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Molecular Docking and Dynamic Simulation of Erythrina fusca Lour Chemical Compounds Targeting VEGFR-2 Receptor for Anti-Liver Cancer Activity Maharani, Dila Aulia; Adelina, Rosa; Aini, Anggun Qurrota; Supandi, Supandi
Jurnal Kimia Valensi Jurnal Kimia VALENSI, Volume 10, No. 1, May 2024
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v10i1.35295

Liver cancer is a serious health concern characterized by abnormal cell growth, but currently, available treatment options are limited, suggesting the need for a new therapeutic method. Therefore, this research aimed to investigate the potential of chemical compounds obtained from the cangkring plant (Erythrina fusca) as anti-liver cancer agents targeting Vascular Endothelial Growth Factor Receptor 2 (VEGFR-2). The investigation was conducted in silico through molecular docking and dynamic method. Molecular docking was performed using AutoDock Tools, followed by visualization with Biovia Discovery Studio. Additionally, molecular dynamics simulation was conducted using GROMACS software and visualized with Grace. A total of 36 chemical compounds from E. fusca were used as ligands for molecular docking. The results showed that Isobavachalcone (ISB) was the most effective test compound with a binding energy of -11.45 kcal/mol, compared to the positive control Sorafenib with a value of - 11.51 kcal/mol. In this context, hydrogen bonding, as well as hydrophobic, electrostatic, and unfavorable molecular interactions were identified. Moreover, molecular dynamics simulation provided RMSD, RMSF, Radius of Gyration (Rg), and hydrogen bond parameters. Analysis of these parameters further confirmed the superior stability of ISB in binding to VEGFR-2, suggesting the potential to suppress angiogenesis by blocking the receptor.

Molecular Docking and Molecular Dynamic Simulation on the Interaction of Saffron’s Active Compunds with HER-2 Protein Adelina, Rosa; Maharani, Dila Aulia; Octaviani, Putri; Putra, Sendi Handika
Indonesian Journal of Cancer Chemoprevention Vol 14, No 2 (2023)
Publisher : Indonesian Society for Cancer Chemoprevention

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14499/indonesianjcanchemoprev14iss2pp117-127

Human epidermal growth factor receptor-2 (HER-2) is an essential oncogene in breast cancer. HER-2 causes 25% of breast cancer, and this type of cancer tends to grow and spread faster than others but had a good response to HER-2 targeted therapy. This study aims to analyze chemical compounds in saffron plants (Crocus sativus) that potential to breast anticancer activity by inhibiting HER-2 receptor (PDB ID: 3RCD). The study employed in silico research such as molecular docking using AutoDock Tools software, and visualization with Biovia Discovery Studio. In addition, molecular dynamic simulation was conducted using GROMACS software, with visualization performed using Grace. The molecular docking results showed that Crocetin has a lower binding energy value of -8.37 kcal/mol compared to Herceptin, which is -7.11 kcal/mol and the lowest energy among Saffron bioactive compounds. These results indicated that the affinity of Crocetin in binding to HER-2 receptor is better than Herceptin. The molecular interactions were hydrogen, hydrophobic, electrostatic, and unfavorable bonds. The MD results showed that the RMSD value meets the 0.2-0.5 nm stability requirements. According to the data analysis, Herceptin appears to have a more stable RMSF value when compares to Crocetin. The Rg graph of both complexes showed stability until the end of the simulation. The H-bond results show that the Herceptin complex has more hydrogen bonds than the Crocetin complex. These results showed that the chemical components of saffron plants have the potential as breast anticancers by inhibiting the HER-2 receptor.Keywords: anticancer, Crocus sativus, HER-2 receptor, molecular docking, molecular dynamic.

The Study of Molecular Docking and Molecular Dynamics Simulation Chemical Compound of Pycnarrhena cauliflora Diels. as Proapoptosis in Cervical Cancer Aini, Anggun Qurrota; Supandi, Supandi; Adelina, Rosa; Maharani, Dila Aulia
Indonesian Journal of Cancer Chemoprevention Vol 15, No 1 (2024)
Publisher : Indonesian Society for Cancer Chemoprevention

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14499/indonesianjcanchemoprev15iss1pp63-75

Cervical cancer is one of the most common cancers among women worldwide and in Indonesia. B-cell lymphoma 2 (Bcl-2) can play a role in causing cancer by inhibiting apoptosis. The purpose of this study was to analyze the chemical compound of the sengkubak plant (Pycnarrhena cauliflora Diels.), which can act as antiapoptotic inhibitor by binding to the B-cell lymphoma 2 (Bcl-2) receptor. The research was conducted in silico with molecular docking methods and molecular dynamics simulations. Molecular docking used the AutoDock 4.2.6 software and visualization used Biovia Discovery Studio. Molecular dynamics simulation used Gromacs 5.1.2 software and result visualization used Grace. Longipinocarvone was the best test ligand with the smallest ΔGbind value of -6.99 kcal/mol compared to the positive control of Doxorubicin and other compounds which indicating Longipinocarvone’s affinity for binding to the Bcl-2 receptor was better than Doxorubicin. The types of interactions involved in the molecular docking of the chemical compounds of the sengkubak plant and Doxorubicin including hydrogen bonds and hydrophobic interactions. The stability of the bond between the ligand protein complex resulting from molecular docking was analyzed based on the parameters RMSD, RMSF, Radius of Gyration (Rg) values through molecular dynamics simulations. The results of the analysis showed that Longipinocarvone and Doxorubicin had a stable bond with Bcl-2 as indicated by the RMSD and RMSF values meeting the requirements, namely <3 Å (0.3 nm). The Rg graph showed both complexes are stable during simulation and have resemblant ligand-protein movements.Keywords: Cervical cancer, B-cell lymphoma 2 (Bcl-2), Pycnarrhena cauliflora Diels., molecular docking, molecular dynamics.

Molecular Docking and Dynamic Simulation of Erythrina fusca Lour Chemical Compounds Targeting VEGFR-2 Receptor for Anti-Liver Cancer Activity Maharani, Dila Aulia; Adelina, Rosa; Aini, Anggun Qurrota; Supandi, Supandi
Jurnal Kimia Valensi Jurnal Kimia VALENSI, Volume 10, No. 1, May 2024
Publisher : Department of Chemistry, Faculty of Science and Technology Syarif Hidayatullah Jakarta State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v10i1.35295

Liver cancer is a serious health concern characterized by abnormal cell growth, but currently, available treatment options are limited, suggesting the need for a new therapeutic method. Therefore, this research aimed to investigate the potential of chemical compounds obtained from the cangkring plant (Erythrina fusca) as anti-liver cancer agents targeting Vascular Endothelial Growth Factor Receptor 2 (VEGFR-2). The investigation was conducted in silico through molecular docking and dynamic method. Molecular docking was performed using AutoDock Tools, followed by visualization with Biovia Discovery Studio. Additionally, molecular dynamics simulation was conducted using GROMACS software and visualized with Grace. A total of 36 chemical compounds from E. fusca were used as ligands for molecular docking. The results showed that Isobavachalcone (ISB) was the most effective test compound with a binding energy of -11.45 kcal/mol, compared to the positive control Sorafenib with a value of - 11.51 kcal/mol. In this context, hydrogen bonding, as well as hydrophobic, electrostatic, and unfavorable molecular interactions were identified. Moreover, molecular dynamics simulation provided RMSD, RMSF, Radius of Gyration (Rg), and hydrogen bond parameters. Analysis of these parameters further confirmed the superior stability of ISB in binding to VEGFR-2, suggesting the potential to suppress angiogenesis by blocking the receptor.

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