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Quantitative Biology

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Quant. Biol.    2019, Vol. 7 Issue (4) : 302-312    https://doi.org/10.1007/s40484-019-0179-4
RESEARCH ARTICLE
Molecular modeling studies of repandusinic acid as potent small molecule for hepatitis B virus through molecular docking and ADME analysis
Vijayakumar Subramaniyan(), Reetha Sekar, Arulmozhi Praveenkumar, Rajalakshmi Selvam
Computational Phytochemistry Lab, PG and Research Department of Botany and Microbiology AVVM Sri Pushpam College (Autonomous), Tamil Nadu, 613503, India
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Abstract

Background: Hepatitis B virus (HBV) has affected over 300 million people worldwide which causes to induce mostly liver disease and liver cancer. It is a member of the family Hepadnaviridae which is a small DNA virus with unusual characters like retroviruses. Generally, hepatoprotective drugs provoke some side effects in human beings. For the reason, this study aims to identify alternative drug molecules from the natural source of medicinal plants with smaller quantity of side effects than those conventional drugs in treating HBV.

Methods: We developed computational methods for calculating drug and target binding resemblance using the Maestro v10.2 of Schrodinger suite. The target and ligand molecules were obtained from recognized databases. Ligand molecules of 40 phytoconstituents were retrieved from variety of plants after we executed crucial analyses such as molecular docking and absorption, distribution, metabolism, and excretion (ADME) analysis.

Results: In the docking analysis, the natural analogues repandusinic acid showed better docking scores of –14.768 with good binding contacts. The remaining bioactive molecules corilagin, furosin, nirurin, iso-quercetin and gallocatechin also showed better docking scores.

Conclusion: This computational analysis reveals that repandusinic acid is a suitable drug candidate for HBV. Therefore, we recommend that this analogue is suitable in further exploration using in vitro studies.

Keywords hepatitis B virus      phytoconstituents      molecular docking      ADMET analysis     
Corresponding Author(s): Vijayakumar Subramaniyan   
Just Accepted Date: 04 September 2019   Online First Date: 18 December 2019    Issue Date: 31 December 2019
 Cite this article:   
Vijayakumar Subramaniyan,Reetha Sekar,Arulmozhi Praveenkumar, et al. Molecular modeling studies of repandusinic acid as potent small molecule for hepatitis B virus through molecular docking and ADME analysis[J]. Quant. Biol., 2019, 7(4): 302-312.
 URL:  
https://academic.hep.com.cn/qb/EN/10.1007/s40484-019-0179-4
https://academic.hep.com.cn/qb/EN/Y2019/V7/I4/302
Fig.1  Ligand active binding cavity HBx.
No. Compound names Name of the plant Number of residues interactions Glide?docking XP?score Glide?e?model (kcal/mol)
1 Repandusinic acid Phyllanthus niruri?L. Asn16, Glu312, Arg263, Lys168, Glu65, Ala62, Thr118 –16.180 –125.993
2 Corilagin Phyllanthus niruri?L.
Phyllanthus emblica L.		 His261, Arg263, Ala221, Cys18, Lys168, Gly122 –13.399 –92.836
3 Furosin Phyllanthus niruri?L. Glu312, Cys18, Asn262, Arg263, Lys168 (salt bridge) –13.454 –98.141
4 Nirurin Phyllanthus niruri?L. Asn262, His261, Cys18, Thr118, Glu65, Tyr171 –12.392 –79.381
5 Iso-quercitin Hemidesmus indicus L. Cys18, Ile124, Glu65, Ala221, Arg263, His261 (salt bridge) –12.299 –86.492
6 Rutin Phyllanthus niruri?L.
Delonix elata L.		 Glu65, Ile124, Cys18, Thr20, Ala221, Arg263, His261(salt bridge) –11.848 –88.335
7 (+)Gallocatechin Phyllanthus niruri?L. His261, Thr118, Lys168, Asn16 –11.216 –95.126
8 Hesperidin Citrus sp. L. Ala221, Cys18, Thr20, Arg263, Leu66 –10.247 –115.29
9 Quercitrin Phyllanthus niruri?L.
Acalypha indica L.		 Leu314, Tyr171, Glu65, Ala262, rg263,His261(salt bridge) –10.009 –105.236
10 Astragalin Phyllanthus niruri?L. Ala221, Lys168, Arg263, Arg262, Glu65, Cys18 –9.503 –94.263
11 Geranin Phyllanthus niruri?L. Arg263, His22, Thr20, Arg68, Leu66, Glu65, Cys18 –9.221 –97.741
12 Fisetin Mangifera indica L. Arg263, Ala221, Glu65, Cys18 –8.870 –82.586
13 Myricetin Holigarna grahamii(Wight)?Kurz. Leu314, Glu65, Lys168, Glu65 –8.346 –82.077
14 Ascorbic acid Nervilia aragona L. Arg263, Tyr271, Ala221, Lys168, His261, Asn262 –8.304 –84.664
15 Astragalin Cuscuta chinensis L. Leu66, Glu65, Ile124, Asn262, Phe169, Lys168 –8.254 –92.314
16 Kaempferol Jatropha curcas, Phyllathus niruri L. Arg263, Ala221, Lys168, Glu168, Glu65, Leu314 –8.109 –98.9
17 Gallic acid Phyllathus niruri L.
Aerva lanata L.		 Arg263, Ala221, Lys168 –7.943 –97.417
18 Tartaric acid Gisekia phannaceides Arg263, Tyr271, His261, Lys168 –7.652 –75.934
19 Nirphyllin Phyllathus niruri L. His261, Cys18, Gly122 ?7.570 ?90.786
20 Quinic acid Holigarna grahamii(Wight)?Kurz. Asn16, Met66, Ile61 ?7.481 ?80.054
21 Chlorogenic acid Eryngium planum L. Asn262, Arg263, Tyr 271, Ile124 ?7.238 ?78.122
22 Caffeic acid Convolvulus gangeticus Arg263, Tyr271, Ile124 ?7.143 ?63.632
23 Isovitexin Jatropha mollissima (pohl) baill Glu312, Asn16, His261, Arg263, Ala221 ?7.006 ?68.914
24 (?) Epicatechin Camellia sinensis L. Thr20, Glu65, Lys168, Ala221, Arg263, His 261 ?6.980 ?91.758
25 (+) Catechin Camellia sinensis L.
Albizia lebbeck L.		 His261, Leu314, Glu65, Met64, Ile61 ?6.650 ?72.007
26 Eriodictyol Lyonia ovalifolia L.
Lythrum salicaria L.		 Thyr20, Thr315, His261, Arg263, Ala221 ?6.531 ?85.558
27 Ferulic acid Beta vulgaris L. Tyr271, Arg263, Ile124 ?6.428 ?81.391
28 Shikonin Lithospermum erythrorhizon Siebold & Zucc Aerg263, Phe169, Ile124 ?6.221 ?86.663
29 Venellic acid Capparis zeylanica L. Asn262, Arg263, Tyr271, Lys168 ?6.118 ?70.845
30 Estrodiol Momordica charantia L. Arg263, Phe169, Ile124 ?6.007 ?69.064
31 Taraxacin Calotropis procera Tyr271, Arg263, Ile124 ?5.743 ?37.129
32 Brevifoin Phyllathus sps. Arg263, Ala221, Lys168 ?5.520 ?65.546
33 Phyltetralin Pilates niruri L. Cys18 ?5.517 ?58.561
34 (?) Limonine Limonia acidissima L. Cys18
Thr20, Leu314, Gly122		 ?5.481 ?69.007
35 Hypophyllanthin Phyllathus niruri L. Phyllathus amarus L. Arg263, Asn262, Lys168, Ile124 ?5.372 ?71.809
36 Taraxastrol Calotropis procora Ile165 ?5.204 ?57.032
37 Niranthin Phyllathus niruri L. Thr20, Cys18, His261 ?5.029 ?54.594
38 Salycilic acid Filipendula ulmoria L. Lys168, Ile124 ?4.858 ?73.773
39 Linolenic acid Nervilia aragona L. Tyr271, Arg263 ?4.629 ?76.13
40 Tridecanol Nervilia aragona L. Tyr271, Ala221 ?4.568 ?51.578
Tab.1  Docking results of 40 natural compounds from medicinal plant sources
Fig.2  Residues and hydrogen bond contacts (yellow dotted line) with their distance values (pink) in repandusinic acid, and the 2D template representing the types of contacts involved between the ligand and target.
Fig.3  Residues and hydrogen bond contacts (yellow dotted line) with their distance values (pink) in corilagin, and the 2D template representing the types of contacts involved between the ligand target.
Fig.4  Residues and hydrogen bond contacts (yellow dotted line) with their distance values (pink) in furosin, at the 2D template representing the types of contacts involved between the ligand and target.
Fig.5  Residues and hydrogen bond contacts (yellow dotted line) with their distance values (pink) in nirurin, and the 2D template representing the types of contacts involved between the ligand and target.
Fig.6  Residues and hydrogen bond contacts (yellow dotted line) with their distance values (pink) in iso-quercetin, and the 2D template representing the types of contacts involved in the ligand and target.
No. Molecular
formula		 Molecular
weight (g/mol)		 Volume SASA Acceptor
H bond
groups		 Donor H bond
groups		 Number of ring
atoms		 Q Plog
Pw
(–2 to 6.5)		 %
Human
oral
absorption		 CNS Rule of five
1 C41H30O28 970.663 2327.586 1050.003 17 29.95 55 –2.557 1 –2 3
2 C27H22O18 634.455 1552.483 778.079 9 20.55 28 –1.354 1 –2 3
3 C27H22O19 650.454 1671.132 866.924 7 20.05 28 –3.007 1 –2 3
4 C32H40O15 664.651 1568.806 821.477 7 22.45 17 –1.397 1 –2 3
5 C21H20O12 464.379 1611.303 837.282 7 19.30 28 1.884 1 –2 3
6 C27H30O16 610.521 2190.041 1057.957 6 21.30 34 0.453 1 –2 3
7 C15H14O7 306.270 1519.296 807.567 10 10.90 32 –0.515 1 –2 3
8 C28H34O15 610.565 995.503 553.076 6 9.65 12 –2.426 1 –2 1
9 C21H20O11 448.380 963.976 535.187 9 12.35 6 –1.76 1 –2 2
10 C21H20O11 448.380 1127.265 634.363 7 13 20 0.957 1 –2 2
11 C41H28O27 952.648 1094.899 637.616 5 7 12 2.223 1 –2 0
12 C15H10O6 286.239 1443.524 746.044 6 9.35 17 0.427 2 –2 1
13 C15H10O8 318.237 856.481 503.931 5 5.45 16 –3.079 2 –2 0
14 C6H8O6 176.124 595.353 369.932 6 10.20 0 –1.245 1 –2 1
15 C21H20O11 448.380 794.879 466.636 5 12.40 6 3.323 1 –2 0
16 C15H10O6 286.239 1093.897 616.277 2 4 16 0.286 3 –2 0
17 C7H6O5 170.120 834.19 477.4 5 5.45 16 1.289 2 –2 0
18 C4H6O6 150.086 1041.592 547.798 3 8.10 15 –0.359 3 –2 0
19 C24H32O8 448.512 836.626 516.586 3 8.60 11 3.561 2 –2 0
20 C7H12O6 192.167 1294.790 378.032 17 29.95 55 –2.557 1 –2 3
21 C16H18O9 354.311 868.249 578.065 9 20.55 28 –1.354 1 –2 3
22 C9H8O4 180.159 831.747 436.980 7 20.05 28 –3.007 1 –2 3
23 C21H20O10 432.381 878.822 578.603 7 22.45 17 –1.397 1 –2 3
24 C15H14O6 290.271 870.576 473.047 7 19.30 28 1.884 1 –2 3
25 C11H12O6 280.712 553.076 668.294 6 21.30 34 0.453 1 –2 3
26 C15H12O6 288.255 525.074 621.747 10 10.90 32 –0.515 1 –2 3
27 C10H10O4 194.186 643.360 873.822 6 9.65 12 –2.426 1 –2 1
28 C16H16O5 288.299 746.044 975.780 9 12.35 6 –1.76 1 –2 2
29 C8H8O4 168.148 396.249 780.638 7 13 20 0.957 1 –2 2
30 C18H24O2 272.388 661.231 535.750 5 7 55 2.223 1 –2 3
31 C15H14O3 242.274 456.890 535.178 6 9.35 28 0.427 2 –2 3
32 C15H12O6 288.255 474.403 643.336 5 5.45 28 –3.079 2 –2 3
33 C10H10O4 194.186 574.897 673.616 6 10.20 17 –1.245 1 –2 3
34 C16H16O5 288.299 561.568 530.931 5 12.40 28 3.323 1 –2 3
35 C8H8O4 168.148 578.158 661.271 2 4 34 0.286 3 –2 3
36 C18H24O2 272.388 562.372 464.663 5 5.45 32 1.289 2 –2 3
37 C24H32O7 432.513 673.661 474.700 3 8.1 12 –0.359 3 –2 1
38 C12H16O3 208.257 530.913 574.879 3 8.6 6 3.561 2 –2 2
39 C18H30O2 278.436 396.932 578.851 17 29.95 20 –2.557 1 –2 2
40 C13H28O 200.366 526.723 562.372 9 20.55 12 –1.354 1 –2 0
Tab.2  Physicochemical properties and biological functions of the 40 bioactive molecules analyzed by using QuikProp
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