References
- Bai, Y., Monzingo, A. F., & Robertus, J. D. (2009). The X-ray structure of ricin A chain with a novel inhibitor. Archives of Biochemistry and Biophysics, 483(1), 23–28. https://doi.org/https://doi.org/10.1016/j.abb.2008.12.013
- Botelho, F. D., dos Santos, M. C., da, S., Gonçalves, A., Kuca, K., Valis, M., LaPlante, S. R., França, T. C. C., & de Almeida, J. S. F. D. (2020). Ligand-based virtual screening, molecular docking, molecular dynamics, and MM-PBSA calculations towards the identification of potential novel ricin inhibitors. Toxins, 12(12), 746. https://doi.org/https://doi.org/10.3390/toxins12120746
- Chaves, E. J. F., Padilha, I. Q. M., Araújo, D. A. M., & Rocha, G. B. (2018). Determining the relative binding affinity of ricin toxin A inhibitors by using molecular docking and nonequilibrium work. Journal of Chemical Information and Modeling, 58(6), 1205–1213. https://doi.org/https://doi.org/10.1021/acs.jcim.8b00036
- Colizzi, F., Perozzo, R., Scapozza, L., Recanatini, M., & Cavalli, A. (2010). Single-molecule pulling simulations can discern active from inactive enzyme inhibitors. Journal of the American Chemical Society, 132(21), 7361–7371. https://doi.org/https://doi.org/10.1021/ja100259r
- Do, P.-C., Lee, E. H., & Le, L. T. (2018). Steered molecular dynamics simulation in rational drug design. Journal of Chemical Information and Modeling, 58(8), 1473–1482. https://doi.org/https://doi.org/10.1021/acs.jcim.8b00261
- Florin, E., Moy, V., & Gaub, H. (1994). Adhesion forces between individual ligand-receptor pairs. Science, 264(5157), 415–417. https://doi.org/https://doi.org/10.1126/science.8153628
- Gal, Y., Mazor, O., Falach, R., Sapoznikov, A., Kronman, C., & Sabo, T. (2017). Treatments for pulmonary ricin intoxication: Current aspects and future prospects. Toxins, 9(10), 311. https://doi.org/https://doi.org/10.3390/toxins9100311
- Gimeno, A., Ojeda-Montes, M. J., Tomás-Hernández, S., Cereto-Massagué, A., Beltrán-Debón, R., Mulero, M., Pujadas, G., & Garcia-Vallvé, S. (2019). The light and dark sides of virtual screening: What is there to know? International Journal of Molecular Sciences, 20(6), 1375. https://doi.org/https://doi.org/10.3390/ijms20061375
- Grela, P., Szajwaj, M., Horbowicz-Drożdżal, P., & Tchórzewski, M. (2019). How ricin damages the ribosome. Toxins, 11(5), 241. https://doi.org/https://doi.org/10.3390/toxins11050241
- Hawkins, P. C. D., Skillman, A. G., & Nicholls, A. (2007). Comparison of shape-matching and docking as virtual screening tools. Journal of Medicinal Chemistry, 50(1), 74–82. https://doi.org/https://doi.org/10.1021/jm0603365
- Hawkins, P. C. D., Skillman, A. G., Warren, G. L., Ellingson, B. A., & Stahl, M. T. (2010). Conformer generation with OMEGA: Algorithm and validation using high quality structures from the protein databank and Cambridge structural database. Journal of Chemical Information and Modeling, 50(4), 572–584. https://doi.org/https://doi.org/10.1021/ci100031x
- Ho, M.-C., Sturm, M. B., Almo, S. C., & Schramm, V. L. (2009). Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins. Proceedings of the National Academy of Sciences of the United States of America, 106(48), 20276–20281. https://doi.org/https://doi.org/10.1073/pnas.0911606106
- Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins, 65, 712–725.
- Hostaš, J., Řezáč, J., & Hobza, P. (2013). On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions. Chemical Physics Letters, 568-569, 161–166. https://doi.org/https://doi.org/10.1016/j.cplett.2013.02.069
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/https://doi.org/10.1016/0263-7855(96)00018-5
- Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., & Coleman, R. G. (2012). ZINC: A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 52(7), 1757–1768. https://doi.org/https://doi.org/10.1021/ci3001277
- Isralewitz, B., Gao, M., & Schulten, K. (2001). Steered molecular dynamics and mechanical functions of proteins. Current Opinion in Structural Biology, 11(2), 224–230. https://doi.org/https://doi.org/10.1016/S0959-440X(00)00194-9
- Jasheway, K., Pruet, J., Anslyn, E. V., & Robertus, J. D. (2011). Structure-based design of ricin inhibitors. Toxins, 3(10), 1233–1248. https://doi.org/https://doi.org/10.3390/toxins3101233
- Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 267(3), 727–748. https://doi.org/https://doi.org/10.1006/jmbi.1996.0897
- Korth, M. (2010). Third-generation hydrogen-bonding corrections for semiempirical QM methods and force fields. Journal of Chemical Theory and Computation, 6(12), 3808–3816. https://doi.org/https://doi.org/10.1021/ct100408b
- Liphardt, J., Dumont, S., Smith, S. B., Tinoco, I., & Bustamante, C. (2002). Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science, 296(5574), 1832–1835. https://doi.org/https://doi.org/10.1126/science.1071152
- Lo, R., Chandar, N. B., Ghosh, S., & Ganguly, B. (2016). The reactivation of tabun-inhibited mutant AChE with Ortho-7: Steered molecular dynamics and quantum chemical studies. Molecular Biosystems, 12(4), 1224–1231. https://doi.org/https://doi.org/10.1039/c5mb00735f
- Lüdemann, S. K., Lounnas, V., & Wade, R. C. (2000a). How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways. Journal of Molecular Biology, 303(5), 813–830. https://doi.org/https://doi.org/10.1006/jmbi.2000.4155
- Lüdemann, S. K., Lounnas, V., & Wade, R. C. (2000b). How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. Journal of Molecular Biology, 303(5), 797–811. https://doi.org/https://doi.org/10.1006/jmbi.2000.4154
- Mai, B. K., Viet, M. H., & Li, M. S. (2010). Top leads for swine influenza A/H1N1 virus revealed by steered molecular dynamics approach. Journal of Chemical Information and Modeling, 50(12), 2236–2247. https://doi.org/https://doi.org/10.1021/ci100346s
- Maia, J. D. C., Urquiza Carvalho, G. A., Mangueira, C. P., Santana, S. R., Cabral, L. A. F., & Rocha, G. B. (2012). GPU linear algebra libraries and GPGPU programming for accelerating MOPAC semiempirical quantum chemistry calculations. Journal of Chemical Theory and Computation, 8(9), 3072–3081. https://doi.org/https://doi.org/10.1021/ct3004645
- Miller, D. J., Ravikumar, K., Shen, H., Suh, J.-K., Kerwin, S. M., & Robertus, J. D. (2002). Structure-based design and characterization of novel platforms for ricin and shiga toxin inhibition. Journal of Medicinal Chemistry, 45(1), 90–98. https://doi.org/https://doi.org/10.1021/jm010186s
- Mlsna, D., Monzingo, A. F., Katzin, B. J., Ernst, S., & Robertus, J. D. (1993). Structure of recombinant ricin A chain at 2.3 A. Protein Science, 2(3), 429–435. https://doi.org/https://doi.org/10.1002/pro.5560020315
- Montfort, W., Villafranca, J. E., Monzingo, A. F., Ernst, S. R., Katzin, B., Rutenber, E., Xuong, N. H., Hamlin, R., & Robertus, J. D. (1987). The three-dimensional structure of ricin at 2.8 A. Journal of Biological Chemistry, 262(11), 5398–5403. https://doi.org/https://doi.org/10.1016/S0021-9258(18)61201-3
- Monzingo, A. F., & Robertus, J. D. (1992). X-ray analysis of substrate analogs in the ricin A-chain active site. Journal of Molecular Biology, 227(4), 1136–1145. https://doi.org/https://doi.org/10.1016/0022-2836(92)90526-P
- Mysinger, M. M., Carchia, M., Irwin, J. J., & Shoichet, B. K. (2012). Directory of useful decoys, enhanced (DUD-E): Better ligands and decoys for better benchmarking. Journal of Medicinal Chemistry, 55(14), 6582–6594. https://doi.org/https://doi.org/10.1021/jm300687e
- Neal, L. M., O’Hara, J., Brey, R. N., & Mantis, N. J. (2010). A monoclonal immunoglobulin G antibody directed against an immunodominant linear epitope on the ricin A chain confers systemic and mucosal immunity to ricin. Infection and Immunity, 78(1), 552–561. https://doi.org/https://doi.org/10.1128/IAI.00796-09
- Ngo, S. T., Hung, H. M., & Nguyen, M. T. (2016). Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work. Journal of Computational Chemistry, 37(31), 2734–2742. https://doi.org/https://doi.org/10.1002/jcc.24502
- Niu, Y., Li, S., Pan, D., Liu, H., & Yao, X. (2016). Computational study on the unbinding pathways of B-RAF inhibitors and its implication for the difference of residence time: Insight from random acceleration and steered molecular dynamics simulations. Physical Chemistry Chemical Physics, 18(7), 5622–5629. https://doi.org/https://doi.org/10.1039/C5CP06257H
- Noy-Porat, T., Alcalay, R., Epstein, E., Sabo, T., Kronman, C., & Mazor, O. (2017). Extended therapeutic window for post-exposure treatment of ricin intoxication conferred by the use of high-affinity antibodies. Toxicon, 127, 100–105. https://doi.org/https://doi.org/10.1016/j.toxicon.2017.01.009
- Noy-Porat, T., Rosenfeld, R., Ariel, N., Epstein, E., Alcalay, R., Zvi, A., Kronman, C., Ordentlich, A., & Mazor, O. (2016). Isolation of anti-ricin protective antibodies exhibiting high affinity from immunized non-human primates. Toxins, 8(3), 64. https://doi.org/https://doi.org/10.3390/toxins8030064
- Oprea, T. I., Davis, A. M., Teague, S. J., & Leeson, P. D. (2001). Is there a difference between leads and drugs? A historical perspective. Journal of Chemical Information and Computer Sciences, 41(5), 1308–1315. https://doi.org/https://doi.org/10.1021/ci010366a
- Pagadala, N. S., Syed, K., & Tuszynski, J. (2017). Software for molecular docking: A review. Biophysical Reviews, 9(2), 91–102. https://doi.org/https://doi.org/10.1007/s12551-016-0247-1
- Park, S., Khalili-Araghi, F., Tajkhorshid, E., & Schulten, K. (2003). Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality. The Journal of Chemical Physics, 119(6), 3559–3566. https://doi.org/https://doi.org/10.1063/1.1590311
- Peng, C., Wang, J., Yu, Y., Wang, G., Chen, Z., Xu, Z., Cai, T., Shao, Q., Shi, J., & Zhu, W. (2019). Improving the accuracy of predicting protein-ligand binding-free energy with semiempirical quantum chemistry charge. Future Medicinal Chemistry, 11(4), 303–321. https://doi.org/https://doi.org/10.4155/fmc-2018-0207
- Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. https://doi.org/https://doi.org/10.1002/jcc.20289
- Polito, L., Bortolotti, M., Battelli, M. G., Calafato, G., & Bolognesi, A. (2019). Ricin: An ancient story for a timeless plant toxin. Toxins, 11(6), 324. https://doi.org/https://doi.org/10.3390/toxins11060324
- Pruet, J. M., Jasheway, K. R., Manzano, L. A., Bai, Y., Anslyn, E. V., & Robertus, J. D. (2011). 7-Substituted pterins provide a new direction for ricin A chain inhibitors. European Journal of Medicinal Chemistry, 46(9), 3608–3615. https://doi.org/https://doi.org/10.1016/j.ejmech.2011.05.025
- Pruet, J. M., Saito, R., Manzano, L. a., Jasheway, K. R., Wiget, P. a., Kamat, I., Anslyn, E. V., & Robertus, J. D. (2012). Optimized 5-membered heterocycle-linked pterins for the inhibition of ricin toxin A. ACS Medicinal Chemistry Letters, 3(7), 588–591. https://doi.org/https://doi.org/10.1021/ml300099t
- Randjelović, J., Erić, S., & Savić, V. (2013). Computational study and peptide inhibitors design for the CDK9 – Cyclin T1 complex. Journal of Molecular Modeling, 19(4), 1711–1725. https://doi.org/https://doi.org/10.1007/s00894-012-1735-2
- Řezáč, J., & Hobza, P. (2012). Advanced corrections of hydrogen bonding and dispersion for semiempirical quantum mechanical methods. Journal of Chemical Theory and Computation, 8(1), 141–151. https://doi.org/https://doi.org/10.1021/ct200751e
- 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. https://doi.org/https://doi.org/10.1002/jcc.20425
- Rocha, S. F. L. S., & Sant’Anna, C. M. R. (2019). A procedure combining molecular docking and semiempirical method PM7 for identification of selective Shp2 inhibitors. Biopolymers, 110(11), 1–8. https://doi.org/https://doi.org/10.1002/bip.23320
- Roe, D. R., & Cheatham, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/https://doi.org/10.1021/ct400341p
- Ruiz-Carmona, S., Schmidtke, P., Luque, F. J., Baker, L., Matassova, N., Davis, B., Roughley, S., Murray, J., Hubbard, R., & Barril, X. (2017). Dynamic undocking and the quasi-bound state as tools for drug discovery. Nature Chemistry, 9(3), 201–206. https://doi.org/https://doi.org/10.1038/nchem.2660
- Rutenber, E., Katzin, B. J., Ernst, S., Collins, E. J., Mlsna, D., Ready, M. P., & Robertus, J. D. (1991). Crystallographic refinement of ricin to 2.5 A. Proteins, 10(3), 240–250. https://doi.org/https://doi.org/10.1002/prot.340100308
- Ryde, U., & Söderhjelm, P. (2016). Ligand-binding affinity estimates supported by quantum-mechanical methods. Chemical Reviews, 116(9), 5520–5566. https://doi.org/https://doi.org/10.1021/acs.chemrev.5b00630
- Saito, R., Pruet, J. M., Manzano, L. A., Jasheway, K., Monzingo, A. F., Wiget, P. A., Kamat, I., Anslyn, E. V., & Robertus, J. D. (2013). Peptide-conjugated pterins as inhibitors of ricin toxin A. Journal of Medicinal Chemistry, 56(1), 320–329. https://doi.org/https://doi.org/10.1021/jm3016393
- Severino, L. S., Auld, D. L., Baldanzi, M., Cândido, M. J. D., Chen, G., Crosby, W., Tan, D., He, X., Lakshmamma, P., Lavanya, C., Machado, O. L. T., Mielke, T., Milani, M., Miller, T. D., Morris, J. B., Morse, S. A., Navas, A. A., Soares, D. J., Sofiatti, V., … Zieler, H. (2012). A review on the challenges for increased production of castor. Agronomy Journal, 104(4), 853–880. https://doi.org/https://doi.org/10.2134/agronj2011.0210
- Sliwoski, G., Kothiwale, S., Meiler, J., & Lowe, E. W. E. (2014). Computational methods in drug discovery. Pharmacological Reviews, 66(1), 334–395. https://doi.org/https://doi.org/10.1124/pr.112.007336
- Sterling, T., & Irwin, J. J. (2015). ZINC 15-ligand discovery for everyone. Journal of Chemical Information and Modeling, 55(11), 2324–2337. https://doi.org/https://doi.org/10.1021/acs.jcim.5b00559
- Stewart, J. J. P. (1990). MOPAC: A semiempirical molecular orbital program. Journal of Computer-Aided Molecular Design, 4(1), 1–103. https://doi.org/https://doi.org/10.1007/BF00128336
- Stewart, J. J. P. (1996). Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations. International Journal of Quantum Chemistry, 58(2), 133–146. https://doi.org/https://doi.org/10.1002/(SICI)1097-461X(1996)58:2<133::AID-QUA2>3.0.CO;2-Z
- Stewart, J. J. P. (2007). Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements. Journal of Molecular Modeling, 13(12), 1173–1213. https://doi.org/https://doi.org/10.1007/s00894-007-0233-4
- Stewart, J. J. P. (2013). Optimization of parameters for semiempirical methods VI: More modifications to the NDDO approximations and re-optimization of parameters. Journal of Molecular Modeling, 19(1), 1–32. https://doi.org/https://doi.org/10.1007/s00894-012-1667-x
- Sulimov, A. V., Kutov, D. C., Katkova, E. V., & Sulimov, V. B. (2017). Combined docking with classical force field and quantum chemical semiempirical method PM7. Advances in Bioinformatics, 2017, 7167691. https://doi.org/https://doi.org/10.1155/2017/7167691
- Trott, O., & Olson, A. J. (2009). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31, 455–461. https://doi.org/https://doi.org/10.1002/jcc.21334
- Urquiza-Carvalho, G. A., Fragoso, W. D., & Rocha, G. B. (2016). Assessment of semiempirical enthalpy of formation in solution as an effective energy function to discriminate native-like structures in protein decoy sets. Journal of Computational Chemistry, 37(21), 1962–1972. https://doi.org/https://doi.org/10.1002/jcc.24415
- Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics & Modelling, 25(2), 247–260. https://doi.org/https://doi.org/10.1016/j.jmgm.2005.12.005
- 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(9), 1157–1174. https://doi.org/https://doi.org/10.1002/jcc.20035
- Weston, S. A., Tucker, A. D., Thatcher, D. R., Derbyshire, D. J., & Pauptit, R. A. (1994). X-ray structure of recombinant ricin A-chain at 1.8 A resolution. Journal of Molecular Biology, 244(4), 410–422. https://doi.org/https://doi.org/10.1006/jmbi.1994.1739
- Wiget, P. A., Manzano, L. A., Pruet, J. M., Gao, G., Saito, R., Monzingo, A. F., Jasheway, K. R., Robertus, J. D., & Anslyn, E. V. (2013). Sulfur incorporation generally improves Ricin inhibition in pterin-appended glycine-phenylalanine dipeptide mimics. Bioorganic & Medicinal Chemistry Letters, 23(24), 6799–6804. https://doi.org/https://doi.org/10.1016/j.bmcl.2013.10.017
- Xiong, H., Crespo, A., Marti, M., Estrin, D., & Roitberg, A. E. (2006). Free energy calculations with non-equilibrium methods: Applications of the Jarzynski relationship. Theoretical Chemistry Accounts, 116(1-3), 338–346. https://doi.org/https://doi.org/10.1007/s00214-005-0072-2
- Yan, X., Hollis, T., Svinth, M., Day, P., Monzingo, A. F., Milne, G. W., & Robertus, J. D. (1997). Structure-based identification of a ricin inhibitor. Journal of Molecular Biology, 266(5), 1043–1049. https://doi.org/https://doi.org/10.1006/jmbi.1996.0865
- Yermakova, A., & Mantis, N. J. (2011). Protective immunity to ricin toxin conferred by antibodies against the toxin's binding subunit (RTB). Vaccine, 29(45), 7925–7935. https://doi.org/https://doi.org/10.1016/j.vaccine.2011.08.075