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Mandova T, Saivish MV, Menezes GDL, Bezerra KS, Fulco UL, da Silva RA, Da Costa FB, Nogueira ML. Antiviral Activity and Molecular Dynamics Simulation of Hops Compounds against Oropouche Virus ( Peribunyaviridae). Pharmaceutics 2023; 15:2769. [PMID: 38140109 PMCID: PMC10747393 DOI: 10.3390/pharmaceutics15122769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The Oropouche virus (OROV) is a member of the family Peribunyaviridae (order Bunyavirales) and the cause of a dengue-like febrile illness transmitted mainly by biting midges and mosquitoes. In this study, we aimed to explore acylphloroglucinols and xanthohumol from hops (Humulus lupulus L.) as a promising alternative for antiviral therapies. The evaluation of the inhibitory potential of hops compounds on the viral cycle of OROV was performed through two complementary approaches. The first approach applies cell-based assay post-inoculation experiments to explore the inhibitory potential on the latest steps of the viral cycle, such as genome translation, replication, virion assembly, and virion release from the cells. The second part covers in silico methods evaluating the ability of those compounds to inhibit the activity of the endonuclease domain, which is essential for transcription, binding, and cleaving RNA. In conclusion, the beta acids showed strongest inhibitory potential in post-treatment assay (EC50 = 26.7 µg/mL). Xanthohumol had the highest affinity for OROV endonuclease followed by colupulone and cohumulone. This result contrasts with that observed for docking and MM/PBSA analysis, where cohumulone was found to have a higher affinity. Finally, among the three tested ligands, Lys92 and Arg33 exhibited the highest affinity with the protein.
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Affiliation(s)
- Tsvetelina Mandova
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-020, SP, Brazil
- Gilson Purification, 22 rue Bourseul, 56890 Saint Avé, France
| | - Marielena Vogel Saivish
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil; (M.V.S.)
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Gabriela de Lima Menezes
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | - Katyanna Sales Bezerra
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | - Umberto Laino Fulco
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | | | - Fernando Batista Da Costa
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-020, SP, Brazil
| | - Maurício Lacerda Nogueira
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil; (M.V.S.)
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
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Prasetyo WE, Triadmojo B, Kusumaningsih T, Marliyana SD, Wibowo FR, Firdaus M. Mechanistic insight into the free radical scavenging and xanthine oxidase (XO) inhibitor potent of monoacetylphloroglucinols (MAPGs). Free Radic Res 2023:1-33. [PMID: 37315300 DOI: 10.1080/10715762.2023.2225731] [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: 02/01/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Three novel antioxidant candidates based on phenolic polyketide, monoacetylphloroglucinol (MAPG), a natural antibiotic compound produced by plant growth-promoting rhizobacteria (PGPR), Pseudomonas fluorescens F113 have been proposed. Initially, a green and highly efficient route to the synthesis of MAPG and its two analogues from phloroglucinol (PG) has been developed. Afterward, their rational mechanism of antioxidant activity has been investigated based on thermodynamic descriptors involved in the double ( 2H+/2e-) radical trapping processes. These calculations have been performed using the systematic density functional theory (DFT) method at the B3LYP/Def2-SVP level of theory in the gas phase and aqueous solution. Our findings reveal that the double formal hydrogen atom transfer (df-HAT) mechanism is preferred in the gas phase, while the double sequential proton loss electron transfer (dSPLET) mechanism is preferred in aqueous solution for all MAPGs. The 6-OH group represents the most favourable site for trapping radical species for all MAPGs, which is supported by the pKa values obtained from DFT calculations. The role of acyl substituents on the PG ring has been comprehensively discussed. The presence of acyl substituents has a strong influence on the thermodynamic parameters of the phenolic O-H bond in PG. These results are supported by frontier molecular orbitals (FMOs) analysis, where the addition of acyl substituents increases the chemical reactivity of MAPGs significantly. Based on molecular docking and molecular dynamics simulations (MDs), MAPGs are also predicted to be promising candidates for xanthine oxidase (XO) inhibition.HighlightsThe antioxidant activity of the three synthesised MAPGs has been investigated using the DFT method.Acyl substituents increase the chemical reactivity and antioxidant activity of MAPGs.df-HAT is the preferred mechanism in the gas phase.dSPLET seems to be more favoured in aqueous solution.MAPGs are expected to be promising xanthine oxidase (XO) inhibitors.
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Affiliation(s)
- Wahyu Eko Prasetyo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Jl. Ir. Sutami No.36A, Surakarta, 57126, Indonesia
| | - Bram Triadmojo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Jl. Ir. Sutami No.36A, Surakarta, 57126, Indonesia
| | - Triana Kusumaningsih
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Jl. Ir. Sutami No.36A, Surakarta, 57126, Indonesia
| | - Soerya Dewi Marliyana
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Jl. Ir. Sutami No.36A, Surakarta, 57126, Indonesia
| | - Fajar Rakhman Wibowo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Jl. Ir. Sutami No.36A, Surakarta, 57126, Indonesia
| | - Maulidan Firdaus
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Jl. Ir. Sutami No.36A, Surakarta, 57126, Indonesia
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Prasetyo WE, Kusumaningsih T, Triadmojo B, Anggraini SD, Marliyana SD, Firdaus M. Investigation of the dual role of acyl phloroglucinols as a new hope for antibacterial and anti-SARS-CoV-2 agents employing integrated in vitro and multi-phase in silico approaches. J Biomol Struct Dyn 2023; 41:15067-15084. [PMID: 36927239 DOI: 10.1080/07391102.2023.2186712] [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: 11/29/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023]
Abstract
With the rapid spread of multi-drug-resistant bacteria and more infectious or aggressive variants of SARS-CoV-2, it is critical to develop drugs that can quickly adapt to evolving bacterial and viral mutations. In this study, encouraged by nature, we synthesized a series of phloroglucinol (PG) derivatives, acyl phloroglucinols (ACPLs) 2a-4c by mimicking the structure of the natural antifungal 2,4-diacetylphloroglucinol 3a (2,4-DAPG). According to the quantum chemical calculation, these compounds were expected to be exceptionally favourable for intermolecular interaction with protein receptors. Intriguingly, the in vitro study of Staphylococcus aureus (S. aureus) ATCC 25923 and Escherichia coli (E. coli) ATCC 25922, showed that the four ACPLs 3a-4a had good antibacterial activity and selectivity against gram-positive bacteria, S. aureus. These results were then supported by in silico molecular docking and molecular dynamics simulations (MDs) between these potent compounds and the S. aureus FtsA protein (PDB ID: 3WQU). Furthermore, with the aid of the knowledge base Virus-CKB along with the molecular docking study, it was found that the three ACPLs 4a-4c showed potential inhibitors against SARS-CoV-2 PLpro (PDB ID: 7CMD). Additionally, 100 ns of MDs was carried out in order to assess the stability behaviour of ACPLs at the docked site. Moreover, in silico ADME/T and drug likeness of all studied ACPLs were also predicted. Finally, shape-based screening of FDA-approved drugs was performed using the most prominent synthesized ACPLs as a template, enabling us to include several medications that could be utilized as antibacterial and antiviral drug candidates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wahyu Eko Prasetyo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Triana Kusumaningsih
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Bram Triadmojo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Septin Dwi Anggraini
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Soerya Dewi Marliyana
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Maulidan Firdaus
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
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Mammino L. Tube-shaped molecular structures built from acylphloroglucinols: an ab initio and DFT study. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1784477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Liliana Mammino
- School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa
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Mammino L. Stacking interactions in cavity-containing molecular structures built from acylphloroglucinols: a computational study. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1800852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Liliana Mammino
- School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa
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