PERTANIKA JOURNAL OF SCIENCE AND TECHNOLOGY

The search for new compounds other than oxime as potential reactivator that is effective upon organophosphate poisoning treatments is desired. The less efficacy of oxime treatment has been the core factor. Fourteen compounds have been screened via in silico approach for their potential as sarin-inhibited human acetylcholinesterase poisoning antidotes. The selection of the compounds to be synthesized based on this computational screening, reduces the time and cost needed. To perform the docking study of sarin-inhibited acetylcholinesterase and reactivator-sarin inhibited acetylcholinesterase complexations, a bioinformatics tool was used. Estimation of the nucleophilic attack distance and binding energy of fourteen potential compounds with sarin inhibited acetylcholinesterase complexes to determine their antidote capacities was carried out using Autodock. A commercially available antidote, 2-PAM was used for the comparison. The best docked-pose was further examined with molecular dynamics simulation. Apart from being lipophilic, a compound with a carboxylic acid, (R)-Boc-nipecotic acid is shown to exhibit 6.29 kcal/mol binding energy with 8.778 Å distance of nucleophilic attack. The stability and flexibility of the sarin-inhibited acetylcholinesterase, complexed with (R)-Boc-nipecotic acid suggests this compound should be tested experimentally as a new, promising antidote for sarin-inhibited acetylcholinesterase poisoning.

• Abou-Donia, M. B., Siracuse, B., Gupta, N., & Sokol, A. S. (2016). Sarin (GB, O isopropyl methylphosphonofluoridate) neurotoxicity: Critical review. Critical Reviews in Toxicology, 46(10), 845-875. https://doi.org/10.1080/10408444.2016.1220916

• Ajami, D., & Rebek, J. (2013). Chemical approaches for detection and destruction of nerve agents. Organic and Biomolecular Chemistry, 11(24), 3936-3942. https://doi.org/10.1039/c3ob40324f

• Artursson, E., Akfur, C., Hornberg, A., Worek, F., & Ekstrom, F. (2009). Reactivation of tabun-hAChE investigated by structurally analogous oximes and mutagenesis. Toxicology, 265(3), 108-114. https://doi.org/10.1016/j.tox.2009.09.002

• Bagaria, A., Jaravine, V., Huang, Y. J., Montelione, G. T., & Guntert, P. (2012). Protein structure validation by generalized linear model root-mean-square deviation prediction. Protein Science, 21(2), 229-238. https://doi.org/10.1002/pro.2007

• Baker, S. R. (1990). The effects of pesticides on human health. In C. F. Wilkinson (Ed.), Advances in modern environmental toxicology (pp. 35-130). Princeton Scientific Publication.

• Barak, D., Kronman, C., Ordentlich, A., Ariel, N., Bromberg, A., Marcus, D., Lazara, A., Velan, B., & Shafferman, A. (1994). Acetylcholinesterase peripheral anionic site degeneracy conferred by amino acid arrays sharing a common core. Journal of Biological Chemistry, 269(9), 6296-6305. https://doi.org/10.1016/S0021-9258(17)37371-4

• Baweja, M., Singh, P. K., Sadaf, A., Tiwari, R., Nain, L., Khare, S. K., & Shukla, P. (2017). Cost effective characterization process and molecular dynamic simulation of detergent compatible alkaline protease from Bacillus pumilus strain MP27. Process Biochemistry, 58, 199-203. https://doi.org/10.1016/j.procbio.2017.04.024

• Bhattacharjee, A. K., Marek, E., Le, H. T., Ratcliffe, R., DeMar, J. C., Pervitsky, D., & Gordon, R. K. (2015). Discovery of non-oxime reactivators using an in silico pharmacophore model of reactivators for DFP-inhibited acetylcholinesterase. European Journal of Medicinal Chemistry, 90, 209-220. https://doi.org/10.1016/j.ejmech.2014.11.013

• Brighente, I. M. C., & Yunes, R. A. (1997). The general mechanisms of attack of nitrogen nucleophiles on carbonyl compounds. Facts that determine the change of the rate-pH profiles. Journal of the Brazillian Chemical Society, 8(5), 549-553. d https://doi.org/10.1590/S0103-50531997000500018

• Cadieux, C. L., Wang, H., Zhang, Y., Koenig, J. A., Shih, T. M., McDonough, J., Koh, J., & Cerasoli, D. (2016). Probing the activity of a non-oxime reactivator for acetylcholinesterase inhibited by organophosphorus nerve agents. Chemico-Biological Interactions, 259(Pt B), 133-141. https://doi.org/10.1016/j.cbi.2016.04.002

• Chen, D. E., Willick, D. L., Ruckel, J. B., & Floriano, W. B. (2015). Principal component analysis of binding energies for single-point mutants of hT2R16 bound to an agonist correlate with experimental mutant cell response. Journal of Computational Biology, 22(1), 37-53. https://doi.org/10.1089/cmb.2014.0192

• Colovic, M. B., Krstic, D. Z., Lazarevic-Pasti, T. D., Bondzic, A. M., & Vasic, V. M. (2013). Acetylcholinesterase inhibitors: Pharmacology and toxicology. Current Neuropharmacology, 11(3), 315-335. https://doi.org/10.2174/1570159x11311030006

• de Almeida, J. S. F. D., Guizado, T. R. C., Guimarães, A. P., Ramalho, T. C., Gonçalves, A. S., de Koning, M. C., & França, T. C. C. (2016). Docking and molecular dynamics studies of peripheral site ligand–oximes as reactivators of sarin-inhibited human acetylcholinesterase. Journal of Biomolecular Structure and Dynamics, 34(12), 1-11. https://doi.org/10.1080/07391102.2015.1124807

• de Koning, M. C., Horn, G., Worek, F., & Grol, M. V. (2018). Discovery of a potent non-oxime reactivator of nerve agent inhibited human acetylcholinesterase. European Journal of Medicinal Chemistry, 157, 151-160. https://doi.org/10.1016/j.ejmech.2018.08.016

• de Koning, M. C., Joosen, M. J. A., Worek, F., Nachon, F., van Grol, M., Klaassen, S. D., Alkema, D. P. W., Wille, T., & de Bruijn, H. M. (2017). Application of the Ugi multicomponent reaction in the synthesis of reactivators of nerve agent inhibited Acetylcholinesterase. Journal of Medicinal Chemistry, 60(22), 9376-9392. https://doi.org/10.1021/acs.jmedchem.7b01083

• de Koning, M. C., van Grol, M., & Noort, D. (2011). Peripheral site ligand conjugation to a non-quaternary oxime enhances reactivation of nerve agent-inhibited human acetylcholinesterase. Toxicology Letters, 206(1), 54-59. https://doi.org/10.1016/j.toxlet.2011.04.004

• de Souza, F. R., Garcia, D. R., Cuya, T., Pimentel, A. S., Gonçalves, A. S., de Alencastro, R. B., & França, T. C. C. (2020). Molecular modeling study of uncharged oximes compared to HI-6 and 2-PAM inside human AChE sarin and VX conjugates. American Chemical Society Omega, 5(9), 4490-4500. https://doi.org/10.1021/acsomega.9b03737

• Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., & Kollman, P. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry, 24(16), 1999-2012. https://doi.org/10.1002/jcc.10349

• Ishak, S. N. H., Aris, S. N. A. M., Halim, K. B. A., Ali, M. S. M., Leow, T. C., Kamarudin, N. H. A., Masomian, M., & Rahman, R. N. Z. R. A. (2017). Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase Geobacillus zalihae revealed a better structure. Molecules, 22(10), Article 1574. https://doi.org/10.3390/molecules22101574

• Johnson, G., & Moore, S. (2006). The peripheral anionic site of acetylcholinesterase: structure, functions and potential role in rational drug design. Current Pharmaceutical Design, 12(2), 217-225. https://doi.org/10.2174/138161206775193127

• Katz, F. S., Pecic, S., Schneider, L., Zhu, Z., Hastings-Robinson, A., Luzac, M., Macdonald, J., Landry, D. W., & Stojanovic, M. N. (2018). New therapeutic approaches and novel alternatives for organophosphate toxicity. Toxicology Letters, 291, 1-10. https://doi.org/10.1016/j.toxlet.2018.03.028

• Katz, F. S., Pecic, S., Tran, T. H., Trakht, I., Schneider, L., Zhu, Z., Ton-That, L., Luzac, M., Zlatanic, V., Damera, S., Macdonald, J., Landry, D. W., Tong, L., & Stojanovic, M. N. (2015). Discovery of new classes of compounds that reactivate acetylcholinesterase inhibited by organophosphates. ChemBioChem, 16(15), 2205-2215. https://doi.org/10.1002/cbic.201500348

• 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-D1213. https://doi.org/10.1093/nar/gkv951

• Konagurthu, A. S., Whisstock, J. C., Stuckey, P. J., & Lesk, A. M. (2006). MUSTANG: A multiple structural alignment algorithm. Proteins: Structure, Function, and Bioinformatics, 64(3), 559-574. https://doi.org/10.1002/prot.20921

• Kovarik, Z., MačEk, N., Sit, R. K., Radić, Z., Fokin, V. V., Sharpless, K., & Taylor, P. (2013). Centrally acting oximes in reactivation of tabun-phosphoramidated AChE. Chemico-Biological Interactions, 203(1), 77-80. https://doi.org/10.1016/j.cbi.2012.08.019

• Krieger, E., Koraimann, G., & Vriend, G. (2002). Increasing the precision of comparative models with YASARA NOVA—A self-parameterizing force field. Proteins, 47(3), 393-402. https://doi.org/10.1002/prot.10104

• Krieger, E., & Vriend, G. (2014). YASARA View - molecular graphics for all devices - from smartphones to workstations. Bioinformatics, 30(20), 2981-2982. https://doi.org/10.1093/bioinformatics/btu426

• Kryger, G., Harel, M., Giles, K., Toker, L., Velan, B., Lazar, A., Kronman, C., Barak, D., Ariel, N., Shafferman, A., Silman, I., & Sussman, J. L. (2000). Structures of recombinant native and E202Q mutant human acetylcholinesterase complexed with the snake-venom toxin fasciculin-II. Acta Crystallographica Section D: Biological Crystallography, 56(11), 1385-1394. https://doi.org/10.1107/S0907444900010659

• Kuca, K., Musilek, K., Jun, D., Karasova, J., Soukup, O., Pejchal, J., & Hrabinova, M. (2013). Structure-activity relationship for the reactivators of acetylcholinesterase inhibited by nerve agent VX. Medicinal Chemistry, 9(5), 689-693. https://doi.org/10.2174/1573406411309050008

• Lotti, M. (2010). Clinical toxicology of anticholinesterase agents in humans. In R. Krieger (Ed.), Hayes’ Handbook of Pesticide Toxicology (pp. 1543-1589). Elsevier Inc.

• Mallender, W. D., Szegletes, T., & Rosenberry, T. L. (2000). Acetylthiocholine binds to Asp74 at the peripheral site of human acetylcholinesterase as the first step in the catalytic pathway. Biochemistry, 39(26), 7753-7763. https://doi.org/10.1021/bi000210o

• Matos, K. S., Mancini, D. T., da Cunha, E. F. F., Kuca, K., Franca, T. C. C., & Ramalho, T. C. (2011). Molecular aspects of the reactivation process of acetylcholinesterase inhibited by cyclosarin. Journal of Brazilian Chemistry Society, 22(10), 1999-2004.

• Mercey, G., Renou, J., Verdelet, T., Kliachyna, M., Baati, R., Gillon, E., Arboleas, M., Loiodice, M., Nachon, F., Jean, L., & Renard, P. Y. (2012a). Phenyltetrahydroisoquinoline-pyridinaldoxime conjugates as efficient uncharged reactivators for the dephosphylation of inhibited human acetylcholinesterase. Journal of Medicinal Chemistry, 55(23), 10791-10795. https://doi.org/10.1021/jm3015519

• Mercey, G., Verdelet, T., Renou, J., Kliachyna, M., Baati, R., Nachon, F., Jean, L., & Renard, P. Y. (2012b). Reactivators of acetylcholinesterase inhibited by organophosphorus nerve agents. Accounts of Chemical Research, 45(5), 756-766. https://doi.org/10.1021/ar2002864

• Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639-1662. d https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B

• Mukherjee, S., & Bahadur, R. P. (2018). An account of solvent accessibility in protein-RNA recognition. Scientific Reports, 8(1), 1-13. https://doi.org/10.1038/s41598-018-28373-2

• Musilek, K., Jun, D., Cabal, J., Kassa, J., Gunn-Moore, F., & Kuca, K. (2007). Design of a potent reactivator of tabun-inhibited acetylcholinesterases-synthesis and evaluation of (E)-1-(4-carbamoylpyridinium)-4-(4-hydroxyiminomethylpyridinium)-but-2-ene dibromide (K203). Journal of Medicinal Chemistry, 50(22), 5514-5518.https://doi.org/10.1021/jm070653r

• Namba, T., Nolte, C. T., Jackrel, J., & Grob, D. (1971). Poisoning due to organophosphate insecticides. Acute and chronic manifestations. The American Journal of Medicine, 50(4), 475-492. https://doi.org/10.1016/0002-9343(71)90337-8

• Ordentlich, A., Barak, D., Sod-Moriah, G., Kaplan, D., Mizrahi, D., Segall, Y., Kronman, C., Karton, Y., Lazar, A., Marcus, D., Velan, B., & Shafferman, A. (2004). Stereoselectivity toward VX is determined by interactions with residues of the acyl pocket as well as of the peripheral anionic site of AChE. Biochemistry, 43(35), 11255-11265. https://doi.org/10.1021/bi0490946

• Patil, N., Ranjan, A., Chauhan, A., & Jindal, T. (2018). Mechanistic of organophosphate mediated inhibition of human acetylcholinesterase by molecular docking. JSM Bioinformatics, Genomics and Proteomics, 3(2), 1032-1040.

• Qiao, Y., Han, K., & Zhan, C. G. (2014). Reaction pathways and free energy profiles for cholinesterase-catalyzed hydrolysis of 6-monoacetylmorphine. Organic and Biomolecular Chemistry, 12(14), 2214-2227. https://doi.org/10.1039/c3ob42464b

• Radić, Z., Sit, R. K., Garcia, E., Zhang, L., Berend, S., Kovarik, Z., Amitai, G., Fokin, V. V., Sharpless, K. B., & Taylor, P. (2013). Mechanism of interaction of novel uncharged, centrally active reactivators with OP-hAChE conjugates. Chemico-Biological Interactions, 203(1), 67-71. https://doi.org/10.1016/j.cbi.2012.08.014

• Radić, Z., Sit, R. K., Kovarik, Z., Berend, S., Garcia, E., Zhang, L., Amitai, G., Green, C., Radic, B., Fokin, V. V., Sharpless K. B., & Taylor, P. (2012). Refinement of structural leads for centrally acting oxime reactivators of phosphylated cholinesterases. Journal of Biological Chemistry, 287(15), 11798-11809. https://doi.org/10.1074/jbc.M111.333732

• Ranjan, A., Kumar, A., Gulati, K., Thakur, S., & Jindal, T. (2015). Role of aromatic amino acids in stabilizing organophosphate and human acetylcholinesterase complex. Journal of Current Pharma Research, 5(4), 1632-1639. https://doi.org/10.33786/JCPR.2015.V05I04.006

• Schaeffer, L. (2008). The role of functional groups in drug–receptor interactions. In C.G. Wermuth, P. Raboisson, D. Aldous, & D. Rognan (Eds.), The practice of medicinal chemistry (pp. 359-378). Elsevier Incorporation. https://doi.org/10.1016/B978-0-12-417205-0.00014-6

• Shafferman, A., Velan, B., Ordentlich, A., Kronman, C., Grosfeld, H., Leitner, M., Flashner, Y., Cohen, S., Barak, D., & Ariel, N. (1992). Substrate inhibition of acetylcholinesterase: Residues affecting signal transduction from the surface to the catalytic center. European Molecular Biology Organization Journal, 11(10), 3561-3568. https://doi.org/10.1002/j.1460-2075.1992.tb05439.x

• Sit, R. K., Radić, Z., Gerardi, V., Zhang, L., Garcia, E., Katalinić, M., Amitai, G., Kovarik, Z., Fokin, V. V., Sharpless, K. B., & Taylor, P. (2011). New structural scaffolds for centrally acting oxime reactivators of phosphylated cholinesterases. Journal of Biological Chemistry, 286(22), 19422-19430. https://doi.org/10.1074/jbc.M111.230656

• Tang, M., Zhou, Y., Xu, W., Li, S., Wang, L., Wei, D., & Qiao, Z. (2013). A novel drug candidate for Alzheimer’s disease treatment: Gx-50 derived from Zanthoxylum bungeanum. Journal of Alzheimer’s Disease, 34(1), 203-213. https://doi.org/10.3233/JAD-121831

• Wlodek, S. T., Shen, T., & McCammon, J. A. (2000). Electrostatic steering of substrate to acetylcholinesterase: Analysis of field fluctuations. Biopolymers, 53(3), 265-271. https://doi.org/10.1002/(SICI)1097-0282(200003)53:3<265::AID-BIP6>3.0.CO;2-N

• Yellapu, N., Gopal, J., Thulasibabu, R., Gunasekaran, K., & Jambulingam, P. (2015). Screening and identification of inhibitors against glutathione synthetase, a potential drug target of Plasmodium falciparum. Combinatorial Chemistry & High Throughput Screening, 18, 492-504.

• Zhang, Y., Zhang, S., Xu, G., Yan, H., Pu, Y., & Zuo, Z. (2016). The discovery of new acetylcholinesterase inhibitors derived from pharmacophore modeling, virtual screening, docking simulation and bioassays. Molecular BioSystems, 12(12), 3734-3742. https://doi.org/10.1039/C6MB00661B