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Jesus EGD, Souza FFD, Andrade JV, Andrade E Silva ML, Cunha WR, Ramos RC, Campos OS, Santos JAN, Santos MFC. In silico and in vitro elastase inhibition assessment assays of rosmarinic acid natural product from Rosmarinus officinalis Linn. Nat Prod Res 2024; 38:879-884. [PMID: 37004998 DOI: 10.1080/14786419.2023.2196077] [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: 12/15/2022] [Accepted: 03/19/2023] [Indexed: 04/04/2023]
Abstract
The use of various herbs and their compounds has been a strategy widely used in the fight against various human diseases. For example, rosmarinic acid, a bioactive phenolic compound commonly found in Rosemary plants (Rosmarinus officinalis Labiatae), has multiple therapeutic benefits in different diseases, such as cancer. Therefore, the study aimed to evaluate in silico and in vitro the inhibition potential of the enzyme Elastase from the porcine pancreas by rosmarinic acid isolated from the plant species R. officinalis Linn. Through Molecular Docking, the mechanism of action was investigated. In addition, rosmarinic acid presented a range of 5-60 µg/mL and significantly inhibited Elastase. At 60 µg/mL, there was an inhibition of 55% on the enzymatic activity. The results demonstrate the inhibition of Elastase by rosmarinic acid, which can lead to the development of new enzyme inhibitors that can be an inspiration for developing various drugs, including anticancer drugs.
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Affiliation(s)
- Ester Gonçalves de Jesus
- Departamento de Química e Física, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil
| | - Fernanda Fernandes de Souza
- Departamento de Química e Física, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil
| | - João Victor Andrade
- Departamento de Química e Física, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil
| | | | - Wilson R Cunha
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, Brazil
| | - Rafael Corrêa Ramos
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, Brazil
| | - Othon Souto Campos
- Departamento de Química e Física, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil
| | - Jorge Alexandre Nogueira Santos
- Departamento de Bioquímica, Instituto Federal de Educação, Ciência e Tecnologia do Sul de Minas Gerais, Minas Gerais, Brazil
| | - Mario F C Santos
- Departamento de Química e Física, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil
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2
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Oliveira APS, Lima DR, Bezerra LL, Monteiro NKV, Loiola OD, Silva MGV. Virtual screening of flavonoids from Chamaecrista genus: ADME and pharmacokinetic properties, interactions of flavonoid-DNA complex by molecular docking and molecular dynamics. J Biomol Struct Dyn 2023; 41:7677-7685. [PMID: 36120963 DOI: 10.1080/07391102.2022.2124455] [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: 05/09/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
This research aimed to conduct an in silico study of compounds, mainly flavonoids, that are found in several plants, including the species of the Chamaecrista genus. The ADME properties, the drug-likeness score and properties of Lipinski and Veber rules of the molecules were determined using online databases. Based on the predicted properties, four flavonoids, apigenin, fisetin, luteolin and ononin were selected for molecular docking and dynamic simulations to study their interactions with DNA (PDB ID: 1BNA). The molecular docking showed that ononin has a high affinity for B-DNA, exhibiting a ΔG value of -9.3 kcal mol-1, compared with the other flavonoids. The molecular dynamic simulations of the flavonoid-DNA complexes showed that the flavonoids interacted with DNA by hydrogen bonding, hydrophobic interaction and π-stacking. The flavonoid ononin showed the best interaction energy value of -291.3490 kJ mol-1, compared with the other flavonoids.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ana Paula S Oliveira
- Department of Organic and Inorganic Chemistry, Federal University of Ceará, Fortaleza, Brazil
| | - Daniele R Lima
- Department of Physico-chemical and Analytic Chemistry, Federal University of Ceará, Fortaleza, Brazil
| | - Lucas L Bezerra
- Department of Physico-chemical and Analytic Chemistry, Federal University of Ceará, Fortaleza, Brazil
| | - Norberto K V Monteiro
- Department of Physico-chemical and Analytic Chemistry, Federal University of Ceará, Fortaleza, Brazil
| | - Otília D Loiola
- Department of Organic and Inorganic Chemistry, Federal University of Ceará, Fortaleza, Brazil
| | - Maria Goretti V Silva
- Department of Organic and Inorganic Chemistry, Federal University of Ceará, Fortaleza, Brazil
- Department of Physico-chemical and Analytic Chemistry, Federal University of Ceará, Fortaleza, Brazil
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3
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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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4
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Gonçalves MA, Gonçalves AS, Franca TCC, Santana MS, da Cunha EFF, Ramalho TC. Improved Protocol for the Selection of Structures from Molecular Dynamics of Organic Systems in Solution: The Value of Investigating Different Wavelet Families. J Chem Theory Comput 2022; 18:5810-5818. [DOI: 10.1021/acs.jctc.2c00593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mateus A. Gonçalves
- Chemistry Department, Federal University of Lavras, 37200-000Lavras, MG, Brazil
| | - Arlan S. Gonçalves
- Federal Institute of Education Science and Technology of Espírito Santo, Vila Velha29100-000, Brazil
- Federal Institute of Education Science and Technology of Espírito Santo, Unit Goiabeiras, 29056-264Vitória, Espírito Santo, Brazil
| | - Tanos C. C. Franca
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMACBD), Military Institute of Engineering (IME), Rio de Janeiro22290-270, Brazil
| | - Mozarte S. Santana
- Chemistry Department, Federal University of Lavras, 37200-000Lavras, MG, Brazil
| | | | - Teodorico C. Ramalho
- Chemistry Department, Federal University of Lavras, 37200-000Lavras, MG, Brazil
- Faculty of Informatics and Management, Center for Basic and Applied Research, University of Hradec Kralove, Hradec Kralove50003, Czech Republic
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5
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Samandar F, Tehranizadeh ZA, Saberi MR, Chamani J. CB1 as a novel target for Ginkgo biloba's terpene trilactone for controlling chemotherapy-induced peripheral neuropathy (CIPN). J Mol Model 2022; 28:283. [PMID: 36044079 DOI: 10.1007/s00894-022-05284-8] [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: 01/28/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022]
Abstract
The application of antineoplastic chemotherapeutic agents causes a common side effect known as chemotherapy-induced peripheral neuropathy (CIPN) that leads to reducing the quality of patient's life. This research involves the performance of molecular docking and molecular dynamic (MD) simulation studies to explore the impact of terpenoids of Ginkgo biloba on the targets (CB-1, TLR4, FAAH-1, COX-1, COX-2) that can significantly affect the controlling of CIPN's symptoms. According to the in-vitro and in-vivo investigations, terpenoids, particularly ginkgolides B, A, and bilobalide, can cause significant effects on neuropathic pain. The molecular docking results disclosed the tendency of our ligands to interact with mainly CB1 and FAAH-1, as well as partly with TLR4, throughout their interactions with targets. Terpene trilactone can exhibit a lower rate of binding energy than CB1's inhibitor (7dy), while being precisely located in the CB1's active site and capable of inducing stable interactions by forming hydrogen bonds. The analyses of MD simulation proved that ginkgolide B was a more suitable activator and inhibitor for CB1 and TLR4, respectively, when compared to bilobalide and ginkgolide A. Moreover, bilobalide is capable of inhibiting FAAH-1 more effectively than the two other ligands. According to the analyses of ADME, every three ligands followed the Lipinski's rule of five. Considering these facts, the exertion of three ligands is recommended for their anti-inflammatory, neuroprotective, and anti-nociception influences caused by primarily activating CB1 and inhibiting FAAH-1 and TLR4; in this regard, these compounds can stand as potential candidates for the control and treatment of CIPN's symptoms.
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Affiliation(s)
- Farzaneh Samandar
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri Tehranizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Reza Saberi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Bioinformatics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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6
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do Bomfim MR, Barbosa DB, de Carvalho PB, da Silva AM, de Oliveira TA, Taranto AG, Leite FHA. Identification of potential human beta-secretase 1 inhibitors by hierarchical virtual screening and molecular dynamics. J Biomol Struct Dyn 2022:1-15. [DOI: 10.1080/07391102.2022.2069155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mayra Ramos do Bomfim
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Deyse Brito Barbosa
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Alisson Marques da Silva
- Departamento de Informática, Gestão e Design, Centro Federal de Educação Tecnológica de Minas Gerais, Divinópolis, Brazil
| | - Tiago Alves de Oliveira
- Departamento de Informática, Gestão e Design, Centro Federal de Educação Tecnológica de Minas Gerais, Divinópolis, Brazil
- Departamento de Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei, Brazil
| | - Alex Gutterres Taranto
- Departamento de Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei, Brazil
- Faculty of Computing, University of Latvia (UL), Riga, Latvia
| | - Franco Henrique Andrade Leite
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
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7
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Costa AN, de Sá ÉRA, Bezerra RDS, Souza JL, Lima FDCA. Constituents of buriti oil ( Mauritia flexuosa L.) like inhibitors of the SARS-Coronavirus main peptidase: an investigation by docking and molecular dynamics. J Biomol Struct Dyn 2021; 39:4610-4617. [PMID: 32567501 PMCID: PMC7332871 DOI: 10.1080/07391102.2020.1778538] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
Statistics show alarming numbers of infected and killed in the world, caused by the Covid-19 pandemic, which still doesn't have a specific treatment and effective in combating all efforts to seek treatments and medications against this disease. Natural products are of relevant interest in the search for new drugs. Thus, Buriti oil (Mauritia flexuosa L.) is a natural product extracted from the fruit of the palm and is quite common in the legal Amazon region, Brazil. In the present work, the anti-Covid-19 biological activity of some constituents of Buriti oil was investigated using in silico methods of Molecular Docking and Molecular Dynamics Simulations. The main results of Molecular Docking revealed favorable interaction energies in the formation of the 2GTB peptidase complex (main peptidase of SARS-CoV) with the 13-cis-β-carotene ligands (ΔGbind = -10.23Kcal mol-1), 9-cis -β-carotene (ΔGbind = -9.82Kcal mol-1), and α-carotene (ΔGbind = -8.34Kcal mol-1). Molecular Dynamics simulations demonstrated considerable interaction for these ligands with emphasis on α-carotene. Such theoretical results encourage and enable a direction for experimental studies in vitro and in vivo, essential in the development of new drugs with enzymatic inhibitory action for Covid-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Allan N. Costa
- Pará/Conceição do Araguaia Campus, Federal Institute of Education, Science and Technology, Conceição do Araguaia, Brazil
| | - Ézio R. A. de Sá
- Piauí/Picos Campus, Federal Institute of Education, Science and Technology, Picos, Brazil
| | - Roosevelt D. S. Bezerra
- Piauí/Teresina-Central Campus, Federal Institute of Education, Science and Technology, Teresina, Brazil
| | - Janilson L. Souza
- Maranhão/Bacabal Campus, Federal Institute of Education, Science and Technology, Bacabal, Brazil
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8
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Investigating an efficient and accurate protocol for sampling structures from molecular dynamics simulations: a close look by different wavelet families. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02816-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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da Silva TU, Pougy KDC, Albuquerque MG, da Silva Lima CH, Machado SDP. Development of parameters compatible with the CHARMM36 force field for [Fe 4S 4] 2+ clusters and molecular dynamics simulations of adenosine-5'-phosphosulfate reductase in GROMACS 2019. J Biomol Struct Dyn 2020; 40:3481-3491. [PMID: 33183173 DOI: 10.1080/07391102.2020.1847687] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
DFT calculations were used to obtain parameters compatible with the CHARMM36 force field for iron-sulfur clusters (Fe-S) of the type [Fe4S4]2+ that are coordinated to dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Classical molecular dynamics (MD) simulations were performed on two APSrAB systems to validate the parameters and verify the stability of the studied systems. The time analysis of the parameters inserted into the force field was in reasonable agreement with the experimental X-ray diffraction data. The analysis of the time evolution of the studied systems indicated that these systems and, in particular, the clusters in their respective cavities had a good stability and were in agreement with what was observed in previous works. The parameters obtained provide the basis for the study of APSrAB as well as other systems that contain [Fe4S4]2+ through the CHARMM36 force field.
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10
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Vasconcelos MA, Orsolin PC, Oliveira VC, Lima PMAP, Naves MPC, de Morais CR, Nicolau-Júnior N, Bonetti AM, Spanó MA. Modulating effect of vitamin D3 on the mutagenicity and carcinogenicity of doxorubicin in Drosophila melanogaster and in silico studies. Food Chem Toxicol 2020; 143:111549. [PMID: 32640329 PMCID: PMC7335493 DOI: 10.1016/j.fct.2020.111549] [Citation(s) in RCA: 4] [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: 05/04/2020] [Revised: 06/18/2020] [Accepted: 06/21/2020] [Indexed: 02/07/2023]
Abstract
Vitamin D3 (VD3) deficiency increases DNA damage, while supplementation may exert a pro-oxidant activity, prevent viral infections and formation of tumors. The aim of this study was to investigate the mutagenicity and carcinogenicity of VD3 alone or in combination with doxorubicin (DXR) using the Somatic Mutation and Recombination Test and the Epithelial Tumor Test, both in Drosophila melanogaster. For better understanding of the molecular interactions of VD3 and receptors, in silico analysis were performed with molecular docking associated with molecular dynamics. Findings revealed that VD3 alone did not increase the frequency of mutant spots, but reduced the frequency of mutant spots when co-administered with DXR. In addition, VD3 did not alter the recombinogenic effect of DXR in both ST and HB crosses. VD3 alone did not increase the total frequency of tumor, but significantly reduced the total frequency of tumor when co-administered with DXR. Molecular modeling and molecular dynamics between calcitriol and Ecdysone Receptor (EcR) showed a stable interaction, indicating the possibility of signal transduction between VD3 and EcR. In conclusion, under these experimental conditions, VD3 has modulatory effects on the mutagenicity and carcinogenicity induced by DXR in somatic cells of D. melanogaster and exhibited satisfactory interactions with the EcR.
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Affiliation(s)
- Mirley Alves Vasconcelos
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil.
| | - Priscila Capelari Orsolin
- Laboratory of Cytogenetic and Mutagenesis, University Center of Patos de Minas, Patos de Minas, MG, Brazil.
| | - Victor Constante Oliveira
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil.
| | | | | | | | - Nilson Nicolau-Júnior
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil.
| | - Ana Maria Bonetti
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil.
| | - Mário Antônio Spanó
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil.
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11
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Albuquerque SO, Barros TG, Dias LRS, Lima CHDS, Azevedo PHRDA, Flores-Junior LAP, Dos Santos EG, Loponte HF, Pinheiro S, Dias WB, Muri EMF, Todeschini AR. Biological evaluation and molecular modeling of peptidomimetic compounds as inhibitors for O-GlcNAc transferase (OGT). Eur J Pharm Sci 2020; 154:105510. [PMID: 32801002 DOI: 10.1016/j.ejps.2020.105510] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/24/2020] [Accepted: 08/10/2020] [Indexed: 01/19/2023]
Abstract
The vital enzyme O-linked β-N-acetylglucosamine transferase (OGT) catalyzes the O-GlcNAcylation of intracellular proteins coupling the metabolic status to cellular signaling and transcription pathways. Aberrant levels of O-GlcNAc and OGT have been linked to metabolic diseases as cancer and diabetes. Here, a new series of peptidomimetic OGT inhibitors was identified highlighting the compound LQMed 330, which presented better IC50 compared to the most potent inhibitors found in the literature. Molecular modeling study of selected inhibitors into the OGT binding site provided insight into the behavior by which these compounds interact with the enzyme. The results obtained in this study provided new perspectives on the design and synthesis of highly specific OGT inhibitors.
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Affiliation(s)
- Suraby O Albuquerque
- Laboratório de Glicobiologia Estrutural e Funcional, IBCCF, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Thalita G Barros
- Laboratório de Química Medicinal, Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Luiza R S Dias
- Laboratório de Química Medicinal, Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Camilo H da S Lima
- Universidade Federal do Rio de Janeiro, Instituto de Química, Rio de Janeiro, RJ, Brazil
| | - Pedro H R de A Azevedo
- Laboratório de Química Medicinal, Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Luiz A P Flores-Junior
- Laboratório de Química Medicinal, Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Eldio G Dos Santos
- Laboratório de Química Medicinal, Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Hector F Loponte
- Laboratório de Glicobiologia Estrutural e Funcional, IBCCF, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Sergio Pinheiro
- Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Wagner B Dias
- Laboratório de Glicobiologia Estrutural e Funcional, IBCCF, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Estela M F Muri
- Laboratório de Química Medicinal, Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Adriane R Todeschini
- Laboratório de Glicobiologia Estrutural e Funcional, IBCCF, Universidade Federal do Rio de Janeiro, RJ, Brazil.
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12
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do Bomfim MR, Araújo JSC, Macêdo WJDC, Santos CBRD, Leite FHA. Identification of potential modulator of Anopheles gambiae odorant binding protein 1 by hierarchical virtual screening and molecular dynamics. J Biomol Struct Dyn 2020; 39:6031-6043. [PMID: 32696721 DOI: 10.1080/07391102.2020.1796807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Malaria is a protozoan infection transmitted by the bite of the infected female mosquito belonging to the genus Anopheles spp., which causes more than 445 million annual deaths worldwide. Available drugs have serious adverse effects (e.g. blurred vision, hypotension and headache) and species-dependent efficacy. An alternative to overcome these problems involve the use of molecules with affinity to the Anopheles gambiae mosquito odor receptors, minimizing the reinfection process as well as reducing the problems related to pharmacological therapy. The vector control can interrupt the epidemiological cycle and, therefore, control the malaria incidence. In the olfactory pathway, odorant binding protein 1 acts on the first level of odor recognition on malarial vector and thus can be used to modulate mosquito behavior and development of new attracts or repellents. Thus, this study applied ligand-based (2D-chemical similarity) and structure-based (docking and molecular dynamics) computational approaches to prioritize potential olfactory modulators on natural products catalogs at ZINC15 database (n = 98,379). Hierarchical virtual screening prioritized a potential olfactory modulator (Z8217) against Anopheles gambiae odorant binding protein 1 (AgOBP1). Next, it was submitted to molecular dynamics routine to identify structural requirements and the interactions profile required for binding-site affinity. This promising natural compound can interact like experimental ligand and will be used in repellency assay to confirm its sensorial behavior.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mayra Ramos do Bomfim
- Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Williams Jorge da Cruz Macêdo
- Laboratorio de Modelagem Molecular e simulação de sistemas, Universidade Federal Rural da Amazônia, Capanema, Brazil
| | | | - Franco Henrique Andrade Leite
- Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil.,Programa de Pós-Graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil.,Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
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13
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Antifungal Agents in Agriculture: Friends and Foes of Public Health. Biomolecules 2019; 9:biom9100521. [PMID: 31547546 PMCID: PMC6843326 DOI: 10.3390/biom9100521] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/12/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
Fungal diseases have been underestimated worldwide but constitute a substantial threat to several plant and animal species as well as to public health. The increase in the global population has entailed an increase in the demand for agriculture in recent decades. Accordingly, there has been worldwide pressure to find means to improve the quality and productivity of agricultural crops. Antifungal agents have been widely used as an alternative for managing fungal diseases affecting several crops. However, the unregulated use of antifungals can jeopardize public health. Application of fungicides in agriculture should be under strict regulation to ensure the toxicological safety of commercialized foods. This review discusses the use of antifungals in agriculture worldwide, the need to develop new antifungals, and improvement of regulations regarding antifungal use.
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Assis LC, de Castro AA, Prandi IG, Mancini DT, de Giacoppo JOS, Savedra RML, de Assis TM, Carregal JB, da Cunha EFF, Ramalho TC. Interactions of cantharidin-like inhibitors with human protein phosphatase-5 in a Mg 2+ system: molecular dynamics and quantum calculations. J Mol Model 2018; 24:303. [PMID: 30280322 DOI: 10.1007/s00894-018-3837-y] [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: 02/08/2018] [Accepted: 09/18/2018] [Indexed: 11/29/2022]
Abstract
The serine/threonine protein phosphatase type 5 (PP5) is a promising target for designing new antitumor drugs. This enzyme is a member of the PPP phosphatases gene family, which catalyzes a dephosphorylation reaction: a regulatory process in the signal transduction pathway that controls various biological processes. The aim of this work is to study and compare the inhibition of PP5 by ten cantharidin-like inhibitors in order to bring about contributions relevant to the better comprehension of their inhibitory activity. In this theoretical investigation, we used molecular dynamics techniques to understand the role of key interactions that occur in the protein active site; QM calculations were employed to study the interaction mode of these inhibitors in the enzyme. In addition, atoms in molecules (AIM) calculations were carried out to characterize the chemical bonds among the atoms involved and investigate the orbital interactions with their respective energy values. The obtained results suggest that the Arg275, Asn303, His304, His352, Arg400, His427, Glu428, Val429, Tyr451, and Phe446 residues favorably contribute to the interactions between inhibitors and PP5. However, the Asp271 and Asp244 amino acid residues do not favor such interactions for some inhibitors. Through the QM calculations, we can suggest that the reactional energy of the coordination mechanism of these inhibitors in the PP5 active site is quite important and is responsible for the inhibitory activity. The AIM technique employed in this work was essential to get a better comprehension of the transition states acquired from the mechanism simulation. This work offers insights of how cantharidin-like inhibitors interact with human PP5, potentially allowing the design of more specific and even less cytotoxic drugs for cancer treatments. Graphical Abstract Interactions of cantharidin-like inhibitors with human protein phosphatase-5 in a Mg2+ system.
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Affiliation(s)
- Letícia C Assis
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), 3027, Campus Universitario, Lavras, 37200000, Minas Gerais, Brazil
| | - Alexandre A de Castro
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), 3027, Campus Universitario, Lavras, 37200000, Minas Gerais, Brazil
| | - Ingrid G Prandi
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), 3027, Campus Universitario, Lavras, 37200000, Minas Gerais, Brazil
| | - Daiana T Mancini
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), 3027, Campus Universitario, Lavras, 37200000, Minas Gerais, Brazil
| | - Juliana O S de Giacoppo
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), 3027, Campus Universitario, Lavras, 37200000, Minas Gerais, Brazil
| | - Ranylson M L Savedra
- Laboratory of Molecular Simulation of Material, Department of Physics, Federal University of Ouro Preto, Campus Universitário Morro do Cruzeiro, Ouro Preto, MG, CEP 35400-000, Brazil
| | - Tamiris M de Assis
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), 3027, Campus Universitario, Lavras, 37200000, Minas Gerais, Brazil
| | - Juliano B Carregal
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of São João del Rei (UFSJ), Rua Sebastião Gonçalves Coelho 400, Divinópolis, MG, 35501-296, Brazil
| | - Elaine F F da Cunha
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), 3027, Campus Universitario, Lavras, 37200000, Minas Gerais, Brazil
| | - Teodorico Castro Ramalho
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), 3027, Campus Universitario, Lavras, 37200000, Minas Gerais, Brazil. .,Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Hradec Kralove, Czech Republic.
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15
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Melo MMA, Daniele-Silva A, Teixeira DG, Estrela AB, Melo KRT, Oliveira VS, Rocha HAO, Ferreira LDS, Pontes DL, Lima JPMS, Silva-Júnior AA, Barbosa EG, Carvalho E, Fernandes-Pedrosa MF. Structure and in vitro activities of a Copper II-chelating anionic peptide from the venom of the scorpion Tityus stigmurus. Peptides 2017; 94:91-98. [PMID: 28552408 DOI: 10.1016/j.peptides.2017.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/09/2023]
Abstract
Anionic Peptides are molecules rich in aspartic acid (Asp) and/or glutamic acid (Glu) residues in the primary structure. This work presents, for the first time, structural characterization and biological activity assays of an anionic peptide from the venom of the scorpion Tityus stigmurus, named TanP. The three-dimensional structure of TanP was obtained by computational modeling and refined by molecular dynamic (MD) simulations. Furthermore, we have performed circular dichroism (CD) analysis to predict TanP secondary structure, and UV-vis spectroscopy to evaluate its chelating activity. CD indicated predominance of random coil conformation in aqueous medium, as well as changes in structure depending on pH and temperature. TanP has chelating activity on copper ions, which modified the peptide's secondary structure. These results were corroborated by MD data. The molar ratio of binding (TanP:copper) depends on the concentration of peptide: at lower TanP concentration, the molar ratio was 1:5 (TanP:Cu2+), whereas in concentrated TanP solution, the molar ratio was 1:3 (TanP:Cu2+). TanP was not cytotoxic to non-neoplastic or cancer cell lines, and showed an ability to inhibit the in vitro release of nitric oxide by LPS-stimulated macrophages. Altogether, the results suggest TanP is a promising peptide for therapeutic application as a chelating agent.
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Affiliation(s)
- Menilla M A Melo
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil
| | - Alessandra Daniele-Silva
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | - Diego G Teixeira
- Laboratório de Sistemas Metabólicos, Centro de Biociências, UFRN, Natal, RN, Brazil
| | - Andréia B Estrela
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | - Karolline R T Melo
- Laboratório de Biotecnologia de Polímeros Naturais, UFRN, Natal, RN, Brazil
| | | | - Hugo A O Rocha
- Laboratório de Biotecnologia de Polímeros Naturais, UFRN, Natal, RN, Brazil
| | | | - Daniel L Pontes
- Laboratório de Química de Coordenação e Polímeros, UFRN, Natal, RN, Brazil
| | - João P M S Lima
- Laboratório de Sistemas Metabólicos, Centro de Biociências, UFRN, Natal, RN, Brazil
| | - Arnóbio A Silva-Júnior
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil
| | - Euzebio G Barbosa
- Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil; Laboratório de Química Farmacêutica, UFRN, Natal, RN, Brazil
| | - Eneas Carvalho
- Centro de Biotecnologia, Instituto Butantan, São Paulo, SP, Brazil
| | - Matheus F Fernandes-Pedrosa
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil.
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16
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Machado N, dos Santos L, Carvalho B, Singh P, Téllez Soto C, Azoia N, Cavaco-Paulo A, Martin A, Favero P. Assessment of penetration of Ascorbyl Tetraisopalmitate into biological membranes by molecular dynamics. Comput Biol Med 2016; 75:151-9. [DOI: 10.1016/j.compbiomed.2016.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/03/2016] [Accepted: 06/01/2016] [Indexed: 11/29/2022]
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17
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Virtual Screening and Molecular Dynamics Simulations from a Bank of Molecules of the Amazon Region Against Functional NS3-4A Protease-Helicase Enzyme of Hepatitis C Virus. Appl Biochem Biotechnol 2015; 176:1709-21. [DOI: 10.1007/s12010-015-1672-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 05/17/2015] [Indexed: 10/23/2022]
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