Generic placeholder image

Letters in Drug Design & Discovery

Editor-in-Chief

ISSN (Print): 1570-1808
ISSN (Online): 1875-628X

Research Article

QSAR Model based Gradient Boosting Regression of N-Arylsulfonyl-Indole-2-Carboxamide Derivatives as Inhibitors for Fructose-1,6-bisphosphatase

Author(s): Ziyi Zhao, Jialong Yang, Hongxiang Ji, Zeyu Liu, Tingting Sun and Tongshang NI*

Volume 21, Issue 7, 2024

Published on: 19 September, 2023

Page: [1274 - 1286] Pages: 13

DOI: 10.2174/1570180820666230726145659

Price: $65

Abstract

Background: Due to the complication caused by conventional drugs, global attention has been focused on the development of novel drugs. As a consequence, a potential theory to put T2DM under control is of great medical significance.

Methods: We used the heuristic method to establish the linear model and used Gradient Boosting Regression to establish the nonlinear model of Fructose-1,6-Bisphosphatse inhibitor successively. In this study, 84 derivatives of N-Arylsulfonyl-Indole-2-Carboxamide were introduced into the models, and two outstanding QSAR models with 2 molecule descriptors were established successfully.

Results: Gradient Boosting Regression rendered a good correlation with R2 of 0.943 and MSE of 0.135 for the training set, 0.916 and 0.213 for the test set, which also proves the feasibility of the implementation of the new method GBR in the field of QSAR. Meanwhile, the optimal model displayed wonderful statistical significance.

Conclusion: This study makes an attempt at the application of a new method of GBR in QSAR and proves GBR as a promising tool for further study of CADD.

« Previous
Graphical Abstract

[1]
Murphy, H.R.; Howgate, C.; O’Keefe, J.; Myers, J.; Morgan, M.; Coleman, M.A.; Jolly, M.; Valabhji, J.; Scott, E.M.; Knighton, P.; Young, B.; Lewis-Barned, N.; Anglioni, E.; Barron, E.; Bell, R.; Berry, A.; Cartright, C.; Colling, S.; Curley, M.; Duggan, A.; Draper, L.; Fargher, L.; Flanagan, M.; Hawdon, J.; Holt, R.; Kurinczuk, J.; Maresh, M.; Pinnock, A.; Shonegeval, L.; Todd, D.; Tomkins, N. Characteristics and outcomes of pregnant women with type 1 or type 2 diabetes: A 5-year national population-based cohort study. Lancet Diabetes Endocrinol., 2021, 9(3), 153-164.
[http://dx.doi.org/10.1016/S2213-8587(20)30406-X] [PMID: 33516295]
[2]
Lim, S.; Oh, T.J.; Dawson, J.; Sattar, N. Diabetes drugs and stroke risk: Intensive versus conventional glucose‐lowering strategies, and implications of recent cardiovascular outcome trials. Diabetes Obes. Metab., 2020, 22(1), 6-15.
[http://dx.doi.org/10.1111/dom.13850] [PMID: 31379119]
[3]
Kaur, R.; Dahiya, L.; Kumar, M. Fructose-1,6-bisphosphatase inhibitors: A new valid approach for management of type 2 diabetes mellitus. Eur. J. Med. Chem., 2017, 141, 473-505.
[http://dx.doi.org/10.1016/j.ejmech.2017.09.029] [PMID: 29055870]
[4]
Padhi, S.; Nayak, A.K.; Behera, A. Type II diabetes mellitus: A review on recent drug based therapeutics. Biomed. Pharmacother., 2020, 131, 110708.
[http://dx.doi.org/10.1016/j.biopha.2020.110708] [PMID: 32927252]
[5]
Exton, J.H. Gluconeogenesis. Metabolism, 1972, 21(10), 945-990.
[http://dx.doi.org/10.1016/0026-0495(72)90028-5] [PMID: 4342011]
[6]
Chen, L.; Zhao, X.; He, Y.; Yang, H. Cloning, purification and characterisation of cytosolic fructose-1,6-bisphosphatase from mung bean (Vigna radiata). Food Chem., 2021, 347, 128973.
[http://dx.doi.org/10.1016/j.foodchem.2020.128973] [PMID: 33444888]
[7]
Barciszewski, J.; Wisniewski, J.; Kolodziejczyk, R.; Jaskolski, M.; Rakus, D.; Dzugaj, A. T-to-R switch of muscle fructose-1,6-bisphosphatase involves fundamental changes of secondary and quaternary structure. Acta Crystallogr. D Struct. Biol., 2016, 72(4), 536-550.
[http://dx.doi.org/10.1107/S2059798316001765] [PMID: 27050133]
[8]
Wright, S.W.; Carlo, A.A.; Danley, D.E.; Hageman, D.L.; Karam, G.A.; Mansour, M.N.; McClure, L.D.; Pandit, J.; Schulte, G.K.; Treadway, J.L.; Wang, I.K.; Bauer, P.H. 3-(2-Carboxy-ethyl)-4,6-dichloro-1H-indole-2-carboxylic acid: An allosteric inhibitor of fructose-1,6-bisphosphatase at the AMP site. Bioorg. Med. Chem. Lett., 2003, 13(12), 2055-2058.
[http://dx.doi.org/10.1016/S0960-894X(03)00310-X] [PMID: 12781194]
[9]
Lai, C.; Gum, R.J.; Daly, M.; Fry, E.H.; Hutchins, C.; Abad-Zapatero, C.; von Geldern, T.W. Benzoxazole benzenesulfonamides as allosteric inhibitors of fructose-1,6-bisphosphatase. Bioorg. Med. Chem. Lett., 2006, 16(7), 1807-1810.
[http://dx.doi.org/10.1016/j.bmcl.2006.01.014] [PMID: 16446092]
[10]
Kitas, E; Mohr, P; Kuhn, B; Hebeisen, P; Wessel, HP; Haap, W Sulfonylureido thiazoles as fructose-1, 6-bisphosphatase inhibitors for the treatment of Type-2 diabetes. Bioorg Med Chem Lett., 2010, 20(2), 549-9.
[http://dx.doi.org/10.1016/j.bmcl.2009.11.093] [PMID: 19969452]
[11]
Hebeisen, P; Haap, W; Kuhn, B; Mohr, P; Wessel, HP; Zutter, U Orally active aminopyridines as inhibitors of tetrameric fructose-1,6-bisphosphatase. Bioorg Med Chem Lett., 2011, 21(11), 3237-42.
[http://dx.doi.org/10.1016/j.bmcl.2011.04.044] [PMID: 21550236]
[12]
Dang, Q.; Van Poelje, P.D.; Erion, M.D. The discovery and development of MB07803, a second-generation fructose-1, 6- bisphosphatase inhibitor with improved pharmacokinetic properties, as a potential treatment of type 2 diabetes. In: New Therapeutic Strategies for Type 2 Diabetes; , 2012; pp. 306-23.
[13]
He, H-B.; Gao, L-X.; Zhou, Y-Y.; Liu, T.; Tang, J.; Gong, X.P. Design, synthesis and biological activity evaluation of 2,5-Diphenyl-1,3,4-oxadiazole Derivatives as Novel Inhibitors of Fructose-1,6-bisphosphatase. ChemInform, 2012, 44(11)
[http://dx.doi.org/10.1002/chin.201311135]
[14]
Liao, B-R.; He, H-B.; Yang, L-L.; Gao, L-X.; Chang, L.; Tang, J Synthesis and structure–activity relationship of non-phosphorus-based fructose-1,6-bisphosphatase inhibitors: 2,5-Diphenyl-1,3,4-oxadiazoles. Eur. J. Med. Chem., 2014, 83, 15-25.
[http://dx.doi.org/10.1016/j.ejmech.2014.06.011]
[15]
Bie, J.; Liu, S.; Zhou, J.; Xu, B.; Shen, Z.J.B.; Chemistry, M. Design, synthesis and biological evaluation of 7-nitro-1H-indole-2-carboxylic acid derivatives as allosteric inhibitors of fructose-1,6-bisphosphatase. Bioorg. Med. Chem., 2014, 22(6), 1850-1862.
[http://dx.doi.org/10.1016/j.bmc.2014.01.047] [PMID: 24530031]
[16]
Dang, Q; Kasibhatla, SR; Xiao, W; Liu, Y; DaRe, J; Taplin, F Fructose-1,6-bisphosphatase Inhibitors. 2. Design, synthesis, and structure-activity relationship of a series of phosphonic acid containing benzimidazoles that function as 5'- adenosinemonophosphate (AMP) mimics. J Med Chem., 2010, 53(1), 441-51.
[http://dx.doi.org/10.1021/jm901420x] [PMID: 20055427]
[17]
Dang, Q; Brown, BS; Liu, Y; Rydzewski, RM; Robinson, ED Fructose-1,6-bisphosphatase inhibitors. 1. Purine phosphonic acids as novel AMP mimics. J Med Chem., 2009, 52(9), 2880-98.
[http://dx.doi.org/10.1021/jm900078f] [PMID: 19348494]
[18]
Zhao, L.; Ciallella, H.L.; Aleksunes, L.M.; Zhu, H. Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. Drug Discov. Today, 2020, 25(9), 1624-1638.
[http://dx.doi.org/10.1016/j.drudis.2020.07.005] [PMID: 32663517]
[19]
Cruz-Monteagudo, M.; Schürer, S.; Tejera, E.; Pérez-Castillo, Y.; Medina-Franco, J.L.; Sánchez-Rodríguez, A.; Borges, F. Systemic QSAR and phenotypic virtual screening: Chasing butterflies in drug discovery. Drug Discov. Today, 2017, 22(7), 994-1007.
[http://dx.doi.org/10.1016/j.drudis.2017.02.004] [PMID: 28274840]
[20]
Zhou, J.; Bie, J.; Wang, X.; Liu, Q.; Li, R.; Chen, H.; Hu, J.; Cao, H.; Ji, W.; Li, Y.; Liu, S.; Shen, Z.; Xu, B. Discovery of n -arylsulfonyl-indole-2-carboxamide derivatives as potent, selective, and orally bioavailable fructose-1,6-bisphosphatase inhibitors—design, synthesis, in vivo glucose lowering effects, and x-ray crystal complex analysis. J. Med. Chem., 2020, 63(18), 10307-10329.
[http://dx.doi.org/10.1021/acs.jmedchem.0c00726] [PMID: 32820629]
[21]
Mendelsohn, L.D. Chemdraw 8 ultra, windows and macintosh versions. J. Chem. Inf. Comput. Sci., 2004, 44(6), 2225-2226.
[http://dx.doi.org/10.1021/ci040123t]
[22]
Froimowitz, M. HyperChem: A software package for computational chemistry and molecular modeling. Biotechniques, 1993, 14(6), 1010-1013.
[PMID: 8333944]
[23]
Stewart, J.J.P. MOPAC: A semiempirical molecular orbital program. J. Comput. Aided Mol. Des., 1990, 4(1), 1-103.
[http://dx.doi.org/10.1007/BF00128336] [PMID: 2197373]
[24]
Wang, Y.; Zhao, C.; Ma, W.; Liu, H.; Wang, T.; Jiang, G. Quantitative structure–activity relationship for prediction of the toxicity of polybrominated diphenyl ether (PBDE) congeners. Chemosphere, 2006, 64(4), 515-524.
[http://dx.doi.org/10.1016/j.chemosphere.2005.11.061] [PMID: 16406101]
[25]
Graybill, F. Ed.; Theory and Application of the Linear Model; Duxbury Press: London., 1976.
[26]
Song, R.; Song, F.; Cui, L.; Si, H.; Zhai, H. Eds.; QSAR study on the IC_(50) of 6-alkenylamides of 4-anilinothieno[2,3-d] pyrimidine as epidermal growth factor receptor inhibitors in lung cancer; , 2015.
[27]
Noble, W.S. What is a support vector machine? Nat. Biotechnol., 2006, 24(12), 1565-1567.
[http://dx.doi.org/10.1038/nbt1206-1565] [PMID: 17160063]
[28]
Pal, M. Random forest classifier for remote sensing classification. Int. J. Remote Sens., 2005, 26(1), 217-222.
[http://dx.doi.org/10.1080/01431160412331269698]
[29]
Si, H.; Lian, N.; Yuan, S.; Fu, A.; Duan, Y.B.; Zhang, K.; Yao, X. Predicting the activity of drugs for a group of imidazopyridine anticoccidial compounds. Eur. J. Med. Chem., 2009, 44(10), 4044-4050.
[http://dx.doi.org/10.1016/j.ejmech.2009.04.039] [PMID: 19482386]
[30]
Zhao, Y; Yang, H; Wu, F; Luo, X; Sun, Q; Feng, W. Exploration of N-arylsulfonyl-indole-2-carboxamide derivatives as novel fructose- 1,6-bisphosphatase inhibitors by molecular simulation. Int J Mol Sci., 2022, 23(18), 10259.
[http://dx.doi.org/10.3390/ijms231810259] [PMID: 36142164]

© 2024 Bentham Science Publishers | Privacy Policy