Multifaceted role of drugs: a potential weapon to outsmart Mycobacterium tuberculosis resistance by targeting its essential ThyX

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Abu El Asrar, R., Margamuljana, L., Klaassen, H., Nijs, M., Marchand, A., Chaltin, P., Myllykallio, H., Becker, H. F., De Jonghe, S., Herdewijn, P., & Lescrinier, E. (2017). Discovery of a new Mycobacterium tuberculosis thymidylate synthase X inhibitor with a unique inhibition profile. Biochemical Pharmacology, 135, 69–78. https://doi.org/10.1016/j.bcp.2017.03.017
   PubMed Web of Science ®Google Scholar
• Bantel, H., Berg, C., Vieth, M., Stolte, M., Kruis, W., & Schulze-Osthoff, K. (2000). Mesalazine inhibits activation of transcription factor NF-kappaB in inflamed mucosa of patients with ulcerative colitis. The American Journal of Gastroenterology, 95(12), 3452–3457. https://doi.org/10.1111/j.1572-0241.2000.03360.x
   PubMed Web of Science ®Google Scholar
• Basta, T., Boum, Y., Briffotaux, J., Becker, H. F., Lamarre-Jouenne, I., Lambry, J. C., Skouloubris, S., Liebl, U., Graille, M., van Tilbeurgh, H., & Myllykallio, H. (2012). Mechanistic and structural basis for inhibition of thymidylate synthase ThyX. Open Biology, 2(10), 120120. https://doi.org/10.1098/rsob.120120
   PubMedGoogle Scholar
• Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J. D., & Zardecki, C. (2002). The protein data bank. Acta Crystallographica. Section D, Biological Crystallography, 58(Pt 6 No 1), 899–907. https://doi.org/10.1107/s0907444902003451
   PubMedGoogle Scholar
• Boguski, M. S., Mandl, K. D., & Sukhatme, V. P. (2009). Drug discovery. Repurposing with a difference. Science (New York, N.Y.), 324(5933), 1394–1395. https://doi.org/10.1126/science.1169920
   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
• Haberle, J. (2011). Role of carglumic acid in the treatment of acute hyperammonemia due to N-acetylglutamate synthase deficiency. Therapeutics and Clinical Risk Management, 7, 327–332.
   PubMedGoogle Scholar
• Harder, E., Damm, W., Maple, J., Wu, C., Reboul, M., Xiang, J. Y., Wang, L., Lupyan, D., Dahlgren, M. K., Knight, J. L., Kaus, J. W., Cerutti, D. S., Krilov, G., Jorgensen, W. L., Abel, R., & Friesner, R. A. (2016). OPLS3: A force field providing broad coverage of drug-like small molecules and proteins. Journal of Chemical Theory and Computation, 12(1), 281–296. https://doi.org/10.1021/acs.jctc.5b00864
   PubMed Web of Science ®Google Scholar
• Hurle, M. R., Yang, L., Xie, Q., Rajpal, D. K., Sanseau, P., & Agarwal, P. (2013). Computational drug repositioning: From data to therapeutics. Clinical Pharmacology and Therapeutics, 93(4), 335–341. https://doi.org/10.1038/clpt.2013.1
   PubMed Web of Science ®Google Scholar
• Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., & Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–1213. https://doi.org/10.1093/nar/gkv951
   PubMed Web of Science ®Google Scholar
• Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V., Djoumbou, Y., Eisner, R., Guo, A. C., & Wishart, D. S. (2011). DrugBank 3.0: A comprehensive resource for 'omics' research on drugs. Nucleic Acids Research, 39(Database issue), D1035–1041. https://doi.org/10.1093/nar/gkq1126
   PubMed Web of Science ®Google Scholar
• LigPrep. (2009). 23 Schrodinger LLC.
   Google Scholar
• Mathews, I. I., Deacon, A. M., Canaves, J. M., McMullan, D., Lesley, S. A., Agarwalla, S., & Kuhn, P. (2003). Functional analysis of substrate and cofactor complex structures of a thymidylate synthase-complementing protein. Structure (London, England : 1993), 11(6), 677–690. https://doi.org/10.1016/S0969-2126(03)00097-2
   PubMed Web of Science ®Google Scholar
• Mayberry, J. (2013). The history of 5-ASA compounds and their use in ulcerative colitis–trailblazing discoveries in gastroenterology. Journal of Gastrointestinal and Liver Diseases : JGLD, 22(4), 375–377.
   PubMed Web of Science ®Google Scholar
• Merrell, B. J., & McMurry, J. P. (2021). Folic acid. StatPearls. StatPearls Publishing.
   Google Scholar
• Myllykallio, H., Lipowski, G., Leduc, D., Filee, J., Forterre, P., & Liebl, U. (2002). An alternative flavin-dependent mechanism for thymidylate synthesis. Science (New York, N.Y.), 297(5578), 105–107. https://doi.org/10.1126/science.1072113
   PubMed Web of Science ®Google Scholar
• Pablos-Mendez, A., Gowda, D. K., & Frieden, T. R. (2002). Controlling multidrug-resistant tuberculosis and access to expensive drugs: A rational framework. Bulletin of the World Health Organization, 80(6), 489–495.
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Phelan, J., de Sessions, P. F., Tientcheu, L., Perdigao, J., Machado, D., Hasan, R., Hasan, Z., Bergval, I. L., Anthony, R., McNerney, R., Antonio, M., Portugal, I., Viveiros, M., Campino, S., Hibberd, M. L., & Clark, T. G. (2018). Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally. Scientific Reports, 8(1), 160. https://doi.org/10.1038/s41598-017-18188-y
   PubMedGoogle Scholar
• Pozzi, C., Lopresti, L., Tassone, G., & Mangani, S. (2019). Targeting methyltransferases in human pathogenic bacteria: Insights into Thymidylate Synthase (TS) and Flavin-Dependent TS (FDTS). Molecules, 24(8), 1638. https://doi.org/10.3390/molecules24081638
   PubMed Web of Science ®Google Scholar
• Rousseaux, C., Lefebvre, B., Dubuquoy, L., Lefebvre, P., Romano, O., Auwerx, J., Metzger, D., Wahli, W., Desvergne, B., Naccari, G. C., Chavatte, P., Farce, A., Bulois, P., Cortot, A., Colombel, J. F., & Desreumaux, P. (2005). Intestinal antiinflammatory effect of 5-aminosalicylic acid is dependent on peroxisome proliferator-activated receptor-gamma. The Journal of Experimental Medicine, 201(8), 1205–1215. https://doi.org/10.1084/jem.20041948
   PubMed Web of Science ®Google Scholar
• Sampathkumar, P., Turley, S., Ulmer, J. E., Rhie, H. G., Sibley, C. H., & Hol, W. G. (2005). Structure of the Mycobacterium tuberculosis flavin dependent thymidylate synthase (MtbThyX) at 2.0A resolution. Journal of Molecular Biology, 352(5), 1091–1104. https://doi.org/10.1016/j.jmb.2005.07.071
   PubMed Web of Science ®Google Scholar
• Sassetti, C. M., Boyd, D. H., & Rubin, E. J. (2003). Genes required for mycobacterial growth defined by high density mutagenesis. Molecular Microbiology, 48(1), 77–84. https://doi.org/10.1046/j.1365-2958.2003.03425.x
   PubMed Web of Science ®Google Scholar
• Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Schrodinger. (2011). Schrodinger software suite. Schrodinger LLC.
   Google Scholar
• Schwab, M., Reynders, V., Loitsch, S., Shastri, Y. M., Steinhilber, D., Schroder, O., & Stein, J. (2008). PPARgamma is involved in mesalazine-mediated induction of apoptosis and inhibition of cell growth in colon cancer cells. Carcinogenesis, 29(7), 1407–1414. https://doi.org/10.1093/carcin/bgn118
   PubMed Web of Science ®Google Scholar
• Stolfi, C., De Simone, V., Pallone, F., & Monteleone, G. (2013). Mechanisms of action of non-steroidal anti-inflammatory drugs (NSAIDs) and mesalazine in the chemoprevention of colorectal cancer. International Journal of Molecular Sciences, 14(9), 17972–17985. https://doi.org/10.3390/ijms140917972
   PubMed Web of Science ®Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
   PubMedGoogle Scholar
• Wang, K., Wang, Q., Chen, J., Chen, L., Jiang, H., & Shen, X. (2011). Crystal structure and enzymatic characterization of thymidylate synthase X from Helicobacter pylori strain SS1. Protein Science : a Publication of the Protein Society, 20(8), 1398–1410. https://doi.org/10.1002/pro.668
   PubMed Web of Science ®Google Scholar
• WHO. (2019). Global tuberculosis report 2019.
   Google Scholar
• Yang, H., Lou, C., Sun, L., Li, J., Cai, Y., Wang, Z., Li, W., Liu, G., & Tang, Y. (2019). admetSAR 2.0: Web-service for prediction and optimization of chemical ADMET properties. Bioinformatics, 35(6), 1067–1069. https://doi.org/10.1093/bioinformatics/bty707
   PubMed Web of Science ®Google Scholar
• Yang, L. W., Eyal, E., Bahar, I., & Kitao, A. (2009). Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinformatics (Oxford, England), 25(5), 606–614. https://doi.org/10.1093/bioinformatics/btp023
   PubMed Web of Science ®Google Scholar