Natural derivatives with dual binding potential against SARS-CoV-2 main protease and human ACE2 possess low oral bioavailability: a brief computational analysis

References

• Farag, A., Wang, P., Ahmed, M., and Sadek, H. (2020). Identification of FDA Approved Drugs Targeting COVID-19 Virus by Structure-Based Drug Repositioning (Version 2). https://doi.org/10.26434/CHEMRXIV.12049647.V1.
   Google Scholar
• Arts, I. C. W., Sesink, A. L. A., Faassen-Peters, M., & Hollman, P. C. H. (2004). The type of sugar moiety is a major determinant of the small intestinal uptake and subsequent biliary excretion of dietary quercetin glycosides. The British Journal of Nutrition, 91(6), 841–847. https://doi.org/https://doi.org/10.1079/BJN20041123
   PubMed Web of Science ®Google Scholar
• Cheng, T., Zhao, Y., Li, X., Lin, F., Xu, Y., Zhang, X., Li, Y., Wang, R., & Lai, L. (2007). Computation of octanol-water partition coefficients by guiding an additive model with knowledge. Journal of Chemical Information and Modeling, 47(6), 2140–2148. https://doi.org/https://doi.org/10.1021/ci700257y
   PubMed Web of Science ®Google Scholar
• Coleman, C. M., Liu, Y. V., Mu, H., Taylor, J. K., Massare, M., Flyer, D. C., Glenn, G. M., Smith, G. E., & Frieman, M. B. (2014). Purified coronavirus spike protein nanoparticles induce coronavirus neutralizing antibodies in mice. Vaccine, 32 (26), 3169–3174. https://doi.org/https://doi.org/10.1016/j.vaccine.2014.04.016
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717–42713. https://doi.org/https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Das, S., Sarmah, S., Lyndem, S., & Roy, A. S. (2020). An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study. ” Journal of Biomolecular Structure and Dynamics, May, 1–11. https://doi.org/10.1080/07391102.2020.1763201.
   Google Scholar
• Delaney, J. S. (2004). ESOL: Estimating aqueous solubility directly from molecular structure. Journal of Chemical Information and Computer Sciences, 44(3), 1000–1005. https://doi.org/https://doi.org/10.1021/ci034243x
   PubMedGoogle Scholar
• Emam, A. M., R. Elias, A. M. Moussa, R. Faure, L. Debrauwer, and G. Balansard. (1998). Two Flavonoid Triglycosides from Buddleja Madagascariensis. Phytochemistry, 48(4), 739–42. https://doi.org/10.1016/S0031-9422(97)01043-1.
   Google Scholar
• FDA. (2020). Hydroxychloroquine fact sheet for health care providers, 1–7.
   Google Scholar
• Filipiak, K., Hidalgo, M., Silvan, J. M., Fabre, B., Carbajo, R. J., Pineda-Lucena, A., Ramos, A., De Pascual-Teresa, B., & De Pascual-Teresa, S. (2014). Dietary gallic acid and anthocyanin cytotoxicity on human fibrosarcoma HT1080 cells. A study on the mode of action. Food & Function, 5(2), 381–389. https://doi.org/https://doi.org/10.1039/c3fo60465a
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/https://doi.org/10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Fujimori, K., & Shibano, M. (2013). Avicularin, a plant flavonoid, suppresses lipid accumulation through repression of C/EBPα-activated GLUT4-mediated glucose uptake in 3T3-L1 cells. Journal of Agricultural and Food Chemistry, 61(21), 5139–5147. https://doi.org/https://doi.org/10.1021/jf401154c
   PubMed Web of Science ®Google Scholar
• Fukunaga, T., Nishiya, K., Kajikawa, I., Takeya, K., & Itokawa, H. (1989). Studies on the constituents of Japanese mistletoes from different host trees, and their antimicrobial and hypotensive properties. Chemical & Pharmaceutical Bulletin, 37(6), 1543–1546. https://doi.org/https://doi.org/10.1248/cpb.37.1543
   PubMed Web of Science ®Google Scholar
• Gautret, P., Lagier, J.-C., Parola, P., Hoang, V. T., Meddeb, L., Mailhe, M., Doudier, B., Courjon, J., Giordanengo, V., Vieira, V. E., Dupont, H. T., Honoré, S., Colson, P., Chabrière, E., La Scola, B., Rolain, J.-M., Brouqui, P., & Raoult, D. (2020). Hydroxychloroquine and azithromycin as a treatment of COVID-19: Results of an open-label non-randomized clinical trial. International Journal of Antimicrobial Agents, 105949. https://doi.org/https://doi.org/10.1016/j.ijantimicag.2020.105949
   Google Scholar
• Guimarães, C. R. W., & Cardozo, M. (2008). MM-GB/SA rescoring of docking poses in structure-based lead optimization. Journal of Chemical Information and Modeling, 48(5), 958–970. https://doi.org/https://doi.org/10.1021/ci800004w
   PubMed Web of Science ®Google Scholar
• Guo, X. F., Liu, J. P., Ma, S. Q., Zhang, P., & De Sun, W. (2018). Avicularin reversed multidrug-resistance in human gastric cancer through enhancing Bax and BOK expressions. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 103, 67–74. https://doi.org/https://doi.org/10.1016/j.biopha.2018.03.110
   PubMed Web of Science ®Google Scholar
• Hu, D., Zhu, C., Ai, L., He, T., Wang, Y., Ye, F., Yang, L., Ding, C., Zhu, X., Lv, R., Zhu, J., Hassan, B., Feng, Y., Tan, W., & Wang, C. (2018). Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats. Emerging Microbes & Infections, 7(1), 1–10. https://doi.org/https://doi.org/10.1038/s41426-018-0155-5
   Web of Science ®Google Scholar
• Islam, R., Parves, R., Paul, A. S., Uddin, N., Rahman, M. S., Mamun, A. A., Hossain, M. N., Ali, M. A., & Halim, M. A. (2020). A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2. Journal of Biomolecular Structure & Dynamics, 1–20. https://doi.org/https://doi.org/10.1080/07391102.2020.1761883.
   PubMed Web of Science ®Google Scholar
• Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of Mpro from COVID-19 virus and discovery of its inhibitors. Nature, 582(7811), 289–293. . https://doi.org/https://doi.org/10.1038/s41586-020-2223-y
   PubMed Web of Science ®Google Scholar
• Khaerunnisa, S., Kurniawan, H., Awaluddin, R., & Suhartati, S. (2020). Potential inhibitor of COVID-19 main protease (M pro) from several medicinal plant compounds by molecular docking study. Preprints, 1–14. https://doi.org/https://doi.org/10.20944/preprints202003.0226.v1.
   Google Scholar
• Lalit, S., & Vyomesh, J. (2020). Comparative docking analysis of rational drugs against COVID-19 main protease. ChemRxiv. https://doi.org/https://doi.org/10.26434/chemrxiv.12136002.v1.
   Google Scholar
• Liu, H., Ye, F., Sun, Q., Liang, H., Li, C., Lu, R., Huang, B., Tan, W., & Lai, L. (2020). Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro. BioRxiv, 2020.04.10.035824. https://doi.org/https://doi.org/10.1101/2020.04.10.035824.
   Google Scholar
• Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., … Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. The Lancet, 395(10224), 565–574. https://doi.org/https://doi.org/10.1016/S0140-6736(20)30251-8
   PubMed Web of Science ®Google Scholar
• Manish, M. (2020). Studies on computational molecular interaction between SARS-CoV-2 main protease and natural products. ChemRxiv, Preprint. https://doi.org/https://doi.org/10.26434/chemrxiv.12024789.v1.
   Google Scholar
• Martin, Y. C. (2005). A bioavailability score. Journal of Medicinal Chemistry, 48(9), 3164–3170. https://doi.org/https://doi.org/10.1021/jm0492002
   PubMed Web of Science ®Google Scholar
• Mazewski, C., Kim, M. S., & Gonzalez de Mejia, E. (2019). Anthocyanins, delphinidin-3-O-glucoside and cyanidin-3-O-glucoside, inhibit immune checkpoints in human colorectal cancer cells in vitro and in silico. Scientific Reports, 9(1), 1–15. https://doi.org/https://doi.org/10.1038/s41598-019-47903-0
   PubMedGoogle Scholar
• McGhie, T. K., & Walton, M. C. (2007). The bioavailability and absorption of anthocyanins: Towards a better understanding. Molecular Nutrition & Food Research, 51(6), 702–713. https://doi.org/https://doi.org/10.1002/mnfr.200700092
   PubMed Web of Science ®Google Scholar
• Mereles, D., & Hunstein, W. (2011). Epigallocatechin-3-Gallate (EGCG) for clinical trials: More pitfalls than promises? International Journal of Molecular Sciences, 12(9), 5592–5603. https://doi.org/https://doi.org/10.3390/ijms12095592
   PubMed Web of Science ®Google Scholar
• Micael, D., de Oliveira, L., & de Oliveira Kelson Mota, T. (2020). Comparative computational study of SARS-CoV-2 receptors antagonists from already approved drugs. ChemRxiv. https://doi.org/https://doi.org/10.26434/chemrxiv.12044538.v2.
   Google Scholar
• Mittal, L., Kumari, A., Srivastava, M., Singh, M., & Asthana, S. (2020). Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach. ChemRxiv, (1). Preprint. https://doi.org/https://doi.org/10.26434/CHEMRXIV.12086565.V2.
   Google Scholar
• Okonogi, S., Kheawfu, K., Holzer, W., Unger, F. M., Viernstein, H., & Mueller, M. (2016). Anti-inflammatory effects of compounds from Polygonum odoratum. Natural Product Communications, 11(11), 1651–1654. https://doi.org/https://doi.org/10.1177/1934578X1601101107
   PubMed Web of Science ®Google Scholar
• Pandit, M. n.d. In silico studies reveal potential antiviral activity of phytochemicals from medicinal plants for the treatment of COVID-19 infection. 1–38. https://doi.org/https://doi.org/10.21203/rs.3.rs-22687/v1.
   Google Scholar
• Paul, A., Banerjee, K., Goon, A., & Saha, S. (2018). Chemo-profiling of anthocyanins and fatty acids present in pomegranate aril and seed grown in Indian condition and its bioaccessibility study. Journal of Food Science and Technology, 55(7), 2488–2496. https://doi.org/https://doi.org/10.1007/s13197-018-3166-2
   PubMed Web of Science ®Google Scholar
• Rehecho, S., Hidalgo, O., García-Iñiguez de Cirano, M., Navarro, I., Astiasarán, I., Ansorena, D., Cavero, R. Y., & Calvo, M. I. (2011). Chemical composition, mineral content and antioxidant activity of Verbena officinalis L. LWT - Food Science and Technology, 44(4), 875–882. https://doi.org/https://doi.org/10.1016/j.lwt.2010.11.035
   Web of Science ®Google Scholar
• Rhoades, A. (2020). Remdesivir EUA letter of authorization. 564, 1–6.
   Google Scholar
• Roh, C. (2012). A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide. International Journal of Nanomedicine, 7, 2173–2179. https://doi.org/https://doi.org/10.2147/IJN.S31379
   PubMed Web of Science ®Google Scholar
• Rota, P. A., Oberste, M. S., Monroe, S. S., Nix, W. A., Campagnoli, R., Icenogle, J. P., Peñaranda, S., Bankamp, B., Maher, K., Chen, M.-H., Tong, S., Tamin, A., Lowe, L., Frace, M., DeRisi, J. L., Chen, Q., Wang, D., Erdman, D. D., Peret, T. C. T., … Bellini, W. J. (2003). Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science, 300(5624), 1394–1399. https://doi.org/https://doi.org/10.1126/science.1085952
   PubMed Web of Science ®Google Scholar
• Stenlid, G. (1976). Effects of substituents in the A-ring on the physiological activity of flavones. Phytochemistry, 15 (6), 911–912. https://doi.org/https://doi.org/10.1016/S0031-9422(00)84368-X
   Web of Science ®Google Scholar
• Tallei, T., Tumilaar, S., Niode, N., Fatimawali, Kepel, B., Idroes, R. & Effendi, Y. (2020). Potential of plant bioactive compounds as SARS-CoV-2 main protease (Mpro) and spike (S) glycoprotein inhibitors: A molecular docking study. Preprints, no. 1–18. https://doi.org/https://doi.org/10.20944/preprints202004.0102.v1.
   Google Scholar
• Towler, P., Staker, B., Prasad, S. G., Menon, S., Tang, J., Parsons, T., Ryan, D., Fisher, M., Williams, D., Dales, N. A., Patane, M. A., & Pantoliano, M. W. (2004). ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis. The Journal of Biological Chemistry, 279(17), 17996–17997. https://doi.org/https://doi.org/10.1074/jbc.M311191200
   PubMed Web of Science ®Google Scholar
• Ubani, A., Agwom, F., Shehu, N. Y., Luka, P., Umera, E. A., Umar, U., Omale, S., Nnadi, E., & Aguiyi, J. C. (2020). Molecular docking analysis of some phytochemicals on two SARS-CoV-2 targets. BioRxiv, 2020.03.31.017657. https://doi.org/https://doi.org/10.1101/2020.03.31.017657.
   Google Scholar
• Walle, T. (2004). Absorption and metabolism of flavonoids. Free Radical Biology & Medicine, 36(7), 829–837. https://doi.org/https://doi.org/10.1016/j.freeradbiomed.2004.01.002
   PubMed Web of Science ®Google Scholar
• Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., Shi, Z., Hu, Z., Zhong, W., & Xiao, G. (2020). Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-NCoV) in vitro. Cell Research, 30(3), 269–271. https://doi.org/https://doi.org/10.1038/s41422-020-0282-0
   PubMed Web of Science ®Google Scholar
• Wang, Q., Zhang, Y., Wu, L., Niu, S., Song, C., Zhang, Z., Lu, G., Qiao, C., Hu, Y., Yuen, K.-Y., Wang, Q., Zhou, H., Yan, J., & Qi, J. (2020). Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell, 181(4), 894–904.e9. https://doi.org/https://doi.org/10.1016/j.cell.2020.03.045
   PubMed Web of Science ®Google Scholar
• Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., Yuan, M.-L., Zhang, Y.-L., Dai, F.-H., Liu, Y., Wang, Q.-M., Zheng, J.-J., Xu, L., Holmes, E. C., & Zhang, Y.-Z. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265–269. https://doi.org/https://doi.org/10.1038/s41586-020-2008-3
   PubMed Web of Science ®Google Scholar
• Yao, X., Ye, F., Zhang, M., Cui, C., Huang, B., Niu, P., Liu, X., Zhao, L., Dong, E., Song, C., Zhan, S., Lu, R., Li, H., Tan, W., & Liu, D. (2020). In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 1–8. Clinical Infectious Diseases. . https://doi.org/https://doi.org/10.1093/cid/ciaa237
   Google Scholar
• Yuan, Y., Cao, D., Zhang, Y., Ma, J., Qi, J., Wang, Q., Lu, G., Wu, Y., Yan, J., Shi, Y., Zhang, X., & Gao, G. F. (2017). Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Nature Communications, 8, 15092–15099. https://doi.org/https://doi.org/10.1038/ncomms15092
   PubMed Web of Science ®Google Scholar
• Yuldashev, M. P. (2002). Flavonoids of the aerial part of Trigonella grandiflora. Chemistry of Natural Compounds, 38(3), 291–292. https://doi.org/https://doi.org/10.1023/A:1020448531522
   Web of Science ®Google Scholar
• Zhang, X. Q., and Xu, L. S. (1989). Determination of avicularin in Polygonum aviculare L. by square wave polarography. Proc Chin Acad Med Sci Peking Union Med Coll, 4(4),193–195.
   Google Scholar
• Zhang, H., Penninger, J. M., Li, Y., Zhong, N., & Slutsky, A. S. (2020). Angiotensin-Converting Enzyme 2 (ACE2) as a SARS-CoV-2 receptor: Molecular mechanisms and potential therapeutic target. Intensive Care Medicine, 46(4), 586–590. https://doi.org/https://doi.org/10.1007/s00134-020-05985-9
   PubMed Web of Science ®Google Scholar
• Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., Chen, H.-D., Chen, J., Luo, Y., Guo, H., Jiang, R.-D., Liu, M.-Q., Chen, Y., Shen, X.-R., Wang, X., … Shi, Z.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi.org/https://doi.org/10.1038/s41586-020-2012-7
   PubMed Web of Science ®Google Scholar
• Zhou, Y., Hou, Y., Shen, J., Huang, Y., Martin, W., & Cheng, F. (2020). Network-based drug repurposing for novel coronavirus 2019-NCoV/SARS-CoV-2. Cell Discovery, 6(1), 14 . https://doi.org/https://doi.org/10.1038/s41421-020-0153-3
   PubMed Web of Science ®Google Scholar