Vegetos

References

Agoni C, Olotu FA, Ramharack P, Soliman ME (2020) Druggability and drug-likeness concepts in drug design: are biomodelling and predictive tools having their say? J Mol Model 26(6). https://doi.org/10.1007/s00894-020-04385-6


Burki TK (2022) Omicron variant and booster COVID-19 vaccines. The Lancet Respiratory Medicine 10(2):e17. https://doi.org/10.1016/S2213-2600(21)00559-2


Cui Z, Liu P, Wang N, Wang L, Fan K, Zhu Q, Wang K, Chen R, Feng R, Jia Z, Yang M, Xu G, Zhu B, Fu W, Chu T, Feng L, Wang Y, Pei X, Yang P, …, Wang X (2022) Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell 185(5):860–871e13. https://doi.org/10.1016/j.cell.2022.01.019


Diaza RG, Manganelli S, Esposito A, Roncaglioni A, Manganaro A, Benfenati E (2015) Comparison of in silico tools for evaluating rat oral acute toxicity. SAR QSAR Environ Res 26(1):1–27. https://doi.org/10.1080/1062936X.2014.977819


Dyer O (2021) Covid-19: Omicron is causing more infections but fewer hospital admissions than delta, south african data show. BMJ (Clinical Research Ed) 375(November):n3104. https://doi.org/10.1136/bmj.n3104


Eberhardt J, Santos-Martins D, Tillack AF, Forli S (2021) AutoDock Vina 1.2.0: new docking methods, expanded force field, and Python Bindings. J Chem Inf Model 61(8):3891–3898. https://doi.org/10.1021/acs.jcim.1c00203


Fan Y, Li X, Zhang L (2022) SARS-CoV-2 Omicron variant: recent progress and future perspectives. April. https://doi.org/10.1038/s41392-022-00997-x


Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KHD, Dingens AS, Nargi RS, Sutton RE, Suryadevara N, Rothlauf PW, Liu Z, Whelan SPJ, Carnahan RH, Crowe JE, Bloom JD (2021) Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Cell Host and Microbe 29(1):44–57e9. https://doi.org/10.1016/j.chom.2020.11.007


Gurung AB, Ali MA, Lee J, Farah MA, Al-Anazi KM (2020) Unravelling lead antiviral phytochemicals for the inhibition of SARS-CoV-2 mpro enzyme through in silico approach. Life Sci 255:117831. https://doi.org/10.1016/j.lfs.2020.117831


Halberstein RA (2005) Medicinal plants: historical and cross-cultural usage patterns. Ann Epidemiol 15(9):686–699. https://doi.org/10.1016/j.annepidem.2005.02.004


Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, Ludden C, Reeve R, Rambaut A, Peacock SJ, Robertson DL (2021) SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol 19(7):409–424. https://doi.org/10.1038/s41579-021-00573-0


Hetz C, Zhang K, Kaufman RJ (2020) Mechanisms, regulation and functions of the unfolded protein response. Nat Rev Mol Cell Biol 21(8):421–438. https://doi.org/10.1038/s41580-020-0250-z


Karim SSA, Karim QA (2021) Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic. The Lancet 398(10317):2126–2128. https://doi.org/10.1016/S0140-6736(21)02758-6


Khalifa SAM, Mohamed BS, Elashal MH, Du M, Guo Z, Zhao C, Musharraf SG, Boskabady MH, El-Seedi HHR, Efferth T, El-Seedi HR (2020) Comprehensive overview on multiple strategies fighting covid-19. Int J Environ Res Public Health 17(16):1–13. https://doi.org/10.3390/ijerph17165813


Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE (2021) PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Res 49(D1):D1388–D1395. https://doi.org/10.1093/nar/gkaa971


López-Blanco JR, Aliaga JI, Quintana-Ortí ES, Chacón P (2014) IMODS: Internal coordinates normal mode analysis server. Nucleic Acids Res 42(W1):271–276. https://doi.org/10.1093/nar/gku339


Mani JS, Johnson JB, Steel JC, Broszczak DA, Neilsen PM, Walsh KB, Naiker M (2020) Natural product-derived phytochemicals as potential agents against coronaviruses: a review. Virus Res 284:197989. https://doi.org/10.1016/j.virusres.2020.197989


Mannar D, Saville JW, Zhu X, Srivastava SS, Berezuk AM, Tuttle KS, Marquez AC, Sekirov I, Subramaniam S (2022) SARS-CoV-2 Omicron variant: antibody evasion and cryo-EM structure of spike protein–ACE2 complex. Science 375(6582):760–764. https://doi.org/10.1126/science.abn7760


May A, Sieker F, Zacharias M (2008) How to efficiently include receptor flexibility during computational docking. Curr Comput Aided-Drug Des 4(2):143–153. https://doi.org/10.2174/157340908784533265


Mukherjee I, Chakrabarti S (2021) Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes. Comput Struct Biotechnol J 19:3779–3795. https://doi.org/10.1016/j.csbj.2021.06.039


Murgueitio MS, Bermudez M, Mortier J, Wolber G (2012) In silico virtual screening approaches for anti-viral drug discovery. Drug Discovery Today: Technologies 9(3):219–225. https://doi.org/10.1016/j.ddtec.2012.07.009


O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel Journal of Cheminformatics 3(33):1–14. https://jcheminf.biomedcentral.com/track/pdf/https://doi.org/10.1186/1758-2946-3-33


Plewczynski D, Hoffmann M, Von Grotthuss M, Ginalski K, Rychewski L (2007) In silico prediction of SARS protease inhibitors by virtual high throughput screening. Chem Biology Drug Des 69(4):269–279. https://doi.org/10.1111/j.1747-0285.2007.00475.x


Rabi FA, Zoubi A, Al-Nasser MS, Kasasbeh AD, G. A., Salameh DM (2020) Sars-cov-2 and coronavirus disease 2019: what we know so far. Pathogens 9(3):1–14. https://doi.org/10.3390/pathogens9030231


Raj U, Varadwaj PK (2016) Flavonoids as multi-target inhibitors for Proteins Associated with Ebola Virus: in Silico Discovery using virtual screening and molecular Docking Studies. Interdisciplinary Sci – Comput Life Sci 8(2):132–141. https://doi.org/10.1007/s12539-015-0109-8


Raschka S, Wolf AJ, Bemister-Buffington J, Kuhn LA (2018) Protein–ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes. J Comput Aided Mol Des 32(4):511–528. https://doi.org/10.1007/s10822-018-0105-2


Sayed AM, Khattab AR, AboulMagd AM, Hassan HM, Rateb ME, Zaid H, Abdelmohsen UR (2020) Nature as a treasure trove of potential anti-SARS-CoV drug leads: a structural/mechanistic rationale. RSC Adv 10(34):19790–19802. https://doi.org/10.1039/d0ra04199h


Sirois S, Wei DQ, Du Q, Chou KC (2004) Virtual screening for SARS-CoV protease based on KZ7088 pharmacophore points. J Chem Inf Comput Sci 44(3):1111–1122. https://doi.org/10.1021/ci034270n


Sun Z, Liu Q, Qu G, Feng Y, Reetz MT (2019) Utility of B-Factors in protein science: interpreting rigidity, flexibility, and Internal Motion and Engineering thermostability [Review-article]. Chem Rev. https://doi.org/10.1021/acs.chemrev.8b00290


Vidal-Limon A, Aguilar-Toalá JE, Liceaga AM (2022) Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for studying Food Proteins and bioactive peptides. J Agric Food Chem 70(4):934–943. https://doi.org/10.1021/acs.jafc.1c06110


Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, Hinsley WR, Laydon DJ, Dabrera G, O’Toole Á, Amato R, Ragonnet-Cronin M, Harrison I, Jackson B, Ariani CV, Boyd O, Loman NJ, McCrone JT, Gonçalves S, …, Ferguson NM (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature 593(7858):266–269. https://doi.org/10.1038/s41586-021-03470-x


Zakaryan H, Arabyan E, Oo A, Zandi K (2017) Flavonoids: promising natural compounds against viral infections. Arch Virol 162(9):2539–2551. https://doi.org/10.1007/s00705-017-3417-y


Zhang XQ, Xu X, Bertrand N, Pridgen E, Swami A, Farokhzad OC (2012) Interactions of nanomaterials and biological systems: implications to personalized nanomedicine. Adv Drug Deliv Rev 64(13):1363–1384. https://doi.org/10.1016/j.addr.2012.08.005


Zhao C, Montaseri MH, Wood GS, Pu SH, Seshia AA, Kraft M (2016) A review on coupled MEMS resonators for sensing applications utilizing mode localization. Sens Actuators A 249:93–111. https://doi.org/10.1016/j.sna.2016.07.015


Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS, Sampson JM, Schön A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry M, Stephens T, Stuckey J, Teng IT, Wang P, …, Kwong PD (2020) Cryo-EM Structures of SARS-CoV-2 spike without and with ACE2 reveal a pH-Dependent switch to mediate endosomal positioning of receptor-binding domains. Cell Host and Microbe 28(6):867–879e5. https://doi.org/10.1016/j.chom.2020.11.004


Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A (2016) Coarse-grained protein models and their applications. Chem Rev 116:7898–7936


Sumera A, Waseem F, Fatima M, Malik A, Ali N, Zahid A, S (2022) Molecular Docking and Molecular Dynamics Studies reveal secretory proteins as novel targets of Temozolomide in Glioblastoma Multiforme. Molecules 27:7198. https://doi.org/10.3390/molecules27217198


Fatriansyah JF, Rizqillah RK, Yandi MY, Fadilah, Sahlan M (2022) Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2. J King Saud Univ - Sci 34(1):101707. https://doi.org/10.1016/J.JKSUS.2021.101707





Pandit A, Shukla AK, Deepika, Vaidya D, Kumari A, Kumar A (2023) In vitro Assessment of Anti-Microbial Activity of Aloe vera (Barbadensis miller) supported through computational studies. Russ J Bioorg Chem. https://doi.org/10.1134/S1068162023020188