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Oncoinformatic screening of the gene clusters involved in the HER2-positive breast cancer formation along with the in silico pharmacodynamic profiling of selective long-chain omega-3 fatty acids as the metastatic antagonists

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Abstract

The HER2-positive patients occupy ~ 30% of the total breast cancer patients globally where no prevalent drugs are available to mitigate the frequent metastasis clinically except lapatinib and neratinib. This scarcity reinforced researchers' quest for new medications where natural substances are significantly considered. Valuing the aforementioned issues, this research aimed to study the ERBB2-mediated string networks that work behind the HER2-positive breast cancer formation regarding co-expression, gene regulation, GAMA-receptor-signaling pathway, cellular polarization, and signal inhibition. Following the overexpression, promotor methylation, and survivability profiles of ERBB2, the super docking position of HER2 was identified using the quantum tunneling algorithm. Supramolecular docking was conducted to study the target specificity of EPA and DHA fatty acids followed by a comprehensive molecular dynamic simulation (100 ns) to reveal the RMSD, RMSF, Rg, SASA, H-bonds, and MM/GBSA values. Finally, potential drug targets for EPA and DHA in breast cancer were constructed to determine the drug–protein interactions (DPI) at metabolic stages. Considering the values resulting from the combinational models of the oncoinformatic, pharmacodynamic, and metabolic parameters, long-chain omega-3 fatty acids like EPA and DHA can be considered as potential-targeted therapeutics for HER2-positive breast cancer treatment.

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Authors and Affiliations

  1. Pathology and Pathophysiology Major, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001, Henan Province, People’s Republic of China

    A K M Helal Morshed

  2. Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu Province, People’s Republic of China

    Salauddin Al Azad

  3. Department of Pharmaceutical Technology, Faculty of Pharmacy, International Islamic University Malaysia, 25200, Pahang, Kuantan, Malaysia

    Md. Abdur Rashid Mia

  4. College of Material Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, People’s Republic of China

    Mohammad Fahim Uddin

  5. Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh

    Tanzila Ismail Ema & Rukaiya Binte Yeasin

  6. School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka, 1212, Bangladesh

    Sanjida Ahmed Srishti

  7. Department of Medicine, Sher-E-Bangla Medical College Hospital, South Alekanda, Barisal, 8200, Bangladesh

    Pallab Sarker

  8. Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Palashi, Dhaka, 1205, Bangladesh

    Rubaita Younus Aurthi

  9. Department of Pharmacy, University of Asia Pacific, Farmgate, Dhaka, 1205, Bangladesh

    Farhan Jamil

  10. School of Environment and Life Sciences, Independent University, Dhaka, 1219, Bangladesh

    Nure Sharaf Nower Samia

  11. Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh

    Partha Biswas

  12. School of Data Sciences, Department of Mathematics & Natural Sciences, BRAC University, 66 Mohakhali, Dhaka, 1212, Bangladesh

    Iffat Ara Sharmeen

  13. School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough, TS1 3BX, Tees Valley, UK

    Rasel Ahmed

  14. State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, People’s Republic of China

    Mahbuba Siddiquy

  15. Department of Mathematics, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh

    Nurunnahar

Authors
  1. A K M Helal Morshed
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  2. Salauddin Al Azad
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Correspondence to Salauddin Al Azad.

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Morshed, A.K.M.H., Al Azad, S., Mia, M.A.R. et al. Oncoinformatic screening of the gene clusters involved in the HER2-positive breast cancer formation along with the in silico pharmacodynamic profiling of selective long-chain omega-3 fatty acids as the metastatic antagonists. Mol Divers 27, 2651–2672 (2023). https://doi.org/10.1007/s11030-022-10573-8

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