Characterization of thiamine pyrophosphokinase of vitamin B1 biosynthetic pathway as a drug target of Leishmania donovani

References

• Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
   PubMed Web of Science ®Google Scholar
• Ansari, S., Bhatt, D. N., Sood, C., & Datta, A. (2021). Functional characterization of the LdNAGD gene in Leishmania donovani. Microbiological Research, 251, 126830. https://doi.org/10.1016/j.micres.2021.126830
   PubMed Web of Science ®Google Scholar
• Baker, L. J., Dorocke, J. A., Harris, R. A., & Timm, D. E. (2001). The crystal structure of yeast thiamin pyrophosphokinase. Structure, 9(6), 539–546. https://doi.org/10.1016/S0969-2126(01)00615-3
   PubMed Web of Science ®Google Scholar
• Bateman, A. (2019). UniProt: A worldwide hub of protein knowledge. Nucleic Acids Research, 47(D1), D506–D515. https://doi.org/10.1093/nar/gky1049
   PubMed Web of Science ®Google Scholar
• Beck, B. J., & Downs, D. M. (1998). The apbE gene encodes a lipoprotein involved in thiamine synthesis in Salmonella typhimurium. Journal of Bacteriology, 180(4), 885–891. https://doi.org/10.1128/JB.180.4.885-891.1998
   PubMed Web of Science ®Google Scholar
• Begley, T. P., Downs, D. M., Ealick, S. E., McLafferty, F. W., Loon, A. P. G. M. V., Taylor, S., Campobasso, N., Chiu, H. J., Kinsland, C., Reddick, J. J., & Xi, J. (1999). Thiamin biosynthesis in prokaryotes. Archives of Microbiology, 171(5), 293–300. https://doi.org/10.1007/s002030050713
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., & Shaw, D. E. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters [Paper presentation]. Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, SC’06. https://doi.org/10.1145/1188455.1188544
   Google Scholar
• Bradford, M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochemistry, 72(1–2), 248–254. https://doi.org/10.1006/abio.1976.9999
   PubMed Web of Science ®Google Scholar
• Buckner, F. S., & Wilson, A. J. (2005). Colorimetric assay for screening compounds against Leishmania amastigotes grown in macrophages. The American Journal of Tropical Medicine and Hygiene, 72(5), 600–605. https://doi.org/10.4269/ajtmh.2005.72.600
   PubMed Web of Science ®Google Scholar
• Bugiardini, E., Pope, S., Feichtinger, R. G., Poole, O. V., Pittman, A. M., Woodward, C. E., Heales, S., Quinlivan, R., Houlden, H., Mayr, J. A., Hanna, M. G., & Pitceathly, R. D. S. (2019). Utility of whole blood thiamine pyrophosphate evaluation in TPK1-related diseases. Journal of Clinical Medicine, 8(7), 991. https://doi.org/10.3390/jcm8070991
   PubMed Web of Science ®Google Scholar
• Campobasso, N., Mathews, I. I., Begley, T. P., & Ealick, S. E. (2000). Crystal structure of 4-methyl-5-β-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 Å resolution. Biochemistry, 39(27), 7868–7877. https://doi.org/10.1021/bi0000061
   PubMed Web of Science ®Google Scholar
• Chawla, B., Kumar, R. R., Tyagi, N., Subramanian, G., Srinivasan, N., Park, M. H., & Madhubala, R. (2012). A unique modification of the eukaryotic initiation factor 5A shows the presence of the complete hypusine pathway in leishmania donovani. PLoS One, 7(3), e33138. https://doi.org/10.1371/journal.pone.0033138
   PubMed Web of Science ®Google Scholar
• Chow, E., Rendleman, C. A., Bowers, K. J., Dror, R. O., H., D., Gullingsrud, J., Sacerdoti, F. D., & Shaw, D. E. (2008). Desmond performance on a cluster of multicore processors. D. E. Shaw Research Technical Report DESRES/TR-2008-01, New York. http://deshawresearch.com.
   Google Scholar
• Corpet, F. (1988). Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research, 16(22), 10881–10890. https://doi.org/10.1093/nar/16.22.10881
   PubMed Web of Science ®Google Scholar
• Dangi, P., Jain, R., Mamidala, R., Sharma, V., Agarwal, S., Bathula, C., Thirumalachary, M., Sen, S., & Singh, S. (2019). Natural product inspired novel indole based chiral scaffold kills human malaria parasites via ionic imbalance mediated cell death. Scientific Reports, 9(1), 17785. https://doi.org/10.1038/s41598-019-54339-z
   Google Scholar
• Du, Q., Wang, H., & Xie, J. (2011). Thiamin (vitamin B1) biosynthesis and regulation: A rich source of antimicrobial drug targets? International Journal of Biological Sciences, 7(1), 41–52. https://doi.org/10.7150/ijbs.7.41
   PubMed Web of Science ®Google Scholar
• Edache, E. I., Uzairu, A., Mamza, P. A., & Shallangwa, G. A. (2022). QSAR, homology modeling, and docking simulation on SARS-CoV-2 and pseudomonas aeruginosa inhibitors, ADMET, and molecular dynamic simulations to find a possible oral lead candidate. Journal, Genetic Engineering & Biotechnology, 20, 88. https://doi.org/10.1186/s43141-022-00362-z
   PubMed Web of Science ®Google Scholar
• Fankhauser, H., Zurlinden, A., Schweingruber, A. M., Edenharter, E., & Schweingruber, M. E. (1995). Schizosaccharomyces pombe thiamine pyrophosphokinase is encoded by gene tnr3 and is a regulator of thiamine metabolism, phosphate metabolism, mating, and growth. The Journal of Biological Chemistry, 270(47), 28457–28462. https://doi.org/10.1074/jbc.270.47.28457
   PubMed Web of Science ®Google Scholar
• Gangolf, M., Czerniecki, J., Radermecker, M., Detry, O., Nisolle, M., Jouan, C., Martin, D., Chantraine, F., Lakaye, B., Wins, P., Grisar, T., & Bettendorff, L. (2010). Thiamine status in humans and content of phosphorylated thiamine derivatives in biopsies and cultured cells. PloS One, 5(10), e13616. https://doi.org/10.1371/journal.pone.0013616
   PubMed Web of Science ®Google Scholar
• Gubler, C. J. (1961). Studies on the physiological functions of thiamine. I. The effects of thiamine deficiency and thiamine antagonists on the oxidation of alpha-keto acids by rat tissues. Journal of Biological Chemistry, 236(12), 3112–3120. https://doi.org/10.1016/S0021-9258(18)93980-3
   PubMed Web of Science ®Google Scholar
• Gubler, C. J., & Murdock, D. S. (1982). Effects of treatment with thiamin antagonists, oxythiamin and pyrithiamin and of thiamin excess on the levels and distribution of thiamin in rat tissues. Journal of Nutritional Science and Vitaminology, 28(3), 217–224. https://doi.org/10.3177/jnsv.28.217
   PubMed Web of Science ®Google Scholar
• Hao, G. F., Xu, W. F., Yang, S. G., & Yang, G. F. (2015). Multiple simulated annealing-molecular dynamics (MSA-MD) for conformational space search of peptide and miniprotein. Scientific Reports, 5, 15568. https://doi.org/10.1038/srep15568
   PubMed Web of Science ®Google Scholar
• Herwaldt, B. L. (1999). Miltefosine—the long-awaited therapy for visceral leishmaniasis? New England Journal of Medicine, 341(24), 1840–1842. https://doi.org/10.1056/NEJM199912093412411
   PubMed Web of Science ®Google Scholar
• Hohmann, S., & Meacock, P. A. (1998). Thiamin metabolism and thiamin diphosphate-dependent enzymes in the yeast Saccharomyces cerevisiae: Genetic regulation. Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology, 1385(2), 201–219. (Issue https://doi.org/10.1016/S0167-4838(98)00069-7
   PubMedGoogle Scholar
• Horácio, E. C. A., Hickson, J., Murta, S. M. F., Ruiz, J. C., & Nahum, L. A. (2021). Perspectives from systems biology to improve knowledge of leishmania drug resistance. Frontiers in Cellular and Infection Microbiology, 11, 653670. https://doi.org/10.3389/fcimb.2021.653670
   PubMed Web of Science ®Google Scholar
• Huang, Z., Wong, C. F., & Wheeler, R. A. (2008). Flexible protein-flexible ligand docking with disrupted velocity simulated annealing. Proteins, 71(1), 440–454. https://doi.org/10.1002/prot.21781
   PubMed Web of Science ®Google Scholar
• Ingelman, M., Ramaswamy, S., Nivière, V., Fontecave, M., & Eklund, H. (1999). Crystal structure of NAD(P)H: Flavin oxidoreductase from Escherichia coli. Biochemistry, 38(22), 7040–7049. https://doi.org/10.1021/bi982849m
   PubMed Web of Science ®Google Scholar
• Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences: CABIOS, 8(3), 275–282. https://doi.org/10.1093/bioinformatics/8.3.275
   PubMedGoogle Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Ju, J., Xu, J., Zhu, Y., Fu, X., Morel, L., & Xu, Z. (2019). A variant of the histone-binding protein SNASP contributes to mouse lupus. Frontiers in Immunology, 10, 637. https://doi.org/10.3389/fimmu.2019.00637
   PubMed Web of Science ®Google Scholar
• Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., … Hassabis, D. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596(7873), 583–589. https://doi.org/10.1038/s41586-021-03819-2
   PubMed Web of Science ®Google Scholar
• Kapla, J., Espigares, I. R., Ballante, F., Selent, J., & Carlsson, J. (2021). Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? PLoS Computational Biology, 17(5), e1008936. https://doi.org/10.1371/journal.pcbi.1008936
   PubMed Web of Science ®Google Scholar
• Kashif, M., & Subbarao, N. (2023). Identification of potential novel inhibitors against glutamine synthetase enzyme of Leishmania major by using computational tools. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2023.2175382
   Google Scholar
• Khan, Y. A., Andrews, N. W., & Mittra, B. (2018). ROS regulate differentiation of visceralizing Leishmania species into the virulent amastigote form. Parasitology Open, 4, e19. https://doi.org/10.1017/pao.2018.15
   Google Scholar
• Knöckel, J., Bergmann, B., Müller, I. B., Rathaur, S., Walter, R. D., & Wrenger, C. (2008). Filling the gap of intracellular dephosphorylation in the Plasmodium falciparum vitamin B1 biosynthesis. Molecular and Biochemical Parasitology, 157(2), 241–243. https://doi.org/10.1016/j.molbiopara.2007.10.010
   PubMed Web of Science ®Google Scholar
• Liu, J. Y., Timm, D. E., & Hurley, T. D. (2006). Pyrithiamine as a substrate for thiamine pyrophosphokinase. Journal of Biological Chemistry, 281(10), 6601–6607. https://doi.org/10.1074/jbc.M510951200
   PubMed Web of Science ®Google Scholar
• Liu, Z. J., Sun, Y. J., Rose, J., Chung, Y. J., Hsiao, C. D., Chang, W. R., Kuo, I., Perozich, J., Lindahl, R., Hempel, J., & Wang, B. C. (1997). The first structure of an aldehyde dehydrogenase reveals novel interactions between NAD and the Rossmann fold. Nature Structural Biology, 4(4), 317–326. https://doi.org/10.1038/nsb0497-317
   PubMedGoogle Scholar
• Lonsdale, D. (2006). A review of the biochemistry, metabolism and clinical benefits of thiamin(e) and its derivatives. Evidence-Based Complementary and Alternative Medicine: eCAM, 3(1), 49–59. https://doi.org/10.1093/ecam/nek009
   PubMed Web of Science ®Google Scholar
• MacArthur, M. W., Laskowski, R. A., & Thornton, J. M. (1994). Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy. Current Opinion in Structural Biology, 4(5), 731–737. https://doi.org/10.1016/S0959-440X(94)90172-4
   Web of Science ®Google Scholar
• Mandal, S., Maharjan, M., Ganguly, S., Chatterjee, M., Singh, S., Buckner, F. S., & Madhubala, R. (2009). High-throughput screening of amastigotes of Leishmania donovani clinical isolates against drugs using a colorimetric β-lactamase assay. Indian Journal of Experimental Biology, 47(6), 475–479.
   PubMed Web of Science ®Google Scholar
• Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Šali, A. (2000). Comparative protein structure modeling of genes and genomes. Annual Review of Biophysics and Biomolecular Structure, 29(1), 291–325. https://doi.org/10.1146/annurev.biophys.29.1.291
   PubMedGoogle Scholar
• Martyna, G. J., Klein, M. L., & Tuckerman, M. (1992). Nosé-Hoover chains: The canonical ensemble via continuous dynamics. The Journal of Chemical Physics, 97(4), 2635–2643. https://doi.org/10.1063/1.463940
   Web of Science ®Google Scholar
• Martyna, G. J., Tobias, D. J., & Klein, M. L. (1994). Constant pressure molecular dynamics algorithms. The Journal of Chemical Physics, 101(5), 4177–4189. https://doi.org/10.1063/1.467468
   Web of Science ®Google Scholar
• Meir, Z., & Osherov, N. (2018). Vitamin biosynthesis as an antifungal target. Journal of Fungi, 4(2), 72. https://doi.org/10.3390/jof4020072
   Web of Science ®Google Scholar
• Melnick, J., Lis, E., Park, J. H., Kinsland, C., Mori, H., Baba, T., Perkins, J., Schyns, G., Vassieva, O., Osterman, A., & Begley, T. P. (2004). Identification of the two missing bacterial genes involved in thiamine salvage: Thiamine pyrophosphokinase and thiamine kinase. Journal of Bacteriology, 186(11), 3660–3662. https://doi.org/10.1128/JB.186.11.3660-3662.2004
   PubMed Web of Science ®Google Scholar
• Mittra, B., Cortez, M., Haydock, A., Ramasamy, G., Myler, P. J., & Andrews, N. W. (2013). Iron uptake controls the generation of leishmania infective forms through regulation of ROS levels. Journal of Experimental Medicine, 210(2), 401–416. https://doi.org/10.1084/jem.20121368
   PubMed Web of Science ®Google Scholar
• Mittra, B., Laranjeira-Silva, M. F., de Menezes, J. P. B., Jensen, J., Michailowsky, V., & Andrews, N. W. (2016). A trypanosomatid iron transporter that regulates mitochondrial function is required for Leishmania amazonensis virulence. PLOS Pathogens, 12(1), e1005340. https://doi.org/10.1371/journal.ppat.1005340
   PubMed Web of Science ®Google Scholar
• Mittra, B., Laranjeira-Silva, M. F., Miguel, D. C., Menezes, J. P. B. D., & Andrews, N. W. (2017). The iron-dependent mitochondrial superoxide dismutase SODA promotes Leishmania virulence. Journal of Biological Chemistry, 292(29), 12324–12338. https://doi.org/10.1074/jbc.M116.772624
   PubMed Web of Science ®Google Scholar
• Mizote, T., & Nakayama, H. (1989). The thiM locus and its relation to phosphorylation of hydroxyethylthiazole in Escherichia coli. Journal of Bacteriology, 171(6), 3228–3232. https://doi.org/10.1128/jb.171.6.3228-3232.1989
   PubMed Web of Science ®Google Scholar
• Mizote, T., Tsuda, M., Smith, D. D. S., Nakayama, H., & Nakazawa, T. (1999). Cloning and characterization of the thiD/J gene of Escherichia coli encoding a thiamin-synthesizing bifunctional enzyme, hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase. Microbiology, 145(2), 495–501. https://doi.org/10.1099/13500872-145-2-495
   PubMedGoogle Scholar
• Morett, E., Korbel, J. O., Rajan, E., Saab-Rincon, G., Olvera, L., Olvera, M., Schmidt, S., Snel, B., & Bork, P. (2003). Systematic discovery of analogous enzymes in thiamin biosynthesis. Nature Biotechnology, 21(7), 790–795. https://doi.org/10.1038/nbt834
   PubMed Web of Science ®Google Scholar
• Mosmann, T. (1983). Rapid colorimetric assay for cellular growth and survival: Application to proliferation and cytotoxicity assays. Journal of Immunological Methods, 65(1–2), 55–63. https://doi.org/10.1016/0022-1759(83)90303-4
   PubMed Web of Science ®Google Scholar
• Murray, H. W., Berman, J. D., Davies, C. R., & Saravia, N. G. (2005). Advances in leishmaniasis. The Lancet, 366(9496), 1561–1577. https://doi.org/10.1016/S0140-6736(05)67629-5
   PubMed Web of Science ®Google Scholar
• Nishimura, H., Kawasaki, Y., Nosaka, K., Kaneko, Y., & Iwashima, A. (1991). A constitutive thiamine metabolism mutation, thi80, causing reduced thiamine pyrophosphokinase activity in Saccharomyces cerevisiae. Journal of Bacteriology, 173(8), 2716–2719. https://doi.org/10.1128/jb.173.8.2716-2719.1991
   PubMed Web of Science ®Google Scholar
• Nosaka, K., Kaneko, Y., Nishimura, H., & Iwashima, A. (1993). Isolation and characterization of a thiamin pyrophosphokinase gene, THI80, from Saccharomyces cerevisiae. The Journal of Biological Chemistry, 268(23), 17440–17447. https://doi.org/10.1016/s0021-9258(19)85354-1
   PubMed Web of Science ®Google Scholar
• Peapus, D. H., Chiu, H. J., Campobasso, N., Reddick, J. J., Begley, T. P., & Ealick, S. E. (2001). Structural characterization of the enzyme-substrate, enzyme-intermediate, and enzyme-product complexes of thiamin phosphate synthase. Biochemistry, 40(34), 10103–10114. https://doi.org/10.1021/bi0104726
   PubMed Web of Science ®Google Scholar
• Pohl, M., Sprenger, G. A., & Müller, M. (2004). A new perspective on thiamine catalysis. Current Opinion in Biotechnology, 15(4), 335–342. https://doi.org/10.1016/j.copbio.2004.06.002
   PubMed Web of Science ®Google Scholar
• Poola, N. R., Kalis, M., Plakogiannis, F. M., & Taft, D. R. (2003). Characterization of pentamidine excretion in the isolated perfused rat kidney. Journal of Antimicrobial Chemotherapy, 52(3), 397–404. https://doi.org/10.1093/jac/dkg341
   PubMed Web of Science ®Google Scholar
• Ranimol, G., Devipriya, C. B., & Sunkar, S. (2023). Docking and molecular dynamics simulation studies for the evaluation of laccase mediated biodegradation of triclosan. In Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022). https://doi.org/10.2991/978-94-6463-020-6_20
   Google Scholar
• Raschke, M., Bürkle, L., Müller, N., Nunes-Nesi, A., Fernie, A. R., Arigoni, D., Amrhein, N., & Fitzpatrick, T. B. (2007). Vitamin B1 biosynthesis in plants requires the essential iron-sulfur cluster protein, THIC. Proceedings of the National Academy of Sciences, 104(49), 19637–19642. https://doi.org/10.1073/pnas.0709597104
   PubMed Web of Science ®Google Scholar
• Rath, J., Gowri, V. S., Chauhan, S. C., Padmanabhan, P. K., Srinivasan, N., & Madhubala, R. (2009). A glutathione-specific aldose reductase of Leishmania donovani and its potential implications for methylglyoxal detoxification pathway. Gene, 429(1–2), 1–9. https://doi.org/10.1016/j.gene.2008.09.037
   PubMed Web of Science ®Google Scholar
• Reddick, J. J., Kinsland, C., Nicewonger, R., Christian, T., Downs, D. M., Winkler, M. E., & Begley, T. P. (1998). Overexpression, purification and characterization of two pyrimidine kinases involved in the biosynthesis of thiamin: 4-amino-5-hydroxymethyl-2- methylpyrimidine kinase and 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase. Tetrahedron, 54(52), 15983–15991. https://doi.org/10.1016/S0040-4020(98)01006-0
   Web of Science ®Google Scholar
• Rindi, G., Degiuseppe, L., & Ventura, U. (1963). Distribution and phosphorylation of oxythiamine in rat tissues. The Journal of Nutrition, 81, 147–154. https://doi.org/10.1093/jn/81.2.147
   PubMed Web of Science ®Google Scholar
• Rindi, G., Patrini, C., Nauti, A., Bellazzi, R., & Magni, P. (2003). Three thiamine analogues differently alter thiamine transport and metabolism in nervous tissue: An in vivo kinetic study using rats. Metabolic Brain Disease, 18(4), 245–263. https://doi.org/10.1023/B:MEBR.0000020187.98238.58
   PubMed Web of Science ®Google Scholar
• Rossmann, M. G., Moras, D., & Olsen, K. W. (1974). Chemical and biological evolution of a nucleotide-binding protein. Nature, 250(463), 194–199. https://doi.org/10.1038/250194a0
   PubMedGoogle Scholar
• Sanemori, H., Egi, Y., & Kawasaki, T. (1976). Pathway of thiamine pyrophosphate synthesis in Micrococcus denitrificans. Journal of Bacteriology, 126(3), 1030–1036. https://doi.org/10.1128/jb.126.3.1030-1036.1976
   PubMed Web of Science ®Google Scholar
• Santini, S., Monchois, V., Mouz, N., Sigoillot, C., Rousselle, T., Claverie, J. M., & Abergel, C. (2008). Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase. BMC Structural Biology, 8(1), 33. https://doi.org/10.1186/1472-6807-8-33
   PubMedGoogle Scholar
• Schyns, G., Potot, S., Geng, Y., Barbosa, T. M., Henriques, A., & Perkins, J. B. (2005). Isolation and characterization of new thiamine-deregulated mutants of bacillus subtilis. Journal of Bacteriology, 187(23), 8127–8136. https://doi.org/10.1128/JB.187.23.8127-8136.2005
   PubMed Web of Science ®Google Scholar
• Settembre, E. C., Dorrestein, P. C., Zhai, H., Chatterjee, A., McLafferty, F. W., Begley, T. P., & Ealick, S. E. (2004). Thiamin biosynthesis in Bacillus subtilis: Structure of the thiazole synthase/sulfur carrier protein complex. Biochemistry, 43(37), 11647–11657. https://doi.org/10.1021/bi0488911
   PubMed Web of Science ®Google Scholar
• Shaw, D. E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R. O., Eastwood, M. P., Bank, J. A., Jumper, J. M., Salmon, J. K., Shan, Y., & Wriggers, W. (2010). Atomic-level characterization of the structural dynamics of proteins. Science, 330(6002), 341–346. https://doi.org/10.1126/science.1187409
   PubMed Web of Science ®Google Scholar
• Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J., & Sherman, W. (2010). Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the opls force field. Journal of Chemical Theory and Computation, 6(5), 1509–1519. https://doi.org/10.1021/ct900587b
   PubMed Web of Science ®Google Scholar
• Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120
   PubMed Web of Science ®Google Scholar
• Towbin, H., Staehelin, T., & Gordon, J. (1979). Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: Procedure and some applications. Proc Natl Acad Sci U S A., 76(9), 4350–4354. https://doi.org/10.1073/pnas.76.9.4350.
   Google Scholar
• Tran, P. H., Korszun, Z. R., Cerritelli, S., Springhorn, S. S., & Lacks, S. A. (1998). Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniae bound to S-adenosylmethionine. Structure, 6(12), 1563–1575. https://doi.org/10.1016/S0969-2126(98)00154-3
   PubMed Web of Science ®Google Scholar
• Tylicki, A., Łempicka, A., Romaniuk-Demonchaux, K., Czerniecki, J., Dobrzyń, P., & Strumiło, S. (2003). Effect of oxythiamin on growth rate, survival ability and pyruvate decarboxylase activity in Saccharomyces cerevisiae. Journal of Basic Microbiology, 43(6), 522–529. https://doi.org/10.1002/jobm.200310290
   PubMed Web of Science ®Google Scholar
• Webb, B., & Sali, A. (2016). Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics, 54(1), 5.6.1–5.6.37. https://doi.org/10.1002/cpbi.3
   PubMedGoogle Scholar
• Weng, Y. L., Naik, S. R., Dingelstad, N., Lugo, M. R., Kalyaanamoorthy, S., & Ganesan, A. (2021). Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 main protease complexes reveal the role of lateral pocket in enhancing the ligand affinity. Scientific Reports, 11(1), 7429. https://doi.org/10.1038/s41598-021-86471-0
   PubMed Web of Science ®Google Scholar
• Wightman, R., & Meacock, P. A. (2003). The THI5 gene family of Saccharomyces cerevisiae: Distribution of homologues among the hemiascomycetes and functional redundancy in the aerobic biosynthesis of thiamin from pyridoxine. Microbiology, 149(6), 1447–1460. (https://doi.org/10.1099/mic.0.26194-0
   PubMedGoogle Scholar
• Wrenger, C., Eschbach, M. L., Müller, I. B., Laun, N. P., Begley, T. P., & Walter, R. D. (2006). Vitamin B1 de novo synthesis in the human malaria parasite Plasmodium falciparum depends on external provision of 4-amino-5-hydroxymethyl- 2-methylpyrimidine. Biological Chemistry, 387(1), 41–51. https://doi.org/10.1515/BC.2006.007
   PubMed Web of Science ®Google Scholar
• Wrenger, C., Knöckel, J., Walter, R. D., & Müller, I. B. (2008). Vitamin B1 and B6 in the malaria parasite: Requisite or dispensable? Brazilian Journal of Medical and Biological Research, 41(2), 82–88. https://doi.org/10.1590/S0100-879X2008005000006
   PubMed Web of Science ®Google Scholar
• Yadav, P., Ayana, R., Garg, S., Jain, R., Sah, R., Joshi, N., Pati, S., & Singh, S. (2019). Plasmodium palmitoylation machinery engineered in E. coli for high-throughput screening of palmitoyl acyl-transferase inhibitors. FEBS Open Bio, 9(2), 248–264. https://doi.org/10.1002/2211-5463.12564
   PubMed Web of Science ®Google Scholar
• Zhang, Y. I., Taylor, S. V., Chiu, H. J., & Begley, T. P. (1997). Characterization of the Bacillus subtilis thiC operon involved in thiamine biosynthesis. Journal of Bacteriology, 179(9), 3030–3035. https://doi.org/10.1128/jb.179.9.3030-3035.1997
   PubMed Web of Science ®Google Scholar