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Review Articles

Pharmacoinformatics approaches in the discovery of drug-like antimicrobials of plant origin

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Pages 7612-7628 | Received 10 Oct 2020, Accepted 21 Feb 2021, Published online: 04 Mar 2021

References

  • Ahmad, I., & Beg, A. Z. (2001). Antimicrobial and phytochemical studies on 45 Indian medicinal plants against multi-drug resistant human pathogens. Journal of Ethnopharmacology, 74(2), 113–123. https://doi.org/10.1016/S0378-8741(00)00335-4
  • Al-Janabi, A. A. H. S. (2011). Potential activity of the purine compounds caffeine and aminophylline on bacteria. Journal of Global Infectious Diseases, 3(2), 133–137. https://doi.org/10.4103/0974-777X.81689
  • Al-Soud, Y. A., Al-Sa’doni, H. H., Amajaour, H. A., Salih, K. S., Mubarakb, M. S., & Al-Masoudic, N. A. (2008). Synthesis, characterization and anti-HIV and antitumor activities of new coumarin derivatives. Zeitschrift Für Naturforschung B, 63(1), 83–89. https://doi.org/10.1515/znb-2008-0112
  • Ayoola, G., Johnson, O., Adelowotan, T., Aibinu, I., Adenipekun, E., Adepoju-Bello, A., Coker, H., & Odugbemi, T. (2008). Evaluation of the chemical constituents and the antimicrobial activity of the volatile oil of Citrus reticulata fruit (Tangerine fruit peel) from South West Nigeria. African Journal of Biotechnology, 7
  • Bag, A., & Chattopadhyay, R. (2017). Synergistic antibacterial and antibiofilm efficacy of nisin in combination with p-coumaric acid against food-borne bacteria Bacillus cereus and Salmonella typhimurium. Letters in Applied Microbiology, 65(5), 366–372. https://doi.org/10.1111/lam.12793
  • Bailey, C. J., & Day, C. (2004). Metformin: Its botanical background. Practical Diabetes International, 21(3), 115–117. https://doi.org/10.1002/pdi.606
  • Balandrin, M. F. (1996). Commercial utilization of plant-derived saponins: An overview of medicinal, pharmaceutical, and industrial applications. Saponins Used in Traditional and Modern Medicine, Springer, 1–14.
  • Balasundram, N., Sundram, K., & Samman, S. (2006). Phenolic compounds in plants and agri-industrial by-products: Antioxidant activity, occurrence, and potential uses. Food Chemistry, 99(1), 191–203. https://doi.org/10.1016/j.foodchem.2005.07.042
  • Bastida, J., Lavilla, R., & Viladomat, F. (2006). Chemical and biological aspects of Narcissus alkaloids. The Alkaloids. Chemistry and Biology, 63, 87–179. https://doi.org/10.1016/s1099-4831(06)63003-4
  • Batista, M. N., Carneiro, B. M., Braga, A. C. S., & Rahal, P. (2015). Caffeine inhibits hepatitis C virus replication in vitro. Archives of Virology, 160(2), 399–407. https://doi.org/10.1007/s00705-014-2302-1
  • Behnia, M., Haghighi, A., Komeilizadeh, H., Tabaei, S. S., & Abadi, A. (2008). In vitro antiamoebic activity of Iranian Allium sativum in comparison with metronidazole against Entamoeba histolytica. Iranian Journal of Parasitology, 3(4), 32–38.
  • Bersani, F. S., Coviello, M., Imperatori, C., Francesconi, M., Hough, C. M., Valeriani, G., De Stefano, G., Bolzan Mariotti Posocco, F., Santacroce, R., Minichino, A., & Corazza, O. (2015). Adverse Psychiatric Effects Associated with Herbal Weight-Loss Products. BioMed Research International, 2015(2015), 120679–120679. https://doi.org/10.1155/2015/120679
  • Broach, J. R., & Thorner, J. (1996). High-throughput screening for drug discovery. Nature, 384(6604 Suppl), 14–16. https://doi.org/10.1038/384014a0
  • Buenz, E., Johnson, H., Beekman, E., Motley, T., & Bauer, B. A. (2005). Bioprospecting Rumphius's Ambonese herbal: Volume I. Journal of Ethnopharmacology, 96(1-2), 57–70. https://doi.org/10.1016/j.jep.2004.08.016
  • Cai, J., Han, C., Hu, T., Zhang, J., Wu, D., Wang, F., Liu, Y., Ding, J., Chen, K., Yue, J., Shen, X., & Jiang, H. (2006). Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation. Protein Science : a Publication of the Protein Society, 15(9), 2071–2081. https://doi.org/10.1110/ps.062238406
  • Califf, R. M., Zarin, D. A., Kramer, J. M., Sherman, R. E., Aberle, L. H., & Tasneem, A. (2012). Characteristics of clinical trials registered in ClinicalTrials.gov, 2007-2010. JAMA, 307(17), 1838–1847. gov, 2007-2010, Jama,) https://doi.org/10.1001/jama.2012.3424
  • Calzada, F., & Alanís, A. D. (2007). Additional antiprotozoal flavonol glycosides of the aerial parts of Helianthemum glomeratum. Phytotherapy Research : PTR, 21(1), 78–80. https://doi.org/10.1002/ptr.2031
  • Champagne, A., & Boutry, M. (2013). Proteomics of nonmodel plant species, Proteomics. Proteomics, 13(3-4), 663–673. https://doi.org/10.1002/pmic.201200312
  • Chang, I. M. (2001). Anti-aging and health-promoting constituents derived from traditional oriental herbal remedies: information retrieval using the TradiMed 2000 DB. Annals of the New York Academy of Sciences, 928, 281–286. https://doi.org/10.1111/j.1749-6632.2001.tb05657.x
  • Chen, Y., & Ung, C. (2001). Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand–protein inverse docking approach. Journal of Molecular Graphics & Modelling, 20(3), 199–218. https://doi.org/10.1016/S1093-3263(01)00109-7
  • Chen, X., Zhou, H., Liu, Y., Wang, J., Li, H., Ung, C., Han, L., Cao, Z., & Chen, Y. (2006). Database of traditional Chinese medicine and its application to studies of mechanism and to prescription validation. Br J Pharmacol, 149(8), 1092–1103. https://doi.org/10.1038/sj.bjp.0706945
  • Chiang, L., Chiang, W., Chang, M., Ng, L., & Lin, C. (2002). Antiviral activity of Plantago major extracts and related compounds in vitro. Antiviral Research, 55(1), 53–62. https://doi.org/10.1016/S0166-3542(02)00007-4
  • Chidambaram, S., El-Sheikh, M. A., Alfarhan, A. H., Radhakrishnan, S., & Akbar, I. (2021). Synthesis of novel coumarin analogues: Investigation of molecular docking interaction of SARS-CoV-2 proteins with natural and synthetic coumarin analogues and their pharmacokinetics studies. Saudi Journal of Biological Sciences, 28(1), 1100–1108. https://doi.org/10.1016/j.sjbs.2020.11.038
  • Chiow, K., Phoon, M., Putti, T., Tan, B. K., & Chow, V. T. (2016). Evaluation of antiviral activities of Houttuynia cordata Thunb. extract, quercetin, quercetrin and cinanserin on murine coronavirus and dengue virus infection. Asian Pacific Journal of Tropical Medicine, 9(1), 1–7. https://doi.org/10.1016/j.apjtm.2015.12.002
  • Daglia, M., Papetti, A., Dacarro, C., & Gazzani, G. (1998). Isolation of an antibacterial component from roasted coffee. Journal of Pharmaceutical and Biomedical Analysis, 18(1-2), 219–225. https://doi.org/10.1016/S0731-7085(98)00177-0
  • Dastan, D., Salehi, P., Aliahmadi, A., Gohari, A. R., Maroofi, H., & Ardalan, A. (2016). New coumarin derivatives from Ferula pseudalliacea with antibacterial activity. Natural Product Research, 30(24), 2747–2753. https://doi.org/10.1080/14786419.2016.1149705
  • de Sousa Luisa, J. A., Barrosb, R. P. C., de Sousab, N. F., Muratovc, E., Scottib, L., & Scottib, M. T. (2020). Virtual Screening of Natural Products Database, Mini Reviews in Medicinal Chemistry, 20, 1.
  • Dodson, H. C., Lyda, T. A., Chambers, J. W., Morris, M. T., Christensen, K. A., & Morris, J. C. (2011). Quercetin, a fluorescent bioflavanoid, inhibits Trypanosoma brucei hexokinase 1. Experimental Parasitology, 127(2), 423–428. https://doi.org/10.1016/j.exppara.2010.10.011
  • Doughari, J. H. Phytochemicals: extraction methods, basic structures and mode of action as potential chemotherapeutic agents, Phytochemicals-A global perspective of their role in nutrition and health, InTech (2012).
  • Doughari, J., Human, I., Benadé, A., & Ndakidemi, P. Phytochemicals as chemotherapeutic agents and antioxidants: Possible solution to the control of antibiotic resistant verocytotoxin producing bacteria, (2009).
  • Edris, A. E. (2007). Pharmaceutical and therapeutic potentials of essential oils and their individual volatile constituents: A review. Phytotherapy Research : PTR, 21(4), 308–323. https://doi.org/10.1002/ptr.2072
  • Egamberdieva, D., & Jabborova, D. (2020). Plant microbiome: Source for biologically active compounds. Biodiversity and Biomedicine, Academic Press, 1–9.
  • Elzupir, A. O. (2020). Caffeine and caffeine-containing pharmaceuticals as promising inhibitors for 3-chymotrypsin-like protease of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 1–8.
  • Emoto, C., Murayama, N., Rostami-Hodjegan, A., & Yamazaki, H. (2009). Utilization of estimated physicochemical properties as an integrated part of predicting hepatic clearance in the early drug-discovery stage: Impact of plasma and microsomal binding. Xenobiotica; the Fate of Foreign Compounds in Biological Systems, 39(3), 227–235. https://doi.org/10.1080/00498250802668863
  • Emran, T. B., Rahman, M. A., Uddin, M. M. N., Dash, R., Hossen, M. F., Mohiuddin, M., & Alam, M. R. (2015). Molecular docking and inhibition studies on the interactions of Bacopa monnieri’s potent phytochemicals against pathogenic Staphylococcus aureus. DARU Journal of Pharmaceutical Sciences, 23(1), 1–8. https://doi.org/10.1186/s40199-015-0106-9
  • Fasinu, P. S., Bouic, P. J., & Rosenkranz, B. (2012). An overview of the evidence and mechanisms of herb-drug interactions. Frontiers in Pharmacology, 3, 69–69. https://doi.org/10.3389/fphar.2012.00069
  • Ferguson, J. J., Stojanovski, E., MacDonald-Wicks, L., & Garg, M. L. (2018). Curcumin potentiates cholesterol-lowering effects of phytosterols in hypercholesterolaemic individuals. A randomised controlled trial. Metabolism, 82, 22–35. https://doi.org/10.1016/j.metabol.2017.12.009
  • Gao, M., Wang, H., & Zhu, L. (2016). Quercetin assists fluconazole to inhibit biofilm formations of fluconazole-resistant Candida albicans in in vitro and in vivo antifungal managements of vulvovaginal candidiasis. Cellular Physiology and Biochemistry : international Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology, 40(3-4), 727–742. https://doi.org/10.1159/000453134
  • Giri, L., C. Andola, H., Purohit, V. K., Rawat, M. S. M., Rawal, R. S., & Bhatt, I. D. (2010). Chromatographic and spectral fingerprinting standardization of traditional medicines: An overview as modern tools. Research Journal of Phytochemistry, 4(4), 234–241. https://doi.org/10.3923/rjphyto.2010.234.241
  • Goldmann, D., Montanari, F., Richter, L., Zdrazil, B., & Ecker, G. F. (2014). Exploiting open data: a new era in pharmacoinformatics. Future Medicinal Chemistry, 6(5), 503–514. https://doi.org/10.4155/fmc.14.13
  • Gu, P., & Chen, H. (2014). Modern bioinformatics meets traditional Chinese medicine. Brief Bioinform, 15(6), 984–1003. https://doi.org/10.1093/bib/bbt063
  • Gu, J., Gui, Y., Chen, L., Yuan, G., & Xu, X. (2013). CVDHD: A cardiovascular disease herbal database for drug discovery and network pharmacology. Journal of Cheminformatics, 5(1), 51 https://doi.org/10.1186/1758-2946-5-51
  • Hakeem, K. R., Malik, A., Vardar-Sukan, F., & Ozturk, M. (2017). Plant Bioinformatics: Decoding the Phyta., Springer.
  • Happi, E. N., Mbosso, E. J. T., Nguemfo, E. L., Zambou, H. R., & Azebaze, A. G. B. (2014). Anti-toxoplasma gondii activity of constituents from Balsamocitrus camerunensis L (Rutaceae). African Journal of Biotechnology, 13(52), 4680-4684.
  • Harvey, A. (2000). Strategies for discovering drugs from previously unexplored natural products. Drug Discov Today, 5(7), 294–300. https://doi.org/10.1016/s1359-6446(00)01511-7
  • Harvey, A. L., Edrada-Ebel, R., & Quinn, R. J. (2015). The re-emergence of natural products for drug discovery in the genomics era. Nature Reviews. Drug Discovery, 14(2), 111–129. https://doi.org/10.1038/nrd4510
  • Hennessy, M., Kelleher, D., Spiers, J. P., Barry, M., Kavanagh, P., Back, D., Mulcahy, F., & Feely, J. (2002). St Johns wort increases expression of P-glycoprotein: Implications for drug interactions. British Journal of Clinical Pharmacology, 53(1), 75–82. https://doi.org/10.1046/j.0306-5251.2001.01516.x
  • Hilaly, J. E., Israili, Z. H., & Lyoussi, B. (2004). Acute and chronic toxicological studies of Ajuga iva in experimental animals. Journal of Ethnopharmacology, 91(1), 43–50. https://doi.org/10.1016/j.jep.2003.11.009
  • Hui-Fang, L., Qing, S., Jian, Z., & Wei, F. (2010). Evaluation of various inverse docking schemes in multiple targets identification. Journal of Molecular Graphics & Modelling, 29(3), 326–330. https://doi.org/10.1016/j.jmgm.2010.09.004
  • Hwu, J. R., Singha, R., Hong, S. C., Chang, Y. H., Das, A. R., Vliegen, I., De Clercq, E., & Neyts, J. (2008). Synthesis of new benzimidazole-coumarin conjugates as anti-hepatitis C virus agents . Antiviral Research, 77(2), 157–162. https://doi.org/10.1016/j.antiviral.2007.09.003
  • Islam, M. A., & Pillay, T. S. (2020). Identification of promising anti-DNA gyrase antibacterial compounds using de novo design, molecular docking and molecular dynamics studies. Journal of Biomolecular Structure & Dynamics, 38(6), 1798–1809. https://doi.org/10.1080/07391102.2019.1617785
  • Jaisinghani, R. N. (2017). Antibacterial properties of quercetin. Microbiology Research, 8(1), 13-14. https://doi.org/10.4081/mr.2017.6877
  • Jang, E., Park, J. A., Kim, Y. H., & Kim, H. (2019). Effect of caffeine on the antibacterial activity of Lactobacillus casei: Caffeine and antibacterial activity of L. Casei, Korean Journal of Agricultural Science, 46, 981–989.
  • Jia, C., Zhang, J., Yu, L., Wang, C., Yang, Y., Rong, X., Xu, K., & Chu, M. (2018). Antifungal activity of coumarin against Candida albicans is related to apoptosis. Frontiers in Cellular and Infection Microbiology, 8, 1–13.https://doi.org/10.3389/fcimb.2018.00445
  • Johari, J., Kianmehr, A., Mustafa, M. R., Abubakar, S., & Zandi, K. (2012). Antiviral activity of baicalein and quercetin against the Japanese encephalitis virus. Int J Mol Sci, 13(12), 16785–16795. https://doi.org/10.3390/ijms131216785
  • Kandi, S., Godishala, V., Rao, P., & Ramana, K. (2015). Biomedical significance of terpenes: An insight. Biomedicine, 3, 8–10.
  • Kanehisa, M. (2009). Representation and analysis of molecular networks involving diseases and drugs, Genome Informatics 2009: Genome Informatics Series. Vol. 23, World Scientific. pp. 212–213.
  • Karunamoorthi, K., Jegajeevanram, K., Vijayalakshmi, J., & Mengistie, E. (2013). Traditional medicinal plants: A source of phytotherapeutic modality in resource-constrained health care settings. Journal of Evidence-Based Complementary & Alternative Medicine, 18(1), 67–74. https://doi.org/10.1177/2156587212460241
  • Kayser, O., & Kolodziej, H. (1999). Antibacterial activity of simple coumarins: Structural requirements for biological activity. Zeitschrift Fur Naturforschung. C, Journal of Biosciences, 54(3-4), 169–174. https://doi.org/10.1515/znc-1999-3-405
  • Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., & Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44, D1202–D1213. https://doi.org/10.1093/nar/gkv951
  • Koehn, F. E., & Carter, G. T. (2005). The evolving role of natural products in drug discovery. Nature Reviews. Drug Discovery, 4(3), 206–220. https://doi.org/10.1038/nrd1657
  • Koleva, I. I., Van Beek, T. A., Linssen, J. P., Groot, Ad., & Evstatieva, L. N. (2002). Screening of plant extracts for antioxidant activity: A comparative study on three testing methods. Phytochemical Analysis : PCA, 13(1), 8–17. https://doi.org/10.1002/pca.611
  • Kraljevic, S., Stambrook, P. J., & Pavelic, K. (2004). Accelerating drug discovery: Although the evolution of ‘‐omics’ methodologies is still in its infancy, both the pharmaceutical industry and patients could benefit from their implementation in the drug development process. EMBO Reports, 5(9), 837–842. https://doi.org/10.1038/sj.embor.7400236
  • Kubmarawa, D., Ajoku, G., Enwerem, N., & Okorie, D. (2007). Preliminary phytochemical and antimicrobial screening of 50 medicinal plants from Nigeria. African Journal of Biotechnology, 6 (14), 1690-1696.‌
  • Kumar Yadav, D., Kalani, K., Khan, F., & Srivastava, S. K. (2013). QSAR and docking based semi-synthesis and in vitro evaluation of 18 β-glycyrrhetinic acid derivatives against human lung cancer cell line A-549. Medicinal Chemistry (Shariqah (United Arab Emirates)), 9(8), 1073–1084. https://doi.org/10.2174/1573406411309080009
  • Lagunin, A., Gloriozova, T., Dmitriev, A., Volgina, N., & Poroikov, V. (2013). Computer evaluation of drug interactions with P-glycoprotein. Bulletin of Experimental Biology and Medicine, 154(4), 521–524. https://doi.org/10.1007/s10517-013-1992-9
  • Lagunin, A. A., Goel, R. K., Gawande, D. Y., Pahwa, P., Gloriozova, T. A., Dmitriev, A. V., Ivanov, S. M., Rudik, A. V., Konova, V. I., Pogodin, P. V., Druzhilovsky, D. S., & Poroikov, V. V. (2014). Chemo- and bioinformatics resources for in silico drug discovery from medicinal plants beyond their traditional use: A critical review. Natural Product Reports, 31(11), 1585–1611. https://doi.org/10.1039/c4np00068d
  • Lagunin, A., Zakharov, A., Filimonov, D., & Poroikov, V. (2011). QSAR modelling of rat acute toxicity on the basis of PASS prediction. Molecular Informatics, 30(2-3), 241–250. https://doi.org/10.1002/minf.201000151
  • Lambrinidis, G., Tsopelas, F., Giaginis, C., & Tsantili-Kakoulidou, A. (2017). QSAR/QSPR modeling in the design of drug candidates with balanced pharmacodynamic and pharmacokinetic properties, Advances in QSAR Modeling., Springer. pp. 339–384.
  • Liu, R. H. (2004). Potential synergy of phytochemicals in cancer prevention: Mechanism of action. The Journal of Nutrition, 134(12 Suppl), 3479S–3485S. https://doi.org/10.1093/jn/134.12.3479S
  • Liu, X., Ouyang, S., Yu, B., Liu, Y., Huang, K., Gong, J., Zheng, S., Li, Z., Li, H., & Jiang, H. (2010). PharmMapper server: A web server for potential drug target identification using pharmacophore mapping approach. Nucleic Acids Research, 38(Web Server issue), W609–W614. https://doi.org/10.1093/nar/gkq300
  • Li, X., Yang, Y., Henry, R. J., Rossetto, M., Wang, Y., & Chen, S. (2015). Plant DNA barcoding: From gene to genome. Biological Reviews of the Cambridge Philosophical Society, 90(1), 157–166. https://doi.org/10.1111/brv.12104
  • Li, S., Zhang, B., & Zhang, N. (2011). Network target for screening synergistic drug combinations with application to traditional Chinese medicine. BMC Systems Biology, 5(Suppl 1), S10. https://doi.org/10.1186/1752-0509-5-S1-S10
  • Lopes, S. P., Yepes, L. M., Pérez-Castillo, Y., Robledo, S. M., & de Sousa, D. P. (2020). Alkyl and Aryl Derivatives Based on p-Coumaric Acid Modification and Inhibitory Action against Leishmania braziliensis and Plasmodium falciparum. Molecules, 25(14), 3178. https://doi.org/10.3390/molecules25143178
  • Lou, S.-K., Wong, K.-L., Li, M., But, P. P.-H., Tsui, S. K.-W., & Shaw, P.-C. (2010). An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database). BMC Genomics, 11, 402 https://doi.org/10.1186/1471-2164-11-402
  • Loub, W., Farnsworth, N., Soejarto, D., & Quinn, M. (1985). NAPRALERT: Computer handling of natural product research data. Journal of Chemical Information and Computer Sciences, 25(2), 99–103. https://doi.org/10.1021/ci00046a009
  • Martín-Navarro, C. M., López-Arencibia, A., Sifaoui, I., Reyes-Batlle, M., Fouque, E., Osuna, A., Valladares, B., Piñero, J. E., Héchard, Y., Maciver, S. K., & Lorenzo-Morales, J. (2017). Amoebicidal activity of caffeine and maslinic acid by the induction of programmed cell death in Acanthamoeba. Antimicrobial Agents and Chemotherapy, 61(6) https://doi.org/10.1128/AAC.02660-16
  • Milani, A., Basirnejad, M., Shahbazi, S., & Bolhassani, A. (2017). Carotenoids: Biochemistry, pharmacology and treatment. British Journal of Pharmacology, 174(11), 1290–1324. https://doi.org/10.1111/bph.13625
  • Mills, S., & Willoughby, M. (1996). The EXTRACT database at the University of Exeter. Complementary Therapies in Medicine, 4(4), 268–270. https://doi.org/10.1016/S0965-2299(96)80090-2
  • Montagner, C., de Souza, S. M., Groposo, C., Delle Monache, F., Smânia, E. F., & Smânia, A. Jr, (2008). Antifungal activity of coumarins. Z Naturforsch C J Biosci, 63(1-2), 21–28. https://doi.org/10.1515/znc-2008-1-205
  • Morales, J., Mendoza, L., & Cotoras, M. (2017). Alteration of oxidative phosphorylation as a possible mechanism of the antifungal action of p-coumaric acid against Botrytis cinerea . Journal of Applied Microbiology, 123(4), 969–976. https://doi.org/10.1111/jam.13540
  • Murayama, M., Tsujimoto, K., Uozaki, M., Katsuyama, Y., Yamasaki, H., Utsunomiya, H., & Koyama, A. H. (2008). Effect of caffeine on the multiplication of DNA and RNA viruses. Molecular Medicine Reports, 1(2), 251–255.
  • Newman, R. A., Yang, P., Pawlus, A. D., & Block, K. I. (2008). Cardiac glycosides as novel cancer therapeutic agents. Molecular Interventions, 8(1), 36–49. https://doi.org/10.1124/mi.8.1.8
  • Ningthoujam, S. S., Talukdar, A. D., Potsangbam, K. S., & Choudhury, M. D. (2012). Challenges in developing medicinal plant databases for sharing ethnopharmacological knowledge. Journal of Ethnopharmacology, 141(1), 9–32. https://doi.org/10.1016/j.jep.2012.02.042
  • Nostro, A., Germanò, M. P., D'angelo, V., Marino, A., & Cannatelli, M. A. (2000). Extraction methods and bioautography for evaluation of medicinal plant antimicrobial activity. Letters in Applied Microbiology, 30(5), 379–384. https://doi.org/10.1046/j.1472-765x.2000.00731.x
  • Nunnari, G., Argyris, E., Fang, J., Mehlman, K. E., Pomerantz, R. J., & Daniel, R. (2005). Inhibition of HIV-1 replication by caffeine and caffeine-related methylxanthines. Virology, 335(2), 177–184. https://doi.org/10.1016/j.virol.2005.02.015
  • Ohyanagi, H., Takano, T., Terashima, S., Kobayashi, M., Kanno, M., Morimoto, K., Kanegae, H., Sasaki, Y., Saito, M., Asano, S., Ozaki, S., Kudo, T., Yokoyama, K., Aya, K., Suwabe, K., Suzuki, G., Aoki, K., Kubo, Y., Watanabe, M., Matsuoka, M., & Yano, K. (2015). Plant Omics Data Center: An integrated web repository for interspecies gene expression networks with NLP-based curation. Plant & Cell Physiology, 56(1), e9 https://doi.org/10.1093/pcp/pcu188
  • Ojha, D., & Patil, K. N. (2019). p-Coumaric acid inhibits the Listeria monocytogenes RecA protein functions and SOS response: An antimicrobial target. Biochemical and Biophysical Research Communications, 517(4), 655–661. https://doi.org/10.1016/j.bbrc.2019.07.093
  • Onwuliri, F., Mawak, J., Wonang, D., & Onwuliri, E. Phytochemical, toxicological and Histopathological studies of some medicinal plants in Nigeria, (2006).
  • Ou-Yang, S-s., Lu, J-y., Kong, X-q., Liang, Z-j., Luo, C., & Jiang, H. (2012). Computational drug discovery. Acta Pharmacologica Sinica, 33(9), 1131–1140. https://doi.org/10.1038/aps.2012.109
  • Ozturk, M., Egamberdieva, D., & Pešić, M. (2020). Biodiversity and Biomedicine: Our Future., Academic Press.
  • Ozturk, M., & Hakeem, K. R. (2019). Plant and Human Health, Volume 2: Phytochemistry and Molecular Aspects., Springer.
  • Ozturk, M., & Hakeem, K. R. (2019). Plant and Human Health, Volume 3: Pharmacology and Therapeutic Uses., Springer.
  • Öztürk, M., Altay, V., Hakeem, K. R., & Akçiçek, E. (2018). Liquorice: from botany to phytochemistry., Springer.
  • Parida, P., Bhowmick, S., Saha, A., & Islam, M. A. (2021). Insight into the screening of potential beta-lactamase inhibitors as anti-bacterial chemical agents through pharmacoinformatics study. Journal of Biomolecular Structure & Dynamics, 39(3), 923–942. https://doi.org/10.1080/07391102.2020.1720819
  • Parulekar, G. (2017). Antibacterial and phytochemical analysis of Ceiba pentandra (L.) seed extracts. Journal of Pharmacognosy and Phytochemistry, 6, 586–589.
  • Patel, N. B., Patel, L. N., Patel, K. D., Patel, M. V., & Kalasariya, H. S. ADMET & Cytotoxicity Prediction of Red Seaweed Gracillaria dura: An In Silico Approach, (2020).
  • Pereira, J. A., Oliveira, I., Sousa, A., Valentão, P., Andrade, P. B., Ferreira, I. C., Ferreres, F., Bento, A., Seabra, R., & Estevinho, L. (2007). Walnut (Juglans regia L.) leaves: Phenolic compounds, antibacterial activity and antioxidant potential of different cultivars. Food and Chemical Toxicology : An International Journal Published for the British Industrial Biological Research Association, 45(11), 2287–2295. https://doi.org/10.1016/j.fct.2007.06.004
  • Plaper, A., Golob, M., Hafner, I., Oblak, M., Šolmajer, T., & Jerala, R. (2003). Characterization of quercetin binding site on DNA gyrase. Biochemical and Biophysical Research Communications, 306(2), 530–536. https://doi.org/10.1016/S0006-291X(03)01006-4
  • Pothineni, V. R., Wagh, D., Babar, M. M., Inayathullah, M., Solow-Cordero, D., Kim, K.-M., Samineni, A. V., Parekh, M. B., Tayebi, L., & Rajadas, J. (2016). Identification of new drug candidates against Borrelia burgdorferi using high-throughput screening, Drug design. Development and Therapy, 10, 1307.
  • Prakash, O., Khan, F., Sangwan, R. S., & Misra, L. (2013). ANN-QSAR model for virtual screening of androstenedione C-skeleton containing phytomolecules and analogues for cytotoxic activity against human breast cancer cell line MCF-7. Combinatorial Chemistry & High Throughput Screening, 16(1), 57–72. https://doi.org/10.2174/1386207311316010008
  • Prassas, I., & Diamandis, E. P. (2008). Novel therapeutic applications of cardiac glycosides. Nature Reviews. Drug Discovery, 7(11), 926–935. https://doi.org/10.1038/nrd2682
  • Qidwai, T., Yadav, D. K., Khan, F., Dhawan, S., & Bhakuni, R. S. (2012). QSAR, docking and ADMET studies of artemisinin derivatives for antimalarial activity targeting plasmepsin II, a hemoglobin-degrading enzyme from P. falciparum. Current Pharmaceutical Design, 18(37), 6133–6154. https://doi.org/10.2174/138161212803582397
  • Ramanavičienė, A., Mostovojus, V., Bachmatova, I., & Ramanavičius, A. (2003). Antibacterial effect of caffeine on Escherichia coli and Pseudomonas fluorescens. Acta Medica Lituanica, 10, 185–188.
  • Rao, B. N. (2003). Bioactive phytochemicals in Indian foods and their potential in health promotion and disease prevention. Asia Pacific Journal of Clinical Nutrition, 12(1), 9-22.
  • Rathod, S., Patel, N., & Patel, P. (2011). A review on modification of analytical techniques in herbal research. International Journal of Research in Ayurveda & Pharmacy, 2(5), 1483-1485.
  • Raut, J. S., Chauhan, N. M., Shinde, R. B., & Karuppayil, S. M. (2013). Inhibition of planktonic and biofilm growth of Candida albicans reveals novel antifungal activity of caffeine. Journal of Medicinal Plants Research, 7, 777–782.
  • Rios, J., & Recio, M. (2005). Medicinal plants and antimicrobial activity. Journal of Ethnopharmacology, 100(1-2), 80–84. https://doi.org/10.1016/j.jep.2005.04.025
  • Rollinger, J. M., Haupt, S., Stuppner, H., & Langer, T. (2004). Combining ethnopharmacology and virtual screening for lead structure discovery: COX-inhibitors as application example. Journal of Chemical Information and Computer Sciences, 44(2), 480–488. https://doi.org/10.1021/ci030031o
  • Rønsted, N., Savolainen, V., Mølgaard, P., & Jäger, A. K. (2008). Phylogenetic selection of Narcissus species for drug discovery. Biochemical Systematics and Ecology, 36(5-6), 417–422. https://doi.org/10.1016/j.bse.2007.12.010
  • Sadeghi-Ghadi, Z., Vaezi, A., Ahangarkani, F., Ilkit, M., Ebrahimnejad, P., & Badali, H. (2020). Potent in vitro activity of curcumin and quercetin co-encapsulated in nanovesicles without hyaluronan against Aspergillus and Candida isolates. Journal de Mycologie Medicale, 30(4), 101014 https://doi.org/10.1016/j.mycmed.2020.101014
  • Sadiq, S., Rana, N. F., Zahid, M. A., Zargaham, M. K., Tanweer, T., Batool, A., Naeem, A., Nawaz, A., Muneer, Z., & Siddiqi, A. R. (2020). Virtual Screening of FDA-Approved Drugs against LasR of Pseudomonas aeruginosa for Antibiofilm Potential. Molecules, 25, 3723. https://doi.org/10.3390/molecules25163723
  • Samie, A., Tambani, T., Harshfield, E., Green, E., Ramalivhana, J., & Bessong, P. (2010). Antifungal activities of selected Venda medicinal plants against Candida albicans, Candida krusei and Cryptococcus neoformans isolated from South African AIDS patients. African Journal of Biotechnology,9(20), 2965-2976.
  • Saslis-Lagoudakis, C. H., Klitgaard, B. B., Forest, F., Francis, L., Savolainen, V., Williamson, E. M., & Hawkins, J. A. (2011). The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: An example from Pterocarpus (Leguminosae). PloS One, 6(7), e22275 https://doi.org/10.1371/journal.pone.0022275
  • Saxena, M. S., Nema, R., Sigh, D., & Gupta, A. (2013). Phytochemsitry of Medicinal Plants. Journal of Pharmacy and Phytochemistry, 1(6), 168–182.
  • Schmidt, R. J. (2001). The Botanical Dermatology Database (http://BoDD. cf. ac. uk): An Electronic Reincarnation of Mitchell and Rook'sBotanical Dermatology. Dermatitis, 12, 40–42.
  • Scotti, L., Ghasemi, J., & Scotti, M. T. (2018). Editorial: In Silico Methodologies Applied to Drug Discovery. Combinatorial Chemistry & High Throughput Screening, 21(3), 150–151. https://doi.org/10.2174/138620732103180423125817
  • Sen, G., Mukhopadhyay, S., Ray, M., & Biswas, T. (2008). Quercetin interferes with iron metabolism in Leishmania donovani and targets ribonucleotide reductase to exert leishmanicidal activity. Journal of Antimicrobial Chemotherapy, 61(5), 1066–1075. https://doi.org/10.1093/jac/dkn053
  • Sharma, V., & Sarkar, I. N. (2013). Bioinformatics opportunities for identification and study of medicinal plants. Briefings in Bioinformatics, 14(2), 238–250. https://doi.org/10.1093/bib/bbs021
  • Shiraki, K., & Rapp, F. (1988). Effects of caffeine on herpes simplex virus. Intervirology, 29(4), 235–240. https://doi.org/10.1159/000150050
  • Snow Setzer, M., Sharifi-Rad, J., & Setzer, W. N. (2016). The search for herbal antibiotics: An in-silico investigation of antibacterial phytochemicals. Antibiotics, 5(3), 30. https://doi.org/10.3390/antibiotics5030030
  • Song, P.-P., Zhao, J., Liu, Z.-L., Duan, Y.-B., Hou, Y.-P., Zhao, C.-Q., Wu, M., Wei, M., Wang, N.-H., Lv, Y., & Han, Z.-J. (2017). Evaluation of antifungal activities and structure-activity relationships of coumarin derivatives. Pest Management Science, 73(1), 94–101. https://doi.org/10.1002/ps.4422
  • Suhitha, S., Gunasekaran, K., & Velmurugan, D. (2012). Structure based design of compounds from natural sources for diabetes and inflammation. Bioinformation, 8(23), 1125–1131. https://doi.org/10.6026/97320630081125
  • Tang, Y., Zhu, W., Chen, K., & Jiang, H. (2006). New technologies in computer-aided drug design: Toward target identification and new chemical entity discovery. Drug Discovery Today. Technologies, 3(3), 307–313. https://doi.org/10.1016/j.ddtec.2006.09.004
  • Tempesti, T. C., Alvarez, M. G., de Araújo, M. F., Júnior, F. E. A. C., de Carvalho, M. G., & Durantini, E. N. (2012). Antifungal activity of a novel quercetin derivative bearing a trifluoromethyl group on Candida albicans. Medicinal Chemistry Research, 21(9), 2217–2222. https://doi.org/10.1007/s00044-011-9750-x
  • Thomas, M. B. (2008). Emerging synergies between information technology and applied ethnobotanical research. Ethnobotany Research and Applications, 1, 065–074. https://doi.org/10.17348/era.1.0.65-74
  • Tiwari, S., Gupta, N., Malairaman, U., & Shankar, J. (2017). Anti-aspergillus properties of phytochemicals against aflatoxin producing Aspergillus flavus and Aspergillus parasiticus. National Academy Science Letters, 40(4), 267–271. https://doi.org/10.1007/s40009-017-0569-y
  • Ulbricht, C., Chao, W., Costa, D., Rusie-Seamon, E., Weissner, W., & Woods, J. (2008). Clinical evidence of herb-drug interactions: A systematic review by the natural standard research collaboration. Current Drug Metabolism, 9(10), 1063–1120. https://doi.org/10.2174/138920008786927785
  • Unlu, A., Kirca, O., Ozdogan, M., & Nayır, E. (2016). High-dose vitamin C and cancer. Journal of Oncological Science, 1, 10–12. https://doi.org/10.1016/j.jons.2015.11.010
  • Valerio, L. G., Jr, Arvidson, K. B., Busta, E., Minnier, B. L., Kruhlak, N. L., & Benz, R. D. (2010). Testing computational toxicology models with phytochemicals. Molecular Nutrition & Food Research, 54(2), 186–194. https://doi.org/10.1002/mnfr.200900259
  • Van Emon, J. M. (2016). The omics revolution in agricultural research. Journal of Agricultural and Food Chemistry, 64(1), 36–44. https://doi.org/10.1021/acs.jafc.5b04515
  • Vijayakumar, S., Prabhu, S., Rajalakhsmi, S., & Manogar, P. (2016). Review on potential phytocompounds in drug development for Parkinson disease: A pharmacoinformatic approach. Informatics in Medicine Unlocked, 5, 15–25. https://doi.org/10.1016/j.imu.2016.09.002
  • W.H. Organization, National policy on traditional medicine and regulation of herbal medicines: Report of a WHO global survey, (2005).
  • Wang, Y., Wang, X., & Cheng, Y. (2006). A computational approach to botanical drug design by modeling quantitative composition-activity relationship. Chemical Biology & Drug Design, 68(3), 166–172. https://doi.org/10.1111/j.1747-0285.2006.00431.x
  • Wang, Y., Yan, W., Chen, Q., Huang, W., Yang, Z., Li, X., & Wang, X. (2017). Inhibition viral RNP and anti-inflammatory activity of coumarins against influenza virus. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 87, 583–588. https://doi.org/10.1016/j.biopha.2016.12.117
  • Wang, S., Yao, J., Zhou, B., Yang, J., Chaudry, M. T., Wang, M., Xiao, F., Li, Y., & Yin, W. (2018). Bacteriostatic effect of quercetin as an antibiotic alternative in vivo and its antibacterial mechanism in vitro. Journal of Food Protection, 81(1), 68–78. https://doi.org/10.4315/0362-028X.JFP-17-214
  • Wolfender, J.-L., Rudaz, S., Choi, Y. H., & Kim, H. K. (2013). Plant metabolomics: From holistic data to relevant biomarkers. Current Medicinal Chemistry, 20(8), 1056–1090. https://doi.org/10.2174/092986713805288932
  • Wootton, J. C. (2002). Development of HerbMed®: An interactive, evidence-based herbal database. Advances in Phytomedicine, Elsevier, 1, 55–60.
  • Wu, W., Li, R., Li, X., He, J., Jiang, S., Liu, S., & Yang, J. (2016). Quercetin as an antiviral agent inhibits influenza A virus (IAV) entry. Viruses, 8(1), 6. https://doi.org/10.3390/v8010006
  • Xue, C., Zhang, X., Liu, M., Hu, Z., & Fan, B. (2005). Study of probabilistic neural networks to classify the active compounds in medicinal plants. Journal of Pharmaceutical and Biomedical Analysis, 38(3), 497–507. https://doi.org/10.1016/j.jpba.2005.01.035
  • Yadav, R., & Agarwala, M. (2011). Phytochemical analysis of some medicinal plants. Journal of Phytology, 3(12), 10-14.
  • Yadav, D. K., Meena, A., Srivastava, A., Chanda, D., Khan, F., & Chattopadhyay, S. (2010). Development of QSAR model for immunomodulatory activity of natural coumarinolignoids, Drug design. Drug Design, Development and Therapy, 4, 173–186. https://doi.org/10.2147/dddt.s10875
  • Yang, S.-Y. (2010). Pharmacophore modeling and applications in drug discovery: Challenges and recent advances. Drug Discovery Today, 15(11-12), 444–450. https://doi.org/10.1016/j.drudis.2010.03.013
  • Yang, D., Du, X., Yang, Z., Liang, Z., Guo, Z., & Liu, Y. (2014). Transcriptomics, proteomics, and metabolomics to reveal mechanisms underlying plant secondary metabolism. Engineering in Life Sciences, 14(5), 456–466. https://doi.org/10.1002/elsc.201300075
  • Ye, H., Ye, L., Kang, H., Zhang, D., Tao, L., Tang, K., Liu, X., Zhu, R., Liu, Q., Chen, Y. Z., Li, Y., & Cao, Z. (2011). HIT: Linking herbal active ingredients to targets. Nucleic Acids Research, 39(Database issue), D1055–D1059. https://doi.org/10.1093/nar/gkq1165
  • Youns, M., Hoheisel, J. D., & Efferth, T. (2010). Toxicogenomics for the prediction of toxicity related to herbs from traditional Chinese medicine. Planta Medica, 76(17), 2019–2025. https://doi.org/10.1055/s-0030-1250432
  • Yue, Q.-X., Cao, Z.-W., Guan, S.-H., Liu, X.-H., Tao, L., Wu, W.-Y., Li, Y.-X., Yang, P.-Y., Liu, X., & Guo, D.-A. (2008). Proteomics characterization of the cytotoxicity mechanism of ganoderic acid D and computer-automated estimation of the possible drug target network. Molecular & Cellular Proteomics : MCP, 7(5), 949–961. https://doi.org/10.1074/mcp.M700259-MCP200
  • Zhao, J., Jiang, P., & Zhang, W. (2010). Molecular networks for the study of TCM pharmacology. Briefings in Bioinformatics, 11(4), 417–430. https://doi.org/10.1093/bib/bbp063

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