Structure–activity across six chemotypes

Cross-referencing the plate against the 184 ligand-bound PXR structures in structure_ground_truth. Five plate compounds are crystallized — matched both on registration ID and, independently, on stereochemistry-stripped structure, which agree exactly. Each is marked ◆ code on its row below.

The potency plotted throughout is the purity-corrected pEC₅₀. It is worth knowing exactly what that correction is, because it is not an independent measurement.

A 1-methylcyclohex-3-enyl amide anchored to a benzenesulfonyl head group. The sulfonyl substituent is varied over nine groups; three analogues also move the sulfonyl to meta or insert a two-atom linker into the amide.

Cyclopropylsulfonamide is the best simple head group (2315472, pEC₅₀ 6.43), and a bulky N-methyl-cyclohexyl sulfonamide matches it. Potency is broadly tolerant of the sulfonyl group — nine variants span only 1.0 log — but the amide linker is not: extending the direct aryl amide to cinnamamide costs 1.9 log and to the saturated homologue 1.6 log. The sulfone (2469067) is 1.0 log worse than the matched sulfonamide, so the S–NH donor is contributing. The series lead 2315472 is the member with a bound structure (x02813-1, 1.96 Å), and none of the eleven new analogues improved on it.

A 1-cyclobutylpyrazole-4-sulfonamide on an aniline that carries a basic amine ortho to the sulfonamide NH. Only that amine is varied.

The tightest series on the plate — all twelve fall within 0.9 log, and every one is at or above pEC₅₀ 5.7. The trend is simple steric: going from NMe₂ (5.71) up through N(Me)Et, N(Me)ⁿPr to N(Me)ⁱPr (6.52) and N(Me)cyclopentyl (6.49) gains ~0.8 log, while tying the amine back into a ring loses it again (pyrrolidine 5.78, piperidine 5.66). A branched acyclic amine is what this pocket wants. The crystallized lead 2318048 (x02698-1, 2.24 Å) carries exactly that N(Me)ⁱPr group and tops the series, so the bound structure is available to explain the preference directly. Note that N(Me)Ac (6.34) rests entirely on a 3% recovery correction and should be re-tested.

A complete 12×2 matrix: twelve N-aryl piperazines, each made twice — once with an α-H mandelamide and once with the α-methyl quaternary version. This is the cleanest single-variable comparison on the plate.

The α-methyl group is worth +0.75 log on average across all twelve matched pairs, and it helps in eleven of them — one of the most consistent single-atom effects in the dataset. It pays most where the aryl is otherwise poor (+1.44 on 2-ⁱPr-6-Me-pyrimidin-4-yl, +1.31 on the aminotriazine, +1.00 on plain pyrimidine) and least where the aryl is already good, which is the signature of two partially redundant contributions to the same binding event. The single exception, 2,3-dimethylphenyl (−0.14), is the one aryl with an ortho substituent — the α-methyl and the ortho-methyl appear to compete for the same space. On the aryl side, 4-ⁱPr-pyrimidin-2-yl is best in both halves of the matrix (6.48 / 5.92); swapping that isopropyl for a methyl ester costs ~1.4 log. That best corner of the matrix is the crystallized lead 2308748 (x03363-1, 2.09 Å) — so the α-methyl whose effect the matrix quantifies is resolved in the bound pose.

A carbonyl bridging an aryl amine or aryl ether to an N-aryl piperazine. The 24 compounds form two arms that cross at 2395416: one holds the left-hand side fixed and walks the piperazine aryl, the other does the reverse.

Arm 1 · left-hand side fixed as the 2-ethoxypyridin-3-yl urea

Remarkably flat — twelve different piperazine aryls span only 0.93 log, and eight of them sit within 0.4 log of each other. 4-ⁱPr-pyrimidin-2-yl is again the best (5.40), and the only real loser is 2-ⁱPr-6-Me-pyrimidin-4-yl (4.47), the same regiochemistry that underperformed in series C.

Arm 2 · right-hand side fixed as the 4-ⁱPr-pyrimidinyl piperazine

The left-hand side matters more, spanning 1.4 log. Two things read clearly: a tertiary urea beats every secondary one (N-ethyl-N-phenyl at 6.25 is the best compound in the series, and the cyclic benzoxazine urea is second at 5.85, both on clean >100% recoveries), and an ortho substituent on the aniline is worth roughly half a log (2-MeO-phenyl 5.40 vs. pyridin-3-yl 4.88). Carbamates are competitive with the secondary ureas but not with the tertiary ones. Four of the weakest rows carry large purity corrections, so the bottom of this ranking is the softest data on the plate. D is also the one series with no crystal structure — not for its lead 2395416, and not for any other compound on this core — so unlike every other series here, its flat SAR cannot be checked against a bound pose.

A 1-(4-fluoro-2-methylphenyl)pyrazol-3-yl urea — constant across all twelve — with a sulfonamide-bearing tail. The tail is the only variable.

This series is pharmacologically distinct from the other five. Its E_max values cluster at 0.63–0.83 (mean 0.68) while every other series averages 0.94–1.07 — these are partial agonists, and the effect tracks the scaffold rather than the tail, so it is the constant pyrazolyl urea head that caps efficacy. If the goal is a ceiling on PXR activation rather than raw potency, this is the series to work on. Within the tail, the two-carbon sulfonamide is the preferred geometry: a plain phenyl sulfonamide leads (6.68), N-benzyl and indoline are close behind, and both conformationally restrained versions — the azetidine (5.86) and the piperazine (5.49) — give the tail up without gaining anything. Replacing the sulfonamide with a carboxamide costs 0.8 log. This is the best-characterized series structurally: the lead 2318616 is crystallized (x02800-1, 1.95 Å) and four further structures keep that phenylsulfonamide tail while varying the pyrazole N-substituent — the one position the plate held fixed.

A 3,4-dimethylphenylsulfonyl acetamide on a 2-aryl morpholine. The morpholine and its aryl vary together.

The most potent series on the plate — median pEC₅₀ 6.47, and it holds the top compound overall. The SAR is a clean read on the 2-aryl group: para substitution is strongly preferred and the effect tracks lipophilicity (4-CF₃ 6.97 > 4-OCHF₂ 6.64 ≈ 4-Me 6.62 > 4-F 6.32), while walking that same fluorine around the ring costs potency at every step (para 6.32 → meta 6.26 → ortho 5.78). Two changes are clearly disfavoured: swapping the phenyl for 2-pyridyl loses 0.8 log, and methylating the morpholine 2-position to a quaternary centre loses 1.3 log — the opposite of what the same substitution did in series C. The 5,5-dimethyl regioisomer (6.89) and the oxazepane homologue (6.62) are both well tolerated, so the ring itself has room to move. F is the series that most clearly moved: its crystallized lead 2310554 (x02793-1, 2.02 Å) sits only 7th of twelve, beaten by six analogues and by 0.64 log at the top — and a bound pose of the parent 4-fluorophenyl exists to rationalize why.

Built from pxr_semi_pure_96_corrected.csv (96 rows). Series assigned by substructure match; R-groups obtained by cutting each molecule at the bonds that define its series, then verified by reconstruction. Potency is the corrected pEC₅₀ with its combined dose–response and recovery error; E_max is the normalized value as supplied. Structure depictions are drawn from the corrected SMILES.

For each of the five crystallized leads, every analogue in that series was given a conformer ensemble (ETKDG, MMFF-minimised), superimposed on the crystal ligand across its shared scaffold, and the single conformer with the best combined shape + feature overlap was kept. Series A, B and C used 200 conformers; the two flexible series, E and F, used 1000. What you see below is that best pose for each analogue, inside the protein it was aligned into.