Generic placeholder image

Current Computer-Aided Drug Design

Editor-in-Chief

ISSN (Print): 1573-4099
ISSN (Online): 1875-6697

Research Article

A Fuzzy System Classification Approach for QSAR Modeling of α- Amylase and α-Glucosidase Inhibitors

Author(s): Karel Diéguez-Santana*, Amilkar Puris, Oscar M. Rivera-Borroto, Gerardo M. Casanola-Martin, Bakhtiyor Rasulev and Humberto González-Díaz

Volume 18, Issue 7, 2022

Published on: 16 November, 2022

Page: [469 - 479] Pages: 11

DOI: 10.2174/1573409918666220929124820

Price: $65

Abstract

Introduction: This report proposes the application of a new Machine Learning algorithm called Fuzzy Unordered Rules Induction Algorithm (FURIA)-C in the classification of druglike compounds with antidiabetic inhibitory ability toward the main two pharmacological targets: α-amylase and α-glucosidase.

Methods: The two obtained QSAR models were tested for classification capability, achieving satisfactory accuracy scores of 94.5% and 96.5%, respectively. Another important outcome was to achieve various α-amylase and α-glucosidase fuzzy rules with high Certainty Factor values. Fuzzyrules derived from the training series and active classification rules were interpreted. An important external validation step, comparing our method with those previously reported, was also included.

Results: The Holm’s test comparison showed significant differences (p-value<0.05) between FURIA-C, Linear Discriminating Analysis (LDA), and Bayesian Networks, the former beating the two latter according to the relative ranking score of the Holm’s test.

Conclusion: From these results, the FURIA-C algorithm could be used as a cutting-edge technique to predict (classify or screen) the α-amylase and α-glucosidase inhibitory activity of new compounds and hence speed up the discovery of new potent multi-target antidiabetic agents.

Keywords: Anti-diabetic agents, induction rule, FURIA-C, QSAR, machine-learning techniques, LDA.

Next »
Graphical Abstract
[1]
Rocha, S.; Sousa, A.; Ribeiro, D.; Correia, C.M.; Silva, V.L.M.; Santos, C.M.M.; Silva, A. M.S.; Araújo, A.N.; Fernandes, E.; Freitas, M. A study towards drug discovery for the management of type 2 diabetes: Mellitus through inhibition of the carbohydrate-hydrolyzing enzymes α-amylase and α-glucosidase by chalcone derivatives. Food Func., 2019, 10(9), 5510-5520.
[http://dx.doi.org/10.1039/C9FO01298B]
[2]
IDF diabetes atlas.. 2019. Available from: http://www.diabetesatlas. org/ (accessed on: 2022 June, 7th).
[3]
Temelkova-Kurktschiev, T.; Stefanov, T. Lifestyle and genetics in obesity and type 2 diabetes. Exp. Clin. Endocrinol. Diabetes, 2012, 120(1), 1-6.
[http://dx.doi.org/10.1055/s-0031-1285832]
[4]
Inzucchi, S.E.; Bergenstal, R.M.; Buse, J.B.; Diamant, M.; Ferrannini, E.; Nauck, M.; Peters, A.L.; Tsapas, A.; Wender, R.; Matthews, D.R. Management of hyperglycemia in type 2 diabetes: A patient-centered approach: Position statement of the American Diabetes Association (ADA) and the European Association for the Study of Diabetes (EASD). Diabetes Care, 2012, 35(6), 1364-1379.
[http://dx.doi.org/10.2337/dc12-0413] [PMID: 22517736]
[5]
Kumar, D.; Gupta, N.; Ghosh, R.; Gaonkar, R.H.; Pal, B.C. α-Glucosidase and α-amylase inhibitory constituent of Carex baccans: Bio-assay guided isolation and quantification by validated RP-HPLC–DAD. J. Funct. Foods, 2013, 5(1), 211-218.
[http://dx.doi.org/10.1016/j.jff.2012.10.007]
[6]
Palanisamy, U.D.; Ling, L.T.; Manaharan, T.; Appleton, D. Rapid isolation of geraniin from Nephelium lappaceum rind waste and its anti-hyperglycemic activity. Food Chem., 2011, 127(1), 21-27.
[http://dx.doi.org/10.1016/j.foodchem.2010.12.070]
[7]
Manaharan, T.; Teng, L.L.; Appleton, D.; Ming, C.H.; Masilamani, T.; Palanisamy, U.D. Antioxidant and antiglycemic potential of Peltophorum pterocarpum plant parts. Food Chem., 2011, 129(4), 1355-1361.
[http://dx.doi.org/10.1016/j.foodchem.2011.05.041]
[8]
Eichler, H.G.; Korn, A.; Gasic, S.; Pirson, W.; Businger, J. The effect of a new specific? -amylase inhibitor on post-prandial glucose and insulin excursions in normal subjects and Type 2 (non-insulin-dependent) diabetic patients. Diabetologia, 1984, 26(4), 278-281.
[http://dx.doi.org/10.1007/BF00283650] [PMID: 6376235]
[9]
Dieguez-Santana, K.; Pham-The, H.; Rivera-Borroto, O.M.; Puris, A.; Le-Thi-Thu, H.; Casanola-Martin, G.M. A two QSAR way for antidiabetic agents targeting using α-amylase and α-glucosidase inhibitors: Model parameters settings in artificial intelligence techniques. Lett. Drug Des. Discov., 2017, 14(8), 862-868.
[http://dx.doi.org/10.2174/1570180814666161128121142]
[10]
Diéguez-Santana, K.; Rivera-Borroto, O.M.; Puris, A.; Pham-The, H.; Le-Thi-Thu, H.; Rasulev, B.; Casañola-Martin, G.M. Beyond model interpretability using LDA and decision trees for α‐amylase and α‐glucosidase inhibitor classification studies. Chem. Biol. Drug Des., 2019, 94(1), 1414-1421.
[http://dx.doi.org/10.1111/cbdd.13518] [PMID: 30908888]
[11]
Diéguez-Santana, K.; Casañola-Martin, G.M.; Green, J.R.; Rasulev, B.; González-Díaz, H. Predicting metabolic reaction networks with Perturbation-Theory Machine Learning (PTML) models. Curr. Top. Med. Chem., 2021, 21(9), 819-827.
[http://dx.doi.org/10.2174/1568026621666210331161144] [PMID: 33797370]
[12]
Rastija, V.; Bešlo, D.; Nikolić, S. Two-dimensional quantitative structure–activity relationship study on polyphenols as inhibitors of α-glucosidase. Med. Chem. Res., 2012, 21(12), 3984-3993.
[http://dx.doi.org/10.1007/s00044-011-9938-0]
[13]
Narayana Moorthy, N. S. H.; Ramos, M. J.; Fernandes, P. A. Prediction of the relationship between the structural features of andro-grapholide derivatives and αî±-glucosidase inhibitory activity: A quantitative structure-activity relationship (QSAR) study. J. Enzyme Inhib. Med. Chem., 2011, 26(1), 78-87.
[http://dx.doi.org/10.3109/14756361003724760]
[14]
Rao, R. R.; Tiwari, A. K.; Reddy, P. P.; Babu, K. S.; Suresh, G.; Ali, A. Z.; Madhusudana, K.; Agawane, S. B.; Badrinarayan, P.; Sastry, G. N. Synthesis of antihyperglycemic, α-glucosidase inhibitory, and DPPH free radical scavenging furanochalcones. Medicinal Chemistry Research, 2012, 21(6), 760-774.
[http://dx.doi.org/10.1007/s00044-011-9583-7]
[15]
Narayana Moorthy, N. S. H.; Ramos, M. J.; Fernandes, P. A. Comparative structural analysis of α-glucosidase inhibitors on difference species: A computational study. Archiv der Pharmazie, 2012, 345(4), 265-274.
[http://dx.doi.org/10.1002/ardp.201100047]
[16]
Masand, V.H.; Mahajan, D.T.; Patil, K.N.; Chinchkhede, K.D.; Jawarkar, R.D.; Hadda, T.B.; Alafeefy, A.A.; Shibi, I.G. k-NN, quantum mechanical and field similarity based analysis of xanthone derivatives as α-glucosidase inhibitors. Med. Chem. Res., 2012, 21(12), 4523-4534.
[http://dx.doi.org/10.1007/s00044-012-9995-z]
[17]
Gómez-Jeria, J.S.; Gazzano, V. A quantum chemical study of the inhibition of a-glucosidase by a group of oxadiazole benzohydrazone derivatives. Pharma Chem., 2016, 8(11), 21-27.
[18]
Wu, P.; Zheng, J.; Huang, T.; Li, D.; Hu, Q.; Cheng, A.; Jiang, Z.; Jiao, L.; Zhao, S.; Zhang, K. Synthesis and evaluation of novel triterpene analogues of ursolic acid as potential antidiabetic agent. PLoS ONE, 2015, 10(9), E0138767.
[http://dx.doi.org/10.1371/journal.pone.0138767]
[19]
Pham-The, H.; Nam, N. H.; Nga, D. V.; Hai, D. T.; Diéguez-Santana, K.; Marrero-Ponce, Y.; Castillo-Garit, J. A.; Casañola-Martin, G. M.; Le-Thi-Thu, H. Learning from multiple classifier systems: Perspectives for improving decision making of QSAR models in medicinal chemistry. Curr. Topics Med. Chem., 2017, 17(30), 3269-3288.
[http://dx.doi.org/10.2174/1568026618666171212111018]
[20]
Thukral, S.; Rana, V. Versatility of fuzzy logic in chronic diseases: A review. Med. Hypotheses, 2019, 122, 150-156.
[http://dx.doi.org/10.1016/j.mehy.2018.11.017] [PMID: 30593401]
[21]
Reghunadhan, R.; Arulmozhi, V. Fuzzy logic for Chemoinformatics - A review. J. Theor. Appl. Inf. Technol., 2013, 47(1), 86-92.
[22]
DrugBank Database V4.0. Available from: http://www.drugbank.ca/
[23]
Statistica (data analysis software system), Version 8.0.1; StatSoft, Inc.: Tulsa, OK 2012. Available from: www.statsoft.com
[24]
McInnes, L.; Healy, J. UMAP: Uniform manifold approximation and projection for dimension reduction. ArXiv e-prints, 2018, 1802.03426.
[25]
MarvinView. 16.3.14.0-master-4840 ed., 2016. Available from: ww.chemaxon.com
[26]
Dragon for Widows; (Software for the Calculation of Molecular Descriptors): Milan, Italy, 2013.
[27]
IMMAN (Information Theory based Chemometric Analysis) Version 1.0, 2011.
[28]
García, A.J.J.; Pikatza, A.J.M.; Ubeda, C.M.; Ansuategi, Z.E. Automatic text classification to support systematic reviews in medicine. Expert Syst. Appl., 2014, 41(4), 1498-1508.
[http://dx.doi.org/10.1016/j.eswa.2013.08.047]
[29]
Quinlan, J. R. C4. 5: Programming for machine learning; Morgan Kaufman Publishers: San Mateo, 1993.
[30]
Diéguez-Santana, K.; Rasulev, B.; González-Díaz, H. Towards rational nanomaterial design by predicting drug–nanoparticle system interaction vs. bacterial metabolic networks. Environ. Sci.: Nano, 2022, 9(4), 1391-1413.
[http://dx.doi.org/10.1039/D1EN00967B]
[31]
Svozil, D.; Kvasnicka, V.; Pospichal, J. Introduction to multi-layer feed-forward neural networks. Chemom. Intell. Lab. Syst., 1997, 39(1), 43-62.
[http://dx.doi.org/10.1016/S0169-7439(97)00061-0]
[32]
Pham-The, H.; Casañola-Martin, G.; Diéguez-Santana, K.; Nguyen-Hai, N.; Ngoc, N.T.; Vu-Duc, L.; Le-Thi-Thu, H. Quantitative structure–activity relationship analysis and virtual screening studies for identifying HDAC2 inhibitors from known HDAC bioactive chemical libraries. SAR QSAR Environ. Res., 2017, 28(3), 199-220.
[http://dx.doi.org/10.1080/1062936X.2017.1294198] [PMID: 28332438]
[33]
Sumpter, B.G.; Getino, C.; Noid, D.W. Theory and applications of neural computing in chemical science. Annu. Rev. Phys. Chem., 1994, 45(1), 439-481.
[http://dx.doi.org/10.1146/annurev.pc.45.100194.002255]
[34]
Witten, I.H.; Frank, E. Data Mining: Practical machine learning tools and techniques; Morgan Kaufmann, 2005.
[35]
Ivanciuc, O. Applications of support vector machines in chemistry. In: Reviews in Computational Chemistry; , 2007; pp. 291-400.
[http://dx.doi.org/10.1002/9780470116449.ch6]
[36]
Cortes, C.; Vapnik, V. Support-vector networks. Machine Learning, 1995, 20(3), 273-297.
[http://dx.doi.org/10.1007/BF00994018]
[37]
Peterson, L. K-nearest neighbor. Scholarpedia J., 2009, 4(2), 1883.
[http://dx.doi.org/10.4249/scholarpedia.1883]
[38]
Fix, E.; Hodges, J.L. Discriminatory analysis: Non-parametric discrimination; USAF School of Aviation Medicine, 1951.
[39]
Michalski, R.S. 4 - A theory and methodology of inductive learning. In: Machine Learning; Morgan Kaufmann, 1983; pp. 83-134.
[40]
Cohen, W.W. Fast effective rule induction. In: Machine Learning Proceedings 1995; Prieditis, A.; Russell, S., Eds.; Morgan Kaufmann, 1995; pp. 115-123.
[http://dx.doi.org/10.1016/B978-1-55860-377-6.50023-2]
[41]
Hühn, J.; Hüllermeier, E.J.D.M.; Discovery, K. FURIA: An algorithm for unordered fuzzy rule induction. Data Min. Knowl. Disc., 2009, 19, 293-319.
[http://dx.doi.org/10.1007/s10618-009-0131-8]
[42]
Trawiński, K.; Cordón, O.; Quirin, A. On designing fuzzy rule-based multiclassification systems by combining furia with bagging and feature selection. Int. J. Uncertain. Fuzziness Knowl. Based Syst., 2011, 19(4), 589-633.
[http://dx.doi.org/10.1142/S0218488511007155]
[43]
Diéguez-Santana, K.; González-Díaz, H. Towards machine learning discovery of dual antibacterial drug–nanoparticle systems. Nanoscale, 2021, 13(42), 17854-17870.
[http://dx.doi.org/10.1039/D1NR04178A]
[44]
Alcalá-Fdez, J.; Sánchez, L.; García, S.; del Jesus, M. J.; Ventura, S.; Garrell, J. M.; Otero, J.; Romero, C.; Bacardit, J.; Rivas, V. M. KEEL: A software tool to assess evolutionary algorithms for data mining problems. Soft Comput., 2009, 13(3), 307-318.
[http://dx.doi.org/10.1007/s00500-008-0323-y]
[45]
Hall, M.; Frank, E.; Holmes, G.; Pfahringer, B.; Reutemann, P.; Witten, I.H. The WEKA data mining software. SIGKDD Explor., 2009, 11(1), 10-18.
[http://dx.doi.org/10.1145/1656274.1656278]
[46]
Baldi, P.; Brunak, S.; Chauvin, Y.; Andersen, C.A.F.; Nielsen, H. Assessing the accuracy of prediction algorithms for classification: An overview. Bioinformatics, 2000, 16(5), 412-424.
[http://dx.doi.org/10.1093/bioinformatics/16.5.412] [PMID: 10871264]
[47]
Roy, K.; Kar, S.; Das, R.N. Statistical methods in QSAR/QSPR. In: A Primer on QSAR/QSPR Modeling: Fundamental Concepts; Springer International Publishing, 2015; pp. 37-59.
[48]
Pearlman, R.S.; Smith, K.M. Novel software tools for chemical diversity. In: 3D QSAR in Drug Design: Ligand-Protein Interactions and Molecular Similarity; Kubinyi, H.; Folkers, G.; Martin, Y.C., Eds.; Springer, 1998, pp. 339-353.
[49]
Kortagere, S.; Krasowski, M. D.; Ekins, S. The importance of discerning shape in molecular pharmacology. Trends Pharmacol. Sci., 2009, 30(3), 138-147.
[http://dx.doi.org/10.1016/j.tips.2008.12.001]
[50]
Valentina, P.; Ilango, K.; Indraja, K. Modified quercetin derivatives as potent anti diabetic agents: A QSAR approach. Res. J. Pharm. Biol. Chem. Sci., 2013, 4(2), 1004-1008.
[51]
Saqib, U.; Siddiqi, M.I. 3D-QSAR studies of xanthone derivatives as human alpha glucosidase inhibitors. Int. J. Integr. Biol., 2009, 5(1), 13-19.
[52]
Kraim, K.; Khatmi, D.; Saihi, Y.; Ferkous, F.; Brahimi, M. Quantitative structure activity relationship for the computational prediction of α-glucosidase inhibitory. Chemometr. Intell. Labor. Syst., 2009, 97(2), 118-126.
[http://dx.doi.org/10.1016/j.chemolab.2009.03.006]
[53]
Saihi, Y.; Kraim, K.; Ferkous, F.; Djeghaba, Z.; Azzouzi, A.; Benouis, S. Nonlinear qsar study of xanthone and curcuminoid derivatives as α-glucosidase inhibitors. Bull. Korean Chem. Soc., 2013, 34(6), 1643-1650.
[http://dx.doi.org/10.5012/bkcs.2013.34.6.1643]
[54]
Jabeen, F.; Oliferenko, P. V.; Oliferenko, A. A.; Pillai, G. G.; Ansari, F. L.; Hall, C. D.; Katritzky, A. R. Dual inhibition of the α-glucosidase and butyrylcholinesterase studied by molecular field topology analysis. Eur. J. Med. Chem., 2014, 80, 228-242.
[http://dx.doi.org/10.1016/j.ejmech.2014.04.018]
[55]
Guptan, N.; Saha, A.K.; Sen, R. QSAR analysis of xanthone derivative in the treatment of carbohydrate mediated diseases. J. Appl. Sci. Res., 2010, 6(5), 415-420. [Article. Scopus.].
[56]
Liu, B.; Ma, J. M.; Chen, H. W.; Li, Z. L.; Sun, L. H.; Zeng, Z.; Jiang, H. α-Glucosidase inhibitory activities of phenolic acid amides with l-amino acid moiety. RSC Adv., 2016, 6(56), 50837-50845.
[http://dx.doi.org/10.1039/C6RA08330G]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy