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Morales BGDV, Dos Reis MC, Gomes TJDS, Zeferino NA, de Oliveira GA, Zanchi FB. A rational in silico approach to identify inhibitors of Batroxrhagin from Bothrops atrox. J Biomol Struct Dyn 2022; 40:9620-9635. [PMID: 34060428 DOI: 10.1080/07391102.2021.1932597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bothrops atrox venom comprises several types of bioactive molecules, enzymatic and non-enzymatic, among those, Batroxrhagin is the most predominant SVMP P-III enzyme, which are responsible for induction of local and systemic hemorrhage and muscle fibers damage, impairing regeneration. Due to great difficulties in establishing an antibothropic drug, new strategies must be addressed to achieve a more effective and efficient treatment. There are no studies of specific catalytic inhibitors of Batroxrhagin. However, there are in vitro studies that have described similar metalloprotease inhibitors. The inhibitor batimastat was used as a leading compound for the search and selection of similar candidates. This molecule is widely cited as a metalloprotease inhibitor and as an antimetastatic. In addition to batimastat-like molecules, four other reported metalloprotease inhibitors were included to compose the study's positive control group. Hence, 580 molecules were tested. The three-dimensional structure of B. atrox Batroxrhagin was predicted based on homologous structures using Modeller 9.20. Molecular docking calculation was performed using Autodock 4.2 and molecular surfaces and interactions were analyzed using Biovia/Discovery Studio 2017. Among 576 molecules, 42 similar to batismast resulted in a better energy of interaction than all positive controls, including batimastat itself. The batimastat-like molecules with lowest energy and positive controls were subjected to molecular dynamics for 30 ns in Gromacs 2019.4. This batimastat-like molecule produced better stability among all the Batroxrhagin-ligand complexes analyzed. Overall, the proposed compounds present justifiable evidence for future in vitro tests aiming to inhibit Batroxrhagin. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bruno Gildo Dalla Vecchia Morales
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz Rondônia, Porto Velho-RO, Brazil.,Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho-RO, Brazil.,FIOCRUZ Rondônia, Porto Velho-RO, Brazil
| | - Marlon Chaves Dos Reis
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz Rondônia, Porto Velho-RO, Brazil.,Faculdades Integradas Aparício Carvalho/FIMCA, Porto Velho-RO, Brazil
| | | | - Nabia Azevedo Zeferino
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz Rondônia, Porto Velho-RO, Brazil.,Faculdades Integradas Aparício Carvalho/FIMCA, Porto Velho-RO, Brazil
| | - George Azevedo de Oliveira
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz Rondônia, Porto Velho-RO, Brazil.,Programa de Doutorado em Ciências - Cooperação IOC/Fiocruz Rondônia: Biologia Computacional e Sistemas (BCS), Porto Velho-RO, Brazil
| | - Fernando Berton Zanchi
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz Rondônia, Porto Velho-RO, Brazil.,Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho-RO, Brazil.,FIOCRUZ Rondônia, Porto Velho-RO, Brazil.,Programa de Doutorado em Ciências - Cooperação IOC/Fiocruz Rondônia: Biologia Computacional e Sistemas (BCS), Porto Velho-RO, Brazil.,Instituto Nacional de Epidemiologia na Amazônia Ocidental - EPIAMO, Porto Velho-RO, Brazil
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Feng XY, Ding TT, Liu YY, Xu WR, Cheng XC. In-silico identification of peroxisome proliferator-activated receptor (PPAR)α/γ agonists from Ligand Expo Components database. J Biomol Struct Dyn 2020; 39:1853-1864. [DOI: 10.1080/07391102.2020.1745279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ting-Ting Ding
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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3
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Identification of novel PPARα/γ dual agonists by pharmacophore screening, docking analysis, ADMET prediction and molecular dynamics simulations. Comput Biol Chem 2019; 78:178-189. [DOI: 10.1016/j.compbiolchem.2018.11.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/20/2018] [Accepted: 11/25/2018] [Indexed: 01/05/2023]
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Computational modeling in glioblastoma: from the prediction of blood-brain barrier permeability to the simulation of tumor behavior. Future Med Chem 2017; 10:121-131. [PMID: 29235374 DOI: 10.4155/fmc-2017-0128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The integrated in silico-in vitro-in vivo approaches have fostered the development of new treatment strategies for glioblastoma patients and improved diagnosis, establishing the bridge between biochemical research and clinical practice. These approaches have provided new insights on the identification of bioactive compounds and on the complex mechanisms underlying the interactions among glioblastoma cells, and the tumor microenvironment. This review focuses on the key advances pertaining to computational modeling in glioblastoma, including predictive data on drug permeability across the blood-brain barrier, tumor growth and treatment responses. Structure- and ligand-based methods have been widely adopted, enabling the study of dynamic and evolutionary aspects of glioblastoma. Their potential applications as predictive tools and the advantages over other well-known methodologies are outlined. Challenges regarding in silico approaches for predicting tumor properties are also discussed.
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Design, sythesis and evaluation of a series of 3- or 4-alkoxy substituted phenoxy derivatives as PPARs agonists. Oncotarget 2017; 8:20766-20783. [PMID: 28186999 PMCID: PMC5400543 DOI: 10.18632/oncotarget.15198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 01/25/2017] [Indexed: 11/25/2022] Open
Abstract
Peroxisome proliferators-activated receptors (PPARα, γ and δ) are potentially effective targets for Type 2 diabetes mellitus therapy. The severe effects of known glitazones and the successfully approved agents (saroglitazar and lobeglitazone) motivated us to study novelly potent PPARs drugs with improved safety profile. In this work, we received 15 carboxylic acids based on the combination principle to integrate the polar head of bezafibrate with the hydrophobic tail of pioglitazone. Another 12 tetrazoles based on the bioisosterism principle were obtained accordingly. Furthermore, in vitro PPARs transactivation assays on these 3- or 4-alkoxy substituted phenoxy derivatives afforded six compounds. Interactions and binding stability from the docking analysis and 20 ns molecular dynamic simulations confirmed the representative compounds to be suitable and plausible for PPARs pockets. The above-mentioned results demonstrated that the compounds may be used as reference for further optimization for enhanced PPARs activities and wide safety range.
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Doménech-Carbó A, Cebrián-Torrejón G, Montoya N, Ueberschaar N, Scotti MT, Benfodda Z, Hertweck C. Electrochemical monitoring of ROS generation by anticancer agents: the case of chartreusin. RSC Adv 2017. [DOI: 10.1039/c7ra08238j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Generation of ROS by anticancer agents is monitored using solid state electrochemical techniques.
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Affiliation(s)
| | | | - Noemí Montoya
- Departament de Química Analítica
- Facultat de Química
- Universitat de València
- Valencia
- Spain
| | - Nico Ueberschaar
- Department of Biomolecular Chemistry
- Leibniz Institute for Natural Product Research and Infection Biology (HKI)
- Jena
- Germany
| | - Marcus Tullius Scotti
- Department of Engineering and the Environment
- Federal University of Paraíba
- Rio Tinto
- Brazil
| | | | - Christian Hertweck
- Department of Biomolecular Chemistry
- Leibniz Institute for Natural Product Research and Infection Biology (HKI)
- Jena
- Germany
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Liu Z, Jiang Z, Huang J, Huang S, Li Y, Yu S, Yu S, Liu X. miR-7 inhibits glioblastoma growth by simultaneously interfering with the PI3K/ATK and Raf/MEK/ERK pathways. Int J Oncol 2014; 44:1571-80. [PMID: 24603851 DOI: 10.3892/ijo.2014.2322] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 02/14/2014] [Indexed: 01/08/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) signaling regulates glioblastoma cell proliferation, survival, migration and invasion and plays a key role in tumor progression. We show that microRNA-7 (miR-7) is a common regulator of the phosphoinositide-3-kinase (PI3K)/ATK and Raf/mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) pathways, both of which are launched by EGFR through its two direct targets, the transcription factors PI3K and Raf-1, respectively. Enforced expression of miR-7 markedly decreased expression of PI3K, phosphorylated Akt, Raf-1, phosphorylated MEK 1/2, and cyclin D1, as well as slightly reduced expression of EGFR. Forced expression of PI3K or Raf-1 transcripts lacking the 3'-untranslated region (3'-UTR) partially reversed the effects of miR-7 on cell growth inhibition and cell cycle arrest in glioma cells. Additionally, transient expression of miR-7 in glioblastoma cells strongly inhibited in vivo glioblastoma xenograft growth. We conclude that miR-7 is a potential tumor suppressor in glioblastoma that acts by targeting multiple oncogenes related to the downstream pathway of EGFR and may serve as a novel therapeutic target for malignant gliomas.
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Affiliation(s)
- Zhenlin Liu
- Department of Neurosurgery, The Fifth Central Hospital of Tianjin, Tianjin, P.R. China
| | - Zhongmin Jiang
- Department of Pathology, The Fifth Central Hospital of Tianjin, Tianjin, P.R. China
| | - Jianyong Huang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Shuqiang Huang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Yanxia Li
- The Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin, P.R. China
| | - Simiao Yu
- Department of Neurosurgery, The Fifth Central Hospital of Tianjin, Tianjin, P.R. China
| | - Shizhu Yu
- Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, P.R. China
| | - Xiaozhi Liu
- Department of Neurosurgery, The Fifth Central Hospital of Tianjin, Tianjin, P.R. China
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Identification of hepatitis C virus inhibitors targeting different aspects of infection using a cell-based assay. Antimicrob Agents Chemother 2012; 56:6109-20. [PMID: 22948883 DOI: 10.1128/aac.01413-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
With 2 to 3% of the worldwide population chronically infected, hepatitis C virus (HCV) infection continues to be a major health care burden. Unfortunately, current interferon-based treatment options are not effective in all patients and are associated with significant side effects. Consequently, there is an ongoing need to identify and develop new anti-HCV therapies. Toward this goal, we previously developed a cell-based HCV infection assay for antiviral compound screening based on a low-multiplicity-of-infection approach that uniquely allows for the identification of antiviral compounds that target cell culture-derived HCV (HCVcc) at any step of the viral infection cycle. Using this assay, here we report the screening of the NCI Diversity Set II library, containing 1,974 synthesized chemical compounds, and the identification of compounds with specific anti-HCV activity. In combination with toxicity counterscreening, we identified 30 hits from the compound library, 13 of which showed reproducible and dose-dependent inhibition of HCV with mean therapeutic indices (50% cytotoxic concentration [CC(50)]/50% effective concentration [EC(50)]) of greater than 6. Using HCV pseudotype and replicon systems of multiple HCV genotypes, as well as infectious HCVcc-based assembly and secretion analysis, we determined that different compounds within this group of candidate inhibitors target different steps of viral infection. The compounds identified not only will serve as biological probes to study and further dissect the biology of viral infection but also should facilitate the development of new anti-HCV therapeutic treatments.
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