Abstract
Not always lead compound and/or derivatives are suitable for the specific biological target for which they are designed but, in some cases, discarded compounds proved to be good binders for other biological targets; therefore, drug repurposing constitute a valid alternative to avoid waste of human and financial resources. Our virtual lock-and-key methods, VLKA and Conf-VLKA, furnish a strong support to predict the efficacy of a designed drug a priori its biological evaluation, or the correct biological target for a set of the selected compounds, allowing thus the repurposing of known and unknown, active and inactive compounds.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Dimasi JA, Feldman L, Seckler A, Wilson A (2010) Trends in risks associated with new drug development: success rates for investigational drugs. Clin Pharmacol Ther 87:272–277. https://doi.org/10.1038/clpt.2009.295
Dickson M, Gagnon JP (2004) Key factors in the rising cost of new drug discovery and development. Nat Rev Drug Discov 3:417–429. https://doi.org/10.1038/nrd1382
Peterson RT (2008) Chemical biology and the limits of reductionism. Nat Chem Biol 4:635–638. https://doi.org/10.1038/nchembio1108-635
Nobeli I, Favia AD, Thornton JM (2009) Protein promiscuity and its implications for biotechnology. Nat Biotechnol 27:157–167. https://doi.org/10.1038/nbt1519
Reddy AS, Zhang S (2013) Polypharmacology: drug discovery for the future. Expert Rev Clin Pharmacol 6:41–77. https://doi.org/10.1586/ecp.12.74
Hopkins AL (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4:682–690. https://doi.org/10.1038/nchembio.118
Peters JU (2013) Polypharmacology—foe or friend? J Med Chem 56:8955–8971. https://doi.org/10.1021/jm400856t
Overington JP, Al-Lazikani B, Hopkins AL (2006) How many drug targets are there? Nat Rev Drug Discov 5:993–996. https://doi.org/10.1038/nrd2199
Hopkins AL, Mason JS, Overington JP (2006) Can we rationally design promiscuous drugs? Curr Opin Struct Biol 15:104–111. https://doi.org/10.1016/j.sbi.2006.01.013
Aislyn DW, Boran RI (2010) Systems approaches to polypharmacology and drug discovery. Curr Opin Drug Discov Devel 13:297–309. https://doi.org/10.1126/scisignal.2001965.Introduction
Anighoro A, Bajorath J, Rastelli G (2014) Polypharmacology: challenges and opportunities in drug discovery. J Med Chem 57:7874–7887. https://doi.org/10.1021/jm5006463
Gujral TS, Peshkin L, Kirschner MW (2014) Exploiting polypharmacology for drug target deconvolution. Proc Natl Acad Sci 111:5048–5053. https://doi.org/10.1073/pnas.1403080111
Fischer E (1895) Ueber den Einfluss der Konfiguration auf die Wirkung der Enzyme III. Berichte der Dtsch Chem Gesellschaft 28:1429–1438. https://doi.org/10.1002/cber.18950280243
Forster MO (1920) Emil Fischer memorial lecture. J Chem Soc Trans 117:1157–1201. https://doi.org/10.1039/CT9201701157
Fischer E (1899) Bedeutung der Stereochemie für die Physiologie. Hoppe Seylers Z Physiol Chem. https://doi.org/10.1515/bchm2.1899.26.1-2.60
Lauria A, Tutone M, Almerico AM (2011) Virtual lock-and-key approach: the in silico revival of Fischer model by means of molecular descriptors. Eur J Med Chem 46:4274–4280. https://doi.org/10.1016/j.ejmech.2011.06.033
Tutone M, Perricone U, Almerico AM (2017) Conf-VLKA: a structure-based revisitation of the Virtual Lock-and-Key Approach. J Mol Graph Model 71:50–57. https://doi.org/10.1016/j.jmgm.2016.11.006
Lauria A, Ippolito M, Almerico AM (2009) Principal component analysis on molecular descriptors as an alternative point of view in the search of new Hsp90 inhibitors. Comput Biol Chem 33:386–390. https://doi.org/10.1016/j.compbiolchem.2009.07.010
Lauria A, Tutone M, Barone G, Almerico AM (2014) Multivariate analysis in the identification of biological targets for designed molecular structures: the BIOTA protocol. Eur J Med Chem 75:106–110. https://doi.org/10.1016/j.ejmech.2014.01.025
Lauria A, Patella C, Abbate I et al (2012) Lead optimization through VLAK protocol: new annelated pyrrolo-pyrimidine derivatives as antitumor agents. Eur J Med Chem 55:375–383. https://doi.org/10.1016/j.ejmech.2012.07.046
Lauria A, Abbate I, Patella C et al (2013) New annelated thieno[2,3-e][1,2,3]triazolo[1,5-a]pyrimidines, with potent anticancer activity, designed through VLAK protocol. Eur J Med Chem 62:416–424. https://doi.org/10.1016/j.ejmech.2013.01.019
Liu T, Lin Y, Wen X et al (2007) BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res 35:D198–D201. https://doi.org/10.1093/nar/gkl999
Karelson M, Lobanov VS, Katritzky AR (1996) Quantum-chemical descriptors in QSAR/QSPR studies. Chem Rev 96:1027–1044. https://doi.org/10.1021/cr950202r
LigPrep, version 2.5. In: Suite. Schrödinger, LLC, New York NY; 2012
Rogers D, Brown RD, Hahn M (2005) Using extended-connectivity fingerprints with Laplacian-modified Bayesian analysis in high-throughput screening follow-up. J Biomol Screen 10:682–686. https://doi.org/10.1177/1087057105281365
Duan J, Dixon SL, Lowrie JF, Sherman W (2010) Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods. J Mol Graph Model 29:157–170. https://doi.org/10.1016/j.jmgm.2010.05.008
Gilbert G (1972) Distance between sets. Nature 239:174. https://doi.org/10.1038/239174c0
Sastry M, Lowrie JF, Dixon SL, Sherman W (2010) Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments. J Chem Inf Model 50:771–784. https://doi.org/10.1021/ci100062n
Dutta S, Berman MH, Bluhm FW (2005) RCSB Protein Data Bank. Curr Prot Bioinformatics chapter 1: Unit 1.9. doi: https://doi.org/10.1002/0471250953.bi0109s20
Maestro, version 9.4, Schrödinger, LLC, New York, NY; 2013
Halgren TA, Murphy RB, Friesner RA et al (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750–1759. https://doi.org/10.1021/jm030644s
Martin YC, Kofron JL, Traphagen LM (2002) Do structurally similar molecules have similar biological activity? J Med Chem 45:4350–4358. https://doi.org/10.1021/jm020155c
Kubinyi H (2002) Chemical similarity and biological activities. J Braz Chem Soc 13:717–726. https://doi.org/10.1590/S0103-50532002000600002
Marona-Lewicka D, Nichols DE (2007) Further evidence that the delayed temporal dopaminergic effects of LSD are mediated by a mechanism different than the first temporal phase of action. Pharmacol Biochem Behav 87:453–461. https://doi.org/10.1016/j.pbb.2007.06.001
Marona-Lewicka D, Nichols DE (2009) WAY 100635 produces discriminative stimulus effects in rats mediated by dopamine D4 receptor activation. Behav Pharmacol 20:114–118. https://doi.org/10.1097/FBP.0b013e3283242f1a
Roth BL, Sheffer DJ, Kroeze WK (2004) Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia. Nat Rev Drug Discov 3:353–359. https://doi.org/10.1038/nrd1346
Bajorath J (2008) Computational analysis of ligand relationships within target families. Curr Opin Chem Biol 12:352–358. https://doi.org/10.1016/j.cbpa.2008.01.044
Oprea TI, Tropsha A, Faulon JL, Rintoul MD (2007) Systems chemical biology. Nat Chem Biol 3:447–450. https://doi.org/10.1038/nchembio0807-447
Newman DJ (2008) Natural products as leads to potential drugs: an old process or the new hope for drug discovery? J Med Chem 51:2589–2599. https://doi.org/10.1021/jm0704090
Siegel MG, Vieth M (2007) Drugs in other drugs: a new look at drugs as fragments. Drug Discov Today 12:71–79. https://doi.org/10.1016/j.drudis.2006.11.011
Young DW, Bender A, Hoyt J et al (2008) Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nat Chem Biol 4:59–68. https://doi.org/10.1038/nchembio.2007.53
Wagner BK, Kitami T, Gilbert TJ et al (2008) Large-scale chemical dissection of mitochondrial function. Nat Biotechnol 26:343–351. https://doi.org/10.1038/nbt1387
Krejsa CM, Horvath D, Rogalski SL et al (2003) Predicting ADME properties and side effects: the BioPrint approach. Curr Opin Drug Discov Devel 6:470–480
Acknowledgements
The work reported in this chapter is based on the reference [17] (Tutone M, Perricone U, Almerico AM (2017) Conf-VLKA: A structure-based revisitation of the virtual lock-and-key approach. J Mol Graph Model 71:50–57. doi: 10.1016/j.jmgm.2016.11.006) and was adapted with permission.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Tutone, M., Almerico, A.M. (2020). The In Silico Fischer Lock-and-Key Model: The Combined Use of Molecular Descriptors and Docking Poses for the Repurposing of Old Drugs. In: Labrou, N. (eds) Targeting Enzymes for Pharmaceutical Development. Methods in Molecular Biology, vol 2089. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0163-1_2
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0163-1_2
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0162-4
Online ISBN: 978-1-0716-0163-1
eBook Packages: Springer Protocols