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Class report 03

Two Doors in One Key

Family C is the only class that tries to be both mechanisms at once — and it is the one most likely to be wrong.

editorial schematic · not experimental data: Two Doors in One Key
EDITORIAL SCHEMATIC · NOT EXPERIMENTAL DATA

The two doors

The research paper names two access routes to the same cellular state: the voltage door and the redox door. The four classic agents sort cleanly between them. Family C fuses a voltage-seeking element and a redox-active element into a single molecule — three compounds deposited.

Why that is attractive

If the target state really is one condition reachable two ways, a molecule carrying both keys should reach it more reliably than either alone, and should be harder for a cell to adapt around.

Why it is the weakest claim in the set

Because it compounds two assumptions instead of testing one. A hybrid that underperforms both parents tells you little; a hybrid that works does not tell you which half did it. If any class in this series deserves scepticism first, it is this one, and the right experiment is the boring one: the hybrid against each parent, separately, same assay.

The deposited compounds

ARF IDNameFormulaMWStatus
ARF-MOX-C1menadione glycolateC50H61NO12868.03Computational design. Not synthesised, assayed or administered.
ARF-MOX-C2plumbagin-type glycolateC49H59NO13870.01Computational design. Not synthesised, assayed or administered.
ARF-MOX-C4trioxane (artemisinin-like) esterC52H75NO11890.17Computational design. Not synthesised, assayed or administered.

Addendum, 5 November 2026 — the branch was rebuilt

Nothing above has been altered. The original listing of four deposited redox-hybrid designs stands as published. What follows is appended.

The deposited lead of this branch, ARF-MOX-C4, was attacked on three grounds and did not survive any of them: the peroxide bond had to survive synthesis and plasma, the C5 ester could be cleaved by esterases before iron could activate the warhead, and the compound carried sixteen stereocentres of which six were unspecified — so it never defined a single synthetic target.

Then it turned out not to be the compound we had described. Ring perception on our own deposited structure gives a peroxide ring of C–O–O–C–C–C: six-membered, two ring oxygens, a 1,2-dioxane. An artemisinin-type 1,2,4-trioxane requires three. The appendage carries one carbonyl, so the linkage is a glutaryl-type monoester and not the succinate diester we reported. The structure governs and our prose was wrong. The correction cuts against the compound rather than for it: a plain dialkyl 1,2-dioxane has no stabilising acetal oxygen and is a poorer peroxide than the one we claimed, so the case for replacing it was stronger than the case made against it. The error never entered the structural record — every property ever published was computed from the correct structure — and it is corrected here by addition, not by deletion.

What improved, and what failed

The obvious repair, reading the antimalarial record, is the spiroadamantane ozonide of the OZ277/OZ439 lineage, where a cage shields the peroxide sterically. On this chassis it is a negative result: every adamantane design is worse than the compound it was meant to rescue on stereochemical definition, and no better on lipophilicity. We publish it as a failure because a reader deserves the dead end as much as the result.

What worked was symmetry. A tetraoxane with identical substitution either side of its peroxide ring has spiro carbons that are not stereocentres at all, so the ambiguity disappears with nothing having to be specified, while the molecule carries two peroxide bonds instead of one. A monospiro warhead bearing a methyl on the opposite ring carbon runs 50–100 Da lighter than the dispiro equivalent, and trading a spiro cyclohexane for an oxane exchanges hydrophobic surface for oxygen. Those moves reach clogP 6.39 where the first series bottomed out at 7.83.

Thirty-four designs, built independently on two planets and reconciled; twelve improve on the deposited lead simultaneously in lipophilicity, stereochemical definition and ester count. The deposited lead now ranks 31st of 34. S04 is the only design in the set to satisfy both Veber criteria with clean stereochemistry and is the lightest by 45 Da; S07 leads on the stated liability at clogP 6.60.

One thing is unresolved and it halves the branch. The C5 ester is the liability and the release mechanism: remove it and the conjugate can never revert to free moxidectin. A primary record has since been found — Naito and co-workers prepared C5-masked milbemycin ethers, esters, sulfonates and carbamates in 1994 and reported activity penalties across that set. That is a warning about retained parent activity, measured in a worm-motility assay rather than in cancer, and it is reported here against our own interest.

The thirty-four C4-branch designs, ranked best in class

IDSeriesFormulaMWclogPO–OUnspec. centresStatus
S07Planet 85C46H66N2O14871.06.6020Computational design. Not synthesised, assayed or administered.
S06Planet 85C45H64N2O13841.06.9720Computational design. Not synthesised, assayed or administered.
S04Planet 85C45H65NO11796.07.7210Computational design. Not synthesised, assayed or administered.
S05Planet 85C47H68N2O13869.17.7520Computational design. Not synthesised, assayed or administered.
S09Planet 85C48H68N2O13881.17.8920Computational design. Not synthesised, assayed or administered.
S10Planet 85C49H71NO13882.18.0620Computational design. Not synthesised, assayed or administered.
S11Planet 85C48H70N2O14899.16.3920Computational design. Not synthesised, assayed or administered.
S03Planet 85C46H66N2O13855.06.6610Computational design. Not synthesised, assayed or administered.
S12Planet 85C48H72N2O14S933.26.9620Computational design. Not synthesised, assayed or administered.
S02Planet 85C47H68N2O12853.17.8210Computational design. Not synthesised, assayed or administered.
C4pPlanet 44C53H78N2O13951.28.7220Computational design. Not synthesised, assayed or administered.
C4qPlanet 44C55H81N3O141008.37.8320Computational design. Not synthesised, assayed or administered.
S08Planet 85C51H73NO12892.18.9226Computational design. Not synthesised, assayed or administered.
C4iPlanet 44C57H82N2O131003.39.2127Computational design. Not synthesised, assayed or administered.
C4kPlanet 44C52H76N2O13937.29.3120Computational design. Not synthesised, assayed or administered.
C4rPlanet 44C54H78N4O12975.29.3920Computational design. Not synthesised, assayed or administered.
C4tPlanet 44C51H75NO12894.29.6020Computational design. Not synthesised, assayed or administered.
S01Planet 85C51H72N2O12905.18.3115Computational design. Not synthesised, assayed or administered.
C4nPlanet 44C57H84N2O14S1053.49.0127Computational design. Not synthesised, assayed or administered.
C4gPlanet 44C56H80N2O13989.39.8027Computational design. Not synthesised, assayed or administered.
C4hPlanet 44C58H82N4O121027.39.8827Computational design. Not synthesised, assayed or administered.
C4fPlanet 44C55H79NO11930.210.1617Computational design. Not synthesised, assayed or administered.
C4uPlanet 44C55H81NO13964.210.5420Computational design. Not synthesised, assayed or administered.
C4sPlanet 44C55H81N3O13992.37.9012Computational design. Not synthesised, assayed or administered.
C4mPlanet 44C59H85N3O131044.38.3917Computational design. Not synthesised, assayed or administered.
C4dPlanet 44C57H82N2O12987.39.2817Computational design. Not synthesised, assayed or administered.
C4jPlanet 44C52H76N2O12921.29.3812Computational design. Not synthesised, assayed or administered.
C4oPlanet 44C54H78N4O11959.29.4612Computational design. Not synthesised, assayed or administered.
C4cPlanet 44C56H80N2O12973.39.8717Computational design. Not synthesised, assayed or administered.
C4ePlanet 44C58H82N4O111011.39.9517Computational design. Not synthesised, assayed or administered.
C4lPlanet 44C61H90N2O131059.410.0317Computational design. Not synthesised, assayed or administered.
C4bPlanet 44C56H79NO12958.210.0817Computational design. Not synthesised, assayed or administered.
C4vPlanet 44C55H81NO12948.210.6112Computational design. Not synthesised, assayed or administered.

In the PDF stack

Published designs, not medicines. Every property is computed. Nothing in either branch has been synthesised, assayed or administered, and no compound has biological data of any kind.

From engineering drawings to molecular blueprints.

One discipline runs underneath all of it: computational engineering — designing the thing completely, and proving out what you can, before anyone cuts metal or runs a reaction. It is the same craft whether the object is a bracket or a molecule. Only the units change.

01 · CAD geometry 02 · Structure 03 · Molecular blueprint 04 · Property set Computational engineering · one continuum
01

AutoCAD engineering

Concept geometry, stage views and engineering drawings — a question turned into something you can inspect and measure. Fabrication readiness still requires validation.

02

Structure and materials

The lattice between the two worlds: geometry that has to obey physics before it is worth costing, let alone building.

03

Biotechnology & molecular research

The same discipline applied to chemistry — scaffolds, conjugates and the design rationale for why a given structure should be made before anyone makes it.

04

Full RDKit molecular blueprints

Every structure parsed, sanitised and reported with its computed property set: isomeric SMILES, mass, lipophilicity, polar surface area, stereocentres. Computed, never quoted.

Our intention is plain: to own this field — computational engineering from the drawing to the molecule. Not by holding patents, but by being the group that does the work in the open, publishes its own corrections, and is the best in the world at deciding what is worth building next.

Computational designs only. Nothing described here has been synthesised, assayed or administered, and every property is a computed descriptor rather than a measurement. Fabrication and clinical readiness require validation that happens outside this factory.