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Almeida MO, Lanza MRV, Honorio KM. A study of possible substitutes for the endocrine disruptor DEHP in two hormone receptors. J Biomol Struct Dyn 2022; 40:12516-12525. [PMID: 34463224 DOI: 10.1080/07391102.2021.1971566] [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] [Indexed: 12/27/2022]
Abstract
Bis(2-ethylhexyl) phthalate (DEHP) has been widely used for the production of plastics, and the compound has also been found to act as endocrine disruptor. Exposure to DEHP has been found to cause several hormonal problems, including decreased fertility. Due to the environmental and health risks posed by the use of DEHP, the present study employed molecular docking, molecular dynamics, and free energy analyses (MM-GBSA, MM-PBSA, and SIE) aiming at evaluating the action of DEHP and that of two other compounds (ATEC and DL9TH), tested as potential DEHP substitutes, on two hormone receptors (sex hormone-binding globulin - SHBG - and progesterone receptor - PR). The results obtained showed that ATEC may be a good substitute for DEHP in the production of plastics, such as PVC, considering that the compound recorded the greatest free energy values with respect to binding with SHBG (-31.36 kcal/mol obtained from MM-GBSA; -20.28 kcal/mol for MM-PBSA, and -7.40 for SIE) and PR (-36.40 kcal/mol for MM-GBSA; -27.00 kcal/mol for MM-PBSA, and -8.51 kcal/mol for SIE) - this shows that ATEC presented the least activity in the two hormone receptors. The findings of this study provide relevant insights on potential substitutes for DEHP and help shed light on the action of these new efficient substances, which have similar properties to DEHP (ATEC and DL9TH) yet do not act as endocrine disruptors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Michell O Almeida
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Marcos R V Lanza
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Kathia M Honorio
- Center of Natural Sciences and Humanities, Federal University of ABC, Santo Andre, São Paulo, Brazil.,School of Arts, Sciences and Humanities, University of São Paulo, Sao Paulo, Brazil
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2
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Farmer SM, Andl CD. Computational modeling of transforming growth factor β and activin a receptor complex formation in the context of promiscuous signaling regulation. J Biomol Struct Dyn 2020; 39:5166-5181. [PMID: 32597324 DOI: 10.1080/07391102.2020.1785330] [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: 10/24/2022]
Abstract
The Transforming growth factor-beta (TGFβ) superfamily is a group of multipotent growth factors that control proliferation, quiescence and differentiation. Aberrant signal transduction and downstream target activation contribute to tumorigenesis and targeted therapy has therefore been considered a promising avenue. Using various modeling pipelines, we analyzed the structure-function relationship between ligand and receptor molecules of the TGFβ family. We further simulated the molecular docking of Galunisertib, a small molecule inhibitor targeting TGFβ signaling in cancer, which is currently undergoing FDA-approved clinical trials. We found that proprotein dimers of Activin isoforms differ at intrachain disulfide bonds, which support prior evidence of varying pro-domain stability and isoform preference. Further, mature proteins possess flexibility around conserved cystine knots to functionally interact with receptors or regulatory molecules in similar but distinct ways to TGFβ. We show that all Activin isoforms are capable of assuming a closed- or open-dimer state, revealing structural promiscuity of their open forms for receptor binding. We propose the first structural landscape for Activin receptor complexes containing a type I receptor (ACVR1B), which shares a pre-helix extension with TGFβ type I receptor (TGFβR1). Here, we artificially demonstrate that Activin can bind TGFβR1 in a TGFβ-like manner and that TGFβ1 can form signaling complexes with ACVR1B. Interestingly, Galunisertib was found to form stable inhibitory structures within the homologous kinase domains of both TGFβR1 and ACVR1B, thus halting receptor-promiscuous signaling. Overall, these observations highlight the challenges of specific TGFβ cascade targeting in the context of cancer therapies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Stephen M Farmer
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Claudia D Andl
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
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3
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An electronic point of view on the inhibition of ALK-5 by bioactive candidates related to cancer. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02602-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Araujo SC, Maltarollo VG, Almeida MO, Ferreira LLG, Andricopulo AD, Honorio KM. Structure-Based Virtual Screening, Molecular Dynamics and Binding Free Energy Calculations of Hit Candidates as ALK-5 Inhibitors. Molecules 2020; 25:molecules25020264. [PMID: 31936488 PMCID: PMC7024315 DOI: 10.3390/molecules25020264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 01/08/2023] Open
Abstract
Activin-like kinase 5 (ALK-5) is involved in the physiopathology of several conditions, such as pancreatic carcinoma, cervical cancer and liver hepatoma. Cellular events that are landmarks of tumorigenesis, such as loss of cell polarity and acquisition of motile properties and mesenchymal phenotype, are associated to deregulated ALK-5 signaling. ALK-5 inhibitors, such as SB505154, GW6604, SD208, and LY2157299, have recently been reported to inhibit ALK-5 autophosphorylation and induce the transcription of matrix genes. Due to their ability to impair cell migration, invasion and metastasis, ALK-5 inhibitors have been explored as worthwhile hits as anticancer agents. This work reports the development of a structure-based virtual screening (SBVS) protocol aimed to prospect promising hits for further studies as novel ALK-5 inhibitors. From a lead-like subset of purchasable compounds, five molecules were identified as putative ALK-5 inhibitors. In addition, molecular dynamics and binding free energy calculations combined with pharmacokinetics and toxicity profiling demonstrated the suitability of these compounds to be further investigated as novel ALK-5 inhibitors.
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Affiliation(s)
- Sheila C. Araujo
- CCNH, Federal University of ABC, Santo Andre, SP 09210-580, Brazil;
| | - Vinicius G. Maltarollo
- Department of Pharmaceutical Products, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, MG 31270-901, Brazil;
| | | | - Leonardo L. G. Ferreira
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of Sao Carlos, University of Sao Paulo, Sao Carlos, SP 13563-120, Brazil; (L.L.G.F.); (A.D.A.)
| | - Adriano D. Andricopulo
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of Sao Carlos, University of Sao Paulo, Sao Carlos, SP 13563-120, Brazil; (L.L.G.F.); (A.D.A.)
| | - Kathia M. Honorio
- CCNH, Federal University of ABC, Santo Andre, SP 09210-580, Brazil;
- EACH, University of São Paulo, Sao Paulo, SP 03828-000, Brazil
- Correspondence: ; Tel.: +55-11-3091-1027
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5
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Soares RF, Antunes D, Santos LHS, Rocha GV, Bastos LS, Guimarães ACR, Caffarena ER. Studying effects of different protonation states of His11 and His102 in ribose-5-phosphate isomerase of Trypanosoma cruzi: an example of cooperative behavior. J Biomol Struct Dyn 2019; 38:2047-2056. [PMID: 31184542 DOI: 10.1080/07391102.2019.1626769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Trypanosoma cruzi ribose-5-phosphate isomerase B (TcRpiB) is a crucial piece in the pentose phosphate pathway and thus is a potential drug target for treatment of Chagas' disease. TcRpiB residues, such as Cys69, Asp45, Glu149 and Pro47, have confirmed their roles in substrate recognition, catalytic reaction and binding site conformation. However, the joint performance of His11 and His102, in the D-ribose-5-phosphate (R5P) in the catalysis is not well understood. In this work, we probed the influence of different protonation states of His11 and His102 on the behavior of the ligand R5P using molecular dynamics simulations, network analysis and thermodynamic integration. Simulations revealed that a protonated His11 combined with a neutral His102 (His11+‒His102) was able to stabilize the ligand R5P in the binding site. Moreover, calculated relative free energy differences showed that when protonated His11 was coupled to a neutral His102 an exergonic process takes place. On the other hand, neutral His11 combined with a protonated His102 (His11‒His102+), sampled conformations that resembled the catalyzed product D-ribulose-5-phosphate (Ru5P). Network analysis also demonstrated some peculiarities for these systems with some negatively correlated nodes in the binding site for His11‒His102+, and exclusive suboptimal paths for His11+‒His102. Therefore, the combined approach presented in this paper proposes two suitable protonation states for the TcRpiB catalytic mechanism, where an extra proton in either histidines might favor R5P binding or influence isomerization reaction to Ru5P. Our results may guide further in silico drug discovery studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rafael F Soares
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brasil
| | - Deborah Antunes
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brasil
| | - Lucianna H S Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
| | - Gisele Vieira Rocha
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brasil
| | - Leonardo Soares Bastos
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brasil
| | - Ana Carolina R Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brasil
| | - Ernesto R Caffarena
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brasil
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Studies on the Dual Activity of EGFR and HER-2 Inhibitors Using Structure-Based Drug Design Techniques. Int J Mol Sci 2018; 19:ijms19123728. [PMID: 30477154 PMCID: PMC6321113 DOI: 10.3390/ijms19123728] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/07/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022] Open
Abstract
HER-2 and EGFR are biological targets related to the development of cancer and the discovery and/or development of a dual inhibitor could be a good strategy to design an effective drug candidate. In this study, analyses of the chemical properties of a group of substances having affinity for both HER-2 and EGFR were carried out with the aim of understanding the main factors involved in the interaction between these inhibitors and the biological targets. Comparative analysis of molecular interaction fields (CoMFA) and comparative molecular similarity index analysis (CoMSIA) techniques were applied on 63 compounds. From CoMFA analyses, we found for both HER-2 (r2 calibration = 0.98 and q2cv = 0.83) and EGFR (r2 calibration = 0.98 and q2cv = 0.73) good predictive models. Good models for CoMSIA technique have also been found for HER-2 (r2 calibration = 0.92 and q2cv = 0.74) and EGFR (r2 calibration = 0.97 and q2cv = 0.72). The constructed models could indicate some important characteristics for the inhibition of the biological targets. New compounds were proposed as candidates to inhibit both proteins. Therefore, this study may guide future projects for the development of new drug candidates for the treatment of breast cancer.
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