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Tecchio KB, Alves FDM, Alves JD, Barbosa CDS, Salgado MAR, Santos VJDSVD, Varotti FDP, Campos-Junior PHDA, Viana GHR, Santos FVD. Evaluation of the in vivo acute toxicity and in vitro genotoxicity and mutagenicity of synthetic β-carboline alkaloids with selective cytotoxic activity against ovarian and breast cancer cell lines. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 899:503808. [PMID: 39326936 DOI: 10.1016/j.mrgentox.2024.503808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 07/24/2024] [Accepted: 08/06/2024] [Indexed: 09/28/2024]
Abstract
The aim of this study was to evaluate the in vitro cytotoxic, genotoxic, and mutagenic potential and to determine the in silico ADME parameters of two synthetic β-carboline alkaloids developed as prototypes of antitumor agents (NQBio-06 and NQBio-21). Additionally, acute toxicity of the compounds was evaluated in mice. The results from the MTT assay showed that NQBio-06 presented higher cytotoxicity in the ovarian cancer cell line TOV-21 G (IC50 = 2.5 µM, selectivity index = 23.7). NQBio-21 presented an IC50 of 6.9 µM and a selectivity index of 14.5 against MDA-MB-231 breast cancer cells. Comet assay results showed that NQBio-06 did not induce chromosomal breaks in vitro, but NQBio-21 was genotoxic with and without metabolic activation (S9 fraction). Micronucleus assay showed that both compounds were mutagenic. In addition, metabolic activation enhanced this effect in vitro. The in silico predictions showed that the compounds met the criteria set by Lipinski's rules, had strong prediction for intestinal absorption, and were possible substrates for P-glycoprotein. The in vivo results demonstrated that both the compounds exhibited low acute toxicity. These results suggest that the mechanisms underlying the cytotoxicity of NQBio-06 and NQBio-21 are related to DNA damage induction and that the use of S9 enhanced these effects. In vivo analysis showed signs of toxicity after a single administration of the compounds in mice. These findings highlight the potential of β-carboline compounds as sources for the development of new anticancer chemotherapeutic agents.
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Affiliation(s)
- Kimberly Brito Tecchio
- Laboratório de Biologia Celular e Mutagênese (LaBCeM), Universidade Federal de São João del Rei (UFSJ), Campus Centro Oeste, Divinópolis, MG 35501-296, Brazil; Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Campus Centro Oeste, Divinópolis, MG 35501-296, Brazil
| | - Fernanda de Moura Alves
- Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Campus Centro Oeste, Divinópolis, MG 35501-296, Brazil
| | - Janaina Domingas Alves
- Laboratório de Pesquisa em Reprodução, Departamento de Ciências Naturais, Universidade Federal de São João del Rei, Campus Dom Bosco, São João del-Rei, MG 36301-160, Brazil
| | - Camila de Souza Barbosa
- Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Campus Centro Oeste, Divinópolis, MG 35501-296, Brazil
| | - Mariana Alves Rezende Salgado
- Laboratório de Biologia Celular e Mutagênese (LaBCeM), Universidade Federal de São João del Rei (UFSJ), Campus Centro Oeste, Divinópolis, MG 35501-296, Brazil
| | - Vanessa Jaqueline da Silva Vieira Dos Santos
- Laboratório de Biologia Celular e Mutagênese (LaBCeM), Universidade Federal de São João del Rei (UFSJ), Campus Centro Oeste, Divinópolis, MG 35501-296, Brazil; Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Campus Centro Oeste, Divinópolis, MG 35501-296, Brazil
| | - Fernando de Pilla Varotti
- Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Campus Centro Oeste, Divinópolis, MG 35501-296, Brazil
| | - Paulo Henrique de Almeida Campos-Junior
- Laboratório de Pesquisa em Reprodução, Departamento de Ciências Naturais, Universidade Federal de São João del Rei, Campus Dom Bosco, São João del-Rei, MG 36301-160, Brazil
| | - Gustavo Henrique Ribeiro Viana
- Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Campus Centro Oeste, Divinópolis, MG 35501-296, Brazil
| | - Fabio Vieira Dos Santos
- Laboratório de Biologia Celular e Mutagênese (LaBCeM), Universidade Federal de São João del Rei (UFSJ), Campus Centro Oeste, Divinópolis, MG 35501-296, Brazil; Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Campus Centro Oeste, Divinópolis, MG 35501-296, Brazil.
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Lanrewaju AA, Enitan-Folami AM, Nyaga MM, Sabiu S, Swalaha FM. Metabolites profiling and cheminformatics bioprospection of selected medicinal plants against the main protease and RNA-dependent RNA polymerase of SARS-CoV-2. J Biomol Struct Dyn 2024; 42:6740-6760. [PMID: 37464870 DOI: 10.1080/07391102.2023.2236718] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023]
Abstract
Despite the existence of some vaccines, SARS-CoV-2 (S-2) infections persist for various reasons relating to vaccine reluctance, rapid mutation rate, and an absence of specific treatments targeted to the infection. Due to their availability, low cost and low toxicity, research into potentially repurposing phytometabolites as therapeutic alternatives has gained attention. Therefore, this study explored the antiviral potential of metabolites of some medicinal plants [Spondias mombin, Macaranga barteri and Dicerocaryum eriocarpum (Sesame plant)] identified using liquid chromatography-mass spectrometry (LCMS) as possible inhibitory agents against the S-2 main protease (S-2 MP) and RNA-dependent RNA polymerase (RP) using computational approaches. Molecular docking was used to identify the compounds with the best affinities for the selected therapeutics targets. Afterwards, compounds with poor physicochemical characteristics, pharmacokinetics, and drug-likeness were screened out. The top-ranked compounds were further subjected to a 120-ns molecular dynamics (MD) simulation. Only quercetin 3-O-rhamnoside (-48.77 kcal/mol) had higher binding free energy than the reference standard (zafirlukast) (-44.99 kcal/mol) against S-2 MP. Conversely, all the top-ranked compounds (ellagic acid hexoside, spiraeoside, apigenin-4'-glucoside and chrysoeriol 7-glucuronide) except gnetin L (-24.24 kcal/mol) had higher binding free energy (-55.19 kcal/mol, -52.75 kcal/mol, -47.22 kcal/mol and -43.35 kcal/mol) respectively, against S-2 RP relative to the reference standard (-34.79 kcal/mol). The MD simulations study further revealed that the investigated inhibitors are thermodynamically stable and form structurally compatible complexes that impede the regular operation of the respective S-2 therapeutic targets. Although, these S-2 therapeutic candidates are promising, further in vitro and in vivo evaluation is required and highly recommended.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adedayo Ayodeji Lanrewaju
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
| | | | - Martin M Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
| | - Feroz Mahomed Swalaha
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
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Scarpa ES, Antonelli A, Balercia G, Sabatelli S, Maggi F, Caprioli G, Giacchetti G, Micucci M. Antioxidant, Anti-Inflammatory, Anti-Diabetic, and Pro-Osteogenic Activities of Polyphenols for the Treatment of Two Different Chronic Diseases: Type 2 Diabetes Mellitus and Osteoporosis. Biomolecules 2024; 14:836. [PMID: 39062550 PMCID: PMC11275061 DOI: 10.3390/biom14070836] [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: 06/03/2024] [Revised: 06/27/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Polyphenols are natural bioactives occurring in medicinal and aromatic plants and food and beverages of plant origin. Compared with conventional therapies, plant-derived phytochemicals are more affordable and accessible and have no toxic side effects. Thus, pharmaceutical research is increasingly inclined to discover and study new and innovative natural molecules for the treatment of several chronic human diseases, like type 2 diabetes mellitus (T2DM) and osteoporosis. These pathological conditions are characterized by a chronic inflammatory state and persistent oxidative stress, which are interconnected and lead to the development and worsening of these two health disorders. Oral nano delivery strategies have been used to improve the bioavailability of polyphenols and to allow these natural molecules to exert their antioxidant, anti-inflammatory, anti-diabetic, and pro-osteogenic biological activities in in vivo experimental models and in patients. Polyphenols are commonly used in the formulations of nutraceuticals, which can counteract the detrimental effects of T2DM and osteoporosis pathologies. This review describes the polyphenols that can exert protective effects against T2DM and osteoporosis through the modulation of specific molecular markers and pathways. These bioactives could be used as adjuvants, in combination with synthetic drugs, in the future to develop innovative therapeutic strategies for the treatment of T2DM and osteoporosis.
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Affiliation(s)
| | - Antonella Antonelli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (A.A.); (M.M.)
| | - Giancarlo Balercia
- Division of Endocrinology, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy;
| | - Sofia Sabatelli
- Clinic of Endocrinology and Metabolic Diseases, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.S.); (G.G.)
| | - Filippo Maggi
- Chemistry Interdisciplinary Project (CHIP) Research Center, School of Pharmacy, University of Camerino, 62032 Camerino, Italy; (F.M.); (G.C.)
| | - Giovanni Caprioli
- Chemistry Interdisciplinary Project (CHIP) Research Center, School of Pharmacy, University of Camerino, 62032 Camerino, Italy; (F.M.); (G.C.)
| | - Gilberta Giacchetti
- Clinic of Endocrinology and Metabolic Diseases, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.S.); (G.G.)
| | - Matteo Micucci
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (A.A.); (M.M.)
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Teixeira De Oliveira J, Brito Tecchio K, Silva Lopes M, Nunes Andrade S, Iara Maciel De Azambuja Ribeiro R, Varotti FDP, Barbosa De Oliveira R, Henrique Ribeiro Viana G, J Da Silva Vieira Dos Santos V, Vieira Dos Santos F. In vitro evaluation of the selective cytotoxicity and genotoxicity of three synthetic ortho-nitrobenzyl derivatives in human cancer cell lines, with and without metabolic activation. Drug Chem Toxicol 2024; 47:404-415. [PMID: 38949608 DOI: 10.1080/01480545.2023.2184478] [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: 07/20/2022] [Accepted: 02/18/2023] [Indexed: 03/11/2023]
Abstract
Although the presence of nitro groups in chemicals can be recognized as structural alerts for mutagenicity and carcinogenicity, nitroaromatic compounds have attracted considerable interest as a class of agents that can serve as source of potential new anticancer agents. In the present study, the in vitro cytotoxicity, genotoxicity, and mutagenicity of three synthetic ortho-nitrobenzyl derivatives (named ON-1, ON-2 and ON-3) were evaluated by employing human breast and ovarian cancer cell lines. A series of biological assays was carried out with and without metabolic activation. Complementarily, computational predictions of the pharmacokinetic properties and druglikeness of the compounds were performed in the Swiss ADME platform. The MTT assay showed that the compounds selectively affected selectively the cell viability of cancer cells in comparison with a nontumoral cell line. Additionally, the metabolic activation enhanced cytotoxicity, and the compounds affected cell survival, as demonstrated by the clonogenic assay. The comet assay, the cytokinesis-block micronucleus assay, and the immunofluorescence of the γ-H2AX foci formation assay have that the compounds caused chromosomal damage to the cancer cells, with and without metabolic activation. The results obtained in the present study showed that the compounds assessed were genotoxic and mutagenic, inducing double-strand breaks in the DNA structure. The high selectivity indices observed for the compounds ON-2 and ON-3, especially after metabolic activation with the S9 fraction, must be highlighted. These experimental biological results, as well as the theoretical properties predicted for the compounds have shown that they are promising anticancer candidates to be exploited in additional studies.
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Affiliation(s)
- Júlia Teixeira De Oliveira
- Laboratório de Biologia Celular e Mutagênese (LaBCeM), Universidade Federal de São João del Rei (UFSJ), Divinópolis, Brazil
- Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Divinópolis, Brazil
| | - Kimberly Brito Tecchio
- Laboratório de Biologia Celular e Mutagênese (LaBCeM), Universidade Federal de São João del Rei (UFSJ), Divinópolis, Brazil
- Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Divinópolis, Brazil
| | - Marcela Silva Lopes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Silmara Nunes Andrade
- Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Divinópolis, Brazil
| | | | - Fernando De Pilla Varotti
- Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Divinópolis, Brazil
| | - Renata Barbosa De Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Fabio Vieira Dos Santos
- Laboratório de Biologia Celular e Mutagênese (LaBCeM), Universidade Federal de São João del Rei (UFSJ), Divinópolis, Brazil
- Núcleo de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del Rei (UFSJ), Divinópolis, Brazil
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Maphumulo NF, Gordon ML. HIV-1 envelope facilitates the development of protease inhibitor resistance through acquiring mutations associated with viral entry and immune escape. Front Microbiol 2024; 15:1388729. [PMID: 38699474 PMCID: PMC11063367 DOI: 10.3389/fmicb.2024.1388729] [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: 02/20/2024] [Accepted: 03/27/2024] [Indexed: 05/05/2024] Open
Abstract
Introduction There is increasing evidence supporting a role for HIV-1 envelope in the development of Protease Inhibitor drug resistance, and a recent report from our group suggested that Env mutations co-evolve with Gag-Protease mutations in the pathway to Lopinavir resistance. In this study, we investigated the effect of co-evolving Env mutations on virus function and structure. Methods Co-receptor usage and n-linked glycosylation were investigated using Geno2Pheno as well as tools available at the Los Alamos sequence database. Molecular dynamics simulations were performed using Amber 18 and analyzed using Cpptraj, and molecular interactions were calculated using the Ring server. Results The results showed that under Protease Inhibitor drug selection pressure, the envelope gene modulates viral entry by protecting the virus from antibody recognition through the increased length and number of N-glycosylation sites observed in V1/V2 and to some extent V5. Furthermore, gp120 mutations appear to modulate viral entry through a switch to the CXCR4 coreceptor, induced by higher charge in the V3 region and specific mutations at the coreceptor binding sites. In gp41, S534A formed a hydrogen bond with L602 found in the disulfide loop region between the Heptad Repeat 1 and Heptad Repeat 2 domains and could negatively affect the association of gp120-gp41 during viral entry. Lastly, P724Q/S formed both intermolecular and intramolecular interactions with residues within the Kennedy loop, a known epitope. Discussion In conclusion, the results suggest that mutations in envelope during Protease Inhibitor treatment failure are related to immune escape and that S534A mutants could preferentially use the cell-to-cell route of infection.
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Affiliation(s)
| | - Michele L. Gordon
- Department of Virology, Doris Duke Medical Research Institute, College of Health Sciences, University of KwaZulu-Natala, Durban, South Africa
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Liu L, Li X. Pharmacokinetic study of the interaction between luteolin and magnoflorine in rats. Chem Biol Drug Des 2024; 103:e14356. [PMID: 37731180 DOI: 10.1111/cbdd.14356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/07/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023]
Abstract
Both luteolin and magnoflorine have been reported to regulate the development of breast cancer, which makes them easier to co-administrate. Luteolin was co-administrated with magnoflorine to evaluate their potential interaction. The pharmacokinetic study was performed on male Sprague-Dawley rats randomly grouped as the single administration of luteolin and the co-administration of luteolin and magnoflorine with six rats of each. CaCO-2 cell transwell assay was employed for transport evaluation, and the metabolic stability of luteolin and CYP3A activity were assessed in rat liver microsomes. The effect of luteolin on MDA-MB-231 cells was assessed with CCK8 assay. Magnoflorine significantly changed the pharmacokinetic profile of luteolin with increased area under the curve (AUC), prolonged t1/2 , and reduced clearance rate. Magnoflorine also suppressed the efflux ratio and improved the in vitro metabolic stability of luteolin. Magnoflorine also enhanced the inhibitory effect of luteolin on MDA-MB-231 cells. Magnoflorine significantly inhibited CYP3A activity with the IC50 of 18.99 μM. Magnoflorine prolonged the system exposure, enhanced the metabolic stability, and enhanced the anti-tumor effect of luteolin through inactivating CYP3A.
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Affiliation(s)
- Lu Liu
- Department of Endocrine, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaohua Li
- Department of Endocrine, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Akoonjee A, Lanrewaju AA, Balogun FO, Makunga NP, Sabiu S. Waste to Medicine: Evidence from Computational Studies on the Modulatory Role of Corn Silk on the Therapeutic Targets Implicated in Type 2 Diabetes Mellitus. BIOLOGY 2023; 12:1509. [PMID: 38132335 PMCID: PMC10740667 DOI: 10.3390/biology12121509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by insulin resistance and/or defective insulin production in the human body. Although the antidiabetic action of corn silk (CS) is well-established, the understanding of the mechanism of action (MoA) behind this potential is lacking. Hence, this study aimed to elucidate the MoA in different samples (raw and three extracts: aqueous, hydro-ethanolic, and ethanolic) as a therapeutic agent for the management of T2DM using metabolomic profiling and computational techniques. Ultra-performance liquid chromatography-mass spectrometry (UP-LCMS), in silico techniques, and density functional theory were used for compound identification and to predict the MoA. A total of 110 out of the 128 identified secondary metabolites passed the Lipinski's rule of five. The Kyoto Encyclopaedia of Genes and Genomes pathway enrichment analysis revealed the cAMP pathway as the hub signaling pathway, in which ADORA1, HCAR2, and GABBR1 were identified as the key target genes implicated in the pathway. Since gallicynoic acid (-48.74 kcal/mol), dodecanedioc acid (-34.53 kcal/mol), and tetradecanedioc acid (-36.80 kcal/mol) interacted well with ADORA1, HCAR2, and GABBR1, respectively, and are thermodynamically stable in their formed compatible complexes, according to the post-molecular dynamics simulation results, they are suggested as potential drug candidates for T2DM therapy via the maintenance of normal glucose homeostasis and pancreatic β-cell function.
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Affiliation(s)
- Ayesha Akoonjee
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Adedayo Ayodeji Lanrewaju
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Fatai Oladunni Balogun
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Nokwanda Pearl Makunga
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa;
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
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Gupta S, Banavath HN, Tejavath KK. Pharmacoinformatic screening of phytoconstituent and evaluation of its anti-PDAC effect using in vitro studies. J Biomol Struct Dyn 2023; 41:10627-10641. [PMID: 36510680 DOI: 10.1080/07391102.2022.2155701] [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: 08/26/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022]
Abstract
With no prominent treatment for pancreatic ductal adenocarcinoma (PDAC) in conventional chemotherapy, recent studies have focused on uniting conventional and traditional medicines including plant phytoconstituents. Herein, we used pharmacoinformatic studies to identify potent phytoconstituent as ligand having inhibition activities against canonical anticancer targets, and evaluated its effect on PDAC cell lines. SwissTargetPrediction and SuperPred tools were utilized to segregate protein targets of ligand in humans, following which FunRich was applied to garner its targets in PDAC. STRING analysis predicted protein-protein interactions and dynamic simulation studies confirmed stability of ligand-protein complex. For in vitro cytotoxic potential, ligand treatment at different concentrations was given to PDAC cell lines both alone and combined with gemcitabine, followed by evaluation of effects on migration. Differential gene expression was checked using PCR for evaluating mechanism of cytotoxicity. Results showed pentagalloylglucose (PGG) with highest docking and MMGBSA scores for Cyclooxygenase 2 (Cox2) inhibition site. SwissTargetPrediction and SuperPred analysis detected 40 targets of PGG in PDAC. Simulation data showed stability of protein-ligand complex. In in vitro experiments Mia-PaCa-2 was more sensitive to PGG than Panc-1. PGG successfully inhibited migration both alone and in combination with gemcitabine. Additionally, PGG treatment induced apoptosis in both the cell lines; but showed antagonism when combined with gemcitabine. In conclusion, our report demonstrates PGG has good binding with Cox2 and showed anti-PDAC activity by inhibiting migration and inducing apoptosis, thus it can be used as a therapy option. But further studies are required to confirm its behaviour as a combination therapy drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shruti Gupta
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Hemanth Naick Banavath
- Department of Sports Bio-Sciences, School of Sports Science MYAS-CURAJ, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Kiran Kumar Tejavath
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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Ilesanmi A, Dairo G, Salimat S, Bodun DS, Awoyale B, Balogun TA. Identification of bioactive compounds from Vaccinium vitis-idaea L. (Lingonberry) as inhibitors for treating KRAS-associated cancer: a computational approach. In Silico Pharmacol 2023; 11:32. [PMID: 37915613 PMCID: PMC10616029 DOI: 10.1007/s40203-023-00165-1] [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: 07/29/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
Lung cancer is the cancer of the lung's epithelial cells typically characterized by difficulty breathing, chest pain, blood-stained coughs, headache, and weight loss. If left unmanaged, lung cancer can spread to other body parts. While several treatment methods exist for managing lung cancer, exploring natural plant sources for developing therapeutics offers great potential in complementing other treatment approaches. In this study, we evaluated the bioactive compounds in Vaccinium vitis-idaea for treating KRAS-associated lung cancer types. In this study, we concentrated on inhibiting the mutated Kirsten rat sarcoma viral oncogene homolog (KRAS) by targeting an associated protein (Phosphodiesterase 6δ) to which KRAS form complexes. We evaluated bioactive compounds from Lingonberry (Vaccinium vitis-idaea L.), adopting computational approaches such as molecular docking, molecular dynamics simulation, molecular mechanics/generalized Born surface area (MM/GBSA) calculations, and pharmacokinetics analysis. A total of 26 out of 39 bioactive compounds of Vaccinium vitis-idaea L. had a higher binding affinity to the target receptor than an approved drug, Sotorasib. Also, further analyses of all lead/top compounds in this study identified (+)-Catechin (Cianidanol), Arbutin, Resveratrol, and Sinapic acid, to be potential drug candidates that could be pursued. In sum, Arbutin, (+)-Catechin, and Sinapic acid are predicted to be the top compound of Vaccinium vitis-idaea L. because of their pharmacokinetic properties and drug-likeness attributes. Also, their stability to the target receptor makes them a potential drug candidate that could be explored for treating KRAS mutation-associated lung cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00165-1.
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Affiliation(s)
- Ayooluwa Ilesanmi
- Department of Sciences and Mathematics, Mississippi University for Women, Columbus, USA
| | - Gbenga Dairo
- Department of Biological Sciences, Western Illinois University, Macomb, IL USA
| | - Sofela Salimat
- Department of Chemistry, University of Lagos, Lagos, Nigeria
| | - Damilola S. Bodun
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Bibiire Awoyale
- Department of Chemistry, University of Ilorin, Ilorin, Nigeria
| | - Toheeb A. Balogun
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
- Department of Biological Sciences, University of California, San Diego, La Jolla, USA
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Kehinde IA, Egbeyemi A, Kaur M, Onyenaka C, Adebusuyi T, Olaleye OA. Inhibitory mechanism of clioquinol and its derivatives at the exopeptidase site of human angiotensin-converting enzyme-2 and receptor binding domain of SARS-CoV-2 viral spike. J Biomol Struct Dyn 2023; 41:2992-3001. [PMID: 35220925 PMCID: PMC11371071 DOI: 10.1080/07391102.2022.2043938] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
The outbreak of SARS-CoV-2 infections around the world has prompted scientists to explore different approaches to develop therapeutics against COVID-19. This study focused on investigating the mechanism of inhibition of clioquinol (CLQ) and its derivatives (7-bromo-5-chloro-8-hydroxyquinoline (CLBQ), 5, 7-Dichloro-8-hydroxyquinoline (CLCQ)) against the viral glycoprotein, and human angiotensin-converting enzyme-2 (hACE-2) involved in SARS-CoV-2 entry. The drugs were docked at the exopeptidase site of hACE-2 and receptor binding domain (RBD) sites of SARS-CoV-2 Sgp to calculate the binding affinity of the drugs. To understand and establish the inhibitory characteristics of the drugs, molecular dynamic (MD) simulation of the best fit docking complex performed. Evaluation of the binding energies of the drugs to hACE-2 after 100 ns MD simulations revealed CLQ to have the highest binding energy value of -40.4 kcal/mol close to MLN-7640 (-45.4 kcal/mol), and higher than the exhibited values for its derivatives: CLBQ (-34.5 kcal/mol) and CLCQ (-24.8 kcal/mol). This suggests that CLQ and CLBQ bind more strongly at the exopeptidase site than CLCQ. Nevertheless, the evaluation of binding affinity of the drugs to SARS-CoV-2 Sgp showed the drugs are weakly bound at the RBD site, with CLBQ, CLCQ, CLQ exhibiting relatively low energy values of -16.8 kcal/mol, -16.34 kcal/mol, -12.5 kcal/mol, respectively compared to the reference drug, Bisoxatin (BSX), with a value of -25.8 kcal/mol. The structural analysis further suggests decrease in systems stability and explain the mechanism of inhibition of clioquinol against SARS-CoV-2 as reported in previous in vitro study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Idowu A Kehinde
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, TX, USA
| | - Anu Egbeyemi
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, TX, USA
| | - Manvir Kaur
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, TX, USA
| | - Collins Onyenaka
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, TX, USA
| | - Tolulope Adebusuyi
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, TX, USA
| | - Omonike A Olaleye
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, TX, USA
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Sales D, Lin E, Stoffel V, Dickson S, Khan ZK, Beld J, Jain P. Apigenin improves cytotoxicity of antiretroviral drugs against HTLV-1 infected cells through the modulation of AhR signaling. NEUROIMMUNE PHARMACOLOGY AND THERAPEUTICS 2023; 2:49-62. [PMID: 37027342 PMCID: PMC10070013 DOI: 10.1515/nipt-2022-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/19/2023]
Abstract
Objectives HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a neuroinflammatory autoimmune disease characterized by high levels of infected immortalized T cells in circulation, which makes it difficult for antiretroviral (ART) drugs to work effectively. In previous studies, we established that Apigenin, a flavonoid, can exert immunomodulatory effects to reduce neuroinflammation. Flavonoids are natural ligands for the aryl hydrocarbon receptor (AhR), which is a ligand activated endogenous receptor involved in the xenobiotic response. Consequently, we tested Apigenin's synergy in combination with ART against the survival of HTLV-1-infected cells. Methods First, we established a direct protein-protein interaction between Apigenin and AhR. We then demonstrated that Apigenin and its derivative VY-3-68 enter activated T cells, drive nuclear shuttling of AhR, and modulate its signaling both at RNA and protein level. Results In HTLV-1 producing cells with high AhR expression, Apigenin cooperates with ARTs such as Lopinavir (LPN) and Zidovudine (AZT), to impart cytotoxicity by exhibiting a major shift in IC50 that was reversed upon AhR knockdown. Mechanistically, Apigenin treatment led to an overall downregulation of NF-κB and several other pro-cancer genes involved in survival. Conclusions This study suggest the potential combinatorial use of Apigenin with current first-line antiretrovirals for the benefit of patients affected by HTLV-1 associated pathologies.
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Affiliation(s)
- Dominic Sales
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Edward Lin
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Victoria Stoffel
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Shallyn Dickson
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Zafar K. Khan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Joris Beld
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Pooja Jain
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
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Kumar N, Acharya V. Machine intelligence-guided selection of optimized inhibitor for human immunodeficiency virus (HIV) from natural products. Comput Biol Med 2023; 153:106525. [PMID: 36603433 DOI: 10.1016/j.compbiomed.2022.106525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/28/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
The human immunodeficiency virus (HIV) connects to the cluster of differentiation (CD4) and any of the entry co-receptors (CCR5 and CXCR4); followed by unloading the viral genome, reverse transcriptase, and integrase enzymes within the host cell. The co-receptors facilitate the entry of virus and vital enzymes, leading to replication and pre-maturation of viral particles within the host. The protease enzyme transforms the immature viral vesicles into the mature virion. The pivotal role of co-receptors and enzymes in homeostasis and growth makes the crucial target for anti-HIV drug discovery, and the availability of X-ray crystal structures is an asset. Here, we used the machine intelligence-driven framework (A-HIOT) to identify and optimize target-based potential hit molecules for five significant protein targets from the ZINC15 database (natural products dataset). Following validation with dynamic motion behavior analysis and molecular dynamics simulation, the optimized hits were evaluated using in silico ADMET filtration. Furthermore, three molecules were screened, optimized, and validated: ZINC00005328058 for CCR5 and protease, ZINC000254014855 for CXCR4 and integrase, and ZINC000000538471 for reverse transcriptase. In clinical trials, the ZINC000254014855 and ZINC000254014855 were passed in primary screens for vif-HIV-1, and we reported the specific receptor as well as interactions. As a result, the validated molecules may be investigated further in experimental studies targeting specific receptors in order to design and synergize an anti-HIV regimen.
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Affiliation(s)
- Neeraj Kumar
- Functional Genomics and Complex System Lab, HiCHiCoB, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research, Ghaziabad, 201002, India.
| | - Vishal Acharya
- Functional Genomics and Complex System Lab, HiCHiCoB, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research, Ghaziabad, 201002, India.
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Rabaan AA, Abas AH, Tallei TE, Al-Zaher MA, Al-Sheef NM, Fatimawali, Al-Nass EZ, Al-Ebrahim EA, Effendi Y, Idroes R, Alhabib MF, Al-Fheid HA, Adam AA, Bin Emran T. Monkeypox outbreak 2022: What we know so far and its potential drug targets and management strategies. J Med Virol 2023; 95:e28306. [PMID: 36372558 DOI: 10.1002/jmv.28306] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/28/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022]
Abstract
Monkeypox is a rare zoonotic disease caused by infection with the monkeypox virus. The disease can result in flu-like symptoms, fever, and a persistent rash. The disease is currently spreading throughout the world and prevention and treatment efforts are being intensified. Although there is no treatment that has been specifically approved for monkeypox virus infection, infected patients may benefit from using certain antiviral medications that are typically prescribed for the treatment of smallpox. The drugs are tecovirimat, brincidofovir, and cidofovir, all of which are currently in short supply due to the spread of the monkeypox virus. Resistance is also a concern, as widespread replication of the monkeypox virus can lead to mutations that produce monkeypox viruses that are resistant to the currently available treatments. This article discusses monkeypox disease, potential drug targets, and management strategies to overcome monkeypox disease. With the discovery of new drugs, it is hoped that the problem of insufficient drugs will be resolved, and it is not anticipated that drug resistance will become a major issue in the near future.
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Affiliation(s)
- Ali A Rabaan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.,Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
| | - Abdul Hawil Abas
- Faculty of Bioscience and Engineering, Ghent University, Ghent, Belgium
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, North Sulawesi, Indonesia
| | - Mona A Al-Zaher
- Department of Commitment management, Directorate of Health Affairs in the Eastern Province, Dammam, Saudi Arabia
| | - Noor M Al-Sheef
- Department of Commitment management, Directorate of Health Affairs in the Eastern Province, Dammam, Saudi Arabia
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, North Sulawesi, Indonesia
| | - Esraa Z Al-Nass
- Department of Commitment management, Directorate of Health Affairs in the Eastern Province, Dammam, Saudi Arabia
| | - Eba A Al-Ebrahim
- Department of Commitment management, Directorate of Health Affairs in the Eastern Province, Dammam, Saudi Arabia
| | - Yunus Effendi
- Department of Biology, Faculty of Science and Technology, Al-Azhar Indonesia University, Jakarta, Indonesia
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Banda Aceh, Aceh, Indonesia
| | - Mather F Alhabib
- Molecular Diagnostic Laboratory, Dammam Regional Laboratory and Blood Bank, Dammam, Saudi Arabia
| | - Hussain A Al-Fheid
- Molecular Diagnostic Laboratory, Dammam Regional Laboratory and Blood Bank, Dammam, Saudi Arabia
| | - Ahmad Akroman Adam
- Dentistry Study Program, Faculty of Medicine, Sam Ratulangi University, Manado, North Sulawesi, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
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Molehin OR, Idowu KA, Olaoye AB, Fakayode AE, Adesua OO. Influence of Clerodendrum volubile leaf extract on doxorubicin-induced toxicity and inhibition of carbonyl reductase mediated metabolism. JOURNAL OF COMPLEMENTARY & INTEGRATIVE MEDICINE 2022; 19:937-946. [PMID: 33977682 DOI: 10.1515/jcim-2020-0231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
OBJECTIVES Doxorubicin (DOX) is a commonly used chemotherapeutic drug. However, its non-target organ toxicities pose a serious problem. This study is to assess the protective role of Clerodendrum volubile leaf extract (CVE) against DOX-induced toxicities in rats. In addition, the inhibitory activities of three phytochemical compounds (Rutin, Gallic acid and Rosmarinic acid) from CVE against Carbonyl reductase 1 (CBR1) were examined. METHODS Rats were randomly divided into 5 groups: (a) Control group rats were given 0.9% NaCl as vehicle, (b) DOX group: A single dose of DOX (25 mg/kg; i.p.) was administered and rats were sacrificed 4 days after DOX injection, while groups (c-e) CVE-treated DOX rat groups were given 125, 250 and 500 mg/kg body weight of extracts orally for 12 consecutive days; 8 days before, and 4 days after the DOX administration. Computational techniques were used to determine the inhibitory activities of the compounds against CBR1. RESULTS DOX intoxication caused a significant increase (p<0.05) in serum marker enzymes: ALT, AST, ALP, LDH, CK activities. The levels of liver and heart tissues antioxidant parameters: GPx, SOD, CAT, and GSH were significantly (p<0.05) decreased in DOX-intoxicated rats with concomitant elevation of malondialdehyde levels. Pretreatment with CVE reversed the above trends. From the structural analysis, Rutin and RSA exhibited the highest binding free energies against CBR1, and also exhibited structural stability when bound with CBR1. CONCLUSIONS Our study indicates the protective effect of CVE when used in combination with doxorubicin thus improving its chemotherapeutic application via inhibition of CBR-mediated metabolism.
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Affiliation(s)
- Olorunfemi R Molehin
- Department of Biochemistry, Faculty of Science, Ekiti State University, Ado-Ekiti, Nigeria
| | - Kehinde A Idowu
- Department of Medical Biochemistry, College of Medicine, Ekiti State University, Ado-Ekiti, Nigeria
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Medical Campus, Durban, South Africa
| | - Ayonposi B Olaoye
- Department of Science Technology, The Federal Polytechnic Ado-Ekiti, Ado-Ekiti, Nigeria
| | - Aderonke E Fakayode
- Department of Biochemistry and Molecular Biology, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Oluwatumininu O Adesua
- Department of Biochemistry, Faculty of Science, Ekiti State University, Ado-Ekiti, Nigeria
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Novel fluorophenyl tethered thiazole and chalcone analogues as potential anti-tubercular agents: Design, synthesis, biological and in silico evaluations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Shode FO, Uhomoibhi JOO, Idowu KA, Sabiu S, Govender KK. Molecular Dynamics Study on Selected Bioactive Phytochemicals as Potential Inhibitors of HIV-1 Subtype C Protease. Metabolites 2022; 12:1155. [PMID: 36422295 PMCID: PMC9695624 DOI: 10.3390/metabo12111155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/05/2022] [Accepted: 11/15/2022] [Indexed: 09/21/2023] Open
Abstract
Acquired immunodeficiency syndrome (AIDS), one of the deadliest global diseases, is caused by the Human Immunodeficiency Virus (HIV). To date, there are no known conventional drugs that can cure HIV/AIDS, and this has prompted continuous scientific efforts in the search for novel and potent anti-HIV therapies. In this study, molecular dynamics simulation (MDS) and computational techniques were employed to investigate the inhibitory potential of bioactive compounds from selected South African indigenous plants against HIV-1 subtype C protease (HIVpro). Of the eight compounds (CMG, MA, UA, CA, BA, UAA, OAA and OA) evaluated, only six (CMG (-9.9 kcal/mol), MA (-9.3 kcal/mol), CA (-9.0 kcal/mol), BA (-8.3 kcal/mol), UAA (-8.5 kcal/mol), and OA (-8.6 kcal/mol)) showed favourable activities against HIVpro and binding landscapes like the reference FDA-approved drugs, Lopinavir (LPV) and Darunavir (DRV), with CMG and MA having the highest binding affinities. Using the structural analysis (root-mean-square deviation (RMSD), fluctuation (RMSF), and radius of gyration (RoG) of the bound complexes with HIVpro after 350 ns, structural evidence was observed, indicating that the six compounds are potential lead candidates for inhibiting HIVpro. This finding was further corroborated by the structural analysis of the enzyme-ligand complexe systems, where structural mechanisms of stability, flexibility, and compactness of the study metabolites were established following binding with HIVpro. Furthermore, the ligand interaction plots revealed that the metabolites interacted hydrophobically with the active site amino residues, with identification of other key residues implicated in HIVpro inhibition for drug design. Overall, this is the first computational report on the anti-HIV-1 activities of CMG and MA, with efforts on their in vitro and in vivo evaluations underway. Judging by the binding affinity, the degree of stability, and compactness of the lead metabolites (CMG, MA, CA, BA, OA, and UAA), they could be concomitantly explored with conventional HIVpro inhibitors in enhancing their therapeutic activities against the HIV-1 serotype.
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Affiliation(s)
- Francis Oluwole Shode
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology (DUT), P.O. Box 1334, Durban 4000, South Africa
| | - John Omo-osagie Uhomoibhi
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology (DUT), P.O. Box 1334, Durban 4000, South Africa
| | - Kehinde Ademola Idowu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology (DUT), P.O. Box 1334, Durban 4000, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology (DUT), P.O. Box 1334, Durban 4000, South Africa
| | - Krishna Kuben Govender
- Department of Chemical Sciences, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg 2028, South Africa
- National Institute for Theoretical and Computational Sciences, NITHeCS, Stellenbosch 7602, South Africa
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17
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Madushanka A, Verma N, Freindorf M, Kraka E. Papaya Leaf Extracts as Potential Dengue Treatment: An In-Silico Study. Int J Mol Sci 2022; 23:12310. [PMID: 36293162 PMCID: PMC9610845 DOI: 10.3390/ijms232012310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
Dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS) cause serious public health problems, with nearly 390 million people affected and 20,000 deaths per year in tropical and subtropical countries. Despite numerous attempts, no antiviral drug or vaccine is currently available to combat the manifestation. The challenge of discovering an efficient vaccine is enhanced by the surplus presence of efficient vectors and drug resistance from the virus. For centuries, papaya (Carica papaya) extracts have been traditionally used to treat DF, DHF, and DSS. In the present study, we systematically investigated seven compounds isolated from papaya leaf extract with regard to their potential as inhibitors for non-structural (NS) proteins, NS3 and NS5, which play a crucial role in viral RNA replication. The computational tools applied stretched across classical molecular docking, molecular dynamics (MD) simulations and SwissADME used to calculate binding affinities; binding free energies; Absorption, Distribution, Metabolism, and Excretion (ADME); and drug-likeness properties, thus, identifying Kaempferol, Chlorogenic acid, and Quercetin as potential candidates, with Kaempferol and Quercetin scoring best. Therefore, for the Kaempferol and Quercetin complexes, hybrid quantum mechanical/molecular mechanical (QM/MM) geometry and frequency calculations were performed, followed by the local mode analysis developed in our group to quantify Kaempferol-NS and Quercetin-NS hydrogen bonding. Given the non-toxic nature and the wide availability of the Kaempferol and Quercetin papaya extract in almost all of the susceptible regions, and our results showing high NS3 and NS5 binding affinities and energies, strong hydrogen bonding with both NS3 and NS5, and excellent ADME properties, we suggest Kaempferol and Quercetin as a strong NS3 and NS5 inhibitor to be further investigated in vitro.
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Affiliation(s)
| | | | | | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, P.O. Box 750314, Dallas, TX 75275, USA
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Jiao M, Liu C, Prieto M, Lu X, Wu W, Sun J, García-Oliveira P, Tang X, Xiao J, Simal-Gandara J, Hu D, Li N. Biological Functions and Utilization of Different Part of the Papaya: A Review. FOOD REVIEWS INTERNATIONAL 2022. [DOI: 10.1080/87559129.2022.2124415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Mingyue Jiao
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Key Laboratory of Agro-Products Processing Technology of Shandong Province/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
- School of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Chao Liu
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Key Laboratory of Agro-Products Processing Technology of Shandong Province/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - M.A. Prieto
- Universidade de Vigo, Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, Ourense, Spain
| | - Xiaoming Lu
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai’an, China
| | - Wenfu Wu
- School of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Jinyue Sun
- Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs/Key Laboratory of Agro-Products Processing Technology of Shandong Province/Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - P. García-Oliveira
- Universidade de Vigo, Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, Ourense, Spain
| | - Xiaozhen Tang
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai’an, China
| | - Jianbo Xiao
- Universidade de Vigo, Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, Ourense, Spain
| | - Jesus Simal-Gandara
- Universidade de Vigo, Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, Ourense, Spain
| | - Dagang Hu
- National Key Laboratory of Crop Biology; Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
| | - Ningyang Li
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai’an, China
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Idowu KA, Onyenaka C, Olaleye OA. A computational evaluation of structural stability of omicron and delta mutations of SARS-CoV-2 spike proteins and human ACE-2 interactions. INFORMATICS IN MEDICINE UNLOCKED 2022; 33:101074. [PMID: 36092780 PMCID: PMC9450468 DOI: 10.1016/j.imu.2022.101074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022] Open
Abstract
Several more infectious SARS-CoV-2 variants have emerged globally since SARS-CoV-2 pandemic and the discovery of the first D614G variant of SARS-CoV-2 spike proteins in 2020. Delta (B.1.617.2) and Omicron (B.1.1.529) variants have proven to be of major concern out of all the reported variants, considering their influence on the virus' transmissibility and severity. This study aimed at evaluating the impact of mutations on these two variants on stability and molecular interactions between the viral Spike protein and human angiotensin converting enzyme-2 (hACE-2). The spike proteins receptor binding domain (RBD) was docked with the hACE-2 using HADDOCK servers. To understand and establish the effects of the mutations on the structural stability and flexibility of the RBD-hACE-2 complex, molecular dynamic (MD) simulation of the docked complex was performed and evaluated. The findings from both molecular docking analysis and binding free energy showed that the Omicron (OM) variant has high receptiveness towards hACE-2 versus Delta variant (DT), thereby, responsible for its increase in transmission. The structural stability and flexibility evaluation of variants' systems showed that mutations on DT and OM variants disturbed the stability of either the spike protein or the RBD-hACE-2 complex, with DT variant having greater instability impact. This study, therefore, assumed this obvious instability observed in DT variant might be associated or responsible for the reported severity in DT variant disease over the OM variant disease. This study provides molecular insight into the effects of OM and DT variants on stability and interactions between SARS-CoV-2 protein and hACE-2.
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Affiliation(s)
- Kehinde A Idowu
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, 3100 Cleburne St, Houston, TX, 77004, USA
| | - Collins Onyenaka
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, 3100 Cleburne St, Houston, TX, 77004, USA
| | - Omonike A Olaleye
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, 3100 Cleburne St, Houston, TX, 77004, USA
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Molecular modeling identification of potential drug candidates from selected African plants against SARS-CoV-2 key druggable proteins. SCIENTIFIC AFRICAN 2022; 17:e01279. [PMID: 35856008 PMCID: PMC9279166 DOI: 10.1016/j.sciaf.2022.e01279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/13/2022] [Accepted: 07/10/2022] [Indexed: 01/18/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is one of the major health threats the world has experienced. In order to stem the tide of the virus and its associated disease, rapid efforts have been dedicated to identifying credible anti-SARS-CoV-2 drugs. This study forms part of the continuing efforts to develop anti-SARS-CoV-2 molecules and employed a computational structure-activity relationship approach with emphasis on 99 plant secondary metabolites from eight selected African medicinal plants with proven therapeutic benefits against respiratory diseases focusing on the viral protein targets [Spike protein (Sgp), Main protease (Mpro), and RNA-dependent RNA polymerase (RdRp)]. The results of the molecular dynamics simulation of the best docked compounds presented as binding free energy revealed that three compounds each against the Sgp (VBS, COG and ABA), and Mpro (COR, QOR and ABG) had higher and better affinity for the proteins than the respective reference drugs, cefoperazone (CSP) and Nelfinavir (NEF), while four compounds (HDG, VBS, COR and KOR) had higher and favorable binding affinity towards RdRp than the reference standard, ramdesivir (RDS). Analysis of interaction with the receptor binding domain amino acid residues of Sgp showed that VBS had the highest number of interactions (17) relative to 14 and 13 for COG and ABA, respectively. For Mpro, COR showed interactions with catalytic dyad residues (His172 and Cys145). Compared to RDS, COR, HDG, VBS and KOR formed 19, 18, 17 and 12 H-bond and Van der Waal bonds, respectively, with RdRp. Furthermore, structural examination of the three proteins after binding to the lead compounds revealed that the compounds formed stable complexes. These observations suggest that the identified compounds might be beneficial in the fight against COVID-19 and are suggested for further in vitro and in vivo experimental validation.
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Shode FO, Idowu ASK, Uhomoibhi OJ, Sabiu S. Repurposing drugs and identification of inhibitors of integral proteins (spike protein and main protease) of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:6587-6602. [PMID: 33590806 PMCID: PMC7898306 DOI: 10.1080/07391102.2021.1886993] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/02/2021] [Indexed: 02/07/2023]
Abstract
The outbreak of Coronavirus infection (COVID-19) has prompted the World Health Organisation (WHO) to declare the outbreak, a Public Health Emergency of International concern. As part of the efforts to discover lead compounds for clinical use, 53 molecules were screened using molecular docking and dynamic simulations (MDS) techniques to identify potential inhibitors of SARS-CoV-2 spike protein (COVID-19 Sgp) and main protease (COVID-19 Mpro) or both. Lopinavir (LPV), nelfinavir (NEF), hydroxychloroquine (HCQ), remdesivir (RDV) and an irreversible inhibitor of SARS-CoV (N3) were used as standard drugs for COVID-19 Mpro, while zafirlukast (ZFK) and cefoperazone (CSP)) as standard drugs for COVID-19 Sgp. After 100 ns of MDS, with reference to standard drugs (N3, -52.463 Kcal/mol, NEF, -51.618 Kcal/mol, RDV, -48.780 Kcal/mol, LPV, -46.788 Kcal/mol, DRV, -33.655 Kcal/mol and HCQ, -21.065 Kcal/mol), five molecules, HCR, GRN, C3G, EGCG, and K7G were predicted to be promising inhibitors of COVID-19 Mpro with binding energies of -53.877 kcal/mol, -50.653 Kcal/mol, -48.600 kcal/mol, -47.798 kcal/mol and -46.902 kcal/mol, respectively. These lead molecules were then docked at receptor-binding domain (RBD) of COVID-19 Sgp to examine their inhibitory effects. C3G, GRN and K7G exhibited higher binding energies of -42.310 kcal/mol, -32.210 kcal/mol, -26.922 kcal/mol than the recorded values for the reference drugs (CSP, -35.509 kcal/mol, ZFK, -24.242 kcal/mol), respectively. The results of the binding energy and structural analyses from this study revealed that C3G, GRN and K7G could serve as potential dual inhibitors of COVID-19 Sgp and COVID-19 Mpro, while HCR and EGCG would be inhibitors of COVID-19 Mpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- F. O. Shode
- Faculty of Applied Sciences, Department of Biotechnology and Food Science, Durban University of Technology (DUT), Durban, South Africa
| | - A. S. K. Idowu
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP)/Genomics Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - O. J. Uhomoibhi
- Faculty of Applied Sciences, Department of Biotechnology and Food Science, Durban University of Technology (DUT), Durban, South Africa
- Department of Family Medicine, Prince Mshiyeni Memorial Hospital, Umlazi, South Africa
| | - S. Sabiu
- Faculty of Applied Sciences, Department of Biotechnology and Food Science, Durban University of Technology (DUT), Durban, South Africa
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22
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Exploring the phytochemicals of Platycodon grandiflorus for TMPRSS2 inhibition in the search for SARS-CoV-2 entry inhibitors. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2022; 34:102155. [PMID: 35702062 PMCID: PMC9181276 DOI: 10.1016/j.jksus.2022.102155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/29/2022] [Accepted: 06/02/2022] [Indexed: 11/29/2022]
Abstract
Platycodon grandiflorus (Jacq.) A. DC. (Campanulaceae) is commonly known as a balloon flower whose rhizomes have been widely utilized in traditional Chinese medicine (TCM) and in various Japanese prescriptions for the treatment of respiratory diseases, diabetes, and inflammatory disorders. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) global pandemic requires priming of the virus's spike (S) protein by cleavage of the S proteins by a multi-domain type II transmembrane serine protease, transmembrane protease serine 2 (TMPRSS2) to gain entry into the host cell. The current research aims at the screening of active phytocompounds of P. grandiflorus as potential inhibitors of cellular TMPRSS2 using molecular docking and molecular dynamics simulations approach. In silico toxicity analyses show that out of a total of 34 phytocompounds selected for the study, 12 compounds obey Lipinski’s rule of five and have favourable pharmacokinetic properties. The top three lead molecules identified here were Apigenin, Luteolin and Ferulic acid which exhibited binding energies of −7.47 kcal/mol, −6.8 kcal/mol and −6.62 kcal/mol respectively with corresponding inhibition constants of 3.33 µM, 10.39 µM and 13.95 µM. The complexes between the lead molecules and the receptor were held by hydrogen bond interactions with key residues such as Gly383, Gly385, Glu389, Lys390, Asp435, Ser436, Ser441, Cys465 and Lys467, and hydrophobic interactions with surrounding residues. The stability of the protein–ligand complexes was evaluated during 100 ns molecular dynamics (MD) simulation by analysing key geometric properties such as RMSD, RMSF, radius of gyration, total solvent accessible surface area and the number of hydrogen bonds. The binding free energies analysis using MD simulations revealed that the compounds and TMPRSS2 have favourable thermodynamic interactions, which are primarily driven by van der Waals forces. As a result, the selected bioactive phytochemicals from P. grandiflorus that target the cellular TMPRSS2 could offer an alternative treatment option against SARS-CoV-2 infections.
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23
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Panda M, Purohit P, Meher BR. Structure-based virtual screening, ADMET profiling, and molecular dynamics simulation studies on HIV-1 protease for identification of active phytocompounds as potential anti-HIV agents. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2060968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
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24
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Kehinde IA, Egbejimi A, Kaur M, Onyenaka C, Adebusuyi T, Olaleye OA. Inhibitory mechanism of Ambroxol and Bromhexine Hydrochlorides as potent blockers of molecular interaction between SARS-CoV-2 spike protein and human angiotensin-converting Enzyme-2. J Mol Graph Model 2022; 114:108201. [PMID: 35487151 PMCID: PMC9022787 DOI: 10.1016/j.jmgm.2022.108201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 12/04/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects the host cells through interaction of its spike protein with human angiotensin-converting enzyme 2 (hACE-2). High binding affinity between the viral spike protein and host cells hACE-2 receptor has been reported to enhance the viral infection. Thus, the disruption of this molecular interaction will lead to reduction in viral infectivity. This study, therefore, aimed to analyze the inhibitory potentials of two mucolytic drugs; Ambroxol hydrochlorides (AMB) and Bromhexine hydrochlorides (BHH), to serve as potent blockers of these molecular interactions and alters the binding affinity/efficiency between the proteins employing computational techniques. The study examined the effects of binding of each drug at the receptor binding domain (RBD) of the spike protein and the exopeptidase site of hACE-2 on the binding affinity (ΔGbind) and molecular interactions between the two proteins. Binding affinity revealed that the binding of the two drugs at the RBD-ACE-2 site does not alter the binding affinity and molecular interaction between the proteins. However, the binding of AMB (−56.931 kcal/mol) and BHH (−46.354 kcal/mol) at the exopeptidase site of hACE-2, significantly reduced the binding affinities between the proteins compared to the unbound, ACE-2-RBD complex (−64.856 kcal/mol). The result further showed the two compounds have good affinity at the hACE-2 site, inferring they might be potent inhibitors of hACE-2. Residue interaction networks analysis further revealed the binding of the two drugs at the exopeptidase site of hACE-2 reduced the number of interacting amino residues, subsequently leading to loss of interactions between the two proteins, with BHH showing better reduction in the molecular interaction and binding affinity than AMB. The result of the structural analyses additionally, revealed that the binding of the drugs considerably influences the dynamic of the complexes when compared to the unbound complex. The findings from this study suggest the binding of the two drugs at the exopeptidase site reduces the binding effectiveness of the proteins than their binding at the RBD site, and consequently might inhibit viral attachment and entry.
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25
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Obakachi VA, Kehinde I, Kushwaha ND, Akinpelu OI, Kushwaha B, Merugu SR, Kayamba F, Kumalo HM, Karpoormath R. Structural based investigation of novel pyrazole-thiazole Hybrids as dual CDK-1 and CDK-2 inhibitors for cancer chemotherapy. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2045016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Vincent A. Obakachi
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Idowu Kehinde
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Narva Deshwar Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Olayinka I. Akinpelu
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Babita Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Srinivas Reddy Merugu
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Francis Kayamba
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M. Kumalo
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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26
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Barreca D, Trombetta D, Smeriglio A, Mandalari G, Romeo O, Felice MR, Gattuso G, Nabavi SM. Food flavonols: Nutraceuticals with complex health benefits and functionalities. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.03.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Mejia-Gutierrez M, Vásquez-Paz BD, Fierro L, Maza JR. In Silico Repositioning of Dopamine Modulators with Possible Application to Schizophrenia: Pharmacophore Mapping, Molecular Docking and Molecular Dynamics Analysis. ACS OMEGA 2021; 6:14748-14764. [PMID: 34151057 PMCID: PMC8209794 DOI: 10.1021/acsomega.0c05984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/30/2021] [Indexed: 05/17/2023]
Abstract
We have performed theoretical calculations with 70 drugs that have been considered in 231 clinical trials as possible candidates to repurpose drugs for schizophrenia based on their interactions with the dopaminergic system. A hypothesis of shared pharmacophore features was formulated to support our calculations. To do so, we have used the crystal structure of the D2-like dopamine receptor in complex with risperidone, eticlopride, and nemonapride. Linagliptin, citalopram, flunarizine, sildenafil, minocycline, and duloxetine were the drugs that best fit with our model. Molecular docking calculations, molecular dynamics outcomes, blood-brain barrier penetration, and human intestinal absorption were studied and compared with the results. From the six drugs selected in the shared pharmacophore features input, flunarizine showed the best docking score with D2, D3, and D4 dopamine receptors and had high stability during molecular dynamics simulations. Flunarizine is a frequently used medication to treat migraines and vertigo. However, its antipsychotic properties have been previously hypothesized, particularly because of its possible ability to block the D2 dopamine receptors.
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Affiliation(s)
- Melissa Mejia-Gutierrez
- Faculty
of Natural and Exact Sciences, Department of Chemistry, and School
of Basic Sciences, Department of Physiological Sciences, Faculty of
Health, Laboratory and Research group - Pharmacology Univalle Group, Universidad del Valle, 25360 Cali, Colombia
| | - Bryan D. Vásquez-Paz
- Faculty
of Natural and Exact Sciences, Department of Chemistry, Laboratory
and Research group - Pharmacology Univalle Group, Universidad del Valle, 25360 Cali, Colombia
| | - Leonardo Fierro
- Faculty
of Health, School of Basic Sciences, Department of Physiological Sciencesh,
Laboratory and Research group - Pharmacology Univalle Group, Universidad del Valle, 25360 Cali, Colombia
| | - Julio R. Maza
- Faculty
of Basic Sciences, Department of Chemistry, Laboratory and Research
group - Organic Chemistry and Biomedical Group, Universidad del Atlántico, 081001 Puerto Colombia, Colombia
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28
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Obakachi VA, Kushwaha ND, Kushwaha B, Mahlalela MC, Shinde SR, Kehinde I, Karpoormath R. Design and synthesis of pyrazolone-based compounds as potent blockers of SARS-CoV-2 viral entry into the host cells. J Mol Struct 2021; 1241:130665. [PMID: 34007088 PMCID: PMC8118388 DOI: 10.1016/j.molstruc.2021.130665] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 05/09/2021] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2 are enveloped positive-stranded RNA viruses that replicate in the cytoplasm. It relies on the fusion of their envelope with the host cell membrane to deliver their nucleocapsid into the host cell. The spike glycoprotein (S) mediates virus entry into cells via the human Angiotensin-converting enzyme 2 (hACE2) protein located on many cell types and tissues' outer surface. This study, therefore, aimed to design and synthesize novel pyrazolone-based compounds as potential inhibitors that would interrupt the interaction between the viral spike protein and the host cell receptor to prevent SARS-CoV 2 entrance into the cell. A series of pyrazolone compounds as potential SARS-CoV-2 inhibitors were designed and synthesized. Employing computational techniques, the inhibitory potentials of the designed compounds against both spike protein and hACE2 were evaluated. Results of the binding free energy from the in-silico analysis, showed that three compounds (7i, 7k and 8f) and six compounds (7b, 7h, 7k, 8d, 8g, and 8h) showed higher and better binding high affinity to SARS-CoV-2 Sgp and hACE-2, respectively compared to the standard drugs cefoperazone (CFZ) and MLN-4760. Furthermore, the outcome of the structural analysis of the two proteins upon binding of the inhibitors showed that the two proteins (SARS-CoV-2 Sgp and hACE-2) were stable, and the structural integrity of the proteins was not compromised. This study suggests pyrazolone-based compounds might be potent blockers of the viral entry into the host cells.
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Affiliation(s)
- Vincent A Obakachi
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Narva Deshwar Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Babita Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Mavela Cleopus Mahlalela
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Suraj Raosaheb Shinde
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Idowu Kehinde
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
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29
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Nag A, Banerjee R, Chowdhury RR, Krishnapura Venkatesh C. Phytochemicals as potential drug candidates for targeting SARS CoV 2 proteins, an in silico study. Virusdisease 2021; 32:98-107. [PMID: 33842673 PMCID: PMC8020371 DOI: 10.1007/s13337-021-00654-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/18/2021] [Indexed: 01/18/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a member of the family Coronaviridae, and the world is currently witnessing a global pandemic outbreak of this viral disease called COVID-19. With no specific treatment regime, this disease is now a serious threat to humanity and claiming several lives daily. In this work, we selected 24 phytochemicals for an in silico docking study as candidate drugs, targeting four essential proteins of SARS-CoV-2 namely Spike glycoprotein (PDB id 5WRG), Nsp9 RNA binding protein (PDB id 6W4B), Main Protease (PDB id 6Y84), and RNA dependent RNA Polymerase (PDB id 6M71). After statistical validation, the results indicated that a total of 11 phytochemicals divided into two clusters might be used as potential drug candidates against SARS-CoV-2.
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Affiliation(s)
- Anish Nag
- Department of Life Sciences, CHRIST (Deemed to be University), Central Campus, Bangalore, 560029 India
| | - Ritesh Banerjee
- Department of Botany, University of Calcutta, Kolkata, 700019 India
| | - Rajshree Roy Chowdhury
- Department of Life Sciences, CHRIST (Deemed to be University), Central Campus, Bangalore, 560029 India
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30
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Eche S, Kumar A, Sonela N, Gordon ML. Acquired HIV-1 Protease Conformational Flexibility Associated with Lopinavir Failure May Shape the Outcome of Darunavir Therapy after Antiretroviral Therapy Switch. Biomolecules 2021; 11:489. [PMID: 33805099 PMCID: PMC8064090 DOI: 10.3390/biom11040489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding the underlying molecular interaction during a therapy switch from lopinavir (LPV) to darunavir (DRV) is essential to achieve long-term virological suppression. We investigated the kinetic and structural characteristics of multidrug-resistant South African HIV-1 subtype C protease (HIV-1 PR) during therapy switch from LPV to DRV using enzyme activity and inhibition assay, fluorescence spectroscopy, and molecular dynamic simulation. The HIV-1 protease variants were from clinical isolates with a combination of drug resistance mutations; MUT-1 (M46I, I54V, V82A, and L10F), MUT-2 (M46I, I54V, L76V, V82A, L10F, and L33F), and MUT-3 (M46I, I54V, L76V, V82A, L90M, and F53L). Enzyme kinetics analysis shows an association between increased relative resistance to LPV and DRV with the progressive decrease in the mutant HIV-1 PR variants' catalytic efficiency. A direct relationship between high-level resistance to LPV and intermediate resistance to DRV with intrinsic changes in the three-dimensional structure of the mutant HIV-1 PR as a function of the multidrug-resistance mutation was observed. In silico analysis attributed these structural adjustments to the multidrug-resistance mutations affecting the LPV and DRV binding landscape. Though DRV showed superiority to LPV, as a lower concentration was needed to inhibit the HIV-1 PR variants, the inherent structural changes resulting from mutations selected during LPV therapy may dynamically shape the DRV treatment outcome after the therapy switch.
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Affiliation(s)
- Simeon Eche
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Ajit Kumar
- Discipline of Microbiology, School of Life Sciences, University of KwaZulu-Natal (Westville Campus), Durban 4000, South Africa;
| | - Nelson Sonela
- School of Medicine, Physical and Natural Sciences, University of Rome Tor Vegata, 1-00133 Rome, Italy;
- Chantal Biya International Reference Center for Research on the Management and Prevention of HIV/AIDS (CIRCB), Yaoundé P.O. Box 3077, Cameroon
| | - Michelle L. Gordon
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa;
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31
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Modulatory influences of antiviral bioactive compounds on cell viability, mRNA and protein expression of cytochrome P450 3A4 and P-glycoprotein in HepG2 and HEK293 cells. Bioorg Chem 2020; 107:104573. [PMID: 33387731 DOI: 10.1016/j.bioorg.2020.104573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/04/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022]
Abstract
The induction of cytochrome P450 3A4 (CYP3A4) and P-glycoprotein (ABCB1) influence drug plasma, and eventually decreases the drugs' therapeutic effects. The effects of Plant-derived compounds (PCs) on drug-metabolising proteins are largely unknown. This study investigated the cytotoxicity, cell viability profiles and regulatory influences of four PCs (epigallocatechin gallate (EGCG), kaempferol-7-glucoside (K7G), luteolin (LUT) and ellagic acid (EGA)) on the mRNA and protein expressions of CYP3A4 and ABCB1 in HepG2 and HEK293 cells. After treatment with the PCs (0-400 µM) for 24 h, 80% (IC20) and 50% (IC50) cell viability were determined. The PCs were not toxic to HepG2 (ATP levels increased at IC20, insignificant change in LDH (lactate dehydrogenase) with the exception of LUT, and ABCB1 protein expressions decreased. The PCs decreased CYP3A4 at IC20 (except LUT), EGCG and K7G at IC20 decreased mRNA expression. For HEK293 cells, no significant change in ATP, except for EGCG IC20 and K7G IC50 which decreased and increased, respectively. LDH decreased at IC20, but LUT IC50 significant increase LDH. ABCB1 protein expression increased at both IC20 and IC50, but LUT and EGA at IC50 decreased mRNA expression. The PCs at IC20, and IC50 of LUT, K7G and of EGCG may enhance drug bioavailability.
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32
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Kehinde I, Ramharack P, Nlooto M, Gordon M. Molecular dynamic mechanism(s) of inhibition of bioactive antiviral phytochemical compounds targeting cytochrome P450 3A4 and P-glycoprotein. J Biomol Struct Dyn 2020; 40:1037-1047. [PMID: 33063648 DOI: 10.1080/07391102.2020.1821780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
P-glycoprotein (ABCB1) and cytochrome P450 3A4 (CYP3A4) metabolize almost all known human immunodeficiency virus' protease inhibitor drugs (PIs). Over induction of these proteins' activities has been linked to rapid metabolism of PIs which are then pumped out of the circulatory system, eventually leading to drug-resistance in HIV-positive patients. This study aims to determine, with the use of computational tools, the inhibitory potential of four phytochemical compounds (PCs) (epigallocatechin gallate (EGCG), kaempferol-7-glucoside (K7G), luteolin (LUT) and ellagic acid (EGA)) in inhibiting the activities of these drug-metabolizing proteins. The comparative analysis of the MM/GBSA results revealed that the binding affinity (ΔGbind) of EGCG and K7G for CYP3A4 and ABCB1 are higher than LUT and EGA and fall between the ΔGbind of the inhibitors of CYP3A4 and ABCB1 (Ritonavir (strong inhibitor) and Lopinavir (moderate inhibitor)). The structural analysis (RMSD, RMSF, RoG and protein-ligand interaction plots) also confirmed that EGCG and K7G showed similar inhibitory activities with the inhibitors. The study has shown that EGCG and K7G have inhibitory activities against the two proteins and assumes they could decrease intracellular efflux of PIs, consequently increasing the optimal concentration of PIs in the systemic circulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Idowu Kehinde
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP)/Genomics Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Pritika Ramharack
- Discipline of Pharmacy, School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Manimbulu Nlooto
- Discipline of Pharmacy, School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Department of Pharmaceutical Sciences, Healthcare Sciences, University of Limpopo, Durban, South Africa
| | - Michelle Gordon
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP)/Genomics Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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33
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Wang L, Song J, Liu A, Xiao B, Li S, Wen Z, Lu Y, Du G. Research Progress of the Antiviral Bioactivities of Natural Flavonoids. NATURAL PRODUCTS AND BIOPROSPECTING 2020; 10:271-283. [PMID: 32948973 PMCID: PMC7500501 DOI: 10.1007/s13659-020-00257-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/24/2020] [Indexed: 05/05/2023]
Abstract
Flavonoids are now considered as an indispensable component in a variety of nutraceutical and pharmaceutical applications. Most recent researches have focused on the health aspects of flavonoids for humans. Especially, different flavonoids have been investigated for their potential antiviral activities, and several natural flavonoids exhibited significant antiviral properties both in vitro and in vivo. This review provides a survey of the literature regarding the evidence for antiviral bioactivities of natural flavonoids, highlights the cellular and molecular mechanisms of natural flavonoids on viruses, and presents the details of most reported flavonoids. Meanwhile, future perspectives on therapeutic applications of flavonoids against viral infections were discussed.
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Affiliation(s)
- Lin Wang
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Junke Song
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Ailin Liu
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Bin Xiao
- Laboratory of Clinical Pharmacy, Ordos Central Hospital, Ordos School of Clinical Medicine, Inner Mongolia Medical University, Ordos, 017000, China
| | - Sha Li
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Zhang Wen
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Yang Lu
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Guanhua Du
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China.
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34
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Oso BJ, Adeoye AO, Olaoye IF. Pharmacoinformatics and hypothetical studies on allicin, curcumin, and gingerol as potential candidates against COVID-19-associated proteases. J Biomol Struct Dyn 2020; 40:389-400. [DOI: 10.1080/07391102.2020.1813630] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Babatunde Joseph Oso
- Department of Biochemistry, McPherson University, Seriki Sotayo, Ogun State, Nigeria
| | | | - Ige Francis Olaoye
- Department of Biochemistry, McPherson University, Seriki Sotayo, Ogun State, Nigeria
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Nag A, Chowdhury RR. Piperine, an alkaloid of black pepper seeds can effectively inhibit the antiviral enzymes of Dengue and Ebola viruses, an in silico molecular docking study. Virusdisease 2020; 31:308-315. [PMID: 32904842 PMCID: PMC7458978 DOI: 10.1007/s13337-020-00619-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022] Open
Abstract
Ebola and Dengue are the critical diseases caused by RNA viruses, especially in the tropical parts of the globe, including Asia and Africa, and no prominent therapeutic options are available so far. Here, an effort was made to evaluate the efficacy of black pepper (Piper nigrum L.) alkaloid Piperine as a potential drug through computational docking simulation. Eight structurally essential proteins of Dengue and Ebola virus were selected as in silico docking targets for Piperine. Absorption, Distribution, Metabolism, and Excretion profile showed that Piperine was safe and possessed significant drug-like properties. Molecular dynamic simulation and binding free energy calculation showed that Piperine could inhibit Methyltransferase (PDB id 1L9K) of Dengue and VP35 Interferon Inhibitory Domain (PDB id 3FKE) of Ebola virus in comparison with the commercial antiviral Ribavirin. Furthermore, statistical analysis based on multivariate and clustering approaches revealed that Piperine had more affinity towards viral proteins than that of Ribavirin.
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Affiliation(s)
- Anish Nag
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore, India
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Ninfali P, Antonelli A, Magnani M, Scarpa ES. Antiviral Properties of Flavonoids and Delivery Strategies. Nutrients 2020; 12:nu12092534. [PMID: 32825564 PMCID: PMC7551920 DOI: 10.3390/nu12092534] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022] Open
Abstract
This review summarizes the latest advancements in phytochemicals as functional antiviral agents. We focused on flavonoids, like apigenin, vitexin, quercetin, rutin and naringenin, which have shown a wide range of biological effects including antiviral activities. The molecular mechanisms of their antiviral effects mainly consist in the inhibition of viral neuraminidase, proteases and DNA/RNA polymerases, as well as in the modification of various viral proteins. Mixtures of different flavonoids or combination of flavonoids with antiviral synthetic drugs provide an enhancement of their antiviral effects. Recent strategies in drug delivery significantly contribute to overcoming the low bioavailability of flavonoids. Frequent viral infections worldwide have led to the need for new effective antiviral agents, which can be identified among the various phytochemicals. In this light, screening the antiviral activities of a cocktail of flavonoids would be advantageous in order to prevent viral infections and improve current antiviral therapies.
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Affiliation(s)
| | | | - Mauro Magnani
- Correspondence: (M.M.); (E.S.S.); Tel.: +39-0722-305-211 (M.M.); +39-0722-305-252 (E.S.S.)
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