Waters, L. S. et al. Eukaryotic translesion polymerases and their roles and regulation in DNA damage tolerance. Microbiol. Mol. Biol. Rev. 73, 134–154. https://doi.org/10.1128/MMBR.00034-08 (2009).
Barnes, R. P., Tsao, W. C., Moldovan, G. L. & Eckert, K. A. DNA polymerase eta prevents tumor cell-cycle arrest and cell death during recovery from replication stress. Cancer Res. 78, 6549–6560. https://doi.org/10.1158/0008-5472.CAN-17-3931 (2018).
Sale, J. E., Lehmann, A. R. & Woodgate, R. Y-family DNA polymerases and their role in tolerance of cellular DNA damage. Nat. Rev. Mol. Cell Biol. 13, 141–152. https://doi.org/10.1038/nrm3289 (2012).
Lange, S. S., Takata, K. I. & Wood, R. D. DNA polymerases and cancer. Nat. Rev. Cancer 11, 96–110. https://doi.org/10.1038/nrc2998 (2011).
Masutani, C., Kusumoto, R., Iwai, S. & Hanaoka, F. Mechanisms of accurate translesion synthesis by human DNA polymerase η. EMBO J. 19, 3100–3109. https://doi.org/10.1093/emboj/19.12.3100 (2000).
Ceppi, P. et al. Polymerase η mRNA expression predicts survival of non-small cell lung cancer patients treated with platinum-based chemotherapy. Clin. Cancer Res. 15, 1039–1045. https://doi.org/10.1158/1078-0432.CCR-08-1227 (2009).
Ummat, A. et al. Structural basis for cisplatin DNA damage tolerance by human polymerase η during cancer chemotherapy. Nat. Struct. Mol. Biol. 19, 628. https://doi.org/10.1038/nsmb.2295 (2012).
Zhao, Y. et al. Structural basis of human DNA polymerase η-mediated chemoresistance to cisplatin. PNAS USA 109, 7269–7274. https://doi.org/10.1073/pnas.1202681109 (2012).
Rechkoblit, O. et al. Structural basis for polymerase η–promoted resistance to the anticancer nucleoside analog cytarabine. Sci. Rep. 8, 1–9. https://doi.org/10.1038/s41598-018-30796-w (2018).
Wiley, J. S., Jones, S. P., Sawyer, W. H. & Paterson, A. R. P. Cytosine arabinoside influx and nucleoside transport sites in acute leukemia. J. Clin. Investig. 69, 479–489. https://doi.org/10.1172/JCI110472 (1982).
Paterson, A. R. P. & Oliver, J. M. Nucleoside transport. II. Inhibition by p-nitrobenzylthioguanosine and related compounds. Can. J. Biochem. Physiol. 49, 271–274. https://doi.org/10.1139/o71-039 (1971).
Goodell, B., Leventhal, B. & Henderson, E. Cytosine arabinoside in acute granulocytic leukemia. Clin. Pharmacol. Ther. 12, 599–606. https://doi.org/10.1002/cpt1971124599 (1971).
Rassiga, A. L., Schwartz, H. J., Forman, W. B. & Crum, E. D. Cytarabine-induced anaphylaxis: demonstration of antibody and successful desensitization. Arch. Intern. Med. 140, 425–426. https://doi.org/10.1001/archinte.1980.0033015013903 (1980).
Pizzo, P. A., Robichaud, K. J., Gill, F. A. & Witebsky, F. G. Empiric antibiotic and antifungal therapy for cancer patients with prolonged fever and granulocytopenia. Am. J. Med. 72, 101–111. https://doi.org/10.1016/0002-9343(82)90594-0 (1982).
Burgdorf, W. H., Gilmore, W. A. & Ganick, R. G. Peculiar acral erythema secondary to high-dose chemotherapy for acute myelogenous leukemia. Ann. Intern. Med. 97, 61–62. https://doi.org/10.7326/0003-4819-97-1-61 (1982).
Jehn, U., Göldel, N., Rienmüller, R. & Wilmanns, W. Non-cardiogenic pulmonary edema complicating intermediate and high-dose Ara C treatment for relapsed acute leukemia. Med. Oncol. Tumor Pharmacother. 5, 41–47. https://doi.org/10.1007/BF03003180 (1988).
Donehower, R. C., Karp, J. E. & Burke, P. J. Pharmacology and toxicity of high-dose cytarabine by 72-hour continuous infusion 1, 2. Cancer Treat. Rep. 70, 1059 (1986) (PMID: 3461882).
Congreve, M., Murray, C. W. & Blundell, T. L. Keynote review: Structural biology and drug discovery. Drug Discov. Today 10, 895–907. https://doi.org/10.1016/S1359-6446(05)03484-7 (2005).
Beddell, C. R., Goodford, P. J., Norrington, F. E., Wilkinson, S. & Wootton, R. Compounds designed to fit a site of known structure in human haemoglobin. Br. J. Pharmacol. 57, 201–209. https://doi.org/10.1111/j.1476-5381 (1976).
Gruner, S. A., Locardi, E., Lohof, E. & Kessler, H. Carbohydrate-based mimetics in drug design: Sugar amino acids and carbohydrate scaffolds. Chem. Rev. 102, 491–514. https://doi.org/10.1021/cr0004409 (2002).
Hirschmann, R. et al. Modulation of receptor and receptor subtype affinities using diastereomeric and enantiomeric monosaccharide scaffolds as a means to structural and biological diversity. J. Med. Chem. 41, 1382–1391. https://doi.org/10.1021/jm9800346 (1998).
Blocks, C. B. & Bols, B. M. Carbohydrate Building Blocks (Wiley, 1996).
Wunberg, T. et al. Carbohydrates as multifunctional chiral scaffolds in combinatorial synthesis. Angew. Chem. 37, 2503–2505. https://doi.org/10.1002/(SICI)1521-3773(19981002)37:18%3c2503::AID-ANIE2503%3e3.0.CO,2-R(1998) (1998).
Schweizer, F. & Hindsgaul, O. Combinatorial synthesis of carbohydrates. Curr. Opin. Chem. Biol. 3, 291–298. https://doi.org/10.1016/s1367-5931(99)80045-3 (1999).
Bednarska, N. G., Wren, B. W. & Willcocks, S. J. The importance of the glycosylation of antimicrobial peptides: natural and synthetic approaches. Drug Discov. Today 22, 919–926. https://doi.org/10.1016/j.drudis.2017.02.001 (2017).
Varamini, P. et al. Synthesis and biological evaluation of an orally active glycosylated endomorphin-1. J. Med. Chem. 55, 5859–5867. https://doi.org/10.1021/jm300418d (2012).
Polt, R., Dhanasekaran, M. & Keyari, C. M. Glycosylated neuropeptides: A new vista for neuropsychopharmacology?. Med. Res. Rev. 25, 557–585. https://doi.org/10.1002/med.20039 (2005).
Ho, H. H., Gilbert, M. T., Nussenzveig, D. R. & Gershengorn, M. C. Glycosylation is important for binding to human calcitonin receptors. Biochemistry 38, 1866–1872. https://doi.org/10.1021/bi981195e (1999).
Herzner, H., Reipen, T., Schultz, M. & Kunz, H. Synthesis of glycopeptides containing carbohydrate and peptide recognition motifs. Chem. Rev. 100, 4495–4538. https://doi.org/10.1021/cr990308c (2000).
Grant, S. Ara-C: Cellular and molecular pharmacology. Adv. Cancer Res. 72, 197–233. https://doi.org/10.1016/S0065-230X (1997).
Maeda, H., Kusuhara, T., Tsuhako, M. & Nakayama, H. Phosphorylation of 5′-deoxy-5-fluorouridine with inorganic phosphorylating agents. Chem. Pharm. Bull. 56, 1698–1703. https://doi.org/10.1248/cpb.59.1447 (2008).
Chanda, D. & Harohally, N. V. Revisiting Amadori and Heyns synthesis: Critical percentage of acyclic form play the trick in addition to catalyst. Tetrahedron Lett. 59, 2983–2988. https://doi.org/10.1016/j.tetlet.2018.06.050 (2018).
Shao, Y., Fusti-Molnar, L., Jung, Y., Kussmann, J., Ochsenfeld, C., Brown, S. T., Gilbert, A. T. B., Slipchenko, L. V., Levchenko, S. V., O’Neill, D. P. & DiStasio Jr, R. A. Wavefunct. Inc. (Irvine CA, 2011).
Trott, O. & Olson, A. J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31, 455–461. https://doi.org/10.1002/jcc.21334 (2010).
Seeliger, D. & de Groot, B. L. Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Comput. Aided Mol. 24, 417–422. https://doi.org/10.1007/s10822-010-9352-6 (2010).
Biovia, D. S. BIOVIA Discovery Studio Client, (v16. 1.0. 15350.) (Dassault Systems, San Diego, 2017).
Páll, S., Abraham, M. J., Kutzner, C., Hess, B. & Lindahl, E. Tackling exascale software challenges in molecular dynamics simulations with GROMACS. EASC https://doi.org/10.1007/978-3-319-15976-8_1 (2014).
Kukol, A. (ed.) Molecular Modeling of Proteins Vol. 443 (Humana Press, 2008).
Humphrey, W., Dalke, A. & Schulten, K. VMD: Visual molecular dynamics. J. Mol. Gr. 14, 33–38. https://doi.org/10.1016/0263-7855(96)00018-5 (1996).
Huey, R. & Morris, G. M. Using AutoDock 4 with AutoDocktools: A Tutorial 54–56 (The Scripps Research Institute, USA, 2008).
Garcia-Diaz, M., Murray, M. S., Kunkel, T. A. & Chou, K. M. Interaction between DNA polymerase λ and anticancer nucleoside analogs. J. Biol. Chem. 285, 16874–16879. https://doi.org/10.1074/jbc.M109.094391 (2010).
Garcıa-Dıaz, M. et al. DNA polymerase λ, a novel DNA repair enzyme in human cells. J. Biol. Chem. 277, 13184–13191. https://doi.org/10.1074/jbc.M111601200 (2002).
Sabini, E. et al. Structure of human dCK suggests strategies to improve anticancer and antiviral therapy. Nat. Struct. Mol. Biol. 10, 513–519. https://doi.org/10.1038/nsb942 (2003).
Mannhold, R. et al. (eds) Molecular Drug Properties: Measurement and Prediction Vol. 37 (Wiley-VCH, 2008).
Lemkul, J. A. & Bevan, D. R. Destabilizing Alzheimer’s Aβ42 protofibrils with morin: mechanistic insights from molecular dynamics simulations. Biochemistry 49, 3935–3946. https://doi.org/10.1021/bi1000855 (2010).
Nedyalkova, M. A., Madurga, S., Tobiszewski, M. & Simeonov, V. Calculating the partition coefficients of organic solvents in octanol/water and octanol/air. J. Chem. Inf. Model. 59, 2257–2263. https://doi.org/10.1021/acs.jcim.9b00212 (2019).
Hoekman, D. Exploring QSAR fundamentals and applications in chemistry and biology, volume 1. Hydrophobic, electronic and steric constants. J. Am. Chem. Soc. 118, 10678–10678. https://doi.org/10.1021/ja965433%2B (1996).
Labnetwork.com. LabNetwork. https://www.labnetwork.com/frontend-app/p/#!/moleculedetails/LN00008170 (2021).
Sangster, J. A databank of evaluated octanol-water partition coefficients (LogP) on microcomputer diskette. Bulletin for Sangster Research Laboratories. Canadian National Committee for CODATA: Montreal, Quebec, Canada (1994).
Thompson, M. Material safety data sheets. Am. J. Nurs. 110, 12–14. https://doi.org/10.1097/01.NAJ.0000390501.84780.e6 (2010).
Schaduangrat, N. et al. Towards reproducible computational drug discovery. J. Cheminform. 12, 9. https://doi.org/10.1186/s13321-020-0408-x (2020).
Marenich, A. V., Cramer, C. J. & Truhlar, D. G. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J. Phys. Chem. B. 113, 6378–6396. https://doi.org/10.1021/jp810292n (2009).
Zhao, Y. & Truhlar, D. G. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor. Chem. Acc. 120, 215–241. https://doi.org/10.1007/s00214-007-0310-x (2008).
Barclay, T., Ginic-Markovic, M., Johnston, M. R., Cooper, P. & Petrovsky, N. Observation of the keto tautomer of D-fructose in D2O using 1H NMR spectroscopy. Carbohydr. Res. 347, 136–141. https://doi.org/10.1016/j.carres.2011.11.003 (2012).
Morris, G. M. et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785–2791. https://doi.org/10.1002/jcc.21256 (2009).
Mansourian, M., Mahnam, K., Madadkar-Sobhani, A., Fassihi, A. & Saghaie, L. Insights into the human A 1 adenosine receptor from molecular dynamics simulation: Structural study in the presence of lipid membrane. Med. Chem. Res. 24, 3645–3659. https://doi.org/10.1007/s00044-015-1409-6 (2015).
Morris, G. M. et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19, 1639–1662. https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14%3c1639::AID-JCC10%3e3.0.CO,2-B (1998).
Davydov, A. S. Solitons in Molecular Systems 113 (Reidel, Dordrecht, 1985).
Yadava, U., Shukla, B. K., Roychoudhury, M. & Kumar, D. Pyrazolo [3, 4-d] pyrimidines as novel inhibitors of O-acetyl-L-serine sulfhydrylase of Entamoeba histolytica: An in-silico study. J. Mol. Model. 21, 96. https://doi.org/10.1007/s00894-015-2631-3 (2015).
Berendsen, H. J., Postma, J. V., van Gunsteren, W. F., DiNola, A. R. H. J. & Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3690. https://doi.org/10.1063/1.448118 (1984).
Yadav, R. K. & Yadava, U. Molecular dynamics simulation of DNA duplex, analog of PPT (polypurine tract), its conformation and hydration: A theoretical study. Med. Chem. Res. 23, 280–286. https://doi.org/10.1007/s00044-013-0631-3 (2014).
Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: An N⋅log (N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089. https://doi.org/10.1063/1.464397 (1993).
Hess, B., Bekker, H., Berendsen, H. J. & Fraaije, J. G. LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463–1472 (1997).
Kumari, R., Kumar, R., Open Source Drug Discovery Consortium, & Lynn, A. g_mmpbsa: A GROMACS tool for high-throughput MM-PBSA calculations. J. Chem. Inf. Model. 54, 1951–1962. https://doi.org/10.1021/ci500020m (2014).
Kessler, D. et al. Drugging an undruggable pocket on KRAS. PNAS USA 116, 15823–15829. https://doi.org/10.1073/pnas.1904529116 (2019).
Karnoub, A. E. et al. Mesenchymal stem cells within tumour stroma promote breast cancer metastasis. Nature 449, 557–563. https://doi.org/10.1038/nature06188 (2007).
Esser, D. et al. Structure determination of the Ras-binding domain of the Ral-specific guanine nucleotide exchange factor Rlf. Biochemistry 37, 13453–13462. https://doi.org/10.1021/bi9811664 (1998).
Zuber, J. et al. A genome-wide survey of RAS transformation targets. Nat. Genet. 24, 144–152. https://doi.org/10.1038/72799 (2000).
Biankin, A. et al. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature 491, 399–405. https://doi.org/10.1038/nature11547 (2012).
Varki, A., Kannagi, R. & Toole, B. P. Glycosylation Changes in Cancer. Essentials of Glycobiology 2nd edn. (Cold Spring Harbor Laboratory Press, 2009).
Brittain, H. G. Profiles of Drug Substances, Excipients, and Related Methodology (Academic press, 2020).
Moldoveanu, S. C. & David, V. Modern Sample Preparation for Chromatography (Elsevier, 2021).
Van Kooyk, Y. & Rabinovich, G. A. Protein-glycan interactions in the control of innate and adaptive immune responses. Nat. Immunol. 9, 593–601. https://doi.org/10.1038/ni.f.203 (2008).
Cummings, R. D. The repertoire of glycan determinants in the human glycome. Mol. Biosyst. 5, 1087–1104. https://doi.org/10.1039/B907931A (2009).
Ernst, B. & Magnani, J. L. From carbohydrate leads to glycomimetic drugs. Nat. Rev. Drug Discov. 8, 661–677. https://doi.org/10.1038/nrd2852 (2009).
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