Structure based design of inhibitory peptides targeting ornithine decarboxylase dimeric interface and in vitro validation in human retinoblastoma Y79 cells

References

• Aier, I., Varadwaj, P. K., & Raj, U. (2016). Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Scientific Reports, 6, 34984. https://doi.org/10.1038/srep34984
   PubMed Web of Science ®Google Scholar
• Allaman-Pillet, N., Oberson, A., & Schorderet, D. F. (2015). BIRO1, a cell-permeable BH3 peptide, promotes mitochondrial fragmentation and death of retinoblastoma cells. Molecular Cancer Research, 13(1), 86–97. https://doi.org/10.1158/1541-7786.MCR-14-0253
   PubMed Web of Science ®Google Scholar
• Almrud, J. J., Oliveira, M. A., Kern, A. D., Grishin, N. V., Phillips, M. A., & Hackert, M. L. (2000). Crystal structure of human ornithine decarboxylase at 2.1 A resolution: Structural insights to antizyme binding. Journal of Molecular Biology, 295(1), 7–16. https://doi.org/10.1006/jmbi.1999.3331
   PubMed Web of Science ®Google Scholar
• Amadasi, A., Bertoldi, M., Contestabile, R., Bettati, S., Cellini, B., Di Salvo, M. L., Borri-Voltattorni, C., Bossa, F., & Mozzarelli, A. (2007). Pyridoxal 5'-phosphate enzymes as targets for therapeutic agents. Current Medicinal Chemistry, 14(12), 1291–1324. https://doi.org/10.2174/092986707780597899
   PubMed Web of Science ®Google Scholar
• Babbar, N., & Gerner, E. W. (2011). Targeting polyamines and inflammation for cancer prevention. Recent Results in Cancer Research. Fortschritte Der Krebsforschung. Progres Dans Les Recherches Sur le Cancer, 188, 49–64. https://doi.org/10.1007/978-3-642-10858-7_4
   PubMedGoogle Scholar
• Bachrach, U. (2004). Polyamines and cancer: Minireview article. Amino Acids, 26(4), 307–309. https://doi.org/10.1007/s00726-004-0076-6
   PubMed Web of Science ®Google Scholar
• Bakan, A., Meireles, L. M., & Bahar, I. (2011). ProDy: Protein dynamics inferred from theory and experiments. Bioinformatics (Oxford, England)), 27(11), 1575–1577. https://doi.org/10.1093/bioinformatics/btr168
   PubMed Web of Science ®Google Scholar
• Bercovich, Z., & Kahana, C. (2004). Degradation of antizyme inhibitor, an ornithine decarboxylase homologous protein, is ubiquitin-dependent and is inhibited by antizyme. The Journal of Biological Chemistry, 279(52), 54097–54102. https://doi.org/10.1074/jbc.M410234200
   PubMed Web of Science ®Google Scholar
• Boonstra, S., Onck, P. R., & van der Giessen, E. (2016). CHARMM TIP3P water model suppresses peptide folding by solvating the unfolded state. The Journal of Physical Chemistry B, 120(15), 3692–3698. https://doi.org/10.1021/acs.jpcb.6b01316
   PubMed Web of Science ®Google Scholar
• Bowers, K., Chow, E., Xu, H., Dror, R., Eastwood, M., Gregersen, B., Klepeis, J., Kolossvary, I., Moraes, M., Sacerdoti, F., Salmon, J., Shan, Y., & Shaw, D. Scalable algorithms for molecular dynamics simulations on commodity clusters [Paper presentation]. ACM/IEEE SC 2006 Conference (SC'06), Tampa, Florida, USA, November 11-17, 2006, p. 43.
   Google Scholar
• Caliandro, R., Rossetti, G., & Carloni, P. (2012). Local fluctuations and conformational transitions in proteins. Journal of Chemical Theory and Computation, 8(11), 4775–4785. https://doi.org/10.1021/ct300610y
   PubMed Web of Science ®Google Scholar
• Chattopadhyay, M. K., Fernandez, C., Sharma, D., McPhie, P., & Masison, D. C. (2011). Yeast ornithine decarboxylase and antizyme form a 1:1 complex in vitro: Purification and characterization of the inhibitory complex. Biochemical and Biophysical Research Communications, 406(2), 177–182. https://doi.org/10.1016/j.bbrc.2011.01.113
   PubMed Web of Science ®Google Scholar
• Childs, A. C., Mehta, D. J., & Gerner, E. W. (2003). Polyamine-dependent gene expression. Cellular and Molecular Life Sciences, 60(7), 1394–1406. https://doi.org/10.1007/s00018-003-2332-4
   PubMed Web of Science ®Google Scholar
• Choi, H., Kyeong, H., Choi, J. M., & Kim, H. (2014). Rational design of ornithine decarboxylase with high catalytic activity for the production of putrescine. Applied Microbiology and Biotechnology, 98(17), 7483–7490. https://doi.org/10.1007/s00253-014-5669-8
   PubMed Web of Science ®Google Scholar
• Cooper, K. D., Shukla, J. B., & Rennert, O. M. (1978). Polyamine compartmentalization in various human disease states. Clinica Chimica Acta; International Journal of Clinical Chemistry, 82(1-2), 1–7. https://doi.org/10.1016/0009-8981(78)90019-0
   PubMed Web of Science ®Google Scholar
• Darden, T., Perera, L., Li, L., & Pedersen, L. (1999). New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure (London, England: 1993), 7(3), R55–R60. https://doi.org/10.1016/s0969-2126(99)80033-1
   PubMed Web of Science ®Google Scholar
• David, C. C., & Jacobs, D. J. (2014). Principal component analysis: A method for determining the essential dynamics of proteins. Methods in Molecular Biology (Clifton, N.J.), 1084, 193–226. https://doi.org/10.1007/978-1-62703-658-0_11
   PubMedGoogle Scholar
• de Beer, T. A. P., Berka, K., Thornton, J. M., & Laskowski, R. A. (2014). PDBsum additions. Nucleic Acids Research, 42(Database issue), D292–D296. https://doi.org/10.1093/nar/gkt940
   PubMed Web of Science ®Google Scholar
• Deepa, P. R., Vandhana, S., Muthukumaran, S., Umashankar, V., Jayanthi, U., & Krishnakumar, S. (2010). Chemical inhibition of fatty acid synthase: Molecular docking analysis and biochemical validation in ocular cancer cells. Journal of Ocular Biology, Diseases, and Informatics, 3(4), 117–128. https://doi.org/10.1007/s12177-011-9065-7
   PubMedGoogle Scholar
• Elkashef, S. M., Allison, S. J., Sadiq, M., Basheer, H. A., Ribeiro Morais, G., Loadman, P. M., Pors, K., & Falconer, R. A. (2016). Polysialic acid sustains cancer cell survival and migratory capacity in a hypoxic environment. Scientific Reports, 6, 33026. https://doi.org/10.1038/srep33026
   PubMed Web of Science ®Google Scholar
• Evans, D. J., & Holian, B. L. (1985). The Nose–Hoover thermostat. The Journal of Chemical Physics, 83(8), 4069–4074. https://doi.org/10.1063/1.449071
   Web of Science ®Google Scholar
• Gautam, A., Chaudhary, K., Kumar, R., & Raghava, G. P. S. (2015). Computer-aided virtual screening and designing of cell-penetrating peptides. Methods in Molecular Biology (Clifton, N.J.), 1324, 59–69. https://doi.org/10.1007/978-1-4939-2806-4_4
   PubMedGoogle Scholar
• Gautam, A., Chaudhary, K., Singh, S., Joshi, A., Anand, P., Tuknait, A., Mathur, D., Varshney, G. C., & Raghava, G. P. S. (2014). Hemolytik: A database of experimentally determined hemolytic and non-hemolytic peptides. Nucleic Acids Res, 42(Database issue), D444–D449. https://doi.org/10.1093/nar/gkt1008
   PubMed Web of Science ®Google Scholar
• Gerner, E. W., & Meyskens, F. L. (2004). Polyamines and cancer: Old molecules, new understanding. Nature Reviews Cancer, 4(10), 781–792. https://doi.org/10.1038/nrc1454
   PubMed Web of Science ®Google Scholar
• Goncearenco, A., Li, M., Simonetti, F. L., Shoemaker, B. A., & Panchenko, A. R. (2017). Exploring protein-protein interactions as drug targets for anti-cancer therapy with in silico workflows. Methods in Molecular Biology (Clifton, N.J.), 1647, 221–236. https://doi.org/10.1007/978-1-4939-7201-2_15
   PubMedGoogle Scholar
• Greenfield, N. J. (2006). Using circular dichroism spectra to estimate protein secondary structure. Nature Protocols, 1(6), 2876–2890. https://doi.org/10.1038/nprot.2006.202
   PubMed Web of Science ®Google Scholar
• Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., & Raghava, G. P. S; Open Source Drug Discovery Consortium (2013). In silico approach for predicting toxicity of peptides and proteins. PLoS One, 8(9), e73957. https://doi.org/10.1371/journal.pone.0073957
   PubMed Web of Science ®Google Scholar
• Hsieh, J., Yang, J., Lin, C., Liu, G., & Hung, H. (2011). Minimal antizyme peptide fully functioning in the binding and inhibition of ornithine decarboxylase and antizyme inhibitor. PLoS One, 6(9), e24366. https://doi.org/10.1371/journal.pone.0024366
   PubMed Web of Science ®Google Scholar
• Hu, H., Liu, X., Jiang, C., Zhang, Y., Bian, J., Lu, Y., Geng, Z., Liu, S., Liu, C., Wang, X., & Wang, W. (2003). Cloning and expression of ornithine decarboxylase gene from human colorectal carcinoma. World Journal of Gastroenterology, 9(4), 714–716. https://doi.org/10.3748/wjg.v9.i4.714
   PubMed Web of Science ®Google Scholar
• Huber, R. (1979). Conformational flexibility in protein molecules. Nature, 280(5723), 538–539. https://doi.org/10.1038/280538a0
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Ivanov, A. A., Khuri, F. R., & Fu, H. (2013). Targeting protein-protein interactions as an anticancer strategy. Trends in Pharmacological Sciences, 34(7), 393–400. https://doi.org/10.1016/j.tips.2013.04.007
   PubMed Web of Science ®Google Scholar
• John, A., Sivashanmugam, M., Natarajan, S. K., & Umashankar, V. (2020). Computational modeling of novel inhibitory peptides targeting proteoglycan like region of carbonic anhydrase IX and in vitro validation in HeLa cells. Journal of Biomolecular Structure & Dynamics, 38(7), 1995–2006. https://doi.org/10.1080/07391102.2019.1623075
   PubMed Web of Science ®Google Scholar
• John, A., Sivashanmugam, M., Umashankar, V., & Natarajan, S. K. (2017). Virtual screening, molecular dynamics, and binding free energy calculations on human carbonic anhydrase IX catalytic domain for deciphering potential leads. Journal of Biomolecular Structure & Dynamics, 35(10), 2155–2168. https://doi.org/10.1080/07391102.2016.1207565
   PubMed Web of Science ®Google Scholar
• John, A., Vetrivel, U., Sivashanmugam, M., & Natarajan, S. K. (2020). Microsecond simulation of the proteoglycan-like region of carbonic anhydrase IX and design of chemical inhibitors targeting ph homeostasis in cancer cells. ACS Omega, 5(8), 4270–4281. https://doi.org/10.1021/acsomega.9b04203
   PubMed Web of Science ®Google Scholar
• Kano, Y., Soda, K., Nakamura, T., Saitoh, M., Kawakami, M., & Konishi, F. (2007). Increased blood spermine levels decrease the cytotoxic activity of lymphokine-activated killer cells: A novel mechanism of cancer evasion. Cancer Immunology, Immunotherapy, 56(6), 771–781. https://doi.org/10.1007/s00262-006-0229-4
   PubMed Web of Science ®Google Scholar
• Kusano, T., Yamaguchi, K., Berberich, T., & Takahashi, Y. (2007). Advances in polyamine research in 2007. Journal of Plant Research, 120(3), 345–350. https://doi.org/10.1007/s10265-007-0074-3
   PubMed Web of Science ®Google Scholar
• Li, X., & Coffino, P. (1992). Regulated degradation of ornithine decarboxylase requires interaction with the polyamine-inducible protein antizyme. Molecular and Cellular Biology, 12(8), 3556–3562. https://doi.org/10.1128/mcb.12.8.3556
   PubMed Web of Science ®Google Scholar
• Lin, J. (2011). Accommodating protein flexibility for structure-based drug design. Current Topics in Medicinal Chemistry, 11(2), 171–178. https://doi.org/10.2174/156802611794863580
   PubMed Web of Science ®Google Scholar
• Liu, H., & Zhou, M. (2017). Antitumor effect of Quercetin on Y79 retinoblastoma cells via activation of JNK and p38 MAPK pathways. BMC Complementary and Alternative Medicine, 17(1), 531. https://doi.org/10.1186/s12906-017-2023-6
   PubMed Web of Science ®Google Scholar
• London, N., Raveh, B., Movshovitz-Attias, D., & Schueler-Furman, O. (2010). Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions? Proteins, 78(15), 3140–3149. https://doi.org/10.1002/prot.22785
   PubMed Web of Science ®Google Scholar
• Lotzová, E., Savary, C. A., Totpal, K., Schachner, J., Lichtiger, B., McCredie, K. B., & Freireich, E. J. (1991). Highly oncolytic adherent lymphocytes: Therapeutic relevance for leukemia. Leukemia Research, 15(4), 245–254. https://doi.org/10.1016/0145-2126(91)90127-f
   PubMed Web of Science ®Google Scholar
• Lozier, A. M., Rich, M. E., Grawe, A. P., Peck, A. S., Zhao, P., Chang, A. T., Bond, J. P., & Sholler, G. S. (2015). Targeting ornithine decarboxylase reverses the LIN28/Let-7 axis and inhibits glycolytic metabolism in neuroblastoma. Oncotarget, 6(1), 196–206. https://doi.org/10.18632/oncotarget.2768
   PubMedGoogle Scholar
• Luqman, S., Luqman, S., Masood, N., Srivastava, S., & Dubey, V. (2013). A modified spectrophotometric and methodical approach to find novel inhibitors of ornithine decarboxylase enzyme: A path through the maze. Protocol Exchange. https://doi.org/10.1038/protex.2013.045
   Google Scholar
• Maisuradze, G. G., Liwo, A., & Scheraga, H. A. (2009). Principal component analysis for protein folding dynamics. Journal of Molecular Biology, 385(1), 312–329. https://doi.org/10.1016/j.jmb.2008.10.018
   PubMed Web of Science ®Google Scholar
• Martyna, G. J. (1994). Remarks on “Constant-temperature molecular dynamics with momentum conservation”. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 50(4), 3234–3236. https://doi.org/10.1103/physreve.50.3234
   PubMed Web of Science ®Google Scholar
• McCann, P. P., & Pegg, A. E. (1992). Ornithine decarboxylase as an enzyme target for therapy. Pharmacology & Therapeutics, 54(2), 195–215. https://doi.org/10.1016/0163-7258(92)90032-u
   PubMed Web of Science ®Google Scholar
• Michael, A. J. (2016). Polyamines in eukaryotes, bacteria, and archaea. The Journal of Biological Chemistry, 291(29), 14896–14903. https://doi.org/10.1074/jbc.R116.734780
   PubMed Web of Science ®Google Scholar
• Mohankumar, A., Renganathan, B., Karunakaran, C., Chidambaram, S., & Konerirajapuram Natarajan, S. (2014). Peptides derived from the copper-binding region of lysyl oxidase exhibit antiangiogeneic properties by inhibiting enzyme activity: An in vitro study. Journal of Peptide Science, 20(11), 837–849. https://doi.org/10.1002/psc.2675
   PubMed Web of Science ®Google Scholar
• Mullard, A. (2012). Protein-protein interaction inhibitors get into the groove. Nature Reviews. Drug Discovery, 11(3), 173–175. https://doi.org/10.1038/nrd3680
   PubMed Web of Science ®Google Scholar
• Muthu, K., Panneerselvam, M., Topno, N. S., & Ramadas, K. (2016). Structural transition of ETS1 from an auto-inhibited to functional state upon association with the p16 INK4a native and mutated promoter region. RSC Advances, 6(19), 15960–15975. https://doi.org/10.1039/C5RA24525G
   Web of Science ®Google Scholar
• Muthukumaran, S., Bhuvanasundar, R., Umashankar, V., & Sulochana, K. N. (2018). Insights on ornithine decarboxylase silencing as a potential strategy for targeting retinoblastoma. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 98, 23–28. https://doi.org/10.1016/j.biopha.2017.12.030
   PubMed Web of Science ®Google Scholar
• Muthukumaran, S., Umashankar, V., & Valliappan, M. R. (2012). Structural studies on AIPL1 and its functional interactions with NUB1 to identify key interacting residues in LCA4. Journal of Ocular Biology, Diseases, and Informatics, 5(3-4), 54–60. https://doi.org/10.1007/s12177-013-9102-9
   PubMedGoogle Scholar
• Nowotarski, S. L., Woster, P. M., & Casero, R. A. (2013). Polyamines and cancer: Implications for chemotherapy and chemoprevention. Expert Reviews in Molecular Medicine, 15, e3. https://doi.org/10.1017/erm.2013.3
   PubMed Web of Science ®Google Scholar
• Oredsson, S. M. (2003). Polyamine dependence of normal cell-cycle progression. Biochemical Society Transactions, 31(2), 366–370. https://doi.org/10.1042/bst0310366
   PubMed Web of Science ®Google Scholar
• Pasic, T. R., Heisey, D., & Love, R. R. (1997). Alpha-difluoromethylornithine ototoxicity. Chemoprevention clinical trial results. Archives of Otolaryngology–Head & Neck Surgery, 123(12), 1281–1286. https://doi.org/10.1001/archotol.1997.01900120031004
   PubMedGoogle Scholar
• Pegg, A. E. (2006). Regulation of ornithine decarboxylase. The Journal of Biological Chemistry, 281(21), 14529–14532. https://doi.org/10.1074/jbc.R500031200
   PubMed Web of Science ®Google Scholar
• Pegg, A. E. (2016). Functions of polyamines in mammals. The Journal of Biological Chemistry, 291(29), 14904–14912. https://doi.org/10.1074/jbc.R116.731661
   PubMed Web of Science ®Google Scholar
• Pegg, A. E., Feith, D. J., Fong, L. Y. Y., Coleman, C. S., O'Brien, T. G., & Shantz, L. M. (2003). Transgenic mouse models for studies of the role of polyamines in normal, hypertrophic and neoplastic growth. Biochemical Society Transactions, 31(2), 356–360. https://doi.org/10.1042/bst0310356
   PubMed Web of Science ®Google Scholar
• Pendeville, H., Carpino, N., Marine, J. C., Takahashi, Y., Muller, M., Martial, J. A., & Cleveland, J. L. (2001). The ornithine decarboxylase gene is essential for cell survival during early murine development. Molecular and Cellular Biology, 21(19), 6549–6558. https://doi.org/10.1128/mcb.21.19.6549-6558.2001
   PubMed Web of Science ®Google Scholar
• Petta, I., Lievens, S., Libert, C., Tavernier, J., & Bosscher, K. d. (2016). Modulation of protein-protein interactions for the development of novel therapeutics. Molecular Therapy: The Journal of the American Society of Gene Therapy, 24(4), 707–718. https://doi.org/10.1038/mt.2015.214
   PubMed Web of Science ®Google Scholar
• Pifl, C., Reither, H., & Hornykiewicz, O. (1991). Lower efficacy of the dopamine D1 agonist, SKF 38393, to stimulate adenylyl cyclase activity in primate than in rodent striatum. European Journal of Pharmacology, 202(2), 273–276. https://doi.org/10.1016/0014-2999(91)90304-9
   PubMed Web of Science ®Google Scholar
• Pommergaard, H., Burcharth, J., Rosenberg, J., & Raskov, H. (2013). Combination chemoprevention with diclofenac, calcipotriol and difluoromethylornithine inhibits development of non-melanoma skin cancer in mice. Anticancer Research, 33(8), 3033–3039.
   PubMed Web of Science ®Google Scholar
• Preeti Tapas, S., Kumar, P., Madhubala, R., & Tomar, S. (2013). Structural insight into DFMO resistant ornithine decarboxylase from Entamoeba histolytica: An inkling to adaptive evolution. PLoS One, 8, e53397. https://doi.org/10.1371/journal.pone.0053397
   PubMed Web of Science ®Google Scholar
• Sadhasivam, A., & Vetrivel, U. (2019). Identification of potential drugs targeting L,L-diaminopimelate aminotransferase of Chlamydia trachomatis: An integrative pharmacoinformatics approach. Journal of Cellular Biochemistry, 120(2), 2271–2288. https://doi.org/10.1002/jcb.27553
   Web of Science ®Google Scholar
• Samdani, A., & Vetrivel, U. (2018). POAP: A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening. Computational Biology and Chemistry, 74, 39–48. https://doi.org/10.1016/j.compbiolchem.2018.02.012
   PubMed Web of Science ®Google Scholar
• Sedan, Y., Marcu, O., Lyskov, S., & Schueler-Furman, O. (2016). Peptiderive server: Derive peptide inhibitors from protein-protein interactions. Nucleic Acids Research, 44(W1), W536–W541. https://doi.org/10.1093/nar/gkw385
   PubMed Web of Science ®Google Scholar
• Singh, S., Singh, H., Tuknait, A., Chaudhary, K., Singh, B., Kumaran, S., & Raghava, G. P. S. (2015). PEPstrMOD: Structure prediction of peptides containing natural, non-natural and modified residues. Biology Direct, 10, 73. https://doi.org/10.1186/s13062-015-0103-4
   PubMed Web of Science ®Google Scholar
• Sivashanmugam, M., Jaidev, J., Umashankar, V., & Sulochana, K. N. (2017). Ornithine and its role in metabolic diseases: An appraisal. Biomedicine & Pharmacotherapy, 86, 185–194. https://doi.org/10.1016/j.biopha.2016.12.024
   PubMed Web of Science ®Google Scholar
• Sivashanmugam, M., Sulochana K. N., & Umashankar, V. (2018). Virtual screening of natural inhibitors targeting ornithine decarboxylase with pharmacophore scaffolding of DFMO and validation by molecular dynamics simulation studies. Journal of Biomolecular Structure and Dynamics, 37, 766–780. https://doi.org/10.1080/07391102.2018.1439772
   PubMed Web of Science ®Google Scholar
• Smith, M. C., Tinling, S., & Doyle, K. J. (2004). Difluoromethylornithine-induced reversible hearing loss across a wide frequency range. The Laryngoscope, 114(6), 1113–1117. https://doi.org/10.1097/00005537-200406000-00029
   PubMed Web of Science ®Google Scholar
• Soda, K. (2011). The mechanisms by which polyamines accelerate tumor spread. Journal of Experimental & Clinical Cancer Research, 30, 95. https://doi.org/10.1186/1756-9966-30-95
   PubMed Web of Science ®Google Scholar
• Takigawa, M., Verma, A. K., Simsiman, R. C., & Boutwell, R. K. (1983). Inhibition of mouse skin tumor promotion and of promoter-stimulated epidermal polyamine biosynthesis by alpha-difluoromethylornithine. Cancer Research, 43(8), 3732–3738.
   PubMed Web of Science ®Google Scholar
• Teilum, K., Olsen, J. G., & Kragelund, B. B. (2011). Protein stability, flexibility and function. Biochimica et Biophysica Acta, 1814(8), 969–976. https://doi.org/10.1016/j.bbapap.2010.11.005
   PubMed Web of Science ®Google Scholar
• Thomas, T., & Thomas, T. J. (2003). Polyamine metabolism and cancer. Journal of Cellular and Molecular Medicine, 7(2), 113–126. https://doi.org/10.1111/j.1582-4934.2003.tb00210.x
   PubMed Web of Science ®Google Scholar
• 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(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Tuckerman, M. E., & Martyna, G. J. (2000). Understanding modern molecular dynamics: Techniques and applications. The Journal of Physical Chemistry B, 104(2), 159–178. https://doi.org/10.1021/jp992433y
   Web of Science ®Google Scholar
• Tyagi, A., KApoor, P., Kumar, R., Chaudhary, K., Gautam, A., & Raghava, G. P. S. (2013). In silico models for designing and discovering novel anticancer peptides. Scientific Reports, 3, 2984. https://doi.org/10.1038/srep02984
   PubMed Web of Science ®Google Scholar
• Ueda, A., Araie, M., & Kubota, S. (2008). Polyamine depletion induces G1 and S phase arrest in human retinoblastoma Y79 cells. Cancer Cell International, 8, 2. https://doi.org/10.1186/1475-2867-8-2
   PubMed Web of Science ®Google Scholar
• Vetrivel, U., Nagarajan, H., & Thirumudi, I. (2018). Design of inhibitory peptide targeting Toxoplasma gondii RON4-human β-tubulin interactions by implementing structural bioinformatics methods. Journal of Cellular Biochemistry, 119(4), 3236–3246. https://doi.org/10.1002/jcb.26480
   PubMed Web of Science ®Google Scholar
• Villoutreix, B. O., Bastard, K., Sperandio, O., Fahraeus, R., Poyet, J., Calvo, F., Déprez, B., & Miteva, M. A. (2008). In silico-in vitro screening of protein-protein interactions: Towards the next generation of therapeutics. Current Pharmaceutical Biotechnology, 9(2), 103–122. https://doi.org/10.2174/138920108783955218
   PubMed Web of Science ®Google Scholar
• Wallace, H. M., Fraser, A. V., & Hughes, A. (2003). A perspective of polyamine metabolism. The Biochemical Journal, 376(Pt 1), 1–14. https://doi.org/10.1042/BJ20031327
   PubMed Web of Science ®Google Scholar
• Wang, J., Liu, X., Yang, Z., Xie, B., & Zhong, Y. (2014). The effect of ROCK-1 activity change on the adhesive and invasive ability of Y79 retinoblastoma cells. BMC Cancer, 14, 89. https://doi.org/10.1186/1471-2407-14-89
   PubMed Web of Science ®Google Scholar
• Wu, H., Chen, S., Hsieh, J., Chou, F., Wang, Y., Lin, W., Lee, P., Yu, Y., Lin, L., Lin, T., Lin, C., Liu, G., Tzeng, S., Hung, H., & Chan, N. (2015). Structural basis of antizyme-mediated regulation of polyamine homeostasis. Proceedings of the National Academy of Sciences of the United States of America, 112(36), 11229–11234. https://doi.org/10.1073/pnas.1508187112
   PubMed Web of Science ®Google Scholar
• Ye, C., Geng, Z., Dominguez, D., Chen, S., Fan, J., Qin, L., Long, A., Zhang, Y., Kuzel, T. M., & Zhang, B. (2016). Targeting ornithine decarboxylase by α-difluoromethylornithine inhibits tumor growth by impairing myeloid-derived suppressor cells. Journal of Immunology, 196(2), 915–923. https://doi.org/10.4049/jimmunol.1500729
   PubMed Web of Science ®Google Scholar
• Yuan, Q., Ray, R. M., Viar, M. J., & Johnson, L. R. (2001). Polyamine regulation of ornithine decarboxylase and its antizyme in intestinal epithelial cells. American Journal of Physiology. Gastrointestinal and Liver Physiology, 280(1), G130–G138. https://doi.org/10.1152/ajpgi.2001.280.1.G130
   PubMed Web of Science ®Google Scholar