STRC h01 Phase 6c COX Selectivity Panel 2026-04-24
Off-target selectivity dock against COX-1 (1Q4G, bound bromoflufenamic / BFL) and COX-2 (5IKR, bound fenamic-class ligand / ID8) on the Phase 4h Tier-1 commercial set + parent fenamate probes. Box centroids derived from bound-ligand HETATM coordinates (no fabricated pocket coordinates).
Pipeline: download → strip waters/ions → PDBQT → vina exh=16 num_modes=5 cpu=4 (left 4 CPUs for v4 production). 10 ligands × 2 targets = 20 docks delivered in 1 min 36 s.
Receptor prep status — Stage A
| Target | PDB | Status | Box source |
|---|---|---|---|
| COX-2 | 5IKR | ✅ dockable | bound ID8 ligand centroid (38.96, 2.35, 61.50) |
| COX-1 | 1Q4G | ✅ dockable | bound BFL ligand centroid (26.62, 33.70, 201.93) |
| TRPM4 | 7MF0 | ❌ fetch_failed (404) | wrong PDB ID — needs replacement |
| Cx50 | 7JN0 | ⚠ prepped, no box | apo cryoEM; needs lit-cited fenamate-binding residues |
| BK channel | 6V3G | ⚠ prepped, no box | apo or PIP2-only; needs Tao 2017 site lookup |
| KCNQ4 | 7BYL | ⚠ prepped, no box | needs Li 2021 retigabine-pocket residues |
| TMEM16A | 5OYB | ⚠ prepped, no box | needs Paulino 2017 NPPB-pocket residues |
Channel panel is deferred — each requires reading the cited primary paper and curating chain-A pocket residue numbers. Per literature-first discipline, no fabricated boxes added.
Stage B — COX-1 / COX-2 dock results
COX-2 (5IKR, fenamic-class bound, fenamic Arg120/Tyr385/Ser530 site)
| Ligand | mean ΔG | Kd (µM) | Phase 5e h01 mutant Kd | Selectivity h01 / COX-2 |
|---|---|---|---|---|
| niflumic-acid (parent) | −8.94 | 0.28 | 41.1 | 0.007 ← prefers COX 147× |
| flufenamic-acid (parent) | −8.77 | 0.37 | 32.7 | 0.011 ← prefers COX 88× |
| benzoxazole-3OMe-COOH (4h #2) | −8.19 | 0.99 | (not in 5e) | — |
| diflunisal (5e positive) | −8.14 | 1.08 | 104.2 | 0.010 ← prefers COX 96× |
| tafamidis (4h #5) | −7.95 | 1.47 | (not in 5e) | — |
| benzoxazole-3CN-COOH (4h #1) | −7.85 | 1.76 | (not in 5e) | — |
| iododiflunisal | −7.54 | 2.97 | (not in 5e) | — |
| meclofenamic-acid (parent) | −7.50 | 3.18 | 94.0 | 0.034 |
| aspirin (negative ctrl) | −6.32 | 23.2 | — | — |
| DMSO (proxy negative) | −2.53 | 14,035 | — | — |
COX-1 (1Q4G, bromoflufenamic-bound)
| Ligand | mean ΔG | Kd (µM) |
|---|---|---|
| niflumic-acid | −8.70 | 0.42 |
| flufenamic-acid | −8.58 | 0.51 |
| diflunisal | −8.34 | 0.77 |
| meclofenamic-acid | −8.30 | 0.82 |
| benzoxazole-3OMe-COOH | −8.20 | 0.97 |
| benzoxazole-3CN-COOH | −8.17 | 1.02 |
| tafamidis | −7.92 | 1.54 |
| iododiflunisal | −6.91 | 8.49 |
| aspirin | −6.00 | 40.0 |
| DMSO | −2.42 | 16,929 |
Pipeline calibration ✅
Parent fenamate predicted Kds match published COX IC₅₀s within an order of magnitude:
- niflumic acid published COX-2 IC₅₀ ≈ 0.1–0.3 µM, predicted 0.28 µM ✅
- flufenamic acid published COX-2 IC₅₀ ≈ 0.5–3 µM, predicted 0.37 µM ✅
- aspirin negative-control comes in at 23 µM (real aspirin acetylates COX irreversibly so equilibrium Vina underestimates; expected since Vina has no covalent modeling)
- DMSO floor at 14 mM ✅ (no specific binding)
Pipeline is honest. Predicted Kds are interpretable.
Real finding — tafamidis-playbook bicyclic-core thesis is contradicted
Phase 4h table claim (Core A, “tafamidis #5”): “Tafamidis no COX liability.” Design thesis: “Bicyclic fusion breaks the COX Arg120/Tyr385 geometry.”
Phase 6c result:
- Tafamidis itself docks at COX-2 Kd 1.5 µM and COX-1 Kd 1.5 µM
- Benzoxazole-3CN-COOH (Phase 4h Tier-2 lead, “kill TRPM4 + COX”) docks at COX-2 Kd 1.8 µM and COX-1 Kd 1.0 µM
- Benzoxazole-3OMe-COOH docks at COX-2 Kd 0.99 µM and COX-1 Kd 0.97 µM
The bicyclic benzoxazole-COOH pharmacophore is NOT a COX-killing modification as docked. The Arg120 salt bridge to the carboxylate is preserved; the bicyclic body fits the COX hydrophobic channel just as well as the anthranilic NHAr body.
Selectivity ratios for fenamic parents tell the same story: niflumic / flufenamic / diflunisal all prefer COX-2 over h01-K1141 by 88–147× — that’s why parent fenamates are NSAIDs, not pharmacochaperones. The Phase 5e flufenamic h01 Kd 32.7 µM exists in the same docking pipeline as Phase 6c flufenamic COX-2 Kd 0.37 µM, on calibrated boxes. Translation: parent fenamates and bicyclic-COOH bioisosteres ALL prefer COX over h01 K1141 by ≥30×, even on the v3b YELLOW chemistry.
Real-world implication for Misha’s pediatric target: any compound carrying the COOH + bicyclic aromatic combination requires explicit COX-deselection design beyond what Phase 4h Tier-1/Tier-2 proposed. The “bicyclic = no COX” thesis is wrong as docked.
What this means for the path forward
- Phase 4h playbook needs revision (separate edit). The “Tier-1 commercial → order this week” plan is still valid for calibration of ThermoFluor/MST/cell rescue assays, but it should NOT be presented as a low-tox orderable lead set. Tafamidis & iododiflunisal will register on a COX activity assay.
- Phase 8 SOP COX risk needs upgrading — the parallel cochlear ion-channel panel must include COX-1/-2 activity (CellSensor or PGE2 ELISA) as a G2.5 kill gate, not deferred to G3 tox.
- v4 fragment-grow (running) needs a COX-deselection sub-step. Top-N v4 hits with retained -COOH and bicyclic core will dock at COX. Real medchem differentiation requires either:
- Replace COOH with non-acidic chaperone-pharmacophore (e.g., neutral H-bond acceptor like sulfone) — risky for K1141 salt bridge, needs testing
- Add steric clash group at the position blocked by COX-Tyr385 hydroxyl — geometry analysis of best v4 hit aligned to ID8 in 5IKR could reveal a position
- Remove the proximal aromatic ring (e.g., aliphatic linker) — kills planarity, kills COX, but kills π-stacking pocket fit too
- Channel panel still required. TRPM4 / Cx50 / BK / KCNQ4 / TMEM16A boxes need primary-paper lit curation in a follow-up turn (each is 30 min of literature reading + JSON edit). Until then, Phase 8 G3 cochlear-channel patch-clamp is the only quantitative kill gate for those targets.
Action items — not done in this turn
- Replace TRPM4 7MF0 with a valid PDB (likely 6BCO or 6BCL — check)
- Curate Cx50 / BK / KCNQ4 / TMEM16A box centres from primary literature (Flores 2020 / Tao 2017 / Li 2021 / Paulino 2017)
- Re-run —dock with the curated 5-target additions
- Phase 4h playbook note — add “COX selectivity contradicted” caveat and revise Tier-1 framing
- Add 1 paragraph to Phase 8 SOP G2.5 COX activity gate
Ranking delta
Tier A held. mech 3 / deliv 4 / misha_fit 4 all held.
- Phase 4h “bicyclic core kills COX” design thesis falsified for tafamidis + 3CN/3OMe benzoxazole bioisosteres. This is a material design constraint, not a tier change — pharmacochaperone monotherapy/adjunct framing per Misha Compound-Het Therapy Stack Model still holds, but the chemistry pipeline now needs explicit COX-deselection beyond what Phase 4h proposed.
- The Phase 5e WT-pocket-validated docking pipeline is now also COX-calibrated (parent fenamates within 1 order of magnitude of published IC₅₀s), giving us a self-consistent selectivity scoring system across h01 and at least 2 off-targets.
next_stepunchanged: Phase 3c v4 still primary; v4 verdict will inform whether a COX-deselect sub-task gets a Phase 3c v4b (fragment-replace COOH cluster) or whether enough v4 leads have alternative pharmacophores to skip it.lit_audit: fixedheld; this is computed on prepared receptors, no new literature claims.
Connections
[part-of]h01 hub[see-also]STRC h01 Phase 4h Tafamidis Playbook Library 2026-04-23 — design thesis contradicted on COX[see-also]STRC h01 Fenamic Scaffold Tox Audit 2026-04-23 — parent fenamate IC₅₀s reproduced[see-also]STRC h01 Phase 5e Mutant Re-Dock Delivery 2026-04-24 — h01 mutant Kd reference[see-also]STRC h01 Phase 8 Wet-Lab Triage SOP — COX needs G2.5 not G3- Misha Compound-Het Therapy Stack Model
- STRC Hypothesis Ranking