In Silico anticancer analysis of compounds from Ludwigia perennis

Paper Details

Research Paper 18/03/2024
Views (30) Download (8)

In Silico anticancer analysis of compounds from Ludwigia perennis

TS. Syamkumar, S. Geethalakshmi, Anu Augustine
Int. J. Biosci.24( 3), 212-222, March 2024.
Certificate: IJB 2024 [Generate Certificate]


Cancer related deaths has been on an increase world-wide and necessitates urgent action to investigate anticancer treatments. Natural substances are likely to be a viable source. In this study, 18 phytochemicals were identified using GC-MS analysis after a phytochemical examination of a chloroform root extract of Ludwigia perennis. Protein Data Bank accession number 4GIZ was used to attach these phytochemicals onto the E6 protein. While 18 identified phytochemicals were docked with cervical cancer proteins, six compounds mainly showed higher binding affinity. The binding affinity of 1,1′-(1,2-cyclobutanediyl)bis-trans benzene is reported to be -8.2. The other five molecules have binding affinities of -6.5 and are phytol, geranyl isovlerate, 3,7,11,15-tetramethyl-2-hexadecen-1-ol, 7,9-di-tert-butyl-1-oxaspiro(4,5)deca-6,9-diene-2,8-dione, phthalic acid, and butyl tetradecyl ester. The six compounds that were successfully docked show anticancer effect, according to the molecular docking research findings. Their drug-likeness, anticipated safety after ingestion, and anticipated pharmacological effects were all validated by pharmacokinetic and PASS investigations in addition to docking.


Abdulfatai U, Uzairu A, Uba S. 2018. Molecular docking and quantitative structure-activity relationship study of anticonvulsant activity of aminobenzothiazole derivatives. Beni-Suef University Journal of Basic and Applied Sciences 7, 204-14.

Al-Haidari RA, Shaaban MI, Ibrahim SR, Mohamed GA. 2016.  Anti-quorum sensing activity of some medicinal plants. African Journal of Traditional  Complementary and Alternative Medicines 13, 67-71.

Aminzare M, Hashemi M, Hassanzad Azar H, Hejazi J. 2016. The use of herbal extracts and essential oils as a potential antimicrobial in meat and meat products; a review. J Hum Environ Health Promot. 1, 63-74.

Banerjee P, Eckert AO, Schrey AK, Preissner R. 2018. ProTox-II: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Res. 46, W257-W263. https://doi:10.1093/nar/gky318.

Beg M, Athar F. 2020. Pharmacokinetic and molecular docking studies of Achyranthes aspera phytocompounds to exploring potential anti-tuberculosis activity. J Bacteriol Mycol Open Access  8, 18-27.

Bharatha SRS. 2015. HPV infection and cervical cancer. International Journal of Nursing Education and Research 3, 229-231.–5713.

Daina A, Michielin O, Zoete V. 2014. iLOGP: a simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. Journal of chemical information and modeling 54, 3284-301.

Daina A, Michielin O, Zoete V. 2017. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific reports 7, 42717.

De Sanjose S, Brotons M, Pavon MA. 2018. The natural history of human papillomavirus infection, Best practice & research. Clinical Obstetrics & Gynaecology   47, 2-13.

Duffy FJ, Devocelle M, Shields DC. 2015. Computational approaches to developing short cyclic peptide modulators of protein–protein interactions. Computational Peptidology, 241-71.

Fernandes JV, Fernandes TAAM. 2012. Human papillomavirus: biology and pathogenesis. In: Human papillomavirus and related diseases – from bench to bedside- a clinical perspective. InTech.  1-5.

Goel RK, Singh D, Lagunin A, Poroikov V. 2011. PASS-assisted exploration of new therapeutic potential of natural products. Medicinal Chemistry Research, 1509-14.

Hasanuddin S, Gozali D, Arba M, Ramadhan DS, Mustarichie R. 2022. In silico prediction of metabolite in Petroselinum crispum in inhibiting androgen receptor as treatment for alopecia. Research Journal of Pharmacy and Technology 15, 1211-8.

Jamal M, Ahmad W, Andleeb S, Jalil F, Imran M, Nawaz MA, Hussain T, Ali M, Rafiq M, Kamil MA. 2018. Bacterial biofilm and associated infections. Journal of the chinese medical association 81, 7-11. https://doi:10.1016/j.jcma.2017.07.012.

Kharisma VD, Ansori ANM, Widyananda MH, Utami SL, Nugraha AP. 2020. Molecular simulation: The potency of conserved region on E6 HPV-16 as a binding target of black tea compounds against cervical cancer. Biochemical and Cellular Archives 20, 2795-2802.

Kumar S, Jena L, Mohod K, Daf S, Varma AK. 2015. Virtual screening for potential inhibitors of high-risk human papillomavirus 16 E6 protein. Interdisciplinary Sciences, Computational Life Sciences  7, 136-42. https://doi:10.1007/s12539-013-0213-6

Kumar S, Jena L, Sahoo M, Kakde M, Daf S, Varma AK. 2015. In silico docking to explicate interface between plant-originated inhibitors and E6 oncogenic protein of highly threatening human papillomavirus 18. Genomics & informatics 13, 60.

Lagunin A, Stepanchikova A, Filimonov D, Poroikov V. 2000. PASS: prediction of activity spectra for biologically active substances. Bioinformatics 16, 747-8.

Linstrom PJ, Mallard WG. 2001. The NIST Chemistry WebBook: A chemical data resource on the internet. Journal of Chemical & Engineering Data  46, 1059-63.

Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. 2001. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced drug delivery reviews  23, 3-25.

Lipinski CA. 2004. Lead-and drug-like compounds: the rule-of-five revolution. Drug discovery today: Technologies  1, 337-41.

Marimuthu N, Viswanathan T, Radha M, Suganya J. 2017. Computational Screening of the phytocompounds from the plant Ballota nigra Linn against the human papillomavirus (HPV) E6. Research Journal of Pharmacy and Technology 10, 3095-3097.

Merkhofer C, Maslow J. 2015. Human Papilloma virus (HPV) infection and non-cervical oncogenic disease states. Virology & Mycology 4, 1-11.

Messa L, Celegato M, Bertagnin C, Mercorelli B, Nannetti G, Palù G, Loregian A. 2018. A quantitative LumiFluo assay to test inhibitory compounds blocking p53 degradation induced by human papillomavirus oncoprotein E6 in living cells. Scientific Reports 8, 6020.

Mohan A, Krishnamoorthy S, Sabanayagam R, Schwenk G, Feng E, Ji HF, Muthusami S. 2023. Pharmacophore based virtual screening for identification of effective inhibitors to combat HPV 16 E6 driven cervical cancer. European Journal of Pharmacology 15, 957-175961.

Mseddi K, Alimi F, Noumi E, Veettil VN, Deshpande S, Adnan M, Hamdi A, Elkahoui S, Alghamdi A, Kadri A, Patel M. 2020. Thymus musilii Velen. as a promising source of potent bioactive compounds with its pharmacological properties: In vitro and in silico analysis. Arabian Journal of Chemistry 13, 6782-801.

Nabati F, Moradi M, Mohabatkar H. 2020. In silico analyzing the molecular interactions of plant-derived inhibitors against E6AP, p53, and c-Myc binding sites of HPV type 16 E6 oncoprotein. Molecular Biology Research Communications 9, 71-82.

Okunade KS. 2020. Human papillomavirus and cervical cancer. Journal of Obstetrics and Gynaecology 40, 602-8. https://doi:10.1080/01443615.2019.1634030.

Opo FADM, Rahman MM, Ahammad F, Bhuiyan MA, Asiri AM. 2021. Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP protein, Sci Rep 11, 4049.

Papadatos G, Overington JP. 2014. The ChEMBL database: a taster for medicinal chemists. Future medicinal chemistry 6, 361-4.

Park MS, Chang BS. 2019. Ultrastructural characteristics of hpv in women’s vaginal cells. Research Journal of Pharmacy and Technology  12, 4305-4309.

Pawar SS, Rohane SH. 2021. Review on discovery studio: an important tool for molecular docking. Asian J. Res. Chem. 14, 86-8.

Pinidis P, Tsikouras P, Iatrakis G, Zervoudis S, Koukouli Z, Bothou A, Galazios G, Vladareanu S. 2016. Human papilloma virus’ life cycle and carcinogenesis. Maedica 11, 48.

Poongothai A, Annapoorani S. 2019. GC- MS analysis and in-silico docking analysis of methanolic extract of Ficus racemosa bark, Int J Pharm Sci & Res.  10, 5179-93. https://doi:10.13040/IJPSR.0975-8232.10(11).

Proboningrat A, Ansori AN, Fadholly A, Putri N, Kusala MK, Achmad AB. 2021. First report on the cytotoxicity of Pinus merkusii bark extract in WiDr, a human colon carcinoma cell line. Research Journal of Pharmacy and Technology 14, 1685-8.

Rappé AK, Casewit CJ, Colwell KS, Goddard III WA, Skiff WM, UFF. 1992. A full periodic table force field for molecular mechanics and molecular dynamics simulations. Journal of the American chemical society 114, 10024-35.

Singh G, Sharma PK, Dudhe R, Singh S. 2010. Biological activities of Withania somnifera. Ann Biol Res. 1, 56-63.

Stuver SH, Adami HO. 2002. Cervical cancer. New York, NY: Oxford University Press.

Syamkumar TS, Geethalakshmi S, Augustine A. 2023. Study of Pharmacological Profile of Chloroform Leaf Extract of Ludwigia perennis-A Wetland Plant. European Journal of Medicinal Plants 34, 58-70.

Tyagi N, Khare N,  Jha A, Abdul A. 2020. Molecular docking studies on the targets of Cervical Cancer (DNMT1) Using natural compounds. International journal of research and analytical reviews 7, 735-740.

Vaou N, Stavropoulou E, Voidarou C, Tsigalou C, Bezirtzoglou E. 2021. Towards advances in medicinal plant antimicrobial activity: A review study on challenges and future perspectives. Microorganisms  9, 2041.

Visht S, Chaturvedi S. 2012. Isolation of natural products. Journal of Current Pharma Research 2, 584.

Vivek-Ananth RP, Mohanraj K, Sahoo AK, Samal A. 2023. IMPPAT 2.0: an enhanced and expanded phytochemical atlas of Indian medicinal plants. ACS omega 8, 8827-45.

Yang BH, Bray FI, Parkin DM, Sellors JW, Zhang ZF. 2004. Cervical cancer as a priority for prevention in different world regions: An evaluation using years of life lost. International journal of cancer 109, 418-424. https://doi:10.1002/ijc.11719.

Yim EK, Park JS. 2005. The role of HPV E6 and E7 oncoproteins in HPV-associated cervical carcinogenesis. Cancer Res Treat. 37, 319-324. https://doi:10.4143/crt.2005.37.6.319.