Comprehensive analysis of protein-protein interactions (PPIs) with structure prediction program for breast cancer determination

Exploring HER2 Protein Structure and Ligand Interactions in Breast Cancer

  • Febrina Margaretha Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
  • Mukti Subagja Department of Biotechnology, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
  • Altri Diana Putri Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
  • Christabel Queentha Salam Department of Biotechnology, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
  • Louis Valenthenardo Department of Biotechnology, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
  • Priscilla Klaresza Adhiwijaya Department of Biotechnology, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
  • Gabriella Zevania Kaitlyn Department of Biotechnology, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
  • Arli Parikesit Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
Keywords: HER2, I-TASSER, ligand, novel treatment, breast cancer, binding affinity

Abstract

Breast cancer is a prevalent disease that primarily affects women, with significant implications for public health. Early detection improves survival rates, and technological advancements can enhance early diagnosis. Protein structure prediction methods can provide valuable insights into the structure of proteins involved in breast cancer, including human epidermal growth factor receptor-2 (HER2). HER2 is a known protein receptor that plays a critical role in breast cancer development and is a target for therapy. Predicting the binding affinity between HER2 and potential ligands can help identify novel treatment options. This study aimed to predict the structure of HER2 using I-TASSER and determine potential ligands using empirical graph neural network-based scoring functions. Molecular docking simulations were performed to evaluate the binding conformation and stability of the HER2-ligand complexes. The results showed the potential ligands identified by I-TASSER: AEE, UUU, and Mg2+. Afterward, their binding affinity with HER2 was assessed, yielding AEE as the best binding with the lowest vina score.

Published
2023-12-07
How to Cite
Margaretha, F., Subagja, M., Diana Putri, A., Salam, C. Q., Valenthenardo, L., Adhiwijaya, P. K., Kaitlyn, G. Z., & Parikesit, A. (2023). Comprehensive analysis of protein-protein interactions (PPIs) with structure prediction program for breast cancer determination. BERKALA PENELITIAN HAYATI JOURNAL OF BIOLOGICAL RESEARCHES, 29(3), 87-94. Retrieved from https://ojs.berkalahayati.org/index.php/jurnal/article/view/745