Acknowledging the importance of studies toward the development of measures against terrorism and bioterrorism, this study aims to contribute to the design of new prototypes of potential drugs against smallpox. Based on a former study, nine synthetic feasible prototypes of selective inhibitors for thymidylate kinase from Variola virus (VarTMPK) were designed and submitted to molecular docking, molecular dynamics simulations and binding energy calculations. The compounds are simplifications of two more complex scaffolds, with a guanine connected to an amide or alcohol through a spacer containing ether and/or amide groups, formerly suggested as promising for the design of selective inhibitors of VarTMPK. Our study showed that, despite the structural simplifications, the compounds presented effective energy values in interactions with VarTMPK and HssTMPK and that the guanine could be replaced by a simpler imidazole ring linked to a -NH2 group, without compromising the affinity for VarTMPK. It was also observed that a positive charge in the imidazole ring is important for the selectivity toward VarTMPK and that an amide group in the spacer does not contribute to selectivity. Finally, prototype 3 was pointed as the most promising to be synthesized and experimentally evaluated. Communicated by Ramaswamy H. Sarma.

Department of Chemistry Federal University of Viçosa Viçosa MG Brazil

Faculty of Informatics and Management Center for Basic and Applied Research University of Hradec Králové Hradec Králove Czech Republic

Laboratory of Computational Chemistry Department of Chemistry UFLA Lavras MG Brazil

Laboratory of Molecular Modeling Applied to Chemical and Biological Defense Military Institute of Engineering Rio de Janeiro RJ Brazil

Laboratory of Organic Synthesis Military Institute of Engineering Rio de Janeiro RJ Brazil

Zobrazit více v PubMed

Abraham, M. J., Murtola, T., Schulz, R., Pall, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS High performance molecular simulations through multi-level parallelism from laptops to supercomputers. Software X, 1-2,19–25. doi: 10.1016/j.softx.2015.06.001 DOI

Almeida, J. S. D., Guizado, T. R. C., Guimarães, A. P., Ramallho, T. C., Goncalves, A. S., Koning, M. C., & Franca, T. C. C. (2015). Docking and molecular dynamics studies of peripheral site ligand-oximes as reactivators of sarin-inhibited human acetylcholinesterase. Journal of Biomolecular Structure and Dynamics, 34,2632–2642. doi: 10.1080/07391102.2015.1124807 PubMed DOI

Almeida, J. S. F. D., Cavalcante, S. F. A., Dolezal, R., Kuca, K., Musilek, K., Jun, D., & Franca, T. C. C. (2018). Molecular modeling studies on the interactions of aflatoxin B1 and its metabolites with the peripheral anionic site (PAS) of human acetylcholinesterase. Journal of Biomolecular Structure and Dynamics, 1–8 [published online]. doi: 10.1080/07391102.2018.1475259 PubMed DOI

Bastos, L. C., Souza, F. R., Guimarães, A. P., Sirouspour, M., Guizado, T. R. C., Forgione, P., … Franca, T. C. C. (2016). Virtual screening, docking and dynamics of potential new inhibitors of dihydrofolate reductase from Yersinia pestis. Journal of Biomolecular Structure and Dynamics, 34(10),2184–2198. 2016. doi: 10.1080/07391102.2015.1110832 PubMed DOI

Berendsen, H. J. C., Van Der Spoel, D., & Van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1-3),43–56. doi: 10.1016/0010-4655(95)00042-E DOI

Berman, H. M., Westbrook, J., Feng, Z., Gilliand, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1),235–242. doi: 10.1093/nar/28.1.235 PubMed DOI PMC

Bismuth, C., Borron, S. W., Baud, F. J., & Barriot, P. (2004). Chemical weapons: Documented use and compounds on the horizon. Toxicology Letters, 149(1-3),11–18. doi: 10.1016/j.toxlet.2003.12.016 PubMed DOI

Byrd, R. H., Lu, P., Nocedal, J., & Zhu, C. (1995). A limited memory algorithm for bound constrained optimization. SIAM Journal on Scientific Computing, 16(5),1190–1208. doi: 10.1137/0916069 DOI

Byrnes, M. E., King, D. A., & Junior, P. M. T. (2003). Nuclear, chemical, and biological terrorism: Emergency response and public protection. Boca Raton, FL: CRC Press.

Caillat, C., Topalis, D., Agrofoglio, L. A., Pochet, S., Balzarini, J., Deville-Bonne, D., & Meyer, P. (2008). Crystal structure of poxvirus thymidylate kinase: An unexpected dimerization has implications for antiviral therapy. Proceedings of the National Academy of Sciences of the United States of America, 105(44),16900–16905. doi: 10.1073/pnas.0804525105 PubMed DOI PMC

Chapman, J. L., Nichols, D. K., Martinez, M. J., & Raymond, J. W. (2010). Animal models of orthopoxvirus infection. Veterinary Pathology, 47(5),852–870. doi: 10.1177/0300985810378649 PubMed DOI

Chaudhuri, S., Symons, J. A., & Deval, J. (2018). Innovation and trends in the development and approval of antiviral medicines: 1987–2017 and beyond. Antiviral Research, 155,76–88. doi: 10.1016/j.antiviral.2018.05.005 PubMed DOI PMC

Chen, Y.-C. (2015). Beware of docking!. Trends in Pharmacological Sciences, 36(2),78–95. doi: 10.1016/j.tips.2014.12.001 PubMed DOI

Chittick, G., Morrison, M., Brundage, T., & Nichols, W. G. (2017). Short-term clinical safety profile of brincidofovir: A favorable benefit risk proposition in the treatment of smallpox. Antiviral Research, 143,269–277. doi: 10.1016/j.antiviral.2017.01.009 PubMed DOI

Crump, R., Korom, M., Buller, R. M., & Parker, S. (2017). Buccal viral DNA as a trigger for brincidofovir therapy in the mousepox model of smallpox. Antiviral Research, 139,112–116. doi: 10.1016/j.antiviral.2016.12.015 PubMed DOI PMC

Damon, I. K., Damaso, C. R., & Mcfadden, G. (2014). Are we there yet? The smallpox research agenda using variola virus. PLoS Pathogens, 10,1–3. doi: 10.1371/journal.ppat.1004108. PubMed DOI PMC

Davenport, R. J., Satchell, M., & Shaw-Taylor, L. M. W. (2018). The geography of smallpox in England before vaccination: A conundrum resolve. Social Science & Medicine, 206,75–85. doi: 10.1016/j.socscimed.2018.04.019 PubMed DOI PMC

Edwards, M. (2002). Origin 7.0: Scientific graphing and data analysis software. Journal of Chemical Information and Computer Sciences, 42,1270–1271. doi: 10.1021/ci0255432 DOI

Evertts, A. G., Zee, B. M., & Garcia, B. A. (2010). Modern approaches for investigating epigenetic signaling pathways. Journal of Applied Physiology, 109(3),927–933. doi: 10.1152/japplphysiol.00007.2010 PubMed DOI PMC

Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5),449–461. doi: 10.1517/17460441.2015.1032936 PubMed DOI PMC

Gonçalves, A. S., Franca, T. C. C., Villar, J. D. F., & Pascutti, P. G. (2010). Conformational analysis of toxogonine, TMB-4 and HI-6 using PM6 and RM1 methods. Journal of the Brazilian Chemical Society, 21(1),179–184. doi: 10.1590/S0103-50532010000100025 DOI

Greenberg, R. N., Overton, E. T., Haas, D. W., Frank, I., Goldman, M., von Krempelhuber, A., … Chaplin, P. (2013). Safety, immunogenicity, and surrogate markers of clinical efficacy for modified vaccinia Ankara as a smallpox vaccine in HIV-infected subjects. The Journal of Infectious Diseases, 207(5),749–758. doi: 10.1093/infdis/jis753 PubMed DOI PMC

Grosenbach, D. W., Honeychurch, K., Rose, E. A., Chinsangaram, J., Frimm, A., Maiti, B., … Hruby, D. E. (2018). Oral tecovirimat for the treatment of smallpox. New England Journal of Medicine, 379(1),44–53. doi: 10.1056/NEJMoa1705688 PubMed DOI PMC

Grossi, I. M., Foster, S. A., Gainey, M. R., Krile, R. T., Dunn, J. A., Brundage, T., & Khouri, J. M. (2017). Efficacy of delayed brincidofovir treatment against a lethal rabbitpox virus challenge in New Zealand White rabbits. Antiviral Research, 143,278–286. doi: 10.1016/j.antiviral.2017.04.002 PubMed DOI

Guex, N., & Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18(15),2714–2723. doi: 10.1002/elps.1150181505 PubMed DOI

Guimarães, A. P., de Souza, F. R., Oliveira, A. A., Gonçalves, A. S., de Alencastro, R. B., Ramalho, T. C., & França, T. C. C. (2015). Design of inhibitors of thymidylate kinase from Variola virus as new selective drugs against smallpox. European Journal of Medicinal Chemistry, 91,72–90. doi: 10.1016/j.ejmech.2014.09.099 PubMed DOI

Guimarães, A. P., Ramalho, T. C., & França, T. C. C. (2014). Preventing the return of smallpox: Molecular modeling studies on thymidylate kinase from Variola virus. Journal of Biomolecular Structure and Dynamics, 32(10),1601–1612. doi: 10.1080/07391102.2013.830578 PubMed DOI PMC

Hammarlund, E., Lewis, M. W., Hanifin, J. M., Mori, M., Koudelka, C. W., & Slifka, M. K. (2010). Antiviral immunity following smallpox virus infection: A case–control study. Journal of Virology, 84(24),12754–12760. doi: 10.1128/JVI.01763-10 PubMed DOI PMC

Hendrickson, R. C., Wang, C., Hatcher, E. L., & Lefkowitz, E. J. (2010). Orthopoxvirus genome evolution: The role of gene loss. Viruses, 2(9),1933–1967. doi: 10.3390/v2091933 PubMed DOI PMC

Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics and Modelling, 14(1),33–38. doi: 10.1016/0263-7855(96)00018-5 PubMed DOI

Jayaram, B., Sprous, D., Young, M. A., & Beveridge, D. L. (1998). Free energy analysis of the conformational preferences of A and B forms of DNA in solution. Journal of the American Chemical Society, 120(41),10629–10633. doi: 10.1021/ja981307p DOI

Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B, 105(28),6474–6487. doi: 10.1021/jp003919d DOI

Kar, P., Lipowsky, R., & Knecht, V. (2013). Importance of polar solvation and configurational entropy for design of antiretroviral drugs targeting HIV-1 protease. The Journal of Physical Chemistry B, 117(19),5793–5805. doi: 10.1021/jp3085292 PubMed DOI

Kennedy, R. B., Ovsyannikova, I. G., Jacobson, R. M., & Poland, G. A. (2009). The immunology of smallpox vaccines. Current Opinion in Immunology, 21(3),314–320. doi: 10.1016/j.coi.2009.04.004 PubMed DOI PMC

Kennedy, R. B., Poland, G. A., Ovsyannikova, I. G., Oberg, A. L., Asmann, Y. W., Grill, D. E., … Jacobson, R. M. (2016). Impaired innate, humoral, and cellular immunity despite a take in smallpox vaccine recipients. Vaccine, 34(28),3283–3290. doi: 10.1016/j.vaccine.2016.05.005 PubMed DOI PMC

Kumari, R., Kumar, R., & Lynn, A. (2014). G_mmpbsa: A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7),1951–1962. doi: 10.1021/ci500020m PubMed DOI

Lee, J., Kumar, S. A., Jhan, Y. Y., & Bishop, C. J. (2018). Engineering DNA vaccines against infectious diseases. Acta Biomaterialia, 80,31–47. doi: 10.1016/j.actbio.2018.08.033 PubMed DOI PMC

Lindler, L. E., Lebeda, F. J., & Korch, G. W. (2004). Biological weapons defense: Infectious diseases and counter bioterrorism. New York, NY: Humana Press.

Lipinski, C. A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today: Technologies, 1(4),337–341. doi: 10.1016/j.ddtec.2004.11.007 PubMed DOI

Liszewski, M. K., Leung, M. K., Hauhart, R., Buller, R. M. L., Bertram, P., Wang, X., … Atkinson, J. P. (2006). Structure and regulatory profile of the monkeypox inhibitor of complement: Comparison to homologs in Vaccinia and variola and evidence for dimer formation. Journal of Immunology, 176(6),3725–3734. doi: 10.4049/jimmunol.176.6.3725 PubMed DOI

Luscombe, N. M., Austin, S. E., Berman, H. M., & Thornton, J. M. (2000). An overview of the structures of protein–DNA complexes. Genome Biology, 1(1), reviews001. doi: 10.1186/gb-2000-1-1-reviews001 PubMed DOI PMC

Manus, J.-M. (2018). La FDA approuve le premier traitement de la variole arme de guerre. Revue Francophone Des Laboratoires, 2018,11. doi: 10.1016/S1773-035X(18)30230-2 PubMed DOI PMC

Norambuena, T., & Melo, F. (2010). The protein–DNA interface database. BMC Bioinformatics, 11,261. doi: 10.1186/1471-2105-11-262. PubMed DOI PMC

Pittman, P. R., Garman, P. M., Kim, S.-H., Schmader, T. J., Nieding, W. J., Pike, J. G., … Meyers, M. S. (2015). Smallpox vaccine, ACAM2000: Sites and duration of viral shedding and effect of povidone iodine on scarification site shedding and immune response. Vaccine, 33(26),2990–2996. 2015. doi: 10.1016/j.vaccine.2015.04.062 PubMed DOI

Prichard, M. N., & Kern, E. R. (2012). Orthopoxvirus targets for the development of new antiviral agents. Antiviral Research, 94(2),111–125. doi: 10.1016/j.antiviral.2012.02.012. doi: 10.1016/j.antiviral.2012.02.012 PubMed DOI PMC

Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., … Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7),845–854. doi: 10.1093/bioinformatics/btt055 PubMed DOI PMC

Rocha, G. B., Freire, R. O., Simas, A. M., & Stewart, J. J. P. (2006). RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. Journal of Computational Chemistry, 27(10),1101–1111. doi: 10.1002/jcc.20425 PubMed DOI

Sakhatskyy, P., Wang, S., Zhang, C., Chou, T.-H., Kishko, M., & Lu, S. (2008). Immunogenicity and protection efficacy of subunit-based smallpox vaccines using Variola major antigens. Virology, 371(1),98–107. doi: 10.1016/j.virol.2007.09.029 PubMed DOI PMC

Shao, Y., Molnar, L. F., Jung, Y., Kussmann, J., Ochsenfeld, C., Brown, S. T., … Head-Gordon, M. (2006). Advances in methods and algorithms in a modern quantum chemistry program package. Physical Chemistry Chemical Physics, 8(27),3172–3319. doi: 10.1039/B517914A PubMed DOI

Silva, A. W. S., & Vranken, W. F. (2012). ACPYPE – AnteChamber Python Parser interfacE. BMC Research Notes, 5,367. doi: 10.1186/1756-0500-5-367 PubMed DOI PMC

Souza, F. R., Guimarães, A. P., Cuya, T., Freitas, M. P., Gonçalves, A. S., Forgione, P., & França, T. C. C. (2017). Analysis of Coxiela burnetti dihydrofolate reductase via in silico docking with inhibitors and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 35(13),2975–2986. doi: 10.1080/07391102.2016.1239550 PubMed DOI

Swain, M. (2012). Chemicalize.org. Journal of Chemical Information and Modeling, 52(2),613–615. doi: 10.1021/ci300046g DOI

Taylor, C. L., & Junior, L. B. T. (1992). Chemical and biological warfare. New York, NY: Franklin Watts.

Thomsen, R., & Christensen, M. H. (2006). MolDock: A new technique for high- accuracy molecular docking. Journal of Medicinal Chemistry, 49(11),3315–3321. doi: 10.1021/jm051197e PubMed DOI

Trost, L. C., Rose, M. L., Khouri, J., Keilholz, L., Long, J., Godin, S. J., & Foster, S. A. (2015). The efficacy and pharmacokinetics of brincidofovir for the treatment of lethal rabbitpox virus infection: A model of smallpox disease. Antiviral Research, 117,115–121. doi: 10.1016/j.antiviral.2015.02.007 PubMed DOI

Vorobjev, Y. N., Almagro, J. C., & Hermans, J. (1998). Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins: Structure, Function, and Genetics, 32(4),399–413. doi: 10.1002/(SICI)1097-0134(19980901)32:4<399::AID-PROT1>3.0.CO;2-C PubMed DOI

Wang, C., Greene, D., Xiao, L., Qi, R., & Luo, R. (2018). Recent developments and applications of the MMPBSA method. Frontiers in Molecular Biosciences, 4,1–18. doi: 10.3389/fmolb.2017.00087. PubMed DOI PMC

In Silico Studies of Potential Selective Inhibitors of Thymidylate Kinase from Variola virus

Molecular Modeling Study of Uncharged Oximes Compared to HI-6 and 2-PAM Inside Human AChE Sarin and VX Conjugates