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Shafiq N, Shakoor B, Yaqoob N, Parveen S, Brogi S, Mohammad Salamatullah A, Rashid M, Bourhia M. A virtual insight into mushroom secondary metabolites: 3D-QSAR, docking, pharmacophore-based analysis and molecular modeling to analyze their anti-breast cancer potential. J Biomol Struct Dyn 2024:1-22. [PMID: 38299565 DOI: 10.1080/07391102.2024.2304137] [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: 08/04/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024]
Abstract
Breast cancer is a major issue of investigation in drug discovery due to its rising frequency and global dominance. Plants are significant natural sources for the development of novel medications and therapies. Medicinal mushrooms have many biological response modifiers and are used for the treatment of many physical illnesses. In this research, a database of 89 macro-molecules with anti-breast cancer activity, which were previously isolated from the mushrooms in literature, has been selected for the three-dimensional quantitative structure-activity relationships (3D-QSAR) studies. The 3D-QSAR model was necessarily used in Pharmacopoeia virtual evaluation of the database to develop novel MCF-7 inhibitors. With the known potential targets of breast cancer, the docking studies were achieved. Using molecular dynamics simulations, the targets' stability with the best-chosen natural product molecule was found. Furthermore, the absorption, distribution, metabolism, excretion, and toxicity of three compounds, resulting after the docking study, were predicted. The compound C1 (Pseudonocardian A) showed the features of effective compounds because it has bioavailability from different coral species and is toxicity-free for the prevention of many dermatological illnesses. C1 is chemically active and possesses charge transfer inside the monomer, as seen by the band gaps of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) electrons. The reactivity descriptors ionization potential, electron affinity, chemical potential (μ), hardness (η), softness (S), electronegativity (χ), and electrophilicity index (ω) have been estimated using the energies of frontier molecular orbitals (HOMO-LUMO). Additionally, molecular electrostatic potential maps were created to show that the C1 is reactive.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nusrat Shafiq
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Bushra Shakoor
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Nazia Yaqoob
- Green Chemistry Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Shagufta Parveen
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Simone Brogi
- Department of Pharmacy, Pisa University, Pisa, Italy
| | - Ahmad Mohammad Salamatullah
- Department of Food Science & Nutrition, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Maryam Rashid
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
- Laboratory of Chemistry-Biochemistry, Environment, Nutrition, and Health, Faculty of Medicine and Pharmacy, University Hassan II, Casablanca, Morocco
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Enzyme Inhibitory Activities of Extracts and Carpachromene from the Stem of Ficus benghalensis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7053655. [PMID: 36582600 PMCID: PMC9794428 DOI: 10.1155/2022/7053655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Ficus benghalensis is one of the potential medicinal plants which is used locally for the treatment of various ailments such as diabetes, antiasthmatic, and wound healing. To provide a scientific background to these folklores, the current study was designed to evaluate the extract and isolated compound against various enzymes such as ureases, tyrosinase, and phosphodiesterase. The methanolic extract and carpachromene demonstrated a significant urease inhibition effect with maximum percent inhibition of 72.09 and 92.87%, respectively. Regarding the tyrosinase inhibition, the percent antagonist effect of carpachromene and the methanolic extract was 84.80 and 70.98%, respectively. The phosphodiesterase was also significantly antagonized by crude extract and carpachromene with a maximum percent inhibition of 82.98% and 89.54%, respectively. The docking study demonstrated that the carpachromene fits well into the active site of all three enzymes with significant interactions. Carpachromene might possess the potential to inhibit all three enzymes and can effectively treat different diseases associated with the hyperactivity of these enzymes. In conclusion, the crude extract and carpachromene exhibit significant urease, tyrosinase, and phosphodiesterase inhibitory activity which might be used against various diseases. In conclusion, the crude extract and carpachromene exhibit significant urease, tyrosinase, and phosphodiesterase inhibitory activity which might be used against diabetes and bronchoconstriction. Further, the current study provides scientific backup to the folklore (antidiabetic and antiasthmatic) of Ficus benghalensis.
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Green Nano-Biotechnology: A New Sustainable Paradigm to Control Dengue Infection. Bioinorg Chem Appl 2022; 2022:3994340. [PMID: 35979184 PMCID: PMC9377959 DOI: 10.1155/2022/3994340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/09/2022] [Indexed: 12/17/2022] Open
Abstract
Dengue is a growing mosquito-borne viral disease prevalent in 128 countries, while 3.9 billion people are at high risk of acquiring the infection. With no specific treatment available, the only way to mitigate the risk of dengue infection is through controlling of vector, i.e., Aedes aegypti. Nanotechnology-based prevention strategies like biopesticides with nanoformulation are now getting popular for preventing dengue fever. Metal nanoparticles (NPs) synthesized by an eco-friendly process, through extracts of medicinal plants have indicated potential anti-dengue applications. Green synthesis of metal NPs is simple, cost-effective, and devoid of hazardous wastes. The recent progress in the phyto-synthesized multifunctional metal NPs for anti-dengue applications has encouraged us to review the available literature and mechanistic aspects of the dengue control using green-synthesized NPs. Furthermore, the molecular bases of the viral inhibition through NPs and the nontarget impacts or hazards with reference to the environmental integrity are discussed in depth. Till date, major focus has been on green synthesis of silver and gold NPs, which need further extension to other innovative composite nanomaterials. Further detailed mechanistic studies are required to critically evaluate the mechanistic insights during the synthesis of the biogenic NPs. Likewise, detailed analysis of the toxicological aspects of NPs and their long-term impact in the environment should be critically assessed.
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Yilmaz H, Gultekin Subasi B, Celebioglu HU, Ozdal T, Capanoglu E. Chemistry of Protein-Phenolic Interactions Toward the Microbiota and Microbial Infections. Front Nutr 2022; 9:914118. [PMID: 35845785 PMCID: PMC9284217 DOI: 10.3389/fnut.2022.914118] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/25/2022] [Indexed: 12/12/2022] Open
Abstract
Along with health concerns, interest in plants as food and bioactive phytochemical sources has been increased in the last few decades. Phytochemicals as secondary plant metabolites have been the subject of many studies in different fields. Breakthrough for research interest on this topic is re-juvenilized with rising relevance in this global pandemics' era. The recent COVID-19 pandemic attracted the attention of people to viral infections and molecular mechanisms behind these infections. Thus, the core of the present review is the interaction of plant phytochemicals with proteins as these interactions can affect the functions of co-existing proteins, especially focusing on microbial proteins. To the best of our knowledge, there is no work covering the protein-phenolic interactions based on their effects on microbiota and microbial infections. The present review collects and defines the recent data, representing the interactions of phenolic compounds -primarily flavonoids and phenolic acids- with various proteins and explores how these molecular-level interactions account for the human health directly and/or indirectly, such as increased antioxidant properties and antimicrobial capabilities. Furthermore, it provides an insight about the further biological activities of interacted protein-phenolic structure from an antiviral activity perspective. The research on the protein-phenolic interaction mechanisms is of great value for guiding how to take advantage of synergistic effects of proteins and polyphenolics for future medical and nutritive approaches and related technologies.
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Affiliation(s)
- Hilal Yilmaz
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey
| | - Busra Gultekin Subasi
- Division of Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
- Hafik Kamer Ornek MYO, Sivas Cumhuriyet University, Sivas, Turkey
| | | | - Tugba Ozdal
- Department of Food Engineering, Faculty of Engineering and Natural Sciences, Istanbul Okan University, Istanbul, Turkey
| | - Esra Capanoglu
- Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering, Istanbul Technical University, Istanbul, Turkey
- *Correspondence: Esra Capanoglu
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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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Lim SYM, Chieng JY, Pan Y. Recent insights on anti-dengue virus (DENV) medicinal plants: review on in vitro, in vivo and in silico discoveries. ALL LIFE 2020. [DOI: 10.1080/26895293.2020.1856192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Sharoen Yu Ming Lim
- Division of Biomedical Science, School of Pharmacy, University of Nottingham Malaysia, Semenyih, Malaysia
| | | | - Yan Pan
- Division of Biomedical Science, School of Pharmacy, University of Nottingham Malaysia, Semenyih, Malaysia
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Antiviral activity of astragaloside II, astragaloside III and astragaloside IV compounds against dengue virus: Computational docking and in vitro studies. Microb Pathog 2020; 152:104563. [PMID: 33098932 DOI: 10.1016/j.micpath.2020.104563] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/26/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022]
Abstract
This study was aimed to identify the phytocompounds possessing anti-dengue virus activity using in silico and in vitro approaches. A total of 7000 phytocompounds were virtually screened against protein targets (envelope, NS2b/NS3, and NS5) of dengue virus using iGEMDOCK and individually docked using Maestro 10.7 module of Schrödinger software. In vitro cytotoxicity and antiviral studies were performed using vero cell line. Finally, three phytocompounds namely astragaloside II, astragaloside III, and astragaloside IV were screened based on their highest binding energy values against protein targets. Astragaloside III exhibited the highest interaction energy value of -8.718 kcal/mol and -8.447 kcal/mol against envelope, and NS2b/NS3 targets, respectively. Astragaloside IV exhibited -7.244 kcal/mol against SAM site, and -9.179 kcal/mol against RNA cap site of NS5 targets. In silico ADMET analysis revealed that astragaloside II, III, and IV were non-mutagenic and non-carcinogenic in nature and these compounds were also non-toxic to vero cells upto 1000 μg/mL. Against dengue virus serotype 3, astragaloside II exhibited substantial antiviral activity at the concentration of 1.56 μg/mL followed by astragaloside III at 6.25 μg/mL and astragaloside IV at 12.5 μg/mL. Also, against dengue serotype 1, astragaloside II showed the maximum antiviral activity at 1.56 μg/mL followed by astragaloside III and IV at 3.125 μg/mL. This study concludes that astragaloside II, III, and IV compounds had potential in vitro anti-dengue virus activity.
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Yan F, Liu G, Chen T, Fu X, Niu MM. Structure-Based Virtual Screening and Biological Evaluation of Peptide Inhibitors for Polo-Box Domain. Molecules 2019; 25:E107. [PMID: 31892137 PMCID: PMC6982974 DOI: 10.3390/molecules25010107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/19/2019] [Accepted: 12/24/2019] [Indexed: 11/25/2022] Open
Abstract
The polo-box domain of polo-like kinase 1 (PLK1-PBD) is proved to have crucial roles in cell proliferation. Designing PLK1-PBD inhibitors is challenging due to their poor cellular penetration. In this study, we applied a virtual screening workflow based on a combination of structure-based pharmacophore modeling with molecular docking screening techniques, so as to discover potent PLK1-PBD peptide inhibitors. The resulting 9 virtual screening peptides showed affinities for PLK1-PBD in a competitive binding assay. In particular, peptide 5 exhibited an approximately 100-fold increase in inhibitory activity (IC50 = 70 nM), as compared with the control poloboxtide. Moreover, cell cycle experiments indicated that peptide 5 effectively inhibited the expression of p-Cdc25C and cell cycle regulatory proteins by affecting the function of PLK1-PBD, thereby inducing mitotic arrest at the G2/M phase. Overall, peptide 5 can serve as a potent lead for further investigation as PLK1-PBD inhibitors.
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Affiliation(s)
| | | | | | | | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (F.Y.); (G.L.); (T.C.); (X.F.)
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Zhou Y, Yan F, Huo X, Niu MM. Discovery of a Potent PLK1-PBD Small-Molecule Inhibitor as an Anticancer Drug Candidate through Structure-Based Design. Molecules 2019; 24:E4351. [PMID: 31795214 PMCID: PMC6930574 DOI: 10.3390/molecules24234351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/29/2022] Open
Abstract
Polo-box domain of polo-like kinase 1 (PLK1-PBD) has a pivotal role in cell proliferation and could be implicated as a potential anticancer target. Although some small-molecule inhibitors have been developed, their clinical application has been restricted by the poor selectivity. Therefore, there is an urgent need to develop effective PLK1-PBD inhibitors. Herein, we have developed a virtual screening protocol to find PLK1-PBD inhibitors by using combination of structure-based pharmacophore modeling and molecular docking. This protocol was successfully applied to screen PLK1-PBD inhibitors from specs database. MTT assay indicated that five screened hits suppressed the growth of HeLa cells. Particularly, hit-5, as a selective PLK1 inhibitor targeting PLK1-PBD, significantly inhibited the progression of HeLa cells-derived xenograft, with no obvious side effects. This work demonstrates that hit-5 may be a potential anticancer agent.
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Affiliation(s)
- Yunjiang Zhou
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (Y.Z.); (F.Y.); (X.H.)
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Fang Yan
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (Y.Z.); (F.Y.); (X.H.)
| | - Xiangyun Huo
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (Y.Z.); (F.Y.); (X.H.)
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (Y.Z.); (F.Y.); (X.H.)
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Zhou Y, Tang S, Chen T, Niu MM. Structure-Based Pharmacophore Modeling, Virtual Screening, Molecular Docking and Biological Evaluation for Identification of Potential Poly (ADP-Ribose) Polymerase-1 (PARP-1) Inhibitors. Molecules 2019; 24:E4258. [PMID: 31766720 PMCID: PMC6930522 DOI: 10.3390/molecules24234258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/13/2019] [Accepted: 11/20/2019] [Indexed: 01/28/2023] Open
Abstract
Poly (ADP-ribose) polymerase-1 (PARP-1) plays critical roles in many biological processes and is considered as a potential target for anticancer therapy. Although some PARP-1 inhibitors have been reported, their clinical application in cancer therapy is limited by some shortcomings such as weak affinity, low selectivity and adverse side effects. To identify highly potent and selective PARP-1 inhibitors, an integrated protocol that combines pharmacophore mapping, virtual screening and molecular docking was constructed. It was then used as a screening query to identify potent leads with unknown scaffolds from an in-house database. Finally, four retrieved compounds were selected for biological evaluation. Biological testing indicated that the four compounds showed strong inhibitory activities on the PARP-1 (IC50 < 0.2 μM). MTT assay confirmed that compounds 1-4 inhibited the growth of human lung cancer A549 cells in a dose-dependent manner. The obtained compounds from this study may be potential leads for PARP-1 inhibition in the treatment of cancer.
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Affiliation(s)
| | | | | | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China; (Y.Z.); (S.T.); (T.C.)
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Zhou Y, Di B, Niu MM. Structure-Based Pharmacophore Design and Virtual Screening for Novel Tubulin Inhibitors with Potential Anticancer Activity. Molecules 2019; 24:E3181. [PMID: 31480625 PMCID: PMC6749218 DOI: 10.3390/molecules24173181] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 12/24/2022] Open
Abstract
Tubulin inhibitors have been considered as potential drugs for cancer therapy. However, their drug resistance and serious side-effects are the main reasons for clinical treatment failure. Therefore, there is still an urgent need to develop effective therapeutic drugs. Herein, a structure-based pharmacophore model was developed based on the co-crystallized structures of the tubulin with a high resolution. The model including one hydrogen-bond acceptor feature, two aromatic features, and one hydrophobic feature was further validated using the Gunner-Henry score method. Virtual screening was performed by an integrated protocol that combines drug-likeness analysis, pharmacophore mapping, and molecular docking approaches. Finally, five hits were selected for biological evaluation. The results indicated that all these hits at the concentration of 40 μM showed an inhibition of more than 50% against five human tumor cells (MCF-7, U87MG, HCT-116, MDA-MB-231, and HepG2). Particularly, hit 1 effectively inhibited the proliferation of these tumor cells, with inhibition rates of more than 80%. The results of tubulin polymerization and colchicine-site competition assays suggested that hit 1 significantly inhibited tubulin polymerization by binding to the colchicine site. Thus, hit 1 could be used as a potential chemotherapeutic agent for cancer treatment. This work also demonstrated the potential of our screening protocol to identify biologically active compounds.
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Affiliation(s)
- Yunjiang Zhou
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Bin Di
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China.
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China.
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Adnan A, Allaudin ZN, Hani H, Loh HS, Khoo TJ, Ting KN, Abdullah R. Virucidal activity of Garcinia parvifolia leaf extracts in animal cell culture. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 19:169. [PMID: 31291936 PMCID: PMC6617885 DOI: 10.1186/s12906-019-2586-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/30/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND Garcinia species contain bioactive compounds such as flavonoids, xanthones, triterpernoids, and benzophenones with antibacterial, antifungal, anti-inflammatory, and antioxidant activities. In addition, many of these compounds show interesting biological properties such as anti-human immunodeficiency virus activity. Garcinia parvifolia is used in traditional medicine. Currently, the antiviral activity of G. parvifolia is not known. METHODS This study was conducted to determine the effects of ethyl acetate (45 L Ea), ethanol (45 L Et), and hexane (45 L H) leaf extracts of G. parvifolia on the infectivity of pseudorabies virus (PrV) in Vero cells. The antiviral effects of the extracts were determined by cytopathic effect (CPE), inhibition, attachment, and virucidal assays. RESULTS The 50% cytotoxicity concentration (CC50) values obtained were 237.5, 555.0, and < 1.25 μg/mL for 45 L Ea, 45 L Et, and 45 L H, respectively. The 45 L Ea showed the greatest viral inhibition potency of 75% at 125 μg/mL. Both 45 L Ea and 45 l Et caused 100% residual viral inhibition at 250 μg/mL. The selectivity index values for 45 L Ea, 45 L Et, and 45 L H were 2.65, 1.75, and 0.10 showing that 45 L Ea had the greatest antiviral activity among the three extracts. CONCLUSION This study showed that ethyl acetate is the best solvent to be used to obtain extract from G. parvifolia leaves with potent antiviral activities.
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Affiliation(s)
- Aziera Adnan
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Zeenathul Nazariah Allaudin
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Homayoun Hani
- Department of Cell Biology and Physiology, School of Medicine, University North Carolina, Chapel Hill, NC 27599 USA
| | - Hwei-San Loh
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Malaysia
| | - Teng-Jin Khoo
- School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Malaysia
| | - Kang Nee Ting
- School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Malaysia
| | - Rasedee Abdullah
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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Tahir Ul Qamar M, Maryam A, Muneer I, Xing F, Ashfaq UA, Khan FA, Anwar F, Geesi MH, Khalid RR, Rauf SA, Siddiqi AR. Computational screening of medicinal plant phytochemicals to discover potent pan-serotype inhibitors against dengue virus. Sci Rep 2019; 9:1433. [PMID: 30723263 PMCID: PMC6363786 DOI: 10.1038/s41598-018-38450-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 12/19/2018] [Indexed: 02/07/2023] Open
Abstract
Emergence of Dengue as one of the deadliest viral diseases prompts the need for development of effective therapeutic agents. Dengue virus (DV) exists in four different serotypes and infection caused by one serotype predisposes its host to another DV serotype heterotypic re-infection. We undertook virtual ligand screening (VLS) to filter compounds against DV that may inhibit inclusively all of its serotypes. Conserved non-structural DV protein targets such as NS1, NS3/NS2B and NS5, which play crucial role in viral replication, infection cycle and host interaction, were selected for screening of vital antiviral drug leads. A dataset of plant based natural antiviral derivatives was developed. Molecular docking was performed to estimate the spatial affinity of target compounds for the active sites of DV’s NS1, NS3/NS2B and NS5 proteins. The drug likeliness of the screened compounds was followed by ADMET analysis whereas the binding behaviors were further elucidated through molecular dynamics (MD) simulation experiments. VLS screened three potential compounds including Canthin-6-one 9-O-beta-glucopyranoside, Kushenol W and Kushenol K which exhibited optimal binding with all the three conserved DV proteins. This study brings forth novel scaffolds against DV serotypes to serve as lead molecules for further optimization and drug development against all DV serotypes with equal effect against multiple disease causing DV proteins. We therefore anticipate that the insights given in the current study could be regarded valuable towards exploration and development of a broad-spectrum natural anti-dengue therapy.
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Affiliation(s)
| | - Arooma Maryam
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Iqra Muneer
- School of Life Sciences, University of Science and Technology of China, Hefei, P.R. China
| | - Feng Xing
- College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Faheem Ahmed Khan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education China, Huazhong Agricultural University, Wuhan, P.R. China
| | - Farooq Anwar
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan
| | - Mohammed H Geesi
- Department of Chemistry, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia.
| | - Rana Rehan Khalid
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sadaf Abdul Rauf
- Department of Computer Science, Fatima Jinnah Women University, Rawalpindi, Pakistan
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan.
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Durdagi S, Tahir Ul Qamar M, Salmas RE, Tariq Q, Anwar F, Ashfaq UA. Investigating the molecular mechanism of staphylococcal DNA gyrase inhibitors: A combined ligand-based and structure-based resources pipeline. J Mol Graph Model 2018; 85:122-129. [PMID: 30176384 DOI: 10.1016/j.jmgm.2018.07.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 01/12/2023]
Abstract
Appropriate therapeutic solutions against Staphylococcal infections are currently limited. To work out the complex task of challenging drug resistance in Staphylococcus aureus, new compounds with novel modes of action are required. In this study, we performed target-driven virtual screening to filter exhaustive phytochemical libraries that can inhibit the activity of S. aureus DNA Gyrase B (Gyr B). Three top-ranked hit molecules (Mangostenone E, Candenatenin A and 2,4,4'-trihydroxydihydrochalcone) were identified from comprehensive molecular docking studies based on their strong spatial affinity with key catalytic residues of the binding pocket of DNA GyrB, especially with the well-known crucial residue Asp81. Molecular dynamics (MD) simulations were performed for these identified hit molecules for better understanding of their dynamical and structural profiles throughout the MD simulations. These compounds can be explored as future lead optimization molecules to discover a new class of antibiotics against resistant Staphylococcus aureus strains.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey.
| | | | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Quratulain Tariq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Farooq Anwar
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan.
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15
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Sarwar MW, Riaz A, Dilshad SMR, Al-Qahtani A, Nawaz-Ul-Rehman MS, Mubin M. Structure activity relationship (SAR) and quantitative structure activity relationship (QSAR) studies showed plant flavonoids as potential inhibitors of dengue NS2B-NS3 protease. BMC STRUCTURAL BIOLOGY 2018; 18:6. [PMID: 29673347 PMCID: PMC5909242 DOI: 10.1186/s12900-018-0084-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 04/11/2018] [Indexed: 12/29/2022]
Abstract
Background Due to dengue virus disease, half of the world population is at severe health risk. Viral encoded NS2B-NS3 protease complex causes cleavage in the nonstructural region of the viral polyprotein. The cleavage is essentially required for fully functional viral protein. It has already been reported that if function of NS2B-NS3 complex is disrupted, viral replication is inhibited. Therefore, the NS2B-NS3 is a well-characterized target for designing antiviral drug. Results In this study docking analysis was performed with active site of dengue NS2B-NS3 protein with selected plant flavonoids. More than 100 flavonoids were used for docking analysis. On the basis of docking results 10 flavonoids might be considered as the best inhibitors of NS2B-NS3 protein. The interaction studies showed resilient interactions between ligand and receptor atoms. Furthermore, QSAR and SAR studies were conducted on the basis of NS2B-NS3 protease complex docking results. The value of correlation coefficient (r) 0.95 shows that there was a good correlation between flavonoid structures and selected properties. Conclusion We hereby suggest that plant flavonoids could be used as potent inhibitors of dengue NS2B-NS3 protein and can be used as antiviral agents against dengue virus. Out of more than hundred plant flavonoids, ten flavonoid structures are presented in this study. On the basis of best docking results, QSAR and SAR studies were performed. These flavonoids can directly work as anti-dengue drug or with little modifications in their structures.
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Affiliation(s)
- Muhammad Waseem Sarwar
- Virology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Jail road, Faisalabad, 38000, Pakistan
| | - Adeel Riaz
- Virology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Jail road, Faisalabad, 38000, Pakistan
| | - Syed Muhammad Raihan Dilshad
- Department of Theriogenology, Faculty of Veterinary and Animal Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Ahmed Al-Qahtani
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Liver Disease Research Center, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Shah Nawaz-Ul-Rehman
- Virology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Jail road, Faisalabad, 38000, Pakistan
| | - Muhammad Mubin
- Virology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Jail road, Faisalabad, 38000, Pakistan.
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16
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Powers CN, Setzer WN. An In-Silico Investigation of Phytochemicals as Antiviral Agents Against Dengue Fever. Comb Chem High Throughput Screen 2017; 19:516-36. [PMID: 27151482 PMCID: PMC5411999 DOI: 10.2174/1386207319666160506123715] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 01/28/2016] [Accepted: 04/13/2016] [Indexed: 01/19/2023]
Abstract
A virtual screening analysis of our library of phytochemical structures with dengue virus protein targets has been carried out using a molecular docking approach. A total of 2194 plant-derived secondary metabolites have been docked. This molecule set comprised of 290 alkaloids (68 indole alkaloids, 153 isoquinoline alkaloids, 5 quinoline alkaloids, 13 piperidine alkaloids, 14 steroidal alkaloids, and 37 miscellaneous alkaloids), 678 terpenoids (47 monoterpenoids, 169 sesquiterpenoids, 265 diterpenoids, 81 steroids, and 96 triterpenoids), 20 aurones, 81 chalcones, 349 flavonoids, 120 isoflavonoids, 74 lignans, 58 stilbenoids, 169 miscellaneous polyphenolic compounds, 100 coumarins, 28 xanthones, 67 quinones, and 160 miscellaneous phytochemicals. Dengue virus protein targets examined included dengue virus protease (NS2B-NS3pro), helicase (NS3 helicase), methyltransferase (MTase), RNA-dependent RNA polymerase (RdRp), and the dengue virus envelope protein. Polyphenolic compounds, flavonoids, chalcones, and other phenolics were the most numerous of the strongly docking ligands for dengue virus protein targets.
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Affiliation(s)
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Tahir ul Q M, Kiran S, Ashfaq UA, Javed MR, Anwar F, Ali MA, Gilani AUH. Discovery of Novel Dengue NS2B/NS3 Protease Inhibitors Using
Pharmacophore Modeling and Molecular Docking Based Virtual
Screening of the ZINC Database. INT J PHARMACOL 2016. [DOI: 10.3923/ijp.2016.621.632] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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18
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Paul A, Vibhuti A, Raj S. Molecular docking NS4B of DENV 1-4 with known bioactive phyto-chemicals. Bioinformation 2016; 12:140-148. [PMID: 28149049 PMCID: PMC5267958 DOI: 10.6026/97320630012140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 02/05/2023] Open
Abstract
Dengue disease is a global disease that has no effective treatment. The dengue virus (DENV) NS4B is a target for designing specific antivirals due to its importance in viral replication. Medicinal plants have been a savior for dengue virus as they consist of a class of phytochemicals having anti-viral activity and can pose a new approach ofstrong drug against viruses. The present study analyzes the activity of compounds against NS4B of DENV (1-4) serotypes. In this study Catechin, Cianidanol, Epicatechin, Eupatoretin, Glabranin, Laurifolin, DL-Catechin, astherapeutic agents were filtered by using Lipinski rule's five and the drug-likeness property of these agents were used for assessment of pharmacological properties. The molecular docking results presented the 2-D structures of bioactive complex, which interacted with especially conserved residues of target domains. Interestingly, we find the Catechin, Laurifolin, Cianidanol have highest binding energy against NS4B in DENV-1,2,4 which is evident by the formation of more hydrogen bonds with the amino acid residues at the binding site of the receptor. Our results revealed that the bioactive compound, especially Catechin has significant anti-dengue activities. In addition, this study may be helpful in further experimental investigations.
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Affiliation(s)
- Anubrata Paul
- Department of Biotechnology, Centre for Drug Design Discovery and Development (C-4D), SRM University, Delhi NCR, Sonepat, Haryana, India
| | - Arpana Vibhuti
- Department of Biotechnology, Centre for Drug Design Discovery and Development (C-4D), SRM University, Delhi NCR, Sonepat, Haryana, India
| | - Samuel Raj
- Department of Biotechnology, Centre for Drug Design Discovery and Development (C-4D), SRM University, Delhi NCR, Sonepat, Haryana, India
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Discovery of antiviral molecules for dengue: In silico search and biological evaluation. Eur J Med Chem 2016; 110:87-97. [PMID: 26807547 DOI: 10.1016/j.ejmech.2015.12.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 11/08/2015] [Accepted: 12/14/2015] [Indexed: 12/24/2022]
Abstract
BACKGROUND Dengue disease is a global disease that has no effective treatment. The dengue virus (DENV) NS2B/NS3 protease complex is a target for designing specific antivirals due to its importance in viral replication and its high degree of conservation. METHODS NS2B/NS3 protease complex structural information was employed to find small molecules that are capable of inhibiting the activity of the enzyme complex. This inhibitory activity was probed with in vitro assays using a fluorescent substrate and the complex NS2B/NS3 obtained by recombinant DNA techniques. HepG2 cells infected with dengue virus serotype 2 were used to test the activity against dengue virus replication. RESULTS A total of 210,903 small molecules from PubChem were docked in silico to the NS2B/NS3 structure (PDB: 2FOM) to find molecules that were capable of inhibiting this protein complex. Five of the best 500 leading compounds, according to their affinity values (-11.6 and -13.5 kcal/mol), were purchased. The inhibitory protease activity on the recombinant protein and antiviral assays was tested. CONCLUSIONS Chemicals CID 54681617, CID 54692801 and CID 54715399 were strong inhibitors of NS2B/NS3, with IC50 values (μM) and percentages of viral titer reductions of 19.9, 79.9%; 17.5, 69.8%; and 9.1, 73.9%, respectively. Multivariate methods applied to the molecular descriptors showed two compounds that were structurally different from other DENV inhibitors. GENERAL SIGNIFICANCE This discovery opens new possibilities for obtaining drug candidates against Dengue virus.
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Qamar MTU, Mumtaz A, Naseem R, Ali A, Fatima T, Jabbar T, Ahmad Z, Ashfaq UA. Molecular Docking Based Screening of Plant Flavonoids as Dengue NS1 Inhibitors. Bioinformation 2014; 10:460-5. [PMID: 25187688 PMCID: PMC4135296 DOI: 10.6026/97320630010460] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 07/01/2014] [Indexed: 12/15/2022] Open
Abstract
Dengue infection has turned into a serious health concern globally due to its high morbidity rate and a high possibility of increase
in its mortality rate on the account of unavailability of any proper treatment for severe dengue infection. The situation demands an
urgent development of efficient and practicable treatment to deal with Dengue virus (DENV). Flavonoids, a class of
phytochemicals present in medicinal plants, possess anti-viral activity and can be strong drug candidates against viruses. NS1
glycoprotein of Dengue virus is involved in its RNA replication and can be a strong target for screening of drugs against this virus.
Current study focuses on the identification of flavonoids which can block Asn-130 glycosylation site of Dengue virus NS1 to inhibit
viral replication as glycosylation of NS1 is required for its biological functioning. Molecular docking approach was used in this
study and the results revealed that flavonoids have strong potential interactions with active site of NS1. Six flavonoids
(Deoxycalyxin A; 3,5,7,3',4'-pentahydroxyflavonol-3-O-beta-D-galactopyranoside; (3R)-3',8-Dihydroxyvestitol; Sanggenon O;
Epigallocatechin gallate; Chamaejasmin) blocked the Asn-130 glycosylation site of NS1 and could be able to inhibit the viral
replication. It can be concluded from this study that these flavonoids could serve as antiviral drugs for dengue infections. Further
in-vitro analyses are required to confirm their efficacy and to evaluate their drug potency.
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Affiliation(s)
- Muhammad Tahir Ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Arooj Mumtaz
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Rabbia Naseem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Amna Ali
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Tabeer Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Tehreem Jabbar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Zubair Ahmad
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
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