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Khatana K, Gupta A, Ghosal A, Dey P, Zafar F, Srivastava A, Verma P. In silico identification and validation of phenolic lipids as potential inhibitor against bacterial and viral strains. J Biomol Struct Dyn 2024; 42:2525-2538. [PMID: 37211872 DOI: 10.1080/07391102.2023.2212811] [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: 03/22/2022] [Accepted: 04/16/2023] [Indexed: 05/23/2023]
Abstract
The recurrence of coronavirus disease and bacterial resistant strains has drawn attention to naturally occurring bioactive molecules that can demonstrate broad-spectrum efficacy against bacteria as well as viral strains. The drug-like abilities of naturally available "anacardic acids" (AA) and their derivatives against different bacterial and viral protein targets through in-silico tools were explored. Three viral protein targets [P DB: 6Y2E (SARS-CoV-2), 1AT3 (Herpes) and 2VSM (Nipah)] and four bacterial protein targets [P DB: 2VF5 (Escherichia coli), 2VEG (Streptococcus pneumoniae), 1JIJ (Staphylococcus aureus) and 1KZN (E. coli)] were selected to evaluate the activity of bioactive AA molecules. The potential ability to inhibit the progression of microbes has been discussed based on the structure, functionality and interaction ability of these molecules on the selected protein targets for multi-disease remediation. The number of interactions, full-fitness value and energy of the ligand-target system were determined from the docked structure in SwissDock and Autodock Vina. In order to compare the efficacy of these active derivatives to that of commonly used drugs against bacteria and viruses, a few of the selected molecules were subjected to 100 ns long MD simulations. It was found that the phenolic groups and alkyl chains of AA derivatives are more likely to bind with microbial targets, that could be responsible for the improved activity against these targets. The results suggest that the proposed AA derivatives have demonstrated potential to become active drug ingredients against microbial protein targets. Further, experimental investigations are essential for clinical verification of the drug-like abilities of AA derivatives.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kavita Khatana
- Department of Chemical Engineering, School of Engineering, Shiv Nadar Institutions of Eminence Deemed to be University, Greater Noida, India
| | - Anjali Gupta
- School of Basic and Applied Science, Galgotias University, Greater Noida, India
| | - Anujit Ghosal
- Department of Chemistry, Jamia Millia Islamia, New Delhi, India
- Department of Food and Human Nutritional Sciences, The University of Manitoba, Winnipeg, MB, Canada
- Richardson Centre for Functional Foods and Nutraceuticals, The University of Manitoba, Winnipeg, MB, Canada
| | - Pinki Dey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Fahmina Zafar
- Department of Chemistry, Jamia Millia Islamia, New Delhi, India
| | | | - Priya Verma
- Department of Physics, University of Lucknow, Lucknow, India
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Bordean ME, Ungur RA, Toc DA, Borda IM, Marțiș GS, Pop CR, Filip M, Vlassa M, Nasui BA, Pop A, Cinteză D, Popa FL, Marian S, Szanto LG, Muste S. Antibacterial and Phytochemical Screening of Artemisia Species. Antioxidants (Basel) 2023; 12:antiox12030596. [PMID: 36978844 PMCID: PMC10045255 DOI: 10.3390/antiox12030596] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Taking into account the increasing number of antibiotic-resistant bacteria, actual research focused on plant extracts is vital. The aim of our study was to investigate leaf and stem ethanolic extracts of Artemisia absinthium L. and Artemisia annua L. in order to explore their antioxidant and antibacterial activities. Total phenolic content (TPC) was evaluated spectrophotometrically. Antioxidant activity was evaluated by DPPH and ABTS. The antibacterial activity of wormwood extracts was assessed by minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) in Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, and Salmonella enteritidis cultures, and by zone of inhibition in Klebsiella carbapenem-resistant enterobacteriaceae (CRE) and Escherichia coli extended-spectrum β-lactamases cultures (ESBL). The Artemisia annua L. leaf extract (AnL) exhibited the highest TPC (518.09 mg/mL) and the highest expression of sinapic acid (285.69 ± 0.002 µg/mL). Nevertheless, the highest antioxidant capacity (1360.51 ± 0.04 µM Trolox/g DW by ABTS and 735.77 ± 0.02 µM Trolox/g DW by DPPH) was found in Artemisia absinthium L. leaf from the second year of vegetation (AbL2). AnL extract exhibited the lowest MIC and MBC for all tested bacteria and the maximal zone of inhibition for Klebsiella CRE and Escherichia coli ESBL. Our study revealed that AbL2 exhibited the best antioxidant potential, while AnL extract had the strongest antibacterial effect.
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Affiliation(s)
- Maria-Evelina Bordean
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 64 Calea Floresti, 400509 Cluj-Napoca, Romania
- Centre for Technology Transfer-BioTech, 64 Calea Florești, 400509 Cluj-Napoca, Romania
| | - Rodica Ana Ungur
- Department of Medical Specialties, Faculty of Medicine, “Iuliu Hațieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania
| | - Dan Alexandru Toc
- Department of Microbiology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Ileana Monica Borda
- Department of Medical Specialties, Faculty of Medicine, “Iuliu Hațieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania
- Correspondence: (I.M.B.); (G.S.M.)
| | - Georgiana Smaranda Marțiș
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 64 Calea Floresti, 400509 Cluj-Napoca, Romania
- Centre for Technology Transfer-BioTech, 64 Calea Florești, 400509 Cluj-Napoca, Romania
- Correspondence: (I.M.B.); (G.S.M.)
| | - Carmen Rodica Pop
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 64 Calea Floresti, 400509 Cluj-Napoca, Romania
- Centre for Technology Transfer-BioTech, 64 Calea Florești, 400509 Cluj-Napoca, Romania
| | - Miuța Filip
- Raluca Ripan Institute for Research in Chemistry, Babeș-Bolyai University, 30 Fântânele Street, 400294 Cluj-Napoca, Romania
| | - Mihaela Vlassa
- Raluca Ripan Institute for Research in Chemistry, Babeș-Bolyai University, 30 Fântânele Street, 400294 Cluj-Napoca, Romania
| | - Bogdana Adriana Nasui
- Department of Community Health, “Iuliu Hațieganu” University of Medicine and Pharmacy, 6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania
| | - Anamaria Pop
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 64 Calea Floresti, 400509 Cluj-Napoca, Romania
- Centre for Technology Transfer-BioTech, 64 Calea Florești, 400509 Cluj-Napoca, Romania
| | - Delia Cinteză
- 9th Department-Physical Medicine and Rehabilitation, Carol Davila Univerity of Medicine and Pharmacy, 050474 București, Romania
| | - Florina Ligia Popa
- Physical Medicine and Rehabilitation Department, Faculty of Medicine, “Lucian Blaga” University of Sibiu, Victoriei Blvd., 550024 Sibiu, Romania
- Academic Emergency Hospital of Sibiu, Coposu Blvd., 550245 Sibiu, Romania
| | - Sabina Marian
- Faculty of Biology and Geology, Babeș-Bolyai University, 44 Republicii Street, 400015 Cluj-Napoca, Romania
| | - Lidia Gizella Szanto
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 64 Calea Floresti, 400509 Cluj-Napoca, Romania
- Centre for Technology Transfer-BioTech, 64 Calea Florești, 400509 Cluj-Napoca, Romania
| | - Sevastița Muste
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 64 Calea Floresti, 400509 Cluj-Napoca, Romania
- Centre for Technology Transfer-BioTech, 64 Calea Florești, 400509 Cluj-Napoca, Romania
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Gumede NJ. Pathfinder-Driven Chemical Space Exploration and Multiparameter Optimization in Tandem with Glide/IFD and QSAR-Based Active Learning Approach to Prioritize Design Ideas for FEP+ Calculations of SARS-CoV-2 PL pro Inhibitors. Molecules 2022; 27:8569. [PMID: 36500659 PMCID: PMC9741453 DOI: 10.3390/molecules27238569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
A global pandemic caused by the SARS-CoV-2 virus that started in 2020 and has wreaked havoc on humanity still ravages up until now. As a result, the negative impact of travel restrictions and lockdowns has underscored the importance of our preparedness for future pandemics. The main thrust of this work was based on addressing this need by traversing chemical space to design inhibitors that target the SARS-CoV-2 papain-like protease (PLpro). Pathfinder-based retrosynthesis analysis was used to generate analogs of GRL-0617 using commercially available building blocks by replacing the naphthalene moiety. A total of 10 models were built using active learning QSAR, which achieved good statistical results such as an R2 > 0.70, Q2 > 0.64, STD Dev < 0.30, and RMSE < 0.31, on average for all models. A total of 35 ideas were further prioritized for FEP+ calculations. The FEP+ results revealed that compound 45 was the most active compound in this series with a ΔG of −7.28 ± 0.96 kcal/mol. Compound 5 exhibited a ΔG of −6.78 ± 1.30 kcal/mol. The inactive compounds in this series were compound 91 and compound 23 with a ΔG of −5.74 ± 1.06 and −3.11 ± 1.45 kcal/mol. The combined strategy employed here is envisaged to be of great utility in multiparameter lead optimization efforts, to traverse chemical space, maintaining and/or improving the potency as well as the property space of synthetically aware design ideas.
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Affiliation(s)
- Njabulo Joyfull Gumede
- Department of Chemistry, Mangosuthu University of Technology, P.O. Box 12363, Jacobs 4026, South Africa
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Molecular docking analysis and evaluation of the antimicrobial properties of the constituents of Geranium wallichianum D. Don ex Sweet from Kashmir Himalaya. Sci Rep 2022; 12:12547. [PMID: 35869098 PMCID: PMC9307801 DOI: 10.1038/s41598-022-16102-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/05/2022] [Indexed: 11/28/2022] Open
Abstract
Geranium wallichianum D. Don ex Sweet is a well-known medicinal plant in Kashmir Himalya. The evidence for its modern medicinal applications remains majorly unexplored. The present study was undertaken to elucidate the detailed antimicrobial promises of different crude extracts (methanolic, ethanolic, petroleum ether, and ethyl acetate) of G. wallichainum against common human bacterial and fungal pathogens in order to scientifically validate its traditional use. The LC–MS analysis of G. wallichainum yielded 141 bioactive compounds with the vast majority of them having therapeutic applications. Determination of minimum inhibitory concentrations (MICs) by broth microdilution method of G. wallichainum was tested against bacterial and fungal pathogens with MICs ranging from 0.39 to 400 µg/mL. Furthermore, virtual ligands screening yielded elatine, kaempferol, and germacrene-A as medicinally most active constituents and the potential inhibitors of penicillin-binding protein (PBP), dihydropteroate synthase (DHPS), elongation factor-Tu (Eu-Tu), ABC transporter, 1,3 beta glycan, and beta-tubulin. The root mean square deviation (RMSD) graphs obtained through the molecular dynamic simulations (MDS) indicated the true bonding interactions which were further validated using root mean square fluctuation (RMSF) graphs which provided a better understanding of the amino acids present in the proteins responsible for the molecular motions and fluctuations. The effective binding of elatine, kaempferol, and germacrene-A with these proteins provides ground for further research to understand the underlying mechanism that ceases the growth of these microbes.
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Chandika P, Khan F, Heo SY, Kim TH, Kim YM, Yi M, Jung WK. Multifunctional dual cross-linked poly (vinyl alcohol)/methacrylate hyaluronic acid/chitooligosaccharide-sinapic acid wound dressing hydrogel. Int J Biol Macromol 2022; 222:1137-1150. [PMID: 36162531 DOI: 10.1016/j.ijbiomac.2022.09.174] [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: 07/02/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022]
Abstract
Wound dressing hydrogel with multifunctional properties, including antioxidant and antimicrobial properties and appropriate mechanical, biological, and physical properties is of great interest in wound healing application and it is still a challenge. In the present study, chitooligosaccharides (COS)/ sinapic acid (SA) conjugate (COS-SA) was synthesized using H2O2-induced grafting polymerization, and photo cross-linkable hyaluronic acid was synthesized using methacrilation (HAMA). The synthesis of COS-SA and HAMA was confirmed by Fourier-transform infrared spectroscopy, proton nuclear magnetic resonance spectroscopy, ultraviolet spectroscopy, and polyphenol assay. Subsequently, we developed duel cross-linked polyvinyl alcohol (PVA)/HAMA composite hydrogel encapsulated with COS-SA as an antioxidant and antimicrobial dressing for full-thickness wound healing application. The chemical, physical, mechanical, antioxidant, antimicrobial, in vitro biocompatibility, and in vivo wound healing properties of hydrogels were subsequently investigated. The results showed that the fabricated composite hydrogel had a uniform porous architecture, excellent fluid absorbability, and appropriate mechanical stability. The introduction of COSs-SA conjugate remarkably enhanced the in vitro biocompatibility, antioxidant, and antimicrobial properties of the hydrogel, leading to the significant promotion of in vivo full-thickness wound closure, re-epithelization, granulation tissue formation, and collagen deposition indicating that COSs-SA incorporated PVA/HAMA hydrogel wound dressing has significant potential for chronic wound healing application.
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Affiliation(s)
- Pathum Chandika
- Major of Biomedical Engineering, Division of Smart Healthcare and New-senior Healthcare Innovation Center (BK21 Plus), Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Seong-Yong Heo
- Jeju Marine Research Center, Korea Institute of Ocean Science & Technology, Jeju 63349, Republic of Korea
| | - Tae-Hee Kim
- Major of Biomedical Engineering, Division of Smart Healthcare and New-senior Healthcare Innovation Center (BK21 Plus), Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Young-Mog Kim
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea; Major of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Myunggi Yi
- Major of Biomedical Engineering, Division of Smart Healthcare and New-senior Healthcare Innovation Center (BK21 Plus), Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Won-Kyo Jung
- Major of Biomedical Engineering, Division of Smart Healthcare and New-senior Healthcare Innovation Center (BK21 Plus), Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
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Rampadarath A, Balogun FO, Pillay C, Sabiu S. Identification of Flavonoid C-Glycosides as Promising Antidiabetics Targeting Protein Tyrosine Phosphatase 1B. J Diabetes Res 2022; 2022:6233217. [PMID: 35782627 PMCID: PMC9249544 DOI: 10.1155/2022/6233217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 06/08/2022] [Indexed: 12/15/2022] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B), a negative regulator of the insulin signaling pathway, has gained attention as a validated druggable target in the management of type 2 diabetes mellitus (T2DM). The lack of clinically approved PTP1B inhibitors has continued to prompt research in plant-derived therapeutics possibly due to their relatively lesser toxicity profiles. Flavonoid C-glycosides are one of the plant-derived metabolites gaining increased relevance as antidiabetic agents, but their possible mechanism of action remains largely unknown. This study investigates the antidiabetic potential of flavonoid C-glycosides against PTP1B in silico and in vitro. Of the seven flavonoid C-glycosides docked against the enzyme, three compounds (apigenin, vitexin, and orientin) had the best affinity for the enzyme with a binding score of -7.3 kcal/mol each, relative to -7.4 kcal/mol for the reference standard, ursolic acid. A further probe (in terms of stability, flexibility, and compactness) of the complexes over a molecular dynamics time study of 100 ns for the three compounds suggested orientin as the most outstanding inhibitor of PTP1B owing to its overall -34.47 kcal/mol binding energy score compared to ursolic acid (-19.24 kcal/mol). This observation was in accordance with the in vitro evaluation result, where orientin had a half maximal inhibitory concentration (IC50) of 0.18 mg/ml relative to 0.13 mg/ml for the reference standard. The kinetics of inhibition of PTP1B by orientin was mixed-type with V max and K m values of 0.004 μM/s and 0.515 μM. Put together, the results suggest orientin as a potential PTP1B inhibitor and could therefore be further explored in the management T2DM as a promising therapeutic agent.
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Affiliation(s)
- Athika Rampadarath
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Fatai Oladunni Balogun
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Charlene Pillay
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
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