DFT Based Pharmacokinetic, Molecular Docking, and ADMET Studies of Some Glucopyranoside Esters

  • Shagir Ahammad Chowdhury Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram, 4331, Bangladesh
  • Sayed M. Kibria Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram, 4331, Bangladesh https://orcid.org/0000-0002-7843-3688
  • Md. Rabiul Alam Department of Chemistry, Comilla University, Cumilla, 3506, Bangladesh https://orcid.org/0000-0001-7185-4773
Keywords: COVID-19, Glucopyranoside ester, DFT calculation, Molecular docking, Pharmacokinetic study.

Abstract

Monosaccharide esters (MEs) are getting more attention from bioorganic chemists due to their biodegradable and drug-likeness properties. As a consequence, carbohydrate derivatives (sugar-based esters, SEs) are an essential part of medicinal chemistry. In this context, density functional theory (DFT) with B3LYP/ 3-21G has been employed to optimize the methyl 4,6-O-benzylidene-α-D-glucopyranoside (3) of methyl α-D-glucopyranoside (2) and its protected acyl esters 4-6. The prediction of activity spectra for substances (PASS) of these compounds showed better antifungal functionalities than the antibacterial potentiality. Thermodynamic properties and molecular electrostatic potential (MEP) of these MEs indicated their stability and both the electrophilic and nucleophilic attack sites. Due to their better antifungal potentiality, molecular docking was conducted against fungal protein lanosterol 14α-demethylase (3JUS), and SARS-CoV-2 main protease (6LU7) along with absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies. The study indicated a better binding affinity of some esters compared to the standard antifungal and COVID-19 related drug hydroxychloroquine (HCQ).

References

Matin, M. M. (2016). Synthesis and Glycosidase Inhibitory Activity of Azasugars. LAP Lambert Academic Publishing, Germany, Vol.2016, pp 1-273. ISBN: 978-3-659-85088-2.

Dhavale, D. D., Matin, M. M., Sharma, T., & Sabharwal, S. G. (2003). N-Hydroxyethyl-piperidine and –pyrrolidine homoazasugars: preparation and evaluation of glycosidase inhibitory activity, Bioorganic & Medicinal Chemistry, 11(15), 3295-3305. https://doi.org/10.1016/S0968-0896(03)00231-1

Varki, A., D Esko, J. D., & Colley, K. J. (2015). Cellular organization of glycosylation. In Essential of Glycobiology, 2nd Edition, Cold Spring Harbor Laboratory Press (NY). https://www.ncbi.nlm.nih.gov/books/NBK1926/

Valverde, P., Ardá, A., Reichardt, N. –C., Jiménez-Barbero, J., & Ana Gimeno, A. (2019). Glycans in drug discovery, MedChemComm, 10, 1678-1691. https://doi.org/10.1039/C9MD00292H

Fernandez-Tejada A., Canada F. J., & Jiménez-Barbero J. (2015). Glycans in medicinal chemistry: An underexploited resource. ChemMedChem, 10, 1291-1295. https://doi.org/10.1002/cmdc.201500107

Matin, M. M., Uzzaman, M., Chowdhury, S. A., & Bhuiyan, M. M. H. (2020). 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, 1-13. https://doi.org/10.1080/07391102.2020.1850358

Staron, J., Dąbrowski , J. M., Cichoń, E., & Guzik, M. (2018). Lactose esters: synthesis and biotechnological applications, Critical Reviews in Biotechnology, 38, 245-258. https://doi.org/10.1080/07388551.2017.1332571

Jones, D., Metzger, H., Schatz, A., & Waksman, S. A. (1944), Control of gram-negative bacteria in experimental animals by streptomycin, Science, 100, 103-105. https://doi.org/10.1126/science.100.2588.103

Magnet, S., & Blanchard, J. S. (2005). Molecular insights into aminoglycoside action and resistance, Chemical Reviews, 105(2), 477-498. https://doi.org/10.1021/cr0301088

Gray, K. C., Palacios, D. S., Dailey, I., Endo, M. M., Uno, B. E., Wilcock, B. C., & Burke, M. D. (2012). Amphotericin primarily kills yeast by simply binding ergosterol. Proceedings of the National Academy of Sciences of the USA, 109(7), 2234-2239. https://doi.org/10.1073/pnas.1117280109

Kabir, A. K. M. S., Rahman, M.S., Matin, M. M., Bhuiyan, M. M. R., & Ali, M. (2001). Antimicrobial activities of some D-glucose derivatives, The Chittagong University Journal of Science, 25(1), 123-128. ISSN 2408-8471

Dhavale, D. D., & Matin, M. M. (2005). Piperidine homoazasugars: Natural occurrence, synthetic aspects and biological activity study, Arkivoc, .2005(3), 110-132. https://doi.org/10.3998/ark.5550190.0006.314

Kabir, A. K. M. S., Matin, M. M., Sanaullah, A. F., Sattar, M. A., Rahman, M. S., & Anwar, M. N. (2001). Antimicrobial activities of some lyxoside derivatives. Bangladesh J. Microbiol, 18(1), 89-95. ISSN 2070-1810

Miljkovic, M. (2010). Amino Sugars. In: Carbohydrates: Synthesis, Mechanisms, and Stereoelectronic Effects, Springer, New York (NY). https://doi.org/10.1007/978-0-387-92265-2_9

Uhrig, M. L., Lantaño, B., & Postigo, A. (2019), Synthetic strategies for fluorination of carbohydrates, Organic & Biomolecular Chemistry, 17(21), 5173-5189. https://doi.org/10.1039/C9OB00405J

Perinelli, D. R., Lucarini, S., Fagioli, L., Campana, R., Vllasaliu, D., Duranti, A., & Casettari, L. (2018). Lactose oleate as new biocompatible surfactant for pharmaceutical applications, European Journal of Pharmaceutics and Biopharmaceutics, 124(55)–62. https://doi.org/10.1016/j.ejpb.2017.12.008

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. https://doi.org/10.18596/jotcsa.83708

Matin, M. M., Bhattacharjee, S. C., Hoque, M. S., & Ahamed, F. (2019). Antibacterial activity of some medicinal plants against carbapenem-resistant Acinetobacter baumannii isolated from patients, European Journal Pharmaceutical and Medical Research, .6(7), 111-116. ISSN 2394-3211

Matin, M. M. (2014). Synthesis and antimicrobial study of some methyl 4-O-palmitoyl-α-L-rhamnopyranoside derivatives, Orbital: The Electronic Journal of Chemistry, 6(1), 20-28. https://doi.org/10.17807/orbital.v6i1.553

Matin, M. M. (2006). Synthesis of some silyl protected 1,4-galactonolactone derivatives, Journal of Applied Sciences Research, 2(10), 753-756. ISSN 1819544X

Matin, M. M., & Ibrahim, M. (2006). Synthesis of 2,3-di-O-substituted derivatives of methyl 4-O-acetyl-α-L-rhamnopyranoside, The Chittagong University Journal of Science, 30(2), 67-76. ISSN 2408-8471

Chowdhury, S. A., Priyanka C., Kawsar, S. M. A., Bhuiyan, M. M. H., & Matin, M. M. (2018). Regioselective acylation,PASS predication and antimicrobial properties of some protected glucopyranosides, Journal of Bangladesh Chemical Society, 30(1), 1-10. ISSN 1022-016X

Fadda, E., & Woods, R. J. (2010). Molecular simulations of carbohydrates and proteincarbohydrate interactions: motivation, issues and prospects, Drug Discovery Today, 15, 596-609. https://doi.org/10.1016/j.drudis.2010.06.001

Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved a-ketoamide inhibitors, Science, 368, 409–412. https://doi.org/10.1126/science.abb3405

Laws, M., Surani, Y. M., Hasan, M. M., Chen, Y., Jin, P., Al-Adhami, T., Chowdhury, M., Imran, A., Psaltis, I., Jamshidi, S., Nahar, K. S., & Rahman, K. M. (2020). Current trends and future approaches in small-molecule therapeutics for COVID-19, Current Medicinal Chemistry, 27, 1-22. https://doi.org/10.2174/0929867327666200721161840

Sharavanan, V. J., Sivaramakrishnan, M., Sivarajasekar, N., Senthilrani, N., Kothandan, R., Dhakal, N., Sivamani, S., Show, P. L., Awual, M. R., & Naushad, M. (2020). Pollutants inducing epigenetic changes and diseases, Environmental Chemistry Letter, 18, 325–343. https://doi.org/10.1007/s10311-019-00944-3

Kabir, A. K. M. S., Matin, M. M., & Majumder, S. (1997). Selective acylation of 3-O-benzyl-1,2-O-isopropylidene-α-D-glucofuranose, Chittagong University Studies, Part II: Science, 21(2), 65-69. ISSN:1561-1167

Kabir, A. K. M. S., Matin, M. M., & Rahman, M. M. (1996). Selective benzoylation of methyl α-D-mannopyranoside using the dibutyltin oxide and direct methods, Chittagong University Studies, Part II: Science, 20(2), 99-104. ISSN:1561-1167

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

Lokman, S. M., Rasheduzzaman, M., Salauddin, A., Barua, R., Tanzina, A. Y., Rumi, M. H., Hossain, M. I., Siddiki, A., Mannan, A., & Hasan, M. M. (2020). Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach. Infection, Genetics and Evolution, Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 84, 104389. https://doi.org/10.1016/j.meegid.2020.104389

Kabir, A. K. M. S., Matin, M. M., & Uddin, M. R. (1998). Selective myristoylation and palmitoylation of uridine, The Chittagong University Journal of Science, 22(2), 27-35. ISSN 2408-8471

Kabir, A. K. M. S., Matin, M. M., Islam, K. R., & Manchur, M. A. (1999). Synthesis and antimicrobial activities of some monosaccharide derivatives, The Chittagong University Journal of Science, 23(2), 1-8. ISSN 2408-8471

Kabir, A. K. M. S., Matin, M. M., Bhuiyan, M. M. R., & Amin, M. N. (2001). Synthesis and characterization of some acylated derivatives of L-lyxose, The Chittagong University Journal of Science, 25(1), 75-84. ISSN 2408-8471

Kabir, A. K. M. S., Matin, M. M., Hossain, M. L., & Anwar, M. N. (2003). Antimicrobial activities of some mannofuranoside derivatives, The Chittagong University Journal of Science, 27(1&2), 119-124. ISSN 2408-8471

Kabir, A. K. M. S., Matin, M. M., Hossain, A., & Sattar, M. A. (2003). Synthesis and antimicrobial activities of some rhamnopyranoside derivatives, Journal of Bangladesh Chemical Society, 16(2), 85-93.

Matin, M. M. (2006). N-Butylation and N-acetylation of a sugar-derived β-aminoester, The Chittagong University Journal of Science, 30(1), 35-39. ISSN 2408-8471

Bhattacharjee, S. C., Matin, M. M., & Nasiruddin, M. (2019). Insecticidal effects of two medicinal plants Polygonum hydropiper L. and Abrus precatorius L. leaves against the rice weevil Sitophilus oryzae L. (Coleoptera: Curculionidae), Journal of Biodiversity Conservation and Bioresource Management, 5(2), 107-114. https://doi.org/10.3329/jbcbm.v5i2.44921

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 2408-8471

Matin, M. M., Chowdhury, S. A., Bhuiyan, M. M. H., Kawsar, S. M. A., & Alam, M. A. (2021). Glucopyranoside dipentanoyl esters: Synthesis, PASS predication, antimicrobial and in silico ADMET studies, Journal of Scientific Research, 13(1), 221-235. http://dx.doi.org/10.3329/jsr.v13i1.48147

Kabir, A. K. M. S., Matin, M. M., Bhuiyan, M. M. R., & Ali, M. (2004). Synthesis and characterization of some D-glucose derivatives, Journal of Bangladesh Chemical Society, 2004, 17(2), 116-123.

Chowdhury, A. Z. M .S, & Matin, M. M. (1997). Synthesis of imidazo[1,2-c]pyrido[4',3':4,5]thieno[3,2-e]-pyrimidine, Chittagong University Studies, Part II: Science, 21(2), 47-52. ISSN:1561-1167

Chowdhury, S. A. (2018). Studies on Regioselective Acylation and Biological Evaluation of Some Monosaccharide and Nucleoside Derivatives, Ph.D. Thesis, University of Chittagong (Bangladesh).

Matin, M. M., Bhattacharjee, S. C., Chakraborty, P., & Alam, M. S. (2019). Synthesis, PASS predication, in vitro antimicrobial evaluation and pharmacokinetic study of novel n-octyl glucopyranoside esters, Carbohydrate Research, 485, 107812. https://doi.org/10.1016/j.carres.2019.107812

Murtazalieva, K. A., Druzhilovskiy, D. S., Goel, R. K., Sastry, G. N., & Poroikov, V. V. (2017). How good are publicly available web services that predict bioactivity profiles for drug repurposing?, SAR and QSAR in Environmental Research, 28(10), 843-862. https://doi.org/10.1080/1062936X.2017.1399448

Matin, M. M., Roshid, M. H. O., Bhattacharjee, S. C., & Azad, A. K. M. S. (2020). PASS predication, antiviral, in vitro antimicrobial, and ADMET studies of rhamnopyranoside esters, Medical Research Archives, 8(7), 2165. https://doi.org/10.18103/mra.v8i7.2165

Azam, F., Alabdullah, N. H., Ehmedat, H. M., Abulifa, A. R., Taban, I., & Upadhyayula, S. (2018). NSAIDs as potential treatment option for preventing amyloid β toxicity in Alzheimer’s disease: an investigation by docking, molecular dynamics, and DFT studies, Journal of Biomolecular Structure and Dynamics, 36, 2099-2117. https://doi.org/10.1080/07391102.2017.1338164

Matin, M. M., Chakraborty, P., Alam, M. S., Islam, M. M., & Hanee, U. (2020). Novel mannopyranoside esters as sterol 14α-demethylase inhibitors: Synthesis, PASS predication, molecular docking, and pharmacokinetic studies, Carbohydrate Research, 496, 108130. https://doi.org/10.1016/j.carres.2020.108130

Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., & Weissig, H. (2000), The Protein Data Bank, Nucleic Acids Research, 28, 235-242. https://doi.org/10.1093/nar/28.1.235

Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, Journal of Computational Chemistry, 31, 455–461.https://doi.org/10.1002/jcc.21334

Matin, M. M., Hasan, M. S., Uzzaman, M., Bhuiyan, M. M. H., Kibria, S. M., Hossain, M. E. & Roshid, M. H. O. (2020). Synthesis, spectroscopic characterization, molecular docking, and ADMET studies of mannopyranoside esters as antimicrobial agents, Journal of Molecular Structure, 1222, 128821. https://doi.org/10.1016/j.molstruc.2020.128821

Matin, M. M., Bhuiyan, M. M. H., Kabir, E., Sanaullah, A. F. M., Rahman, M. A., Hossain, M. E., & Uzzaman, M. (2019). Synthesis, characterization, ADMET, PASS predication, and antimicrobial study of 6-O-lauroyl mannopyranosides, Journal of Molecular Structure, 1195, 189-197. https://doi.org/10.1016/j.molstruc.2019.05.102

Matin, M. M., & Iqbal, M. Z. (2021). Methyl 4-O-(2-chlorobenzoyl)-α-L-rhamnopyranosides: Synthesis, characterization, and thermodynamic studies, Orbital: The Electronic Journal of Chemistry, 13(1), 19-27. http://dx.doi.org/10.17807/orbital.v13i1.1532

Matin, M. M., Islam, N., Siddika, A., & Bhattacharjee, S. C. (2021). Regioselective synthesis of some rhamnopyranoside esters for PASS predication, and ADMET studies, Journal of the Turkish Chemical Society Section A: Chemistry, 8(1), 363-374. https://doi.org/10.18596/jotcsa.829658

Published
2021-04-30
How to Cite
Chowdhury, S. A., Kibria, S. M., & Alam, M. R. (2021). DFT Based Pharmacokinetic, Molecular Docking, and ADMET Studies of Some Glucopyranoside Esters. Journal of Applied Science & Process Engineering, 8(1), 671-683. https://doi.org/10.33736/jaspe.2940.2021