Cost-Effective Pipeline for a Rational Design and Selection of Capsaicin Analogues Targeting TRPV1 Channels

Abstract

Transient receptor potential (TRP) channels constitute a large group of membrane receptors associated with sensory pathways in vertebrates. One of the most studied is TRPV1, a polymodal receptor tuned for detecting heat and pungent compounds. Specific inhibition of the nociceptive transduction at the peripheral nerve represents a convenient approach to pain relief. While acting as a chemoreceptor, TRPV1 shows high sensitivity and selectivity for capsaicin. In contrast to the drugs available on the market that target the inflammatory system, TRPV1 antagonists act as negative modulators of nociceptive transduction. Therefore, the development of compounds modulating TRPV1 activity has expanded dramatically over time. Experimental data suggest that most agonist and antagonist drugs interact at or near capsaicin's binding site. In particular, the properties of capsaicin's head play an essential role in modulating potency and affinity. Here, we explored a cost-efficient pipeline to predict the effects of introducing chemical modifications into capsaicin's head region. An extensive set of molecules was selected by first considering the geometrical properties of capsaicin's binding site and then molecular docking. Finally, the novel ligands were ranked by combining molecular and pharmacokinetic predictions.

Figure 1

Vanilloid-binding site dimensions. (A)shows three different sites in the TRPV1 channel; the conduction pore is presented along the transmembrane helix with a volumetric representation in gray color and the vanilloid-binding site formed by two adjoining regions in purple and orange color. (B) represents the average ±standard deviation of the vanilloid-binding site dimensions located in regions I and II in parallel and orthogonal positions regarding the conduction pore, respectively. (C,D) are depicted as the binding site of capsaicin (CAP) and capsazepine (CZP) molecules into the TRPV1 structure (PDBs id: 7LR0 and 5IS0). Both molecules are stabilized by HB interactions (dashed pink line) with the residue E572.

Figure 2

Capsaicin modifications. (A) Chemical modifications introduced into the head region of the CAP structure (embedded into the green rectangle) in atoms 8 and 9 to (B) R1 and (C) R2 substituents, respectively. The tail and neck regions (highlighted by the pink and purple rectangles) were not modified.

Figure 3

Capsaicin derivatives in their binding site. In (A), the best 24 compounds selected through the pipeline are positioned into the vanilloid-binding site in a “tail up, head down” configuration. 2D representation of the binding site of (B) CAP and (C) CZP molecules docked into the TRPV1 channel. The numbering of the structure of TRPV1 in the presence of CAP begins two positions after that in TRPV1 in the presence of CZP because they belong to different organisms described in Table 1.

Figure 4

Intermolecular interactions between protein and ligand: (A–F) represent the intermolecular interactions of TRPV1 channel and capsaicin (CAP), capsazepine (CZP), and the CAP analogues 10A, 12A, 5A, and 1A calculated along with the simulation time (100 ns).

Figure 5

Clustering of all docking poses CAP (faded red–orange color), CZP (blue color), RTX (gray color), and the best four CAP analogues ranked by the MSM: 10A (magenta color), 12A (faded salmon color), 5A (red color), and 1A (yellow color) were docked into the monomer A of TRPV1 (PDB id: 7LR0), TRPV2 (PDB id: 6OO7), 5C is TRPV3 (PDB id: 6UW6), and 5D is TRPV4 (PDB id: 7AA5) channels. Green and cyan ribbons represent the monomers A and B of every channel, respectively. At most, 10 docking poses of each ligand are shown.