Naturally Occurring Rhamnopyranosides as Anticancer Agents: Molecular Docking and ADMET Study
Abstract
After heart disease, cancer continues to be the second most prevalent cause of death in the USA. Several chemotherapeutic treatments (drugs) are available for cancer that use powerful chemicals to kill the body's rapidly proliferating cells. However, recent research disclosed that many clinically viable anticancer drugs have been developed with the help of chemicals originating from plants. A number of phytochemicals isolated from plants possess rhamnopyranoses and some of them are acyl rhamnopyranoses. Encouragingly, such compounds were reported for their cell proliferation and migration inhibition activities against invasive human triple-negative breast cancer cells. In this study, four naturally occurring rhamnopyranose esters were checked against three cancer-related proteins (PDB IDs: 3TJM, 4OAR, and 5FGK) via molecular docking. Rhamnose compounds 3-6 showed better binding energy compared to the related standard drugs in use in the hospitals. Compound 6 was found highly potential against all the proteins (-8.5 to -11.3 kcal/mol). ADMET studies have also been discussed in this respect. This study indicated that natural rhamnopyranose esters could be used to stop the spreading of cancer cells like other reported sugar fatty acid esters (SFAEs).
References
WHO Cancer, (2022). Available online: https://www.who.int/health-topics/cancer (accessed on 2 October, 2022).
Giovannucci, E., Harlan, D.M., Archer, M.C., Bergenstal, R.M., Gapstur, S.M., Habel, L.A., Pollak, M., Regensteiner, J.G., & Yee, D. (2010). Diabetes and cancer: a consensus report. Ca-Cancer J. Clin., 60, 207–221. https://doi.org/10.3322/caac.20078.
Leporini, M., Catinella, G., Bruno, M., Falco, T., TundisR., & Loizzo, M.R. (2018). Investigating the antiproliferative and antioxidant properties of Pancratium maritimum L. (Amaryllidaceae) stems, flowers, bulbs, and fruits extracts. J. Evidence-Based Complementary Altern. Med., 2018, 1–8. https://doi.org/10.1155/2018/9301247
Sharma, N., Sharma, A., Bhatia, G., Landi, M., Brestic, M., Singh, B., Singh, J., Kaur, S., & Bhardwaj, R. (2019). Isolation of phytochemicals from Bauhinia variegata l. Bark and their in vitro antioxidant and cytotoxic potential. Antioxidants, 2019(8), 492. https://doi.org/10.3390/antiox8100492
Khan, T., & Gurav, P. (2018). Phyto nanotechnology: Enhancing delivery of plant based anticancer drugs. Frontiers in Pharmacology, 8, 1002. https://doi.org/10.3389/fphar.2017.01002
Cragg, G.M., & Pezzuto, J.M., (2016). Natural products as a vital source for the discovery of cancer chemotherapeutic and chemopreventive agents. Medical Principles and Practice, 25, 41-59. https://doi.org/10.1159/000443404
Koumba Ibinga, S.K., Fabre, J-.F., Bikanga, R., & Mouloungui, Z. (2019). Atypical reaction media and organized systems for the synthesis of low-substitution sugar esters. Front. Chem., 7, 587. https://doi.org/10.3389/fchem.2019.00587
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
Matin, M.M., Bhuiyan, M.M.H., Azad, A.K.M.S., & Rashid, M.H.O. (2015). Synthesis of 6-O-stearoyl-1,2-O-isopropylidene-α-D-gluco-furanose derivatives for antimicrobial evaluation. Journal of Physical Science, 26(1), 1-12. ISSN: 2180-4230
El-Baz, H.A., Elazzazy, A.M., Saleh, T.S., Dourou, M., Mahyoub, J.A., Baeshen, M.N., Madian, H.R., & Aggelis, G. (2021). Enzymatic synthesis of glucose fatty acid esters using SCOs as acyl group-donors and their biological activities. Appl. Sci., 11, 2700. https://doi.org/10.3390/app11062700
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., & 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. https://doi.org/10.33736/jaspe.2603.2020
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
Kabir, A.K.M.S., Matin, M.M., & Uddin, M.R. (1998). Comparative studies on selective acylation of uridine using the dibutyltin oxide and direct methods. The Chittagong University Journal of Science, 22(1), 97-103. ISSN: 1561-1167
Yang, Z., & Huang, Z-.L. (2012). Enzymatic synthesis of sugar fatty acid esters in ionic liquids. Catalysis Science & Technology, 2, 1767-1775. http://dx.doi.org/10.1039/C2CY20109G
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. (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
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.http://dx.doi.org/10.18596/jotcsa.83708
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
Gumel, A.M., Annuar, M.S.M., Heidelberg, T., & Chisti, Y. (2011). Lipase mediated synthesis of sugar fatty acid esters. Process Biochemistry, 46, 2079-2090. https://doi.org/10.1016/j.procbio.2011.07.021
Hannessian, S. (1983). Total Synthesis of Natural Producrs: The 'Chiron' Approach. Pergamon Press (Oxford). ISBN: 978-0080307152
Dhavale, D.D., & Matin, M.M. (2005). Piperidine homoazasugars: Natural occurrence, synthetic aspects and biological activity study. ARKIVOC, 2005(3), 110-132. ISSN: 1424-6376
Kinnaert, C., Daugaard, M., Nami, F., & Clausen, M.H., (2017). Chemical synthesis of oligosaccharides related to the cell walls of plants and algae. Chemical Reviews, 117, 11337–11405. https://doi.org/10.1021/acs.chemrev.7b00162
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
Komatsu, K., Tsuda, M., Tanaka, Y., Mikami, Y., & Kobayashi, J. (2005). SAR studies of brasilicardin A for immunosuppressive and cytotoxic activities. Bioorganic & Medicinal Chemistry, 13(5), 1507-1513. https://doi.org/10.1016/j.bmc.2004.12.029
Kim, S.R., & Kim, Y.C. (2000). Neuroprotective phenylpropanoid esters of rhamnose isolated from roots of Scrophularia buergeriana. Phytochemistry, 54(5), 503-509. https://doi.org/10.1016/s0031-9422(00)00110-2
Grond, S., Langer, H.J., Henne, P., Sattler, I., Thiericke, R., Grabley, S., et al. (2000). Secondary metabolites by chemical screening, 39 acyl α-L-rhamnopyranosides, a novel family of secondary metabolites from Streptomyces sp.: Isolation and biosynthesis. European Journal of Organic Chemistry, 2000, 929–937. https://doi.org/10.1002/(SICI)1099-0690(200003)2000:6%3C929::AID-EJOC929%3E3.0.CO;2-U
Hu, J.F., Wunderlich, D., Sattler, I., Hartl, A., Papastavrou, I., Grond, S., et al. (2000). New 1-Oacyl alpha-L-rhamnopyranosides and rhamnosylated lactones from Streptomyces sp., inhibitors of 3 alpha-hydroxysteroid-dehydrogenase (3alpha-HSD). Journal of Antibiotics, 53, 944–953. https://doi.org/10.7164/antibiotics.53.944
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 1560–8530
Platel, R., Chaveriat, L., Le Guenic, S., Pipeleers, R., Magnin-Robert, M., Randoux, B., Trapet, P., Lequart, V., Joly, N., Halama, P., Martin, P., et al. (2021). Importance of the C12 carbon chain in the biological activity of rhamnolipids conferring protection in wheat against Zymoseptoria tritici. Molecules, 26, 40. https://dx.doi.org/10.3390/molecules26010040
Matin, M,M., Ibrahim, M., & Rahman, M.S. (2008). Antimicrobial evaluation of methyl 4-O-acetyl-α-L-rhamnopyranoside derivatives. Chittagong Univ. J. Biol. Sci., 3(1&2), 33-43. http://dx.doi.org/10.3329/cujbs.v3i1.13404
Kabir, A.K.M.S., & Matin, M.M. (1997). Regioselective monoacylation of a derivative of L-rhamnose. J. Bangladesh Acad. Sci., 21(1), 83-88.
Matin, M.M., & Ibrahim, M. (2006). Synthesis of 2,3-di-O-substituted derivatives of methyl 4-O-acetyl-α-L-rhamnopyranoside. Chittagong Univ. J. Sci., 30(2), 67-76. ISSN 1561-1167
Krishnamoorthy, M., & Balakrishnan, R., (2014). Docking studies for screening anticancer compounds of Azadirachta indica using Saccharomyces cerevisiae as model system. J. Nat. Sci. Biol. Med., Vol.5, No.1, 108-111. https://doi.org/10.4103/0976-9668.127298.
Hussain, S., Liufang, H., Shah, S.M., Ali, F., Khan, S.A., Shah, F.A., Li, J.B., & Li, S. (2022). Cytotoxic effects of extracts and isolated compounds from Ifloga spicata (forssk.) sch. bip against HepG-2 cancer cell line: Supported by ADMET analysis and molecular docking. Front. Pharmacol., 13, 986456. https://doi.org/10.3389/fphar.2022.986456
Snoch, W., Wnuk, D., Witko, T., Staro´n, J.,Bojarski, A.J., Jarek, E., Plou, F.J., Guzik, M. (2021). In search of effective anticancer agents—Novel sugar esters based on polyhydroxyalkanoate monomers. Int. J. Mol. Sci., 22, 7238. https://doi.org/10.3390/ijms22137238
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., 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
Uzzaman, M., Hasan, M.K., Mahmud, S., Fatema, K., & Matin, M.M. (2021). Structure-based design of new diclofenac: Physicochemical, spectral, moleculardocking, dynamics simulation and ADMET studies. Informatics in Medicine Unlocked, 25, 100677. https://doi.org/10.1016/j.imu.2021.100677
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 J. Microbiol., 18(1), 89-95. ISSN: 1011-9981
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
Tazeddinova, D., Rahman, M.R., Hamdan, S.B., Matin, Bin Bakri, M.K., & Rahman, M.M. (2022). Plant based polyphenol assiciations with protein: A prospective review. BioResources, 17(4). https://doi.org/10.15376/biores.17.4.Tazeddinova2
Tazeddinova, D., Toshev, A.D., Abylgazinova, A., Rahman, M., Matin, M.M., Bin Bakri, M.K., & Ayan, O. (2022). A review of polyphenol and whey protein-based conjugates. BioResources, 17(4). https://doi.org/10.15376/biores.17.4.Tazeddinova1
Mehdia, R.B.A, Shaabanb, K.A, Rebaia, I.K., Smaouia, S., Bejara, S., & Mellouli, L. (2009). Five naturally bioactive molecules including two rhamnopyranoside derivatives isolated from the Streptomyces sp. strain TN58. Natural Product Research, 23(12), 1095–1107. https://doi.org/10.1080/14786410802362352
Elmaidomy, A.H., Mohammed, R., Owis, A.I., Hetta, M.H., AboulMagd, A.M., Siddique, A.B., Abdelmohsen, U.R., Rateb, M.E., Sayed, K.A.E., Hassan, H.M. (2020). Triple-negative breast cancer suppressive activities, antioxidants and pharmacophore model of new acylated rhamnopyranoses from Premna odorata. RSC Advances, 10, 10584. https://doi.org/10.1039/d0ra01697g
Bartuzi, D., Kaczor, A.A., Targowska-Duda, K.M., & Matosiuk, D. (2017). Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors. Molecules, 22(2), 340. https://doi.org/10.3390/molecules22020340.
Kumer, A., Chakma, U., Chandro, A., Howlader, D., Akash, S., Kobir, M.E., Hossain, T., & Matin, M.M. (2022). Modified D-glucofuranose computationally screening for inhibitor of breast cancer and triple breast cancer: Chemical descriptor, molecular docking, molecular dynamics and QSAR. J. Chil. Chem. Soc., 67(3), 5623-5635. http://dx.doi.org/10.4067/S0717-97072022000305623
Kaewmeesri, P., Pocasap, P., Kukongviriyapan, V., Prawan, A., Kongpetch, S., & Senggunprai, L. (2022) Anti-metastatic Potential of Natural Triterpenoid Cucurbitacin B Against Cholangiocarcinoma Cells by Targeting Src Protein. Integrative Cancer Therapies, 21, 15347354221124861. https://doi.org/10.1177/15347354221124861.
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
El Aissouq, A., Chedadi, O., Bouachrine, M., & Ouammou, A. (2021). Identification of novel SARS-CoV-2 inhibitors: A structure-based virtual screening approach. Journal of Chemistry, 2021, 1901484. https://doi.org/10.1155/2021/1901484
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. https://doi.org/10.5267/j.ccl.2022.3.003
Islam, F., Rahman, M.R., & Matin, M.M. (2021). The effects of protecting and acyl groups on the conformation of benzyl α-L-rhamnopyranosides: An in silico study. Turkish Computational and Theoretical Chemistry, 5(1), 39-50. https://doi.org/10.33435/tcandtc.914768
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
Guan, L., Yang, H., Cai, Y., Sun, L., Di, P., Li ,W., Liu, G., & Tang, Y. (2018). ADMET-score - a comprehensive scoring function for evaluation of chemical drug-likeness. Medchemcomm, 10(1), 148-157. https://doi.org/10.1039/c8md00472b.
Ali, M., Karim, M.H., & Matin, M.M. (2021). Efficient synthetic technique, PASS predication, and ADMET studies of acylated n-octyl glucopyranosides. Journal of Applied Science & Process Engineering, 8(1), 648-659. https://doi.org/10.33736/jaspe.2823.2021
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
Pires, D.E.V., Blundell, T.L., & Ascher, D.B. (2015). pkCSM: predicting small-molecule pharmacokinetic properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
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 Report, 7, 42717. https://doi.org/10.1038/srep42717
Ferrer, M., Perez, G., Plou, F.J., Castell, J.V., & Ballesteros, A. (2005). Antitumour activity of fatty acid maltotriose esters obtained by enzymatic synthesis. Biotechnol. Appl. Biochem., 42(1), 35–39. https://doi.org/10.1042/BA20040122
Zhang, W., Chakravarty, B., Zheng, F., Gu, Z., Wu, H., Mao, J., Wakil, S.J., & Quiocho, F.A. (2011). Crystal structure of the human fatty acid synthase thioesterase domain with an activate site-specific polyunsaturated fatty acyl adduct. Proc. Natl. Acad. Sci. USA, 108(38), 15757-62. https://doi.org/10.1073/pnas.1112334108.
Petit-Topin, I., Fay, M., Resche-Rigon, M., Ulmann, A., Gainer, E., Rafestin-Oblin, M.-E., & Fagart, J. (2014). Molecular determinants of the recognition of ulipristal acetate by oxo-steroid receptors, Journal of Steroid Biochemistry and Molecular Biology, 144(B), 427-435. https://doi.org/10.1016/j.jsbmb.2014.08.008
Mallinger, A., Schiemann, K., Rink, C., Stieber, F., Calderini, M., Crumpler, S., et al. (2016). Discovery of Potent, Selective, and Orally Bioavailable Small-Molecule Modulators of the Mediator Complex-Associated Kinases CDK8 and CDK19. J. Med. Chem., 59(3), 1078–1101. https://doi.org/10.1021/acs.jmedchem.5b01685
Nagai, Y., Kawano , S., Motoda, K., Tomida, M., Tatebe, C., Sato, K., & Akiyama, H. (2017). Solubility Testing of Sucrose Esters of Fatty Acids in International Food Additive Specifications. Biological and Pharmaceutical Bulletin, 40(3), 284-289. https://doi.org/10.1248/bpb.b16-00738
Kumar, H., Aggarwal, N., Marwaha, M.G., Deep, A., Chopra, H., et al. (20222). Thiazolidin-2,4-dione scaffold: An insight into recent advances as antimicrobial, antioxidant, hypoglycemic agents, mechanism of action and patents granted. Molecules, 27, 6763. https://doi.org/10.3390/molecules27196763
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