Synthesis and characterization of new potent TLR7 antagonists based on analysis of the binding mode using biomolecular simulations

• Published in: European journal of medicinal chemistry Vol. 210; p. 112978
• Main Authors: Pal, Sourav, Paul, Barnali, Bandopadhyay, Purbita, Preethy, Nagothy, Sarkar, Dipika, Rahaman, Oindrila, Goon, Sunny, Roy, Swarnali, Ganguly, Dipyaman, Talukdar, Arindam
• Format: Journal Article
• Language: English
• Published: France Elsevier Masson SAS 15-01-2021
• Subjects: Antagonist; Binding model; Binding Sites - drug effects; Dendritic Cells - drug effects; Dose-Response Relationship, Drug; Drug design; HEK293 Cells; Humans; Molecular docking; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Molecular Structure; Quinazolines - chemical synthesis; Quinazolines - chemistry; Quinazolines - pharmacology; Structure-Activity Relationship; Toll-like receptor 7; Toll-Like Receptor 7 - antagonists & inhibitors; Toll-Like Receptor 7 - metabolism; Molecular dynamics; Toll-like receptor 7; Drug design; Binding model; Antagonist; Molecular docking
• ISSN: 0223-5234; 1768-3254
• DOI: 10.1016/j.ejmech.2020.112978

Aberrant activation of the endosomal Toll-like receptor 7 (TLR7) has been implicated in myriad autoimmune diseases and is an established therapeutic target in such conditions. Development of diverse TLR7 antagonists is mainly accomplished through random screening. To correlate human TLR7 (hTLR7) antagonistic activity with the structural features in different chemotypes, we derived a hypothetical binding model based on molecular docking analysis along with molecular dynamics (MD) simulations study. The binding hypothesis revealed different pockets, grooves and a central cavity where ligand-receptor interaction with specific residues through hydrophobic and hydrogen bond interactions take place, which correlate with TLR7 antagonistic activity thus paving the way for rational design using varied chemotypes. Based on the structural insight thus gained, TLR7 antagonists with quinazoline were designed to understand the effect of engagement of these pockets as well as boundaries of the chemical space associated with them. The newly synthesized most potent hTLR7 antagonist, i.e. compound 63, showed IC50 value of 1.03 ± 0.05 μM and was validated by performing primary assay in human plasmacytoid dendritic cells (pDC) (IC50pDC: 1.42 μM). The biological validation of the synthesized molecules was performed in TLR7-reporter HEK293 cells as well as in human plasmacytoid dendritic cells (pDCs). Our study provides a rational design approach thus facilitating further development of novel small molecule hTLR7 antagonists based on different chemical scaffolds.
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•hTLR7 antagonist binding hypothesis based on docking analysis of known antagonists.•Significance of engaging different pockets and grooves for hTLR7 antagonism.•MD simulation showed ligand binding stability and protein conformational change.•Newly designed ligands based on binding model showed potent hTLR7 antagonism.•Interaction pattern can correlate the structural change in molecule with the activity.