Assessing the structural dynamics of the glucose-6-phosphate dehydrogenase dimer interface using molecular dynamics simulation and ligand screening using computer aided drug discovery

References

• Au SWN, Gover S, Lam VMS, et al. Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP + molecule and provides insights into enzyme deficiency. Structure. 2000;8(3):293–303. doi:10.1016/S0969-2126(00)00104-0
   PubMed Web of Science ®Google Scholar
• Özaslan MS, Balcı N, Demir Y, et al. Inhibition effects of some antidepressant drugs on pentose phosphate pathway enzymes. Environ Toxicol Pharmacol. 2019;72:103244. doi:10.1016/j.etap.2019.103244
   PubMed Web of Science ®Google Scholar
• Lee J, Kim TI, Kang J-M, et al. Prevalence of glucose-6-phosphate dehydrogenase (G6PD) deficiency among malaria patients in upper Myanmar. BMC Infect Dis. 2018;18(1):131. doi:10.1186/s12879-018-3031-y
   PubMedGoogle Scholar
• Yıldız ML, Demir Y, Küfrevioğlu ÖI. Screening of in vitro and in silico effect of fluorophenylthiourea compounds on glucose 6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase enzymes. J Mol Recognit. 2022;35(12):e2987. doi:10.1002/jmr.2987
   PubMed Web of Science ®Google Scholar
• Horikoshi N, Hwang S, Gati C, et al. Designing angle-independent structural colors using Monte Carlo simulations of multiple scattering. Proc Natl Acad Sci. 2021;118(4):e2022790118. doi:10.1073/pnas.2015551118
   PubMed Web of Science ®Google Scholar
• Çalışkan B, Öztürk Kesebir A, Demir Y, et al. The effect of brimonidine and proparacaine on metabolic enzymes: glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, and glutathione reductase. Biotechnol Appl Biochem. 2022;69(1):281–288. doi:10.1002/bab.2107
   PubMed Web of Science ®Google Scholar
• Gómez-Manzo S, Terrón-Hernández J, De la Mora-De la Mora I, et al. The stability of G6PD is affected by mutations with different clinical phenotypes. Int J Mol Sci. 2014;15(11):21179–21201. doi:10.3390/ijms151121179
   PubMed Web of Science ®Google Scholar
• Tiwari M. Glucose 6 phosphatase dehydrogenase (G6PD) and neurodegenerative disorders: mapping diagnostic and therapeutic opportunities. Genes Dis. 2017;4(4):196–203. doi:10.1016/j.gendis.2017.09.001
   PubMed Web of Science ®Google Scholar
• Gaskin RS, Estwick D, Peddi R. G6PD deficiency: its role in the high prevalence of hypertension and diabetes mellitus. Ethn Dis. 2001;11(4):749–754.
   PubMedGoogle Scholar
• Youssef JG, Zahiruddin F, Youssef G, et al. G6PD deficiency and severity of COVID19 pneumonia and acute respiratory distress syndrome: tip of the iceberg? Ann Hematol. 2021;100(3):667–673. doi:10.1007/s00277-021-04395-1
   PubMed Web of Science ®Google Scholar
• Gautam K. Glusoce-6-phosphate dehydrogenase- history and diagnosis. J Pathol Nepal. 2016;6:1034. doi:10.3126/jpn.v6i12.16260
   Google Scholar
• Cunningham AD, Mochly-Rosen D. Structural analysis of clinically relevant pathogenic G6PD variants reveals the importance of tetramerization for G6PD activity. Matters (Zur). 2017; doi:10.19185/matters.201705000008
   PubMedGoogle Scholar
• Hwang S, Mruk K, Rahighi S, et al. Correcting glucose-6-phosphate dehydrogenase deficiency with a small-molecule activator. Nat Commun. 2018;9(1):4045. doi:10.1038/s41467-018-06447-z
   PubMedGoogle Scholar
• Kotaka M, Gover S, Vandeputte-Rutten L, et al. Structural studies of glucose-6-phosphate and NADP+ binding to human glucose-6-phosphate dehydrogenase. Acta Crystallogr D Biol Crystallogr. 2005;61(Pt 5):495–504. doi:10.1107/S0907444905002350
   PubMedGoogle Scholar
• Chen J, Sawyer N, Regan L. Protein-protein interactions: general trends in the relationship between binding affinity and interfacial buried surface area. Protein Sci. 2013;22(4):510–515. doi:10.1002/pro.2230
   PubMed Web of Science ®Google Scholar
• Gómez-Manzo S, Quino J, Ortega-Cuellar D, et al. Functional and biochemical analysis of glucose-6-phosphate dehydrogenase (G6PD) variants: elucidating the molecular basis of G6PD deficiency. Catalysts. 2017;7:135. doi:10.3390/catal7050135
   Web of Science ®Google Scholar
• Li Q, Yang F, Liu R, et al. Prevalence and molecular characterization of glucose-6-phosphate dehydrogenase deficiency at the China-Myanmar border. PLoS One. 2015;10(7):e0134593.
   PubMed Web of Science ®Google Scholar
• Raub AG, Hwang S, Horikoshi N, et al. Small-molecule activators of glucose-6-phosphate dehydrogenase (G6PD) bridging the dimer interface. ChemMedChem. 2019;14(14):1321–1324. doi:10.1002/cmdc.201900341
   PubMed Web of Science ®Google Scholar
• Saddala MS, Lennikov A, Huang H. Discovery of small-molecule activators for glucose-6-phosphate dehydrogenase (G6PD) using machine learning approaches. Int J Mol Sci. 2020;21(4):1523.
   PubMed Web of Science ®Google Scholar
• PyMOL. Available from: https://www.pymol.org/.
   Google Scholar
• Hanwell MD, Curtis DE, Lonie DC, et al. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform. 2012;4(1):17. doi:10.1186/1758-2946-4-17
   PubMed Web of Science ®Google Scholar
• Morris GM, Huey R, Lindstrom W, et al. Autodock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785–2791. doi:10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Trott O, Olson AJ. Autodock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455–461. doi:10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Anuar NFSK, Wahab RA, Huyop F, et al. Molecular docking and molecular dynamics simulations of a mutant Acinetobacter haemolyticus alkaline-stable lipase against tributyrin. J Biomol Struct Dyn. 2021;39(6):2079–2091. doi:10.1080/07391102.2020.1743364
   PubMed Web of Science ®Google Scholar
• Buza A, Türkeş C, Arslan M, et al. Discovery of novel benzenesulfonamides incorporating 1,2,3-triazole scaffold as carbonic anhydrase I, II, IX, and XII inhibitors. Int J Biol Macromol. 2023;239:124232. doi:10.1016/j.ijbiomac.2023.124232
   PubMed Web of Science ®Google Scholar
• Kakakhan C, Türkeş C, Güleç Ö, et al. Exploration of 1,2,3-triazole linked benzenesulfonamide derivatives as isoform selective inhibitors of human carbonic anhydrase. Bioorg. Med. Chem. 2023;77:117111. doi:10.1016/j.bmc.2022.117111
   PubMed Web of Science ®Google Scholar
• Doss CG, Alasmar DR, Bux RI, et al. Genetic epidemiology of glucose-6-phosphate dehydrogenase deficiency in the Arab world. Sci Rep. 2016;6:37284. doi:10.1038/srep37284
   PubMed Web of Science ®Google Scholar
• Minucci A, Moradkhani K, Hwang MJ, et al. Glucose-6-phosphate dehydrogenase (G6PD) mutations database: review of the “old” and update of the new mutations. Blood Cells Mol Dis. 2012;48(3):154–165. doi:10.1016/j.bcmd.2012.01.001
   PubMed Web of Science ®Google Scholar
• Hirono A, Miwa S, Fujii H, et al. Molecular study of eight Japanese cases of glucose-6-phosphate dehydrogenase deficiency by nonradioisotopic single-strand conformation polymorphism analysis [see comments]. Blood. 1994;83:3363–3368. doi:10.1182/blood.V83.11.3363.3363
   PubMed Web of Science ®Google Scholar
• Boonyuen U, Chamchoy K, Swangsri T, et al. A trade off between catalytic activity and protein stability determines the clinical manifestations of glucose-6-phosphate dehydrogenase (G6PD) deficiency. Int J Biol Macromol. 2017;104:145–156. doi:10.1016/j.ijbiomac.2017.06.002
   PubMed Web of Science ®Google Scholar
• Fu C, Luo S, Li Q, et al. Newborn screening of glucose-6-phosphate dehydrogenase deficiency in Guangxi, China: determination of optimal cutoff value to identify heterozygous female neonates. Sci Rep. 2018;8(1):833. doi:10.1038/s41598-017-17667-6
   PubMedGoogle Scholar
• Chao LT, Du CS, Louie E, et al. A to G substitution identified in exon 2 of the G6PD gene among G6PD deficient Chinese. Nucleic Acids Res. 1991;19(21):6056. doi:10.1093/nar/19.21.6056
   PubMed Web of Science ®Google Scholar
• Chang J-G, Chiou S-S, Perng L-I, et al. Molecular characterization of glucose-6-phosphate dehydrogenase (G6PD) deficiency by natural and amplification created restriction sites: five mutations account for most G6PD deficiency cases in Taiwan. Blood. 1992;80(4):1079–1082. doi:10.1182/blood.V80.4.1079.1079
   PubMed Web of Science ®Google Scholar
• Iwai K, Hirono A, Matsuoka H, et al. Distribution of glucose-6-phosphate dehydrogenase mutations in Southeast Asia. Hum Genet. 2001;108(6):445–449. doi:10.1007/s004390100527
   PubMed Web of Science ®Google Scholar
• Hess B, Kutzner C, van der Spoel D, et al. Gromacs 4:  algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4(3):435–447. doi:10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Malde AK, Zuo L, Breeze M, et al. An automated force field topology builder (ATB) and repository: version 1.0. J Chem Theory Comput. 2011;7(12):4026–4037. doi:10.1021/ct200196m
   PubMed Web of Science ®Google Scholar
• Louis NE, Hamza MA, Baharuddin PNSDE, et al. Preliminary study of structural changes of glucose-6-phosphate dehydrogenase deficiency variants. BioMedicine. 2022;12(3):12–19. doi:10.37796/2211-8039.1355
   PubMedGoogle Scholar
• Güleç Ö, Türkeş C, Arslan M, et al. Novel beta-lactam substituted benzenesulfonamides: in vitro enzyme inhibition, cytotoxic activity and in silico interactions. J Biomol Struct Dyn: 1–19. doi:10.1080/07391102.2023.2240889. PMID: 37540185.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 2005;33(7):2302–2309. doi:10.1093/nar/gki524
   PubMed Web of Science ®Google Scholar
• Huynh T, Khan JM, Ranganathan S. A comparative structural bioinformatics analysis of inherited mutations in β-D-mannosidase across multiple species reveals a genotype-phenotype correlation. BMC Genom. 2011;12(Suppl 3):S22.
   PubMedGoogle Scholar
• Khan JM, Ranganathan S. A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation. BMC Genom. 2009;10(Suppl 3):S33.
   PubMedGoogle Scholar
• Nantasenamat C, Prachayasittikul V. Maximizing computational tools for successful drug discovery. Expert Opin Drug Discov. 2015;10(4):321–329. doi:10.1517/17460441.2015.1016497
   PubMed Web of Science ®Google Scholar
• Yaşar Ü, Gönül İ, Türkeş C, et al. Transition-Metal complexes of bidentate Schiff-base ligands: In vitro and In silico evaluation as non-classical carbonic anhydrase and potential acetylcholinesterase inhibitors. Chem Select. 2021;6(29):7278–7284.
   Google Scholar
• Laskowski RA, Swindells MB. Ligplot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model. 2011;51(10):2778–2786. doi:10.1021/ci200227u
   PubMed Web of Science ®Google Scholar
• P T. Grace-5.1. 22/qtGrace v 0.2. 4. (2018).
   Google Scholar
• Pereira GRC, BdAA V, De Mesquita JF. Comprehensive in silico analysis and molecular dynamics of the superoxide dismutase 1 (SOD1) variants related to amyotrophic lateral sclerosis. PLoS One. 2021;16(2):e0247841-e.
   Web of Science ®Google Scholar
• Kumar CV, Swetha RG, Anbarasu A, et al. Computational analysis reveals the association of threonine 118 methionine mutation in PMP22 resulting in CMT-1A. Adv Bioinform. 2014;2014:502618.
   PubMedGoogle Scholar
• Basic characteristics of the 20 amino acids: hydrophobic, hydrophilic, polar and charged.
   Google Scholar
• Shamsi A, Shahwan M, Khan MS, et al. Mechanistic insight into binding of huperzine A with human serum albumin. Comput Spectrosc Approaches Mol. 2022;27(3):797.
   Google Scholar
• Nagasundaram N, Zhu H, Liu J, et al. Analysing the effect of mutation on protein function and discovering potential inhibitors of CDK4: molecular modelling and dynamics studies. PLoS One. 2015;10(8):e0133969.
   PubMed Web of Science ®Google Scholar
• Gómez-Manzo S, Marcial-Quino J, Vanoye-Carlo A, et al. Glucose-6-Phosphate dehydrogenase: update and analysis of New mutations around the world. Int J Mol Sci. 2016;17(12).
   Web of Science ®Google Scholar
• Chagas CM, Moss S, Alisaraie L. Drug metabolites and their effects on the development of adverse reactions: revisiting Lipinski's rule of five. Int J Pharm. 2018;549(1-2):133–149. doi:10.1016/j.ijpharm.2018.07.046
   PubMed Web of Science ®Google Scholar