Probing the chemical interaction space governed by 4-amino-substituted benzenesulfonamides and carbonic anhydrase isoforms

Behnam Rasti, Yeganeh Entezari Heravi

Abstract


Isoform diversity, critical physiological roles and involvement in major diseases/disorders such as glaucoma, epilepsy, Alzheimer’s disease, obesity, and cancers have made carbonic anhydrase (CA), one of the most interesting case studies in the field of computer aided drug design. Since applying non-selective inhibitors can result in major side effects, there have been considerable efforts so far to achieve selective inhibitors for different isoforms of CA. Using proteochemometrics approach, the chemical interaction space governed by a group of 4-amino-substituted benzenesulfonamides and human CAs has been explored in the present study. Several validation methods have been utilized to assess the validity, robustness and predictivity power of the proposed proteochemometric model. Our model has offered major structural information that can be applied to design new selective inhibitors for distinct isoforms of CA. To prove the applicability of the proposed model, new compounds have been designed based on the offered discriminative structural features.


Keywords


Carbonic anhydrases; Proteochemometrics; Selectivity; GRINDs; Z-scales

Full Text:

PDF

References


Supuran CT. Carbonic anhydrases: novel therapeutic applications for inhibitors and activators. Nat Rev Drug Discov. 2008;7(2):168-181.

Henry RP. Multiple roles of carbonic anhydrase in cellular transport and metabolism. Annu Rev Physiol. 1996;58:523-538.

Henry RP, Swenson ER. The distribution and physiological significance of carbonic anhydrase in vertebrate gas exchange organs. Respir Physiol. 2000;121(1):1-12.

Kose LP, Gülçin İ, Özdemir H, Atasever A, Alwasel SH, Supuran CT. The effects of some avermectins on bovine carbonic anhydrase enzyme. J Enzyme Inhib Med Chem. 2016;31(5):773-778.

Nishimori I. Acatalytic CAs: Carbonic Anhydrase-Related Proteins. In: Supuran CT, Scozzafava A, Conway J, editors. Carbonic Anhydrase: Its Inhibitors and Activators. New York: CRC Press; 2004. pp. 12-14.

Supuran CT, Scozzafava A, Casini A. Carbonic anhydrase inhibitors. Med Res Rev. 2003;23(2): 146-189.

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.

Schulze Wischeler J, Innocenti A, Vullo D, Agrawal A, Cohen S M, Heine A, et al. Bidentate Zinc chelators for alpha‐carbonic anhydrases that produce a trigonal bipyramidal coordination geometry. ChemMedChem. 2010;5(9):1609-1615.

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.

McKenna R, Supuran CT. Carbonic Anhydrase Inhibitor Drug Design. In: Frost SC, McKenna R, editors. Carbonic Anhydrase: Mechanism, Regulation, Links to Disease, and Industrial Applications. Netherlands: Springer Science+Business Media Dordrecht; 2013. pp. 291-323.

Lindahl M, Vidgren J, Eriksson E, Habash J, Harrop S, Helliwell J, et al. Crystallographic Studies of Carbonic Anhydrase Inhibition. In: Botre F, Gros G, Storey BT, editors. Carbonic Anhydrase: From Biochemistry and Genetics to Physiology and Clinical Medicine. Weinheim: VCH; 1991. pp. 111-118.

Prusis P, Muceniece R, Andersson P, Post C, Lundstedt T, Wikberg JE. PLS modeling of chimeric MS04/MSH-peptide and MC1/MC 3-receptor interactions reveal a novel method for the analysis of ligand-receptor interactions. Biochim Biophys Acta. 2001;1544(1-2):350-357.

Lapinsh M, Prusis P, Lundstedt T, Wikberg JE. Proteochemometrics modeling of the interaction of amine G-protein coupled receptors with a diverse set of ligands. Mol Pharmacol. 2002;61(6):1465-1475.

Prusis P, Lapins M, Yahorava S, Petrovska R, Niyomrattanakit P, Katzenmeier G, et al. Proteochemometrics analysis of substrate interactions with dengue virus NS3 proteases. Bioorg Med Chem. 2008;16(20):9369-9377.

Rasti B, Shahangian SS. Proteochemometric modeling of the origin of thymidylate synthase inhibition. Chem Biol Drug Des. 2017. DOI: 10.1111/cbdd.13163.

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.

Rasti B, Karimi‐Jafari M H, 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, Namazi M, Karimi‐Jafari M, 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. 2017;36(4). DOI: 10.1002/minf.201600102.

Rasti B, Schaduangrat N, Shahangian SS, Nantasenamat C. Exploring the origin of phosphodiesterase inhibition via proteochemometric modeling. RSC Adv. 2017;7(45):28056-28068.

Rutkauskas K, Zubrienė A, Tumosienė I, Kantminienė K, Kažemėkaitė M, Smirnov A, et al. 4-amino-substituted benzenesulfonamides as inhibitors of human carbonic anhydrases. Molecules. 2014;19(11):17356-17380.

Durán A, Zamora I, Pastor M. Suitability of GRIND-based principal properties for the description of molecular similarity and ligand-based virtual screening. J Chem Inf Model. 2009;49(9):2129-2138.

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.

Durán Á, Martínez GC, Pastor. M. Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in molecular interaction fields. J Chem Inf Model. 2008;48(9):1813-1823.

Fedorov VV. Theory of Optimal Experiments. New York: Academic Press; 1972. pp. 292.

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. bioinformatics. 2007;23(21):2947-2948.

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.

Beasley D, Bull DR, Martin RR. An overview of genetic algorithms: Part 1, fundamentals. University Computing.1993;15(2):58-69.

Van de Waterbend H. Chemometric Methods in Molecular Design. In: Van de Waterbend, Timmerman H, Mannhold R, Krogsgaard-Larsen P, editors. Methods and Principles in Medicinal Chemistry. New York: VCH: Publishers; 1995. pp. 195-219.

Parish M, Hemmateenejad B, Miri R, Edraki N, Elyasi M, Khoshneviszadeh M, et al. Qsar study of N-acyl-3,5-bis(arylidene)-4-piperidones as cytotoxic agents. Res Pharm Sci. 2012;7(5):s557.

Karbakhsh R, Sabet R. Application of different chemometric tools in QSAR study of azolo-adamantanes against influenza A virus. Res Pharm Sci. 2011;6(1):23-33.

Kennard RW, Stone LA. Computer aided design of experiments. Technometrics. 1969;11(1):137-148.

Gramatica P. Principles of QSAR models validation: internal and external. Mol Inform. 2007;26(5): 694-701.

Eriksson L, Jaworska J, Worth AP, Cronin MTD, 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.


Refbacks

  • There are currently no refbacks.


Creative Commons Attribution-NonCommercial 3.0

This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License which allows users to read, copy, distribute and make derivative works for non-commercial purposes from the material, as long as the author of the original work is cited properly.