fantasy121
commented
2 years ago For Fenarimols, so far other heterocyclic rings (Ring 1) (such as 5-pyrimidyl) have resulted in poor in vitro activity and I cannot explain why this is. One paper mentions that basicity (pKa) of the heterocycles may enhance binding affinity of the drug to the haeme-iron but I don't really understand their reasoning (see passage quoted below). In the literature, CYP51 inhibition for other pathogens appears to tolerate other heterocyclic rings apart from 3-pyridyl. This could be a mycetoma-specific interaction. However, we haven't specifically synthesised compounds that test for changes in the ring 1 position while keeping all the other parts strictly the same. For instance, take the most active leads and only change the Ring 1 to a different heterocyclic aromatic ring.
Passage referring to the basicity of pyridine compared to other Heterocycles (T. cruzi paper): "Although the apparent Kds determined by spectral titration are useful for primary identification of new binding ligands, they do not always correlate with inhibition of 14DM activity (12). Thus, we found that several imidazole derivatives that reveal nanomolar Kds were easily replaced in the enzyme reaction by substrate, whereas VNF derivatives were not (12). On the other hand, some pyridine derivatives, which induce moderate spectral responses (the apparent Kds ~ 0.2–0.5 uM), turned out to be rather strong inhibitors of TC14DM (38). This contradiction might be explained by the fact that because 14DM spectral responses to azoles (an exam- ple is shown in supplemental Fig. S1a) only reflect displacement of a weaker ligand (water) from the sixth iron coordination sphere (28), they might be enhanced by basicity of the iron-coordinating atom (imidazole > triazole > pyridine (39)), whereas the effects of additional lipophilic interactions with the protein residues may sometimes remain unrecognized."
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MFernflower
wwjvdsande
From: 
(Sorry pdf was too large to upload it)
mattodd
A bit of a recap from what I mentioned in the January meeting #67
I found these crystal structures from the Protein Data Bank. These provide more evidence that Fenarimol analogues inhibits CYP51 of mycetoma in a similar fashion to the azoles.
What's needed for activity (in vitro) for other pathogens: – A heterocyclic aromatic ring containing an atom that can coordinates to the haeme-iron residing in the CYP51 active pocket. – A disubstituted phenyl group near the heterocyclic ring. Forms additional interaction with residues in the active pocket (stabilising drug binding). Also disrupts the haeme-support (usually Tyr residues that stabilise the haeme). This can also change the oxidation state of the iron which may enhance binding affinity of the drug Heterocycles. – A H-bond acceptor/donor near the heterocyclic ring. Similar function to the disub Ph group above. – The rest of the compounds (would be at the Ring 3 Tail position for the fenarimol analogues) forms additional interaction with residues at the entry to the active pocket. The pocket usually can only accommodate 2 aromatic rings and the H-bond donor/acceptor (the previous three dot points) so everything else just sticks out of the active site.
In the case of Fenarimols, we have:
– The nitrogen atom of the 3-pyiridyl ring (Ring 1). [Haeme-iron binding] – At least one phenyl ring (mono- or disubstituted) (Ring 2/Ring3). [Disrupts haeme-support. Stabilise binding of Ring 1] – Hydroxy group in the Core. [Disrupts haeme-support. Stabilise binding of Ring 1] – The other bit at the tail position (Ring 3/Ring2). [Further stabilise Binding of Ring 1, by interacting with the residues at the entry to the active site]
Literature of the structures:
You can search the protein data bank to look up existing crystal structures of drug-bound enzymes (just type in the organism, the enzymes and the drug names into search for eg "Azole t cruzi CYP51", or type in the unique PDB codes (each crystal structure has one) which I lacked the foresight to record for the five instances above, oof XD). There's no literature on Mycetoma crystal structures as of 27 Jan 2022)