In Silico Testing of Some Protected Galactopyranose as SARS-CoV-2 Main Protease Inhibitors

Authors

DOI:

https://doi.org/10.33736/jaspe.4970.2022

Keywords:

COVID-19, Protected galactose, Molecular docking, Remdesivir, Sugar esters

Abstract

An outbreak of novel Coronavirus disease (COVID-19 or 2019-nCoV) due to the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has already demonstrated a fatal death toll all over the world. To cure this viral infection, a number of compounds of different categories have been investigated in silico. Some of the compounds showed better binding energy with COVID-19-related proteins. However, until now there is no appropriate drug except a vaccine. It was found that many antifungal drugs are used for COVID-19 patients in hospitals. Many monosaccharide esters have been reported to have antifungal potential. Thus, in the present study, some protected galactopyranose esters are chosen for molecular docking with SARS-CoV-2 main proteases (PDB id: 7BQY and 6LU7). A docking study revealed that galactopyranose esters 5-8 have very good docking scores (-8.4 to -6.5 kcal/mol) compared to the standard drugs azithromycin, remdesivir, and hydroxychloroquine. To explain such good scores interaction between amino acid residues of proteins and compounds in their docked complexes are calculated and duly discussed in this study.

References

Peng, Z., Xing-Lou, Y., Xian-Guang, W., Ben, H., Lei, Z., & Wei, Z. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi.org/10.1038/s41586-020-2012-7.

Dhumad, A.M., Majeed, H.J., Harismah, K., & Zandi, H. (2021). In silico Approach on ribavirin inhibitors for COVID-19 main protease. Bioint. Res. Appl. Chem., 11(6), 13924–13933. https://doi.org/10.33263/BRIAC116.1392413933

Rout, J., Swain, B.C., & Tripathy, U. (2022) In silico investigation of spice molecules as potent inhibitor of SARS-CoV-2, Journal of Biomolecular Structure and Dynamics, 40(2), 860–874, https://doi.org/10.1080/07391102.2020.1819879

Rashdan, H.R.M, Abdelmonsef, A.H., Abou-Krisha, M.M., & Yousef, T.A. (2022). Synthesis and identification of novel potential thiadiazole based molecules containing 1,2,3-triazole moiety against COVID-19 main protease through structure-guided virtual screening approach. Bioint. Res. Appl. Chem., 12(6), 8258–8270. https://doi.org/10.33263/BRIAC126.82588270

Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., et al. (2020). A novel Coronavirus from patients with pneumonia in China, 2019. New Engl. J. Med., 382, 727–733. https://doi.org/10.1056/NEJMoa2001017

Prescott, H.C. (2021). Outcomes for patients following hospitalization for COVID-19. JAMA. 325(15), 1511–1512. https://doi.org/10.1001/jama.2021.3430

Kordzadeh, A., & Saadatabadi, A.R. (2022). Effects of the temperature and the pH on the main protease of SARS-CoV-2: A molecular dynamics simulation study. Bioint. Res. Appl. Chem., 12(6), 7239–7248. https://doi.org/10.33263/BRIAC126.72397248

Zhang, L., Hou, J., Ma, F.Z. et al. (2021). The common risk factors for progression and mortality in COVID-19 patients: a meta-analysis. Arch. Virol., 166, 2071–2087. https://doi.org/10.1007/s00705-021-05012-2

Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., et al. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet, 395, 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5

Mehta, P., McAuley, D.F., Brown, M., Sanchez, E., Tattersall, R.S., Manson, J.J., et al. (2020).COVID-19: consider cytokine storm syndromes and immunosuppression. Lancet, 395, 1033–1034. https://doi.org/10.1016/S0140-6736(20)30628-0

Chen, C., Zhang, Y., Huang, J., Yin, P., Cheng, Z., Wu, J., Chen, S., Zhang, Y., Chen, B., Lu, M., Luo, Y., Ju, L., Zhang, J., & Wang, X. (2020). Favipiravir versus Arbidol for COVID-19: A randomized clinical trial. MedRxiv. https://doi.org/10.1101/2020.03.17.20037432

Md Nayeem, S., Sohail, E. M., Srihari, N. V., Indira, P., & Srinivasa Reddy, M. (2021). Target SARS-CoV-2: theoretical exploration on clinical suitability of certain drugs. Journal of Biomolecular Structure and Dynamics, 1-8. https://doi.org/10.1080/07391102.2021.1924262

Hu, B., Guo, H., Zhou, P., & Shi, Z.-L. (2021). Characteristics of SARS-CoV-2 and COVID-19. Nat. Rev. Microbiol., 19, 141–154. https://doi.org/10.1038/s41579-020-00459-7

Shah, A.S., Gribben, C., Bishop, J., Hanlon, P., Caldwell, D., Wood, R., Reid, M., McMenamin, J., Goldberg, D., Stockton, D., et al. (2021). Effect of vaccination on transmission of SARS-CoV-2. New Engl. J. Med., 385, 1718–1720. https://doi.org/10.1056/NEJMc2106757

Tarighi, P., Eftekhari, S., Chizari, M., Sabernavaei, M., Jafari, D., & Mirzabeigi, P. (2021). A review of potential suggested drugs for coronavirus disease (COVID-19) treatment. Eur. J. Pharmacol., 895, 173890. https://doi.org/10.1016/j.ejphar.2021.173890

Ghosh, R., Chakraborty, A., Biswas, A., & Chowdhuri, S. (2021). Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors – An in silico docking and molecular dynamics simulation study. Journal of Biomolecular Structure & Dynamics, 39, 4362–4374. https://doi.org/10.1080/07391102.2020.1779818

Fischer, W., Eron, J.J., Holman, W., Cohen, M.S., Fang, L., Szewczyk, L.J., Sheahan, T.P., Baric, R., Mollan, K.R., Wolfe, C.R., et al. (2021). Molnupiravir, an Oral Antiviral Treatment for COVID-19. medRxiv, https://doi.org/10.1101/2021.06.17.21258639

Rothan, H.A., Stone, S., Natekar, J., Kumari, P., Arora, K., & Kumar, M. (2020). The FDA-approved gold drug auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells. Virology, 547, 7–11. https://doi.org/10.1016/j.virol.2020.05.002

Cirri, D., Marzo, T., Tolbatov, I., Marrone, A., Saladini, F., Vicenti, I., Dragoni, F., Boccuto, A., & Messori, L. (2021). In vitro anti-SARS-CoV-2 activity of selected metal compounds and potential molecular basis for their actions based on computational study. Biomolecules, 11, 1858. https://doi.org/10.3390/biom11121858

Lee, Y.-K., Chang, W.-C., Prakash, E., Peng, Y.-J., Tu, Z.-J., Lin, C.-H., Hsu, P.-H., & Chang, C.-F. (2022). Carbohydrate Ligands for COVID-19 spike proteins. Viruses, 14, 330. https://doi.org/10.3390/v14020330

Kasthuri, M., Li, C., Verma, K., Russell, O.O., Dickson, L., McCormick, L., Bassit, L., Amblard, F., & Schinazi, R.F. (2020). Synthesis of 4'-substituted-2'-deoxy-2'-alpha-fluoro nucleoside analogs as potential antiviral agents. Molecules, 25, 1258. https://doi.org/10.3390/molecules25061258

Sari, O., Bassit, L., Gavegnano, C., McBrayer, T.R., McCormick, L., Cox, B., Coats, S.J., Amblard, F., & Schinazi, R.F. (2017). Synthesis and antiviral evaluation of 2',2',3',3'-tetrafluoro nucleoside analogs. Tetrahedron Lett., 58, 642–644. https://doi.org/10.1016/j.tetlet.2017.01.006

Schultz, D.C., Johnson, R.M., Ayyanathan, K. et al. (2022). Pyrimidine inhibitors synergize with nucleoside analogues to block SARS-CoV-2. Nature, 604, 134–140. https://doi.org/10.1038/s41586-022-04482-x

Zenchenko, A.A., Drenichev, M.S., Il’icheva, I.A., & Mikhailov, S.N. (2021). Antiviral and Antimicrobial Nucleoside Derivatives: Structural Features and Mechanisms of Action. Molecular Biology, 55, 786–812. https://doi.org/10.1134/S0026893321040105

Kabir, A.K.M.S., Matin, M.M., Mridha, M.A.U., & Shahed, S.M. (1998). Antifungal activities of some methyl 6-O-trityl-α-D-mannopyranosides, The Chittagong University Journal of Science, 22(1), 41–46. ISSN: 1561-1167

Matin, M.M., & Ibrahim, M. (2010). Synthesis of some methyl 4-O-octanoyl-α-L-rhamnopyranoside derivatives. Journal of Applied Sciences Research, 6(10), 1527–1532. ISSN: 1816-157X

Matin, M.M., & Chakraborty, P. (2020). Synthesis, spectral and DFT characterization, PASS predication, antimicrobial, and ADMET studies of some novel mannopyranoside esters. Journal of Applied Science & Process Engineering, 7(2), 572–586. e-ISSN: 2289-7771

Matin, M.M., Bhuiyan, M.M.H., Hossain, M.M., & Roshid M.H.O. (2015). Synthesis and comparative antibacterial studies of some benzylidene monosaccharide benzoates. Journal of the Turkish Chemical Society Section A: Chemistry, 2(4), 12–21. e-ISSN: 2149-0120

Rahman, M.A., Chakma, U., Kumer, A., Rahman, M.R., & Matin, M.M. (2023). Uridine-derived 4-aminophenyl 1-thioglucosides: DFT optimized FMO, ADME, and antiviral activities study. Biointerface Research in Applied Chemistry, 13(1), 52.https://doi.org/10.33263/BRIAC131.052

Kabir, A.K.M.S., Matin, M.M., & Kawsar, S.M.A. (1998). Synthesis and antibacterial activities of some uridine derivatives. The Chittagong University Journal of Science, 22(1), 13–18. ISSN: 1561-1167

Kabir, A.K.M.S., Matin, M.M., Sanaullah, A.F.M., Sattar, M.A., & Rahman, M.S. (2001). Antimicrobial activities of some lyxoside derivatives. Bangladesh Journal of Microbiology, 18(1), 89–95. ISSN: 1011-9981

Kabir, A.K.M.S., Matin, M.M., Bhuiyan, M.M.R., Rahim, M.A., & Rahman, M.S. (2005). Biological evaluation of some monosaccharide derivatives. International Journal of Agriculture & Biology, 7(2), 218-221. ISSN: 1814-9596

Hanee, U., Rahman, M.R., & Matin, M.M. (2021). Synthesis, PASS, in silico ADMET, and thermodynamic studies of some galactopyranoside esters. Physical Chemistry Research, 9(4), 591-603.

https://doi.org/10.22036/pcr.2021.282956.1911

Siddikey, F., Roni, M.A.H., Kumer, A., Chakma, U., & Matin, M.M. (2022). Computational investigation of Betalain derivatives as natural inhibitor against food borne bacteria. Current Chemistry Letters, 11(3), 309–320. http://dx.doi.org/10.5267/j.ccl.2022.3.003

Rahman, M.A., Matin, M.M., Kumer, A., Chakma, U., & Rahman, M.R. (2022). Modified D-Glucofuranoses as New Black Fungus Protease Inhibitors: Computational Screening, Docking, Dynamics, and QSAR Study. Physical Chemistry Research, 10(2), 195–209. https://doi.org/10.22036/pcr.2021.294078.1934

Kumer, A., Chakma, U., & Matin, M.M. (2022). Bilastine based drugs as SARS-CoV-2 protease inhibitors: Molecular docking, dynamics, and ADMET related studies. Orbital: The Electronic Journal of Chemistry, 14(1), 15–23. http://dx.doi.org/10.17807/orbital.v14i1.1642

Zago, E., Joly, N., Chaveriat, L., Vincent Lequart, V., & Martin, P., (2021). Enzymatic synthesis of amphiphilic carbohydrate esters: Influence of physicochemical and biochemical parameters, Biotechnology Reports, 30, e00631, https://doi.org/10.1016/j.btre.2021.e00631

Kim, H. J., Kang, S. H., Choi, S. S., & Kim, E. S. (2017). Redesign of antifungal polyene glycosylation: engineered biosynthesis of disaccharide-modified NPP. Applied Microbiology & Biotechnology, 101, 5131–5137. https://doi.org/10.1007/s00253-017-8303-8

Kabir, A.K.M.S., & Matin, M.M. (1994). Regioselective acylation of a derivative of L-rhamnose using the dibutyltin oxide method. Journal of the Bangladesh Chemical Society, 7(1), 73–79. ISSN: 1022-016X

Matin, M.M. (2008). Synthesis of D-glucose derived oxetane: 1,2-O-isopropylidene-4-(S)-3-O,4-C-methylene-5-O-methanesulfonyl-β-L-threo-pento-1,4-furanose. Journal of Applied Sciences Research, 4(11), 1478–1482. ISSN: 1816-157X

Kabir, A.K.M.S., Matin, M.M., Hossain, A., & Sattar, M.A. (2003). Synthesis and antimicrobial activities of some rhamno-pyranoside derivatives. Journal of the Bangladesh Chemical Society, 16(2), 85–93. ISSN: 1022-016X

Matin, M.M. (2006). Synthesis of some silyl protected 1,4-galactonolactone derivatives. Journal of Applied Sciences Research, 2(10), 753–756. ISSN: 1816-157X

Kumbhar, P.S., Pandya, A.K., Manjappa, A.S., Disouza, J.I., & Patravale, V.B. (2021). Carbohydrates-based diagnosis, prophylaxis and treatment of infectious diseases: Special emphasis on COVID-19. Carbohydrate Polymer Technologies and Applications, 2, 100052. https://doi.org/10.1016/j.carpta.2021.100052

Islam, N, Islam, M.D., Rahman, M.R., & Matin, M.M. (2021). Octyl 6-O-hexanoyl-β-D-glucopyranosides: Synthesis, PASS, antibacterial, in silico ADMET, and DFT studies. Current Chemistry Letters, 10(4), 413–426. http://dx.doi.org/10.5267/j.ccl.2021.5.003

Matin, M.M., Uzzaman, M., Chowdhury, S.A., & Bhuiyan, M.M.H. (2022). In vitro antimicrobial, physicochemical, pharmacokinetics, and molecular docking studies of benzoyl uridine esters against SARS-CoV-2 main protease. Journal of Biomolecular Structure and Dynamics, 40(8), 3668-3680. https://doi.org/10.1080/07391102.2020.1850358

Matin, P., Matin, M.M., Rahman, M.R., & Kumer, A. (2023). Synthesis, antifungal, and molecular docking studies of some new di-O-isopentanoyl glucopyranosides. Physical Chemistry Research, 11(1), 149–157. https://doi.org/10.22036/PCR.2022.334577.2057

Kumer, A., Chakma, U., Matin, M.M., Akash, S., Chando, A., & Howlader, D. (2021). The computational screening of inhibitor for black fungus and white fungus by D-glucofuranose derivatives using in silico and SAR study. Organic Communications, 14(4), 305–322. https://doi.org/10.25135/agc.oc.116.2108.2188

Matin, M. M., Bhuiyan, M. M. H., Debnath, D. C., & Manchur, M. A. (2013). Synthesis and comparative antimicrobial studies of some acylated D-glucofuranose and D-glucopyranose derivatives. International Journal of Biosciences, 3(8), 279–287. http://dx.doi.org/10.12692/ijb/3.8.279-287

Matin, P., Rahman, M.R., Huda, D., Bakri, M.K.B., Uddin, J., Yurkin, Y., Burko, A., Kuok, K.K., & Matin, M.M. (2022). Application of synthetic acyl glucopyranosides for white-rot and brown-rot fungal decay resistance in aspen and pine wood. BioResources, 17(2), 3025–3041. https://doi.org/10.15376/biores.17.2.3025-3041

James, A.A., Rahman, M.R., Huda, D., Aqlan, M.F.M., Matin, M.M., Bakri, M.K.B., Kuok, K.K., Rahman, M.M. (2022). Synthesis and characterization of novel nano-carbon mixture from Dabai (Canarium odontophyllum) nutshell. BioResources, 17(3), 4452–4469. https://doi.org/10.15376/biores.17.3.4452-4469

Khui, P.L.N., Rahman, M.R., Matin, M.M., & Bakri, M.K.B. (2022). Recycled Rubber Waste Plastic and its Composites. In: Recycled Plastic Biocomposites, Rahman, M.R. & Bakri, M.K.B. (Eds), 1st Ed, Woodhead Publishing/Elsevierpp 147–163. https://doi.org/10.1016/B978-0-323-88653-6.00014-6

Matin, P., Hanee, U., Alam, M.S., Jeong, J.E., Matin, M.M., Rahman, M.R., Mahmud, S., Alshahrani, M.M., & Kim, B. (2022). Novel galactopyranoside esters: Synthesis, mechanism, in vitro antimicrobial evaluation and molecular docking studies. Molecules, 27(13), 4125. https://doi.org/10.3390/molecules27134125

Matin, M.M., & Azad, A.K.M.S. (2006). Synthesis of some protected 6-O-acyl-galactopyranose derivatives. Journal of Applied Sciences Research, 2(12), 1199–1202. ISSN: 1816-157X

Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., et al. (2013). Gaussian 09W, Revision D.01. Gaussian, Inc., Wallingford CT.

Lu, L., Hu, H., Hou, H., & Wang, B. (2013). An improved B3LYP method in the calculation of organic thermochemistry and reactivity. Computational and Theoretical Chemistry, 1015, 64-71. https://doi.org/10.1016/j.comptc.2013.04.009.

Veronika Temml, Zsofia Kutil, Z. (2021). Structure-based molecular modeling in SAR analysis and lead optimization. Computational and Structural Biotechnology Journal, 19, 1431-1444. https://doi.org/10.1016/j.csbj.2021.02.018.

Matin, M. M., Ibrahim, M., Anisa, T. R., & Rahman, M. R. (2022). Synthesis, characterization, in silico optimization, and conformational studies of methyl 4-O-palmitoyl-α-L-rhamnopyranosides. Malaysian Journal of Science, 41(1), 91-105. https://doi.org/10.22452/mjs.vol41no1.6

Torneri, A., Libin, P., Vanderlocht, J., Vandamme, A.-M., Neyts, J., & Hens, N. (2020). A prospect on the use of antiviral drugs to control local outbreaks of COVID-19. BMC Medicine, 18(191). https://doi.org/10.1186/s12916-020-01636-4

Matin, M. M., Bhuiyan, M. M. H., Kibria, S. M., & Hasan, M. S. (2022). Synthesis, PASS predication of antimicrobial activity and pharmacokinetic properties of hexanoyl galactopyranosides and experimental evaluation of their action against four human pathogenic bacteria and four fungal strains. Pharmaceutical Chemistry Journal, 56(5), 627-637. https://doi.org/10.1007/s11094-022-02687-y

Ristovski, J.T., Matin, M.M., Kong, R., Kusturica, M.P., Zhang, H. (2022). In vitro testing and computational analysis of specific phytochemicals with antiviral activities considering their possible applications against COVID-19. South African Journal of Botany, 1–11. https://doi.org/10.1016/j.sajb.2022.02.009

Narayanan, A., Narwal, M., Majowicz, S.A. et al. (2022). Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay. Communications Biology, 5, 169. https://doi.org/10.1038/s42003-022-03090-9

Niknam, Z., Jafari, A., Golchin, A., Pouya, F.D., Nemati, M., Rezaei-Tavirani, M., & Rasmi, Y. 2022). Potential therapeutic options for COVID-19: an update on current evidence. Eur. J. Med. Res., Vol.27, No.6. https://doi.org/10.1186/s40001-021-00626-3

Mirtaleb, M.S., Mirtaleb, A.H., Nosrati, H., Heshmatnia, J., Falak, R., & Emameh, R.M. (2021). Potential therapeutic agents to COVID-19: An update review on antiviral therapy, immunotherapy, and cell therapy, Biomedicine & Pharmacotherapy, 138, 111518. https://doi.org/10.1016/j.biopha.2021.111518

Downloads

Published

2022-10-31

How to Cite

Azad, A. K. ., Islam, M. N. ., Chowdhury, M. A. I. ., & Kabir, E. (2022). In Silico Testing of Some Protected Galactopyranose as SARS-CoV-2 Main Protease Inhibitors. Journal of Applied Science &Amp; Process Engineering, 9(2), 1281–1294. https://doi.org/10.33736/jaspe.4970.2022