1
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Baltazar-García EA, Vargas-Guerrero B, Lima A, Boavida Ferreira R, Mendoza-Magaña ML, Ramírez-Herrera MA, Baltazar-Díaz TA, Domínguez-Rosales JA, Salazar-Montes AM, Gurrola-Díaz CM. Deflamin Attenuated Lung Tissue Damage in an Ozone-Induced COPD Murine Model by Regulating MMP-9 Catalytic Activity. Int J Mol Sci 2024; 25:5063. [PMID: 38791100 PMCID: PMC11121448 DOI: 10.3390/ijms25105063] [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: 03/28/2024] [Revised: 04/26/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is comprised of histopathological alterations such as pulmonary emphysema and peribronchial fibrosis. Matrix metalloproteinase 9 (MMP-9) is one of the key enzymes involved in both types of tissue remodeling during the development of lung damage. In recent studies, it was demonstrated that deflamin, a protein component extracted from Lupinus albus, markedly inhibits the catalytic activity of MMP-9 in experimental models of colon adenocarcinoma and ulcerative colitis. Therefore, in the present study, we investigated for the first time the biological effect of deflamin in a murine COPD model induced by chronic exposure to ozone. Ozone exposure was carried out in C57BL/6 mice twice a week for six weeks for 3 h each time, and the treated group was orally administered deflamin (20 mg/kg body weight) after each ozone exposure. The histological results showed that deflamin attenuated pulmonary emphysema and peribronchial fibrosis, as evidenced by H&E and Masson's trichrome staining. Furthermore, deflamin administration significantly decreased MMP-9 activity, as assessed by fluorogenic substrate assay and gelatin zymography. Interestingly, bioinformatic analysis reveals a plausible interaction between deflamin and MMP-9. Collectively, our findings demonstrate the therapeutic potential of deflamin in a COPD murine model, and suggest that the attenuation of the development of lung tissue damage occurs by deflamin-regulated MMP-9 catalytic activity.
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Affiliation(s)
- Elia Ana Baltazar-García
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
| | - Belinda Vargas-Guerrero
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
| | - Ana Lima
- CECAV—Centro de Ciência Animal e Veterinária, Faculty of Veterinary Medicine, Lusófona University, Campo Grande, 376, 1749-024 Lisbon, Portugal;
| | - Ricardo Boavida Ferreira
- LEAF—Landscape Environment Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal;
| | - María Luisa Mendoza-Magaña
- Laboratorio de Neurofisiología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (M.L.M.-M.); (M.A.R.-H.)
| | - Mario Alberto Ramírez-Herrera
- Laboratorio de Neurofisiología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (M.L.M.-M.); (M.A.R.-H.)
| | - Tonatiuh Abimael Baltazar-Díaz
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
| | - José Alfredo Domínguez-Rosales
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
| | - Adriana María Salazar-Montes
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
| | - Carmen Magdalena Gurrola-Díaz
- Instituto de Investigación en Enfermedades Crónico-Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Puerta peatonal 7, Col. Independencia, Guadalajara 44350, Jalisco, Mexico; (E.A.B.-G.); (B.V.-G.); (T.A.B.-D.); (J.A.D.-R.); (A.M.S.-M.)
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2
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Yırtıcı Ü, Ergene A, Adem Ş, Atalar MN, Eyüpoğlu V, Rawat R, Arat E, Hamzaoğlu E. Centaurea mersinensis phytochemical composition and multi-dimensional bioactivity properties supported by molecular modeling. J Biomol Struct Dyn 2024; 42:2341-2357. [PMID: 37098809 DOI: 10.1080/07391102.2023.2204496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/14/2023] [Indexed: 04/27/2023]
Abstract
Various studies conducted on Centaurea species indicate that the relevant plant is good source of bioactive phytochemicals. In this study, in vitro studies were used to determine bioactivity properties of methanol extract of Centaurea mersinensis - endemic species in Turkey - on extensive basis. Furthermore, the interaction of target molecules, identified for breast cancer and phytochemicals in the extract, was investigated via in silico analyses to support findings received in vitro. Scutellarin, quercimeritrin, chlorogenic acid and baicalin were primary phytochemicals in the extract. Methanol extract and scutellarin had higher cytotoxic effects against MCF-7 (IC50=22.17 µg/mL, and IC50=8.25 µM, respectively), compared to other breast cancer cell lines (MDA-MB-231, SKBR-3). The extract had strong antioxidant properties and inhibited target enzymes, especially α-amylase (371.69 mg AKE/g extract). The results of molecular docking indicate that main compounds of extract show high-strength bonding to the c-Kit tyrosine among target molecules identified in breast cancer, compared to other target molecules (MMP-2, MMP-9, VEGFR2 kinase, Aurora-A kinase, HER2). The tyrosinase kinase (1T46)-Scutellarin complex showed considerable stability in 150 ns simulation as per MD findings, and it was coherent with optimal docking findings. Docking findings and HOMO-LUMO analysis results corresponds with in vitro experiments. Medicinal properties of phytochemicals, which was determined to be suitable for oral use along with ADMET, were found to be within normal limits except for their polarity properties. In conclusion, in vitro and in silico studies indicated that the relevant plant yields promising results regarding its potential to develop novel and effective medicational products.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ümit Yırtıcı
- Department of Medical Laboratory, Kırıkkale University, Kırıkkale, Turkey
| | - Aysun Ergene
- Department of Biology, Kırıkkale University, Kırıkkale, Turkey
| | - Şevki Adem
- Department of Chemistry, Çankırı Karatekin University, Çankırı, Turkey
| | | | - Volkan Eyüpoğlu
- Department of Chemistry, Çankırı Karatekin University, Çankırı, Turkey
| | - Ravi Rawat
- School of Health Sciences & Technology, UPES University, Dehradun, India
| | - Esra Arat
- Scientific and Technological Researches Application and Research Center Directorate, Kırıkkale University, Kırıkkale, Turkey
| | - Ergin Hamzaoğlu
- Department of Science Education, Gazi Faculty of Education, Gazi University, Ankara, Turkey
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3
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Shoari A, Khalili-Tanha G, Coban MA, Radisky ES. Structure and computation-guided yeast surface display for the evolution of TIMP-based matrix metalloproteinase inhibitors. Front Mol Biosci 2023; 10:1321956. [PMID: 38074088 PMCID: PMC10702220 DOI: 10.3389/fmolb.2023.1321956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 11/13/2023] [Indexed: 01/03/2024] Open
Abstract
The study of protein-protein interactions (PPIs) and the engineering of protein-based inhibitors often employ two distinct strategies. One approach leverages the power of combinatorial libraries, displaying large ensembles of mutant proteins, for example, on the yeast cell surface, to select binders. Another approach harnesses computational modeling, sifting through an astronomically large number of protein sequences and attempting to predict the impact of mutations on PPI binding energy. Individually, each approach has inherent limitations, but when combined, they generate superior outcomes across diverse protein engineering endeavors. This synergistic integration of approaches aids in identifying novel binders and inhibitors, fine-tuning specificity and affinity for known binding partners, and detailed mapping of binding epitopes. It can also provide insight into the specificity profiles of varied PPIs. Here, we outline strategies for directing the evolution of tissue inhibitors of metalloproteinases (TIMPs), which act as natural inhibitors of matrix metalloproteinases (MMPs). We highlight examples wherein design of combinatorial TIMP libraries using structural and computational insights and screening these libraries of variants using yeast surface display (YSD), has successfully optimized for MMP binding and selectivity, and conferred insight into the PPIs involved.
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Affiliation(s)
| | | | | | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, United States
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4
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Kumar I, Silva M, Choudhary DA, Ali SF, Rusak R, Cotzomi P, Wiecek S, Sato I, Khundoker R, Donmez B, Gabriel S, Bobila M, Leonida MD, Traba C. Small molecular exogenous modulators of active forms of MMPs. Biochimie 2023:S0300-9084(23)00292-4. [PMID: 37944661 DOI: 10.1016/j.biochi.2023.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/13/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023]
Abstract
Matrix metalloproteinases (MMPs) are endopeptidases, and their activity depends on calcium and zinc metal ions. These enzymes are expressed originally in zymogenic form, where the active site of proteins is closed by a prodomain which is removed during activation. A homeostatic balance of their activity is primarily regulated by a 'cysteine switch' located on a consensus sequence of the prodomain and natural endogenous inhibitors, called tissue inhibitors of metalloproteinases (TIMPs). Breakage of this homeostasis may lead to various pathological conditions, which may require further activation and/or inhibition of these enzymes to regenerate that balance. Here, we report four modulators, more specifically, three inhibitors (I1, I2 and I3), and one exogenous activator (L) of the active form of human collagenase MMP-1 (without prodomain). The results were confirmed by binding studies using fluorescence-based enzyme assays.
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Affiliation(s)
- Ish Kumar
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA.
| | - Melissa Silva
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Dinesh A Choudhary
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Syeda F Ali
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Raymond Rusak
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Paulina Cotzomi
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Suzanne Wiecek
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Iwon Sato
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Rinat Khundoker
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Bora Donmez
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Samantha Gabriel
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Monica Bobila
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Mihaela D Leonida
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
| | - Christian Traba
- Department of Chemistry, Biochemistry & Physics, Fairleigh Dickinson University, 1000 River Rd, Teaneck, NJ, 07666, USA
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5
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Deryusheva EI, Machulin AV, Galzitskaya OV. Diversity and features of proteins with structural repeats. Biophys Rev 2023; 15:1159-1169. [PMID: 37974986 PMCID: PMC10643770 DOI: 10.1007/s12551-023-01130-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/28/2023] [Indexed: 11/19/2023] Open
Abstract
The review provides information on proteins with structural repeats, including their classification, characteristics, functions, and relevance in disease development. It explores methods for identifying structural repeats and specialized databases. The review also highlights the potential use of repeat proteins as drug design scaffolds and discusses their evolutionary mechanisms.
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Affiliation(s)
- Evgeniya I. Deryusheva
- Institute for Biological Instrumentation, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
| | - Andrey V. Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
| | - Oxana V. Galzitskaya
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Russia
- Institute of Theoretical and Experimental Biophysics of the Russian Academy of Sciences, Pushchino, Russia
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6
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Shi X, Huang B, Zhu J, Yamaguchi T, Hu A, Tabuchi M, Watanabe D, Yoshikawa S, Mizushima S, Mizushima A, Xia S. A network pharmacology-based investigation of emodin against pancreatic adenocarcinoma. Medicine (Baltimore) 2023; 102:e33521. [PMID: 37335741 DOI: 10.1097/md.0000000000033521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Pancreatic adenocarcinoma (PAAD) is one of the most common malignancies worldwide with an increasing incidence and poor outcome due to the lack of effective diagnostic and treatment methods. Emerging evidence implicates that emodin displays extensive spectrum anticancer properties. Differential expression genes in PAAD patients were analyzed by Gene Expression Profiling Interactive Analysis (GEPIA) website, and the targets of emodin were obtained via Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. Subsequently, enrichment analyses were performed using R software. A protein-protein interaction (PPI) network was constructed by STRING database and Cytoscape software was used to identify the hub genes. Prognostic value and immune infiltration landscapes were explored through Kaplan-Meier plotter (KM plotter) website and the Single-Sample Gene Set Enrichment Analysis package of R. Finally, molecular docking was used to computationally verify the interaction of ligand and receptor proteins. A total of 9191 genes were significantly differentially expressed in PAAD patients and 34 potential targets of emodin were obtained. Intersections of the 2 groups were considered as potential targets of emodin against PAAD. Functional enrichment analyses illustrated that these potential targets were linked to numerous pathological processes. Hub genes identified through PPI networks were correlated with poor prognosis and infiltration level of different immune cells in PAAD patients. Perhaps emodin interacted with the key molecules and regulate the activity of them. We revealed the inherent mechanism of emodin against PAAD with the aid of network pharmacology, which provided reliable evidence and a novel guideline for clinical treatment.
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Affiliation(s)
- Xueying Shi
- Clinical Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Bingqian Huang
- Clinical Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Jingyi Zhu
- Clinical Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Takuji Yamaguchi
- Department of Palliative Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Ailing Hu
- Department of Palliative Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Masahiro Tabuchi
- Department of Palliative Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Daisuke Watanabe
- Department of Palliative Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Seiichiro Yoshikawa
- Cancer therapeutic center, Juntendo University Urayasu Hospital, Chiba, Japan
| | | | - Akio Mizushima
- Department of Palliative Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Shilin Xia
- Clinical Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Department of Palliative Medicine, Juntendo University School of Medicine, Tokyo, Japan
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7
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Yang RQ, Chen YL, Sun LC, Ou W, Liu HY, Zhang LJ, Liu GM, Zhao G, Cao MJ. Involvement of MMP-9 in collagen degradation of sea bass (Lateolabrax japonicus): Cloning, expression, and characterization. J Food Sci 2023; 88:638-649. [PMID: 36576136 DOI: 10.1111/1750-3841.16402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/20/2022] [Accepted: 11/10/2022] [Indexed: 12/29/2022]
Abstract
Disintegration of intramuscular connective tissue is responsible for postmortem tenderization of fish muscles during chilled storage. Matrix metalloproteinase-9 (MMP-9) was reported to be involved in this process, whereas the mechanism has not been revealed. In the present study, purified type I and V collagens from the connective tissues of sea bass (Lateolabrax japonicus) muscles were first prepared. These two kinds of collagens comprise three polypeptide chains (α), forming a typical triple-helical domain as determined by circular dichroism. The complete coding region of MMP-9 containing an open reading frame of 2070 bp encoding 689 amino acid residues was then cloned. The recombinant MMP-9 catalytic domain (rcMMP-9) was expressed in Escherichia coli and exhibited high hydrolyzing activity toward gelatin. Besides, rcMMP-9 was effective in degrading type V collagen rather than type I collagen at 4°C. The enzymatic activity of rcMMP-9 was highly pH-dependent, and its enzymatic activity under neutral and basic conditions was higher than that under acidic conditions. Metal ion Ca2+ was necessary for the maintenance of rcMMP-9 activity, whereas Zn2+ inhibited its activity. Our present study indicated that MMP-9 is responsible for the disintegration of intramuscular connective tissues by cleaving type V collagen during postmortem tenderization of fish muscle. PRACTICAL APPLICATION: Elucidation the involvement of MMP-9 in collagen degradation will deliver a reference for the prevention of muscular protein decomposition during chilled storage of fish fillets.
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Affiliation(s)
- Ru-Qing Yang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
| | - Yu-Lei Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China.,Collaborative Innovation Center of Marine Food Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Le-Chang Sun
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China.,Collaborative Innovation Center of Marine Food Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Wei Ou
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
| | - Hai-Yan Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
| | - Ling-Jing Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China.,Collaborative Innovation Center of Marine Food Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Guang-Ming Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China.,Collaborative Innovation Center of Marine Food Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Guanghua Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China.,Collaborative Innovation Center of Marine Food Deep Processing, Dalian Polytechnic University, Dalian, China
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8
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Lau RK, Enustun E, Gu Y, Nguyen JV, Corbett KD. A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage. EMBO J 2022; 41:e111540. [PMID: 36156805 PMCID: PMC9670203 DOI: 10.15252/embj.2022111540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 01/13/2023] Open
Abstract
To protect themselves from the constant threat of bacteriophage (phage) infection, bacteria have evolved diverse immune systems including restriction-modification, CRISPR-Cas, and many others. Here, we describe the discovery of a two-protein transcriptional regulator module associated with hundreds of CBASS immune systems and demonstrate that this module drives the expression of its associated CBASS system in response to DNA damage. We show that the helix-turn-helix transcriptional repressor CapH binds the promoter region of its associated CBASS system to repress transcription until it is cleaved by the metallopeptidase CapP. CapP is activated in vitro by single-stranded DNA, and in cells by DNA-damaging drugs. Together, CapH and CapP drive increased expression of their associated CBASS system in response to DNA damage. We identify CapH- and CapP-related proteins associated with diverse known and putative bacterial immune systems including DISARM and Pycsar antiphage operons. Overall, our data highlight a mechanism by which bacterial immune systems can sense and respond to a universal signal of cell stress, potentially enabling multiple immune systems to mount a coordinated defensive response against an invading pathogen.
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Affiliation(s)
- Rebecca K Lau
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaCAUSA
| | - Eray Enustun
- Department of Molecular Biology, School of Biological SciencesUniversity of California, San DiegoLa JollaCAUSA
| | - Yajie Gu
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaCAUSA
| | - Justin V Nguyen
- Department of Molecular Biology, School of Biological SciencesUniversity of California, San DiegoLa JollaCAUSA
| | - Kevin D Corbett
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaCAUSA
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9
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Liu D, Saikam V, Skrada KA, Merlin D, Iyer SS. Inflammatory bowel disease biomarkers. Med Res Rev 2022; 42:1856-1887. [PMID: 35603998 PMCID: PMC10321231 DOI: 10.1002/med.21893] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 11/16/2021] [Accepted: 05/05/2022] [Indexed: 12/16/2022]
Abstract
Inflammatory bowel disease (IBD) is characterized as chronic inflammation in the gastrointestinal tract, which includes two main subtypes, Crohn's disease and ulcerative colitis. Endoscopy combined with biopsy is the most effective way to establish IBD diagnosis and disease management. Imaging techniques have also been developed to monitor IBD. Although effective, the methods are expensive and invasive, which leads to pain and discomfort. Alternative noninvasive biomarkers are being explored as tools for IBD prognosis and disease management. This review focuses on novel biomarkers that have emerged in recent years. These serological biomarkers and microRNAs could potentially be used for disease management in IBD, thereby decreasing patient discomfort and morbidity.
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Affiliation(s)
- Dandan Liu
- Department of Chemistry, 788 Petit Science Center, Georgia State University, Atlanta, Georgia, USA
| | - Varma Saikam
- Department of Chemistry, 788 Petit Science Center, Georgia State University, Atlanta, Georgia, USA
| | - Katie A Skrada
- Department of Chemistry, 788 Petit Science Center, Georgia State University, Atlanta, Georgia, USA
| | - Didier Merlin
- 790 Petit Science Center, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
- Atlanta Veterans Medical Center, Decatur, Georgia, USA
| | - Suri S Iyer
- Department of Chemistry, 788 Petit Science Center, Georgia State University, Atlanta, Georgia, USA
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10
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Molecularly Imprinted Nanoparticles towards MMP9 for Controlling Cardiac ECM after Myocardial Infarction: A Predictive Experimental-Computational Chemistry Investigation. Biomedicines 2022; 10:biomedicines10092070. [PMID: 36140171 PMCID: PMC9495980 DOI: 10.3390/biomedicines10092070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/14/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022] Open
Abstract
The recent advances in nanotechnology are revolutionizing preventive and therapeutic approaches to treating cardiovascular diseases. Controlling the extracellular matrix metalloproteinase (MMP) activation and expression in the failing human left ventricular myocardium represents a significant therapeutic target for heart disease. In this study, we used molecularly imprinting polymers (MIPs) to restore the correct balance between MMPs and their tissue inhibitors (TIMPs), and explored the potential of this technique exhaustively through chemical synthesis, physicochemical and biological characterizations, and computational chemistry methods. By molecular dynamics simulations based on classical force fields, we simulated the early stages of the imprinting process in solution disclosing the pivotal interaction established between the monomers and the MMP9 protein template. The average interaction energies of methacrylic acid (MAA) and poly (ethylene glycol) ethyl ether methacrylate (PEG) units were in the ranges 17–22 and 30–37 kcal/mol, respectively. At low coverage, the PEG monomers seemed firmly anchored to the protein surface and were not displaced by water, while only about 20% of MAA was replaced by water. The synthesis of MIPs was successfully with a monomer conversion higher than 99% and the production of spherical particles with average diameter of 344 ± 33 nm. HPLC analysis showed a specific recognition factor of MMP9 on MIPs of about 1.3. FT-IR Chemical Imaging confirmed the mechanisms necessary to generate a “selective memory” of the MIPs towards the enzyme. HPLC results indicated that the rebound amount of both TIMP1 and MMP2 to MIPs is lower than that of the template, showing a selectivity factor of 2.1 and 2.3, respectively. Preliminary tests on the effect of MIPs on H9C2 cells revealed that this treatment has no cytotoxic effects.
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Pavan M, Bassani D, Bolcato G, Bissaro M, Sturles M, Moro S. Computational strategies to identify new drug candidates against neuroinflammation. Curr Med Chem 2022; 29:4756-4775. [PMID: 35135446 DOI: 10.2174/0929867329666220208095122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 11/22/2022]
Abstract
The even more increasing application of computational approaches in these last decades has deeply modified the process of discovery and commercialization of new therapeutic entities. This is especially true in the field of neuroinflammation, in which both the peculiar anatomical localization and the presence of the blood-brain barrier makeit mandatory to finely tune the candidates' physicochemical properties from the early stages of the discovery pipeline. The aim of this review is therefore to provide a general overview to the readers about the topic of neuroinflammation, together with the most common computational strategies that can be exploited to discover and design small molecules controlling neuroinflammation, especially those based on the knowledge of the three-dimensional structure of the biological targets of therapeutic interest. The techniques used to describe the molecular recognition mechanisms, such as molecular docking and molecular dynamics, will therefore be eviscerated, highlighting their advantages and their limitations. Finally, we report several case studies in which computational methods have been applied in drug discovery on neuroinflammation, focusing on the last decade's research.
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Affiliation(s)
- Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Giovanni Bolcato
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Maicol Bissaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Mattia Sturles
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
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12
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Raeeszadeh-Sarmazdeh M, Coban M, Mahajan S, Hockla A, Sankaran B, Downey GP, Radisky DC, Radisky ES. Engineering of tissue inhibitor of metalloproteinases TIMP-1 for fine discrimination between closely-related stromelysins MMP-3 and MMP-10. J Biol Chem 2022; 298:101654. [PMID: 35101440 PMCID: PMC8902619 DOI: 10.1016/j.jbc.2022.101654] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 12/03/2022] Open
Abstract
Matrix metalloproteinases (MMPs) have long been known as key drivers in the development and progression of diseases, including cancer and neurodegenerative, cardiovascular, and many other inflammatory and degenerative diseases, making them attractive potential drug targets. Engineering selective inhibitors based upon tissue inhibitors of metalloproteinases (TIMPs), endogenous human proteins that tightly yet nonspecifically bind to the family of MMPs, represents a promising new avenue for therapeutic development. Here, we used a counter-selective screening strategy for directed evolution of yeast-displayed human TIMP-1 to obtain TIMP-1 variants highly selective for the inhibition of MMP-3 in preference over MMP-10. As MMP-3 and MMP-10 are the most similar MMPs in sequence, structure, and function, our results thus clearly demonstrate the capability for engineering full-length TIMP proteins to be highly selective MMP inhibitors. We show using protein crystal structures and models of MMP-3-selective TIMP-1 variants bound to MMP-3 and counter-target MMP-10 how structural alterations within the N-terminal and C-terminal TIMP-1 domains create new favorable and selective interactions with MMP-3 and disrupt unique interactions with MMP-10. While our MMP-3-selective inhibitors may be of interest for future investigation in diseases where this enzyme drives pathology, our platform and screening strategy can be employed for developing selective inhibitors of additional MMPs implicated as therapeutic targets in disease.
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Affiliation(s)
| | - Mathew Coban
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224
| | - Shivansh Mahajan
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224
| | - Alexandra Hockla
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Gregory P Downey
- Departments of Medicine, Pediatrics, and Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado 80206; Departments of Medicine, and Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Derek C Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224
| | - Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224.
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Udrea AM, Gradisteanu Pircalabioru G, Boboc AA, Mares C, Dinache A, Mernea M, Avram S. Advanced Bioinformatics Tools in the Pharmacokinetic Profiles of Natural and Synthetic Compounds with Anti-Diabetic Activity. Biomolecules 2021; 11:1692. [PMID: 34827690 PMCID: PMC8615418 DOI: 10.3390/biom11111692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
Diabetes represents a major health problem, involving a severe imbalance of blood sugar levels, which can disturb the nerves, eyes, kidneys, and other organs. Diabes management involves several synthetic drugs focused on improving insulin sensitivity, increasing insulin production, and decreasing blood glucose levels, but with unclear molecular mechanisms and severe side effects. Natural chemicals extracted from several plants such as Gymnema sylvestre, Momordica charantia or Ophiopogon planiscapus Niger have aroused great interest for their anti-diabetes activity, but also their hypolipidemic and anti-obesity activity. Here, we focused on the anti-diabetic activity of a few natural and synthetic compounds, in correlation with their pharmacokinetic/pharmacodynamic profiles, especially with their blood-brain barrier (BBB) permeability. We reviewed studies that used bioinformatics methods such as predicted BBB, molecular docking, molecular dynamics and quantitative structure-activity relationship (QSAR) to elucidate the proper action mechanisms of antidiabetic compounds. Currently, it is evident that BBB damage plays a significant role in diabetes disorders, but the molecular mechanisms are not clear. Here, we presented the efficacy of natural (gymnemic acids, quercetin, resveratrol) and synthetic (TAK-242, propofol, or APX3330) compounds in reducing diabetes symptoms and improving BBB dysfunctions. Bioinformatics tools can be helpful in the quest for chemical compounds with effective anti-diabetic activity that can enhance the druggability of molecular targets and provide a deeper understanding of diabetes mechanisms.
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Affiliation(s)
- Ana Maria Udrea
- Laser Department, National Institute for Laser, Plasma and Radiation Physics, 077125 Maurele, Romania; (A.M.U.); (A.D.)
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, 1 B. P. Hașdeu St., 50567 Bucharest, Romania;
| | - Gratiela Gradisteanu Pircalabioru
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, 1 B. P. Hașdeu St., 50567 Bucharest, Romania;
| | - Anca Andreea Boboc
- “Maria Sklodowska Curie” Emergency Children’s Hospital, 20, Constantin Brancoveanu Bd., 077120 Bucharest, Romania;
- Department of Pediatrics 8, “Carol Davila” University of Medicine and Pharmacy, Eroii Sanitari Bd., 020021 Bucharest, Romania
| | - Catalina Mares
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independentei, 050095 Bucharest, Romania; (C.M.); (S.A.)
| | - Andra Dinache
- Laser Department, National Institute for Laser, Plasma and Radiation Physics, 077125 Maurele, Romania; (A.M.U.); (A.D.)
| | - Maria Mernea
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independentei, 050095 Bucharest, Romania; (C.M.); (S.A.)
| | - Speranta Avram
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91–95 Splaiul Independentei, 050095 Bucharest, Romania; (C.M.); (S.A.)
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Choi H, Kim E, Choi JY, Park E, Lee HJ. Potent therapeutic targets for treatment of Alzheimer's disease: Amyloid degrading enzymes. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hang Choi
- Department of Chemistry Education Kongju National University Gongju Republic of Korea
| | - Eungchan Kim
- Department of Chemistry Education Kongju National University Gongju Republic of Korea
| | - Jae Yoon Choi
- Department of Chemistry Education Kongju National University Gongju Republic of Korea
| | - Eunsik Park
- Department of Life Sport Education Kongju National University Gongju Republic of Korea
| | - Hyuck Jin Lee
- Department of Chemistry Education Kongju National University Gongju Republic of Korea
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Liu N, Wang X, Wu H, Lv X, Xie H, Guo Z, Wang J, Dou G, Zhang C, Sun M. Computational study of effective matrix metalloproteinase 9 (MMP9) targeting natural inhibitors. Aging (Albany NY) 2021; 13:22867-22882. [PMID: 34607974 PMCID: PMC8544340 DOI: 10.18632/aging.203581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/10/2021] [Indexed: 02/06/2023]
Abstract
Object: The present study screened ideal lead natural compounds that could target and inhibit matrix metalloproteinase 9 (MMP9) protein from the ZINC database to develop drugs for clear cell renal cell carcinoma (CCRCC)-targeted treatment. Methods: Discovery Studio 4.5 was used to compare and screen the ligands with the reference drug, solasodine, to identify ideal candidate compounds that could inhibit MMP9. The LibDock module was used to analyze compounds that could strongly bind to MMP9, and the top 20 compounds determined by the LibDock score were selected for further research. ADME and TOPKAT modules were used to choose the safe compounds from these 20 compounds. The selected compounds were analyzed using the CDOCKER module for molecular docking and feature mapping for pharmacophore prediction. The stability of these compound–MMP9 complexes was analyzed by molecular dynamic simulation. Cell counting kit-8, colony-forming, and scratch assays were used to analyze the anti-CCRCC effects of these ligands. Results: Strong binding to MMP9 was exhibited by 6,762 ligands. Among the top 20 compounds, sappanol and sventenin exhibited nearly undefined blood–brain barrier level and lower aqueous solubility, carcinogenicity, and hepatotoxicity than the positive control drug, solasodine. Additionally, these compounds exhibited lower potential energies with MMP9, and the ligand–MMP9 complexes were stable in the natural environment. Furthermore, sappanol inhibited CCRCC cell migration and proliferation. Conclusion: Sappanol and sventenin are safe and reliable compounds to target and inhibit MMP9. Sappanol can CCRCC cell migration and proliferation. These two compounds may give new thought to the targeted therapy for patients with CCRCC.
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Affiliation(s)
- Naimeng Liu
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, China
| | - Xinhui Wang
- Department of Oncology, The First Hospital of Jilin University, Changchun, China
| | - Hao Wu
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
| | - Xiaye Lv
- Department of Hematology, The First Clinical Medical School of Lanzhou University, Lanzhou, Gansu, China
| | - Haoqun Xie
- Clinical College, Jilin University, Changchun, China
| | - Zhen Guo
- Clinical College, Jilin University, Changchun, China
| | - Jing Wang
- Clinical College, Jilin University, Changchun, China
| | - Gaojing Dou
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, China.,Clinical College, Jilin University, Changchun, China
| | - Chenxi Zhang
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
| | - Mindan Sun
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
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Production of a Soluble Recombinant Antibody Fragment against MMP9 Using Escherichia coli. ACTA ACUST UNITED AC 2021; 57:medicina57090981. [PMID: 34577904 PMCID: PMC8468072 DOI: 10.3390/medicina57090981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022]
Abstract
Matrix metalloproteinase 9 (MMP9) is involved in several aspects of the pathology of cancer, including invasion, metastasis, and angiogenesis. In this study, we expressed a recombinant scFv-type anti-MMP9 antibody in soluble form using Escherichia coli, purified it, and confirmed its antigen-binding ability. The convenient, rapid, inexpressive system used in this study for producing recombinant antibody fragments needs only five days, and thus can be used for the efficient production of scFv against MMP9, which can be used in a range of applications and industrial fields, including diagnosis and treatment of inflammatory and cancer-related diseases.
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17
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Rahman F, Nguyen TM, Adekoya OA, Campestre C, Tortorella P, Sylte I, Winberg JO. Inhibition of bacterial and human zinc-metalloproteases by bisphosphonate- and catechol-containing compounds. J Enzyme Inhib Med Chem 2021; 36:819-830. [PMID: 33757387 PMCID: PMC7993378 DOI: 10.1080/14756366.2021.1901088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Compounds containg catechol or bisphosphonate were tested as inhibitors of the zinc metalloproteases, thermolysin (TLN), pseudolysin (PLN) and aureolysin (ALN) which are bacterial virulence factors, and the human matrix metalloproteases MMP-9 and -14. Inhibition of virulence is a putative strategy in the development of antibacterial drugs, but the inhibitors should not interfere with human enzymes. Docking indicated that the inhibitors bound MMP-9 and MMP-14 with the phenyl, biphenyl, chlorophenyl, nitrophenyl or methoxyphenyl ringsystem in the S1'-subpocket, while these ringsystems entered the S2'- or S1 -subpockets or a region involving amino acids in the S1'- and S2'-subpockets of the bacterial enzymes. An arginine conserved among the bacterial enzymes seemed to hinder entrance deeply into the S1'-subpocket. Only the bisphosphonate containing compound RC2 bound stronger to PLN and TLN than to MMP-9 and MMP-14. Docking indicated that the reason was that the conserved arginine (R203 in TLN and R198 in PLN) interacts with phosphate groups of RC2.
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Affiliation(s)
- Fatema Rahman
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Tra-Mi Nguyen
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Olayiwola A Adekoya
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Cristina Campestre
- Department of Pharmacy, University of "G. d'Annunzio" Chieti, Chieti, Italy
| | - Paolo Tortorella
- Department of Pharmacy, Science of Pharmacy, University "A. Moro" Bari, Bari, Italy
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Jan-Olof Winberg
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
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18
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Sun P, Scharnweber T, Wadhwani P, Rabe KS, Niemeyer CM. DNA-Directed Assembly of a Cell-Responsive Biohybrid Interface for Cargo Release. SMALL METHODS 2021; 5:e2001049. [PMID: 34927983 DOI: 10.1002/smtd.202001049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 05/06/2021] [Indexed: 05/24/2023]
Abstract
The development of a DNA-based cell-responsive biohybrid interface that can be used for spatially confined release of molecular cargo is reported. To this end, tailored DNA-protein conjugates are designed as gatekeepers that can be specifically cleaved by matrix metalloproteases (MMPs), which are secreted by many cancer cells. These gatekeepers can be installed by DNA hybridization on the surface of mesoporous silica nanoparticles (MSNs). The MSNs display another orthogonal DNA oligonucleotide that can be exploited for site-selective immobilization on solid glass surfaces to yield micropatterned substrates for cell adhesion. Using the human fibrosarcoma cell line HT1080 that secretes MMPs, it is demonstrated that the biohybrid surface is specifically modified by the cells to release both MSN-bound gatekeeper proteins and the encapsulated cargo peptide KLA. In view of the enormously high modularity of the system presented here, this approach promising for applications in drug delivery, tissue engineering, or other areas of nanobiotechnology is considered.
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Affiliation(s)
- Pengchao Sun
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz-1, D-76344, Eggenstein-Leopoldshafen, Germany
- School of Pharmaceutical Sciences, Zhengzhou University, No.100 Science Avenue, Zhengzhou, 450001, China
| | - Tim Scharnweber
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz-1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Parvesh Wadhwani
- Institute for Biological Interfaces (IBG 2), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz-1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz-1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz-1, D-76344, Eggenstein-Leopoldshafen, Germany
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Charzewski Ł, Krzyśko KA, Lesyng B. Structural characterisation of inhibitory and non-inhibitory MMP-9-TIMP-1 complexes and implications for regulatory mechanisms of MMP-9. Sci Rep 2021; 11:13376. [PMID: 34183752 PMCID: PMC8238946 DOI: 10.1038/s41598-021-92881-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 05/12/2021] [Indexed: 12/18/2022] Open
Abstract
MMP-9 plays a number of important physiological functions but is also responsible for many pathological processes, including cancer invasion, metastasis, and angiogenesis. It is, therefore, crucial to understand its enzymatic activity, including activation and inhibition mechanisms. This enzyme may also be partially involved in the "cytokine storm" that is characteristic of COVID-19 disease (SARS-CoV-2), as well as in the molecular mechanisms responsible for lung fibrosis. Due to the variety of processing pathways involving MMP-9 in biological systems and its uniqueness due to the O-glycosylated domain (OGD) and fibronectin-like (FBN) domain, specific interactions with its natural TIMP-1 inhibitor should be carefully studied, because they differ significantly from other homologous systems. In particular, earlier experimental studies have indicated that the newly characterised circular form of a proMMP-9 homotrimer exhibits stronger binding properties to TIMP-1 compared to its monomeric form. However, molecular structures of the complexes and the binding mechanisms remain unknown. The purpose of this study is to fill in the gaps in knowledge. Molecular modelling methods are applied to build the inhibitory and non-inhibitory MMP-9-TIMP-1 complexes, which allows for a detailed description of these structures and should allow for a better understanding of the regulatory processes in which MMP-9 is involved.
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Affiliation(s)
- Łukasz Charzewski
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Krystiana A Krzyśko
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.
| | - Bogdan Lesyng
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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21
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An interplay of microglia and matrix metalloproteinase MMP9 under hypoxic stress regulates the opticin expression in retina. Sci Rep 2021; 11:7444. [PMID: 33811221 PMCID: PMC8018966 DOI: 10.1038/s41598-021-86302-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 03/12/2021] [Indexed: 02/07/2023] Open
Abstract
Inflammation plays a key role in the pathogenesis of retinal vascular diseases. We have shown earlier an increase in the activity of matrix metalloproteinases in the vitreous and tears of preterm born babies with retinopathy of prematurity (ROP) compared to those with no-ROP leading to a shift in the balance of angiogenic (vascular endothelial growth factor [VEGF], matrix metalloproteinase [MMPs], complement component [C3]) and anti-angiogenic (opticin, thrombospondin) in ROP eyes. We now confirmed that tear MMP levels in premature infants perfectly correlates with disease severity. Next, we demonstrated that a reduced opticin levels in ROP vitreous are regulated by MMPs secreted by activated microglia. Upon exposing the human microglia cell line (CHME3) to hypoxia, an increased expression of inflammatory proteins (MMP9, VEGF) was noticed while opticin reduced significantly (p = 0.005). Further, the reduced opticin’s expression by microglial cells under hypoxia could be rescued by inhibiting the MMP activity using doxycycline and EDTA. The inhibition of MMP activity altered the expression of other key signaling molecules under hypoxia. Our study clearly explains that increased activity of MMPs under hypoxia regulates the expression of opticin as seen in the vitreous humor of ROP and could serve as a potential target for ROP management.
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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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Bayona-Serrano JD, Viala VL, Rautsaw RM, Schramer TD, Barros-Carvalho GA, Nishiyama MY, Freitas-de-Sousa LA, Moura-da-Silva AM, Parkinson CL, Grazziotin FG, Junqueira-de-Azevedo ILM. Replacement and Parallel Simplification of Nonhomologous Proteinases Maintain Venom Phenotypes in Rear-Fanged Snakes. Mol Biol Evol 2020; 37:3563-3575. [PMID: 32722789 PMCID: PMC8525196 DOI: 10.1093/molbev/msaa192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Novel phenotypes are commonly associated with gene duplications and neofunctionalization, less documented are the cases of phenotypic maintenance through the recruitment of novel genes. Proteolysis is the primary toxic character of many snake venoms, and ADAM metalloproteinases, named snake venom metalloproteinases (SVMPs), are largely recognized as the major effectors of this phenotype. However, by investigating original transcriptomes from 58 species of advanced snakes (Caenophidia) across their phylogeny, we discovered that a different enzyme, matrix metalloproteinase (MMP), is actually the dominant venom component in three tribes (Tachymenini, Xenodontini, and Conophiini) of rear-fanged snakes (Dipsadidae). Proteomic and functional analyses of these venoms further indicate that MMPs are likely playing an "SVMP-like" function in the proteolytic phenotype. A detailed look into the venom-specific sequences revealed a new highly expressed MMP subtype, named snake venom MMP (svMMP), which originated independently on at least three occasions from an endogenous MMP-9. We further show that by losing ancillary noncatalytic domains present in its ancestors, svMMPs followed an evolutionary path toward a simplified structure during their expansion in the genomes, thus paralleling what has been proposed for the evolution of their Viperidae counterparts, the SVMPs. Moreover, we inferred an inverse relationship between the expression of svMMPs and SVMPs along the evolutionary history of Xenodontinae, pointing out that one type of enzyme may be substituting for the other, whereas the general (metallo)proteolytic phenotype is maintained. These results provide rare evidence on how relevant phenotypic traits can be optimized via natural selection on nonhomologous genes, yielding alternate biochemical components.
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Affiliation(s)
| | - Vincent Louis Viala
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC
| | | | | | - Milton Yutaka Nishiyama
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
| | | | - Ana Maria Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC
| | | | - Inácio L M Junqueira-de-Azevedo
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
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Mary Rajathei D, Parthasarathy S, Selvaraj S. HPREP: a comprehensive database for human proteome repeats. J Integr Bioinform 2020; 0:/j/jib.ahead-of-print/jib-2020-0024/jib-2020-0024.xml. [PMID: 33136065 DOI: 10.1515/jib-2020-0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/17/2020] [Indexed: 11/15/2022] Open
Abstract
Amino acid repeats are found to play important roles in both structures and functions of the proteins. These are commonly found in all kingdoms of life, especially in eukaryotes and a larger fraction of human proteins composed of repeats. Further, the abnormal expansions of shorter repeats cause various diseases to humans. Therefore, the analysis of repeats of the entire human proteome along with functional, mutational and disease information would help to better understand their roles in proteins. To fulfill this need, we developed a web database HPREP (http://bioinfo.bdu.ac.in/hprep) for human proteome repeats using Perl and HTML programming. We identified different categories of well-characterized repeats and domain repeats that are present in the human proteome of UniProtKB/Swiss-Prot by using in-house Perl programming and novel repeats by using the repeat detection T-REKS tool as well as XSTREAM web server. Further, these proteins are annotated with functional, mutational and disease information and grouped according to specific repeat types. The developed database enables the users to search by specific repeat type in order to understand their involvement in proteins. Thus, the HPREP database is expected to be a useful resource to gain better insight regarding the different repeats in human proteome and their biological roles.
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Affiliation(s)
- David Mary Rajathei
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, India
| | - Subbiah Parthasarathy
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, India
| | - Samuel Selvaraj
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, India
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Mohammadi M, Rezaie E, Sakhteman A, Zarei N. A highly potential cleavable linker for tumor targeting antibody-chemokines. J Biomol Struct Dyn 2020; 40:2546-2556. [PMID: 33118476 DOI: 10.1080/07391102.2020.1841025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chemokines are the large family of chemotactic cytokines that play an important role in leukocyte movement and migration stimulation. Until now, several antibody-cytokine (chemokine) fusion proteins have been investigated in clinical trials because of their ability to evoke the circulating leukocytes far from the tumor site. In this case, creating the concentration gradient regarding the chemokine is very important to recruit the circulating leukocytes with maximum performance to the tumor environment. To achieve a proper gradient, the chemokine separation from the tumor antigen-bounded antibody can be very crucial. Thus, we designed a novel linker that can be cleaved by enzymes presented around the tumor site including cathepsin B, urokinase-type plasminogen activator (uPA) and matrix metalloproteinases (MMPs). Also, it can inhibit tumor progression by competing with the native substrate of key proteases in the tumor microenvironment. The proposed linker was evaluated using some bioinformatics approaches. In silico results showed that the linker is structurally stable and could be detected and cleaved using the mentioned enzymes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mozafar Mohammadi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ehsan Rezaie
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Neda Zarei
- Department of Biology, Farhangian University, Tehran, Iran
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26
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The Role of Matrix Metalloproteinase-9 in Atherosclerotic Plaque Instability. Mediators Inflamm 2020; 2020:3872367. [PMID: 33082709 PMCID: PMC7557896 DOI: 10.1155/2020/3872367] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/10/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
Matrix metalloproteinase-9 (MMP-9) belongs to the MMP family and has been widely investigated. Excessive MMP-9 expression can enhance extracellular matrix degradation and promote plaque instability. Studies have demonstrated that MMP-9 levels are higher in vulnerable plaques than in stable plaques. Additionally, several human studies have demonstrated that MMP-9 may be a predictor of atherosclerotic plaque instability and a risk factor for future adverse cardiovascular and cerebrovascular events. MMP-9 deficiency or blocking MMP-9 expression can inhibit plaque inflammation and prevent atherosclerotic plaque instability. All of these results suggest that MMP-9 may be a useful predictive biomarker for vulnerable atherosclerotic plaques, as well as a therapeutic target for preventing atherosclerotic plaque instability. In this review, we describe the structure, function, and regulation of MMP-9. We also discuss the role of MMP-9 in predicting and preventing atherosclerotic plaque instability.
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Molecular Interactions Stabilizing the Promatrix Metalloprotease-9·Serglycin Heteromer. Int J Mol Sci 2020; 21:ijms21124205. [PMID: 32545641 PMCID: PMC7352350 DOI: 10.3390/ijms21124205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 12/13/2022] Open
Abstract
Previous studies have shown that THP-1 cells produced an SDS-stable and reduction-sensitive complex between proMMP-9 and a chondroitin sulfate proteoglycan (CSPG) core protein. The complex could be reconstituted in vitro using purified serglycin (SG) and proMMP-9 and contained no inter-disulfide bridges. It was suggested that the complex involved both the FnII module and HPX domain of proMMP-9. The aims of the present study were to resolve the interacting regions of the molecules that form the complex and the types of interactions involved. In order to study this, we expressed and purified full-length and deletion variants of proMMP-9, purified CSPG and SG, and performed in vitro reconstitution assays, peptide arrays, protein modelling, docking, and molecular dynamics (MD) simulations. ProMMP-9 variants lacking both the FnII module and the HPX domain did not form the proMMP-9∙CSPG/SG complex. Deletion variants containing at least the FnII module or the HPX domain formed the proMMP-9∙CSPG/SG complex, as did the SG core protein without CS chains. The interacting parts covered large surface areas of both molecules and implicated dynamic and complementary ionic, hydrophobic, and hydrogen bond interactions. Hence, no short single interacting linear motifs in the two macromolecules could explain the strong SDS-stable and reduction-sensitive binding.
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28
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Roque W, Boni A, Martinez-Manzano J, Romero F. A Tale of Two Proteolytic Machines: Matrix Metalloproteinases and the Ubiquitin-Proteasome System in Pulmonary Fibrosis. Int J Mol Sci 2020; 21:ijms21113878. [PMID: 32485920 PMCID: PMC7312171 DOI: 10.3390/ijms21113878] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 01/19/2023] Open
Abstract
Pulmonary fibrosis is a chronic and progressive lung disease characterized by the activation of fibroblasts and the irreversible deposition of connective tissue matrices that leads to altered pulmonary architecture and physiology. Multiple factors have been implicated in the pathogenesis of lung fibrosis, including genetic and environmental factors that cause abnormal activation of alveolar epithelial cells, leading to the development of complex profibrotic cascade activation and extracellular matrix (ECM) deposition. One class of proteinases that is thought to be important in the regulation of the ECM are the matrix metalloproteinases (MMPs). MMPs can be up- and down- regulated in idiopathic pulmonary fibrosis (IPF) lungs and their role depends upon their location and function. Furthermore, alterations in the ubiquitin-proteosome system (UPS), a major intracellular protein degradation complex, have been described in aging and IPF lungs. UPS alterations could potentially lead to the abnormal accumulation and deposition of ECM. A better understanding of the specific roles MMPs and UPS play in the pathophysiology of pulmonary fibrosis could potentially drive to the development of novel biomarkers that can be as diagnostic and therapeutic targets. In this review, we describe how MMPs and UPS alter ECM composition in IPF lungs and mouse models of pulmonary fibrosis, thereby influencing the alveolar epithelial and mesenchymal cell behavior. Finally, we discuss recent findings that associate MMPs and UPS interplay with the development of pulmonary fibrosis.
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Affiliation(s)
- Willy Roque
- Department of Medicine, Rutgers—New Jersey Medical School, 185 S Orange Ave, Newark, NJ 07103, USA; (W.R.); (A.B.)
| | - Alexandra Boni
- Department of Medicine, Rutgers—New Jersey Medical School, 185 S Orange Ave, Newark, NJ 07103, USA; (W.R.); (A.B.)
| | - Jose Martinez-Manzano
- Brigham and Women’s Hospital—Pulmonary and Critical Care Medicine, Boston, MA 02115, USA;
| | - Freddy Romero
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care and the Center for Translational Medicine, The Jane & Leonard Korman Respiratory Institute, Philadelphia, PA 19107, USA
- Correspondence:
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Gifre-Renom L, Ugarte-Berzal E, Martens E, Boon L, Cano-Garrido O, Martínez-Núñez E, Luque T, Roca-Pinilla R, Conchillo-Solé Ò, Ferrer-Miralles N, Villaverde A, Opdenakker G, Garcia-Fruitós E, Arís A. Recombinant Protein-Based Nanoparticles: Elucidating their Inflammatory Effects In Vivo and their Potential as a New Therapeutic Format. Pharmaceutics 2020; 12:pharmaceutics12050450. [PMID: 32414218 PMCID: PMC7284881 DOI: 10.3390/pharmaceutics12050450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/29/2020] [Accepted: 05/11/2020] [Indexed: 12/29/2022] Open
Abstract
Bacterial inclusion bodies (IBs) are protein-based nanoparticles of a few hundred nanometers formed during recombinant protein production processes in different bacterial hosts. IBs contain active protein in a mechanically stable nanostructured format that has been broadly characterized, showing promising potential in different fields such as tissue engineering, protein replacement therapies, cancer, and biotechnology. For immunomodulatory purposes, however, the interference of the format immunogenic properties—intrinsic to IBs—with the specific effects of the therapeutic protein is still an uncovered gap. For that, active and inactive forms of the catalytic domain of a matrix metalloproteinase-9 (MMP-9 and mutMMP-9, respectively) have been produced as IBs and compared with the soluble form for dermal inflammatory effects in mmp9 knock-out mice. After protein injections in air-pouches in the mouse model, MMP-9 IBs induce local neutrophil recruitment and increase pro-inflammatory chemokine levels, lasting for at least two days, whereas the effects triggered by the soluble MMP-9 format fade out after 3 h. Interestingly, the IB intrinsic effects (mutMMP-9 IBs) do not last more than 24 h. Therefore, it may be concluded that IBs could be used for the delivery of therapeutic proteins, such as immunomodulating proteins while preserving their stability in the specific tissue and without triggering important unspecific inflammatory responses due to the protein format.
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Affiliation(s)
- Laia Gifre-Renom
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08140 Caldes de Montbui, Spain; (L.G.-R.); (R.R.-P.)
| | - Estefania Ugarte-Berzal
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, University of Leuven, 3000 Leuven, Belgium; (E.U.-B.); (E.M.); (L.B.); (G.O.)
| | - Erik Martens
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, University of Leuven, 3000 Leuven, Belgium; (E.U.-B.); (E.M.); (L.B.); (G.O.)
| | - Lise Boon
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, University of Leuven, 3000 Leuven, Belgium; (E.U.-B.); (E.M.); (L.B.); (G.O.)
| | - Olivia Cano-Garrido
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.C.-G.); (E.M.-N.); (T.L.); (Ò.C.-S.); (N.F.-M.); (A.V.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Esther Martínez-Núñez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.C.-G.); (E.M.-N.); (T.L.); (Ò.C.-S.); (N.F.-M.); (A.V.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 08193 Barcelona, Spain
| | - Teresa Luque
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.C.-G.); (E.M.-N.); (T.L.); (Ò.C.-S.); (N.F.-M.); (A.V.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Ramon Roca-Pinilla
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08140 Caldes de Montbui, Spain; (L.G.-R.); (R.R.-P.)
| | - Òscar Conchillo-Solé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.C.-G.); (E.M.-N.); (T.L.); (Ò.C.-S.); (N.F.-M.); (A.V.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.C.-G.); (E.M.-N.); (T.L.); (Ò.C.-S.); (N.F.-M.); (A.V.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (O.C.-G.); (E.M.-N.); (T.L.); (Ò.C.-S.); (N.F.-M.); (A.V.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Ghislain Opdenakker
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, University of Leuven, 3000 Leuven, Belgium; (E.U.-B.); (E.M.); (L.B.); (G.O.)
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08140 Caldes de Montbui, Spain; (L.G.-R.); (R.R.-P.)
- Correspondence: (E.G.-F.); (A.A.); Tel.: +34-934-674-040 (E.G.-F. & A.A.)
| | - Anna Arís
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08140 Caldes de Montbui, Spain; (L.G.-R.); (R.R.-P.)
- Correspondence: (E.G.-F.); (A.A.); Tel.: +34-934-674-040 (E.G.-F. & A.A.)
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Anthraquinone: a promising scaffold for the discovery and development of therapeutic agents in cancer therapy. Future Med Chem 2020; 12:1037-1069. [PMID: 32349522 DOI: 10.4155/fmc-2019-0198] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cancer, characterized by uncontrolled malignant neoplasm, is a leading cause of death in both advanced and emerging countries. Although, ample drugs are accessible in the market to intervene with tumor progression, none are totally effective and safe. Natural anthraquinone (AQ) equivalents such as emodin, aloe-emodin, alchemix and many synthetic analogs extend their antitumor activity on different targets including telomerase, topoisomerases, kinases, matrix metalloproteinases, DNA and different phases of cell lines. Nano drug delivery strategies are advanced tools which deliver drugs into tumor cells with minimum drug leakage to normal cells. This review delineates the way AQ derivatives are binding on these targets by abolishing tumor cells to produce anticancer activity and purview of nanoformulations related to AQ analogs.
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Kotta JC, Lestari ABS, Candrasari DS, Hariono M. Medicinal Effect, In Silico Bioactivity Prediction, and Pharmaceutical Formulation of Ageratum conyzoides L.: A Review. SCIENTIFICA 2020; 2020:6420909. [PMID: 33110668 PMCID: PMC7578719 DOI: 10.1155/2020/6420909] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/22/2020] [Accepted: 09/26/2020] [Indexed: 05/05/2023]
Abstract
Goat weed (Ageratum conyzoides L.), or bandotan in Indonesia, is an herbaceous plant that broadly grows up in both subtropical as well as tropical areas. This herb contains many phytoconstituents which have many benefits in different aspects. The essential oil contains phytochemicals such as phenol, phenolic ester, and coumarin, whereas many compounds can been identified in the whole part such as terpenoid, steroid, chromene, pyrrolizidine alkaloid, and flavonoid. Empirically, this herb has been used as an antihemorrhagic, antiseptic, antileprosy, and wound-healing agent. This article reviews the potency of the herb in medication according to the chemical substances being deposited, which are collected from numerous studies, followed by its in silico bioactivity prediction as well as its pharmaceutical dosage form formulation.
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Affiliation(s)
- Jasvidianto C. Kotta
- Faculty of Pharmacy, Sanata Dharma University, Yogyakarta Campus III, Depok 55282, Indonesia
| | - Agatha B. S. Lestari
- Faculty of Pharmacy, Sanata Dharma University, Yogyakarta Campus III, Depok 55282, Indonesia
| | - Damiana S. Candrasari
- Faculty of Pharmacy, Sanata Dharma University, Yogyakarta Campus III, Depok 55282, Indonesia
| | - Maywan Hariono
- Faculty of Pharmacy, Sanata Dharma University, Yogyakarta Campus III, Depok 55282, Indonesia
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32
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Cuesta SA, Mora JR, Zambrano CH, Torres FJ, Rincón L. Comparative study of the nucleophilic attack step in the proteases catalytic activity: A theoretical study. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1705412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Sebastián A. Cuesta
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - José R. Mora
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Cesar H. Zambrano
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - F. Javier Torres
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Luis Rincón
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
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33
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Deryusheva EI, Machulin AV, Matyunin MA, Galzitskaya OV. Investigation of the Relationship between the S1 Domain and Its Molecular Functions Derived from Studies of the Tertiary Structure. Molecules 2019; 24:E3681. [PMID: 31614904 PMCID: PMC6832287 DOI: 10.3390/molecules24203681] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022] Open
Abstract
S1 domain, a structural variant of one of the "oldest" OB-folds (oligonucleotide/oligosaccharide-binding fold), is widespread in various proteins in three domains of life: Bacteria, Eukaryotes, and Archaea. In this study, it was shown that S1 domains of bacterial, eukaryotic, and archaeal proteins have a low percentage of identity, which indicates the uniqueness of the scaffold and is associated with protein functions. Assessment of the predisposition of tertiary flexibility of S1 domains using computational and statistical tools showed similar structural features and revealed functional flexible regions that are potentially involved in the interaction of natural binding partners. In addition, we analyzed the relative number and distribution of S1 domains in all domains of life and established specific features based on sequences and structures associated with molecular functions. The results correlate with the presence of repeats of the S1 domain in proteins containing the S1 domain in the range from one (bacterial and archaeal) to 15 (eukaryotic) and, apparently, are associated with the need for individual proteins to increase the affinity and specificity of protein binding to ligands.
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Affiliation(s)
- Evgenia I Deryusheva
- Institute for Biological Instrumentation, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Moscow Region, Russia.
| | - Andrey V Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Moscow Region, Russia.
| | - Maxim A Matyunin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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34
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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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35
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Moscoso CG, Steer CJ. "Let my liver rather heat with wine" - a review of hepatic fibrosis pathophysiology and emerging therapeutics. Hepat Med 2019; 11:109-129. [PMID: 31565001 PMCID: PMC6731525 DOI: 10.2147/hmer.s213397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/17/2019] [Indexed: 12/12/2022] Open
Abstract
Cirrhosis is characterized by extensive hepatic fibrosis, and it is the 14th leading cause of death worldwide. Numerous contributing conditions have been implicated in its development, including infectious etiologies, medication overdose or adverse effects, ingestible toxins, autoimmunity, hemochromatosis, Wilson’s disease and primary biliary cholangitis to list a few. It is associated with portal hypertension and its stigmata (varices, ascites, hepatic encephalopathy, combined coagulopathy and thrombophilia), and it is a major risk factor for hepatocellular carcinoma. Currently, orthotopic liver transplantation has been the only curative modality to treat cirrhosis, and the scarcity of donors results in many people waiting years for a transplant. Identification of novel targets for pharmacologic therapy through elucidation of key mechanistic components to induce fibrosis reversal is the subject of intense research. Development of robust models of hepatic fibrosis to faithfully characterize the interplay between activated hepatic stellate cells (the principal fibrogenic contributor to fibrosis initiation and perpetuation), hepatocytes and extracellular matrix components has the potential to identify critical components and mechanisms that can be exploited for targeted treatment. In this review, we will highlight key cellular pathways involved in the pathophysiology of fibrosis from extracellular ligands, effectors and receptors, to nuclear receptors, epigenetic mechanisms, energy homeostasis and cytokines. Further, molecular pathways of hepatic stellate cell deactivation are discussed, including apoptosis, senescence and reversal or transdifferentiation to an inactivated state resembling quiescence. Lastly, clinical evidence of fibrosis reversal induced by biologics and small molecules is summarized, current compounds under clinical trials are described and efforts for treatment of hepatic fibrosis with mesenchymal stem cells are highlighted. An enhanced understanding of the rich tapestry of cellular processes identified in the initiation, perpetuation and resolution of hepatic fibrosis, driven principally through phenotypic switching of hepatic stellate cells, should lead to a breakthrough in potential therapeutic modalities.
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Affiliation(s)
- Carlos G Moscoso
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition
| | - Clifford J Steer
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition.,Department of Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, MN 55455, USA
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36
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Shoari A, Rasaee MJ, Kanavi MR, Daraei B. Functional mimetic peptide discovery isolated by phage display interacts selectively to fibronectin domain and inhibits gelatinase. J Cell Biochem 2019; 120:19699-19711. [DOI: 10.1002/jcb.29276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Alireza Shoari
- Department of Medical Biotechnology, Faculty of Medical Sciences Tarbiat Modares University Tehran Iran
| | - Mohammad J. Rasaee
- Department of Medical Biotechnology, Faculty of Medical Sciences Tarbiat Modares University Tehran Iran
| | - Mozhgan R. Kanavi
- Ophthalmic Research Center Shahid Beheshti University of Medical Sciences Tehran Iran
| | - Bahram Daraei
- Department of Toxicology and Pharmacology, Faculty of Pharmacy Shahid Beheshti University of Medical Sciences Tehran Iran
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37
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Machulin A, Deryusheva E, Lobanov M, Galzitskaya O. Repeats in S1 Proteins: Flexibility and Tendency for Intrinsic Disorder. Int J Mol Sci 2019; 20:ijms20102377. [PMID: 31091666 PMCID: PMC6566611 DOI: 10.3390/ijms20102377] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 11/16/2022] Open
Abstract
An important feature of ribosomal S1 proteins is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. For S1 proteins, little is known about the contribution of flexible regions to protein domain function. We exhaustively studied a tendency for intrinsic disorder and flexibility within and between structural domains for all available UniProt S1 sequences. Using charge–hydrophobicity plot cumulative distribution function (CH-CDF) analysis we classified 53% of S1 proteins as ordered proteins; the remaining proteins were related to molten globule state. S1 proteins are characterized by an equal ratio of regions connecting the secondary structure within and between structural domains, which indicates a similar organization of separate S1 domains and multi-domain S1 proteins. According to the FoldUnfold and IsUnstruct programs, in the multi-domain proteins, relatively short flexible or disordered regions are predominant. The lowest percentage of flexibility is in the central parts of multi-domain proteins. Our results suggest that the ratio of flexibility in the separate domains is related to their roles in the activity and functionality of S1: a more stable and compact central part in the multi-domain proteins is vital for RNA interaction, terminals domains are important for other functions.
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Affiliation(s)
- Andrey Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia.
| | - Evgenia Deryusheva
- Institute for Biological Instrumentation, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia.
| | - Mikhail Lobanov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia.
| | - Oxana Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia.
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38
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Boon L, Ugarte-Berzal E, Martens E, Vandooren J, Rybakin V, Colau D, Gordon-Alonso M, van der Bruggen P, Stöcker W, Becker-Pauly C, Witters P, Morava E, Jaeken J, Proost P, Opdenakker G. Propeptide glycosylation and galectin-3 binding decrease proteolytic activation of human proMMP-9/progelatinase B. FEBS J 2018; 286:930-945. [PMID: 30422384 PMCID: PMC7379967 DOI: 10.1111/febs.14698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/21/2018] [Accepted: 11/09/2018] [Indexed: 01/06/2023]
Abstract
Matrix metalloproteinases (MMPs) are secreted as proenzymes, containing propeptides that interact with the catalytic zinc, thereby controlling MMP activation. The MMP‐9 propeptide is unique in the MMP family because of its post‐translational modification with an N‐linked oligosaccharide. ProMMP‐9 activation by MMP‐3 occurs stepwise by cleavage of the propeptide in an aminoterminal (pro‐AT) and carboxyterminal (pro‐CT) peptide. We chemically synthesized aglycosyl pro‐AT and pro‐CT and purified recombinant glycosylated pro‐ATSf−9. First, we report new cleavage sites in the MMP‐9 propeptide by MMP‐3 and neutrophil elastase. Additionally, we demonstrated with the use of western blot analysis a higher resistance of glycosylated versus aglycosyl pro‐AT against proteolysis by MMP‐3, MMP‐9, meprin α, neutrophil elastase and by protease‐rich synovial fluids from rheumatoid arthritis patients. Moreover, we investigated the effect of glycosylation on proteolytic activation of human proMMP‐9 with the use of zymography and dye‐quenched gelatin cleavage analysis. Compared to recombinant Sf‐9 proMMP‐9 glycoforms, larger oligosaccharides of human neutrophil proMMP‐9 increased resistance against proteolytic activation. Additionally, proMMP‐9 from Congenital Disorder of Glycosylation patients, compared to healthy controls, showed a higher activation rate by MMP‐3. Finally, we demonstrated that glycan‐galectin‐3 interactions reduced proMMP‐9 activation. In conclusion, modification of MMP‐9 propeptide glycosylation is a fine‐tuning mechanism and co‐determines the specific activity of MMP‐9 in physiology and pathology. Enzymes MMP‐9 EC 3.4.24.35, MMP‐3 EC 3.4.24.17, meprin α EC 3.4.24.18, neutrophil elastase EC 3.4.21.37, trypsin EC 3.4.21.4 and PNGase F EC 3.5.1.52.
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Affiliation(s)
- Lise Boon
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Belgium
| | | | - Erik Martens
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Jennifer Vandooren
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Vasily Rybakin
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Didier Colau
- Ludwig Institute for Cancer Research, Brussels, Belgium
| | | | | | - Walter Stöcker
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz, Germany
| | | | - Peter Witters
- Department of Pediatrics, University Hospitals Leuven, KU Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Belgium
| | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, ON, USA
| | - Jaak Jaeken
- Department of Pediatrics, University Hospitals Leuven, KU Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Ghislain Opdenakker
- Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Belgium
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39
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Yan W, Li SX, Wei M, Gao H. Identification of MMP9 as a novel key gene in mantle cell lymphoma based on bioinformatic analysis and design of cyclic peptides as MMP9 inhibitors based on molecular docking. Oncol Rep 2018; 40:2515-2524. [PMID: 30226602 PMCID: PMC6151885 DOI: 10.3892/or.2018.6682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive disease. MCL is associated with poor patient prognosis and limited survival. To identify key genes and explore targeting cyclic peptide inhibitors for the treatment of MCL, we downloaded two gene expression profiles (GSE32018 and GSE9327) from the Gene Expression Omnibus (GEO) database. We screened 84 differentially expressed genes (DEGs). Pathway analysis showed that DEMs were mainly enriched in the ‘Pathway in cancer’, ‘PI3K-Akt signaling pathway’, ‘Cytokine-cytokine receptor interaction’, ‘Rap1 signaling pathway’, ‘NF-κB signaling pathway’ and ‘Leukocyte trans-endothelial migration’. We subsequently constructed a protein-protein interaction (PPI) network of DEGs. In addition, matrix metalloproteinase 9 (MMP9) with a high degree in the PPI network was identified as a hub gene in MCL. Meanwhile in the Molecular Complex Detection (MCODE) analysis, MMP9 was located in the important cluster. Thus, MMP9 can be used as a therapeutic target for MCL and we designed cyclic peptides as MMP9 inhibitors. MMP9 protein structure was gathered from the Protein Data Bank (PDB), with a PDB ID: 1L6J. MMP9 and cyclic peptides were docked using Molecular Operating Environment (MOE) software after structural optimization. It was revealed that cyclic peptide 2 bound deeply in the binding pocket of MMP9 and had interaction with the active-site Zn2+ ion in the catalytic domain. Cyclic peptides 1, 2, 4–6 also displayed potential interaction with active residues of MMP9; thus, these cyclic peptides can serve as potential drug candidates to block MMP9 activity and future studies are warranted to confirm their efficacy.
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Affiliation(s)
- Wei Yan
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Shawn Xiang Li
- International College, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Hua Gao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P.R. China
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40
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Hariono M, Yuliani SH, Istyastono EP, Riswanto FD, Adhipandito CF. Matrix metalloproteinase 9 (MMP9) in wound healing of diabetic foot ulcer: Molecular target and structure-based drug design. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.wndm.2018.05.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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41
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Arolas JL, Goulas T, Cuppari A, Gomis-Rüth FX. Multiple Architectures and Mechanisms of Latency in Metallopeptidase Zymogens. Chem Rev 2018; 118:5581-5597. [PMID: 29775286 DOI: 10.1021/acs.chemrev.8b00030] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metallopeptidases cleave polypeptides bound in the active-site cleft of catalytic domains through a general base/acid mechanism. This involves a solvent molecule bound to a catalytic zinc and general regulation of the mechanism through zymogen-based latency. Sixty reported structures from 11 metallopeptidase families reveal that prosegments, mostly N-terminal of the catalytic domain, block the cleft regardless of their size. Prosegments may be peptides (5-14 residues), which are only structured within the zymogens, or large moieties (<227 residues) of one or two folded domains. While some prosegments globally shield the catalytic domain through a few contacts, others specifically run across the cleft in the same or opposite direction as a substrate, making numerous interactions. Some prosegments block the zinc by replacing the solvent with particular side chains, while others use terminal α-amino or carboxylate groups. Overall, metallopeptidase zymogens employ disparate mechanisms that diverge even within families, which supports that latency is less conserved than catalysis.
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Affiliation(s)
- Joan L Arolas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - Theodoros Goulas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - Anna Cuppari
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
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42
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Abstract
Matrix metalloproteinases (MMPs) are structurally related endopeptidases. They are also known as metzincins due to their interaction with zinc ion of the conserved methionine (Met) at the active site. MMPs play an important role in physiological and signaling processes of wound healing, bone resorption and angiogenesis. The structure of MMPs consists of signal peptide, propeptide, catalytic domain, hinge region and hemopexin-like domain. MMP-9 shares high structural and functional similarities with MMP-2, therefore designing selective MMP-9 inhibitors (MMPIs) is challenging. The selectivity can be achieved by targeting S2 subsite of MMP-9 that is having difference with MMP-2. Further, targeting its exosite and protein disulfide isomerase may also provide selective MMPIs. The review highlights the molecular features and basis of MMP-9 enzyme action. The MMPIs reported in the recent years have also been included.
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43
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Grosche J, Meißner J, Eble JA. More than a syllable in fib-ROS-is: The role of ROS on the fibrotic extracellular matrix and on cellular contacts. Mol Aspects Med 2018; 63:30-46. [PMID: 29596842 DOI: 10.1016/j.mam.2018.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/16/2018] [Accepted: 03/21/2018] [Indexed: 01/01/2023]
Abstract
Fibrosis is characterized by excess deposition of extracellular matrix (ECM). However, the ECM changes during fibrosis not only quantitatively but also qualitatively. Thus, the composition is altered as the expression of various ECM proteins changes. Moreover, also posttranslational modifications, secretion, deposition and crosslinkage as well as the proteolytic degradation of ECM components run differently during fibrosis. As several of these processes involve redox reactions and some of them are even redox-regulated, reactive oxygen species (ROS) influence fibrotic diseases. Redox regulation of the ECM has not been studied intensively, although evidences exist that the alteration of the ECM, including the redox-relevant processes of its formation and degradation, may be of key importance not only as a cause but also as a consequence of fibrotic diseases. Myofibroblasts, which have differentiated from fibroblasts during fibrosis, produce most of the ECM components and in return obtain important environmental cues of the ECM, including their redox-dependent fibrotic alterations. Thus, myofibroblast differentiation and fibrotic changes of the ECM are interdependent processes and linked with each other via cell-matrix contacts, which are mediated by integrins and other cell adhesion molecules. These cell-matrix contacts are also regulated by redox processes and by ROS. However, most of the redox-catalyzing enzymes are localized within cells. Little is known about redox-regulating enzymes, especially the ones that control the formation and cleavage of redox-sensitive disulfide bridges within the extracellular space. They are also important players in the redox-regulative crosstalk between ECM and cells during fibrosis.
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Affiliation(s)
- Julius Grosche
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149 Münster, Germany
| | - Juliane Meißner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149 Münster, Germany
| | - Johannes A Eble
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149 Münster, Germany.
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44
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Kumar S, Cieplak P. Role of N-glycosylation in activation of proMMP-9. A molecular dynamics simulations study. PLoS One 2018; 13:e0191157. [PMID: 29329315 PMCID: PMC5766141 DOI: 10.1371/journal.pone.0191157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/01/2018] [Indexed: 12/20/2022] Open
Abstract
Human matrix metalloproteinase proMMP-9 is secreted as latent zymogen, which requires two-steps proteolytic activation. The secreted proMMP-9 is glycosylated at two positions: Asn38 and Asn120 located in the prodomain and catalytic domain, respectively. It has been demonstrated that glycosylation at Asn120 is required for secretion of the enzyme, while the role of Asn38 glycosylation is not well understood, but is usually linked to the activation process. One hypothesis stated that the Asn38 glycosylation might protect against proteolytic activation. However, the activation process occurs with or without the presence of this glycosylation. We conducted molecular dynamics (MD) simulations on the glycosylated and non-glycosylated proMMP-9 to elucidate the effect of Asn38 glycosylation on this two-step activation process. The simulation results suggest that Asn38 glycosylation does not hinder the activation process directly, but induces conformational changes in the vicinity of the first proteolytic region in such a way that E59-M60 cleavage is processed before R106-F107. These results correlate with analysis provided by Boon et al. and experimental data from Ogata et al. who attempted to determine the order of events in activation of proMMP-9. Results from additional MD simulations for the model of glycosylated proMMP-9 bound to galectin-8 N-domain suggest that Gal-8 by interacting with Asn38 glycan might further facilitate processing of the first cleavage between E59-M60. Thus, our simulation results suggest that both Asn38 glycosylation and interaction with Gal-8N may be involved in facilitating and the temporal order of the activation process of pro-MMP9. The aim of this report is to provide an inspiration for future detailed experiments aimed at explaining the role of N-glycosylation in the activation process of prodomain of MMP-9.
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Affiliation(s)
- Sonu Kumar
- SBP Medical Discovery Institute, La Jolla, California, United States of America
| | - Piotr Cieplak
- SBP Medical Discovery Institute, La Jolla, California, United States of America
- * E-mail:
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45
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Scannevin RH, Alexander R, Haarlander TM, Burke SL, Singer M, Huo C, Zhang YM, Maguire D, Spurlino J, Deckman I, Carroll KI, Lewandowski F, Devine E, Dzordzorme K, Tounge B, Milligan C, Bayoumy S, Williams R, Schalk-Hihi C, Leonard K, Jackson P, Todd M, Kuo LC, Rhodes KJ. Discovery of a highly selective chemical inhibitor of matrix metalloproteinase-9 (MMP-9) that allosterically inhibits zymogen activation. J Biol Chem 2017; 292:17963-17974. [PMID: 28860188 DOI: 10.1074/jbc.m117.806075] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/11/2017] [Indexed: 11/06/2022] Open
Abstract
Aberrant activation of matrix metalloproteinases (MMPs) is a common feature of pathological cascades observed in diverse disorders, such as cancer, fibrosis, immune dysregulation, and neurodegenerative diseases. MMP-9, in particular, is highly dynamically regulated in several pathological processes. Development of MMP inhibitors has therefore been an attractive strategy for therapeutic intervention. However, a long history of failed clinical trials has demonstrated that broad-spectrum MMP inhibitors have limited clinical utility, which has spurred the development of inhibitors selective for individual MMPs. Attaining selectivity has been technically challenging because of sequence and structural conservation across the various MMPs. Here, through a biochemical and structural screening paradigm, we have identified JNJ0966, a highly selective compound that inhibited activation of MMP-9 zymogen and subsequent generation of catalytically active enzyme. JNJ0966 had no effect on MMP-1, MMP-2, MMP-3, MMP-9, or MMP-14 catalytic activity and did not inhibit activation of the highly related MMP-2 zymogen. The molecular basis for this activity was characterized as an interaction of JNJ0966 with a structural pocket in proximity to the MMP-9 zymogen cleavage site near Arg-106, which is distinct from the catalytic domain. JNJ0966 was efficacious in reducing disease severity in a mouse experimental autoimmune encephalomyelitis model, demonstrating the viability of this therapeutic approach. This discovery reveals an unprecedented pharmacological approach to MMP inhibition, providing an opportunity to improve selectivity of future clinical drug candidates. Targeting zymogen activation in this manner may also allow for pharmaceutical exploration of other enzymes previously viewed as intractable drug targets.
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Affiliation(s)
- Robert H Scannevin
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Richard Alexander
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | | | - Sharon L Burke
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Monica Singer
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Cuifen Huo
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Yue-Mei Zhang
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Diane Maguire
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - John Spurlino
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Ingrid Deckman
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Karen I Carroll
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Frank Lewandowski
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Eric Devine
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Keli Dzordzorme
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Brett Tounge
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Cindy Milligan
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Shariff Bayoumy
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Robyn Williams
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Celine Schalk-Hihi
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Kristi Leonard
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Paul Jackson
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Matthew Todd
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Lawrence C Kuo
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
| | - Kenneth J Rhodes
- From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477
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Pugacheva V, Korotkov A, Korotkov E. Search of latent periodicity in amino acid sequences by means of genetic algorithm and dynamic programming. Stat Appl Genet Mol Biol 2017; 15:381-400. [PMID: 27337743 DOI: 10.1515/sagmb-2015-0079] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aim of this study was to show that amino acid sequences have a latent periodicity with insertions and deletions of amino acids in unknown positions of the analyzed sequence. Genetic algorithm, dynamic programming and random weight matrices were used to develop a new mathematical algorithm for latent periodicity search. A multiple alignment of periods was calculated with help of the direct optimization of the position-weight matrix without using pairwise alignments. The developed algorithm was applied to analyze amino acid sequences of a small number of proteins. This study showed the presence of latent periodicity with insertions and deletions in the amino acid sequences of such proteins, for which the presence of latent periodicity was not previously known. The origin of latent periodicity with insertions and deletions is discussed.
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Activation of MMP-9 activity by acrolein in saliva from patients with primary Sjögren’s syndrome and its mechanism. Int J Biochem Cell Biol 2017; 88:84-91. [DOI: 10.1016/j.biocel.2017.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 03/18/2017] [Accepted: 05/04/2017] [Indexed: 11/21/2022]
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48
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Vandooren J, Knoops S, Aldinucci Buzzo JL, Boon L, Martens E, Opdenakker G, Kolaczkowska E. Differential inhibition of activity, activation and gene expression of MMP-9 in THP-1 cells by azithromycin and minocycline versus bortezomib: A comparative study. PLoS One 2017; 12:e0174853. [PMID: 28369077 PMCID: PMC5378356 DOI: 10.1371/journal.pone.0174853] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/16/2017] [Indexed: 01/22/2023] Open
Abstract
Gelatinase B or matrix metalloproteinase-9 (MMP-9) (EC 3.4.24.35) is increased in inflammatory processes and cancer, and is associated with disease progression. In part, this is due to MMP-9-mediated degradation of extracellular matrix, facilitating influx of leukocytes into inflamed tissues and invasion or metastasis of cancer cells. MMP-9 is produced as proMMP-9 and its propeptide is subsequently removed by other proteases to generate proteolytically active MMP-9. The significance of MMP-9 in pathologies triggered the development of specific inhibitors of this protease. However, clinical trials with synthetic inhibitors of MMPs in the fight against cancer were disappointing. Reports on active compounds which inhibit MMP-9 should be carefully examined in this regard. In a considerable set of recent publications, two antibiotics (minocycline and azythromycin) and the proteasome inhibitor bortezomib, used in cancers, were reported to inhibit MMP-9 at different stages of its expression, activation or activity. The current study was undertaken to compare and to verify the impact of these compounds on MMP-9. With exception of minocycline at high concentrations (>100 μM), the compounds did not affect processing of proMMP-9 into MMP-9, nor did they affect direct MMP-9 gelatinolytic activity. In contrast, azithromycin specifically reduced MMP-9 mRNA and protein levels without affecting NF-κB in endotoxin-challenged monocytic THP-1 cells. Bortezomib, although being highly toxic, had no MMP-9-specific effects but significantly upregulated cyclooxygenase-2 (COX-2) activity and PGE2 levels. Overall, our study clarified that azithromycin decreased the levels of MMP-9 by reduction of gene and protein expression while minocycline inhibits proteolytic activity at high concentrations.
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Affiliation(s)
- Jennifer Vandooren
- Laboratory of Immunobiology, Rega Institute for Medical Research, University of Leuven, KU Leuven, Leuven, Belgium
| | - Sofie Knoops
- Laboratory of Immunobiology, Rega Institute for Medical Research, University of Leuven, KU Leuven, Leuven, Belgium
| | - João L. Aldinucci Buzzo
- Laboratory of Immunobiology, Rega Institute for Medical Research, University of Leuven, KU Leuven, Leuven, Belgium
| | - Lise Boon
- Laboratory of Immunobiology, Rega Institute for Medical Research, University of Leuven, KU Leuven, Leuven, Belgium
| | - Erik Martens
- Laboratory of Immunobiology, Rega Institute for Medical Research, University of Leuven, KU Leuven, Leuven, Belgium
| | - Ghislain Opdenakker
- Laboratory of Immunobiology, Rega Institute for Medical Research, University of Leuven, KU Leuven, Leuven, Belgium
| | - Elzbieta Kolaczkowska
- Laboratory of Immunobiology, Rega Institute for Medical Research, University of Leuven, KU Leuven, Leuven, Belgium
- Department of Evolutionary Immunology, Jagiellonian University, Krakow, Poland
- * E-mail:
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49
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Using Small Angle X-Ray Scattering (SAXS) to Characterize the Solution Conformation and Flexibility of Matrix Metalloproteinases (MMPs). Methods Mol Biol 2017. [PMID: 28299734 DOI: 10.1007/978-1-4939-6863-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Small angle X-ray scattering (SAXS) provides information about the conformation and flexibility of proteins in solution, and hence provides complementary structural information to that obtained from X-ray crystallography and nuclear magnetic resonance spectroscopy. In this chapter, we describe the methods for the preparation of matrix metalloproteinase (MMP) samples for SAXS analyses, and for the acquisition, processing and interpretation of the SAXS data.
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50
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Appleby TC, Greenstein AE, Hung M, Liclican A, Velasquez M, Villaseñor AG, Wang R, Wong MH, Liu X, Papalia GA, Schultz BE, Sakowicz R, Smith V, Kwon HJ. Biochemical characterization and structure determination of a potent, selective antibody inhibitor of human MMP9. J Biol Chem 2017; 292:6810-6820. [PMID: 28235803 DOI: 10.1074/jbc.m116.760579] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/15/2017] [Indexed: 12/31/2022] Open
Abstract
Matrix metalloproteinase 9 (MMP9) is a member of a large family of proteases that are secreted as inactive zymogens. It is a key regulator of the extracellular matrix, involved in the degradation of various extracellular matrix proteins. MMP9 plays a pathological role in a variety of inflammatory and oncology disorders and has long been considered an attractive therapeutic target. GS-5745, a potent, highly selective humanized monoclonal antibody inhibitor of MMP9, has shown promise in treating ulcerative colitis and gastric cancer. Here we describe the crystal structure of GS-5745·MMP9 complex and biochemical studies to elucidate the mechanism of inhibition of MMP9 by GS-5745. GS-5745 binds MMP9 distal to the active site, near the junction between the prodomain and catalytic domain, and inhibits MMP9 by two mechanisms. Binding to pro-MMP9 prevents MMP9 activation, whereas binding to active MMP9 allosterically inhibits activity.
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Affiliation(s)
- Todd C Appleby
- From Gilead Sciences, Inc., Foster City, California 94404
| | | | | | | | | | | | - Ruth Wang
- From Gilead Sciences, Inc., Foster City, California 94404
| | - Melanie H Wong
- From Gilead Sciences, Inc., Foster City, California 94404
| | - Xiaohong Liu
- From Gilead Sciences, Inc., Foster City, California 94404
| | | | | | - Roman Sakowicz
- From Gilead Sciences, Inc., Foster City, California 94404
| | - Victoria Smith
- From Gilead Sciences, Inc., Foster City, California 94404
| | - Hyock Joo Kwon
- From Gilead Sciences, Inc., Foster City, California 94404
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