Topic automatically created for discussing the designs at:
https://covid.postera.ai/covid/submissions/PET-UNK-5ecb6237
I’ll mention @mc-robinson and @londonir (this submission is analogous to NIR-WEI-75ed5c39). While there are not enough examples in the Cambridge Structural Database (CSD) to permit meaningful statistical analysis of torsional distributions, entries POKFON POKGEE WUCXUN suggest that substitution of anilide nitrogen with nitrile will not ‘invert’ the amide cis/trans geometrical preference in the same way that substitution with sp3 carbon does.
First apologies for the length of the message and I’ll mention @mc-robinson @edgriffen @Ben_DNDi @alphalee @RGlen @JSPEN @miko_a @anandrewleach.
I noticed that ALP-POS-5fe48310 | ALP-POS-4483ae88 | ALP-POS-4483ae88 | EDG-MED-e300b289 submissions refer to potential Ames liability and I’d like to flag up a potential tactic with which we might address the issue.
The most obvious way to address a potential Ames liability like this is simply to methylate the offending nitrogen. However, this is kiss of death for the potency of ADA-UCB-6c2cb422-1 (I believe this is due to the inversion of the trans/cis geometric preference of the amide that results from N-methylation). I would not expect substitution of the amide nitrogen with cyano to ‘flip’ the amide like N-methylation does and submitted the N-cyano analog of ADA-UCB-6c2cb422-1 as PET-UNK-5ecb6237-1 about this time last year with a view to targeting the catalytic cysteine. My assessment is that the covalent bond is more likely to form than not to form although I did note at the time of submission that the geometry appeared suboptimal for covalent bond formation. Covalent bond formation between the nitrile warhead and a catalytic cysteine is typically reversible.
Even if the covalent bond doesn’t form, the nitrile offers potential advantages beyond addressing potential Ames liability. First, I think that the cyano group would help push the P1 isoquinoline away from coplanarity with respect to the amide. Second, I would anticipate increased aqueous solubility since the only hydrogen bond donor in the molecular structure is eliminated (slide 15 from my UK-QSAR presentation shows the effects N-methylation on aqueous solubility for three classes of secondary amide). Third, active efflux will be reduced if the amide NH is a transporter recognition element (benefits of the methoxy configurational lock for translation of enzyme inhibition to cell-based activity may reflect active efflux). There are potential downsides in that hydrogen bond basicity of the amide carbonyl oxygen will be reduced and reactivity with glutathione could be a problem. There is also the possibility that the compound might transfer the cyano group to the catalytic cysteine (depending on the hydrolysis rate of the S-cyano cysteine this could be good or bad) or to glutathione (definitely bad).
Typically, cyanogen bromide is used to attach cyano groups to nitrogen (the group I work with at USP in Brazil used it in the synthesis of azapeptide nitriles and our main difficulty was that importation of cyanogen bromide is controlled by the Brazilian army). I understand that there were synthesis and stability difficulties with acrylamides such as MAT-POS-e69ad64a-2 although I see these as largely due to two acyl groups competing for the nitrogen lone pair in a sterically crowded environment. If MAT-POS-bb423b95-7 can be synthesized by methylation of ADA-UCB-6c2cb422-1 then I’d be optimistic that PET-UNK-5ecb6237-1 could be synthesized in an analogous manner. The nitrile can be seen as a molecular recognition element that you can bolt on at the end which means that it could be used with other scaffolds.
I believe that PET-UNK-5ecb6237-1 would give us a good idea of the benefits (and costs) of N-cyano substitution. Covalent binding if it does occur is likely to be reversible and I don’t see it as presenting any special challenges beyond assessment of glutathione reactivity.
Good point. We’ve made N-CN before and it certainly worked in cimetidine (although… nowadays seen as a d-d interaction + control!). NCH2CN is easier but has one more bond and may suffer from +++ entropy. N-formylation etc is also a strategy as is N-NO2 but N-CHO, NCO2Me would be preferable…but we might be dealing with prodrugs in these cases…
Hi @JSPEN, The pKa of guanidine is extremely sensitive to substitution and is rendered non-basic by substitution with cyano or nitro. I submitted the formyl analog PET-UNK-12d8d43f-1 after the nitrile and I would anticipate that it would present some of the synthesis/stability difficulties that that were experienced for the acrylamides. Also I would guess that it would be more likely to function as a formyl transfer agent rather than forming a covalently-bound adduct reversibly.
From my perspective, substituting the amide with cyano has the potential to create room to manoeuvre although reversible covalent bond formation would be a very welcome bonus.