An in silico approach towards the identification of novel inhibitors of the TLR-4 signaling pathway

Abstract

Precise functioning and fine-tuning of Toll-like receptor 4 (TLR4) signaling is a critical requirement for the smooth functioning of the innate immune system, since aberrant TLR4 activation causes excessive production of pro-inflammatory cytokines and interferons. This can result in life threatening conditions such as septic shock and other inflammatory disorders. The TRIF-related adaptor molecule (TRAM) adaptor protein is unique to the TLR4 signaling pathway and abrogation of TRAM-mediated TLR4 signaling is a promising strategy for developing therapeutics aimed at disrupting TRAM interactions with other components of the TLR4 signaling complex. The VIPER motif from the vaccinia virus-producing protein, A46 has been reported to disrupt TRAM-TLR4 interactions. We have exploited this information, in combination with homology modeling and docking approaches, to identify a potential binding site on TRAM lined by the BB loop and αC helix. Virtual screening of commercially available small molecules targeting the binding site enabled to short-list 12 small molecules to abrogate TRAM-mediated TLR4 signaling. Molecular dynamics and molecular mechanics calculations have been performed for the analysis of these receptor-ligand interactions.

Keywords:

• innate immunity
• TLR4
• TRAM
• A46
• VIPER
• sepsis
• homology modeling
• docking
• virtual screening
• MM-GBSA
• molecular dynamics simulations
• induced-fit docking
• therapeutics

Acknowledgements

Authors thank NCBS (TIFR) for infrastructural support.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the Centre for Excellence Grant [grant number BT/01/COE/09/01], Department of Biotechnology, India to RS and a Senior Research Fellowship [grant number 09/860(0139)/2012-EMR-I] awarded by the Council of Scientific and Industrial Research (CSIR) to JM.