Integration of Ligand-Based and Structure-Based Methods for the Design of Small-Molecule TLR7 Antagonists

Abstract

Toll-like receptor 7 (TLR7) is activated in response to the binding of single-stranded RNA. Its over-activation has been implicated in several autoimmune disorders, and thus, it is an established therapeutic target in such circumstances. TLR7 small-molecule antagonists are not yet available for therapeutic use. We conducted a ligand-based drug design of new TLR7 antagonists through a concerted effort encompassing 2D-QSAR, 3D-QSAR, and pharmacophore modelling of 54 reported TLR7 antagonists. The developed 2D-QSAR model depicted an excellent correlation coefficient (R2training: 0.86 and R2test: 0.78) between the experimental and estimated activities. The ligand-based drug design approach utilizing the 3D-QSAR model (R2training: 0.95 and R2test: 0.84) demonstrated a significant contribution of electrostatic potential and steric fields towards the TLR7 antagonism. This consolidated approach, along with a pharmacophore model with high correlation (Rtraining: 0.94 and Rtest: 0.92), was used to design quinazoline-core-based hTLR7 antagonists. Subsequently, the newly designed molecules were subjected to molecular docking onto the previously proposed binding model and a molecular dynamics study for a better understanding of their binding pattern. The toxicity profiles and drug-likeness characteristics of the designed compounds were evaluated with in silico ADMET predictions. This ligand-based study contributes towards a better understanding of lead optimization and the future development of potent TLR7 antagonists.

Development, Optimization, and In Vivo Validation of New Imidazopyridine Chemotypes as Dual TLR7/TLR9 Antagonists through Activity-Directed Sequential Incorporation of Relevant Structural Subunits

“…The conceptual design of the compounds was influenced by our previous experience with the essential structural features and geometrical arrangements in different chemotypes such as benzoxazole, , oxoadenine, − imidazoquinoline, quinazoline, − and other cores. − To identify the minimal substitutions required to attain TLR7/9 antagonism, initially, 7–11 were prepared with small substituents at the C4′ and C2′ positions. The C2′ substitution was to impart obvious geometrical restrictions in the molecule.…”

“…70,71 Plasma Stability. Compounds 24,26,38,41,42,53, 54, and 60 showed good plasma stability in both human and mouse plasma (Table 5).…”

“…In Vitro Cellular Toxicity Assay. From our library, we selected 10 hit compounds 24,26,27,35,38,42,53,54, 60, and 64 for cytotoxicity assessment. We checked the in vitro toxicity in various cell lines of different tissue origins, for example, human peripheral blood mononuclear cells (PBMCs) (hematopoietic origin) and HEK293 cells, by propidium iodide (PI) staining.…”

“…4(M) HCl in 1,4-dioxane (1.0 mL) was added to a solution of compound 50 (0.25 g, 0.47 mmol) in 1,4-dioxane (2.0 mL) at 0−5 °C, and the reaction was carried out following general procedure H. Pure compound 52 appeared as a greenish solid (67%, mp 72 °C). 1 (53). To a mixture of compound 51 (0.12 g, 0.27 mmol) and K 2 CO 3 (0.074 g, 0.53 mmol) in dry DMF (1.5 mL), bromocyclopentane (0.035 mL, 0.35 mmol) was added following the general procedure I.…”

“…TLR7 and TLR9 activation with their respective ligands lead to identical downstream signaling pathways initiated by the association with their adaptor protein Myd88 and culminating in the transcriptional activation of several inflammatory genes such as type I interferons or pro-inflammatory cytokines depending on the cell type and the endosomal localization of the ligands. , Dual antagonists targeting TLR7/9 serve as important tools to prevent undesirable activation and production of type I interferons in various inflammatory disease contexts. Antimalarial drugs chloroquine and hydroxychloroquine, with established inhibitory action on endosomal TLR activation, have been in clinical use against several major autoimmune diseases such as rheumatoid arthritis. , Several oligonucleotide TLR7/TLR9 antagonists such as IMO-8400, IMO-3100, and IMO-9200 have undergone evaluation in clinical trials to monitor their safety and efficacy in patients diagnosed with autoimmune disorders. − Pfizer initiated a clinical trial of a small molecule (CpG-52364) with a quinazoline core, but it failed to pass the phase I stage. ,, Several groups along with us have also previously demonstrated systematic development of potent TLR7 and TLR9 small-molecule antagonists based on benzoxazole, , quinazoline, − imidazoquinoline, and purine − scaffolds by employing different medicinal chemistry strategies. − Through agonist-to-antagonist strategy, we identified a chemical switch in the purine scaffold leading to a switch from TLR7 agonism to antagonism . An activity-guided strategy was employed for the development of selective TLR9 and dual TLR7/TLR9 antagonists in the quinazoline scaffold. , …”