Ligand-Based Virtual Screening, Molecular Docking, Molecular Dynamics, and MM-PBSA Calculations towards the Identification of Potential Novel Ricin Inhibitors
Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články, práce podpořená grantem
Grantová podpora
VT2019-2021
UHK - International
CEP - Centrální evidence projektů
308225/2018-0
Conselho Nacional de Pesquisa (CNPq) - International
E-02/202.961/2017
Fundação de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ) - International
FN HK 00179906
Ministry of Health of the Czech - International
PROGRES Q40
Charles University in Prague, Czech Republic - International
PubMed
33256167
PubMed Central
PMC7761309
DOI
10.3390/toxins12120746
PII: toxins12120746
Knihovny.cz E-zdroje
- Klíčová slova
- chemical/biological warfare agents, ligand-based virtual screening, molecular dynamics, ricin, ricin inhibitors,
- MeSH
- algoritmy MeSH
- chemické bojové látky chemie MeSH
- ligandy MeSH
- molekulární konformace MeSH
- molekulární struktura MeSH
- objevování léků MeSH
- ricin antagonisté a inhibitory chemie MeSH
- simulace molekulární dynamiky MeSH
- simulace molekulového dockingu MeSH
- vazebná místa MeSH
- vodíková vazba MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- chemické bojové látky MeSH
- ligandy MeSH
- ricin MeSH
Ricin is a toxin found in the castor seeds and listed as a chemical weapon by the Chemical Weapons Convention (CWC) due to its high toxicity combined with the easiness of obtention and lack of available antidotes. The relatively frequent episodes of usage or attempting to use ricin in terrorist attacks reinforce the urge to develop an antidote for this toxin. In this sense, we selected in this work the current RTA (ricin catalytic subunit) inhibitor with the best experimental performance, as a reference molecule for virtual screening in the PubChem database. The selected molecules were then evaluated through docking studies, followed by drug-likeness investigation, molecular dynamics simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations. In every step, the selection of molecules was mainly based on their ability to occupy both the active and secondary sites of RTA, which are located right next to each other, but are not simultaneously occupied by the current RTA inhibitors. Results show that the three PubChem compounds 18309602, 18498053, and 136023163 presented better overall results than the reference molecule itself, showing up as new hits for the RTA inhibition, and encouraging further experimental evaluation.
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Endo Y., Mitsui K., Motizuki M., Tsurugi K. The Mechanism of Action of Ricin and Related Toxic Lectins on Eukaryotic Ribosomes. J. Biol. Chem. 1987;262:5908–5912. PubMed
Endo Y., Tsurugi K. The RNA N-glycosidase activity of ricin A-chain. The characteristics of the enzymatic activity of ricin A-chain with ribosomes and with rRNA. J. Biol. Chem. 1988;263:8735–8739. PubMed
Audi J., Belson M. Ricin Poisoning—A comprehensive review. JAMA. 2005;294 doi: 10.1001/jama.294.18.2342. PubMed DOI
Argent R.H., Roberts L.M., Wales R., Robertus J.D., Lord J.M. Introduction of a disulfide bond into ricin A chain decreases the cytotoxicity of the ricin holotoxin. J. Biol. Chem. 1994;269:26705–26710. PubMed
Spooner R.A., Watson P.D., Marsden C.J., Smith D.C., Moore K.A.H., Cook J.P., Lord J.M., Roberts L.M. Protein disulphide-isomerase reduces ricin to its A and B chains in the endoplasmic reticulum. Biochem. J. 2004;383:285–293. doi: 10.1042/BJ20040742. PubMed DOI PMC
Olsnes S., Fernandez-Puentes C., Carrasco L., Vazquez D. Ribosome Inactivation by the Toxic Lectins Abrin and Ricin. Eur. J. Biochem. 1975;60:281–288. doi: 10.1111/j.1432-1033.1975.tb21001.x. PubMed DOI
Franke H., Scholl R., Aigner A. Ricin and Ricinus communis in pharmacology and toxicology-from ancient use and “Papyrus Ebers” to modern perspectives and “poisonous plant of the year 2018”. Naunyn Schmiedebergs Arch. Pharmacol. 2019;392:1181–1208. doi: 10.1007/s00210-019-01691-6. PubMed DOI
Chemical Weapons Convention | OPCW. [(accessed on 30 October 2020)]; Available online: https://www.opcw.org/chemical-weapons-convention.
Nehring C. Umbrella or pen? The murder of Georgi Markov. New facts and old questions. J. Intell. Hist. 2017;16:47–58. doi: 10.1080/16161262.2016.1258248. DOI
Benner K., Draper R. Arrest Is Made In Connection To Ricin Letter Sent to Trump. New York Times. Sep 21, 2020. p. 20.
Patel V.R., Dumancas G.G., Viswanath L.C.K., Maples R., Subong B.J.J. Castor Oil: Properties, Uses, and Optimization of Processing Parameters in Commercial Production. Lipid Insights. 2016;9:1–12. doi: 10.4137/LPI.S40233. PubMed DOI PMC
Lord J.M., Roberts L.M., Robertus J.D. Ricin: Structure, mode of action, and some current applications. FASEB J. 1994;8:201–208. doi: 10.1096/fasebj.8.2.8119491. PubMed DOI
Ho M., Sturm M.B., Almo S.C., Schramm V.L. Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins. Proc. Natl. Acad. Sci. USA. 2009;106:20276–20281. doi: 10.1073/pnas.0911606106. PubMed DOI PMC
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. Sulfur incorporation generally improves Ricin inhibition in pterin-appended glycine-phenylalanine dipeptide mimics. Bioorg. Med. Chem. Lett. 2013;23:6799–6804. doi: 10.1016/j.bmcl.2013.10.017. PubMed DOI
Saito R., Pruet J.M., Manzano L.A., Jasheway K., Monzingo A.F., Wiget P.A., Kamat I., Anslyn E.V., Robertus J.D. Peptide-conjugated pterins as inhibitors of ricin toxin A. J. Med. Chem. 2013;56:320–329. doi: 10.1021/jm3016393. PubMed DOI PMC
Pruet J.M., Saito R., Manzano L.A., Jasheway K.R., Wiget P.A., Kamat I., Anslyn E.V., Robertus J.D. Optimized 5-membered heterocycle-linked pterins for the inhibition of Ricin Toxin A. ACS Med. Chem. Lett. 2012;3:588–591. doi: 10.1021/ml300099t. PubMed DOI PMC
Kim S., Chen J., Cheng T., Gindulyte A., He J., He S., Li Q., Shoemaker B.A., Thiessen P.A., Yu B., et al. PubChem 2019 update: Improved access to chemical data. Nucleic Acids Res. 2019;47:D1102–D1109. doi: 10.1093/nar/gky1033. PubMed DOI PMC
Wang L., Chen L., Yu M., Xu L.H., Cheng B., Lin Y.S., Gu Q., He X.H., Xu J. Discovering new mTOR inhibitors for cancer treatment through virtual screening methods and in vitro assays. Sci. Rep. 2016;6:1–13. doi: 10.1038/srep18987. PubMed DOI PMC
Park H., Choe H., Hong S. Virtual screening and biochemical evaluation to identify new inhibitors of mammalian target of rapamycin (mTOR) Bioorg. Med. Chem. Lett. 2014;24:835–838. doi: 10.1016/j.bmcl.2013.12.081. PubMed DOI
Nagpal I., Raj I., Subbarao N., Gourinath S. Virtual Screening, Identification and In Vitro Testing of Novel Inhibitors of O-Acetyl-L-Serine Sulfhydrylase of Entamoeba histolytica. PLoS ONE. 2012;7 doi: 10.1371/journal.pone.0030305. PubMed DOI PMC
De Paula R.L., De Almeida J.S.F.D., Cavalcante S.F.A., Gonçalves A.S., Simas A.B.C., Franca T.C.C., Valis M., Kuca K., Nepovimova E., Granjeir J.M. Molecular Modeling and In Vitro Studies of a Neutral Oxime as a Potential Reactivator for Acetylcholinesterase Inhibited by Paraoxon. Molecules. 2018;23:2954. doi: 10.3390/molecules23112954. PubMed DOI PMC
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
Kontoyianni M., McClellan L.M., Sokol G.S. Evaluation of Docking Performance: Comparative Data on Docking Algorithms. J. Med. Chem. 2004;47:558–565. doi: 10.1021/jm0302997. PubMed DOI
Douguet D. e-LEA3D: A computational-aided drug design web server. Nucleic Acids Res. 2010;38:615–621. doi: 10.1093/nar/gkq322. PubMed DOI PMC
Korb O., Stützle T., Exner T.E. Empirical scoring functions for advanced Protein-Ligand docking with PLANTS. J. Chem. Inf. Model. 2009;49:84–96. doi: 10.1021/ci800298z. PubMed DOI
Schrödinger LigPrep . Schrödinger Release 2019-4. LLC; New York, NY, USA: 2019.
Abad-Zapatero C. A Sorcerer’s apprentice and The Rule of Five: From rule-of-thumb to commandment and beyond. Drug Discov. Today. 2007;12:995–997. doi: 10.1016/j.drudis.2007.10.022. PubMed DOI
Keller T.H., Pichota A., Yin Z. A practical view of ‘druggability’. Curr. Opin. Chem. Biol. 2006;10:357–361. doi: 10.1016/j.cbpa.2006.06.014. PubMed DOI
Homayun B., Lin X., Choi H.-J. Challenges and Recent Progress in Oral Drug Delivery Systems for Biopharmaceuticals. Pharmaceutics. 2019;11:129. doi: 10.3390/pharmaceutics11030129. PubMed DOI PMC
Yan X., Hollis T., Svinth M., Day P., Monzingo A.F., Milne G.W., Robertus J.D. Structure-based identification of a ricin inhibitor. J. Mol. Biol. 1997;266:1043–1049. doi: 10.1006/jmbi.1996.0865. PubMed DOI
Bai Y., Watt B., Wahome P.G., Mantis N.J., Robertus J.D. Identification of new classes of ricin toxin inhibitors by virtual screening. Toxicon. 2010;56:526–534. doi: 10.1016/j.toxicon.2010.05.009. PubMed DOI PMC
Jin Z., Du X., Xu Y., Deng Y., Liu M., Zhao Y., Zhang B., Li X., Zhang L., Peng C., et al. Structure of Mpro from COVID-19 virus and discovery of its inhibitors. Nature. 2020 doi: 10.1038/s41586-020-2223-y. PubMed DOI
Klemm T., Ebert G., Calleja D.J., Allison C.C., Richardson L.W., Bernardini J.P., Lu B.G., Kuchel N.W., Grohmann C., Shibata Y., et al. Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2. EMBO J. 2020;39:1–17. doi: 10.15252/embj.2020106275. PubMed DOI PMC
Ferreira Neto D.C., Alencar Lima J., Sobreiro Francisco Diz de Almeida J., Costa França T.C., Jorge do Nascimento C., Figueroa Villar J.D. New semicarbazones as gorge-spanning ligands of acetylcholinesterase and potential new drugs against Alzheimer’s disease: Synthesis, molecular modeling, NMR, and biological evaluation. J. Biomol. Struct. Dyn. 2018;36:4099–4113. doi: 10.1080/07391102.2017.1407676. PubMed DOI
Chaves E.J.F., Padilha I.Q.M., Araújo D.A.M., Rocha G.B. Determining the Relative Binding Affinity of Ricin Toxin A Inhibitors by Using Molecular Docking and Nonequilibrium Work. J. Chem. Inf. Model. 2018;58:1205–1213. doi: 10.1021/acs.jcim.8b00036. PubMed DOI
Vass M., Kooistra A.J., Ritschel T., Leurs R., de Esch I.J., de Graaf C. Molecular interaction fingerprint approaches for GPCR drug discovery. Curr. Opin. Pharmacol. 2016;30:59–68. doi: 10.1016/j.coph.2016.07.007. PubMed DOI
Wildman S.A. Approaches to Virtual Screening and Screening Library Selection. Curr. Pharm. Des. 2013;19:4787–4796. doi: 10.2174/1381612811319260009. PubMed DOI
Jorgensen W.L., Maxwell D.S., Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 1996;118:11225–11236. doi: 10.1021/ja9621760. DOI
Lipinski C.A., Lombardo F., Dominy B.W., Feeney P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 1997;23:3–25. doi: 10.1016/S0169-409X(96)00423-1. PubMed DOI
Hess B., Kutzner C., Spoel D., van der Lindahl E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 2008;4:435–447. doi: 10.1021/ct700301q. PubMed DOI
Sousa Da Silva A.W., Vranken W.F. ACPYPE—AnteChamber PYthon Parser interfacE. BMC Res. Notes. 2012;5:1–8. doi: 10.1186/1756-0500-5-367. PubMed DOI PMC
Ribeiro A.A.S.T., Horta B.A.C., De Alencastro R.B. MKTOP: A program for automatic construction of molecular topologies. J. Braz. Chem. Soc. 2008;19:1433–1435. doi: 10.1590/S0103-50532008000700031. DOI
Abraham M.J., van der Spoel D., Lindahl E., Hess B. GROMACS User Manual version 2018.8. Royal Institue of Technology and Uppsala University; Uppsala, Sweden: 2019.
Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983;79:926–935. doi: 10.1063/1.445869. DOI
Bussi G., Donadio D., Parrinello M. Canonical sampling through velocity rescaling. J. Chem. Phys. 2007;126 doi: 10.1063/1.2408420. PubMed DOI
Parrinello M., Rahman A. Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys. 1981;52:7182–7190. doi: 10.1063/1.328693. DOI
Humphrey W., Dalke A., Schulten K. VMD: Visual molecular dynamics. J. Mol. Graph. 1996;14:33–38. doi: 10.1016/0263-7855(96)00018-5. PubMed DOI
Turner P.J. XMGRACE. Center for Coastal and Land-margin Research, Oregon Graduate Institute of Science and Technology; Beaverton, OR, USA: 2005. Version 5.1.25.
Gilson M.K., Honig B. Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis. Proteins Struct. Funct. Bioinform. 1988;4:7–18. doi: 10.1002/prot.340040104. PubMed DOI
Rizzo R.C., Aynechi T., Case D.A., Kuntz I.D. Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. J. Chem. Theory Comput. 2006;2:128–139. doi: 10.1021/ct050097l. PubMed DOI
Sitkoff D., Sharp K.A., Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 1994;98:1978–1988. doi: 10.1021/j100058a043. DOI
Still W.C., Tempczyk A., Hawley R.C., Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 1990;112:6127–6129. doi: 10.1021/ja00172a038. DOI
Kumari R., Kumar R., Lynn A. g_mmpbsa: A GROMACS Tool for High- Throughput MM-PBSA Calculations. J. Chem. Inf. Model. 2014;54:1951–1962. doi: 10.1021/ci500020m. PubMed DOI
The Search for Antidotes Against Ricin