Built to
Bind.
A first-in-class covalent heparanase inhibitor designed to protect the glomerular filtration barrier. This is VL166, visualized within the active site of the enzyme it irreversibly inactivates.
Kidney disease starts at the filter.
Every day, the kidney filters ~180 litres of blood through a single-cell-thick barrier. Heparan sulfate is the scaffold that holds that barrier together.
In diabetic kidney disease and several rare nephropathies, the enzyme heparanase is chronically elevated. It is the only human enzyme that cleaves heparan sulfate, and as it does, the glomerular filtration barrier loses its structural integrity. Protein leaks into the urine. Inflammation and fibrosis follow. Kidney function erodes, irreversibly.
Today's standard of care (RAAS blockade, SGLT2 inhibitors) slows the trajectory but does not address the enzyme doing the damage. Millions of patients still progress to dialysis or transplant.
One enzyme. Reusable. Relentless.
Heparanase adopts a (β/α)8 TIM-barrel with a positively charged groove that grips heparan sulfate. Within it, two catalytic glutamates do the work: Glu225 as acid/base, Glu343 as nucleophile. Hydrolysis proceeds through a retaining double-displacement: a transient covalent intermediate, then release.
Then the enzyme resets. A single heparanase molecule processes substrate chain after substrate chain in succession. Reversible inhibitors compete momentarily, then wash out, and the cleavage resumes. To stop the damage, the catalytic machinery itself has to be taken offline.
VL166: the enzyme's own chemistry, turned against it.
A rationally designed disaccharide the enzyme cannot help but engage, and cannot release.
VL166 is shaped like heparanase's natural substrate, so it slides into the −1 subsite of the catalytic cleft with near-perfect complementarity. But where the real substrate carries a glycosidic bond ready for hydrolysis, VL166 carries a strained epoxide warhead at the same position: chemically inviting to heparanase, behaviourally a trap.
The enzyme attacks. The trap closes.
Scroll to watch the inactivation, atom by atom.
Heparanase recognises VL166 as substrate and initiates the same nucleophilic attack it has performed millions of times before. Glu343 reaches for the electrophilic C1 of the warhead. Glu225 donates a proton to the departing oxygen, exactly as it would in normal turnover.
But the epoxide is not a glycosidic bond. The ring opens onto VL166 itself, and Glu343 finds itself fused to the inhibitor through a stable covalent ester. The reaction the enzyme started cannot finish.
Locked. Permanently.
The covalent ester between Glu343 and VL166 (highlighted bond) is not a transient intermediate. The enzyme cannot regenerate its catalytic nucleophile, cannot release the inhibitor, cannot re-enter the hydrolytic cycle. One molecule of VL166 takes one heparanase out of circulation, for good.
Inhibition is stoichiometric and permanent. Recovery requires the body to synthesise new enzyme from scratch: pharmacodynamics decoupled from pharmacokinetics. That is what makes covalent capture different in kind, not in degree, from a reversible inhibitor.
What this changes for the patient.
Heparanase activity is an early and sustained driver of glomerular basement membrane degradation. Shut it down durably, and the upstream cause of barrier loss is removed, not its symptoms. Preclinically, this translates to reduced proteinuria, attenuated inflammatory signalling, and slowed fibrotic progression.
For the millions of patients with diabetic nephropathy, and for those with rare kidney diseases driven by the same enzyme, the prospect is a therapy that intervenes at the point of injury, not after the kidney has already scarred.
In Kidney Disease.
A spin-out of Leiden University ·
Leiden, The Netherlands
Structure: PDB 7PR7, de Boer,
Armstrong, Lit, et al.,
PNAS 119 (2022)
Human heparanase in complex with VL166, 1.52 Å · Visualization by
AVIGI Therapeutics
An educational visualization. Atom positions for the bound complex are taken from the deposited 1.52 Å crystal structure; the reaction trajectory is a smooth interpolation between the resting inhibitor and the covalently bound end-state, so intermediate frames are illustrative rather than measured.