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Paul D, Mahanta S, Tag H, Das SK, Das Gupta D, Tanti B, Ananthan R, Das R, Jambhulkar S, Hui PK. Identification of tyrosine kinase inhibitors from Panax bipinnatifidus and Panax pseudoginseng for RTK-HER2 and VEGFR2 receptors, by in silico approach. Mol Divers 2021; 26:1933-1955. [PMID: 34554395 DOI: 10.1007/s11030-021-10304-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/24/2021] [Indexed: 11/26/2022]
Abstract
Breast and stomach cancer is reported as a leading cause for human mortality across the world. The overexpression of receptor tyrosine kinase (RTK) proteins, namely the human epidermal growth factor receptor2 (HER2) and the vascular endothelial growth factor receptor2 (VEGFR2), is reported to be responsible for development and metastasis of breast and stomach cancer. Although several synthetic tyrosine kinase inhibitors (TKIs) as drug candidates targeting RTK-HER2 and VEGFR2 are currently available in the market, these are expensive with the reported side effects. This confers an opportunity for development of alternative novel tyrosine kinase inhibitors (TKIs) for RTK-HER2 and VEGFR2 receptors from the botanical sources. In the present study, we characterized 47 bioactive phytocompounds from the methanol extracts of the rhizomes of Asiatic traditional medicinal herbs-Panax bipinnatifidus and Panax pseudoginseng, of Indian Himalayan landraces using HPLC, GC-MS and high-sensitivity LC-MS tools. We performed molecular docking and molecular dynamics simulation analysis using Schrödinger suite 2020-3 to confirm the TKI phytocompounds showing the best binding affinity towards RTK-HER2 and VEGFR2 receptors. The results of molecular docking studies confirmed that the phytocompound (ligand) luteolin 7-O-glucoside (IHP15) showed the highest binding affinity towards receptor HER2 (PDB ID: 3PP0) with docking score and Glide g score (G-Score) of - 13.272, while chlorogenic acid (IHP12) showed the highest binding affinity towards receptor VEGFR2 (PDB ID: 4AGC) with docking score and Glide g score (G-Score) of - 10.673. Molecular dynamics (MD) simulation analysis carried out for 100 ns has confirmed strong binding interaction between the ligand and receptor complex [luteolin 7-O-glucoside (IHP15) and HER2 (PDB ID: 3PP0)] and is found to be stabilized within 40 to 100 ns of MD simulation, whereas ligand-receptor complex [chlorogenic acid (IPH12) and VEGFR2 (PDB ID: 4AGC)] also showed strong binding interaction and is found to be stabilized within 18-30 ns but slightly deviated during 100 ns of MD simulation. In silico ADME-Tox study using SwissADME revealed that the ligands luteolin 7-O-glucoside (IHP15) and chlorogenic acid (IHP12) have passed majority parameters of the common drug discovery rules. The present study has confirmed luteolin 7-O-glucoside (IHP15) and chlorogenic acid (IHP12) as potential tyrosine kinase inhibitors (TKIs) which were found to inhibit RTKs-HER2 and VEGFR2 receptor proteins, and thus paving the way for development of alternative potential TKIs (drug molecules) for treatment of HER2- and VEGFR2-positive breast and stomach cancer.
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Affiliation(s)
- Dipayan Paul
- Department of Biotechnology, National Institute of Technology Arunachal Pradesh, Yupia, Papum Pare, Arunachal Pradesh, 791112, India
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology, Guwahati, Assam, 781008, India
| | - Hui Tag
- Pharmacognosy and Phytochemistry Research Laboratory, Department of Botany, Rajiv Gandhi University, Rono Hills, Doimukh, Arunachal Pradesh, 791112, India.
| | - Sanjib Kumar Das
- Department of Biotechnology, National Institute of Technology Arunachal Pradesh, Yupia, Papum Pare, Arunachal Pradesh, 791112, India
| | - Debmalya Das Gupta
- Department of Biotechnology, National Institute of Technology Arunachal Pradesh, Yupia, Papum Pare, Arunachal Pradesh, 791112, India
| | - Bhaben Tanti
- Department of Botany, Gauhati University, Guwahati, Assam, 781014, India
| | - Rajendran Ananthan
- Food Chemistry Division, ICMR National Institute of Nutrition, Jamai-Osmania PO, Hyderabad, Telangana, 500007, India
| | - Ranjan Das
- Department of Crop Physiology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Sanjay Jambhulkar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, 400085, India
| | - Pallabi Kalita Hui
- Department of Biotechnology, National Institute of Technology Arunachal Pradesh, Yupia, Papum Pare, Arunachal Pradesh, 791112, India.
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