Identification of Novel Human Serum Albumin (SA) Inhibitors from Scoparia Dulsis for Urolithiasis

Author(s): Divya Shaji*

Journal Name: Current Computer-Aided Drug Design

Volume 16 , Issue 3 , 2020


Become EABM
Become Reviewer
Call for Editor

Graphical Abstract:


Abstract:

Background: Urolithiasis is the process of forming stones in the kidney, bladder, and/or urinary tract. It has been reported that kidney stones are the third most common disorder among urinary diseases. At present, surgical procedures and Extracorporeal Shock Wave Lithotripsy (ESWL) are commonly employed for the treatment of Urolithiasis. The major drawback of these procedures is the recurrence of stones.

Methods: This study aimed to identify potential natural inhibitors against human Serum Albumin (SA) from the plant Scoparia Dulsis for Urolithiasis. As protein-ligand interactions play a key role in structure- based drug design, this study screened 26 compounds from Scoparia Dulsis and investigated their binding affinity against SA by using molecular docking. The three dimensional (3D) structure of SA was retrieved from Protein Data Bank (PDB) and docked with PubChem structures of 26 compounds using PyRX docking tool through Autodock Vina. Moreover, a 3D similarity search on the PubChem database was performed to find the analogs of best scored compound and docking studies were performed. Drug-likeness studies were made using Swiss ADME and Lipinski’s rule of five was performed for the compounds to evaluate their anti-urolithiatic activity.

Results: The results showed that citrusin c (Eugenyl beta-D-glucopyranoside) exhibited best binding energy of -8.1 kcal/mol with SA followed by aphidicolin, apigenin, luteolin and scutellarein. Two compounds (PubChem CID 46186820, PubChem CID 21579141) analogous to citrusin c were selected based on the lowest binding energy.

Conclusion: This study, therefore, reveals that these compounds could be promising candidates for further evaluation for Urolithiasis prevention or management.

Keywords: Urolithiasis, kidney stone, molecular docking, Scoparia Dulsis, serum albumin, extracorporeal shock wave lithotripsy.

[1]
Sakhaee, K. Nephrolithiasis as a systemic disorder. Curr. Opin. Nephrol. Hypertens., 2008, 17(3), 304-309.
[http://dx.doi.org/10.1097/MNH.0b013e3282f8b34d] [PMID: 18408483]
[2]
Aggarwal, KP; Narula, S; Kakkar, M; Tandon, C Nephrolithiasis: molecular mechanism of renal stone formation and the critical role played by modulators. Biomed Res. Int. 2013; 2013.,
[http://dx.doi.org/10.1155/2013/292953]
[3]
Heilberg, I.P.; Schor, N. Renal stone disease: Causes, evaluation and medical treatment. Arq. Bras. Endocrinol. Metabol, 2006, 50(4), 823-831.
[http://dx.doi.org/10.1590/S0004-27302006000400027] [PMID: 17117307]
[4]
Brener, Z.; Bergman, M.O. Nephrolithiasis management and prevention: current perspectives. J. Clin. Outcomes Manag., 2012, 19, 328-335.
[5]
Nirumand, M.C.; Hajialyani, M.; Rahimi, R.; Farzaei, M.H.; Zingue, S.; Nabavi, S.M.; Bishayee, A. Dietary plants for the prevention and management of kidney stones: preclinical and clinical evidence and molecular mechanisms. Int. J. Mol. Sci., 2018, 19(3), 765.
[http://dx.doi.org/10.3390/ijms19030765] [PMID: 29518971]
[6]
Ramaswamy, K.; Killilea, D.W.; Kapahi, P.; Kahn, A.J.; Chi, T.; Stoller, M.L. The elementome of calcium-based urinary stones and its role in urolithiasis. Nat. Rev. Urol., 2015, 12(10), 543-557.
[http://dx.doi.org/10.1038/nrurol.2015.208] [PMID: 26334088]
[7]
Saxena, A.; Sharma, R.K. Nutritional aspect of nephrolithiasis. Indian J. Urol., 2010, 26(4), 523-530.
[http://dx.doi.org/10.4103/0970-1591.74451] [PMID: 21369385]
[8]
McAteer, J.A.; Evan, A.P. The acute and long-term adverse effects of shock wave lithotripsy. Semin. Nephrol., 2008, 28(2), 200-213. [WB Saunders.
[http://dx.doi.org/10.1016/j.semnephrol.2008.01.003] [PMID: 18359401]
[9]
Willis, L.R.; Evan, A.P.; Connors, B.A.; Shao, Y.; Blomgren, P.M.; Pratt, J.H.; Fineberg, N.S.; Lingeman, J.E. Shockwave lithotripsy: dose-related effects on renal structure, hemodynamics, and tubular function. J. Endourol., 2005, 19(1), 90-101.
[http://dx.doi.org/10.1089/end.2005.19.90] [PMID: 15735392]
[10]
Samy, R.P.; Pushparaj, P.N.; Gopalakrishnakone, P. A compilation of bioactive compounds from Ayurveda. Bioinformation, 2008, 3(3), 100-110.
[http://dx.doi.org/10.6026/97320630003100] [PMID: 19238245]
[11]
Yadav, R.D.; Jain, S.K.; Alok, S.; Mahor, A.; Bharti, J.P.; Jaiswal, M. Herbal plants used in the treatment of urolithiasis: a review. Int. J. Pharm. Sci. Res., 2011, 2, 1412.
[12]
Rajan, R.; Vedi, M.; Sridharan, B.; Himaja, M.; Sabina, E.P.; Raj, N.A. In vitro and In vivo study on the effect of Scoparia Dulcis in inhibiting the growth of urinary crystals. Int. J. Phytomed., 2015, 6, 617-624.
[13]
Farook, N.A.; Rajesh, S.; Jamuna, M. Inhibition of mineralization of urinary stone forming minerals by medicinal plants. J. Chem., 2009, 6, 938-942.
[14]
Mathew, A; Retna, AM Antilithiatic activity and pharmacognostic studies of scoparia dulcis. Green Chemistry & Technology Letters. 2016; 2:01-10,
[http://dx.doi.org/10.18510/gctl.2016.211]
[15]
Pathak, P.; Naik, P.K.; Sengupta, D.; Singh, S.K.; Tandon, C. Mode of interaction of calcium oxalate crystal with human phosphate cytidylyltransferase 1: a novel inhibitor purified from human renal stone matrix. J. Biomed. Sci. Eng., 2011, 4, 591.
[http://dx.doi.org/10.4236/jbise.2011.49075]
[16]
Basavaraj, D.R.; Biyani, C.S.; Browning, A.J.; Cartledge, J.J. The role of urinary kidney stone inhibitors and promoters in the pathogenesis of calcium containing renal stones. EAU-EBU Update Ser., 2007, 5, 126-136.
[http://dx.doi.org/10.1016/j.eeus.2007.03.002]
[17]
Okumura, N.; Tsujihata, M.; Momohara, C.; Yoshioka, I.; Suto, K.; Nonomura, N.; Okuyama, A.; Takao, T. Diversity in protein profiles of individual calcium oxalate kidney stones. PLoS One, 2013, 8(7)e68624
[http://dx.doi.org/10.1371/journal.pone.0068624] [PMID: 23874695]
[18]
Devesh, R.; Pragya, K.; Tanya, S.; Trisha, P.; Priyadarshini, R. Albumin and its role in Urolithiasis. Asian J Pharm Clin Res., 2017, 10, 32-35.
[http://dx.doi.org/10.22159/ajpcr.2017.v10i10.20059]
[19]
Fasano, M.; Curry, S.; Terreno, E.; Galliano, M.; Fanali, G.; Narciso, P.; Notari, S.; Ascenzi, P. The extraordinary ligand binding properties of human serum albumin. IUBMB Life, 2005, 57(12), 787-796.
[http://dx.doi.org/10.1080/15216540500404093] [PMID: 16393781]
[20]
Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The protein data bank. Nucleic Acids Res., 2000, 28(1), 235-242.
[http://dx.doi.org/10.1093/nar/28.1.235] [PMID: 10592235]
[21]
Mishra, M.R.; Behera, R.K.; Jha, S.; Panda, A.K.; Mishra, A.; Pradhan, D.K.; Choudary, P.R. A brief review on phytoconstituents and ethnopharmacology of Scoparia dulcis Linn.(Scrophulariaceae). Int. J. Phytomed., 2011, 3, 422-438.
[22]
Pamunuwa, G; Karunaratne, D Waisundara, VY ntidiabetic Properties, bioactive constituents, and other therapeutic effects of scoparia dulcis. Evid Based Complement Alternat Med. 2016;2016
[23]
Saikia, R.; Choudhury, M.D.; Talukdar, A.D.; Chetia, P. Antidiabetic activity of ethno medicinal plant Scoparia dulcis L.(Family: Scrophulariaceae): a review. Assam University Journal of Science and Technology., 2011, 7, 173-180.
[24]
Kim, S.; Thiessen, P.A.; Bolton, E.E.; Chen, J.; Fu, G.; Gindulyte, A.; Han, L.; He, J.; He, S.; Shoemaker, B.A.; Wang, J.; Yu, B.; Zhang, J.; Bryant, S.H. PubChem substance and compound databases. Nucleic Acids Res., 2016, 44(D1), D1202-D1213.
[http://dx.doi.org/10.1093/nar/gkv951] [PMID: 26400175]
[25]
Dallakyan, S.; Olson, A.J. Small-molecule library screening by docking with PyRx. Methods Mol. Biol., 2015, 1263, 243-250.
[http://dx.doi.org/10.1007/978-1-4939-2269-7_19] [PMID: 25618350]
[26]
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., 2010, 31(2), 455-461.
[PMID: 19499576]
[27]
O’Boyle, N.M.; Banck, M.; James, C.A.; Morley, C.; Vandermeersch, T.; Hutchison, G.R. Open Babel: An open chemical toolbox. J. Cheminform., 2011, 3, 33.
[http://dx.doi.org/10.1186/1758-2946-3-33] [PMID: 21982300]
[28]
Discovery Studio Visualizer, version 16.1. 0.15350; Dassault Systèmes: San Diego, 2016.
[29]
Wallace, A.C.; Laskowski, R.A.; Thornton, J.M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng., 1995, 8(2), 127-134.
[http://dx.doi.org/10.1093/protein/8.2.127] [PMID: 7630882]
[30]
Daina, A.; Michielin, O.; Zoete, V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep., 2017, 7, 42717.
[http://dx.doi.org/10.1038/srep42717] [PMID: 28256516]
[31]
Lipinski, C.A. Drug-like properties and the causes of poor solubility and poor permeability. J. Pharmacol. Toxicol. Methods, 2000, 44(1), 235-249.
[http://dx.doi.org/10.1016/S1056-8719(00)00107-6] [PMID: 11274893]


Rights & PermissionsPrintExport Cite as

Article Details

VOLUME: 16
ISSUE: 3
Year: 2020
Published on: 02 June, 2020
Page: [308 - 317]
Pages: 10
DOI: 10.2174/1573409915666190808125518
Price: $65

Article Metrics

PDF: 12
HTML: 1