Ab-initio modelling and docking evaluation of geographically derived coat proteins of chilli leaf curl virus with flavonoids and chemical compounds

Gnanaprakash Jeyaraj; Habeeb Shaik Mohideen; A. Swapna Geetanjali

doi:10.7324/JABB.2021.95.1s7

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Abstract

Chilli leaf curl virus (ChiLCV) belongs to the genus begomovirus (Family Geminiviridae), can infect chilli and many other crops. The coat protein (CP) of ChiLCV binds with the genomic viral ssDNA and shuttles it in and out of the cell nucleus. The distinct role of CP genes is viral capsid formation and transmission by whitefly. In this study, the interaction of CP with selected plant flavonoids and chemical compounds is explained. The CP of ChiLCV were selected from India, Pakistan, Oman, and Sri Lanka. This study focuses on understanding the structure of CPs from different regions and molecular docking studies to inhibit ssDNA binding for transportation of CP AV1 of ChiLCV. Molecular docking is carried between proteins and selected flavonoids and chemical compounds. Flavonoids show potent inhibition at the binding site of AV1. The outcomes obtained from this study direct that flavonoids' performance promises as compare with other chemical compounds. This information might be interesting to study plant defense mechanisms based on the plants' unique compounds.

Keyword: Coat protein AV1 flavonoids molecular docking plant virus chilli leaf curl virus

Citation:

Jeyaraj G, Mohideen HS, Geetanjali AS. Ab-initio modelingmodelling and docking evaluation of geographically derived coat proteins of chilli leaf curl virus with flavonoids and chemical compounds. J Appl Biol Biotech, 2021;9(S1):40-51.

Copyright: Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike license.

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2. Senanayake DMJB, Varma A, Mandal B. Virus-vector relationships, host range, detection and sequence comparison of chilli leaf curl virus associated with an epidemic of leaf curl disease of chilli in Jodhpur, India. J Phytopathol 2012;160:146-55. https://doi.org/10.1111/j.1439-0434.2011.01876.x
3. Chakraborti S, Bhowmik S, Senapati A. Assessing the impacts of safer management strategies against brinjal pests with emphasis on understorey repellent crop. J Entomol Res 2014;38:201-8.
4. Chattopadhyay B, Singh AK, Yadav T, Fauquet CM, Sarin NB, Chakraborty S. Infectivity of the cloned components of a begomovirus: DNA beta complex causing chilli leaf curl disease in India. Arch Virol 2008;153:533-9. https://doi.org/10.1007/s00705-007-0017-2
5. George B, Alam CM, Kumar RV, Gnanasekaran P, Chakraborty S. Potential linkage between compound microsatellites and recombination in geminiviruses: evidence from comparative analysis. Virology 2015;482:41-50. https://doi.org/10.1016/j.virol.2015.03.003
6. Gnanasekaran P, Kumar RK, Bhattacharyya D, Kumar RV, Chakraborty S. Multifaceted role of geminivirus associated betasatellite in pathogenesis. Mol Plant Pathol 2019;20:1019-33. https://doi.org/10.1111/mpp.12800
7. Sinha DP, Saxena S, Kumar S, Singh M. Detection of pepper leaf curl virus through PCR amplification and expression of its coat protein in Escherichia coli for antiserum production. Afr J Biotechnol 2011;10:3290-5. https://doi.org/10.5897/AJB10.1529
8. Padidam M, Beachy RN, Fauquet CM. A phage single-stranded DNA (ssDNA) binding protein complements ssDNA accumulation of a geminivirus and interferes with viral movement. J Virol 1999;73:1609- 16. https://doi.org/10.1128/JVI.73.2.1609-1616.1999
9. Singh Y, Gupta R. Novel S-enantioselective lipase TALipB from Trichosporon asahii MSR54: heterologous expression, characterization, conformational stability and homology modeling. Enzyme Microb Technol, 2016;83: 29-39. https://doi.org/10.1016/j.enzmictec.2015.11.003
10. Gaur RK, Prajapat R, Marwal A, Sahu A, Rathore MS. First report of a begomovirus infecting Mimosa pudica in India. J Plant Pathol 2011; Vol.93 No.4, Supplement pp.S4.80 ref.2.
11. Zakaryan H, Arabyan E, Oo A, Zandi K. Flavonoids: promising natural compounds against viral infections. Arch Virol 2017;162:2539-51. https://doi.org/10.1007/s00705-017-3417-y
12. Brown CR. Antioxidants in potato. Am J Potato Res 2005;82:163-72. https://doi.org/10.1007/BF02853654
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14. Kartasasmita RE, Herowati R, Gusdinar T. Docking study of quercetin derivatives on inducible nitric oxide synthase and prediction of their absorption and distribution properties. J Appl Sci 2010;10:3098-104. https://doi.org/10.3923/jas.2010.3098.3104
15. Zhang S, Yang X, Sun M, Sun F, Deng S, Dong H. Riboflavin-induced priming for pathogen defense in Arabidopsis thaliana. J Integr Plant Biol 2009;51:167-74. https://doi.org/10.1111/j.1744-7909.2008.00763.x
16. Ferreyra MLF, Rius SP, Casati P. Flavonoids: biosynthesis, biological functions, and biotechnological applications. Front Plant Sci 2012;3:1-5.
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18. Yamasaki H, Sakihama Y, Ikehara N. Flavonoid-peroxidase reaction as a detoxification mechanism of plant cells against H2 O2 . Plant Physiol 1997;115:1405-12. https://doi.org/10.1104/pp.115.4.1405
19. Jansen MAK, den Noort REV, Adillah Tan MYA, Prinsen E, Lagrimini LM, Thorneley RNF. Phenol-oxidizing peroxidases contribute to the protection of plants from ultraviolet radiation stress. Plant Physiol 2001;126:1012-23. https://doi.org/10.1104/pp.126.3.1012
20. Parniske M, Ahlborn B, Werner D. Isoflavonoid-inducible resistance to the phytoalexin glyceollin in soybean rhizobia. J Bacteriol 1991;173:3432-9. https://doi.org/10.1128/jb.173.11.3432-3439.1991
21. Zubair M, Ali Zaidi SSE, Shakir S, Amin I, Mansoor S. An insight into cotton leaf curl multan betasatellite, the most important component of cotton leaf curl disease complex. Viruses 2017;9:1-2. https://doi.org/10.3390/v9100280
22. Samanta A, Das G, Das SK. Roles of flavonoids in plants. Carbon N Y 2011;100:6.
23. Singh RP, Gu M, Agarwal R. Silibinin inhibits colorectal cancer growth by inhibiting tumor cell proliferation and angiogenesis. Cancer Res 2008;68:2043-50. https://doi.org/10.1158/0008-5472.CAN-07-6247
24. Kusano R, Ogawa S, Matsuo Y, Tanaka T, Yazaki Y, Kouno I. Α-amylase and lipase inhibitory activity and structural characterization of Acacia Bark Proanthocyanidins. J Nat Prod 2011;74:119-28. https://doi.org/10.1021/np100372t
25. Bazylko A, Stolarczyk M, Derwiska M, Kiss AK. Determination of antioxidant activity of extracts and fractions obtained from Galinsoga parviflora and Galinsoga quadriradiata, and a qualitative study of the most active fractions using TLC and HPLC methods. Nat Prod Res 2012;26:1584-93. https://doi.org/10.1080/14786419.2011.582469
26. Urbain A, Marston A, Grilo LS, Bravo J, Purev O, Purevsuren B, et al. Xanthones from Gentianella amarella ssp. acuta with acetylcholinesterase and monoamiiu oxidase inhibitory activities. J Nat Prod 2008;71:895-7. https://doi.org/10.1021/np070690l
27. Luca VD, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. I. Partial purification and some properties of S-adenosyl-l-methionine: flavonol 3-, 6-, 7-, and 4′-O-methyltransferases. Arch Biochem Biophys 1985;238:596-605. https://doi.org/10.1016/0003-9861(85)90205-X
28. Anand KK, Gupta VN, Rangari V, Singh B, Chandan BK. Structure and hepatoprotective activity of a biflavonoid from Canarium manii. Planta Med 1992;58:493-5. https://doi.org/10.1055/s-2006-961533
29. Tang W, Hioki H, Harada K, Kubo M, Fukuyama Y. Antioxidant phenylpropanoid-substituted epicatechins from Trichilia catigua. J Nat Prod 2007;70:2010-3. https://doi.org/10.1021/np0703895
30. Ovenden SPB, Cobbe M, Kissell R, Birrell GW, Chavchich M, Edstein MD. Phenolic glycosides with antimalarial activity from Grewillea "Poorinda Queen." J Nat Prod 2011;74:74-8. https://doi.org/10.1021/np100737q
31. Dapkevicius A, Beek TAV, Lelyveld GP, Veldhuizen AV, Groot AD, Linssen JPH, et al. Isolation and structure elucidation of radical scavengers from Thymus vulgaris leaves. J Nat Prod 2002;65:892-6. https://doi.org/10.1021/np010636j

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1. Maurya PK, Srivastava A, Mangal M, Talukdar A, Mondal B, Solanki V, et al. Genetic analysis for resistance to leaf curl disease in chilli peppers (Capsicum annuum L.) under specific situations. Indian J Genet Plant Breed 2019;79:741-8.

2. Senanayake DMJB, Varma A, Mandal B. Virus-vector relationships, host range, detection and sequence comparison of chilli leaf curl virus associated with an epidemic of leaf curl disease of chilli in Jodhpur, India. J Phytopathol 2012;160:146-55. https://doi.org/10.1111/j.1439-0434.2011.01876.x

3. Chakraborti S, Bhowmik S, Senapati A. Assessing the impacts of safer management strategies against brinjal pests with emphasis on understorey repellent crop. J Entomol Res 2014;38:201-8.

4. Chattopadhyay B, Singh AK, Yadav T, Fauquet CM, Sarin NB, Chakraborty S. Infectivity of the cloned components of a begomovirus: DNA beta complex causing chilli leaf curl disease in India. Arch Virol 2008;153:533-9. https://doi.org/10.1007/s00705-007-0017-2

5. George B, Alam CM, Kumar RV, Gnanasekaran P, Chakraborty S. Potential linkage between compound microsatellites and recombination in geminiviruses: evidence from comparative analysis. Virology 2015;482:41-50. https://doi.org/10.1016/j.virol.2015.03.003

6. Gnanasekaran P, Kumar RK, Bhattacharyya D, Kumar RV, Chakraborty S. Multifaceted role of geminivirus associated betasatellite in pathogenesis. Mol Plant Pathol 2019;20:1019-33. https://doi.org/10.1111/mpp.12800

7. Sinha DP, Saxena S, Kumar S, Singh M. Detection of pepper leaf curl virus through PCR amplification and expression of its coat protein in Escherichia coli for antiserum production. Afr J Biotechnol 2011;10:3290-5. https://doi.org/10.5897/AJB10.1529

8. Padidam M, Beachy RN, Fauquet CM. A phage single-stranded DNA (ssDNA) binding protein complements ssDNA accumulation of a geminivirus and interferes with viral movement. J Virol 1999;73:1609- 16. https://doi.org/10.1128/JVI.73.2.1609-1616.1999

9. Singh Y, Gupta R. Novel S-enantioselective lipase TALipB from Trichosporon asahii MSR54: heterologous expression, characterization, conformational stability and homology modeling. Enzyme Microb Technol, 2016;83: 29-39. https://doi.org/10.1016/j.enzmictec.2015.11.003

10. Gaur RK, Prajapat R, Marwal A, Sahu A, Rathore MS. First report of a begomovirus infecting Mimosa pudica in India. J Plant Pathol 2011; Vol.93 No.4, Supplement pp.S4.80 ref.2.

11. Zakaryan H, Arabyan E, Oo A, Zandi K. Flavonoids: promising natural compounds against viral infections. Arch Virol 2017;162:2539-51. https://doi.org/10.1007/s00705-017-3417-y

12. Brown CR. Antioxidants in potato. Am J Potato Res 2005;82:163-72. https://doi.org/10.1007/BF02853654

13. Prabahar A, Swaminathan S, Loganathan A, Jegadeesan R. Identification of novel inhibitors for tobacco mosaic virus infection in Solanaceae plants. Adv Bioinformatics 2015;2015, Article ID 198214.

14. Kartasasmita RE, Herowati R, Gusdinar T. Docking study of quercetin derivatives on inducible nitric oxide synthase and prediction of their absorption and distribution properties. J Appl Sci 2010;10:3098-104. https://doi.org/10.3923/jas.2010.3098.3104

15. Zhang S, Yang X, Sun M, Sun F, Deng S, Dong H. Riboflavin-induced priming for pathogen defense in Arabidopsis thaliana. J Integr Plant Biol 2009;51:167-74. https://doi.org/10.1111/j.1744-7909.2008.00763.x

16. Ferreyra MLF, Rius SP, Casati P. Flavonoids: biosynthesis, biological functions, and biotechnological applications. Front Plant Sci 2012;3:1-5.

17. Kikuchi K, Matsushita N, Suzuki K, Hogetsu T. Flavonoids induce germination of basidiospores of the ectomycorrhizal fungus Suillus bovinus. Mycorrhiza 2007;17: 563-70. https://doi.org/10.1007/s00572-007-0131-8

18. Yamasaki H, Sakihama Y, Ikehara N. Flavonoid-peroxidase reaction as a detoxification mechanism of plant cells against H2 O2 . Plant Physiol 1997;115:1405-12. https://doi.org/10.1104/pp.115.4.1405

19. Jansen MAK, den Noort REV, Adillah Tan MYA, Prinsen E, Lagrimini LM, Thorneley RNF. Phenol-oxidizing peroxidases contribute to the protection of plants from ultraviolet radiation stress. Plant Physiol 2001;126:1012-23. https://doi.org/10.1104/pp.126.3.1012

20. Parniske M, Ahlborn B, Werner D. Isoflavonoid-inducible resistance to the phytoalexin glyceollin in soybean rhizobia. J Bacteriol 1991;173:3432-9. https://doi.org/10.1128/jb.173.11.3432-3439.1991

21. Zubair M, Ali Zaidi SSE, Shakir S, Amin I, Mansoor S. An insight into cotton leaf curl multan betasatellite, the most important component of cotton leaf curl disease complex. Viruses 2017;9:1-2. https://doi.org/10.3390/v9100280

22. Samanta A, Das G, Das SK. Roles of flavonoids in plants. Carbon N Y 2011;100:6.

23. Singh RP, Gu M, Agarwal R. Silibinin inhibits colorectal cancer growth by inhibiting tumor cell proliferation and angiogenesis. Cancer Res 2008;68:2043-50. https://doi.org/10.1158/0008-5472.CAN-07-6247

24. Kusano R, Ogawa S, Matsuo Y, Tanaka T, Yazaki Y, Kouno I. Α-amylase and lipase inhibitory activity and structural characterization of Acacia Bark Proanthocyanidins. J Nat Prod 2011;74:119-28. https://doi.org/10.1021/np100372t

25. Bazylko A, Stolarczyk M, Derwiska M, Kiss AK. Determination of antioxidant activity of extracts and fractions obtained from Galinsoga parviflora and Galinsoga quadriradiata, and a qualitative study of the most active fractions using TLC and HPLC methods. Nat Prod Res 2012;26:1584-93. https://doi.org/10.1080/14786419.2011.582469

26. Urbain A, Marston A, Grilo LS, Bravo J, Purev O, Purevsuren B, et al. Xanthones from Gentianella amarella ssp. acuta with acetylcholinesterase and monoamiiu oxidase inhibitory activities. J Nat Prod 2008;71:895-7. https://doi.org/10.1021/np070690l

27. Luca VD, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. I. Partial purification and some properties of S-adenosyl-l-methionine: flavonol 3-, 6-, 7-, and 4′-O-methyltransferases. Arch Biochem Biophys 1985;238:596-605. https://doi.org/10.1016/0003-9861(85)90205-X

28. Anand KK, Gupta VN, Rangari V, Singh B, Chandan BK. Structure and hepatoprotective activity of a biflavonoid from Canarium manii. Planta Med 1992;58:493-5. https://doi.org/10.1055/s-2006-961533

29. Tang W, Hioki H, Harada K, Kubo M, Fukuyama Y. Antioxidant phenylpropanoid-substituted epicatechins from Trichilia catigua. J Nat Prod 2007;70:2010-3. https://doi.org/10.1021/np0703895

30. Ovenden SPB, Cobbe M, Kissell R, Birrell GW, Chavchich M, Edstein MD. Phenolic glycosides with antimalarial activity from Grewillea "Poorinda Queen." J Nat Prod 2011;74:74-8. https://doi.org/10.1021/np100737q

31. Dapkevicius A, Beek TAV, Lelyveld GP, Veldhuizen AV, Groot AD, Linssen JPH, et al. Isolation and structure elucidation of radical scavengers from Thymus vulgaris leaves. J Nat Prod 2002;65:892-6. https://doi.org/10.1021/np010636j