27 November 2023

Beware of fused tetrahydroquinolines

Practical Fragments has written frequently about pan-assay interference compounds, or PAINS. These molecules contain substructures that frequently show up in hits that tend not to be advanceable, often wasting considerable effort. One criticism of the PAINS concept is that the original definitions were based on a limited number of screens in one assay format. In a new (open-access) J. Med. Chem. paper, Alison Axtman and collaborators at University of North Carolina Chapel Hill, Emory University, and Oxford University characterize one class of PAINS in more detail.
The researchers focused on fused tetrahydroquinolines, or THQs. Of the 51 molecules containing this substructure in the original 2010 PAINS paper, 34 hit in at least one of the assays, and one hit all six. At the time Jonathan Baell and Georgina Holloway noted that “it is not clear for some PAINS, such as the fused tetrahydroquinolines, what the relevant mechanisms of interference may be.” 

The new paper notes that fused THQs are common in screening libraries, with more than 15,000 commercially available. They also frequently show up as hits: the researchers summarize more than two dozen examples against a wide variety of targets including phosphatases, kinases, protein-protein-interactions, and more. In most cases the hits are modestly active, with low to mid micromolar IC50 values, though a few are high nanomolar. 
Promiscuity per se is not necessarily bad. Just last week we noted that the 7-azaindole fragment was the starting point for three approved drugs. However, despite showing up as hits in so many screens, only one peer-reviewed paper reports a crystal structure of a fused THQ bound to a protein, and the researchers note that “no optimized chemical probes or approved drugs contain the chemotype.”
Importantly, fused THQs hit in a variety of different assay formats, including spectrophotometric, chemiluminescent, SPR, and radiochemical. Thus, these are not merely problematic in the AlphaScreen format studied in the original PAINS paper.
So what’s going on? The researchers found that, while molecules containing the fused THQ core were initially colorless, they darkened when dissolved in DMSO or chloroform, turning purple within 72 hours. Interestingly, the reaction seems to be light-dependent: solutions stored in the dark remained colorless. Thin layer chromatography and NMR showed new species forming, and mass spectrometry revealed oxidation with loss of two or four hydrogen atoms. The isolated double bond in the cyclopentene ring seemed to be the culprit, as the saturated analog was stable. Indeed, all of the hits shown in the paper contain the double bond, so fused THQs that lack this feature may be fine – if they ever show up in your assay.
It is still not clear exactly how the decomposition products light up so many assays, but in general it’s a good idea to steer clear of molecules that fall apart in ambient light, unless you’re trying to make a photosensitizer.
The researchers conclude that “it is tragic to continue to watch groups invest time and resources in dead-end hit-to-lead campaigns, and the medicinal chemistry community will benefit everyone if the cycle stops.”
This concludes our public service announcement.

20 November 2023

Capivasertib: the seventh approved fragment-derived drug

On Thursday last week the FDA approved capivasertib for certain breast cancer patients. This marks the seventh fragment-derived drug to be approved. It is also the first approved drug targeting the kinase AKT.
Practical Fragments first wrote about capivasertib, then called AZD5363, way back in 2013, where we described the decade-long odyssey from fragment to drug. Interestingly that fragment, 7-azaindole, was also the starting point for two other approved drugs, pexidartinib and vemurafenib. As we noted at the time, “high-affinity molecules were obtained relatively quickly, but these still required a huge amount of effort to achieve selectivity, oral bioavailability, and other properties.”
What happened next is a poster child to counter one of the false beliefs Christopher Austin noted as being widespread outside industry: “Once an investigational therapy gets into humans for the first time, regulatory approval and marketing are all but assured.”
Capivasertib entered the clinic in 2010 in the first of more than 30 studies listed on ClinicalTrials.gov to date. One challenge was finding patients that would benefit sufficiently to offset a long list of side effects, including diarrhea and glucose fluctuations. In the end, the current approval is in combination with fulvestrant for “adult patients with hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative locally advanced or metastatic breast cancer with one or more PIK3CA/AKT1/PTEN-alterations, as detected by an FDA-approved test, following progression on at least one endocrine-based regimen in the metastatic setting or recurrence on or within 12 months of completing adjuvant therapy.”
Needless to say, these were not the first patients tested. Use of genetic testing to match patients with a drug likely to help them is not routine even today, let alone in 2010. Managing side effects also required figuring out how much of the drug to dose and how often. But additional combination trials are ongoing. Perhaps, as with venetoclax, capivasertib will eventually prove to be useful for a wider range of patients.
The first marketed fragment-derived drug, vemurafenib, sprinted from program initiation to approval in just six years. Capivasertib took twenty. As we previously noted, success in drug discovery is not necessarily fast or inevitable. Every year more than 40,000 people die of breast cancer in the US alone, but the death rate has slowly been declining. Hopefully the introduction of capivasertib will continue to reduce this.
Congratulations to all the researchers at AstraZeneca, Astex, and the Institute for Cancer Research for participating and persisting in this 20-year marathon to bring a new treatment to people with cancer.

13 November 2023

An update on the COVID Moonshot

On March 18, 2020, a group called the COVID Moonshot released crystal structures of 71 fragments bound to the SARS-CoV2 Mpro protein. The same day, they launched an online crowdsourcing initiative seeking ideas for how to advance these fragments, none of which had activity in an enzymatic assay. The results of this experiment in open science have just been published in Science, appropriately open-access.
Within the first week, the group received more than 2000 submissions. Ultimately more than 20,000 molecules were submitted, and all of these were evaluated in “alchemical free-energy calculations.” These are computationally intensive, requiring ~80 GPU hours per compound, so the consortium used the volunteer-based distributed computing network Folding@home. Compounds were evaluated not just for potency but also synthetic accessibility, and those that passed were synthesized at Enamine and tested in various functional assays.
In addition to accepting submissions for how to advance fragments, a core group of researchers proposed their own ideas. Interestingly, at least in the early stages of the project, this elite group did no better at coming up with more potent or synthetically accessible molecules, despite being intimately involved with the project. This finding validates the open-sourcing of ideas from the larger scientific community.
Ultimately more than 2400 compounds were synthesized, and more than 500 crystal structures were determined. All experimental results were posted online to help guide the synthesis of additional compounds. Speed was consistently prioritized, not just with high-throughput crystallography but also high-throughput chemistry and "direct-to-biology" screening of crude reaction mixtures.
The paper highlights one lead series, which originated from a community submission (TRY-UNI-714a760b-6, itself fragment-sized) inspired by merging overlapping fragments. This mid micromolar inhibitor was ultimately optimized to MAT-POS-e194df51-1, with mid-nanomolar activity in both biochemical and cell assays. (Despite a chloroacetamide in one of the original fragments and a nitrile in the final molecule, which is the warhead found in the approved covalent Mpro inhibitor nirmatrelvir, MAT-POS-e194df51-1 is non-covalent.) 

The molecule is potent against known SARS-CoV-2 variants, including recent ones such as Omicron. A crystal structure of the final molecule also overlays remarkably well onto the initial fragments.
The paper notes that there is still considerable work to do, particularly optimizing the pharmacokinetics to lower clearance and improve bioavailability. These efforts can take vast sums of time and money, and the lead series has been adopted by the Drugs for Neglected Diseases initiative for further development. Although a handful of drugs are already approved against SARS-CoV-2, there is room for improvement: Derek Lowe posted a vivid personal account of his experience on nirmatrelvir here.
When we wrote about the COVID Moonshot in March of 2020, we correctly predicted that vaccines would be approved before drugs from this effort emerged. Fortunately, our warning that “there will be a SARS-CoV-3” has not proven correct – yet. But open science endeavors such as the COVID Moonshot will help us prepare for this eventuality. We may not have made it to the moon yet, but perhaps we’ve learned how to leave Earth’s orbit.

06 November 2023

Finding weak fragments for membrane proteins with WAC

Last week we wrote about NMR, one of the most popular fragment-finding methods. This week we turn to a less common technique: weak affinity chromatography, or WAC. As we’ve written previously, WAC involves immobilizing a protein of interest in a chromatography column and flowing a ligand-containing solution through the column. If the ligand interacts with the protein, its elution time will be delayed in proportion to its affinity. In a new (open-access) Molecules paper, Claire Demesmay and collaborators at Universite Claude Bernard Lyon and Ecole SupĂ©rieure de Biotechnologie de Strasbourg extend the technique to membrane proteins.
Membrane proteins are themselves tricky to study, since removing them from their membranes often denatures them. One trick is to use nanodiscs, which are tiny lipid bilayer islands surrounded by proteins that keep them soluble in water. These scaffolding proteins can also be biotinylated so that the nanondiscs can be attached to streptavidin, which itself can be linked to a surface or matrix. Each nanodisc holds one or at most a few membrane proteins.
When we first wrote about WAC in 2011 the technique used standard HPLC columns, which required non-negligible amounts of protein. Here, the technique has been miniaturized to use glass capillaries with volumes of less than 1 microliter, requiring only a few tens of picomoles of protein. The researchers fill the capillaries with a bio-compatible polymer, functionalize it with streptavidin, and then capture biotinylated nanodiscs containing the membrane protein of interest.
A long-recognized challenge with WAC is nonspecific binding of the fragments to the column or matrix. Here, the researchers chose a filling (or monolith) that is more hydrophilic (for aficionados, they picked poly(DHPMA-co-MBA)) and found it superior to the previous polymer both with regards to capacity and non-specific binding.
Another challenge with WAC is detecting low-affinity binders: because interactions with the protein are weak, the shift in retention time is harder to detect. One solution is to pack more protein in the column, and the researchers develop a clever way of doing this with a “multilayer grafting” approach in which successive injections of streptavidin and nanodiscs more effectively fill the capillary. The combination of a more hydrophilic filling and multilayer grafting increased the column capacity for nanodiscs by three-fold.
The researchers tested their approach on the adenosine-A2A receptor (AA2AR), which has frequently been used as a model GPCR. Two previously reported weak ligands, both with affinities around 0.2 mM, could be detected, and competition with an orthosteric binder revealed that they were binding specifically.
This is a nice, how-to guide for performing WAC on membrane proteins, and the paper includes detailed equations for calculating affinities from differences in retention times. I look forward to seeing the technique used in de novo screens.