149
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

Identification of selective LdDHFR inhibitors using quantum chemical and molecular modeling approach

ORCID Icon, &
Pages 8687-8695 | Received 30 Dec 2020, Accepted 05 Apr 2021, Published online: 27 Apr 2021

References

  • Adane, L., Bhagat, S., Arfeen, M., Bhatia, S., Sirawaraporn, R., Sirawaraporn, W., Chakraborti, A. K., & Bharatam, P. V. (2014). Design and synthesis of guanylthiourea derivatives as potential inhibitors of Plasmodium falciparum dihydrofolate reductase enzyme. Bioorganic & Medicinal Chemistry Letters, 24, 613–617. https://doi.org/10.1016/j.bmcl.2013.12.009
  • Abbat, S., Bhagat, S., & Bharatam, P. V. (2015). PfDHFR enzyme inhibitors: Rational design using pharmacoinformatic tools. Frontiers in Medicinal Chemistry, 7, 228–273.
  • Abbat, S., & Bharatam, P. V. (2016). Electronic structure and conformational analysis of P218: An antimalarial drug candidate. International Journal of Quantum Chemistry, 116, 1362–1369. https://doi.org/10.1002/qua.25189
  • Adane, L., & Bharatam, P. V. (2008). Modelling and informatics in the analysis of P. falciparum DHFR enzyme inhibitors. Current Medicinal Chemistry, 15, 1552–1569. https://doi.org/10.2174/092986708784911551
  • Adane, L., & Bharatam, P. V. (2011). Computer-aided molecular design of 1H-imidazole-2, 4-diamine derivatives as potential inhibitors of Plasmodium falciparum DHFR enzyme. Journal of Molecular Modeling, 17, 657–667.
  • Bartolotti, L., & Fluchick, K. (1996). In K. B Lipkowitz & D. B. Boyd (Eds.), Reviews in computational chemistry (Vol. 7, p. 187). VCH Publishers.
  • Becke, A. (1993). Density-functional thermochemistry. III. The role of exact exchange. Journal of Chemical Physics, 98, 5648. https://doi.org/10.1063/1.464913
  • Bhagat, S., Arfeen, M., Adane, L., Singh, S., Singh, P. P., Chakraborti, A. K., & Bharatam, P. V. (2017). Guanylthiourea derivatives as potential antimalarial agents: Synthesis, in vivo and molecular modelling studies. European Journal of Medicinal Chemistry, 135, 339–348.
  • Bhagat, S., Arfeen, M., Das, G., Ramkumar, M., Khan, S. I., Tekwani, B. L., & Bharatam, P. V. (2019). Design, synthesis and biological evaluation of 4-aminoquinoline-guanylthiourea derivatives as antimalarial agents. Bioorganic Chemistry, 91, 103094.
  • Case, D. A., Darden, T. A., Cheatham Iii, T. E., Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Walker, R. C., Zhang, W., & Merz, K. M. (2012). AMBER 12; University of California.
  • Cocco, L., Groff, J. P., Temple, C., Jr., Montgomery, J. A., London, R. E., Matwiyoff, N., & Blakley, R. (1981). Carbon-13 nuclear magnetic resonance study of protonation of methotrexate and aminopterin bound to dihydrofolate reductase. Biochemistry, 20, 3972–3978. https://doi.org/10.1021/bi00517a005
  • Cocco, L., Roth, B., Temple, C., Montgomery, J. A., London, R. E., & Blakley, R. L. (1983). Protonated state of methotrexate, trimethoprim, and pyrimethamine bound to dihydrofolate reductase. Archives of Biochemistry and Biophysics, 226, 567–577.
  • de Lima, W. E., Pereira, A. F., de Castro, A. A., da Cunha, E. F., & Ramalho, T. C. (2016). Flexibility in the molecular design of acetylcholinesterase reactivators: Probing representative conformations by chemometric techniques and docking/QM calculations. Letters in Drug Design & Discovery, 13, 360–371.
  • DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter On Protein Crystallography, 40, 82–92.
  • Eldridge, M. D., Murray, C. W., Auton, T. R., Paolini, G. V., & Mee, R. P. (1997). Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. Journal of Computer-Aided Molecular Design, 11, 425–445.
  • 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. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47, 1739–1749.
  • Frisch, M., Trucks, G., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., & Petersson, G. (2009). Gaussian 09, Revision d. 01. Gaussian. Inc.
  • Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on drug discovery, 10, 449–461. https://doi.org/10.1517/17460441.2015.1032936
  • Gilbert, I. H. (2002). Inhibitors of dihydrofolate reductase in Leishmania and trypanosomes. Biochimica et Biophysica Acta, Molecular Basis of Disease, 1587, 249–257.
  • Glide 6.7. (2015). Schrödinger, LLC.
  • Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51, 69–82. https://doi.org/10.1021/ci100275a
  • https://www.ebi.ac.uk/chembl
  • Huc, I., & Lehn, J.-M. (1997). Virtual combinatorial libraries: Dynamic generation of molecular and supramolecular diversity by self-assembly. Proceedings of the National Academy of Sciences, 94, 2106–2110. https://doi.org/10.1073/pnas.94.6.2106
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14, 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
  • Jaladanki, C. K., Gahlawat, A., Rathod, G., Sandhu, H., Jahan, K., & Bharatam, P. V. (2020). Mechanistic studies on the drug metabolism and toxicity originating from cytochromes P450. Drug Metabolism Reviews, 52, 366–394. https://doi.org/10.1080/03602532.2020.1765792
  • Kathuria, D., Bankar, A. A., & Bharatam, P. V. (2018). “What's in a structure?” The story of biguanides. Journal of Molecular Structure, 1152, 61–78. https://doi.org/10.1016/j.molstruc.2017.08.100
  • Khabnadideh, S., Pez, D., Musso, A., Brun, R., Pérez, L. M. R., González-Pacanowska, D., & Gilbert, I. H. (2005). Design, synthesis and evaluation of 2, 4-diaminoquinazolines as inhibitors of trypanosomal and leishmanial dihydrofolate reductase. Bioorganic & Medicinal Chemistry, 13, 2637–2649.
  • Knighton, D. R., Kan, C.-C., Howland, E., Janson, C. A., Hostomska, Z., Welsh, K. M., & Matthews, D. A. (1994). Structure of and kinetic channelling in bifunctional dihydrofolate reductase – thymidylate synthase. Nature Structural & Molecular Biology, 1, 186–194. https://doi.org/10.1038/nsb0394-186
  • Kuca, K., Musilek, K., Jun, D., Zdarova-Karasova, J., Nepovimova, E., Soukup, O., Hrabinova, M., Mikler, J., Franca, T. C., & Da Cunha, E. F. (2018). A newly developed oxime K203 is the most effective reactivator of tabun-inhibited acetylcholinesterase. BMC Pharmacology and Toxicology, 19(1), 10. https://doi.org/10.1186/s40360-018-0196-3
  • Laird, B. B., Ross, R. B., & Ziegler, T. (1996). Density-functional methods in chemistry: An overview. ACS Publications.
  • Lee, C., Yang, W., & Parr, R. G. (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37, 785. https://doi.org/10.1103/physrevb.37.785
  • Lehn, J. M. (1999). Dynamic combinatorial chemistry and virtual combinatorial libraries. Chemistry – A European Journal, 5, 2455–2463. https://doi.org/10.1002/(SICI)1521-3765(19990903)5:9<2455::AID-CHEM2455>3.0.CO;2-H
  • LigPrep. (2015). Version 3.5, Schrodinger LLC.
  • Lindorff‐Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side‐chain torsion potentials for the Amber ff99SB protein force field. Proteins: Structure, Function, and Bioinformatics, 78, 1950–1958.
  • Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105, 9954–9960.
  • Parr, R., & Yang, W. (1989). Density-functional theory of atoms and molecules. Oxford University Press.
  • Prime. (2015). Version 4.0, Schrödinger LLC.
  • QikProp. (2015). Version 4.3, Schrödinger LLC.
  • Ramström, O., & Lehn, J.-M. (2002). Drug discovery by dynamic combinatorial libraries. Nature Reviews Drug Discovery, 1, 26. https://doi.org/10.1038/nrd704
  • Roe, D. R., & Cheatham, T. E., III. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9, 3084–3095. https://doi.org/10.1021/ct400341p
  • Schnell, J. R., Dyson, H. J., & Wright, P. E. (2004). Structure, dynamics, and catalytic function of dihydrofolate reductase. Annual Review of Biophysics and Biomolecular Structure, 33, 119–140.
  • Sharma, V. K., Abbat, S., & Bharatam, P. (2017). Pharmacoinformatic study on the selective inhibition of the protozoan dihydrofolate reductase enzymes. Molecular Informatics, 36, 1600156. https://doi.org/10.1002/minf.201600156
  • Sharma, V. K., & Bharatam, P. V. (2021). Identification of selective inhibitors of LdDHFR enzyme using pharmacoinformatic methods. Journal of Computational Biology, 28, 43–59. https://doi.org/10.1089/cmb.2019.0332
  • Tawari, N. R., Bag, S., & Degani, M. S. (2011). A review of molecular modelling studies of dihydrofolate reductase inhibitors against opportunistic microorganisms and comprehensive evaluation of new models. Current Pharmaceutical Design, 17, 712–751. https://doi.org/10.2174/138161211795428966
  • Tjong, E., Dimri, M., & Mohiuddin, S. S. (2019). Biochemistry, tetrahydrofolate. StatPearls Publishing.
  • Vickers, T. J., & Beverley, S. M. (2011). Folate metabolic pathways in Leishmania. Essays in Biochemistry, 51, 63–80. https://doi.org/10.1042/bse0510063
  • Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25, 1157–1174. https://doi.org/10.1002/jcc.20035
  • Zuccotto, F., Martin, A. C. R., Laskowski, R. A., Thornton, J. M., & Gilbert, I. H. (1998). Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania. Journal of Computer-Aided Molecular Design, 12, 241–257. https://doi.org/10.1023/A:1016085005275

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.