Quantitative Characterization of the Chemical Space Governed by Human Carbonic Anhydrases and selenium-containing derivatives of solfonamides
DOI:
https://doi.org/10.1590/s2175-97902022e19704%20%20Keywords:
Carbonic anhydrase, Proteochemometric modeling, Grid Independent Descriptors, Z-scales, Isoform selectivityAbstract
Due to the fact that different isoforms of carbonic anhydrase play distinct physiological roles, their diseases/disorders involvement are different as well. Involvement in major disorders such as glaucoma, epilepsy, Alzheimer’s disease, obesity and cancers, have turned carbonic anhydrase into a popular case study in the field of rational drug design. Since carbonic anhydrases are highly similar with regard to their structures, selective inhibition of different isoforms has been a significant challenge. By applying a proteochemometrics approach, herein the chemical interaction space governed by acyl selenoureido benzensulfonamides and human carbonic anhydrases is explored. To assess the validity, robustness and predictivity power of the proteochemometrics model, a diverse set of validation methods was used. The final model is shown to provide valuable structural information that can be considered for new selective inhibitors design. Using the supplied information and to show the applicability of the constructed model, new compounds were designed. Monitoring of selectivity ratios of new designs shows very promising results with regard to their selectivity for a specific isoform of carbonic anhydrase.
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Angeli A, Carta F, Bartolucci G, Supuran CT. Synthesis of novel acyl selenoureido benzensulfonamides as carbonic anhydrase I, II, VII and IX inhibitors. Bioorg Med Chem. 2017;25(13):3567-3573.
Bonneau A, Maresca A, Winum JY, Supuran CT. Metronidazole-coumarin conjugates and 3-cyano-7-hydroxy-coumarin act as isoform-selective carbonic anhydrase inhibitors. J Enzyme Inhib Med Chem. 2013;28(2):397-401.
Carta F, Temperini C, Innocenti A, Scozzafava A, Kaila K, Supuran CT. Polyamines inhibit carbonic anhydrases by anchoring to the zinc-coordinated water molecule. J Med Chem. 2010;53(15):5511-5522.
Carta F, Vullo D, Maresca A, Scozzafava A, Supuran CT. Mono-/dihydroxybenzoic acid esters and phenol pyridinium derivatives as inhibitors of the mammalian carbonic anhydrase isoforms I, II, VII, IX, XII and XIV. Bioorg Med Chem . 2013;21(6):1564-1569.
Ditte P, Dequiedt F, Svastova E, Hulikova A, Ohradanova-Repic A, Zatovicova M, et al. Phosphorylation of carbonic anhydrase IX controls its ability to mediate extracellular acidification in hypoxic tumors. Cancer Res. 2011;71(24):7558-7567.
Eriksson L, Jaworska J, Worth AP, Cronin MT, McDowell RM, Gramatica P. Methods for reliability and uncertainty assessment and for applicability evaluations of classification-and regression-based QSARs. Environ Health Perspect. 2003;111(10):1361-1375.
Gramatica P. Principles of QSAR models validation: internal and external. Mol Inf. 2007;26(5):694-701.
Hariri S, Ghasemi JB, Shirini F, Rasti B. Probing the Origin of Dihydrofolate Reductase Inhibition via Proteochemometric Modeling. J Chemom. 2019;33(2):e3090.
Hellberg S, Sjöström M, Skagerberg B, Wold S. Peptide quantitative structure-activity relationships, a multivariate approach. J Med Chem . 1987;30(7):1126-1135.
Henry RP. Multiple roles of carbonic anhydrase in cellular transport and metabolism. Annu Rev Physiol. 1996;58:523-538.
Kennard RW, Stone LA. Computer aided design of experiments. Technometrics. 1969;11(1):137-148.
Lapinsh M, Eklund M, Spjuth O, Prusis P, Wikberg JE. Proteochemometric modeling of HIV protease susceptibility. BMC Bioinf. 2008;9:181.
Lapinsh M, Prusis P, Uhlén S, Wikberg JE. Improved approach for proteochemometrics modeling: application to organic compound-amine G protein-coupled receptor interactions. Bioinformatics. 2005;21(23):4289-4296.
Pastor M, Cruciani G, McLay I, Pickett S, Clementi S. GRid-INdependent descriptors (GRIND): a novel class of alignment-independent three-dimensional molecular descriptors. J Med Chem . 2000;43(17):3233-3243.
Prusis P, Muceniece R, Andersson P, Post C, Lundstedt T, Wikberg JE. PLS modeling of chimeric MS04/MSH-peptide and MC 1/MC 3-receptor interactions reveals a novel method for the analysis of ligand-receptor interactions. Biochim Biophys Acta. 2001;1544(1-2):350-357.
Purkerson J, Schwartz G. The role of carbonic anhydrases in renal physiology. Kidney Int. 2007;71(2):103-115.
Rasti B, Entezari Heravi Y. Probingthechemicalinteraction space governed by 4-aminosubstituted benzenesulfonamides and carbonic anhydrase isoforms. Res Pharm Sci. 2018;13(3):192-204.
Rasti B, Karimi-Jafari MH, Ghasemi JB. Quantitative characterization of the interaction space of the mammalian carbonic anhydrase isoforms I, II, VII, IX, XII, and XIV and their inhibitors, using the proteochemometric approach. Chem Biol Drug Des. 2016;88(3):341-353.
Rasti B, Mazraedoost S, Panahi H, Falahati M, Attar F. New insights into the selective inhibition of the β-carbonic anhydrases of pathogenic bacteria Burkholderia pseudomallei and Francisella tularensis: a proteochemometrics study. Mol Divers. 2019;23(2):263-273.
Rasti B, Namazi M, Karimi-Jafari MH, Ghasemi JB. Proteochemometric modeling of the interaction space of carbonic anhydrase and its inhibitors: an assessment of structure-based and sequence-based descriptors. Mol Info. 2017a;36(4):1600102.
Rasti B, Schaduangrat N, Shahangian SS, Nantasenamat C. Exploring the origin of phosphodiesterase inhibition via proteochemometric modeling. RSC Adv. 2017b;7:28056-28068.
Rasti B, Shahangian SS. Proteochemometric Modeling of the Origin of Thymidylate Synthase Inhibition. Chem Biol Drug Des . 2018;91(5):1007-1016.
Rogers D, Hopfinger AJ. Application of genetic function approximation to quantitative structure-activity relationships and quantitative structure-property relationships. J Chem Inf Comput Sci. 1994;34(4):854-866.
Sandberg M, Eriksson L, Jonsson J, Sjöström M, Wold S. New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids. J Med Chem . 1998;41(14):2481-2491.
Simeon S, Spjuth O, Lapins M, Nabu S, Anuwongcharoen N, Prachayasittikul V, et al. Origin of aromatase inhibitory activity via proteochemometric modeling. PeerJ. 2016;4:e1979.
Subramanian V, Prusis P, Pietilä LO, Xhaard H, Wohlfahrt G. Visually interpretable models of kinase selectivity related features derived from field-based proteochemometrics. J Chem Inf Model. 2013;53(11):3021-3030.
Supuran CT, Scozzafava A, Casini A. Carbonic anhydrase inhibitors. Med Res Rev. 2003;23(2):146-189.
Supuran CT, Scozzafava A, Conway J. Carbonic anhydrase: its inhibitors and activators. Vol. 1. 2004: CRC Press.
Wischeler JS, Innocenti A, Vullo D, Agrawal A, Cohen SM, Heine A, et al. Bidentate zinc chelators for α-carbonic anhydrases that produce a trigonal bipyramidal coordination geometry. Chem Med Chem. 2010;5(9):1609-1615.
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