Structure based drug design and fragment based approach to identify potential methotrexate analogues as dual inhibitors for management of psoriasis

References

• Baggott, J. E., Vaughn, W. H., & Hudson, B. B. (1986). Inhibition of 5-aminoimidazole-4-carboxamide ribotide transformylase, adenosine deaminase and 5’-adenylate deaminase by polyglutamates of methotrexate and oxidized folates and by 5-aminoimidazole-4-carboxamide riboside and ribotide. The Biochemical Journal, 236(1), 193–200. https://doi.org/10.1042/bj2360193
   PubMed Web of Science ®Google Scholar
• Bedoui, Y., Guillot, X., Sélambarom, J., Guiraud, P., Giry, C., Jaffar-Bandjee, M. C., Ralandison, S., & Gasque, P. (2019). Methotrexate an old drug with new tricks. International Journal of Molecular Sciences, 20(20), 5023. https://doi.org/10.3390/ijms20205023
   PubMed Web of Science ®Google Scholar
• Bhabha, G., Ekiert, D. C., Jennewein, M., Zmasek, C. M., Tuttle, L. M., Kroon, G., Dyson, H. J., Godzik, A., Wilson, I. A., & Wright, P. E. (2013). Divergent evolution of protein conformational dynamics in dihydrofolate reductase. Nature Structural & Molecular Biology, 20(11), 1243–1249. https://doi.org/10.1038/nsmb.2676
   PubMed Web of Science ®Google Scholar
• Cheong, C. G., Wolan, D. W., Greasley, S. E., Horton, P. A., Beardsley, G. P., & Wilson, I. A. (2004). Crystal structures of human bifunctional enzyme aminoimidazole-4-carboxamide ribonucleotide transformylase/IMP cyclohydrolase in complex with potent sulfonyl-containing antifolates. The Journal of Biological Chemistry, 279(17), 18034–18045. https://doi.org/10.1074/jbc.M313691200
   PubMed Web of Science ®Google Scholar
• Fales, K. R., Njoroge, F. G., Brooks, H. B., Thibodeaux, S., Torrado, A., Si, C., Toth, J. L., Mc Cowan, J. R., Roth, K. D., Thrasher, K. J., Frimpong, K., Lee, M. R., Dally, R. D., Shepherd, T. A., Durham, T. B., Margolis, B. J., Wu, Z., Wang, Y., Atwell, S., … Geeganage, S. (2017). Discovery of N-(6-Fluoro-1-oxo-1,2-dihydroisoquinolin-7-yl)-5-[(3R)-3-hydroxypyrrolidin-1-yl]thiophene-2-sulfonamide (LSN 3213128), a potent and selective nonclassical antifolate aminoimidazole-4-carboxamide ribonucleotide formyltransferase (AICARFT) inhibitor effective at tumor suppression in a cancer xenograft model. Journal of Medicinal Chemistry, 60(23), 9599–9616. https://doi.org/10.1021/acs.jmedchem.7b01046
   PubMed Web of Science ®Google Scholar
• Ferreira, L. G., Dos Santos, R. N., Oliva, G., & Andricopulo, A. D. (2015). Molecular docking and structure-based drug design strategies. Molecules (Basel, Switzerland), 20(7), 13384–13421. https://doi.org/10.3390/molecules200713384
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Garg, T., Rath, G., & Goyal, A. K. (2014). Ancient and advanced approaches for the treatment of an inflammatory autoimmune disease-psoriasis. Critical Reviews in Therapeutic Drug Carrier Systems, 31(4), 331–364. https://doi.org/10.1615/CritRevTherDrugCarrierSyst.2014010122
   PubMed Web of Science ®Google Scholar
• Hanaa, S. M., El-Serwy, W. S., & El-Serwy, W. S. (2021). Synthesis, molecular docking, in silico ADME predictions, and toxicity studies of n-substituted-5-(4-chloroquinolin-2-yl)-1,3,4-thiadiazol-2-amine derivatives as COVID-19 inhibitors. Russian Journal of Bioorganic Chemistry, 47(1), 158–165. https://doi.org/10.1134/S1068162021010155
   PubMed Web of Science ®Google Scholar
• Hoffman, M. B., Hill, D., & Feldman, S. R. (2016). Current challenges and emerging drug delivery strategies for the treatment of psoriasis. Expert Opinion on Drug Delivery, 13(10), 1461–1473. https://doi.org/10.1080/17425247.2016.1188801
   PubMed Web of Science ®Google Scholar
• Hopper, A. T., Brockman, A., Wise, A., Gould, J., Barks, J., Radke, J. B., Sibley, L. D., Zou, Y., & Thomas, S. (2019). Discovery of selective Toxoplasma gondii dihydrofolate reductase inhibitors for the treatment of toxoplasmosis. Journal of Medicinal Chemistry, 62(3), 1562–1576. https://doi.org/10.1021/acs.jmedchem.8b01754
   PubMed Web of Science ®Google Scholar
• Kirsch, P., Hartman, A. M., Hirsch, A. K. H., & Empting, M. (2019). Concepts and core principles of fragment-based drug design. Molecules, 24(23), 4309. https://doi.org/10.3390/molecules24234309
   PubMed Web of Science ®Google Scholar
• Koźmiński, P., Halik, P. K., Chesori, R., & Gniazdowska, E. (2020). Overview of dual-acting drug methotrexate in different neurological diseases, autoimmune pathologies and cancers. International Journal of Molecular Sciences, 21(10), 3483. https://doi.org/10.3390/ijms21103483
   PubMed Web of Science ®Google Scholar
• Langley, R. G., Cherman, A. M., & Gupta, A. K. (2005). Alefacept: An expert review concerning the treatment of psoriasis. Expert Opinion on Pharmacotherapy, 6(13), 2327–2333. https://doi.org/10.1517/14656566.6.13.2327
   PubMed Web of Science ®Google Scholar
• Malik, R., Mehta, P., Srivastava, S., Choudhary, B., & Sharma, M. (2017). Structure-based screening, ADMET profiling, and molecular dynamic studies on mGlu2 receptor for identification of newer antiepileptic agents. Journal of Biomolecular Structure & Dynamics, 35(16), 3433–3448. https://doi.org/10.1080/07391102.2016.1257440
   PubMed Web of Science ®Google Scholar
• Matthews, D. A., Alden, R. A., Bolin, J. T., Freer, S. T., Hamlin, R., Xuong, N., Kraut, J., Poe, M., Williams, M., & Hoogsteen, K. (1977). Dihydrofolate reductase: X-ray structure of the binary complex with methotrexate. Science (New York, N.Y.), 197(4302), 452–455. https://doi.org/10.1126/science.17920
   PubMed Web of Science ®Google Scholar
• Meijer, F. A., Oerlemans, G. J. M., & Brunsveld, L. (2021). Orthosteric and allosteric dual targeting of the nuclear receptor RORγt with a bitopic ligand. ACS Chemical Biology, 16(3), 510–519. https://doi.org/10.1021/acschembio.0c00941
   PubMed Web of Science ®Google Scholar
• Nath, V., Agrawal, R., & Kumar, V. (2020). Structure based docking and molecular dynamics studies: Peroxisome proliferator-activated receptors –α/γ dual agonists for treatment of metabolic disorders. Journal of Biomolecular Structure & Dynamics, 38(2), 511–523. https://doi.org/10.1080/07391102.2019.1581089
   PubMed Web of Science ®Google Scholar
• Nath, V., Ramchandani, M., Kumar, N., Agrawal, R., & Kumar, V. (2021). Computational identification of potential dipeptidyl peptidase (DPP)-IV inhibitors: Structure based virtual screening, molecular dynamics simulation and knowledge based SAR studies. Journal of Molecular Structure, 1224, 129006. https://doi.org/10.1016/j.molstruc.2020.129006
   Web of Science ®Google Scholar
• Nemat, A., Iqbal, M., Mehmood, T.(2020). A comprehensive review of synthesized derivatives of methotrexate in relation to their anticancer potential. Journal of Medical Oncology and Therapeutics, 5(1). https://doi.org/10.35841/medical-oncology.
   Google Scholar
• Opo, F. A. D. M., Rahman, M. M., Ahammad, F., Ahmed, I., Bhuiyan, M. A., & Asiri, A. M. (2021). Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP protein. Scientific Reports, 11(1), 1–18. https://doi.org/10.1038/s41598-021-83626-x
   PubMed Web of Science ®Google Scholar
• Parnami, N., Garg, T., Rath, G., & Goyal, A. K. (2014). Development and characterization of nanocarriers for topical treatment of psoriasis by using combination therapy. Artificial Cells, Nanomedicine, and Biotechnology, 42(6), 406–412. https://doi.org/10.3109/21691401.2013.837474
   PubMed Web of Science ®Google Scholar
• Rahman, L. K. A., & Chhabra, S. R. (1988). The chemistry of methotrexate and its analogues. Medicinal Research Reviews, 8(1), 95–155. https://doi.org/10.1002/med.2610080106
   PubMed Web of Science ®Google Scholar
• Rajagopalan, P. T. R., Zhang, Z., McCourt, L., Dwyer, M., Benkovic, S. J., & Hammes, G. G. (2002). Interaction of dihydrofolate reductase with methotrexate: Ensemble and single-molecule kinetics. Proceedings of the National Academy of Sciences of the United States of America, 99(21), 13481–13486. https://doi.org/10.1073/pnas.172501499
   PubMed Web of Science ®Google Scholar
• Salam, N. K., Huang, T. H. W., Kota, B. P., Kim, M. S., Li, Y., & Hibbs, D. E. (2008). Novel PPAR-gamma agonists identified from a natural product library: A virtual screening, induced-fit docking and biological assay study. Chemical Biology & Drug Design, 71(1), 57–70. https://doi.org/10.1111/j.1747-0285.2007.00606.x
   PubMed Web of Science ®Google Scholar
• Sandoval, L. F., Tuchayi, S. M., & Alinia, H. (2014). PTT-54068-emerging-treatment-options-for-psoriasis–focus-on-il-17-bl. 27–35.
   Google Scholar
• Shaikh, F., Zhao, Y., Alvarez, L., Iliopoulou, M., Lohans, C., Schofield, C. J., Padilla-Parra, S., Siu, S. W. I., Fry, E. E., Ren, J., & Stuart, D. I. (2019). Structure-based in silico screening identifies a potent ebolavirus inhibitor from a traditional Chinese medicine library. Journal of Medicinal Chemistry, 62(6), 2928–2937. https://doi.org/10.1021/acs.jmedchem.8b01328
   PubMed Web of Science ®Google Scholar
• Singh, A., Deshpande, N., Pramanik, N., Jhunjhunwala, S., Rangarajan, A., & Atreya, H. S. (2018). Optimized peptide based inhibitors targeting the dihydrofolate reductase pathway in cancer. Scientific Reports, 8(1), 1–8. https://doi.org/10.1038/s41598-018-21435-5
   PubMedGoogle Scholar
• Vyas, V. K., Ghate, M., & Goel, A. (2013). Pharmacophore modeling, virtual screening, docking and in silico ADMET analysis of protein kinase B (PKB β) inhibitors. Journal of Molecular Graphics & Modelling, 42, 17–25. https://doi.org/10.1016/j.jmgm.2013.01.010
   PubMed Web of Science ®Google Scholar
• Zachariae, H. (1990). Methotrexate side-effects. British Journal of Dermatology, 122(S36), 127–133. https://doi.org/10.1111/j.1365-2133.1990.tb02890.x
   PubMedGoogle Scholar