Identification of potent COVID-19 main protease inhibitors by loading of favipiravir on Mg₁₂O₁₂ and Zn₁₂O₁₂ nanoclusters: an in silico strategy for COVID-19 treatment

References

• Abd El-Mageed, H. R. (2020). Zinc oxide nanoclusters and nanoparticles as a drug carrier for cisplatin and nedaplatin anti-cancer drugs, insights from DFT methods and MC simulation. Molecular Physics, e1842533.
   Web of Science ®Google Scholar
• Ahmed, S. A., Rahman, A. A., Elsayed, K. N. M., Abd El-Mageed, H. R., Mohamed, H. S., & Ahmed, S. A. (2021). Cytotoxic activity, molecular docking, pharmacokinetic properties and quantum mechanics calculations of the brown macroalga Cystoseiratrinodis compounds. Journal of Biomolecular Structure and Dynamics, 39(11), 3855–3873. https://doi.org/10.1080/07391102.2020.1774418
   PubMed Web of Science ®Google Scholar
• AIMAll (Version 19.02.13) (2019). Todd A. Keith, TK Gristmill Software, Overland Park KS, USA, aim.tkgristmill.com
   Google Scholar
• Ali, T. T., Narasimharao, K., Parkin, I. P., Carmalt, C. J., Sathasivam, S., Basahel, S. N., Bawaked, S. M., & Al-Thabaiti, S. A. (2015). Effect of pretreatment temperature on the photocatalytic activity of microwave irradiated porous nanocrystalline ZnO. New Journal of Chemistry, 39(1), 321–332. https://doi.org/10.1039/C4NJ01465K
   Web of Science ®Google Scholar
• Al-Masoudi, N. A., Elias, R. S., & Saeed, B. (2020). Molecular docking studies of some antiviral and antimalarial drugs via bindings to 3CL-protease and polymerase enzymes of the novel coronavirus (SARS-CoV-2). Biointerface Research in Applied Chemistry, 10(5), 6444–6459.
   Web of Science ®Google Scholar
• Azam, A., Ahmed, A. S., Oves, M., Khan, M. S., Habib, S. S., & Memic, A. (2012). Antimicrobial activity of metal oxide nanoparticles against Gram-positive and Gram-negative bacteria: a comparative study. International Journal of Nanomedicine, 7, 6003–6009. https://doi.org/10.2147/IJN.S35347
   PubMed Web of Science ®Google Scholar
• Baker, N. A., Sept, D., Joseph, S., Holst, M. J., & McCammon, J. A. (2001). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences, 98(18), 10037–10041. 181342398 https://doi.org/10.1073/pnas
   PubMed Web of Science ®Google Scholar
• Bastikar, V. A., Bastikar, A. V., & Chhajed, S. S. (2020). Understanding the role of natural medicinal compounds such as curcumin and allicin against SARS-CoV-2 proteins as potential treatment against COVID-19: An in silico approach. Journal of Proteomics and Bioinformatics, 13, 7. https://doi.org/10.35248/0974-276X.1000510
   Google Scholar
• Bhardwaj, V. K., Singh, R., Das, P., & Purohit, R. (2021). Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs. Computers in Biology and Medicine, 128, 104117. https://doi.org/10.1016/j.compbiomed.2020.104117
   PubMed Web of Science ®Google Scholar
• Cai, Q., Yang, M., Liu, D., Chen, J., Shu, D., Xia, J., Liao, X., Gu, Y., Cai, Q., Yang, Y., Shen, C., Li, X., Peng, L., Huang, D., Zhang, J., Zhang, S., Wang, F., Liu, J., Chen, L., … Liu, L. (2020). Experimental treatment with favipiravir for COVID-19: An open-label control study. Engineering, 6(10), 1192–1198. https://doi.org/10.1016/j.eng.2020.03.007
   Web of Science ®Google Scholar
• Chai, J.-D., & Head-Gordon, M. (2008). Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Physical Chemistry Chemical Physics : PCCP, 10(44), 6615e6620–6615e6620. https://doi.org/10.1039/b810189b
   Web of Science ®Google Scholar
• Chandraboss, V. L., Karthikeyan, B., & Senthilvelan, S. (2014). Experimental and first principle study of guanine adsorption on ZnO clusters. Physical Chemistry Chemical Physics : PCCP, 16(42), e23461–e23475. https://doi.org/10.1039/c4cp03274h
   PubMed Web of Science ®Google Scholar
• Chen, X., Sun, Z., Zhang, H., & Onsori, S. (2020). Effect of metal atoms on the electronic properties of metal oxide nanoclusters for use in drug delivery applications: A density functional theory study. Molecular Physics, 118(13), e1692150. https://doi.org/10.1080/00268976.2019.1692150
   Web of Science ®Google Scholar
• Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. In Chemical biology (pp. 243–250). Springer.
   Google Scholar
• El-Mageed, H. A., Mustafa, F. M., & Abdel-Latif, M. K. (2020). Boron nitride nanoclusters, nanoparticles and nanotubes as a drug carrier for isoniazid anti-tuberculosis drug, computational chemistry approaches. Journal of Biomolecular Structure and Dynamics, 1–10.
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M. … Fox, D. J. (2003). Gaussian 09, Revision A.1. Gaussian Inc.
   Google Scholar
• Haertelt, M., Fielicke, A., Meijer, G., Kwapien, K., Sierka, M., & Sauer, J. (2012). Structure determination of neutral MgO clusters—hexagonal nanotubes and cages. Physical Chemistry Chemical Physics : PCCP, 14(8), 2849–2856. https://doi.org/10.1039/c2cp23432g
   PubMed Web of Science ®Google Scholar
• Javarsineh, S. A., Vessally, E., Bekhradnia, A., Hosseinian, A., & Ahmadi, S. (2018). A Computational study on the purinethol drug adsorption on the AlN nanocone and nanocluster. Journal of Cluster Science, 29(4), 767–775. https://doi.org/10.1007/s10876-018-1381-7
   Web of Science ®Google Scholar
• Kalia, M., Singh, P. K., Yadav, V. K., Yadav, B. S., Sharma, D., Narvi, S. S., Mani, A., & Agarwal, V. (2017). Structure based virtual screening for identification of potential quorum sensing inhibitors against LasR master regulator in Pseudomonas aeruginosa. Microbial Pathogenesis, 107, 136–143. https://doi.org/10.1016/j.micpath.2017.03.026
   PubMed Web of Science ®Google Scholar
• Khaerunnisa, S., Kurniawan, H., Awaluddin, R., Suhartati, S., & Soetjipto, S. (2020). Potential inhibitor of COVID-19 main protease (Mpro) from several medicinal plant compounds by molecular docking study. Preprints, 20944, 1–14. https://doi.org/10.20944/preprints202003.0226
   Google Scholar
• Koopmans, T. (1933). Physica, 1, 104.
   Google Scholar
• Kumar, S., Song, T. K., Gautam, S., Chae, K. H., Kim, S. S., & Jang, K. W. (2015). Structural, magnetic and electronic structure properties of Co doped ZnO nanoparticles. Materials Research Bulletin, 66, 76–82. https://doi.org/10.1016/j.materresbull.2015.02.020
   Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A. (2014). g_mmpbsa-A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Lopes, S. M., de Medeiros, H. I., Scotti, M. T., & Scotti, L. (2022). Natural products against COVID-19 inflammation: A mini-review. Combinatorial Chemistry & High Throughput Screening, 25(14), 2358–2369. https://doi.org/10.2174/1386207325666220128114547
   PubMed Web of Science ®Google Scholar
• Martínez, L., Andrade, R., Birgin, E. G., & Martínez, J. M. (2009). PACKMOL: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13), 2157–2164. https://doi.org/10.1002/jcc.21224
   PubMed Web of Science ®Google Scholar
• Mohammadreza, A., Molaakbari, E., Mostafavi, P., Salarizadeh, N., Eshaghi Maleksah, R., & Afzali, D. (2022). Investigation of Cu metal nanoparticles with different morphologies to inhibit SARS-CoV-2 main protease and spike glycoprotein using Molecular Docking and Dynamics Simulation. Journal of Molecular Structure, 1253, 132301.
   PubMed Web of Science ®Google Scholar
• Needle, D., Lountos, G. T., & Waugh, D. S. (2015). Structures of the Middle East respiratory syndrome 274 coronavirus 3C-like protease reveal insights into substrate specificity. Acta Crystallographica. Section D, Biological Crystallography, 71(Pt 5), 1102–1111. https://doi.org/10.1107/S1399004715003521
   PubMedGoogle Scholar
• Oliveira, L. D., Davi, M., Oliveira, T. D., & Mota, K. (2020). Comparative computational study of SARS-CoV2 receptors antagonists from already approved drugs. ChemRxiv, 10.
   Google Scholar
• Padash, A., Esfahani, M. R., & Rad, A. S. (2020). The computational quantum mechanical study of sulfamide drug adsorption onto X12Y12 fullerenelikenanocages: Detailed DFT and QTAIM investigations. Journal of Biomolecular Structure and Dynamics. https://doi.org/10.1080/07391102.2020.1792991
   PubMedGoogle Scholar
• Padash, R., Esfahani, M. R., & Rad, A. S. (2021). The computational quantum mechanical study of sulfamide drug adsorption onto X12Y12 fullerenelikenanocages: detailed DFT and QTAIM investigations. Journal of Biomolecular Structure and Dynamics, 39(15), 5427–5437. https://doi.org/10.1080/07391102.2020.1792991
   PubMed Web of Science ®Google Scholar
• Padash, R., Sobhani-Nasab, A., Rahimi-Nasrabadi, M., Mirmotahari, M., Ehrlich, H., Rad, A. S., & Peyravi, M. (2018). Is it possible to use X12Y12 (X = Al, B, and Y = N, P) nanocages for drug-delivery systems? A DFT study on the adsorption property of 4-aminopyridine drug. Applied Physics A, 124(9), 582. https://doi.org/10.1007/s00339-018-1965-y
   Web of Science ®Google Scholar
• Rasmussen, J. W., Martinez, E., Louka, P., & Wingett, D. G. (2010). Zinc oxide nanoparticles for selective destruction of tumor cells and potential for drug delivery applications. Expert Opinion on Drug Delivery, 7(9), 1063–1077. https://doi.org/10.1517/17425247.2010.502560
   PubMed Web of Science ®Google Scholar
• Saha, S., & Sarkar, P. (2014). Understanding the interaction of DNAeRNA nucleobases with different ZnO nanomaterials. Physical Chemistry Chemical Physics : PCCP, 16(29), 15355–e15366. https://doi.org/10.1039/c4cp01041h
   PubMed Web of Science ®Google Scholar
• Schmid, N., Eichenberger, A. P., Choutko, A., Riniker, S., Winger, M., Mark, A. E., & van Gunsteren, W. F. (2011). Definition and testing of the GROMOS force-field versions 54A7 and 54B7. European Biophysics Journal : EBJ, 40(7), 843–856. https://doi.org/10.1007/s00249-011-0700-9
   PubMed Web of Science ®Google Scholar
• Schuttelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for € high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Shewale, V., Joshi, P., Mukhopadhyay, S., Deshpande, M., Pandey, R., Hussain, S., & Karna, S. P. (2011). First-principles study of nanoparticleebiomolecular interactions: Anchoring of a (ZnO)12 cluster on nucleobases. The Journal of Physical Chemistry C, 115(21), 10426–e10430. https://doi.org/10.1021/jp2013545
   Web of Science ®Google Scholar
• Shiraki, K., & Daikoku, T. (2020). Favipiravir, an anti- influenza drug against life-threatening RNA virus infections. Pharmacology & Therapeutics, 209, 107512. https://doi.org/10.1016/j.pharmthera.2020.107512
   PubMed Web of Science ®Google Scholar
• Singh, R., Bhardwaj, V. K., & Purohit, R. (2022). Inhibition of nonstructural protein 15 of SARS‐CoV‐2 by golden spice: A computational insight. Cell Biochemistry and Function, 40(8), 926–934. https://doi.org/10.1002/cbf.3753
   PubMed Web of Science ®Google Scholar
• Singh, R., Bhardwaj, V. K., Sharma, J., Kumar, D., & Purohit, R. (2021). Identification of potential plant bioactive as SARS-CoV-2 Spike protein and human ACE2 fusion inhibitors. Computers in Biology and Medicine, 136, 104631. https://doi.org/10.1016/j.compbiomed.2021.104631
   PubMed Web of Science ®Google Scholar
• Sisakht, M., Solhjoo, A., Mahmoodzadeh, A., Fathalipour, M., Kabiri, M., & Sakhteman, A. (2021). Potential inhibitors of the main protease of SARS-CoV-2 and modulators of arachidonic acid pathway: Non-steroidal anti-inflammatory drugs against COVID-19. Computers in Biology and Medicine, 136, 104686. https://doi.org/10.1016/j.compbiomed.2021.104686
   PubMed Web of Science ®Google Scholar
• Taha, M., & Haboub, L. (2020). Novel coronavirus disease (COVID-19): Causes, pathogenesis and efforts of treatment. FABAD Journal of Pharmaceutical Sciences, 45(3), 279–296.
   Google Scholar
• Taha, M., & Lee, M.-J. (2019). Does the peptide backbone unit interact with gold nanoclusters? Insights from computational modeling. Journal of Biomolecular Structure and Dynamics, 37(16), 4258–4266. https://doi.org/10.1080/07391102.2018.1546231
   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/10.1038/s41422-020-0282-0
   PubMed Web of Science ®Google Scholar
• Wu, C., Liu, Y., Yang, Y., Zhang, P., Zhong, W., Wang, Y., Wang, Q., Xu, Y., Li, M., Li, X., Zheng, M., Chen, L., & Li, H. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica. B, 10(5), 766–788. https://doi.org/10.1016/j.apsb.2020.02.008
   PubMed Web of Science ®Google Scholar
• Yadava, U., Singh, M., & Roychoudhury, M. (2013). Pyrazolo[3,4-d]pyrimidines as inhibitor of anti-coagulation and inflammation activities of phospholipase A2: Insight from molecular docking studies. Journal of Biological Physics, 39(3), 419–438. https://doi.org/10.1007/s10867-013-9299-7
   PubMed Web of Science ®Google Scholar
• Zhang, H., Saravanan, K. M., Yang, Y., Hossain, M. T., Li, J., Ren, X., & Wei, Y. (2020). Deep learning based drug screening for novel coronavirus 2019-nCov. Preprints.
   Google Scholar
• Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G. F., & Tan, W. (2020). A novel coronavirus from patients with pneumonia in China, 2019. The New England Journal of Medicine, 382(8), 727–733. https://doi.org/10.1056/NEJMoa2001017
   PubMed Web of Science ®Google Scholar
• Zumla, A., Chan, J. F. W., Azhar, E. I., Hui, D. S. C., & Yuen, K.-Y. (2016). Coronaviruses - drug discovery and therapeutic options. Nature Reviews. Drug Discovery, 15(5), 327–347. https://doi.org/10.1038/nrd.2015.37
   PubMed Web of Science ®Google Scholar