Host-pathogen protein-nucleic acid interactions: A comprehensive review

Anuja Jain, Shikha Mittal, Lokesh P. Tripathi, Ruth Nussinov*, Shandar Ahmad

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review


Recognition of pathogen-derived nucleic acids by host cells is an effective host strategy to detect pathogenic invasion and trigger immune responses. In the context of pathogen-specific pharmacology, there is a growing interest in mapping the interactions between pathogen-derived nucleic acids and host proteins. Insight into the principles of the structural and immunological mechanisms underlying such interactions and their roles in host defense is necessary to guide therapeutic intervention. Here, we discuss the newest advances in studies of molecular interactions involving pathogen nucleic acids and host factors, including their drug design, molecular structure and specific patterns. We observed that two groups of nucleic acid recognizing molecules, Toll-like receptors (TLRs) and the cytoplasmic retinoic acid-inducible gene (RIG)-I-like receptors (RLRs) form the backbone of host responses to pathogen nucleic acids, with additional support provided by absent in melanoma 2 (AIM2) and DNA-dependent activator of Interferons (IFNs)-regulatory factors (DAI) like cytosolic activity. We review the structural, immunological, and other biological aspects of these representative groups of molecules, especially in terms of their target specificity and affinity and challenges in leveraging host-pathogen protein-nucleic acid interactions (HP-PNI) in drug discovery.

Original languageEnglish
Pages (from-to)4415-4436
Number of pages22
JournalComputational and Structural Biotechnology Journal
StatePublished - Jan 2022


  • Drug design
  • Host pathogen interactions
  • Immunological response
  • Protein-nucleic acid interactions
  • Structural biology
  • Toll-like receptors


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