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Dos Santos AF, Martins MO, Lameira J, de Oliveira Araújo J, Frizzo MS, Davidson CB, de Souza DV, Machado AK, Mortari SR, Druzian DM, Tonel MZ, da Silva IZ, Fagan SB. Evaluation interaction of graphene oxide with heparin for antiviral blockade: a study of ab initio simulations, molecular docking, and experimental analysis. J Mol Model 2023; 29:235. [PMID: 37418181 DOI: 10.1007/s00894-023-05645-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/30/2023] [Indexed: 07/08/2023]
Abstract
CONTEXT Heparin, one of the drugs reused in studies with antiviral activity, was chosen to investigate a possible blockade of the SARS-CoV-2 spike protein for viral entry through computational simulations and experimental analysis. Heparin was associated to graphene oxide to increase in the binding affinity in biological system. First, the electronic and chemical interaction between the molecules was analyzed through ab initio simulations. Later, we evaluate the biological compatibility of the nanosystems, in the target of the spike protein, through molecular docking. The results show that graphene oxide interacts with the heparin with an increase in the affinity energy with the spike protein, indicating a possible increment in the antiviral activity. Experimental analysis of synthesis and morphology of the nanostructures were carried out, indicating heparin absorption by graphene oxide, confirming the results of the first principle simulations. Experimental tests were conducted on the structure and surface of the nanomaterial, confirming the heparin aggregation on the synthesis with a size between the GO layers of 7.44 Å, indicating a C-O type bond, and exhibiting a hydrophilic surface characteristic (36.2°). METHODS Computational simulations of the ab initio with SIESTA code, LDA approximations, and an energy shift of 0.05 eV. Molecular docking simulations were performed in the AutoDock Vina software integrated with the AMDock Tools Software using the AMBER force field. GO, GO@2.5Heparin, and GO@5Heparin were synthesized by Hummers and impregnation methods, respectively, and characterized by X-ray diffraction and surface contact angle.
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Affiliation(s)
- André Flores Dos Santos
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil.
| | - Mirkos Ortiz Martins
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences, Federal University of Pará-UFPA, Belém, PA, Brazil
| | | | - Marcela Sagrilo Frizzo
- Postgraduate Program in Chemical Engineering-PosENQ, Federal University of Santa Catarina-UFSC, Florianopolis, SC, Brazil
| | - Carolina Bordin Davidson
- Postgraduate Program in Nanosciences: Laboratory of Cell Culture and Bioactive Effects, Franciscan University-UFN, Santa Maria, RS, Brazil
| | - Diulie Valente de Souza
- Postgraduate Program in Nanosciences: Laboratory of Cell Culture and Bioactive Effects, Franciscan University-UFN, Santa Maria, RS, Brazil
| | - Alencar Kolinski Machado
- Postgraduate Program in Nanosciences: Laboratory of Cell Culture and Bioactive Effects, Franciscan University-UFN, Santa Maria, RS, Brazil
| | - Sérgio Roberto Mortari
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
| | - Daniel Moro Druzian
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
| | - Mariana Zancan Tonel
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
| | - Ivana Zanella da Silva
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
| | - Solange Binotto Fagan
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
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Araújo JDO, Dos Santos AM, Lameira J, Alves CN, Lima AH. Computational Investigation of Bisphosphate Inhibitors of 3-Deoxy-d- manno-octulosonate 8-phosphate Synthase. Molecules 2019; 24:E2370. [PMID: 31252580 PMCID: PMC6650799 DOI: 10.3390/molecules24132370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/24/2019] [Accepted: 05/29/2019] [Indexed: 11/23/2022] Open
Abstract
The synthase, 3-deoxy-d-manno-octulosonate 8-phosphate (KDO8P), is a key enzyme for the lipopolysaccharide (LPS) biosynthesis of gram-negative bacteria and a potential target for developing new antimicrobial agents. In this study, computational molecular modeling methods were used to determine the complete structure of the KDO8P synthase from Neisseria meningitidis and to investigate the molecular mechanism of its inhibition by three bisphosphate inhibitors: BPH1, BPH2, and BPH3. Our results showed that BPH1 presented a protein-ligand complex with the highest affinity, which is in agreement with experimental data. Furthermore, molecular dynamics (MD) simulations showed that BPH1 is more active due to the many effective interactions, most of which are derived from its phosphoenolpyruvate moiety. Conversely, BPH2 exhibited few hydrogen interactions during the MD simulations with key residues located at the active sites of the KDO8P synthase. In addition, we hydroxylated BPH2 to create the hypothetical molecule named BPH3, to investigate the influence of the hydroxyl groups on the affinity of the bisphosphate inhibitors toward the KDO8P synthase. Overall, we discuss the main interactions between the KDO8P synthase and the bisphosphate inhibitors that are potential starting points for the design of new molecules with significant antibiotic activities.
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Affiliation(s)
- Jéssica de Oliveira Araújo
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Belém 66075-110, Brasil
| | - Alberto Monteiro Dos Santos
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Belém 66075-110, Brasil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Belém 66075-110, Brasil
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Belém 66075-110, Brasil
| | - Anderson Henrique Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Belém 66075-110, Brasil.
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