Organophosphorus compounds (OP) are part of a group of compounds that may be hazardous to health. They are called neurotoxic agents because of their action on the nervous system, inhibiting the acetylcholinesterase (AChE) enzyme and resulting in a cholinergic crisis. Their high toxicity and rapid action lead to irreversible damage to the nervous system, drawing attention to developing new treatment methods. The diisopropyl fluorophosphatase (DFPase) enzyme has been considered as a potent biocatalyst for the hydrolysis of toxic OP and has potential for bioremediation of this kind of intoxication. In order to investigate the degradation process of the nerve agents Tabun, Cyclosarin and Soman through the wild-type DFPase, and taking into account their stereochemistry, theoretical studies were carried out. The intermolecular interaction energy and other parameters obtained from the molecular docking calculations were used to construct a data matrix, which were posteriorly treated by statistical analyzes of chemometrics, using the PCA (Principal Components Analysis) multivariate analysis. The analyzed parameters seem to be quite important for the reaction mechanisms simulation (QM/MM). Our findings showed that the wild-type DFPase enzyme is stereoselective in hydrolysis, showing promising results for the catalytic degradation of the neurotoxic agents under study, with the degradation mechanism performed through two proposed pathways.

Center for Basic and Applied Research Faculty of Informatics and Management University Hradec Kralove 50003 Hradec Kralove Czech Republic

Department of Health Sciences Federal University of Espírito Santo 29932 540 São Mateus ES Brazil

Laboratory of Molecular Modeling Chemistry Department Federal University of Lavras 37200 000 Lavras MG Brazil

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Chauhan S., Chauhan S., D’Cruz R., Faruqi S., Singh K.K., Varma S., Singh M., Karthik V. Chemical warfare agents. Environ. Toxicol. Pharmacol. 2008;26:113–122. doi: 10.1016/j.etap.2008.03.003. PubMed DOI

Chambers J.E., Carr R.L. Biochemical mechanisms contributing to species differences in insecticidal toxicity. Toxicology. 1995;105:291–304. doi: 10.1016/0300-483X(95)03225-5. PubMed DOI

Li J.N., Liu L., Fu Y., Guo Q.X. What are the pKa values of organophosphorus compounds? Tetrahedron. 2006;62:4453–4462. doi: 10.1016/j.tet.2006.02.049. DOI

Jaga K., Dharmani C. Sources of exposure to and public health implications of organophosphate pesticides. Rev. Panam. Salud Pública. 2003;14:171–185. doi: 10.1590/S1020-49892003000800004. PubMed DOI

Giacoppo J.O.S., França T.C.C., Kuča K., Cunha E.F.F., Abagyan R., Mancini D.T., Ramalho T.C. Molecular modeling and in vitro reactivation study between the oxime BI-6 and acetylcholinesterase inhibited by different nerve agents. J. Biomol. Struct. Dyn. 2015;33:2048–2058. doi: 10.1080/07391102.2014.989408. PubMed DOI

Chen J.C.H., Mustyakimov M., Schoenborn B.P., Langan P., Blum M.M. Neutron structure and mechanistic studies of diisopropyl fluorophosphatase (DFPase) Acta Crystallogr. Sect. D Biol. Crystallogr. 2010;66:1131–1138. doi: 10.1107/S0907444910034013. PubMed DOI PMC

Melzer M., Chen J.C.H., Heidenreich A., Gäb J., Koller M., Kehe K., Blum M.M. Reversed Enantioselectivity of Diisopropyl Fluorophosphatase against Organophosphorus Nerve Agents by Rational Design. J. Am. Chem. Soc. 2009;131:17226–17232. doi: 10.1021/ja905444g. PubMed DOI

Romero A.M. Commercializing chemical warfare: Citrus, cyanide, and an endless war. Agric. Hum. Values. 2016;33:3–26. doi: 10.1007/s10460-015-9591-1. DOI

Ordentlich A., Barak D., Sod-Moriah G., Kaplan D., Mizrahi D., Segall Y., Kronman C., Karton Y., Lazar A., Marcus D., et al. Stereoselectivity toward VX is determined by interactions with residues of the acyl pocket as well as of the peripheral anionic site of AChE. Biochemistry. 2004;43:11255–11265. doi: 10.1021/bi0490946. PubMed DOI

Ramalho T.C., Castro A.A., Silva D.R., Silva M.C., França T.C.C., Bennion B.J., Kuca K. Computational Enzymology and Organophosphorus Degrading Enzymes: Promising Approaches Toward Remediation Technologies of Warfare Agents and Pesticides. Curr. Med. Chem. 2016;23:1041–1061. doi: 10.2174/0929867323666160222113504. PubMed DOI

Xu C., Yang L., Yu J.-G., Liao R.-Z. What roles do the residue Asp229 and the coordination variation of calcium play of the reaction mechanism of the diisopropyl-fluorophosphatase? A DFT investigation. Theor. Chem. Acc. 2016;135:138. doi: 10.1007/s00214-016-1896-7. DOI

Wymore T., Field M.J., Langan P., Smith J.C., Parks J.M. Hydrolysis of DFP and the Nerve Agent (S)-Sarin by DFPase Proceeds along Two Different Reaction Pathways: Implications for Engineering Bioscavengers. J. Phys. Chem. B. 2014;118:4479–4489. doi: 10.1021/jp410422c. PubMed DOI PMC

Blum M.M., Löhr F., Richardt A., Ruterjans H., Chen J.C.H. Binding of a Designed Substrate Analogue to Diisopropyl Fluorophosphatase:  Implications for the Phosphotriesterase Mechanism. J. Am. Chem. Soc. 2006;128:12750–12757. doi: 10.1021/ja061887n. PubMed DOI

Castro A.A., Caetano M.S., Silva T.C., Mancini D.T., Rocha E.P., Cunha E.F.F., Ramalho T.C. Molecular Docking, Metal Substitution and Hydrolysis Reaction of Chiral Substrates of Phosphotriesterase. Comb. Chem. High Throughput Screen. 2016;19:334–344. doi: 10.2174/1386207319666160325113844. PubMed DOI

Sartorelli J., Castro A.A., Ramalho T.C., Giacoppo J.O.S., Mancini D.T., Caetano M.S., Cunha E.F.F. Asymmetric biocatalysis of the nerve agent VX by human serum paraoxonase 1: Molecular docking and reaction mechanism calculations. Med. Chem. Res. 2016;25:2521–2533. doi: 10.1007/s00044-016-1704-x. DOI

Dawson R.M., Pantelidis S., Rose H.R., Kotsonis S.E. Degradation of nerve agents by an organophosphate-degrading agent (OpdA) J. Hazard. Mater. 2008;157:308–314. doi: 10.1016/j.jhazmat.2007.12.099. PubMed DOI

Hanselman D., Littlefield B. Mastering MATLAB 5: A Comprehensive Tutorial and Reference. Prentice-Hall; Bergen, NJ, USA: 1998.

Lima W.E.A., Pereira A.F., Castro A.A., Cunha E.F.F., Ramalho T.C. Flexibility in the Molecular Design of Acetylcholinesterase Reactivators: Probing Representative Conformations by Chemometric Techniques and Docking/QM Calculations. Lett. Drug Des. Discov. 2016;13:360–371. doi: 10.2174/1570180812666150918191550. DOI

Castro A.A., Assis L.C., Silva D.R., Corrêa S., Assis T.M., Gajo G.C., Soares F.V., Ramalho T.C. Computational enzymology for degradation of chemical warfare agents: Promising technologies for remediation processes. AIMS Microbiol. 2017;3:108–135. doi: 10.3934/microbiol.2017.1.108. PubMed DOI PMC

Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Scalmani G., Barone V., Petersson G.A., Nakatsuji H., et al. Gaussian 09, Revision A.02. Gaussian, Inc.; Wallingford, CT, USA: 2016.

Thomsen R., Christensen M.H. MolDock:  A New Technique for High-Accuracy Molecular Docking. J. Med. Chem. 2006;49:3315–3321. doi: 10.1021/jm051197e. PubMed DOI

Silva T.C., Pires M.S., Castro A.A., Cunha E.F.F., Caetano M.S., Ramalho T.C. Molecular insight into the inhibition mechanism of plant and rat 4-hydroxyphenylpyruvate dioxygenase by molecular docking and DFT calculations. Med. Chem. Res. 2015;24:3958–3971. doi: 10.1007/s00044-015-1436-3. DOI

Guimarães A.P., Oliveira A.A., Cunha E.F.F., Ramalho T.C., França T.C.C. Analysis of Bacillus anthracis nucleoside hydrolase via in silico docking with inhibitors and molecular dynamics simulation. J. Mol. Model. 2011;17:2939–2951. doi: 10.1007/s00894-011-0968-9. PubMed DOI

Matos K.S., Mancini D.T., Cunha E.F.F., Kuca K., França T.C.C., Ramalho T.C. Molecular aspects of the reactivation process of acetylcholinesterase inhibited by cyclosarin. J. Braz. Chem. Soc. 2011;22:1999–2004. doi: 10.1590/S0103-50532011001000023. DOI

Ramalho T.C., Caetano M.S., Cunha E.F.F., Souza T.C.S., Rocha M.V.J. Construction and Assessment of Reaction Models of Class I EPSP Synthase: Molecular Docking and Density Functional Theoretical Calculations. J. Biomol. Struct. Dyn. 2009;27:195–207. doi: 10.1080/07391102.2009.10507309. PubMed DOI

Cunha E.F.F., Barbosa E.F., Oliveira A.A., Ramalho T.C. Molecular Modeling of Mycobacterium Tuberculosis DNA Gyrase and its Molecular Docking Study with Gatifloxacin Inhibitors. J. Biomol. Struct. Dyn. 2010;27:619–625. doi: 10.1080/07391102.2010.10508576. PubMed DOI

Souza T.C.S., Josa D., Ramalho T.C., Caetano M.S., Cunha E.F.F. Molecular modelling of Mycobacterium tuberculosis acetolactate synthase catalytic subunit and its molecular docking study with inhibitors. Mol. Simul. 2008;34:707–713. doi: 10.1080/08927020802129974. DOI

Goncalves A.S., França T.C.C., Caetano M.S., Ramalho T.C. Reactivation steps by 2-PAM of tabun-inhibited human acetylcholinesterase: Reducing the computational cost in hybrid QM/MM methods. J. Biomol. Struct. Dyn. 2014;32:301–307. doi: 10.1080/07391102.2013.765361. PubMed DOI

Matos K.S., Cunha E.F.F., Abagyan R., Ramalho T.C. Computational Evidence for the Reactivation Process of Human Acetylcholinesterase Inhibited by Carbamates. Comb. Chem. High Throughput Screen. 2014;17:554–564. doi: 10.2174/1386207316666131217100416. PubMed DOI

Ramalho T.C., Alencastro R.B., La-Scalea M.A., Figueroa-Villar J.D. Theoretical evaluation of adiabatic and vertical electron affinity of some radiosensitizers in solution using FEP, ab initio and DFT methods. Biophys. Chem. 2004;110:267–279. doi: 10.1016/j.bpc.2004.03.002. PubMed DOI

Besler B.H., Merz K.M., Kollman P.A. Atomic charges derived from semiempirical methods. J. Comput. Chem. 1990;11:431–439. doi: 10.1002/jcc.540110404. DOI

Singh U.C., Kollman P.A. An approach to computing electrostatic charges for molecules. J. Comput. Chem. 1984;5:129–145. doi: 10.1002/jcc.540050204. DOI

Gustin D.J., Mattei P., Kast P., Wiest O., Lee L., Cleland W.W., Hilvert D. Heavy Atom Isotope Effects Reveal a Highly Polarized Transition State for Chorismate Mutase. J. Am. Chem. Soc. 1999;121:1756–1757. doi: 10.1021/ja9841759. DOI

Giacoppo J.O.S., Mancini D.T., Guimarães A.P., Gonçalves A.S., Cunha E.F.F., França T.C.C., Ramalho T.C. Molecular modeling toward selective inhibitors of dihydrofolate reductase from the biological warfare agent Bacillus anthracis. Eur. J. Med. Chem. 2015;91:63–71. doi: 10.1016/j.ejmech.2014.06.025. PubMed DOI

Li R., Liu Y., Zhang J., Chen K., Li S., Jiang J. An isofenphos-methyl hydrolase (Imh) capable of hydrolyzing the P–O–Z moiety of organophosphorus pesticides containing an aryl or heterocyclic group. Appl. Microbiol. Biotechnol. 2012;94:1553–1564. doi: 10.1007/s00253-011-3709-1. PubMed DOI

Cunha E.F.F., Ramalho T.C., Reynolds R.C. Binding Mode Analysis of 2,4-diamino-5-methyl-5-deaza-6-substituted Pteridines with Mycobacterium tuberculosis and Human Dihydrofolate Reductases. J. Biomol. Struct. Dyn. 2008;25:377–385. doi: 10.1080/07391102.2008.10507186. PubMed DOI

Van der Kamp M.W., Mulholland A.J. Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology. Biochemistry. 2013;52:2708–2728. doi: 10.1021/bi400215w. PubMed DOI

Lonsdale R., Ranaghan K.E., Mulholland A.J. Computational enzymology. Chem. Commun. 2010;46:2354–2372. doi: 10.1039/b925647d. PubMed DOI

Senthilkumar K., Mujika J.I., Ranaghan K.E., Manby F.R., Mulholland A.J., Harvey J.N. Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds. J. R. Soc. Interface. 2008;5:S207–S216. doi: 10.1098/rsif.2008.0243.focus. PubMed DOI PMC

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