A molecular docking and dynamics study to screen phytochemicals that target mutant thymidine phosphorylase for colon cancer therapy

Brown, 2020, Surgical management of recurrent colon cancer, J. Gastrointest. Oncol., 11, 513, 10.21037/jgo-2019-ccm-09 Patil, 2017, Colorectal cancer in India: an audit from a tertiary center in a low prevalence area, Indian J. Surg. Oncol., 8, 484, 10.1007/s13193-017-0655-0 Siegel, 2020, 70 DuHadaway, 2016, Antimetabolite TTL-315 selectively kills glucose-deprived cancer cells and enhances responses to cytotoxic chemotherapy in preclinical models of cancer, Oncotarget, 7, 7372, 10.18632/oncotarget.7058 Lee, 2016, Therapeutic drug monitoring of 5-fluorouracil, Cancer Chemother. Pharmacol., 78, 447, 10.1007/s00280-016-3054-2 Mori, 2019, The inhibition of thymidine phosphorylase can reverse acquired 5FU-resistance in gastric cancer cells, Gastric Cancer : Off. J. Int. Gastric Cancer Assoc. Jpn. Gastric Cancer Assoc., 22, 497, 10.1007/s10120-018-0881-3 Bronckaers, 2009, The dual role of thymidine phosphorylase in cancer development and chemotherapy, Med. Res. Rev., 29, 903, 10.1002/med.20159 Shahrokni, 2009, Toxicity and efficacy of 5-fluorouracil and capecitabine in a patient with TYMS gene polymorphism: a challenge or a dilemma?, Clin. Colorectal Cancer, 8, 231, 10.3816/CCC.2009.n.039 Lindskog, 2014, Thymidine phosphorylase expression is associated with time to progression in patients with metastatic colorectal cancer, BMC Clin. Pathol., 14, 25, 10.1186/1472-6890-14-25 Kugimiya, 2019, Determination of thymidine phosphorylase expression level facilitates recurrence risk stratification in stage II/III colorectal cancer following adjuvant chemotherapy with oral fluoropyrimidines, Oncol. Lett., 17, 5267 Rejhová, 2018, Natural compounds and combination therapy in colorectal cancer treatment, Eur. J. Med. Chem., 144, 582, 10.1016/j.ejmech.2017.12.039 Mitsiki, 2009, Structures of native human thymidine phosphorylase and in complex with 5-iodouracil, Biochem. Biophys. Res. Commun., 386, 666, 10.1016/j.bbrc.2009.06.104 Akkol, 2021, Is emodin with anticancer effects completely innocent? Two sides of the coin, Cancers, 13, 2733, 10.3390/cancers13112733 Pagano, 2021, Palmitoylethanolamide reduces colon cancer cell proliferation and migration, influences tumor cell cycle and exerts in vivo chemopreventive effects, Cancers, 13, 1923, 10.3390/cancers13081923 Silva, 2020, Toxicological, chemopreventive, and cytotoxic potentialities of rare vegetal species and supporting findings for the Brazilian Unified Health System (SUS), J. Toxicol. Environ. Health Part A, 83, 525, 10.1080/15287394.2020.1780658 Küpeli Akkol, 2020, Coumarins and coumarin-related compounds in pharmacotherapy of cancer, Cancers, 12, 1959, 10.3390/cancers12071959 Ahmed, 2020, Anticancer potential of furanocoumarins: mechanistic and therapeutic aspects, Int. J. Mol. Sci., 21, 5622, 10.3390/ijms21165622 Farooq, 2021, Isolation, characterization and neuroprotective activity of folecitin: an in vivo study, Life (Basel, Switzerland), 11, 825 Bari, 2021, Ethnomedicinal uses, phytochemistry, and biological activities of plants of the genus Gynura, J. Ethnopharmacol., 271, 10.1016/j.jep.2021.113834 Hossain, 2021, Andrographis paniculata (burm. f.) wall. ex nees: an updated review of phytochemistry, antimicrobial pharmacology, and clinical safety and efficacy, Life (Basel, Switzerland), 11, 348 Chakraborty, 2021, Bromelain a potential bioactive compound: a comprehensive overview from a pharmacological perspective, Life (Basel, Switzerland), 11, 317 Martínez, 2020, Cannabidiol and other non-psychoactive cannabinoids for prevention and treatment of gastrointestinal disorders: useful nutraceuticals?, Int. J. Mol. Sci., 21, 3067, 10.3390/ijms21093067 Sahu, 2021, Computational study to evaluate the potency of phytochemicals in Boerhavia diffusa and the impact of point mutation on cyclin-dependent kinase 2-associated protein 1, J. Biomol. Struct. Dynam., 1, 10.1080/07391102.2021.1914169 Bristy, 2020, Deciphering the pharmacological properties of methanol extract of Psychotria calocarpa leaves by in vivo, in vitro and in silico approaches, Pharmaceuticals (Basel, Switzerland), 13, 183, 10.3390/ph13080183 Sahin, 2021, Modulation of inflammation by phytochemicals to enhance efficacy and reduce toxicity of cancer chemotherapy, Crit. Rev. Food Sci. Nutr., 1, 10.1080/10408398.2021.1976721 Fernández, 2021, Antiproliferative and palliative activity of flavonoids in colorectal cancer, Biomed. Pharmacother. = Biomedecine & pharmacotherapie, 143 Tong, 2019, Apigenin inhibits epithelial-mesenchymal transition of human colon cancer cells through NF-κB/Snail signalling pathway, Biosci. Rep., 39, 10.1042/BSR20190452 Zhou, 2019, Worldwide research trends on aristolochic acids (1957-2017): suggestions for researchers, PLoS One, 14, 10.1371/journal.pone.0216135 Iqbal, 2018, Isolation and characterization of aristolactam alkaloids from the stem bark of Goniothalamus velutinus (Airy Shaw) and their biological activities, J. King Saud Univ. Sci., 30, 41, 10.1016/j.jksus.2016.12.008 Tayarani-Najaran, 2021, A review of auraptene as an anticancer agent, Front. Pharmacol., 12, 698352, 10.3389/fphar.2021.698352 Mou, 2019, Berbamine exerts anticancer effects on human colon cancer cells via induction of autophagy and apoptosis, inhibition of cell migration and MEK/ERK signalling pathway, Journal of BUON : Off. J. Balk. Union Oncol., 24, 1870 Zhuang, 2018, Crocetin treatment inhibits proliferation of colon cancer cells through down-regulation of genes involved in the inflammation, Saudi J. Biol. Sci., 25, 1767, 10.1016/j.sjbs.2017.04.005 Rahmani, 2020, Synthesis and characterisation of chitosan-encapsulated genistein: its anti-proliferative and anti-angiogenic activities, J. Microencapsul., 37, 305, 10.1080/02652048.2020.1740804 Mi, 2017, Imperatorin suppresses proliferation and angiogenesis of human colon cancer cell by targeting HIF-1α via the mTOR/p70S6K/4E-BP1 and MAPK pathways, J. Ethnopharmacol., 203, 27, 10.1016/j.jep.2017.03.033 Riahi-Chebbi, 2019, The Phenolic compound Kaempferol overcomes 5-fluorouracil resistance in human resistant LS174 colon cancer cells, Sci. Rep., 9, 195, 10.1038/s41598-018-36808-z Muthusamy, 2020, Synergistic effect of 5-fluorouracil combined with naringin in MDA-MB-231 human breast cancer cells, Int. Res. J. Oncol., 13 Chung, 2018, Combination of resveratrol and 5-flurouracil enhanced anti-telomerase activity and apoptosis by inhibiting STAT3 and Akt signalling pathways in human colorectal cancer cells, Oncotarget, 9, 32943, 10.18632/oncotarget.25993 Chen, 1996, New dimeric aporphine alkaloids and cytotoxic constituents of Hernandia nymphaeifolia, Planta Med., 62, 528, 10.1055/s-2006-957963 Timofeev, 2013, Three-dimensional structure of thymidine phosphorylase from E. coli in complex with 3′-azido-2′-fluoro-2′, 3′-dideoxyuridine, Crystallogr. Rep., 58, 842, 10.1134/S1063774513060230 Bendl, 2014, PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations, PLoS Comput. Biol., 10, 10.1371/journal.pcbi.1003440 Pires, 2014, DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach, Nucleic Acids Res., 42, W314, 10.1093/nar/gku411 Szklarczyk, 2021, The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets, Nucleic Acids Res., 49, D605, 10.1093/nar/gkaa1074 Jo, 2008, CHARMM-GUI: a web-based graphical user interface for CHARMM, J. Comput. Chem., 29, 1859, 10.1002/jcc.20945 Daina, 2017, SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules, Sci. Rep., 7, 42717, 10.1038/srep42717 Sander, 2015, DataWarrior: an open-source program for chemistry aware data visualization and analysis, J. Chem. Inf. Model., 55, 460, 10.1021/ci500588j Ramaiah, 2020, Synthesis, in vitro and structural aspects of benzothiazole analogs as anti-oxidants and potential neuroprotective agents, Environ. Toxicol. Pharmacol., 79, 103415, 10.1016/j.etap.2020.103415 Tian, 2018, CASTp 3.0: computed atlas of surface topography of proteins, Nucleic Acids Res., 46, W363, 10.1093/nar/gky473 Trott, 2010, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem., 31, 455, 10.1002/jcc.21334 Sravani, 2021, Computational molecular docking analysis and visualisation of anthocyanins for anticancer activity, Int. J. Res. Appl. Sci. Biotechnol., 8, 154, 10.31033/ijrasb.8.1.18 Pattanayak, 2011, Effect of water on solvation structure and dynamics of ions in the peptide bond environment: importance of hydrogen bonding and dynamics of the solvents, J. Phys. Chem. B, 115, 13241, 10.1021/jp206027e Pattanayak, 2013, Pressure and temperature dependence on the hydrogen bonding and dynamics of ammonium ion in liquid water: a molecular dynamics simulations study, J. Mol. Liq., 186, 98, 10.1016/j.molliq.2013.05.010 Pattanayak, 2014, Effects of methanol on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution, J. Mol. Liq., 194, 141, 10.1016/j.molliq.2014.01.012 Van Der Spoel, 2005, GROMACS: fast, flexible, and free, J. Comput. Chem., 26, 1701, 10.1002/jcc.20291 Huang, 2017, CHARMM36m: an improved force field for folded and intrinsically disordered proteins, Nat. Methods, 14, 71, 10.1038/nmeth.4067 Wu, 2006, Flexible simple point-charge water model with improved liquid-state properties, J. Chem. Phys., 124, 10.1063/1.2136877 Fletcher, 1963, A rapidly convergent descent method for minimization, Comput. J., 6, 163, 10.1093/comjnl/6.2.163 Ewald, 1921, Evaluation of optical and electrostatic lattice potentials, Ann. Phys., 64, 253, 10.1002/andp.19213690304 Rodrigues, 2018, DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability, Nucleic Acids Res., 46, W350, 10.1093/nar/gky300 Wang, 2018, A quantum mechanical computational method for modeling electrostatic and solvation effects of protein, Sci. Rep., 8, 5475, 10.1038/s41598-018-23783-8 Sahu, 2020, Molecular dynamics simulation perception study of the binding affinity performance for main protease of SARS-CoV-2, J. Biomol. Struct. Dynam., 1 Sahu, 2019, Molecular docking and molecular dynamics simulation studies on PLCE1 encoded protein, J. Mol. Struct., 1198, 10.1016/j.molstruc.2019.126936 Taherimehr, 2020, New insight into the molecular mechanism of the trehalose effect on urate oxidase stability, J. Biomol. Struct. Dynam., 1 Zhang, 2018, Berbamine suppresses cell viability and induces apoptosis in colorectal cancer via activating p53-dependent apoptotic signaling pathway, Cytotechnology, 70, 321, 10.1007/s10616-017-0146-8 Parhi, 2017, Enhanced anti-metastatic and anti-tumorigenic efficacy of Berbamine loaded lipid nanoparticles in vivo, Sci. Rep., 7, 5806, 10.1038/s41598-017-05296-y