Tc-43/VHL_NonProline_Binder_Designs_9GIO

VHL Non-Proline Binder Designs (9GIO)

279 generatively designed small molecules docked into the VHL substrate-recognition pocket of the VHL–ElonginC–ElonginB (VCB) complex, using PDB 9GIO as the receptor.

Molecules were generated by the Technetium TC-43.ai engine (GA-II generation). Target selection, structural analysis and dataset curation were performed with Claude Code.

Why these designs matter for PROTAC development

Essentially every VHL-recruiting PROTAC in the literature is built on the same (4R)-hydroxyproline warhead — VH032 and its close analogues. That warhead is an excellent binder but an expensive one to carry: it contributes a large polar surface area to a molecule that is already far outside Rule-of-5 space, and PROTAC permeability is TPSA- and HBD-limited.

These designs are a different chemical proposition. 278 of 279 contain no 4-hydroxypyrrolidine and none contain a prolinamide — they occupy the same pocket through genuinely non-proline chemotypes (252 distinct Murcko scaffolds across 274 unique molecules).

Lower TPSA than the proline-based standard

	TPSA (Ų)	MW	HBD	rot. bonds
These designs (median)	89.6	450.6	2	4
VH032 / 3JF — proline warhead in 9GIO	111.6	472.6	3	6
87A — VHL PROTAC (proline-based)	208.6	936.1	5	16
Q43 — VHL PROTAC (proline-based)	209.4	1060.2	6	15

• 227 of 279 (81%) fall below VH032's TPSA, interquartile range 72.0–107.9 Ų.
• Median TPSA is 22 Ų lower than VH032, with one fewer H-bond donor and two fewer rotatable bonds.

Because the warhead's polarity is carried directly into the assembled degrader, a ~22 Ų TPSA reduction and the loss of an H-bond donor propagate into the full PROTAC — the property axis on which proline-based VHL degraders such as 87A and Q43 (TPSA ≈ 209 Ų) are most constrained. Lower donor count and reduced flexibility also ease the conformational and desolvation penalties that dominate bRo5 permeability.

They bind where VH032 binds — by a different, more robust mechanism

Superposed on 9GIO, the designed ligands overlap the VH032 site to within 0.13 Å (closest approach), and sit 19.8 Å away from the covalent C77 site also present in that structure. But they hold that site differently. Running the same interaction analysis on VH032 in 9GIO and on all 279 designs:

	VH032 (3JF, proline-based)	these designs
H-bonds	3, all sidechain: Ser111 OG (2.61 Å), His115 ND1 (2.67 Å), Tyr98 OH (2.73 Å)	2.0 per design, 97% anchored on the His110 backbone
π-stacking	none	95% of designs — Tyr112, Phe76, Tyr98, Trp88, Phe91, His115
hydrophobic	5	5.8 per design

VH032 binds as a hydroxyproline mimic of hydroxylated HIF-1α Pro564, and its affinity rests on three sidechain hydrogen bonds. Sidechain donors and acceptors are rotatable and entropically expensive, and one of the three is geometrically marginal in this structure (His115, geometry score 0.08).

These designs instead converge on a backbone hydrogen bond to His110 — present in 271 of 279 — combined with aromatic stacking against a pocket that is unusually rich in it (Tyr98, Tyr112, Trp88, Trp117, Phe76, Phe91). Backbone carbonyl geometry is fixed by the fold rather than by a rotatable sidechain, and stacking carries no desolvation penalty. Notably, VH032 makes no π-stacking at all — the designs exploit a source of binding energy the substrate-mimetic warhead leaves on the table.

Only 4 of 279 designs hydrogen-bond Ser111. That is by construction, not by omission: reproducing the hydroxyproline–Ser111 contact is not required once a ligand has a conserved backbone anchor and good stacking, and abandoning it is precisely what frees these scaffolds from the proline core and its polar-surface cost.

Pocket contacts (heavy-atom, 4.5 Å) across all 279 designs:

residue	engaged
Tyr98	100%
His110	100%
Tyr112	99%
Trp117	99%
Trp88	94%
His115	78%

Every design presents a linker vector

All 279 carry at least one well solvent-exposed heavy atom (≥20 Ų SASA in the complex; median 6 such atoms per molecule, most-exposed atom median 43.5 Ų), so each offers a defined attachment point for linker growth toward the E3–target interface.

Honest limitations

These are computational designs, not measured binders. Please read them as hypotheses:

• No experimental data. No binding affinity, no ternary complex formation, no degradation. Docking scores (AutoDock Vina, −13.5 to −10.0 kcal/mol) rank poses; they are not affinities and should not be read as such.
• A different binding mode is an untested binding mode. The His110-backbone-plus- stacking anchor set is mechanistically sound and more geometrically reliable than VH032's three sidechain hydrogen bonds, but whether it delivers comparable affinity has not been measured. That is the open question in this set.
• The TPSA gain is partly traded for lipophilicity. Median cLogP is 3.4 against VH032's 2.2, and median QED is 0.4 against 0.6. Solubility and off-target risk should be assessed alongside permeability.
• Rigid, aromatic-rich. Median 6 rings vs VH032's 3 — consistent with a stacking-driven binding mode, but worth watching for planarity and solubility.
• Single rigid receptor. All poses were docked into one 9GIO conformation with no induced fit; VHL's pocket accommodates ligands with some plasticity.

Contents

file	description
designs.csv	one row per design — SMILES, docking score, ligand efficiency, computed properties including tpsa_vs_VH032, and per-design interaction counts (his110_backbone_hbond, n_pi_stacking, best_pi_score, ser111_hbond, …) so every claim above is checkable
ligands.sdf	279 ligands with 3D docked coordinates, bond orders and formal charges; all verified against their source SMILES
receptor_9GIO.pdb	the shared VHL–EloC–EloB receptor
structures/	279 full complex PDBs; REMARK records carry ligand ID, Vina score and SMILES

Reference structure

9GIO — Crystal structure of the VHL–EloC–EloB complex with a covalent compound bound to C77 of VHL. Contains both 3JF (VH032, the proline-based VHL ligand) and A1IMD (the covalent C77 binder). These designs target the 3JF site.

Citation

Designs generated by the Technetium TC-43.ai engine. Analysis and curation by Claude Code. Released under CC-BY-4.0.