Fragments vs herpesviridae

The name herpes makes most people think of painful ulcers in the mouth, or worse. But herpesviruses are actually a family of viruses that can also cause chicken pox, mononucleosis, and other diseases. Some 95% of adults are infected by at least one type of herpesvirus, and these can become deadly if people become immunocompromised, such as during an organ transplant. A drug that would inhibit all forms of herpesviruses would be useful, and the first steps are described in a recent ACS Med. Chem. Lett. paper by Michael Plotkin and colleagues at Merck.

 

The details of the primary screen are sparse, though the researchers did say they physically screened more than 100,000 compounds to identify molecules such as compound 5, a modest inhibitor of the DNA polymerases from both cytomegalovirus (CMV) and varicella zoster virus (VZV). (For most compounds the paper reports biochemical activity towards both of these polymerases as well as antiviral activity for CMV, VZV, herpes simplex virus 1 (HSV-1), and HSV-2, but for simplicity I’ll only show data for CMV here. The compounds generally have comparable activity towards different viruses.)

 

Hydrogen bond acceptors such as the ketone in compound 5 were found to be essential for activity, and exploring a variety of analogs led to compound 12, which in addition to submicromolar biochemical activity against the DNA polymerases also showed antiviral activity against CMV and other herpesviruses.

 

The paper goes into considerable detail on the lead optimization. The (S) enantiomer of compound 12 was an order of magnitude more potent than the (R) enantiomer. Modifications made to both of the phenyl rings ultimately led to compound 44, with low nanomolar biochemical activity against the polymerases and sub-micromolar antiviral activity against CMV, VZV, HSV-1, and HSV-2. Importantly, the researchers note that they did not have crystal structures during optimization, a useful reminder that structural information is not always necessary.

 

Compound 44 had modest oral bioavailability in rodents, but closely related compound 42 containing a trifluoromethyl group in place of the bromine was better, albeit with slightly lower biochemical potency. This molecule led to high survival rates in mice when dosed either before or after being exposed to HSV-1. In separate studies, the compound reduced CMV viral load. For both HSV-1 and CMV compound 42 compared favorably to acyclovir and ganciclovir, two commonly used drugs.

 

Although there is still some way to go to a drug, the researchers end by promising to describe “further progress of this series.” I look forward to reading about this.

It's A Start

As the readers of this blog know, I tend to be harsh on academic "Drug discovery" papers.  Sometimes, there is a really worthwhile academic paper, but by and large I find that they tend to publish things that are barely "drug discovery" and more the For Dummies...of what they think drug discovery is.  Which way will I swing on this paper from researchers Down Under?  

The bacterial Sliding Clamp, aka polymerase 3beta, is a key player in bacterial replication and is an "emerging" target. It interacts with other proteins via LM (Linear Motifs): 4-10 amino acid disordered regions.  This is typically a weak interaction (1-100 uM). These LM exist at termini, but sometimes in loops.  A consensus sequence for the LM that interacts with the Sliding Clamp has been identified: QLx1Lx2F/L (S/D preferred at x1; x2 may be absent).  Two classes of compounds have been identified previously but with >10 uM affinity and no -cidal activity. 

So, these authors went after this target using X-ray as the primary screen.  The Zenobia Fragment Library was used (352 molecules) to soak into crystal in pools of 4 fragments.  Four fragments (below) were found to bind to Subsite I on Chain A.  However, no changes in the main chain density were observed.

They also found several other fragments with weak density, and several that were deemed crystallographic artifacts.  None of these compounds showed significant activity below 1 mM in their competition assay.  So, the story then continues that they "sought to improve binding affinity by identifying fragments that could more completely occupy" the binding site.  

[An aside:  To me, this brings up an important point about the choice of fragment collection.  Fragments that are designed for X-ray soaking tend to be small (10-12 HAC).  Just from a theoretical standpoint, those fragment would have to have an affinity in the 250 uM range (LEAN 0.3).   This was covered in a poll and most most people are happy going < 10 HAC.  My question is how often is a very small fragment found as an active?]

To do this, they noted that the fluoro-phenyl group in 1 was previously reported, leading to investigations with compound 5. It was found to fully occupy the binding site.

They searched ZINC for compounds similar to 1-5.  Their initial purchases failed to find any compounds with activity < 1mM.  Eventually, they landed on the hypothesis that chlorocarbazoles were "promising", leading to compound 6.  At this point, I think Dan's head exploded, Scanners-style.  Yes, that is an epoxide.  The co-crystal structure showed that it was binding in the active, albeit with weak electron density.  Their SAR, wisely, did not include the N-alkyl epoxide. 

Both 7 and 8 show good LE and LLEAT.  Only the R enantiomer of 8 caused movement in the main chain.  It also was the most potent in the replication inhibition assay (64 uM).  It was also the most potent in terms of -cidal activity against both Gram positive and negative microbes. 

So, is this a good or bad paper?  I would say it is a start, but if I had been a reviewer I would have made them change the title "Discovery of Lead Compounds Targeting the Bacterial Sliding Clamp
Using a Fragment-Based Approach" to "Discovery of ACTIVE Compounds Targeting the Bacterial Sliding Clamp Using a Fragment-Based Approach".