Molecular structure similarity analysis using Tanimoto coefficient and its correlation analysis with Maltase-glucoamylase inhibitory activity of Nigella sativa’s compounds
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Abstract
Nigella sativa is one of the medicinal plants that are efficacious for treating diabetes mellitus. Diabetes mellitus is a chronic metabolic disorder characterized by hyperglycemia due to damage of insulin action, insulin production, and/or both. In this study, the molecular structure similarity analysis of the compounds in Nigella sativa to acarbose and the correlation analysis of the similarity with its activity as antidiabetic with the mechanism of maltase glucoamylase (MGAM) inhibition was carried out. Similarity analysis has been done used Tanimoto coefficient. The prediction of MGAM inhibitory activity has been done using molecular docking with molegro virtual docker. The Kaempferol 3-glucosyl-(1-2)-galactosyl-(1-2)-glucoside; (S)-2,3-Epoxysqualene; Quercetin 3-glucosyl-(1-2)-galactosyl-(1-2)-glucoside; Oleic Acid has activity as an inhibitor of MGAM with rerank score -107.8770, -102.1760, -95.7338, -92.4246 respectively and these has Tanimoto score 0.426, 0.319, 0.413, 0.357 respectively. The correlation analysis obtained that there is a significant relationship between the Tanimoto Coefficient and Rerank Score with the opposite relationship because the correlation value is negative. Greater the degree of molecular structure similarity of Nigella sativa’s compounds to acarbose more likely has the similar biological activity as MGAM inhibitory
References
WHO, “Diabetes.” [Online]. Available: https://www.who.int/health-topics/diabetes?gad_source=1&gclid=EAIaIQobChMI36un4KmeiAMVkqJmAh1jkRPREAAYASAAEgJCHvD_BwE#tab=tab_1
D. O. F. Diabetes, “Diagnosis and classification of diabetes mellitus,” Diabetes Care, vol. 32, no. SUPPL. 1, 2009, doi: 10.2337/dc09-S062.
A. Hamdan, R. H. Idrus, and M. H. Mokhtar, “Effects of Nigella sativa on type-2 diabetes mellitus: A systematic review,” Int. J. Environ. Res. Public Health, vol. 16, no. 24, 2019, doi: 10.3390/ijerph16244911.
A. Benhaddou-Andaloussi et al., “Antidiabetic activity of Nigella sativa seed extract in cultured pancreatic β-cells, skeletal muscle cells, and adipocytes,” Pharm. Biol., vol. 46, no. 1–2, pp. 96–104, 2008, doi: 10.1080/13880200701734810.
P. N. R. Rachman, Akrom, and E. Darmawan, “The efficacy of black cumin seed (Nigella sativa) oil and hypoglycemic drug combination to reduce HbA1c level in patients with metabolic syndrome risk,” IOP Conf. Ser. Mater. Sci. Eng., vol. 259, no. 1, 2017, doi: 10.1088/1757-899X/259/1/012018.
C. J. Ozougwu and E. J. Eyo, “Studies on the anti-diabetic activity of allium sativum (garlic) aqueous extracts on alloxan-induced diabetic albino rat,” Pharmacologyonline, vol. 2, no. October, pp. 1079–1088, 2010.
N. Dwi Apriliani and F. Amelia Saputri, “REVIEW : Potensi Penghambatan Enzim Α-Glukosidase Pada Tanaman Obat Tradisional Indonesia,” Farmaka, vol. 16, no. 1, pp. 169–177, 2018.
Susianti, “The Effectiveness of Consuming Bitter Melon Juice on Reducing Blood Sugar Levels In People with Type 2 Diabetes Mellitus,” Jounal Public Heal., vol. 6, no. 2, pp. 93–98, 2023.
A. Yuniarto and N. Selifiana, “Aktivitas Inhibisi Enzim Alfa-glukosidase dari Ekstrak Rimpang Bangle (Zingiber cassumunar Roxb.) secara In vitro,” MPI (Media Pharm. Indones., vol. 2, no. 1, pp. 22–25, 2018, doi: 10.24123/mpi.v2i1.1299.
S. Pujiyanto, R. S. Ferniah, and S. S, “Produksi Dan Ekstraksi Inhibitor Alfa Glukosidase Dari Isolat Aktinomiset Jp-3,” Bioma Berk. Ilm. Biol., vol. 17, no. 2, p. 123, 2016, doi: 10.14710/bioma.17.2.123-129.
H. Fallah Huseini, R. Mohtashami, Z. Sadeqi, Y. Saidi, and A. Fallah Huseini, “A review on pharmacological effects of Nigella sativa L. seeds,” J. Med. Plants, vol. 10, no. 38, pp. 1–18, 2011.
A. S. Jamil, “Pemanfataan Biji Nigella sativa Dalam Terapi Penyembuhan Kanker dan Gangguan Metabolisme,” Farmasains J. Farm. dan Ilmu Kesehat., vol. 1, no. 1, 2010, doi: 10.22219/far.v1i1.422.
K. S. Zaher, W. Ahmed, and S. N. Zerizer, “Observations on the Biological Effects of Black Cumin Seed (Nigella sativa) and Green Tea (Camellia sinensis),” Glob. Vet., vol. 2, no. 4, pp. 198–204, 2008.
R. Bakri, H. Wijayanto, and F. M. Afendi, “Statistical study of chemical structure similarity based on binary data,” Int. J. Comput. Optim., vol. 2, no. 2, pp. 105–112, 2015, doi: 10.12988/ijco.2015.5826.
N. Hilal A. Syahrir, “Uji permutasi efek sinergis bahan aktif tanaman obat berbasiskan jejaring dengan protein target nur hilal a. syahrir,” Inst. Pertan. Bogor, 2015.
C. FADILLAH, “Prediksi efek sinergis tiga senyawa aktif tanaman obat untuk penyakit diabetes mellitus dengan menggunakan metode nims cici fadillah,” [skripsi]. Bogor Inst. Pertan. Bogor., 2018.
J. Klekota and F. P. Roth, “Chemical substructures that enrich for biological activity,” Bioinformatics, vol. 24, no. 21, pp. 2518–2525, 2008, doi: 10.1093/bioinformatics/btn479.
G. M. M. Mark A. Johnson, Concepts and Applications of Molecular Similarity. Wiley, 1991.
L. Ren et al., “Structural insight into substrate specificity of human intestinal maltase-glucoamylase,” Protein Cell, vol. 2, no. 10, pp. 827–836, 2011, doi: 10.1007/s13238-011-1105-3.
“http://www.knapsackfamily.com/knapsack_core/top.php.” 2020.
“https://go.drugbank.com/drugs/DB00284.” 2020.
“https://www.rcsb.org/structure/3TOP,” 2020.
J. Kirchmair, P. Markt, S. Distinto, G. Wolber, and T. Langer, “Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection--what can we learn from earlier mistakes?,” J. Comput. Aided. Mol. Des., vol. 22, no. 3–4, pp. 213–228, 2008, doi: 10.1007/s10822-007-9163-6.
