IMPACT OF TYPE 2 DIABETES-ASSOCIATED DIPEPTIDYL PEPTIDASE-4 (DPP-4) MUTATIONS ON LIGAND BINDING AND ENZYME ACTIVITY MODULATED BY NATURAL COMPOUNDS

Yıl 2025, Cilt: 11 Sayı: 2, 169 - 178, 31.12.2025

Gizem Köprülülü Küçük

https://doi.org/10.22531/muglajsci.1783212

Öz

Type 2 diabetes is a chronic metabolic disorder marked by insulin resistance and β-cell dysfunction. DPP-4 inhibitors help regulate glucose by prolonging the effects of GLP-1 and GIP. This study examined how three mutations in the DPP-4 enzyme, V266I, G189E, and S437T, affect binding affinity with natural ligands (caffeic acid, proanthocyanidin, and palmatine) using in silico methods. The amino acid sequence of DPP-4 was obtained from UniProt, and mutation effects were assessed via HOPE. 3D models were generated through Swiss-Model and validated with SAVES v6.1, showing high structural accuracy (e.g., ERRAT: 97.3%). Molecular docking with AutoDock Vina showed strong binding of palmatine and Caffeic Acid Phenethyl Ester (CAPE) to wild-type DPP-4 (–7.6 kcal/mol). However, all three mutations led to reduced binding affinity, with scores ranging from –5.3 to –6.9 kcal/mol. The G189E mutation, in particular, caused a notable drop in binding energy due to the disruption of electrostatic and hydrophobic interactions. These structural changes suggest that such mutations may decrease the efficacy of DPP-4 inhibitors. Therefore, they represent critical factors to consider in drug design targeting this enzyme.

Anahtar Kelimeler

Type 2 diabetes , DPP-4 , Point mutation , Molecular docking , Natural compounds

TİP 2 DİYABET İLE İLİŞKİLİ DİPEPTİDİL PEPTİDAZ-4 (DPP-4) MUTASYONLARININ DOĞAL BILEŞİKLER TARAFINDAN DÜZENLENEN LİGAND BAĞLANMASI VE ENZİM AKTİVITESİ ÜZERİNDEKİ ETKİSİ

Öz

Tip 2 diyabet, insülin direnci ve β-hücre disfonksiyonu ile karakterize edilen kronik bir metabolik bozukluktur. DPP-4 inhibitörleri, GLP-1 ve GIP’in etkilerini uzatarak glukozu düzenlemeye yardımcı olur. Bu çalışma, DPP-4 enzimindeki üç mutasyonun (V266I, G189E ve S437T) doğal ligandlarla (kafeik asit, proantosiyanidin ve palmatin) bağlanma afinitesini in silico yöntemlerle nasıl etkilediğini incelemiştir. DPP-4’ün amino asit dizisi UniProt’tan elde edilmiş, mutasyon etkileri HOPE aracılığıyla değerlendirilmiştir. 3D modeller Swiss-Model kullanılarak oluşturulmuş ve SAVES v6.1 ile doğrulanmış, yüksek yapısal doğruluk göstermiştir (örneğin, ERRAT: %97,3). AutoDock Vina ile yapılan moleküler yerleştirme çalışmaları, palmatin ve CAPE’nin yabanıl tip DPP-4’e güçlü bağlandığını göstermiştir (–7,6 kcal/mol). Ancak, üç mutasyonun tamamı bağlanma afinitesinde azalmaya yol açmıştır; skorlar –5,3 ile –6,9 kcal/mol arasında değişmiştir. Özellikle G189E mutasyonu, elektrostatik ve hidrofobik etkileşimlerin bozulması nedeniyle bağlanma enerjisinde belirgin bir düşüşe sebep olmuştur. Bu yapısal değişiklikler, bu tür mutasyonların DPP-4 inhibitörlerinin etkinliğini azaltabileceğini göstermektedir. Bu nedenle, bu mutasyonlar bu enzimi hedefleyen ilaç tasarımında dikkate alınması gereken kritik faktörleri temsil etmektedir.

Anahtar Kelimeler

Tip 2 diyabet , DPP-4 , Nokta mutasyonu , Moleküler yerleştirme , Doğal bileşikler

Kaynakça

• Hossain, M. J., Al-Mamun, M., Islam, M. R., "Diabetes mellitus, the fastest growing global public health concern: Early detection should be focused", Health Science Reports, 7(3), 22, 2004.
• Altuntaş, Y., "Approach Toward Diabetes Treatment in the Elderly", Şişli Etfal Hastanesi Tıp Bülteni, 53(2), 96, 2019.
• Nauck, M. A., Quast, D. R., Wefers, J., Pfeiffer, A. F. H., "The evolving story of incretins (GIP and GLP-1) in metabolic and cardiovascular disease: A pathophysiological update", Diabetes Obesity Metabolism, 2021.
• Ezcurra, M., Reimann, F., Gribble, F. M., Emery, E., "Molecular mechanisms of incretin hormone secretion", Current Opinion in Pharmacology (COPHAR), 2013.
• Nauck, M. A., Vardarli, I., Deacon, C. F., Holst, J. J., Meier, J. J., "Secretion of glucagon-like peptide-1 (GLP-1) in type 2 diabetes: What is up, what is down?", Diabetologia, 54, 2011.
• Singh, A. K., Yadav, D., Sharma, N., Jin, J. O., "Dipeptidyl peptidase (Dpp)-iv inhibitors with antioxidant potential isolated from natural sources: A novel approach for the management of diabetes", Pharmaceuticals, 14, 586, 2021.
• Godinho, R., Mega, C., Teixeira-de-Lemos, E., Carvalho, E., Teixeira, F., Fernandes, R., Reis, F., "The Place of Dipeptidyl Peptidase-4 Inhibitors in Type 2 Diabetes Therapeutics: A ‘Me Too’ or ‘the Special One’ Antidiabetic Class?", Journal of Diabetes Research, 2015.
• Xu, W., Luo, Q., Wen, X., Xiao, M., Mei, Q., "Antioxidant and anti-diabetic effects of caffeic acid in a rat model of diabetes", Tropical Journal of Pharmaceutical Research (TJPR), 19(6), 1227–1232, 2020.
• Muhammad Abdul Kadar, N. N., Ahmad, F., Teoh, S. L., Yahaya, M. F., "Caffeic Acid on Metabolic Syndrome: A Review", Molecules, 26(9), 2021.
• Unusan, N., "Proanthocyanidins in grape seeds: An updated review of their health benefits and potential uses in the food industry", Journal of Functional Foods (JFF), 67, 2020.
• Domínguez Avila, J. A., Rodrigo García, J., González Aguilar, G. A., de la Rosa, L. A., "The Antidiabetic Mechanisms of Polyphenols Related to Increased Glucagon-Like Peptide-1 (GLP1) and Insulin Signaling", Molecules, 22, 903, 2017.
• Ekeuku, S. O., Pang, K. L., Chin, K. Y., "Palmatine as an Agent Against Metabolic Syndrome and Its Related Complications: A Review", Drug Design, Development and Therapy, 14, 4963, 2020.
• Grabarska, A., Wróblewska-Łuczka, P., Kukula-Koch, W., Łuszczki, J. J., Kalpoutzakis, E., Adamczuk, G., Skaltsounis, A. L., Stepulak, A., "Palmatine, a Bioactive Protoberberine Alkaloid Isolated from Berberis cretica, Inhibits the Growth of Human Estrogen Receptor-Positive Breast Cancer Cells and Acts Synergistically and Additively with Doxorubicin", Molecules, 26, 6253, 2021.
• UniProt: the Universal Protein Knowledgebase, Available: https://www.uniprot.org/, Accessed: Feb. 01, 2025.
• Venselaar, H., Te Beek, T. A., Kuipers, R. K., Hekkelman, M. L., Vriend, G., "Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist-friendly interfaces", BMC Bioinformatics, 8, 548, 2010.
• Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T., "SWISS-MODEL: homology modelling of protein structures and complexes", Nucleic Acids Research, 46, 296, 2018.
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., Ferrin, T. E., "UCSF Chimera--a visualization system for exploratory research and analysis", Journal of Computational Chemistry, 25, 1605, 2004.
• Structural Analysis and Verification Server, "ERRAT", Available: https://saves.mbi.ucla.edu/ERRAT, Accessed: Feb. 12, 2025.
• Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., Bolton, E. E., "PubChem 2025 update", Nucleic Acids Research, 53, 1516, 2025.
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., Olson, A. J., "AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility", Journal of Computational Chemistry, 16, 2785, 2009.
• Adasme, M. F., et al., "PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA", Nucleic Acids Research, 49, 530, 2021.
• Lee, H. K., Kim, M. K., Kim, H. D., Kim, H. J., Kim, J. W., Lee, J. O., Kim, E. E. K., "Unique binding mode of Evogliptin with human dipeptidyl peptidase IV", Biochemical and Biophysical Research Communications, 494, 452–459, 2017.
• Istyastono, E. P., Yuniarti, N., Prasasty, V. D., Mungkasi, S., Waskitha, S. S. W., Yanuar, M. R. S., Riswanto, F. D. O., "Caffeic Acid in Spent Coffee Grounds as a Dual Inhibitor for MMP-9 and DPP-4 Enzymes", Molecules, 28, 7182, 2023.
• Zhao, Z., Ma, R., Ma, Y., Zhao, L., Wang, L., Fang, Y., Zhang, Y., Wu, X., Wang, X., "Discovery of Nine Dipeptidyl Peptidase-4 Inhibitors from Coptis chinensis Using Virtual Screening, Bioactivity Evaluation, and Binding Studies", Molecules, 29, 2304, 2024.
• National Center for Biotechnology Information (NCBI) dbSNP entry: rs56179129 (DPP4: c.796G>A, p.Val266Ile), Available: https://www.ncbi.nlm.nih.gov/snp/rs56179129, Accessed: Nov.11, 2025.
• Bouchard, L., Faucher, G., Tchernof, A., Deshaies, Y., Marceau, S., Lescelleur, O., Biron, S., & Vohl, M.C., “Comprehensive genetic analysis of the dipeptidyl peptidase-4 gene and cardiovascular disease risk factors in obese individuals”, Acta Diabetology, 46, 13, 2009.
• National Center for Biotechnology Information (NCBI) dbSNP entry: rs1129599 (DPP4: c.1310G>C, p.Ser437Thr), Available: https://www.ncbi.nlm.nih.gov/snp/rs1129599, Accessed: Nov. 11, 2025.
• Chen, S., Francioli, L. C., Goodrich, J. K., Collins, R. L., Kanai, M., Wang, Q., Alföldi, J., Watts, N. A., Vittal, C., Gauthier, L. D., Poterba, T., Wilson, M. W., Tarasova, Y., Phu, W., Grant, R., Yohannes, M. T., Koenig, Z., Farjoun, Y., Banks, E., Donnelly, S., Gabriel, S., Gupta, N., Ferriera, S., Tolonen, C., Novod, S., Bergelson, L., Roazen, D., Ruano-Rubio, V., Covarrubias, M., Llanwarne, C., Petrillo, N., Wade, G., Jeandet, T., Munshi, R., Tibbetts, K., Genome Aggregation Database (gnomAD) Consortium, O’Donnell-Luria, A., Solomonson, M., Seed, C., Martin, A. R., Talkowski, M. E., Rehm, H. L., Daly, M. J., Tiao, G., Neale, B. M.†, MacArthur, D. G.† & Karczewski, K. J. A, “genomic mutational constraint map using variation in 76,156 human genomes”, Nature, 625, 92, 2024.
• National Center for Biotechnology Information (NCBI), Available: https://www.ncbi.nlm.nih.gov/, Accessed: Nov. 11, 2025.
• Landrum MJ, Chitipiralla S, Kaur K, Brown G, Chen C, Hart J, Hoffman D, Jang W, Liu C, Maddipatla Z, Maiti R, Mitchell J, Rezaie T, Riley G, Song G, Yang J, Ziyabari L, Russette A, Kattman BL. “ClinVar: updates to support classifications of both germline and somatic variants”, Nucleic Acids Research, Nov 23, 2024.
• Ensembl, Available: http://www.ensembl.org/, Accessed date: Nov. 11, 2025.