Targeted anticancer pre-vinylsulfone covalent inhibitors of carbonic anhydrase IX

Reviewer #1 (Public review):

Summary:

This paper describes the covalent interactions of small molecule inhibitors of carbonic anhydrase IX, utilizing a pre-cursor molecule capable of undergoing beta-elimination to form the vinyl sulfone and covalent warhead.

Strengths:

The use of a novel covalent pre-cursor molecule that undergoes beta-elimination to form the vinyl sulfone in situ. Sufficient structure-activity relationships across a number of leaving groups, as well as binding moieties that impact binding and dissociation constants.

Overall, the paper is clearly written and provides sufficient data to support the hypothesis and observations. The findings and outcomes are significant for covalent drug discovery applications and could have long-term impacts on related covalent targeting approaches.

Weaknesses:

No major weaknesses were noted by this reviewer.

Reviewer #2 (Public review):

Summary:

The authors utilized a "ligand-first" targeted covalent inhibition approach to design potent inhibitors of carbonic anhydrase IX (CAIX) based on a known non-covalent primary sulfonamide scaffold. The novelty of their approach lies in their use of a protected pre(pro?)-vinylsulfone as a precursor to the common vinylsulfone covalent warhead to target a nonstandard His residue in the active site of CAIX. In addition to a biochemical assessment of their inhibitors, they showed that their compounds compete with a known probe on the surface of HeLa cells.

Strengths:

The authors use a protected warhead for what would typically be considered an "especially hot" or even "undevelopable" vinylsulfone electrophile. This would be the first report of doing so making it a novel targeted covalent inhibition approach specifically with vinylsulfones.

The authors used a number of orthogonal biochemical and biophysical methods including intact MS, 2D NMR, x-ray crystallography, and an enzymatic stopped-flow setup to confirm the covalency of their compounds and even demonstrate that this novel pre-vinylsulfone is activated in the presence of CAIX. In addition, they included a number of compelling analogs of their inhibitors as negative controls that address hypotheses specific to the mechanism of activation and inhibition.

The authors employed an assay that allows them to assess target engagement of their compounds with the target on the surface of cells and a fluorescent probe which is generally a critical tool to be used in tandem with phenotypic cellular assays.

Weaknesses:

While the authors show that the pre-vinyl moiety is shown biochemically to be transformed into the vinylsulfone, they do not show what the fate of this -SO2CH2CH2OCOR group is in a cellular context. Does the pre-vinylsulfone in fact need to be in the active site of CAIX on the surface of the cell to be activated or is the vinylsulfone revealed prior to target engagement?

I appreciate the authors acknowledging the limitations of using an assay such as thermal shift to derive an apparent binding affinity, however, it is not entirely convincing and leaves a gap in our understanding of what is happening biochemically with these inhibitors, especially given the two-step inhibitory mechanism. It is very difficult to properly understand the activity of these inhibitors without a more comprehensive evaluation of kinact and Ki parameters. This can then bring into question how selective these compounds actually are for CAIX over other carbonic anhydrases.

The authors did not provide any cellular data beyond target engagement with a previously characterized competitive fluorescent probe. It would be critical to know the cytotoxicity profile of these compounds or even how they affect the biology of interest regarding CAIX activity if the intention is to use these compounds in the future as chemical probes to assess CAIX activity in the context of tumor metastasis.

Reviewer #3 (Public review):

Summary:

Targeted covalent inhibition of therapeutically relevant proteins is an attractive approach in drug development. This manuscript now reports a series of covalent inhibitors for human carbonic anhydrase (CA) isozymes (CAI, CAII, and CAIX, CAXIII) for irreversible binding to a critical histidine amino acid in the active site pocket. To support their findings, they included co-crystal structures of CAI, CAII, and CAIX in the presence of three such inhibitors. Mass spectrometry and enzymatic recovery assays validate these findings, and the results and cellular activity data are convincing.

Strengths:

The authors designed a series of covalent inhibitors and carefully selected non-covalent counterparts to make their findings about the selectivity of covalent inhibitors for CA isozymes quite convincing. The supportive X-ray crystallography and MS data are significant strengths. Their approach of targeted binding of the covalent inhibitors to histidine in CA isozyme may have broad utility for developing covalent inhibitors.

Weaknesses:

This reviewer did not find any significant weaknesses. However, I suggest several points in the recommendation for the authors' section for authors to consider.