1
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Hu G, Guo H, Lu L, Zhang Z, Tang Y, Zuo J, Wang X. Unveiling esophageal cancer treatment mechanisms: network pharmacology and molecular docking of Physcion. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03283-5. [PMID: 39023545 DOI: 10.1007/s00210-024-03283-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024]
Abstract
This study investigates the effects of Physcion on esophageal cancer and its possible mechanisms of action. Potential Physcion targets were identified using databases. Transcriptomic data from 17 esophageal cancer and adjacent tissues were analyzed to find differentially expressed genes, intersecting with potential targets to select 16 key genes. Their expression and distribution were evaluated in patient sequencing data. Diagnostic potential was assessed through differential gene expression and ROC curves. Pathway enrichment analysis was performed using KEGG, and molecular docking simulations were conducted to assess Physcion's binding affinity to key genes. In vitro assays complemented these findings. A total of 161 drug targets were identified, narrowing down to 16 pivotal genes. Expression patterns were examined across cell populations, and enrichment analysis showed significant PI3K/AKT pathway involvement. Molecular docking indicated strong binding of Physcion to HSP90AA1 and MMP2. In vitro assays confirmed Physcion's dose- and time-dependent impact on esophageal cancer cells, with significant DAPI staining effects. Physcion shows promise as a therapeutic agent for esophageal cancer. The study supports its potential for clinical development and future research in esophageal cancer treatment.
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Affiliation(s)
- Guangbing Hu
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Haiyang Guo
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Liuyi Lu
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - ZongYao Zhang
- Department of General Surgery, The First Affiliated Hospital of Anhui University of Science and Technology, No. 203 Huai Bin Road, Tian Jia'an District, Huainan, 232007, China
| | - Yong Tang
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Ji Zuo
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Xianfei Wang
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, Sichuan, China.
- Digestive Endoscopy Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, Sichuan, China.
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2
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Oka Y, Abe-Sato K, Tabuse H, Yasukawa Y, Yahara T, Nishimoto T, Kamitani M, Fukunaga T, Ochiai N, Kumasaka-Abe T, Hitaka K, Gunji E, Ohara H, Takeda T, Kojima N, Asami T. Discovery of TP0628103: A Highly Potent and Selective MMP-7 Inhibitor with Reduced OATP-Mediated Clearance Designed by Shifting Isoelectric Points. J Med Chem 2024; 67:1406-1420. [PMID: 38214909 DOI: 10.1021/acs.jmedchem.3c01967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Matrix metalloproteinase-7 (MMP-7) has been shown to play an important role in pathophysiological processes such as cancer and fibrosis. We previously discovered selective MMP-7 inhibitors by molecular hybridization and structure-based drug design. However, the systemic clearance (CLtot) of the biologically active lead compound was very high. Because our studies revealed that hepatic uptake by organic anion transporting polypeptide (OATP) was responsible for the high CLtot, we found a novel approach to reducing their uptake based on isoelectric point (IP) values as an indicator for substrate recognition by OATP1B1/1B3. Our "IP shift strategy" to adjust the IP values culminated in the discovery of TP0628103 (18), which is characterized by reduced in vitro OATP-mediated hepatic uptake and in vivo CLtot. Our in vitro-in vivo extrapolation of OATP-mediated clearance and the "IP shift strategy" provide crucial insights for a new medicinal chemistry approach to reducing the systemic clearance of OATP1B1/1B3 substrates.
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Affiliation(s)
- Yusuke Oka
- Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Kumi Abe-Sato
- Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Hideaki Tabuse
- Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Yoshifumi Yasukawa
- Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Tohru Yahara
- Drug Metabolism and Pharmacokinetics Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Tomohiro Nishimoto
- Drug Metabolism and Pharmacokinetics Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Masafumi Kamitani
- Discovery Technologies Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Takuya Fukunaga
- Discovery Technologies Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Nagahiro Ochiai
- Discovery Technologies Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Tomoko Kumasaka-Abe
- Discovery Technologies Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Kosuke Hitaka
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Emi Gunji
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Hiroki Ohara
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Takuya Takeda
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Naoki Kojima
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Taiji Asami
- Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
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3
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Aduriz-Arrizabalaga J, Mercero JM, De Sancho D, Lopez X. Rules governing metal coordination in Aβ-Zn(II) complex models from quantum mechanical calculations. Phys Chem Chem Phys 2023; 25:27618-27627. [PMID: 37811710 DOI: 10.1039/d3cp02070c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Transition metals directly contribute to the neurotoxicity of the aggregates of the amyloid-forming Aβ peptide. The understanding and rationalization of the coordination modes of metals to Aβ amyloid is, therefore, of paramount importance to understand the capacity of a given metal to promote peptide aggregation. Experimentally, multiple Aβ-metal structures have been resolved, which exhibit different modes of coordination in both the monomeric and oligomeric forms of Aβ. Although Zn(II) metalloproteins are very abundant and often involve cysteine residues in the first coordination shell, in the case of Aβ-Zn(II), though, Zn(II) is coordinated by glutamic/aspartic acid and/or histidine residues exclusively, making for an interesting case study. Here we present a systematic analysis of the underlying chemistry on Aβ-Zn(II) coordination, where relative stabilities of different coordination arrangements indicate that a mixture of Glu/Asp and His residues is favored. A detailed comparison between different coordination shell geometries shows that tetrahedral coordination is generally favored in the aqueous phase. Our calculations show an interplay between dative covalent interactions and electrostatics which explains the observed trends. Multiple structures deposited in the Protein Data Bank support our findings, suggesting that the trends found in our work may be transferable to other Zn(II) metalloproteins with this type of coordination.
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Affiliation(s)
- Julen Aduriz-Arrizabalaga
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), PK 1072, 20018 Donostia-San Sebastian, Euskadi, Spain.
| | - Jose M Mercero
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), PK 1072, 20018 Donostia-San Sebastian, Euskadi, Spain.
| | - David De Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), PK 1072, 20018 Donostia-San Sebastian, Euskadi, Spain.
| | - Xabier Lopez
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), PK 1072, 20018 Donostia-San Sebastian, Euskadi, Spain.
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4
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Hayun H, Coban M, Bhagat AK, Ozer E, Alfonta L, Caulfield TR, Radisky ES, Papo N. Utilizing genetic code expansion to modify N-TIMP2 specificity towards MMP-2, MMP-9, and MMP-14. Sci Rep 2023; 13:5186. [PMID: 36997589 PMCID: PMC10063552 DOI: 10.1038/s41598-023-32019-3] [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: 01/05/2023] [Accepted: 03/21/2023] [Indexed: 04/01/2023] Open
Abstract
Matrix metalloproteinases (MMPs) regulate the degradation of extracellular matrix (ECM) components in biological processes. MMP activity is controlled by natural tissue inhibitors of metalloproteinases (TIMPs) that non-selectively inhibit the function of multiple MMPs via interaction with the MMPs' Zn2+-containing catalytic pocket. Recent studies suggest that TIMPs engineered to confer MMP specificity could be exploited for therapeutic purposes, but obtaining specific TIMP-2 inhibitors has proved to be challenging. Here, in an effort to improve MMP specificity, we incorporated the metal-binding non-canonical amino acids (NCAAs), 3,4-dihydroxyphenylalanine (L-DOPA) and (8-hydroxyquinolin-3-yl)alanine (HqAla), into the MMP-inhibitory N-terminal domain of TIMP2 (N-TIMP2) at selected positions that interact with the catalytic Zn2+ ion (S2, S69, A70, L100) or with a structural Ca2+ ion (Y36). Evaluation of the inhibitory potency of the NCAA-containing variants towards MMP-2, MMP-9 and MMP-14 in vitro revealed that most showed a significant loss of inhibitory activity towards MMP-14, but not towards MMP-2 and MMP-9, resulting in increased specificity towards the latter proteases. Substitutions at S69 conferred the best improvement in selectivity for both L-DOPA and HqAla variants. Molecular modeling provided an indication of how MMP-2 and MMP-9 are better able to accommodate the bulky NCAA substituents at the intermolecular interface with N-TIMP2. The models also showed that, rather than coordinating to Zn2+, the NCAA side chains formed stabilizing polar interactions at the intermolecular interface with MMP-2 and MMP-9. Our findings illustrate how incorporation of NCAAs can be used to probe-and possibly exploit-differential tolerance for substitution within closely related protein-protein complexes as a means to improve specificity.
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Affiliation(s)
- Hezi Hayun
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, 84105, Beer-Sheva, Israel
| | - Matt Coban
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, 310 Griffin Building, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Ashok Kumar Bhagat
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Eden Ozer
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Lital Alfonta
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Thomas R Caulfield
- Departments of Neuroscience, Artificial Intelligence and Informatics, Computational Biology and Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Jacksonville, FL, 32224, USA.
| | - Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, 310 Griffin Building, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
| | - Niv Papo
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, 84105, Beer-Sheva, Israel.
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5
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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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6
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Cyclic peptides as an inhibitor of metastasis in breast cancer targeting MMP-1: Computational approach. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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7
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Tabuse H, Abe-Sato K, Kanazawa H, Yashiro M, Tamura Y, Kamitani M, Hitaka K, Gunji E, Mitani A, Kojima N, Oka Y. Discovery of Highly Potent and Selective Matrix Metalloproteinase-7 Inhibitors by Hybridizing the S1' Subsite Binder with Short Peptides. J Med Chem 2022; 65:13253-13263. [PMID: 36137271 DOI: 10.1021/acs.jmedchem.2c01088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Matrix metalloproteinase-7 (MMP-7) has emerged as a protein playing important roles in both physiological and pathophysiological processes. Despite the growing interest in MMP-7 as a potential therapeutic target for diseases including cancer and fibrosis, potent and selective MMP-7 inhibitors have yet to be identified. Compound 1, previously reported by Edman and co-workers, binds to the S1' subsite of MMP-7, exhibiting moderate inhibitory activity and selectivity. To achieve both higher inhibitory activity and selectivity, we conceived hybridizing 1 with short peptides. The initially designed compound 6, which was a hybrid molecule between 1 and a tripeptide (Ala-Leu-Met) derived from an MMP-2-inhibitory peptide (APP-IP), showed enhanced MMP-7-inhibitory activity. Subsequent optimization of the peptide moiety led to the development of compound 18 with remarkable potency for MMP-7 and selectivity over other MMP subtypes.
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Affiliation(s)
- Hideaki Tabuse
- Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Kumi Abe-Sato
- Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Harumi Kanazawa
- Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Miyoko Yashiro
- Discovery Technologies Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Yunoshin Tamura
- Discovery Technologies Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Masafumi Kamitani
- Discovery Technologies Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Kosuke Hitaka
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Emi Gunji
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Akiko Mitani
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Naoki Kojima
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Yusuke Oka
- Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
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8
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Takeuchi T, Hayashi M, Tamita T, Nomura Y, Kojima N, Mitani A, Takeda T, Hitaka K, Kato Y, Kamitani M, Mima M, Toki H, Ohkubo M, Nozoe A, Kakinuma H. Discovery of Aryloxyphenyl-Heptapeptide Hybrids as Potent and Selective Matrix Metalloproteinase-2 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis. J Med Chem 2022; 65:8493-8510. [PMID: 35687819 DOI: 10.1021/acs.jmedchem.2c00613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Matrix metalloproteinase-2 (MMP2) is a zinc-dependent endopeptidase that plays important roles in the degradation of extracellular matrix proteins. MMP2 is considered to be an attractive target for the treatment of various diseases such as cancer, arthritis, and fibrosis. In this study, we have developed a novel class of MMP2-selective inhibitors by hybridizing the peptide that binds to a zinc ion and S2-S5 pockets with small molecules that bind to the S1' pocket. Structural modifications based on X-ray crystallography revealed that the introduction of 2,4-diaminobutanoic acid (Dab) at position 4 dramatically enhanced MMP2 selectivity by forming an electrostatic interaction with Glu130. After improving the metabolic and chemical stability, TP0556351 (9) was identified. It exhibited potent MMP2 inhibitory activity (IC50 = 0.20 nM) and extremely high selectivity. It suppressed the accumulation of collagen in a bleomycin-induced idiopathic pulmonary fibrosis model in mice, demonstrating the efficacy of MMP2-selective inhibitors for fibrosis.
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Affiliation(s)
| | - Masato Hayashi
- Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan
| | - Tomoko Tamita
- Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan
| | - Yusaku Nomura
- Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan
| | - Naoki Kojima
- Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan
| | - Akiko Mitani
- Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan
| | - Takuya Takeda
- Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan
| | - Kosuke Hitaka
- Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan
| | - Yuki Kato
- Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan
| | | | - Masashi Mima
- Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan
| | - Hidetoh Toki
- Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan
| | | | - Akiko Nozoe
- Taisho Pharmaceutical Co., Ltd., Saitama 331-9530, Japan
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9
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A fragment-based structural analysis of MMP-2 inhibitors in search of meaningful structural fragments. Comput Biol Med 2022; 144:105360. [DOI: 10.1016/j.compbiomed.2022.105360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 11/21/2022]
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10
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Tsaban T, Varga JK, Avraham O, Ben-Aharon Z, Khramushin A, Schueler-Furman O. Harnessing protein folding neural networks for peptide-protein docking. Nat Commun 2022; 13:176. [PMID: 35013344 PMCID: PMC8748686 DOI: 10.1038/s41467-021-27838-9] [Citation(s) in RCA: 228] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/10/2021] [Indexed: 12/31/2022] Open
Abstract
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2 and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we show that, although these deep learning approaches have originally been developed for the in silico folding of protein monomers, AlphaFold2 also enables quick and accurate modeling of peptide-protein interactions. Our simple implementation of AlphaFold2 generates peptide-protein complex models without requiring multiple sequence alignment information for the peptide partner, and can handle binding-induced conformational changes of the receptor. We explore what AlphaFold2 has memorized and learned, and describe specific examples that highlight differences compared to state-of-the-art peptide docking protocol PIPER-FlexPepDock. These results show that AlphaFold2 holds great promise for providing structural insight into a wide range of peptide-protein complexes, serving as a starting point for the detailed characterization and manipulation of these interactions.
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Affiliation(s)
- Tomer Tsaban
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Julia K Varga
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orly Avraham
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ziv Ben-Aharon
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alisa Khramushin
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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11
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Xia Y, To J, Chan N, Hu S, Liew HT, Balamkundu S, Zhang X, Lescar J, Bhattacharjya S, Tam JP, Liu C. N
γ
‐Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yiyin Xia
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Janet To
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Ning‐Yu Chan
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Side Hu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Heng Tai Liew
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Seetharamsing Balamkundu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
- Singapore-MIT Alliance for Research and Technology Singapore 138602 Singapore
| | - Xiaohong Zhang
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Julien Lescar
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - James P. Tam
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Chuan‐Fa Liu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
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12
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Xia Y, To J, Chan NY, Hu S, Liew HT, Balamkundu S, Zhang X, Lescar J, Bhattacharjya S, Tam JP, Liu CF. N γ -Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases. Angew Chem Int Ed Engl 2021; 60:22207-22211. [PMID: 34396662 DOI: 10.1002/anie.202108125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 11/10/2022]
Abstract
Peptidyl asparaginyl ligases (PALs) are powerful tools for peptide macrocyclization. Herein, we report that a derivative of Asn, namely Nγ -hydroxyasparagine or Asn(OH), is an unnatural P1 substrate of PALs. By Asn(OH)-mediated cyclization, we prepared cyclic peptides as new matrix metalloproteinase 2 (MMP2) inhibitors displaying the hydroxamic acid moiety of Asn(OH) as the key pharmacophore. The most potent cyclic peptide (Ki =2.8±0.5 nM) was built on the hyperstable tetracyclic scaffold of rhesus theta defensin-1. The Asn(OH) residue in the cyclized peptides can also be readily oxidized to Asp. By this approach, we synthesized several bioactive Asp-containing cyclic peptides (MCoTI-II, kB2, SFTI, and integrin-targeting RGD peptides) that are otherwise difficult targets for PAL-catalyzed cyclization owing to unfavorable kinetics of the P1-Asp substrates. This study demonstrates that substrate engineering is a useful strategy to expand the application of PAL ligation in the synthesis of therapeutic cyclic peptides.
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Affiliation(s)
- Yiyin Xia
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Janet To
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Ning-Yu Chan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Heng Tai Liew
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Seetharamsing Balamkundu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.,Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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13
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Daood U, Bapat RA, Sidhu P, Ilyas MS, Khan AS, Mak KK, Pichika MR, Nagendrababu V, Peters OA. Antibacterial and antibiofilm efficacy of k21-E in root canal disinfection. Dent Mater 2021; 37:1511-1528. [PMID: 34420798 DOI: 10.1016/j.dental.2021.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/21/2021] [Accepted: 08/04/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES The aim of the current project was to study the antimicrobial efficacy of a newly developed irrigant, k21/E against E. faecalis biofilm. METHODS Root canals were instrumented and randomly divided into the following groups: irrigation with saline, 6% NaOCl (sodium hypochlorite), 6% NaOCl+2% CHX (Chlorhexidine), 2% CHX, 0.5% k21/E (k21 - quaternary ammonium silane) and 1% k21/E. E. faecalis were grown (3-days) (1×107CFU mL-1), treated, and further cultured for 11-days. Specimens were subjected to SEM, confocal and Raman analysis and macrophage vesicles characterized along with effect of lipopolysaccharide treatment. 3T3 mouse-fibroblasts were cultured for alizarin-red with Sortase-A active sites and Schrödinger docking was performed. TEM analysis of root dentin substrate with matrix metalloproteinases profilometry was also included. A cytotoxic test analysis for cell viability was measured by absorbance of human dental pulp cells after exposure to different irrigant solutions for 24h. The test percentages have been highlighted in Table 1. RESULTS Among experimental groups, irrigation with 0.5% k21/E showed phase separation revealing significant bacterial reduction and lower phenylalanine 1003cm-1 and Amide III 1245cm-1 intensities. Damage was observed on bacterial cell membrane after use of k21/E. No difference in exosomes distribution between control and 0.5%k21/E was observed with less TNFα (*p<0.05) and preferential binding of SrtA. TEM images demonstrated integrated collagen fibers in control and 0.5%k21/E specimens and inner bacterial membrane damage after k21/E treatment. The k21 groups appeared to be biocompatible to the dental pulpal cells grown for 24h. SIGNIFICANCE Current investigations highlight potential advantages of 0.5% k21/E as irrigation solution for root canal disinfection.
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Affiliation(s)
- Umer Daood
- Division of Clinical Dentistry, School of Dentistry, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000 Bukit Jalil, Wilayah Persekutuan Kuala Lumpur, Malaysia.
| | - Ranjeet Ajit Bapat
- Division of Clinical Dentistry, School of Dentistry, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000 Bukit Jalil, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Preena Sidhu
- Division of Clinical Dentistry, School of Dentistry, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000 Bukit Jalil, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Muhammad Sharjeel Ilyas
- Department of Oral Biology, Post Graduate Medical Institute, 6 Birdwood Road, Lahore, Pakistan
| | - Abdul Samad Khan
- Department of Restorative Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Kit-Kay Mak
- School of Pharmacy, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000 Bukit Jalil, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Mallikarjuna Rao Pichika
- School of Pharmacy, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000 Bukit Jalil, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | | | - Ove A Peters
- School of Dentistry, University of Queensland, Herston, Qld 4006, Australia; Department of Endodontics, Arthur A Dugoni School of Dentistry, University of the Pacific, San Francisco, CA, USA
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14
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Kulakova AM, Khrenova MG. Relationship Between Matrix Metalloproteinase-2 Inhibition Constants With APP-IP Oligopeptide and Its Mutant Forms and Electronic Binding Descriptors. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2021. [DOI: 10.1134/s1990793121030246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Bassiouni W, Ali MAM, Schulz R. Multifunctional intracellular matrix metalloproteinases: implications in disease. FEBS J 2021; 288:7162-7182. [PMID: 33405316 DOI: 10.1111/febs.15701] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that were first discovered as proteases, which target and cleave extracellular proteins. During the past 20 years, however, intracellular roles of MMPs were uncovered and research on this new aspect of their biology expanded. MMP-2 is the first of this protease family to be reported to play a crucial intracellular role where it cleaves several sarcomeric proteins inside cardiac myocytes during oxidative stress-induced injury. Beyond MMP-2, currently at least eleven other MMPs are known to function intracellularly including MMP-1, MMP-3, MMP-7, MMP-8, MMP-9, MMP-10, MMP-11, MMP-12, MMP-14, MMP-23 and MMP-26. These intracellular MMPs are localized to different compartments inside the cell including the cytosol, sarcomere, mitochondria, and the nucleus. Intracellular MMPs contribute to the pathogenesis of various diseases. Cardiovascular renal disorders, inflammation, and malignancy are some examples. They also exert antiviral and bactericidal effects. Interestingly, MMPs can act intracellularly through both protease-dependent and protease-independent mechanisms. In this review, we will highlight the intracellular mechanisms of MMPs activation, their numerous subcellular locales, substrates, and roles in different pathological conditions. We will also discuss the future direction of MMP research and the necessity to exploit the knowledge of their intracellular targets and actions for the design of targeted inhibitors.
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Affiliation(s)
- Wesam Bassiouni
- Department of Pharmacology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Mohammad A M Ali
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, State University of New York-Binghamton, NY, USA
| | - Richard Schulz
- Department of Pharmacology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada.,Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
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16
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Yano H, Nishimiya D, Kawaguchi Y, Tamura M, Hashimoto R. Discovery of potent and specific inhibitors targeting the active site of MMP-9 from the engineered SPINK2 library. PLoS One 2020; 15:e0244656. [PMID: 33373399 PMCID: PMC7771667 DOI: 10.1371/journal.pone.0244656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/14/2020] [Indexed: 11/19/2022] Open
Abstract
Matrix metalloproteinases (MMPs) contribute to many physiological and pathological phenomena via the proteolysis of extracellular matrix components. Specific blocking of the active site of each MMP sheds light on its particular role. However, it remains difficult to acquire an active-site inhibitor with high specificity for only the target MMP due to the highly conserved structure around the active site of MMPs. Recently, we reported that potent and specific inhibitors of serine proteases were obtained from our proprietary engineered serine protease inhibitor Kazal type 2 (SPINK2) library. In this research, using this library, we succeeded in obtaining potent and specific MMP-9 inhibitors. The obtained inhibitors bound to the active site of MMP-9 and inhibited MMP-9 with low nanomolar Ki values. The inhibitors did not cross-react with other MMPs that we tested. Further analysis using MMP-9 mutants demonstrated that the inhibitors recognize not only the residues around the conserved active site of MMP-9 but also different and unique residues in exosites that are distant from each other. This unique recognition manner, which can be achieved by the large interface provided by engineered SPINK2, may contribute to the generation of specific active-site inhibitors of MMPs.
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Affiliation(s)
- Hidenori Yano
- Modality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Daisuke Nishimiya
- Modality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Yoshirou Kawaguchi
- Modality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Masakazu Tamura
- Modality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Ryuji Hashimoto
- Modality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., Tokyo, Japan
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17
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Zipfel P, Rochais C, Baranger K, Rivera S, Dallemagne P. Matrix Metalloproteinases as New Targets in Alzheimer's Disease: Opportunities and Challenges. J Med Chem 2020; 63:10705-10725. [PMID: 32459966 DOI: 10.1021/acs.jmedchem.0c00352] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although matrix metalloproteinases (MMPs) are implicated in the regulation of numerous physiological processes, evidence of their pathological roles have also been obtained in the last decades, making MMPs attractive therapeutic targets for several diseases. Recent discoveries of their involvement in central nervous system (CNS) disorders, and in particular in Alzheimer's disease (AD), have paved the way to consider MMP modulators as promising therapeutic strategies. Over the past few decades, diverse approaches have been undertaken in the design of therapeutic agents targeting MMPs for various purposes, leading, more recently, to encouraging developments. In this article, we will present recent examples of inhibitors ranging from small molecules and peptidomimetics to biologics. We will also discuss the scientific knowledge that has led to the development of emerging tools and techniques to overcome the challenges of selective MMP inhibition.
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Affiliation(s)
- Pauline Zipfel
- Normandie Univ, UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), F-14032 Caen, France
| | - Christophe Rochais
- Normandie Univ, UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), F-14032 Caen, France
| | - Kévin Baranger
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, Marseille, France
| | - Santiago Rivera
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, Marseille, France
| | - Patrick Dallemagne
- Normandie Univ, UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), F-14032 Caen, France
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18
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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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19
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Cerofolini L, Fragai M, Luchinat C. Mechanism and Inhibition of Matrix Metalloproteinases. Curr Med Chem 2019; 26:2609-2633. [PMID: 29589527 DOI: 10.2174/0929867325666180326163523] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 01/02/2023]
Abstract
Matrix metalloproteinases hydrolyze proteins and glycoproteins forming the extracellular matrix, cytokines and growth factors released in the extracellular space, and membrane-bound receptors on the outer cell membrane. The pathological relevance of MMPs has prompted the structural and functional characterization of these enzymes and the development of synthetic inhibitors as possible drug candidates. Recent studies have provided a better understanding of the substrate preference of the different members of the family, and structural data on the mechanism by which these enzymes hydrolyze the substrates. Here, we report the recent advancements in the understanding of the mechanism of collagenolysis and elastolysis, and we discuss the perspectives of new therapeutic strategies for targeting MMPs.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
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20
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Maola K, Wilbs J, Touati J, Sabisz M, Kong X, Baumann A, Deyle K, Heinis C. Engineered Peptide Macrocycles Can Inhibit Matrix Metalloproteinases with High Selectivity. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Khan Maola
- Institute of Chemical Sciences and Engineering École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Jonas Wilbs
- Institute of Chemical Sciences and Engineering École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Jeremy Touati
- Institute of Chemical Sciences and Engineering École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Michal Sabisz
- Institute of Chemical Sciences and Engineering École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Xu‐Dong Kong
- Institute of Chemical Sciences and Engineering École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Alice Baumann
- Institute of Chemical Sciences and Engineering École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Kaycie Deyle
- Institute of Chemical Sciences and Engineering École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
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21
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Maola K, Wilbs J, Touati J, Sabisz M, Kong XD, Baumann A, Deyle K, Heinis C. Engineered Peptide Macrocycles Can Inhibit Matrix Metalloproteinases with High Selectivity. Angew Chem Int Ed Engl 2019; 58:11801-11805. [PMID: 31251434 DOI: 10.1002/anie.201906791] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Indexed: 11/10/2022]
Abstract
Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases at the intersection of health and disease due to their involvement in processes such as tissue repair and immunity as well as cancer and inflammation. Because of the high structural conservation in the catalytic domains and shallow substrate binding sites, selective, small-molecule inhibitors of MMPs have remained elusive. In a tour-de-force peptide engineering approach combining phage-display selections, rational design of enhanced zinc chelation, and d-amino acid screening, we succeeded in developing a first synthetic MMP-2 inhibitor that combines high potency (Ki =1.9±0.5 nm), high target selectivity, and proteolytic stability, and thus fulfills all the required qualities for in cell culture and in vivo application. Our work suggests that selective MMP inhibition is achievable with peptide macrocycles and paves the way for developing specific inhibitors for application as chemical probes and potentially therapeutics.
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Affiliation(s)
- Khan Maola
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Jonas Wilbs
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Jeremy Touati
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Michal Sabisz
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Xu-Dong Kong
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Alice Baumann
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Kaycie Deyle
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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22
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Fischer T, Senn N, Riedl R. Design and Structural Evolution of Matrix Metalloproteinase Inhibitors. Chemistry 2019; 25:7960-7980. [DOI: 10.1002/chem.201805361] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/09/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Thomas Fischer
- Center of Organic and Medicinal Chemistry, Institute of Chemistry, and BiotechnologyZurich University of Applied Sciences (ZHAW) Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - Nicole Senn
- Center of Organic and Medicinal Chemistry, Institute of Chemistry, and BiotechnologyZurich University of Applied Sciences (ZHAW) Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - Rainer Riedl
- Center of Organic and Medicinal Chemistry, Institute of Chemistry, and BiotechnologyZurich University of Applied Sciences (ZHAW) Einsiedlerstrasse 31 8820 Wädenswil Switzerland
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23
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Dioscin-6’-O-acetate impairs migration of lung cancer cells through attenuations of MMP-2 and MMP-9 via NF-κB suppression. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2257-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Abstract
Structure-based virtual screening (SBVS) is a common method for the fast identification of hit structures at the beginning of a medicinal chemistry program in drug discovery. The SBVS, described in this manuscript, is focused on finding small molecule hits that can be further utilized as a starting point for the development of inhibitors of matrix metalloproteinase 13 (MMP-13) via structure-based molecular design. We intended to identify a set of structurally diverse hits, which occupy all subsites (S1'-S3', S2, and S3) centering the zinc containing binding site of MMP-13, by the virtual screening of a chemical library comprising more than ten million commercially available compounds. In total, 23 compounds were found as potential MMP-13 inhibitors using Glide docking followed by the analysis of the structural interaction fingerprints (SIFt) of the docked structures.
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25
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Affiliation(s)
- Xun Li
- Department of Medicinal Chemistry, Key laboratory of Chemistry and Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, PR China
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26
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Zhong Y, Lu YT, Sun Y, Shi ZH, Li NG, Tang YP, Duan JA. Recent opportunities in matrix metalloproteinase inhibitor drug design for cancer. Expert Opin Drug Discov 2017; 13:75-87. [PMID: 29088927 DOI: 10.1080/17460441.2018.1398732] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION The overexpression of matrix metalloproteinase (MMP) plays an important role in the context of tumor invasion and metastasis, and MMP-2 has been characterized as the most validated target for cancer. Therefore, it is necessary to design matrix metalloproteinase inhibitors (MMPIs) that would be active and selective against MMP-2 but non-selective toward other MMPs. Areas covered: This article clearly describes the structural character of MMP-2 followed by a review of the recent development of selective MMP-2 inhibitors based on their basic structures. Expert opinion: Over the past 30 years, MMPs have been considered to be attractive cancer targets, and several different types of synthetic inhibitors have been identified as anticancer agents, but only a small number of small MMPIs have been examined in clinical trials, and none of these molecules has been established as anticancer drugs due to their adverse effects. One major possibility is that the MMPIs used in clinical trials were broad-spectrum drugs that also inhibited the anti-tumor effects and influenced the mediation of the normal physiological processes of MMPs. MMP-2 has recently been characterized as the most validated target for cancer. Therefore, the design and synthesis of selective MMP-2 inhibitors would be helpful for the treatment of cancer.
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Affiliation(s)
- Yue Zhong
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China
| | - Yu-Ting Lu
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China
| | - Ying Sun
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China
| | - Zhi-Hao Shi
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China.,b Department of Organic Chemistry , China Pharmaceutical University , Nanjing , China
| | - Nian-Guang Li
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China
| | - Yu-Ping Tang
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China.,c Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization and College of Pharmacy , Shaanxi University of Chinese Medicine , Xianyang , China
| | - Jin-Ao Duan
- a Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae , Nanjing University of Chinese Medicine , Nanjing , China
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27
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Khrenova MG, Solovyev ID, Lapshin GD, Savitsky AP. Molecular mechanism of interactions between MMP-2 and its oligopeptide-based inhibitors. MENDELEEV COMMUNICATIONS 2017. [DOI: 10.1016/j.mencom.2017.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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Pethe MA, Rubenstein AB, Khare SD. Large-Scale Structure-Based Prediction and Identification of Novel Protease Substrates Using Computational Protein Design. J Mol Biol 2016; 429:220-236. [PMID: 27932294 DOI: 10.1016/j.jmb.2016.11.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/23/2016] [Accepted: 11/30/2016] [Indexed: 12/16/2022]
Abstract
Characterizing the substrate specificity of protease enzymes is critical for illuminating the molecular basis of their diverse and complex roles in a wide array of biological processes. Rapid and accurate prediction of their extended substrate specificity would also aid in the design of custom proteases capable of selectively and controllably cleaving biotechnologically or therapeutically relevant targets. However, current in silico approaches for protease specificity prediction, rely on, and are therefore limited by, machine learning of sequence patterns in known experimental data. Here, we describe a general approach for predicting peptidase substrates de novo using protein structure modeling and biophysical evaluation of enzyme-substrate complexes. We construct atomic resolution models of thousands of candidate substrate-enzyme complexes for each of five model proteases belonging to the four major protease mechanistic classes-serine, cysteine, aspartyl, and metallo-proteases-and develop a discriminatory scoring function using enzyme design modules from Rosetta and AMBER's MMPBSA. We rank putative substrates based on calculated interaction energy with a modeled near-attack conformation of the enzyme active site. We show that the energetic patterns obtained from these simulations can be used to robustly rank and classify known cleaved and uncleaved peptides and that these structural-energetic patterns have greater discriminatory power compared to purely sequence-based statistical inference. Combining sequence and energetic patterns using machine-learning algorithms further improves classification performance, and analysis of structural models provides physical insight into the structural basis for the observed specificities. We further tested the predictive capability of the model by designing and experimentally characterizing the cleavage of four novel substrate motifs for the hepatitis C virus NS3/4 protease using an in vivo assay. The presented structure-based approach is generalizable to other protease enzymes with known or modeled structures, and complements existing experimental methods for specificity determination.
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Affiliation(s)
- Manasi A Pethe
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Aliza B Rubenstein
- Computational Biology & Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Computational Biology & Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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Oxoethylene derivative of the natural substrate as an inhibitor of matrix metalloproteinase MMP-2. MENDELEEV COMMUNICATIONS 2016. [DOI: 10.1016/j.mencom.2016.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Eckhard U, Huesgen PF, Schilling O, Bellac CL, Butler GS, Cox JH, Dufour A, Goebeler V, Kappelhoff R, Keller UAD, Klein T, Lange PF, Marino G, Morrison CJ, Prudova A, Rodriguez D, Starr AE, Wang Y, Overall CM. Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses. Matrix Biol 2015; 49:37-60. [PMID: 26407638 DOI: 10.1016/j.matbio.2015.09.003] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 02/07/2023]
Abstract
Secreted and membrane tethered matrix metalloproteinases (MMPs) are key homeostatic proteases regulating the extracellular signaling and structural matrix environment of cells and tissues. For drug targeting of proteases, selectivity for individual molecules is highly desired and can be met by high yield active site specificity profiling. Using the high throughput Proteomic Identification of protease Cleavage Sites (PICS) method to simultaneously profile both the prime and non-prime sides of the cleavage sites of nine human MMPs, we identified more than 4300 cleavages from P6 to P6' in biologically diverse human peptide libraries. MMP specificity and kinetic efficiency were mainly guided by aliphatic and aromatic residues in P1' (with a ~32-93% preference for leucine depending on the MMP), and basic and small residues in P2' and P3', respectively. A wide differential preference for the hallmark P3 proline was found between MMPs ranging from 15 to 46%, yet when combined in the same peptide with the universally preferred P1' leucine, an unexpected negative cooperativity emerged. This was not observed in previous studies, probably due to the paucity of approaches that profile both the prime and non-prime sides together, and the masking of subsite cooperativity effects by global heat maps and iceLogos. These caveats make it critical to check for these biologically highly important effects by fixing all 20 amino acids one-by-one in the respective subsites and thorough assessing of the inferred specificity logo changes. Indeed an analysis of bona fide MEROPS physiological substrate cleavage data revealed that of the 37 natural substrates with either a P3-Pro or a P1'-Leu only 5 shared both features, confirming the PICS data. Upon probing with several new quenched-fluorescent peptides, rationally designed on our specificity data, the negative cooperativity was explained by reduced non-prime side flexibility constraining accommodation of the rigidifying P3 proline with leucine locked in S1'. Similar negative cooperativity between P3 proline and the novel preference for asparagine in P1 cements our conclusion that non-prime side flexibility greatly impacts MMP binding affinity and cleavage efficiency. Thus, unexpected sequence cooperativity consequences were revealed by PICS that uniquely encompasses both the non-prime and prime sides flanking the proteomic-pinpointed scissile bond.
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Affiliation(s)
- Ulrich Eckhard
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Pitter F Huesgen
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Oliver Schilling
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Caroline L Bellac
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Swissmedic, Swiss Agency for Therapeutic Products, Bern, Switzerland
| | - Georgina S Butler
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jennifer H Cox
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Inception Sciences, Vancouver, BC, Canada
| | - Antoine Dufour
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Verena Goebeler
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ulrich Auf dem Keller
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | - Theo Klein
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Philipp F Lange
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Giada Marino
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Charlotte J Morrison
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Anna Prudova
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - David Rodriguez
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Department of Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Amanda E Starr
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Ottawa Institute of Systems Biology, University of Ottawa, Canada
| | - Yili Wang
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Christopher M Overall
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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Abbasi M, Ramezani F, Elyasi M, Sadeghi-Aliabadi H, Amanlou M. A study on quantitative structure-activity relationship and molecular docking of metalloproteinase inhibitors based on L-tyrosine scaffold. ACTA ACUST UNITED AC 2015; 23:29. [PMID: 25925871 PMCID: PMC4423142 DOI: 10.1186/s40199-015-0111-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 04/12/2015] [Indexed: 12/14/2022]
Abstract
Background MMP-2 enzyme is a kind of matrix metalloproteinases that digests the denatured collagens and gelatins. It is highly involved in the process of tumor invasion and has been considered as a promising target for cancer therapy. The structural requirements of an MMP-2 inhibitor are: (1) a functional group that binds the zinc ion, and (2) a functional group which interacts with the enzyme backbone and the side chains which undergo effective interactions with the enzyme subsites. Methods In the present study, a QSAR model was generated to screen new inhibitors of MMP-2 based on L–hydroxy tyrosine scaffold. Descriptors generation were done by Hyperchem 8, DRAGON and Gaussian98W programs. SPSS and MATLAB programs have been used for multiple linear regression (MLR) and genetic algorithm partial least squares (GA-PLS) analyses and for theoretical validation. Applicability domain of the model was performed to screen new compounds. The binding site potential of all inhibitors was verified by structure-based docking according to their binding energy and then the best inhibitors were selected. Results The best QSAR models in MLR and GA-PLS were reported, with the square correlation coefficient for leave-one-out cross-validation (Q2LOO) larger than 0.921 and 0.900 respectively. The created MLR and GA-PLS models indicated the importance of molecular size, degree of branching, flexibility, shape, three-dimensional coordination of different atoms in a molecule in inhibitory activities against MMP-2. The docking study indicated that lipophilic and hydrogen bonding interactions among the inhibitors and the receptor are involved in a ligand-receptor interaction. The oxygen of carbonyl and sulfonyl groups is important for hydrogen bonds of ligand with Leu82 and Ala83. R2 and R3 substituents play a main role in hydrogen bonding interactions. R1 is sited in the hydrophobic pocket. Methylene group can help a ligand to be fitted in the lipophilic pocket, so two methylene groups are better than one. The Phenyl group can create a π-π interaction with Phe86. Conclusions The QSAR and docking analyses demonstrated to be helpful tools in the prediction of anti-cancer activities and a guide to the synthesis of new metalloproteinase inhibitors based on L-tyrosine scaffold.
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Affiliation(s)
- Maryam Abbasi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Pharmaceutical Science Research Center, Tehran University of Medical Science, Tehran, Iran. .,Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, 81746-73461, Isfahan, Iran.
| | - Fatemeh Ramezani
- Department of Medicinal Chemistry, Faculty of Pharmacy, Pharmaceutical Science Research Center, Tehran University of Medical Science, Tehran, Iran.
| | - Maryam Elyasi
- Medicinal & Natural Product Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Hojjat Sadeghi-Aliabadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, 81746-73461, Isfahan, Iran.
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Pharmaceutical Science Research Center, Tehran University of Medical Science, Tehran, Iran.
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Abbasi M, Ramezani F, Elyasi M, Sadeghi-Aliabadi H, Amanlou M. A study on quantitative structure–activity relationship and molecular docking of metalloproteinase inhibitors based on L-tyrosine scaffold. Daru 2015. [DOI: 10.1186/s40199-015-0111-z pmid: 25925871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
MMP-2 enzyme is a kind of matrix metalloproteinases that digests the denatured collagens and gelatins. It is highly involved in the process of tumor invasion and has been considered as a promising target for cancer therapy. The structural requirements of an MMP-2 inhibitor are: (1) a functional group that binds the zinc ion, and (2) a functional group which interacts with the enzyme backbone and the side chains which undergo effective interactions with the enzyme subsites.
Methods
In the present study, a QSAR model was generated to screen new inhibitors of MMP-2 based on L–hydroxy tyrosine scaffold. Descriptors generation were done by Hyperchem 8, DRAGON and Gaussian98W programs. SPSS and MATLAB programs have been used for multiple linear regression (MLR) and genetic algorithm partial least squares (GA-PLS) analyses and for theoretical validation. Applicability domain of the model was performed to screen new compounds. The binding site potential of all inhibitors was verified by structure-based docking according to their binding energy and then the best inhibitors were selected.
Results
The best QSAR models in MLR and GA-PLS were reported, with the square correlation coefficient for leave-one-out cross-validation (Q2
LOO) larger than 0.921 and 0.900 respectively. The created MLR and GA-PLS models indicated the importance of molecular size, degree of branching, flexibility, shape, three-dimensional coordination of different atoms in a molecule in inhibitory activities against MMP-2.
The docking study indicated that lipophilic and hydrogen bonding interactions among the inhibitors and the receptor are involved in a ligand-receptor interaction. The oxygen of carbonyl and sulfonyl groups is important for hydrogen bonds of ligand with Leu82 and Ala83. R2 and R3 substituents play a main role in hydrogen bonding interactions. R1 is sited in the hydrophobic pocket. Methylene group can help a ligand to be fitted in the lipophilic pocket, so two methylene groups are better than one. The Phenyl group can create a π-π interaction with Phe86.
Conclusions
The QSAR and docking analyses demonstrated to be helpful tools in the prediction of anti-cancer activities and a guide to the synthesis of new metalloproteinase inhibitors based on L-tyrosine scaffold.
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Khrenova M, Savitsky AP, Topol IA, Nemukhin AV. Exploration of the zinc finger motif in controlling activity of matrix metalloproteinases. J Phys Chem B 2014; 118:13505-12. [PMID: 25375834 PMCID: PMC4254000 DOI: 10.1021/jp5088702] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/05/2014] [Indexed: 12/19/2022]
Abstract
Discovering ways to control the activity of matrix metalloproteinases (MMPs), zinc-dependent enzymes capable of degrading extracellular matrix proteins, is an important field of cancer research. We report here a novel strategy for assembling MMP inhibitors on the basis of oligopeptide ligands by exploring the pattern known as the zinc finger motif. Advanced molecular modeling tools were used to characterize the structural binding motifs of experimentally tested MMP inhibitors, as well as those of newly proposed peptidomimetics, in their zinc-containing active sites. The results of simulations based on the quantum mechanics/molecular mechanics (QM/MM) approach and Car-Parrinello molecular dynamics with QM/MM potentials demonstrate that, upon binding of Regasepin1, a known MMP-9 inhibitor, the Zn(2+)(His3) structural element is rearranged to the Zn(2+)(Cys2His2) zinc finger motif, in which two Cys residues are borrowed from the ligand. Following consideration of the crystal structure of MMP-2 with its inhibitor, the oligopeptide APP-IP, we proposed a new peptidomimetic with two replacements in the substrate, Tyr3Cys and Asp6Cys. Simulations show that this peptide variant blocks an enzyme active site by the Zn(2+)(Cys2His2) zinc finger construct. Similarly, a natural substrate of MMP-2, Ace-Gln-Gly ∼ Ile-Ala-Gly-Nme, can be converted to an inhibiting compound by two replacements, Ile by Cys and Gly by the d isomer of Cys, favoring formation of the zinc finger motif.
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Affiliation(s)
- Maria
G. Khrenova
- A.N. Bach Institute
of Biochemistry of the Russian Academy of Science, Leninsky Prospect, 33, Moscow 119071, Russian Federation
- Chemistry
Department, M.V. Lomonosov Moscow State
University, Leninskie
Gory 1/3, Moscow, 119991, Russian Federation
| | - Alexander P. Savitsky
- A.N. Bach Institute
of Biochemistry of the Russian Academy of Science, Leninsky Prospect, 33, Moscow 119071, Russian Federation
| | - Igor A. Topol
- Advanced
Biomedical Computing Center, Information Systems Program, Leidos Biomedical
Research Inc., Frederick National Laboratory
for Cancer Research, Frederick, Maryland 21702, United States
| | - Alexander V. Nemukhin
- Chemistry
Department, M.V. Lomonosov Moscow State
University, Leninskie
Gory 1/3, Moscow, 119991, Russian Federation
- N.M.
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation
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34
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Fabre B, Ramos A, de Pascual-Teresa B. Targeting Matrix Metalloproteinases: Exploring the Dynamics of the S1′ Pocket in the Design of Selective, Small Molecule Inhibitors. J Med Chem 2014; 57:10205-19. [DOI: 10.1021/jm500505f] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Benjamin Fabre
- Departamento de Química
y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo, Urbanización Monteprincipe, 28668 Madrid, Spain
| | - Ana Ramos
- Departamento de Química
y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo, Urbanización Monteprincipe, 28668 Madrid, Spain
| | - Beatriz de Pascual-Teresa
- Departamento de Química
y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo, Urbanización Monteprincipe, 28668 Madrid, Spain
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35
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Azzollini J, Rovina D, Gervasini C, Parenti I, Fratoni A, Cubellis MV, Cerri A, Pietrogrande L, Larizza L. Functional characterisation of a novel mutation affecting the catalytic domain of MMP2 in siblings with multicentric osteolysis, nodulosis and arthropathy. J Hum Genet 2014; 59:631-7. [PMID: 25273674 DOI: 10.1038/jhg.2014.84] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/03/2014] [Accepted: 09/05/2014] [Indexed: 01/16/2023]
Abstract
Multicentric osteolysis, nodulosis and arthropathy (MONA) is a rare autosomal recessive disorder. To date, 13 mutations of the matrix metalloproteinase 2 (MMP2) gene have been detected in 26 patients with MONA and other osteolytic syndromes. Here, we describe the molecular and functional analysis of a novel MMP2 mutation in two adult Italian siblings with MONA. Both siblings displayed palmar-plantar subcutaneous nodules, tendon retractions, limb arthropathies, osteolysis in the toes and pigmented fibrous skin lesions. Molecular analysis identified a homozygous MMP2 missense mutation in exon 8 c.1228G>C (p.G410R), not detected in 260 controls and predicted by several bioinformatic tools to be pathogenic. By protein modelling, the mutant residue was predicted to affect the main chain conformation of the catalytic domain. Gelatin zymography, the gold standard test for MMP2 function, of serum-free conditioned medium from G410R-MMP2-expressing human embryonic kidney (HEK) cells, showed a complete loss of gelatinolytic activity. The novel mutation is located in the catalytic domain, as are 3 (p.E404K, p.V400del and p.G406D) of the other 13 MMP2 mutations described to date; however, p.G410R underlies a phenotype that is only partially overlapping that of other MMP2 exon 8 mutation carriers. Our results further delineate the complexity of genotype-phenotype correlations in MONA, broaden the repertoire of reported MMP2 mutation and enhance the comprehension of the protein motifs crucial for MMP2 catalytic activity.
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Affiliation(s)
- Jacopo Azzollini
- Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy
| | - Davide Rovina
- Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy
| | - Ilaria Parenti
- Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy
| | - Alessia Fratoni
- Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy
| | | | - Amilcare Cerri
- Dermatologic Unit, Department of Health Sciences, San Paolo Hospital, University of Milan, Milan, Italy
| | - Luca Pietrogrande
- Operative Unit of Orthopaedics and Traumatology, Department of Health Sciences, San Paolo Hospital, University of Milan, Milan, Italy
| | - Lidia Larizza
- 1] Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy [2] Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
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Alzheimer's disease--a panorama glimpse. Int J Mol Sci 2014; 15:12631-50. [PMID: 25032844 PMCID: PMC4139864 DOI: 10.3390/ijms150712631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/26/2014] [Accepted: 07/10/2014] [Indexed: 01/05/2023] Open
Abstract
The single-mutation of genes associated with Alzheimer's disease (AD) increases the production of Aβ peptides. An elevated concentration of Aβ peptides is prone to aggregation into oligomers and further deposition as plaque. Aβ plaques and neurofibrillary tangles are two hallmarks of AD. In this review, we provide a broad overview of the diverses sources that could lead to AD, which include genetic origins, Aβ peptides and tau protein. We shall discuss on tau protein and tau accumulation, which result in neurofibrillary tangles. We detail the mechanisms of Aβ aggregation, fibril formation and its polymorphism. We then show the possible links between Aβ and tau pathology. Furthermore, we summarize the structural data of Aβ and its precursor protein obtained via Nuclear Magnetic Resonance (NMR) or X-ray crystallography. At the end, we go through the C-terminal and N-terminal truncated Aβ variants. We wish to draw reader's attention to two predominant and toxic Aβ species, namely Aβ4-42 and pyroglutamate amyloid-beta peptides, which have been neglected for more than a decade and may be crucial in Aβ pathogenesis due to their dominant presence in the AD brain.
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37
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Matrix metalloproteinases and their multiple roles in Alzheimer's disease. BIOMED RESEARCH INTERNATIONAL 2014; 2014:908636. [PMID: 25050378 PMCID: PMC4094696 DOI: 10.1155/2014/908636] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 01/09/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent type of dementia. Pathological changes in the AD brain include amyloid-β (Aβ) plaques and neurofibrillary tangles (NFTs), as well as neuronal death and synaptic loss. Matrix metalloproteinases (MMPs) play an important role as inflammatory components in the pathogenesis of AD. MMP-2 might be assumed to have a protective role in AD and is the major MMP which is directly linked to Aβ in the brain. Synthesis of MMP-9 can be induced by Aβ, and the enzymes appear to exert multiple effects in AD in senile plaque homoeostasis. The proaggregatory influence on tau oligomer formation in strategic brain regions may be a potential neurotoxic side effect of MMP-9. MMP-3 levels are correlated to the duration of AD and correlate with the CSF T-tau and P-tau levels in the elderly controls. Elevated brain levels of MMP-3 might result in increased MMP-9 activity and indirectly facilitate tau aggregation. At present, the clinical utility of these proteins, particularly in plasma or serum, as potential early diagnostic biomarkers for AD remains to be established. More research is needed to understand the diverse roles of these proteases to design specific drugs and devise therapeutic strategies for AD.
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Shi L, Wang Q, Wang H, Zhou H, Li Y, Li X. Sulphonamide 1,4-dithia-7-azaspiro[4,4]nonane derivatives as gelatinase A inhibitors. Bioorg Med Chem 2013; 21:7752-62. [DOI: 10.1016/j.bmc.2013.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/11/2013] [Accepted: 10/12/2013] [Indexed: 10/26/2022]
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Nuti E, Casalini F, Santamaria S, Fabbi M, Carbotti G, Ferrini S, Marinelli L, La Pietra V, Novellino E, Camodeca C, Orlandini E, Nencetti S, Rossello A. Selective Arylsulfonamide Inhibitors of ADAM-17: Hit Optimization and Activity in Ovarian Cancer Cell Models. J Med Chem 2013; 56:8089-103. [DOI: 10.1021/jm4011753] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elisa Nuti
- Dipartimento
di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Francesca Casalini
- Dipartimento
di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | - Marina Fabbi
- Dipartimento
di Terapie Oncologiche Integrate, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Largo R. Benzi 10, 16132 Genova, Italy
| | - Grazia Carbotti
- Dipartimento
di Terapie Oncologiche Integrate, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Largo R. Benzi 10, 16132 Genova, Italy
| | - Silvano Ferrini
- Dipartimento
di Terapie Oncologiche Integrate, IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Largo R. Benzi 10, 16132 Genova, Italy
| | - Luciana Marinelli
- Dipartimento
di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Valeria La Pietra
- Dipartimento
di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- Dipartimento
di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Caterina Camodeca
- Dipartimento
di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | - Susanna Nencetti
- Dipartimento
di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Armando Rossello
- Dipartimento
di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
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40
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Fischer T, Riedl R. Strategic targeting of multiple water-mediated interactions: a concise and rational structure-based design approach to potent and selective MMP-13 inhibitors. ChemMedChem 2013; 8:1457-61, 1572. [PMID: 23894097 PMCID: PMC4281860 DOI: 10.1002/cmdc.201300278] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Fischer
- Institute for Chemistry and Biological Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820 Wädenswil (Switzerland) www.icbc.zhaw.ch/organic‐chemistry
| | - Rainer Riedl
- Institute for Chemistry and Biological Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820 Wädenswil (Switzerland) www.icbc.zhaw.ch/organic‐chemistry
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41
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Stura EA, Visse R, Cuniasse P, Dive V, Nagase H. Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain. FASEB J 2013; 27:4395-405. [PMID: 23913860 DOI: 10.1096/fj.13-233601] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Matrix metalloproteinase (MMP)-13 is one of the mammalian collagenases that play key roles in tissue remodelling and repair and in progression of diseases such as cancer, arthritis, atherosclerosis, and aneurysm. For collagenase to cleave triple helical collagens, the triple helical structure has to be locally unwound before hydrolysis, but this process is not well understood. We report crystal structures of catalytically inactive full-length human MMP-13(E223A) in complex with peptides of 14-26 aa derived from the cleaved prodomain during activation. Peptides are bound to the active site of the enzyme by forming an extended β-strand with Glu(40) or Tyr(46) inserted into the S1' specificity pocket. The structure of the N-terminal part of the peptides is variable and interacts with different parts of the catalytic domain. Those areas are designated substrate-dependent exosites, in that they accommodate different peptide structures, whereas the precise positioning of the substrate backbone is maintained in the active site. These modes of peptide-MMP-13 interactions have led us to propose how triple helical collagen strands fit into the active site cleft of the collagenase.
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Affiliation(s)
- Enrico A Stura
- 2H.N., Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK.
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42
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Higashi S, Hirose T, Takeuchi T, Miyazaki K. Molecular design of a highly selective and strong protein inhibitor against matrix metalloproteinase-2 (MMP-2). J Biol Chem 2013; 288:9066-76. [PMID: 23395821 DOI: 10.1074/jbc.m112.441758] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Synthetic inhibitors of matrix metalloproteinases (MMPs), designed previously, as well as tissue inhibitors of metalloproteinases (TIMPs) lack enzyme selectivity, which has been a major obstacle for developing inhibitors into safe and effective MMP-targeted drugs. Here we designed a fusion protein named APP-IP-TIMP-2, in which the ten amino acid residue sequence of APP-derived MMP-2 selective inhibitory peptide (APP-IP) is added to the N terminus of TIMP-2. The APP-IP and TIMP-2 regions of the fusion protein are designed to interact with the active site and the hemopexin-like domain of MMP-2, respectively. The reactive site of the TIMP-2 region, which has broad specificity against MMPs, is blocked by the APP-IP adduct. The recombinant APP-IP-TIMP-2 showed strong inhibitory activity toward MMP-2 (Ki(app) = 0.68 pm), whereas its inhibitory activity toward MMP-1, MMP-3, MMP-7, MMP-8, MMP-9, or MT1-MMP was six orders of magnitude or more weaker (IC50 > 1 μm). The fusion protein inhibited the activation of pro-MMP-2 in the concanavalin A-stimulated HT1080 cells, degradation of type IV collagen by the cells, and the migration of stimulated cells. Compared with the decapeptide APP-IP (t½ = 30 min), APP-IP-TIMP-2 (t½ ≫ 96 h) showed a much longer half-life in cultured tumor cells. Therefore, the fusion protein may be a useful tool to evaluate contributions of proteolytic activity of MMP-2 in various pathophysiological processes. It may also be developed as an effective anti-tumor drug with restricted side effects.
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Affiliation(s)
- Shouichi Higashi
- Department of Genome System Science, Graduate School of Nanobioscience, Yokohama City University, 641-12, Maioka-cho, Totsuka-ku, Yokohama 244-0813, Japan.
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Computational insights into the selectivity mechanism of APP-IP over matrix metalloproteinases. J Comput Aided Mol Des 2012; 26:1327-42. [PMID: 23224743 DOI: 10.1007/s10822-012-9617-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 11/06/2012] [Indexed: 12/20/2022]
Abstract
In this work, selectivity mechanism of APP-IP inhibitor (β-amyloid precursor protein-derived inhibitory peptide) over matrix metalloproteinases (MMPs including MMP-2, MMP-7, MMP-9 and MMP-14) was investigated by molecular modeling methods. Among MMPs, MMP-2 is the most favorable one for APP-IP interacting based on our calculations. The predicted binding affinities can give a good explanation of the activity difference of inhibitor APP-IP. In Comparison with MMP-2/APP-IP complex, the side chain of Tyr214(MMP-7) makes the binding pocket so shallow that the whole side chain of Tyr3(APP-IP) can not be fully embraced, thus unfavorable for the N-terminal of APP-IP binding to MMP-7. The poor selectivity of APP-IP toward MMP-9 is mainly related with the decrease of interaction between the APP-IP C-terminal and MMP-9 due to the bulky side chains of Pro193 and Gln199, which is in agreement with experiment. The mutations at residues P193A and Q199G of MMP-9 alternate the binding pattern of the C-terminal of APP-IP by forming two new hydrogen bonds and hydrophobic interactions with MMP-9. The mutants favor the binding affinity of MMP-9 largely. For MMP-14/APP-IP, the large steric effect of Phe204(MMP-14) and the weak contributions of the polar residues Asn231(MMP-14) and Thr190(MMP-14) could explain why MMP-14 is non-selective for APP-IP interacting. Here, the molecular modeling methods were successfully employed to explore the selective inhibitor of MMPs, and our work gives valuable information for future rational design of selective peptide inhibitors toward individual MMP.
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Abstract
The matrix metalloproteinases (MMPs) exhibit a broad array of activities, some catalytic and some non-catalytic in nature. An overall lack of selectivity has rendered small molecule, active site targeted MMP inhibitors problematic in execution. Inhibitors that favor few or individual members of the MMP family often take advantage of interactions outside the enzyme active site. We presently focus on peptide-based MMP inhibitors and probes that do not incorporate conventional Zn2+ binding groups. In some cases, these inhibitors and probes function by binding only secondary binding sites (exosites), while others bind both exosites and the active site. A myriad of MMP mediated-activities beyond selective catalysis can be inhibited by peptides, particularly cell adhesion, proliferation, motility, and invasion. Selective MMP binding peptides comprise highly customizable, unique imaging agents. Areas of needed improvement for MMP targeting peptides include binding affinity and stability.
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Ji XN, Yang F, Sui XM, Wang FG, Ge RG, Quan XL, Zhao T, Gao BW, Wang RY. Effect of fractionated irradiation on the expression of multidrug resistance genes in the CNE1 human nasopharyngeal carcinoma cell line. Mol Med Rep 2012; 7:187-94. [PMID: 23128850 DOI: 10.3892/mmr.2012.1148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 09/20/2012] [Indexed: 11/05/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) often develops drug resistance following radiotherapy. The molecular basis of radiotherapy-related multidrug resistance (MDR) remains unclear. In the present study, we investigated the effect of fractionated irradiation on the expression of the MDR-1 gene and the MDR-associated protein P-glycoprotein (P-gp) in CNE1 human NPC cells. CNE1 cells were treated with fractionated X-rays. Drug resistance was determined by MTT assay. The expression levels of MDR-1 and P-gp were analyzed by RT-PCR and western blot analysis, respectively. Differential expression was analyzed by gene chips. The results revealed that low levels of mRNA expression of MDR1 were present in non-irradiated CNE1 cells. Compared with the control, the expression of MDR1 mRNA was gradually increased following fractionated irradiation. On day 21, the expression of MDR1 mRNA was increased 1.59- and 2.19-fold, compared with the control, by treatment with 10 and 20 Gy, respectively. We observed decreased MDR1 expression following treatment with 10 and 20 Gy irradiation on days 28 and 35, compared with day 21. On days 21, 28 and 35, expression was increased 1.37-, 1.40- and 1.15-fold by treatment with 20 Gy compared with 10 Gy. Expression of MDR1 was significantly upregulated by treatment with 50 Gy irradiation compared with the control on days 78 and 106. P-gp expression was consistent with that of MDR1 mRNA expression. The sensitivity of CNE1 cells to cisplatin was reduced following irradiation compared with the control. A total of 26 genes were significantly upregulated and 8 genes were significantly downregulated compared with the control. Results of the present study have shown that MDR1 and P-gp are upregulated in CNE1 cells following irradiation. Multiple genes were involved in the mechanism of radiation-induced drug resistance.
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Affiliation(s)
- Xue-Ning Ji
- Department of Oncology, Zhongshan Hospital, Dalian University, Dalian 116001, PR China
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