Due to transition in the journal platform, the previously submitted articles, which are under process can be re-submitted here for quick process, kindly co-operate


Volume: 44 Issue: 1

  • Open Access
  • Original Article

Molecular docking and dynamic studies of Indian blackberry in contrast to X-ray structure of human PPAR gamma

Aghil Soorya Aravindakshan1, Suraj Katole2, Sameer Sharma2, Susha Dinesh2, Manjula Shantaram3, Raghavendra L. S. Hallur4


1Department of Botany, St. Teresa's College, Ernakulam, Kerala, India
2Department of Bioinformatics, BioNome, Hennur Cross Road, Bengaluru, 560 043, Karnataka, India
3A.J. Research Centre, A.J.Institute of Medical Sciences & Research Centre, Kuntikana, Mangalore, 575 004, Karnataka, India
4College of Biosciences and Technology, Pravara Institute of Medical Sciences (Deemed to be University),
Loni, 413736, Rahata Taluk, Ahmednagar District, Maharashtra, India

Corresponding author: Raghavendra L.S. Hallur. Email: [email protected]


Year: 2024, Page: 71-78, Doi: https://doi.org/10.51248/.v44i1.4116

Received: Dec. 6, 2023 Accepted: Feb. 11, 2024 Published: May 1, 2024


Introduction and Aim: This study aims to elucidate the phytopharmacological and pharmacokinetic characteristics of Indian blackberries about human PPAR gamma receptors through in silico analyses. The protein receptor known as human PPAR gamma was retrieved, along with phytochemicals to perform molecular docking techniques to analyze the inhibitory effects of Indian blackberries.
Methods: The human PPAR gamma receptor was obtained from the Protein Data Bank, and a set of phytochemicals was sourced from the IMPPAT database, and subsequently retrieved through the PubChem database. Molecular docking studies were conducted to assess the inhibitory interactions between Indian blackberry constituents and human PPAR gamma.
Results: Among the various ligands investigated, ligand 12304985 exhibited the highest binding affinity towards the human PPAR gamma receptor. Subsequent analyses involved the assessment of ADMET profiling, secondary structure analysis, and Ramachandran plot analysis at the molecular level for human PPAR gamma.
Conclusion: Our findings suggest that Indian blackberry, particularly ligand 12304985, exhibits promising inhibitory interactions with human PPAR gamma receptors. This in silico investigation provides valuable insights into the potential phytopharmacological and pharmacokinetic properties of Indian blackberries, paving the way for further in vitro and in vivo studies to validate these findings.

Keywords: Indian blackberry; PPAR gamma; MD simulation; ADMET.


1. Gregory, G.A., Robinson, T.I.G., Linklater, S.E., Wang, F., Colagiuri, S., de Beaufort, C., et al., Global incidence, prevalence, and mortality of type 1 diabetes in 2021 with projection to 2040: a modelling study. Lancet Diabetes Endocrinol. 2022;10(10):741-760.
2. Harding, J.L., Wander, P.L., Zhang, X., Li, X., Karuranga, S., Chen, H., et al., The incidence of adult-onset type 1 diabetes: A systematic review from 32 countries and regions. Diabetes Care. 2022;45(4):994-1006.
3. Chhabra. M., Sharma, S. Potential role of peroxisome proliferator activated receptor gamma analogues in regulation of endothelial progenitor cells in diabetes mellitus: An overview. Diabetes Metab Syndr. 2019;13(2):1123-1129.
4. Soni, N.O., Pawar, S.V., Kale, S., Mane, U.A., Bhosale, P.U., Phandhare, K., et al., Peroxisome proliferator-activated receptors and thiazolidinediones in diabetic nephropathy. Int J Basic Clin Pharmacol. 2019;8(10):2344.
5. Zhang, K., Yuan, Q., Xie, J., Yuan, L., Wang, Y. PPAR-γ activation increases insulin secretion independent of CASK in INS-1 cells. Acta Biochim Biophys Sin (Shanghai), 2019; 51(7):715-722.
6. Santini, E., Fallahi, P., Ferrari, S.M., Masoni, A., Antonelli, A., Ferrannini, E. Effect of PPAR-γ activation and inhibition on glucose-stimulated insulin release in INS-1e cells. Diabetes. 2004;53(suppl_3):S79-S83.
7. Evans-Molina, C. Peroxisome proliferator-activated receptor γ activation restores islet function in diabetic mice through reduction of endoplasmic reticulum stress and maintenance of euchromatin structure. Molecular and Cellular Biology. 2009; 29:2053-2067.
8. Yang, H., Tian, T., Wu, D., Guo, D., Lu, J. Prevention and treatment effects of edible berries for three deadly diseases: cardiovascular disease, cancer and diabetes. Crit Rev Food Sci Nutr. 2019;59(12):1903-1912.
9. Jayasurya, Swathy, Susha, Sharma, S. Molecular docking and investigation of Boswellia serrata phytocompounds as cancer therapeutics to target growth factor receptors: An in-silico approach. Int J Appl Pharm. 2023;15(4):173-183.
10. Galgale, S., Zainab, R., Kumar, A. P., Nithya, Susha, Sharma, S. Molecular docking and dynamic simulation-based screening identifies inhibitors of targeted SARS-CoV-2 3CLpro and human ACE2. Int J Appl Pharm. 2023;15(6):297-308.
11. DiMeglio, L.A., Evans-Molina, C., Oram, R.A. Type 1 diabetes. Lancet. 2018;391(10138):2449-2462.
12. Calvano, A., Izuora, K., Oh, E.C., Ebersole, J.L., Lyons, T.J., Basu, A. Dietary berries, insulin resistance and type 2 diabetes: An overview of human feeding trials. Food Funct. 2019; 10(10):6227-6243.
13. Aqil, F. Antioxidant and antiproliferative activities of anthocyanin/ellagitannin-enriched extracts from Syzygium cumini L.(Jamun, the Indian Blackberry). Nutrition and Cancer. 2012;64(3):428-438.
14. Sarkar, D., Orwat, J., Hurburt, T., Woods, F., Pitts, J.A., Shetty, K. Evaluation of phenolic bioactive-linked functionality of blackberry cultivars targeting dietary management of early stages type-2 diabetes using in vitro models. Sci Hortic (Amsterdam). 2016;212:193-202.
15. Jimenez-Garcia, S.N., Vazquez-Cruz, M.A., Garcia-Mier, L., Contreras-Medina, L.M., Guevara-González, R.G., Garcia-Trejo, J.F., et al., Phytochemical and pharmacological properties of secondary metabolites in berries. In: Therapeutic Foods. Elsevier; 2018. p. 397-427.
16. Azofeifa, G., Quesada, S., Navarro, L., Hidalgo, O., Portet, K., Pérez, A.M.,et al., Hypoglycaemic, hypolipidaemic and antioxidant effects of blackberry beverage consumption in streptozotocin-induced diabetic rats. J Funct Foods. 2016;26: 330-337.
17. Loza-Rodríguez, H., Estrada-Soto, S., Alarcón-Aguilar, F.J., Huang, F., Aquino-Jarquín, G., Fortis-Barrera, Á., et al., Oleanolic acid induces a dual agonist action on PPARγ/α and GLUT4 translocation: A pentacyclic triterpene for dyslipidemia and type 2 diabetes. Eur J Pharmacol. 2020;883: 173252.
18. Sung, H.Y., Kang, S.W., Kim, J.L., Li, J., Lee, E.S., Gong, J.H., et al., Oleanolic acid reduces markers of differentiation in 3T3-L1 adipocytes. Nutr Res. 2010;30(12):831-839.
19. Marcelino, G., Machate, D.J., Freitas, K., de C, Hiane, P.A., Maldonade, I.R., Pott, A., et al., β-carotene: Preventive role for type 2 diabetes mellitus and obesity: A review. Molecules. 2020;25(24):5803.
20. Gharib, A., Faezizadeh, Z., Godarzee, M. Treatment of diabetes in the mouse model by delphinidin and cyanidin hydrochloride in free and liposomal forms. Planta Med. 2013; 79(17):1599-1604.
21. Vinayagam, R., Xu, B. Antidiabetic properties of dietary flavonoids: a cellular mechanism review. Nutr Metab (Lond). 2015;12(1):60.

Cite this article

Aghil Soorya Aravindakshan, Suraj Katole, Sameer Sharma, Susha Dinesh, Manjula Shantaram, Raghavendra L. S. Hallur. Molecular docking and dynamic studies of Indian blackberry in contrast to X-ray structure of human PPAR gamma. Biomedicine: 2024; 44(1): 71-78