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Borges RS, Aguiar CPO, Oliveira NLL, Amaral INA, Vale JKL, Chaves Neto AMJ, Queiroz AN, da Silva ABF. Antioxidant capacity of simplified oxygen heterocycles and proposed derivatives by theoretical calculations. J Mol Model 2023; 29:232. [PMID: 37407749 DOI: 10.1007/s00894-023-05602-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 05/22/2023] [Indexed: 07/07/2023]
Abstract
CONTEXT Some structural properties can be involved in the antioxidant capacity of several polyphenol derivatives, among them their simplified structures. This study examines the contribution of simplified structure for the antioxidant capacity of some natural and synthetic antioxidants. The resonance structures were related to the π-type electron system of carbon-carbon double bonds between both phenyl rings. Trans-resveratrol, phenyl-benzofuran, phenyl-indenone, and benzylidene-benzofuranone are the best basic antioxidant templates among the simplified derivatives studied here. Additionally, the stilbene moiety was found on the molecules with the best antioxidant capacity. Furthermore, our investigation suggests that these compounds can be used as antioxidant scaffold for designing and developing of new promising derivatives. METHODS To investigate the structure-antioxidant capacity for sixteen simplified natural and proposed derivatives we have employed density functional theory and used Gaussian 09. Our DFT calculations were performed using the B3LYP functional and the 6-31+G(d,p) basis set. All electron transfer mechanisms were investigated by using values of HOMO, ionization potential, energy affinity, stabilization energies, and spin density distributions.
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Affiliation(s)
- Rosivaldo S Borges
- Núcleo de Estudos e Seleção de Compostos Bioativos, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos, SP, 13560-970, Brazil.
| | - Christiane P O Aguiar
- Núcleo de Estudos e Seleção de Compostos Bioativos, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Nicole L L Oliveira
- Núcleo de Estudos e Seleção de Compostos Bioativos, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Israel N A Amaral
- Núcleo de Estudos e Seleção de Compostos Bioativos, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Joyce K L Vale
- Núcleo de Estudos e Seleção de Compostos Bioativos, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Antonio M J Chaves Neto
- Faculdade de Física, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Auriekson N Queiroz
- Núcleo de Estudos e Seleção de Compostos Bioativos, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Albérico B F da Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos, SP, 13560-970, Brazil
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Che Z, Guo X, Huang X, Wang T, Zhou L, Liu S, Chen G, Tian Y. Synthesis, anti-oomycete activity of 1-sulfonyloxy/acyloxysesamol derivatives. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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Inversion Theory Leveling as a New Methodological Approach to Antioxidant Thermodynamics: A Case Study on Phenol. Antioxidants (Basel) 2023; 12:antiox12020282. [PMID: 36829841 PMCID: PMC9952401 DOI: 10.3390/antiox12020282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023] Open
Abstract
Antioxidants are various types of compounds that represent a link between biology and chemistry. With the development of theoretical and computational methods, antioxidants are now being studied theoretically. Here, a novel method is presented that aims to reduce the estimated wall times for DFT calculations that result in the same or higher degree of accuracy in the second derivatives over energy than is the case with the regular computational route (i.e., optimizing the reaction system at a lower model and then recalculating the energies at a higher level of theory) by applying the inversion of theory level to the universal chemical scavenger model, i.e., phenol. The resulting accuracy and wall time obtained with such a methodological setup strongly suggest that this methodology could be generally applied to antioxidant thermodynamics for some costly DFT methods with relative absolute deviation.
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Canavieira LM, Brasil EM, Silva TDME, Borges RDS, Silva JRA, Lameira J, Bernhardt PV, Williams CM, Alves CN. Experimental and theoretical approaches for the development of 4H-Chromene derivatives as inhibitors of tyrosinase. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1926455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Luciana Morais Canavieira
- Programa de Pós-Graduação em Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Edikarlos Macedo Brasil
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - Thiago de Melo e Silva
- Programa de Pós-Graduação em Química, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Rosivaldo dos Santos Borges
- Núcleo de Estudos e Seleção de Moléculas Bioativas, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, Brazil
| | - José Rogério Araújo Silva
- Programa de Pós-Graduação em Química, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Jerônimo Lameira
- Programa de Pós-Graduação em Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- Programa de Pós-Graduação em Química, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Cláudio Nahum Alves
- Programa de Pós-Graduação em Química, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
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Leão RP, Cruz JV, da Costa GV, Cruz JN, Ferreira EFB, Silva RC, de Lima LR, Borges RS, dos Santos GB, Santos CBR. Identification of New Rofecoxib-Based Cyclooxygenase-2 Inhibitors: A Bioinformatics Approach. Pharmaceuticals (Basel) 2020; 13:E209. [PMID: 32858871 PMCID: PMC7559105 DOI: 10.3390/ph13090209] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023] Open
Abstract
The cyclooxygenase-2 receptor is a therapeutic target for planning potential drugs with anti-inflammatory activity. The selective cyclooxygenase-2 (COX-2) inhibitor rofecoxib was selected as a pivot molecule to perform virtual ligand-based screening from six commercial databases. We performed the search for similarly shaped Rapid Overlay of Chemical Structures (ROCS) and electrostatic (EON) compounds. After, we used pharmacokinetic and toxicological parameters to determine the best potential compounds, obtained through the softwares QikProp and Derek, respectively. Then, the compounds proceeded to the molecular anchorage study, which showed promising results of binding affinity with the hCOX-2 receptor: LMQC72 (∆G = -11.0 kcal/mol), LMQC36 (∆G = -10.6 kcal/mol), and LMQC50 (∆G = -10.2 kcal/mol). LMQC72 and LMQC36 showed higher binding affinity compared to rofecoxib (∆G = -10.4 kcal/mol). Finally, molecular dynamics (MD) simulations were used to evaluate the interaction of the compounds with the target hCOX-2 during 150 ns. In all MD simulation trajectories, the ligands remained interacting with the protein until the end of the simulation. The compounds were also complexing with hCOX-2 favorably. The compounds obtained the following affinity energy values: rofecoxib: ΔGbind = -45.31 kcal/mol; LMQC72: ΔGbind = -38.58 kcal/mol; LMQC36: ΔGbind = -36.10 kcal/mol; and LMQC50: ΔGbind = -39.40 kcal/mol. The selected LMQC72, LMQC50, and LMQC36 structures showed satisfactory pharmacokinetic results related to absorption and distribution. The toxicological predictions of these compounds did not display alerts for possible toxic groups and lower risk of cardiotoxicity compared to rofecoxib. Therefore, future in vitro and in vivo studies are needed to confirm the anti-inflammatory potential of the compounds selected here with bioinformatics approaches based on rofecoxib ligand.
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Affiliation(s)
- Rozires P. Leão
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil; (R.P.L.); (R.C.S.); (L.R.d.L.); (R.S.B.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.; (J.V.C.); (G.V.d.C.); (J.N.C.); (E.F.B.F.)
| | - Josiane V. Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.; (J.V.C.); (G.V.d.C.); (J.N.C.); (E.F.B.F.)
| | - Glauber V. da Costa
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.; (J.V.C.); (G.V.d.C.); (J.N.C.); (E.F.B.F.)
| | - Jorddy N. Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.; (J.V.C.); (G.V.d.C.); (J.N.C.); (E.F.B.F.)
| | - Elenilze F. B. Ferreira
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.; (J.V.C.); (G.V.d.C.); (J.N.C.); (E.F.B.F.)
- Laboratory of Organic Chemistry and Biochemistry, University of State of Amapá, Macapá 68900-070, AP, Brazil
| | - Raí C. Silva
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil; (R.P.L.); (R.C.S.); (L.R.d.L.); (R.S.B.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.; (J.V.C.); (G.V.d.C.); (J.N.C.); (E.F.B.F.)
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14090-901, SP, Brazil
| | - Lúcio R. de Lima
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil; (R.P.L.); (R.C.S.); (L.R.d.L.); (R.S.B.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.; (J.V.C.); (G.V.d.C.); (J.N.C.); (E.F.B.F.)
| | - Rosivaldo S. Borges
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil; (R.P.L.); (R.C.S.); (L.R.d.L.); (R.S.B.)
| | - Gabriela B. dos Santos
- Institute of Collective Health, Federal University of Western Pará, Santarém 68040-255, PA, Brazil;
| | - Cleydson B. R. Santos
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal University of Pará, Belém 66075-110, PA, Brazil; (R.P.L.); (R.C.S.); (L.R.d.L.); (R.S.B.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.; (J.V.C.); (G.V.d.C.); (J.N.C.); (E.F.B.F.)
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