chem Lett 2011; 2:455-60. [PMID: 24900330 DOI: 10.1021/ml200031m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 03/29/2011] [Indexed: 12/13/2022] Open
Abstract
The influence of ionization states of hydroxamates and retrohydroxamates and the presence of zinc ions in the active site were investigated using the wild-type and E402Q mutant of MMP-9. The deprotonated hydroxamates showed a significantly enhanced enrichment factor in the presence of zinc ions. A pharmacophore model was developed based on the deprotonated compounds and was used to identify four structurally diverse compounds with antiproliferative activities.
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Affiliation(s)
- Haizhen Zhong
- Department of Chemistry, University of Nebraska at Omaha, DSC362, 6001 Dodge Street, Omaha, Nebraska 68182, United States
| | - Melissa A. Wees
- Department of Chemistry, University of Nebraska at Omaha, DSC362, 6001 Dodge Street, Omaha, Nebraska 68182, United States
| | - Theresa D. Faure
- Department of Chemistry, University of Nebraska at Omaha, DSC362, 6001 Dodge Street, Omaha, Nebraska 68182, United States
| | - Carol Carrillo
- Department of Dermatology, School of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Jack Arbiser
- Department of Dermatology, School of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - J. Phillip Bowen
- Center for Drug Discovery, Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, 2901 East Lee Street, Suite 2200, Greensboro, North Carolina 27401, United States
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Moroy G, Bourguet E, Decarme M, Sapi J, Alix AJP, Hornebeck W, Lorimier S. Inhibition of human leukocyte elastase, plasmin and matrix metalloproteinases by oleic acid and oleoyl-galardin derivative(s). Biochem Pharmacol 2011; 81:626-35. [PMID: 21146503 DOI: 10.1016/j.bcp.2010.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 11/29/2010] [Accepted: 12/01/2010] [Indexed: 10/18/2022]
Abstract
Molecular modeling was undertaken at aims to analyze the interactions between oleic acid and human leukocyte elastase (HLE), plasmin and matrix metalloproteinase-2 (MMP-2), involved in the inhibitory capacity of fatty acid towards those proteases. The carboxylic acid group of the fatty acid was found to form a salt bridge with Arg(217) of HLE while unsaturation interacted with Phe(192) and Val(216) at the S(3) subsite, and alkyl end group occupied S(1) subsite. In keeping with the main contribution of kringle 5 domain in plasmin-oleic acid interaction [Huet E et al. Biochem Pharmacol 2004;67(4):643-54], docking computations revealed that the long alkyl chain of fatty acid inserted within an hydrophobic groove of this domain with the carboxylate forming a salt bridge with Arg(512). Finally, blind docking revealed that oleic acid could occupy both S'(1) subsite and Fn(II)(3) domain of MMP-2. Several residues involved in Fn(II)(3)/oleic acid interaction were similarly implicated in binding of this domain to collagen. Oleic acid was covalently linked to galardin (at P'(2) position): OL-GAL (CONHOH) or to its carboxylic acid counterpart: OL-GAL (COOH), with the idea to obtain potent MMP inhibitors able to also interfere with elastase and plasmin activity. OL-GALs were found less potent MMP inhibitors as compared to galardin and no selectivity for MMP-2 or MMP-9 could be demonstrated. Docking computations indicated that contrary to oleic acid, OL-GAL binds only to MMP-2 active site and surprisingly, hydroxamic acid was unable to chelate Zn, but instead forms a salt bridge with the N-terminal Tyr(110). Interestingly, oleic acid and particularly OL-GALs proved to potently inhibit MMP-13. OL-GAL was found as potent as galardin (K(i) equal to 1.8nM for OL-GAL and 1.45nM for GAL) and selectivity for that MMP was attained (2-3 log orders of difference in inhibitory potency as compared to other MMPs). Molecular modeling studies indicated that oleic acid could be accommodated within S'(1) pocket of MMP-13 with carboxylic acid chelating Zn ion. OL-GAL also occupied such pocket but hydroxamic acid did not interact with Zn but instead was located at 2.8Å from Tyr(176). Since these derivatives retained, as their oleic acid original counterpart, the capacity to inhibit the amidolytic activity of HLE and plasmin as well as to decrease HLE- and plasmin-mediated pro MMP-3 activation, they might be of therapeutic value to control proteolytic cascades in chronic inflammatory disorders.
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Affiliation(s)
- Gautier Moroy
- Université Paris Diderot, Molécules thérapeutiques in silico, INSERM UMR-S-973, Bât. Lamarck, 35 rue Hélène Brion, 75205 Paris Cedex 13, France.
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Abstract
IMPORTANCE OF THE FIELD Bones play many roles in the body, providing structure, protecting organs, anchoring muscles and storing calcium. Over 100 million people worldwide suffer from bone diseases, mainly osteoporosis, cancer-related bone loss, osteoarthritis and inflammatory arthritis. Osteoporosis itself has no specific symptoms, and the main consequence is the increased risk of bone fractures. Therefore, the prevention of bone diseases is important to maintain the quality of life in the human society. However, treatment options are still insufficient. AREAS COVERED IN THIS REVIEW This review article gives a summary of the low molecular mass modulators of bone diseases targets disclosed in patent applications and articles, mainly during the last 5 years. WHAT THE READER WILL GAIN Readers will rapidly gain an overview of these modulators not only for historical targets, but also of emerging and re-visited targets. Readers will also be able to see the current research trend and the main players in this field. TAKE HOME MESSAGE Drug discovery for bone diseases has made progress in the last years. The research area has dynamically shifted from historical targets (bisphosphonate, parathyroid hormone and calcitonin) to newly confirmed targets or targets re-visited which were biologically validated in the past. Cathepsin K inhibitors should be very close to launching in the market.
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Affiliation(s)
- Keiichi Masuya
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
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Rouffet M, Denhez C, Bourguet E, Bohr F, Guillaume D. In silico study of MMP inhibition. Org Biomol Chem 2009; 7:3817-25. [DOI: 10.1039/b910543c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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LeDour G, Moroy G, Rouffet M, Bourguet E, Guillaume D, Decarme M, ElMourabit H, Augé F, Alix AJ, Laronze JY, Bellon G, Hornebeck W, Sapi J. Introduction of the 4-(4-bromophenyl)benzenesulfonyl group to hydrazide analogs of Ilomastat leads to potent gelatinase B (MMP-9) inhibitors with improved selectivity. Bioorg Med Chem 2008; 16:8745-59. [DOI: 10.1016/j.bmc.2008.07.041] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 07/08/2008] [Accepted: 07/16/2008] [Indexed: 11/17/2022]
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