STM Article Repository

Background: Uncontrolled activity of tumor necrosis factor alpha (TNF-α) as pro-inflammatory cytokine has been linked with pathogenesis of autoimmune/inflammatory diseases. Therefore, modulating of TNF-α associated biological pathways is a promising strategy for alleviating of such diseases. In view of this, the use of antibody fragments such as single-chain variable fragments (scFv) in therapeutic applications has been gained much attention in terms of pharmacokinetic as well as production and therapeutic costs.

Methods: In the current investigation, the previously designed and humanized hD2 antibody was modeled and docked onto the TNF-α structure. The binding free energy was predicted for the complex of hD2-TNF-α using molecular dynamics calculation followed by per-residue energy decomposition for residues of hD2. In addition in silico mutations of important amino acids at the binding site of enzyme were performed and the binding free energy was calculated for mutant forms of scFv in complex with TNF-α.

Results: The analyses of the results proposed Y27F mutation in heavy chain CDR1 of hD2 scFv antibody may be considered as a promising substitution.

Conclusion: The results may be used for designing new anti-TNF-α antibody with improved activity.