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Updated: Feb 28, 2026

Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods
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AI-Guided Binding Mechanisms and Molecular Dynamics for MERS-CoV

Pradyumna Kumar1, Lingtao Chen1, Rachel Yuanbao Chen2

  • 1College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA.

International Journal of Molecular Sciences
|February 27, 2026
PubMed

Insights

Middle East respiratory syndrome coronavirus (MERS-CoV) entry into human cells relies on DPP4 receptor interactions. Molecular Dynamics simulations identified key residues for MERS-CoV-DPP4 binding, aiding antiviral drug design.

Area of Science:

  • Virology and Computational Biology
  • Drug Discovery and Development

Background:

  • Middle East respiratory syndrome coronavirus (MERS-CoV) poses a significant public health threat due to its high mortality rate and limited treatment options.
  • Viral entry mechanisms, specifically the interaction between MERS-CoV surface proteins and the human Dipeptidyl Peptidase-4 (DPP4) receptor, are crucial for understanding and combating infection.

Purpose of the Study:

  • To identify critical interface residues involved in the MERS-CoV and DPP4 receptor interaction using computational methods.
  • To provide a molecular basis for developing targeted antiviral therapies against MERS-CoV.

Main Methods:

  • Utilized Molecular Dynamics (MD) simulations on a high-performance computing (HPC) platform to analyze MERS-CoV-DPP4 interactions.
  • Identified key residue pairs by analyzing salt bridge and hydrogen bond occupancy.
  • Validated residue stability through independent MD simulations at human body temperature and pressure.
  • Calculated binding affinities to quantify interaction strength.

Main Results:

  • Identified seven key interaction pairs between MERS-CoV and the DPP4 receptor.
  • Confirmed two previously reported interaction pairs (Asp510-Arg317 and Arg511-Asp393).
  • Proposed five novel interaction pairs for future experimental validation in antiviral drug discovery.

Conclusions:

  • The study provides crucial molecular insights into the MERS-CoV-DPP4 binding mechanism.
  • Findings support the rational design of structure-based inhibitors to disrupt viral entry.
  • This research facilitates the translation of computational discoveries into potential MERS-CoV antiviral therapeutics.
Keywords:
Artificial Intelligence (AI)MERS-CoVbinding affinitycoronavirusdrug targethigh performance computing (HPC)hydrogen bondsmolecular simulationsprotein–protein interaction (PPI)salt bridge analysis

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