Utilizing the Pyrx Program to Conduct in Silico Screening of Polyphenol Compounds as Potential Inhibitors of the Epidermal Growth Factor Receptor (EGFR) in Mango Plants(Mangifera Indica)

Mango (Mangifera indica) is a tropical plant from Asia with the potential to cure diseases including colorectal cancer. The research aimed to determine the amount of free energy (ΔG) from the polyphenol compounds of mango plants on Epidermal Growth Factor Receptor (EGFR) in silico using PyRx program with molecular docking method. The receptor used was downloaded from the Protein Data Bank (PDB) database with 1YY9 codes and the ligands used were downloaded from the KNApSAcK database. The validation of the docking method showed the RMSD value of 1.645 Å in the Alpha-Mannose; 1.381 Å in Beta-D-Mannose; 1.605 Å at 2-(Aetylamino)-2-Deoxy-A-D-Glucopyronose; and 1.334 Å in N-Acetyl-D-Glucosamine. As the standard, Cetuximab was used as a therapy for colorectal cancer. The polyphenol compounds in mango plants showed bond-free energy (ΔG) with a range of values between -8.5 kcal/molto -6.0 kcal/mol, and the best value was Aurasperone D (-8.5 kcal/mol). Compared to Cetuximab (-6.4 kcal/mol), the value of bond-free energy (ΔG) of Aurasperoune compounds was smaller with quite a farther range of values -2.5 kcal/mol. Polyphenolic compounds discovered in Mango plants displayed potential as inhibitors for the Epidermal Growth Factor Receptor (EGFR).

Keywords:In Silico, Mangifera indica, Epidermal Growth Factor Receptor, Root Mean Square Deviation

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Langkah Docking Dengan Autodock Vina

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1-Click Docking From mcule

Python Prescription

PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process – from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. PyRx also includes chemical spreadsheet-like functionality and powerful visualization engine that are essential for Rational Drug Design.Visit Videos page for Getting Started Screencasts. See also Starting Virtual Screening and Getting Started with PyRx tutorials.

PyRx is using large body of established open source software such as:

Autodock Vina

AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.

AutoDock Vina has been designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute.

The image on the left illustrates the results of flexible docking (green) superimposed on the crystal structures of (a) indinavir, (b) atorvastatin, (c) imatinib, and (d) oseltamivir bound to their respective targets.

Url : http://vina.scripps.edu/index.html

Autodock Tutorial

Argus Lab

Titik awal untuk membantu penelitian permodelan molekul  umumnya merupakan gambar dua dimensi dari molekul yang diperlukan . Diagram data ini berkisar dari sketsa buku catatan untuk koneksi tabel yang disimpan secara eletronik dimana satu sama lain saling  mendefisinikan Jenis atom. Kemudian struktur dua dimensi  diubah menjadi tiga dimensi untuk mempelajari sifat kimia, namun struktur molekul lebih akurat  diubah menjadi tiga dimensi yang respresentasi tersedia di cabridge X.ray kristalografi data base   (sekitar 50.000 struktur). Salah satu aplikasi bantuan Permodelan molekul di lihat disini http://www.arguslab.com/.