GC–MS analysis, molecular docking, and pharmacokinetic studies on Dalbergia sissoo barks extracts for compounds with anti-diabetic potential

Li, W., Yuan, G., Pan, Y., Wang, C. & Chen, H. Network pharmacology studies on the bioactive compounds and action mechanisms of natural products for the treatment of diabetes mellitus: A review. Front. Pharmacol. 8, 74 (2017).PubMed 
PubMed Central 

Google Scholar 
Ali, J. et al. Overall clinical features of type 2 diabetes mellitus with respect to gender. Cureus https://doi.org/10.7759/cureus.35771 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Artasensi, A., Pedretti, A., Vistoli, G. & Fumagalli, L. Type 2 diabetes mellitus: A review of multi-target drugs. Molecules 25, 1987. https://doi.org/10.3390/molecules25081987 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cui, J., Liu, Y., Li, Y., Xu, F. & Liu, Y. Type 2 Diabetes and myocardial infarction: Recent clinical evidence and perspective. Front. Cardiovasc. Med. 8, 644189 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Hung, H.-Y., Qian, K., Morris-Natschke, S. L., Hsu, C.-S. & Lee, K.-H. Recent discovery of plant-derived anti-diabetic natural products. Nat. Prod. Rep. 29, 580–606. https://doi.org/10.1039/C2NP00074A (2012).Article 
CAS 
PubMed 

Google Scholar 
Nawaz, M. et al. Structural elucidation, molecular docking, α-amylase and α-glucosidase inhibition studies of 5-amino-nicotinic acid derivatives. BMC Chem. 14, 43. https://doi.org/10.1186/s13065-020-00695-1 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Adnan, M. et al. Network pharmacology study to reveal the potentiality of a methanol extract of Caesalpinia sappan L. wood against type-2 diabetes mellitus. Life 12, 277. https://doi.org/10.3390/life12020277 (2022).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Alam, S. et al. Antidiabetic phytochemicals from medicinal plants: Prospective candidates for new drug discovery and development. Front. Endocrinol. 13, 800714. https://doi.org/10.3389/fendo.2022.800714 (2022).Article 

Google Scholar 
Singh, S., Bansal, A., Singh, V., Chopra, T. & Poddar, J. Flavonoids, alkaloids and terpenoids: A new hope for the treatment of diabetes mellitus. J. Diabetes Metab. Disord. 21, 941–950. https://doi.org/10.1007/s40200-021-00943-8 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Asafo-Agyei, T., Appau, Y., Barimah, K. B. & Asase, A. Medicinal plants used for management of diabetes and hypertension in Ghana. Heliyon 9, e22977. https://doi.org/10.1016/j.heliyon.2023.e22977 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bailey, C. J. Metformin: Historical overview. Diabetologia 60, 1566–1576. https://doi.org/10.1007/s00125-017-4318-z (2017).Article 
CAS 
PubMed 

Google Scholar 
Al-Snaf, P. D. A. E. Chemical constituents and pharmacological effects of Dalbergia sissoo—A review. IOSR J. Pharm. 07, 59–71. https://doi.org/10.9790/3013-0702015971 (2017).Article 

Google Scholar 
Mannan, Md. A., Khatun, A. & Khan, Md. F. H. Antinociceptive effect of methanol extract of Dalbergia sissoo leaves in mice. BMC Complement. Altern. Med. 17, 72. https://doi.org/10.1186/s12906-017-1565-y (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Thakkar, A. B., RamalingamB, S., Thakkar, V. R. & Thakor, P. Hydromethanolic leaves extract of Dalbergia sissoo Roxb. ex DC. induces apoptosis in lung adenocarcinoma cells. Process Biochem. 134, 250–261. https://doi.org/10.1016/j.procbio.2023.10.006 (2023).Article 
CAS 

Google Scholar 
Naik, H. N. et al. LC–MS profiling, in vitro and in silico C-ABL kinase inhibitory approach to identify potential anticancer agents from Dalbergia sissoo leaves. Sci. Rep. 14, 73. https://doi.org/10.1038/s41598-023-49995-1 (2024).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
El-Azzazy, E. A., Ibrahim, M. T. & Reda, M. A. LC/MS profile and biological evaluation of Dalbergia sissoo growing in Egypt desert. Azhar Int. J. Pharm. Med. Sci. https://doi.org/10.21608/aijpms.2023.190847.1190 (2024).Article 

Google Scholar 
Dixit, S. Investigation of immunomodulation activity in the leaves of Dalbergia dissoo. Glob. J. Pharm. Pharm. Sci. https://doi.org/10.19080/GJPPS.2018.05.555655 (2018).Article 

Google Scholar 
Interaction of Selected Terpenoids From Dalbergia sissoo With Catalytic Domain of Matrix Metalloproteinase-1: An In Silico Assessment of Their Anti-wrinkling Potential – Shagufta Yasmeen, Promila Gupta. https://doi.org/10.1177/1177932219896538 (2019). Accessed 24 Sep 2024Devi, P., Singh, S. & Promila. Isolation and characterization of chemical constituents from Dalbergia sissoo Roxb. Stem. Int J Chem Stud. (2017).Saini, S., & Sharma, S. Antidiabetic activity of different extracts of Dalbergia Sissoo Dc. Stem Bark On Streptozotocin-Nicotinamide Induced Type 2 Diabetic Rats. 5.Pund, K. V., Vyawahare, N. S., Gadakh, R. T. & Murkute, V. K. Antidiabetic evaluation of Dalbergia sissoo against alloxan induced diabetes mellitus in wistar albino rats (2012).Savithramma, N., Rao, M. L. & Suhrulatha, D. Screening of medicinal plants for secondary metabolites (2011).Orole, O. O. GC-MS evaluation phytochemical and antinutritional screening of Ganoderma lucidum. J. Adv. Biol. Biotechnol. https://doi.org/10.9734/JABB/2016/24261 (2016).Article 

Google Scholar 
Gul, R., Jan, S. U., Faridullah, S., Sherani, S. & Jahan, N. Preliminary phytochemical screening, quantitative analysis of alkaloids, and antioxidant activity of crude plant extracts from Ephedra intermedia Indigenous to Balochistan. Sci. World J. 2017, e5873648. https://doi.org/10.1155/2017/5873648 (2017).Article 
CAS 

Google Scholar 
Kancherla, N., Dhakshinamoothi, A., Chitra, K. & Komaram, R. B. Preliminary analysis of phytoconstituents and evaluation of anthelminthic property of Cayratia auriculata (In Vitro). Mædica 14, 350–356. https://doi.org/10.26574/maedica.2019.14.4.350 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Singleton, V. L. & Rossi, J. A. Colorimetry of total phenolics with phosphomolybdic-phosphotungstic acid reagents. Am. J. Enol. Vitic. 16, 144–158. https://doi.org/10.5344/ajev.1965.16.3.144 (1965).Article 
CAS 

Google Scholar 
Woisky, R. G. & Salatino, A. Analysis of propolis: Some parameters and procedures for chemical quality control. J. Apic. Res. 37, 99–105. https://doi.org/10.1080/00218839.1998.11100961 (1998).Article 
CAS 

Google Scholar 
Mahboubi, M., Kazempour, N. & Boland Nazar, A. R. Total phenolic, total flavonoids, antioxidant and antimicrobial activities of scrophularia striata boiss extracts. Jundishapur J. Nat. Pharm. Prod. 8, 15–19 (2013).Article 
PubMed 
PubMed Central 

Google Scholar 
Wongsa, P., Phatikulrungsun, P. & Prathumthong, S. FT-IR characteristics, phenolic profiles and inhibitory potential against digestive enzymes of 25 herbal infusions. Sci. Rep. 12, 6631. https://doi.org/10.1038/s41598-022-10669-z (2022).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chaturvedi, S. & Gupta, P. Functional components in extracts of Beta vulgaris (Chukandar) parts for antioxidant effect and antiobesity potential with lipase inhibition. Food Biosci. 41, 100983. https://doi.org/10.1016/j.fbio.2021.100983 (2021).Article 
CAS 

Google Scholar 
SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep. https://www.nature.com/articles/srep42717. Accessed 11 Mar 2024Banerjee, P., Eckert, A. O., Schrey, A. K. & Preissner, R. ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Res. 46, W257–W263. https://doi.org/10.1093/nar/gky318 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Burley, S. K. et al. RCSB Protein Data Bank: Powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Nucleic Acids Res. 49, D437–D451. https://doi.org/10.1093/nar/gkaa1038 (2021).Article 
CAS 
PubMed 

Google Scholar 
Bolton, E. E., Wang, Y., Thiessen, P. A. & Bryant, S. H. PubChem: Integrated platform of small molecules and biological activities. Ann. Rep. Comput. Chem. 4, 217–241. https://doi.org/10.1016/S1574-1400(08)00012-1 (2008).Article 
CAS 

Google Scholar 
O’Boyle, N. M. et al. Open Babel: An open chemical toolbox. J. Cheminform. 3, 33. https://doi.org/10.1186/1758-2946-3-33 (2011).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Trott, O. & Olson, A. J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31, 455–461. https://doi.org/10.1002/jcc.21334 (2010).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1, 19–25. https://doi.org/10.1016/j.softx.2015.06.001 (2015).Article 
ADS 

Google Scholar 
Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B. & Lindahl, E. Implementation of the CHARMM Force Field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models. J. Chem. Theory Comput. 6, 459–466. https://doi.org/10.1021/ct900549r (2010).Article 
CAS 
PubMed 

Google Scholar 
Zoete, V., Cuendet, M. A., Grosdidier, A. & Michielin, O. SwissParam: A fast force field generation tool for small organic molecules. J. Comput. Chem. 32, 2359–2368. https://doi.org/10.1002/jcc.21816 (2011).Article 
CAS 
PubMed 

Google Scholar 
Humphrey, W., Dalke, A. & Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graph. 14, 33–38. https://doi.org/10.1016/0263-7855(96)00018-5 (1996).Article 
CAS 
PubMed 

Google Scholar 
Adinortey, C. A. et al. Molecular structure-based screening of the constituents of Calotropis procera identifies potential inhibitors of diabetes mellitus target alpha glucosidase. Curr. Issues Mol. Biol. 44, 963–987. https://doi.org/10.3390/cimb44020064 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kong, M. et al. Anti-inflammatory phytochemicals for the treatment of diabetes and its complications: Lessons learned and future promise. Biomed. Pharmacother. 133, 110975. https://doi.org/10.1016/j.biopha.2020.110975 (2021).Article 
CAS 
PubMed 

Google Scholar 
Saleem, S., Muhammad, G., Hussain, M. A., Altaf, M. & Bukhari, S. N. A. Withania somnifera L.: Insights into the phytochemical profile, therapeutic potential, clinical trials, and future prospective. Iran J. Basic Med. Sci. 23, 1501–1526. https://doi.org/10.22038/IJBMS.2020.44254.10378 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Martín, M. Á. & Ramos, S. Dietary flavonoids and insulin signaling in diabetes and obesity. Cells 10, 1474. https://doi.org/10.3390/cells10061474 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Putta, S. et al. Therapeutic potentials of triterpenes in diabetes and its associated complications. Curr. Top Med. Chem. 16, 2532–2542. https://doi.org/10.2174/1568026616666160414123343 (2016).Article 
CAS 
PubMed 

Google Scholar 
Sousa, L. R. et al. Use of monoterpenes as potential therapeutics in diabetes mellitus: A prospective review. Adv. Pharmacol. Pharm. Sci. 2023, e1512974. https://doi.org/10.1155/2023/1512974 (2023).Article 
CAS 

Google Scholar 
Deka, H., Choudhury, A. & Dey, B. K. An overview on plant derived phenolic compounds and their role in treatment and management of diabetes. J. Pharmacopuncture 25, 199–208. https://doi.org/10.3831/KPI.2022.25.3.199 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Allagui, I. et al. Phytochemical screening, antioxidant properties, anti-apoptotic effects and molecular docking study of Tunisian cleome (Cleome arabica L.) fruits extract under optimized extraction conditions. Int. J. Food Prop. 25, 2107–2120. https://doi.org/10.1080/10942912.2022.2125009 (2022).Article 
CAS 

Google Scholar 
Sabandar, C. W., Jalil, J., Ahmat, N. & Aladdin, N.-A. Medicinal uses, chemistry and pharmacology of Dillenia species (Dilleniaceae). Phytochemistry 134, 6–25. https://doi.org/10.1016/j.phytochem.2016.11.010 (2017).Article 
CAS 
PubMed 

Google Scholar 
Rohman, A., Setyaningrum, D. L. & Riyanto, S. FTIR spectroscopy combined with partial least square for analysis of red fruit oil in ternary mixture system. Int. J. Spectrosc. 2014, e785914. https://doi.org/10.1155/2014/785914 (2014).Article 
CAS 

Google Scholar 
Alrubaie, L. A., Muhasin, R. J. & Mousa, M. N. Synthesis, characterization and evaluation of antiinflammatory properties of novel α, β-unsaturated ketones. Trop J. Pharm. Res. 19, 147–154. https://doi.org/10.4314/tjpr.v19i1.22 (2020).Article 
CAS 

Google Scholar 
Ralte, L., Khiangte, L., Thangjam, N. M., Kumar, A. & Singh, Y. T. GC–MS and molecular docking analyses of phytochemicals from the underutilized plant, Parkia timoriana revealed candidate anti-cancerous and anti-inflammatory agents. Sci. Rep. 12, 3395. https://doi.org/10.1038/s41598-022-07320-2 (2022).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
de Almeida, P. D. O. et al. Anti-inflammatory activity of triterpenes isolated from protium paniculatum oil-resins. Evid. Based Complement. Altern. Med. https://doi.org/10.1155/2015/293768 (2015).Article 

Google Scholar 
Lin, Y., Shen, C., Wang, F., Fang, Z. & Shen, G. Network pharmacology and molecular docking study on the potential mechanism of Yi-Qi-Huo-Xue-Tong-Luo formula in treating diabetic peripheral neuropathy. J. Diabetes Res. 2021, 9941791. https://doi.org/10.1155/2021/9941791 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Iqbal, D. et al. Soyasapogenol-B as a potential multitarget therapeutic agent for neurodegenerative disorders: Molecular docking and dynamics study. Entropy https://doi.org/10.3390/e24050593 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Oselusi, S. O., Christoffels, A. & Egieyeh, S. A. Cheminformatic characterization of natural antimicrobial products for the development of new lead compounds. Molecules 26, 3970. https://doi.org/10.3390/molecules26133970 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Tian, S. et al. The application of in silico drug-likeness predictions in pharmaceutical research. Adv. Drug. Deliv. Rev. 86, 2–10. https://doi.org/10.1016/j.addr.2015.01.009 (2015).Article 
CAS 
PubMed 

Google Scholar 
Benet, L. Z., Hosey, C. M., Ursu, O. & Oprea, T. I. BDDCS, the rule of 5 and drugability. Adv. Drug. Deliv. Rev. 101, 89–98. https://doi.org/10.1016/j.addr.2016.05.007 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wairata, J. et al. Evaluation of the antioxidant, antidiabetic, and antiplasmodial activities of xanthones isolated from garcinia forbesii and their in silico studies. Biomedicines 9, 1380. https://doi.org/10.3390/biomedicines9101380 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Mechchate, H., Es-safi, I., Al Kamaly, M.O., & Bousta D. Insight into gentisic acid antidiabetic potential using in vitro and in silico approaches. Molecules 26, 1932. https://doi.org/10.3390/molecules26071932 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Hsiu, J., Fischer, E. H. & Stein, E. A. Alpha-amylases as calcium-metalloenzymes. II. Calcium and the catalytic activity*. Biochemistry 3, 61–66. https://doi.org/10.1021/bi00889a011 (1964).Article 
CAS 
PubMed 

Google Scholar 
Ragunath, C. et al. Probing the role of aromatic residues at the secondary saccharide-binding sites of human salivary α-amylase in substrate hydrolysis and bacterial binding. J. Mol. Biol. 384, 1232–1248. https://doi.org/10.1016/j.jmb.2008.09.089 (2008).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chien, C.-H., Tsai, C.-H., Lin, C.-H., Chou, C.-Y. & Chen, X. Identification of hydrophobic residues critical for DPP-IV dimerization. Biochemistry 45, 7006–7012. https://doi.org/10.1021/bi060401c (2006).Article 
CAS 
PubMed 

Google Scholar 
Lomize, A. L. & Pogozheva, I. D. Physics-based method for modeling passive membrane permeability and translocation pathways of bioactive molecules. J. Chem. Inf. Model 59, 3198–3213. https://doi.org/10.1021/acs.jcim.9b00224 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kuzmanic, A. & Zagrovic, B. Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophys. J. 98, 861–871. https://doi.org/10.1016/j.bpj.2009.11.011 (2010).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kashyap, J. & Datta, D. Drug repurposing for SARS-CoV-2: A high-throughput molecular docking, molecular dynamics, machine learning, and DFT study. J. Mater. Sci. 57, 10780–10802. https://doi.org/10.1007/s10853-022-07195-8 (2022).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Stratton, C. F., Newman, D. J. & Tan, D. S. Cheminformatic comparison of approved drugs from natural product versus synthetic origins. Bioorg. Med. Chem. Lett. 25, 4802–4807. https://doi.org/10.1016/j.bmcl.2015.07.014 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Iwamoto, K. et al. Soyasapogenols reduce cellular triglyceride levels in 3T3-L1 mouse adipocyte cells by accelerating triglyceride lipolysis. Biochem. Biophys. Rep. 16, 44–49. https://doi.org/10.1016/j.bbrep.2018.09.006 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Timalsina, D., Bhusal, D., Devkota, H. P., Pokhrel, K. P. & Sharma, K. R. α-Amylase inhibitory activity of Catunaregam spinosa (Thunb.) Tirveng.: In vitro and in silico studies. BioMed. Res. Int. 2021, 4133876. https://doi.org/10.1155/2021/4133876 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kamruzzaman, M., Horowitz, M., Jones, K. L. & Marathe, C. S. Gut-based strategies to reduce postprandial glycaemia in type 2 diabetes. Front. Endocrinol. 12, 661877. https://doi.org/10.3389/fendo.2021.661877 (2021).Article 

Google Scholar 
Salmaso, V. & Moro, S. Bridging molecular docking to molecular dynamics in exploring ligand-protein recognition process: An overview. Front. Pharmacol. 9 (2018).Dirir, A. M., Daou, M., Yousef, A. F. & Yousef, L. F. A review of alpha-glucosidase inhibitors from plants as potential candidates for the treatment of type-2 diabetes. Phytochem. Rev. 21, 1049–1079. https://doi.org/10.1007/s11101-021-09773-1 (2022).Article 
CAS 
PubMed 

Google Scholar 
Saini, K., Sharma, S. & Khan, Y. DPP-4 inhibitors for treating T2DM – hype or hope? An analysis based on the current literature. Front. Mol. Biosci. 10, 1130625 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Yang, L. et al. Exploration in the mechanism of Kaempferol for the treatment of gastric cancer based on network pharmacology. BioMed. Res. Int. 2020, e5891016. https://doi.org/10.1155/2020/5891016 (2020).Article 
CAS 

Google Scholar 
Blakaj, D. M., McConnell, K. J., Beveridge, D. L. & Baranger, A. M. Molecular dynamics and thermodynamics of protein−RNA interactions: Mutation of a conserved aromatic residue modifies stacking interactions and structural adaptation in the U1A−stem loop 2 RNA complex. J. Am. Chem. Soc. 123, 2548–2551. https://doi.org/10.1021/ja005538j (2001).Article 
CAS 
PubMed 

Google Scholar 
Pecsi, I., Leveles, I., Harmat, V., Vertessy, B. G. & Toth, J. Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase. Nucleic Acids Res. 38, 7179–7186. https://doi.org/10.1093/nar/gkq584 (2010).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Patil, R. et al. Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing. PLOS ONE 5, e12029. https://doi.org/10.1371/journal.pone.0012029 (2010).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ejaz, S. A., Aziz, M., Zafar, Z., Akhtar, N. & Ogaly, H. A. Revisiting the inhibitory potential of protein kinase inhibitors against NEK7 protein via comprehensive computational investigations. Sci. Rep. 13, 4304. https://doi.org/10.1038/s41598-023-31499-7 (2023).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Lobanov, MYu., Bogatyreva, N. S. & Galzitskaya, O. V. Radius of gyration as an indicator of protein structure compactness. Mol. Biol. 42, 623–628. https://doi.org/10.1134/S0026893308040195 (2008).Article 
CAS 

Google Scholar 
Li, M.-H., Luo, Q., Xue, X.-G. & Li, Z.-S. Molecular dynamics studies of the 3D structure and planar ligand binding of a quadruplex dimer. J. Mol. Model. 17, 515–526. https://doi.org/10.1007/s00894-010-0746-0 (2011).Article 
CAS 
PubMed 

Google Scholar