16 October 2017

Docking for finding and optimizing fragments

Docking can sometimes seem like the Rodney Dangerfield of FBDD: it don’t get no respect. In last year’s poll of fragment finding methods, computational approaches ranked in seventh place. This partly reflects the largely biophysical origins of FBDD, but it is also true that ranking low affinity fragments is inherently challenging. Still, the continuing rise in computational power means that methods are rapidly improving. A recent paper in J. Med. Chem. by Jens Carlsson and collaborators at Uppsala University, the Karolinska Institute, and Stockholm University illustrates just how far they can take you.

The researchers were interested in the enzyme MTH1, whose role in DNA repair makes it a potential anti-cancer target. The crystal structure of the protein bound to an inhibitor had previously been reported, and this was used for a virtual screen (using DOCK3.6) of 300,000 commercially available molecules, all with < 15 non-hydrogen atoms, from the ZINC database.

Finding fragments is one thing, but one really wants slightly larger, more potent compounds to begin lead optimization. Thus, the top 5000 fragments were analyzed to look for analogs with up to 6 additional non-hydrogen atoms among the 4.4 million commercial possibilities. This led to 118,421 compounds, each of which was then virtually screened against MTH1. Of the initial 5000 fragments, the top 1000 that had at least 5 analogs with (predicted) higher affinity were manually inspected. Of 22 fragments purchased and tested in an enzymatic assay, 12 showed some activity, with the 5 most active showing IC50 values between 5.6 and 79 µM and good ligand efficiencies.

Since each of these fragments had commercially available larger analogs, the researchers purchased several to see if these did indeed have better affinities. Impressively, this turned out to be the case: both compounds 1a and 4a bound more than two orders of magnitude more tightly than their fragments. Interestingly, while the researchers were unable to obtain crystal structures of fragments 1 and 4 bound to MTH1, they were able to obtain crystal structures of 1a and a close analog of 4a, and these bound as predicted.

Of course, not everything worked: in the case of one fragment, among 19 commercial analogs purchased, the best was only 7-fold better. The crystal structure of this initial fragment bound to MTH1 was eventually solved, revealing that it bound in a different manner than predicted, thus explaining the modest results. In another case the most interesting commercial analogs turned out not to be available after all, but during the course of the study a different research group published a low nanomolar inhibitor with the same scaffold.

One notable aspect of this work is going from fragments to more potent leads without using experimentally determined structural information, something the majority of respondents in our poll earlier this year said they would not attempt. Although such advancement is not unprecedented, published examples are still rare.

In some ways this work is similar to the Fragment Network approach we highlighted last month, the key difference being that while Fragment Network was focused on looking for other fragments, this is focused on finding larger molecules. But how general is it? The researchers found that, while there are a median of just 3 commercial analogs in which a fragment is an exact substructure of a larger molecule, this increases to 700 when the criterion is relaxed to similarity (for example compound 1 and 1a). These numbers undoubtedly become even more favorable for organizations with large internal screening decks.

Eight years ago I ended a post about another successful computational screen with the statement that “the computational tools are ready, as long as they are applied to appropriate systems.” This new paper demonstrates that the tools have continued to improve. I expect we will see computational fragment finding and optimization methods move increasingly to the fore.

09 October 2017

Fragments vs ketohexokinase (KHK) deliver a chemical probe

Anyone who has paid any attention to health news will be aware of concerns over high fructose corn syrup. Just a few years ago the stuff was ubiquitous. Today, due to consumer backlash, it is less common, though still widely used as a cheap sweetener in foods and beverages.

In humans fructose metabolism, unlike glucose metabolism, is not regulated by feedback inhibition, so the sugar is metabolized preferentially. Overconsumption of fructose has been correlated with all sorts of metabolic disorders, from insulin resistance to obesity. But even if you avoid consuming any fructose, your body can still convert glucose into fructose.

The rate-determining step in fructose metabolism is the enzyme ketohexokinase (KHK). Mice lacking this enzyme are healthy and resistant to metabolic diseases. Could a pill do the same thing? Although previous KHK inhibitors have been reported – one starting from fragments discussed here – these did not seem suitable for in vivo studies, not least because they are considerably less potent on rat KHK than human KHK. In a recent J. Med. Chem. paper, Kim Huard and her colleagues at Pfizer describe a chemical probe for KHK.

The researchers used STD NMR to screen their 2592-fragment library in pools of 4 or 10 compounds, with each at 240 µM. This resulted in a formidable 451 hits, of which 448 were screened in full dose response curves using SPR. Of these, 179 confirmed, and 114 had affinities better than 100 µM. All of the SPR-validated hits were tested in an enzymatic assay, leading to 23 fragments with IC50 values from 46 to 439 µM. All 23 of these were soaked into crystals of KHK, and all of them yielded structures showing them bound in the ATP-binding pocket. (Incidentally, this is a lovely example of a successful screening cascade using multiple orthogonal methods, though it would be interesting to know what the outcome would have been had the researchers jumped directly to the X-ray screen.)

But what do you do with 23 fragment hits, all with decent ligand efficiencies and experimentally determined binding modes? Rather than focusing on a single fragment, the researchers noticed that many shared common features, for instance a central heterocycle surrounded by various lipophilic substituents, as in compounds 4 and 5. Many, such as compound 4, also contained a nitrile that made a hydrogen bond to a conserved water molecule.

Next, the researchers combed the full Pfizer screening library for compounds that merged common elements of the fragment hits. This led to more potent inhibitors, such as compound 9 (which was present in the library as a racemate – make sure to vote in the poll on the right!). Parallel chemistry around analogs of this and another hit led to compound 12. In contrast to previously reported molecules, this compound is equipotent on rat and human KHK. It also has decent pharmacokinetics, is orally bioavailable, and is quite selective against a broad panel of off-targets. Rat experiments revealed that the compound inhibits fructose metabolism in vivo.

This story is a nice illustration of how lots of different crystal structures can enable fragment merging. There is still some way to go – the potency in particular could be improved. Also, there are actually two human isoforms of KHK, and compound 12 hits both equally – which may or may not be desirable. Nonetheless, this chemical probe should help further elucidate KHK biology, and help to address whether the enzyme is druggable, or merely ligandable.

02 October 2017

Dynamic combinatorial chemistry revisited: why it’s so difficult

Last year we discussed the application of dynamic combinatorial chemistry (DCC) to fragment linking. The idea is that a protein will shift the equilibrium of a reversible reaction, selecting the tightest binder. Over the past twenty years practitioners of DCC have generated plenty of papers, some quite nice, but I do not recall seeing examples of the technique generating novel and attractive chemical leads. A new paper in Chem. Eur. J. by Beat Ernst and colleagues at the University of Basel explains why it is so difficult.

The researchers were interested in the bacterial protein FimH, which helps microbes colonize the urinary tract by adhering to human proteins that are decorated with mannose. The chemistry the researchers decided to explore for DCC was the reaction of aldehydes with hydrazides to form acylhydrazones. This reaction is slowly reversible at pH 7, allowing exchange between library members to occur, but it can be essentially frozen by raising the pH.

To try to understand every aspect of their system, the researchers focused on a tiny library. Two aldehydes were chosen, one based on mannose, the other based on glucose. Four (quite similar) commercially available hydrazides were purchased.

The researchers made and tested the affinity of each of the eight possible library members using surface plasmon resonance (SPR). The four acylhydrazones based on mannose had dissociation constants (KD) ranging from 0.33 to 0.76 µM, while the mannose aldehyde came in at 3.2 µM. In contrast, the four acylhydrazones based on glucose had KD values between 152 and 735 µM, comparable to the glucose aldehyde itself (194 µM). Since mannose is the natural ligand for FimH while glucose is not, this was expected.

One challenge of DCC is separating library members from the protein for analysis; releasing bound ligands can be particularly challenging if they bind tightly to the protein. A variety of methods were tested, including microfiltration, but this gave “massive alterations in composition.” Various attempts at protein denaturation and precipitation using organic solvents or heat also failed. The fact that this step was so difficult, even for closely related ligands (the difference between mannose and glucose is the stereochemistry around a single hydroxyl group) underscores the challenge of analyzing DCC mixtures.

The problem was finally solved by using a biotinylated version of FimH which could be captured using commercial streptavidin agarose beads.

The most general approach works as follows.

1. Incubate 100 µM FimH protein with library (with each aldehyde and hydrazide at 50-200 µM) at pH 7 for 3 days in the presence of 10 mM aniline, which catalyzes the acylhydrazone exchange.

2. Raise the pH to 8.5 to stop the reaction, add streptavidin agarose, centrifuge, and discard the supernatant containing the unbound molecules.

3. Resuspend the agarose beads containing the protein, add a competitor to release bound ligands, increase the pH to 12 to ensure release, and analyze the product ratios using HPLC.

Although cumbersome, this protocol does work: mannose-derived compounds were enriched relative to glucose-derived compounds, as expected due to their higher affinities, and the most potent compound was enriched over the less potent ones. That said, the robustness of the results were dependent on the ratios of library components.

So will DCC ever be practical? I’m not so sure. But, as the researchers end hopefully but not hypefully, their work “is a contribution to this challenge.”

25 September 2017

Flipping fragments in CDK8

The cyclin-dependent kinases (CDKs) are targets for a variety of diseases, particularly cancers. One of the earliest posts at Practical Fragments discussed the clinical-stage AT7519, which inhibits several CDKs. A new paper in Bioorg. Med. Chem. Lett. by Xingchun Han, Song Yang, and their colleagues at Roche Innovation Center Shanghai describes the discovery of a selective CDK8 inhibitor.

The researchers started with a biochemical screen (at 100 µM) of ~6500 fragments, all with less than 19 non-hydrogen atoms. A whopping 403 compounds showed >70% inhibition, and of 227 tested in full dose-response curves, 48 had IC50 < 50 µM with ligand efficiency > 0.3 kcal/mol/atom. Compound 1 was both potent and structurally interesting.

SAR by catalog led to several more active analogs, including compound 4, which was crystallographically characterized bound to CDK8 (blue). The pyridine nitrogen makes a hydrogen bond with the hinge-region of the kinase, while the pyrrole nitrogen makes a water-mediated bond to the protein. Interestingly though, benzylation of the pyrrole slightly improved affinity, suggesting that the molecule can bind in a flipped orientation, with the pyrrole nitrogen pointing out towards solvent. This binding mode would provide easy access to a small hydrophobic pocket, a hypothesis that was supported when compound 17 showed a dramatic increase in affinity. A crystal structure of compound 17 bound to CDK8 confirmed the flipped binding mode.

A closely related molecule (replacing the chlorine atom with a trifluoromethyl group) showed oral bioavailability and good pharmacokinetics in mice. And another closely related compound (methyl instead of chlorine) showed excellent selectivity against a panel of 43 kinases.

There are several practical lessons in this brief paper. First, very minor changes can lead to massive improvements in affinity. Indeed, compound 17 has the same number of non-hydrogen atoms as the initial fragment, yet binds almost 1000-fold more tightly. Second, it is possible to discover selective kinase inhibitors while staying well within the ATP-binding pocket, and doing so may cut down on molecular obesity too (compare this paper with the CK2 story highlighted last week.) And finally, while structural information can be enabling, it is always important to remember that molecules – even reasonably potent ones – can dramatically change binding modes with the slightest modification. Remaining alert to this possibility can open new opportunities.

18 September 2017

Fragment linking to a selective CK2 inhibitor

The kinase CK2 is an intriguing anti-cancer target, but most of the reported inhibitors bind in the conserved hinge region and so also hit other kinases, complicating interpretation of the biology. A team based at the University of Cambridge has taken a fragment-linking approach to discover more selective inhibitors. The first report was published last year by Marko Hyvönen, David Spring, and colleagues in Chem. Sci., and they have now published a more complete account in Bioorg. Med. Chem.

A crystallographic screen identified compound 1, which bound to six different sites! One of these sites was particularly interesting as it appeared to be a previously undiscovered “αD” pocket near the ATP-binding site. A couple cycles of SAR by catalog, informed by computational screening, led to compound 7, which binds in the desired pocket but not at other sites.

Although compound 7 has measureable affinity for CK2α as judged by ITC, it does not inhibit the enzyme, which is not surprising because it does not bind in the ATP-binding site. Thus, the researchers screened 352 fragments from Zenobia in cocktails of 4, each at 5 mM, and found 23 that bound in the ATP site. Reasoning that the hinge region is the most conserved portion of the ATP-binding site, the researchers avoided fragments that bound there. This led them to focus on compound 8, which has a synthetic handle pointing towards the αD pocket.

Next, modeling was used to generate a series of appendages from compound 7 to try to reach compound 8. Compound 19 looked like it could bridge the gap, a hypothesis which was confirmed when linking led to a low micromolar binder. Tweaking the linker led to CAM4066, which showed nanomolar binding as well as inhibition of CK2. Crystallography revealed that the linked molecule bound as expected.

CAM4066 was tested against 52 other kinases at 2 µM and showed at most only 20% inhibition, suggesting that it is indeed quite selective for CK2. Unfortunately, perhaps because of its carboxylic acid, it did not show any cell activity. This was addressed by making a methyl ester prodrug – a strategy that was also taken for another fragment linking campaign on a very different target.

As the researchers point out, CAM4066 follows the Evotec model of a largely lipophilic fragment linked to a more polar fragment. There is still much more to do: no pharmacokinetic data are provided, and the potency still falls short of what is needed for a chemical probe. Still, this is a nice illustration of the power of fragment linking, guided by both modeling and crystallography, to generate molecules with interesting properties.

11 September 2017

Chiral fragments – and poll!

Chirality underpins all life. Nineteen of the twenty amino acids contain at least one stereocenter, as do all nucelosides, sugars, and most metabolites. The very first fragment I ever found was chiral, but that is not typical, at least judged by those that show up in publications. Only 5 of the 27 fragment to lead success stories published in 2015 started with a fragment containing a chiral center. This probably reflects what people choose to screen and pursue. Chiral centers can lead to challenging chemistry, and chiral centers also add to molecular complexity.

All of which brings us to the topic of our new poll: do you include chiral fragments in your primary screening collection? If so, do you include both enantiomers? Please vote in the poll to the right.

If you do include chiral fragments, do you screen racemic mixtures? Crystallography can sometimes reveal which enantiomer is active if the quality of the structure is good enough, but woe betide anyone screening racemic mixtures by ITC! In a new paper in Magn. Res. Chem., Claudio Dalvit (University of Neuchatel) and Stefan Knapp (Goethe University Frankfurt) show that fluorine NMR can also be used to screen racemic mixtures.

As Teddy wrote more than five years ago, 19F NMR is “just like 1H NMR”. Most applications of 19F rely on detecting the line broadening that occurs when a fluorine-containing fragment binds to a protein. However, the chemical shift of the fluorine atom(s) can also change, particularly if the ligand forms hydrogen bonds to the protein. This “chemical shift perturbation” can be large enough to be detectable.

In the absence of protein, 19F NMR shows the same signal for different enantiomers, so a racemic ligand containing a single trifluoromethyl group gives a single sharp peak. However, upon addition of a protein that binds one enantiomer, the signal splits into two; one remains sharp and retains essentially the same chemical shift, while the other becomes broader and moves. The researchers show this both theoretically and experimentally with a racemic fragment that binds to the bromodomain BRD4. Adding a high-affinity ligand that binds to the same site displaces the fragment, causing the two signals to again converge.

Unfortunately there is no X-ray structure of the ligand bound to the protein, and the two pure enantiomers were not tested individually. And of course, unlike crystallography, 19F NMR does not reveal which enantiomer in a racemic mixture binds. Still, enantioselective binding can itself be indicative of specific binding, as opposed to various artifacts, and the researchers recommend that “racemates should always be included in the generation of the fluorinated fragment libraries.” What do you think?

04 September 2017

Efficiently searching for fragments

What do you do when you find a fragment? After checking for artifacts and getting as much structural information as possible, the next step is usually to test analogs for improved potency. But how do you go about that? Richard Hall and his colleagues at Astex provide their approach in a recent paper in J. Med. Chem.

Readily available analogs can come from two sources. Larger organizations generally have massive libraries of compounds, and it’s easy enough to order these for testing. There are also plenty of commercial vendors, enabling SAR by catalog. But how do you sort through the millions of possibilities to find those that are most likely to improve potency?

Sub-structure searches are generally the first approach: look for fragments containing a central core, perhaps differently decorated. A nice example of this is described here, where a search for related pyrimidines led to an increase in potency by replacing one atom. Sometimes more dramatic changes are necessary though. Searching for similar molecules that do not share the same core can be successful, as in this case, but often requires multiple searches. Also, particularly for smaller fragments, “similarity” can encompass significant differences.

The Astex researchers have created a computational tool to streamline this search procedure. It is called the Fragment Network, which is a “graph database,” a type of database in which information is stored as nodes and edges – like the webpages (nodes) and links (edges) used in Google searches. In the Fragment Network, each fragment is computationally dissected into component parts (such as a phenyl ring or a hydroxyl), with edges representing the connections between the parts (such as carbon-carbon bonds). The database contains about 5 million compounds of up to 24 non-hydrogen atoms, and these are further annotated as to whether they are available in-house or from more or less reliable vendors.

A search of the Fragment Network – which takes just a fraction of a second – can be customized depending on the goal. A default search returns compounds that are up to two edges away from the query, which can yield quite a large number of compounds, many of which would not come up in a substructure query, as shown for the simple but useful 4-hydroxybiphenyl.

Plodding through lists of compounds can be tedious, and one nice feature of the Fragment Network is that it groups compounds by type – so for example the ring substitutions are grouped separately from the linker replacements. Compounds are also sorted by commonality of replacement: for example, published data reveals that the most common replacement of a methyl group is a chlorine atom, followed by a methoxy group, with an amine way down the list.

The researchers applied the Fragment Network retrospectively to two previously disclosed programs, campaigns against protein kinase B and HCV NS3. In both cases the program identified most of the changes explored by the medicinal chemists on the project, as well as some that were not tested. Of course, often times the best fragments are not available and need to be synthesized, and the grouping of results returned by the Fragment Network quickly highlights these regions of less-populated chemical space.

Those of you who have seen Astex researchers present at conferences will be familiar with AstexViewer, a powerful open-source molecular visualization program. Hopefully the code for the Fragment Network will also be publically released. If not, it might be worth talking to your computationally gifted colleagues to see if they can create something similar. In the meantime, how many of you are using something similar?

28 August 2017

Fragments vs BET Bromodomains: FORMA’s story

Five years ago Teddy highlighted a paper from GlaxoSmithKline that reported the discovery and characterization of several different fragments that bind to members of the BET family of bromodomains, epigenetic readers that recognize acetylated lysine residues in histones. Researchers at FORMA were among those paying attention to these developments. David Millan and his colleagues have now published in ACS Med. Chem. Lett. their account of how they were able to advance one of these fragments to a chemical probe.

As the researchers note, many different BET inhibitors have been reported; we discussed two separate series just a few months ago. Chemical novelty was thus a challenge, particularly as they were starting with a fragment (compound 1) reported by a large company. They thus chose to tweak the fragment slightly to intermediate 2. Importantly, introduction of the second nitrogen also introduces another synthetic vector with potential to pick up interactions with the so-called “WPF shelf”. This explicit consideration of synthetic tractability in fragment design enables rapid progress.

Parallel chemistry led to compound 6, with measurable biochemical activity against BRD4. Further growing from the phenyl ring led to compound 8, with sub-micromolar biochemical and antiproliferative activity. A crystal structure revealed that the newly introduced amide functionality was pointed toward solvent, which would allow modulation of the physicochemical properties.

More medicinal chemistry followed, with considerable effort on improving the plasma and liver microsome stability. This campaign involved a combination of rational design and parallel synthesis along with a keen focus on minimizing lipophilicity. Ultimately the researchers arrived at FT001, with good activity and stability. This compound was also selective for BET family members over other bromodomains and displayed reasonable pharmacokinetics and impressive activity in a mouse xenograft model.

Last week we highlighted a paper that also started from a previously disclosed fragment to generate novel chemical matter. This paper provides another example of how useful public fragments can be in the hands of creative scientists.

20 August 2017

Fragments vs histone KDM4 lysine demethylases: Celgene’s story

Last year we highlighted a paper from academia in which modeling was used to discover potent inhibitors of the lysine demethylase KDM4C, a potential anti-cancer target. In a recent paper in ACS Med. Chem. Lett., Michael Wallace and collaborators at Celgene, the European Institute of Oncology, and the University of Chicago report a chemical probe for KDM4 family members.

The researchers started with a literature screen of fragments known to bind to KDM4, leading them to compound 1, which previous work had shown binds to the catalytic iron through the pyridine ring nitrogen. Researchers from GlaxoSmithKline had also reported that growing off compound 1 could lead to more potent compounds, a strategy that proved successful here in the case of chiral compound 2a, which improved affinity by more than two orders of magnitude. Interestingly, the enantiomer had dramatically lower activity.

Armed with this information but no crystal structure, modeling suggested that further growing off the tetrahydronaphthalene would be productive, which turned out to be the case for compound 3, with similar affinity but improved activity in an antiproliferative cell assay. Further experiments showed that the compound increased levels of trimethyl-lysine on lysines 9 and 36 of histone 3, known substrates of KDM4 family members.

A crystal structure of compound 3 bound to KDM4A, which is closely related to KDM4C, suggested further room to grow. Compound 3 contains a carboxylic acid and has a low cLogD, traits that tend to reduce cell permeability. The researchers thus focused on increasing the lipophilicity of the molecules, leading to QC6352. Despite the fact that this molecule is less potent in the enzymatic assay, it has significantly improved cellular potency. It also has reasonable pharmacokinetics and oral bioavailability, and showed activity in a mouse xenograft model. QC6352 hits KDM4A, 4B, 4C, and 4D, but is quite selective against most other KDMs.

This paper illustrates three important points. First, as discussed previously, you don’t need a novel fragment to get to novel leads – you just need creative scientists. Indeed, the increasing number of fragment hits reported for various targets provides a wealth of starting points even for organizations that don’t do in-house fragment screening. Second, you don’t necessarily need a crystal structure as long as you have good modelers. And finally, while excess lipophilicity is rightly avoided, it is important to remember that compounds can also be too polar. As Oscar Wilde noted, “everything in moderation, including moderation.”

14 August 2017

Fragments distinguish allosteric from active site binders

As discussed last year, secondary binding sites on proteins appear to be quite common. Some of these sites have no functional relevance, but others are allosteric sites, which can modulate the activity of proteins. Allosteric ligands can be useful for several reasons. First, unlike molecules that bind at the active (that is, catalytic) site of an enzyme, which usually inhibit activity, allosteric site binders can increase activity. Second, allosteric sites are usually less conserved than active sites, allowing greater selectivity. Finally, combining an allosteric inhibitor with an active site inhibitor can lead to synergy as well as lower the incidence of resistance mutations for cancer and anti-infectives. In a recent ACS Med. Chem. Lett. paper, Lukasz Skora and Wolfgang Jahnke at Novartis describe a simple NMR approach to differentiate these two classes of ligands.

The researchers used 19F NMR to screen 540 fragments containing a CF3 group, each at 25 µM, in pools of 30 against the kinase ABL1 (at 4 µM); the BCR-ABL1 mutant form of this protein is a key driver for chronic myelogenous leukemia. Several approved drugs target the active site of ABL1, and Novartis researchers have recently launched clinical studies of a compound called ABL001, which binds to an allosteric pocket.

Fragments that bind to ABL1 showed a decreased 19F NMR signal due to line broadening. Adding ABL001 displaced fragments that bind to the allosteric site, thereby increasing their NMR signals, while adding the active-site binding drug imatinib displaced fragments that bind to the catalytic site. Follow-up experiments with individual fragments identified a selective catalytic-site binder (CAT-1) and a selective allosteric site binder (ALLO-1). Both fragments are commercially available and quite weak (Kd = 43 µM for ALLO-1 and IC50 = 380 µM for CAT-1), which in this case is a feature because they can easily be displaced.

Mixing these two fluorine-containing probes with ABL1, adding test compounds, and performing 19F NMR thus provides a simple means to determine whether a ligand binds to the allosteric site, the active site, or both sites. The researchers confirmed that the approved catalytic-site binding drugs nilotinib, dasatinib, and ponatinib displace CAT-1 but not ALLO-1, while allosteric-site binders such as ABL001 displaced ALLO-1 but not CAT-1.

Interestingly, a crystal structure of imatinib with the highly related protein ABL2 shows the compound binding to both the catalytic and allosteric sites, yet although imatinib clearly displaced CAT-1 it could not displace ALLO-1. This is a useful reminder that crystal structures say nothing about affinity.

The drug crizotinib, which binds to the active site of multiple kinases, has been reported by other researchers to bind to the allosteric pocket of BCR-ABL1, but this was not borne out in the competition assays. Similarly, the drug fingolimod has also been reported as an allosteric inhibitor of ABL1. This molecule did indeed displace ALLO-1, but only at concentrations so high as to be biologically irrelevant.

This is a nice paper, and a good reminder that fragments can make useful biophysical probes in and of themselves, even without the need for optimization.

07 August 2017

Assessing ligandability by thermal scanning

Ligandability refers to the ability to find small-molecule leads against a target. A protein might be ligandable but not druggable if, for example, potent inhibitors of the target do not affect a disease state. But knowing in advance whether a target is ligandable can be useful, both to decide whether to embark on a campaign and to plan the resources it will likely require. Fragment screens by NMR have been shown to be good predictors of ligandability, but not everyone has access to this technology. Computational methods (such as FTMap) are also useful, but require a structure of the target. In a recent paper in J. Med. Chem., Stefan Geschwindner and colleagues at AstraZeneca describe high-throughput thermal scanning (HTTS) for assessing ligandability.

Thermal scanning (alternately called, as the researchers note, thermal shift, differential scanning fluorimetry (DSF), or thermofluor) relies on the preferential binding of a fluorescent dye to protein that is heat-denatured. Since ligands generally stabilize a protein against denaturation, an increase in melting temperature (Tm) is taken as an indication of binding. The assays can be plate-based and thus very fast.

The researchers chose 16 diverse targets (mostly enzymes) and screened their 763-ligandability fragment set (described here) at 1 mM by HTTS. Hits were defined as compounds that increased  thermal stability at least 3-fold above the standard deviation of controls. Targets were then categorized as follows:

Low ligandability: hit rate < 1.5%
Medium ligandability: hit rate between 1.5 and 4.5%
High ligandability: hit rate > 4.5%

Nine targets ranked low, and all of these failed high throughput screening (HTS), while 5 out of the 7 targets ranked medium or high by HTTS yielded useful HTS hits. Of course, failure in an HTS does not preclude target advancement by other means – including FBLD. Ultimately all but three targets (including all of those ranked medium or high and 6 of 9 ranked low) went on to enter hit-to-lead optimization programs.

Encouragingly, HTTS and NMR agreed perfectly for low and high ligandability targets, but NMR assigned three targets as medium where HTTS assigned them as low. The researchers thus set out to increase the sensitivity of HTTS.

It turns out that entropically-driven binders tend to cause greater thermal shifts than enthalpically driven binders. The observation that most fragments bind largely enthalpically, and with low affinity too, makes them particularly challenging to detect. To try to shift the balance, the researchers repeated the HTTS assay for three of the low-scoring targets in D2O instead of H2O, which enhances entropic interactions at the expense of enthalpic interactions. Indeed, all three targets showed enhanced hit rates, and two moved from low to medium ligandability.

Another way to improve sensitivity of a thermal shift assay is to add urea, which destabilizes proteins by lowering the unfolding enthalpy. Adding non-denaturing amounts of urea (0.8 to 2.4 M concentration) to the three low-scoring targets above did indeed increase the hit rate for two of them.

One interesting tidbit is the observation that particularly stable targets, with unfolding temperatures >70 °C, tend to produce lower hit rates in HTTS than less stable targets. This could account for the very different experiences people have had with the technique.

This is a nice paper, and the approach may be worth implementing, as the researchers note has already happened at AstraZeneca. Although HTTS is unlikely to ever be as robust as SPR, NMR, or crystallography, it is hard to beat the low cost and high speed.

31 July 2017

Fragments in the clinic: PF-06650833

Of the more than 30 fragment-derived drugs that have entered clinical development, more than a third target kinases. While most of these are being developed against various types of cancer, a new paper in J. Med. Chem. by Katherine Lee, Stephen Wright, and their Pfizer colleagues describes the discovery of a compound that inhibits interleukin-1 receptor associated kinase 4 (IRAK4), a target for chronic autoimmune diseases. (Katherine also spoke about this project at FBLD 2016.) This details the earliest screens through development of the active clinical candidate.

The researchers started by screening their 2592-member Global Fragment Initiative library at 236 µM using STD NMR, resulting in 169 hits. A biochemical screen of the same library at 909 µM produced 160 hits, with 95 in common. Further triage using another assay along with modeling prioritized 15 fragments, of which 10 produced structures in co-crystallization trials. Fragment 51 was particularly interesting due to its impressive ligand efficiency and unusual binding mode to the hinge region of the kinase.

The crystal structure suggested that fragment growing could be productive, and indeed simply expanding the phenyl ring to a naphthyl improved the affinity to low micromolar for compound 10. Adding a nitrogen into the ring to lower lipophilicity while also adding a substituent to pick up additional interactions improved the affinity another order of magnitude (compound 14).

Guided by a co-crystal structure of compound 14 bound to IRAK4, the researchers used parallel chemistry to further improve the molecule, resulting in compound 20, which crystallography confirmed makes multiple interactions with the protein. Compound 20 also had promising selectivity and pharmacokinetic properties, but despite low nanomolar activity in a biochemical assay it had only high nanomolar potency in human peripheral blood mononuclear cells (PBMC).

At this point the medicinal chemistry began in earnest, again guided by structure and with a keen eye on maintaining good physicochemical properties. To a non-chemist the changes between compound 20 and PF-06650833 may appear subtle, but chemists will appreciate that you don’t introduce two new stereocenters without darn good reasons, which are discussed in depth in the paper. The results paid off, with the final molecule showing low nanomolar potency in the PBMC assay, excellent selectivity against a broad panel of kinases and other targets, and attractive ADME properties. It was also orally active in an acute rat inflammation model.

Sometimes publications only appear after a compound has dropped out of development, but that is not the case here. Indeed, after completing four phase 1 studies, PF-06650833 is currently being tested in a phase 2 trial for rheumatoid arthritis. Watch this space!

24 July 2017

Fragments vs Trypanosoma parasites

Last month we highlighted how fragments could be used to discover inhibitors of protein-protein interactions (PPIs). Today we continue the theme of fragments vs PPIs, in this case the interaction between PEX14 and PEX5, proteins which are important for glucose metabolism in disease-causing protists such as Trypanosoma.

The research, published recently in Science, was done by a large multinational team led by Grzegorz Popowicz, Michael Sattler (both at Helmholtz Zentrum München), and Ralf Erdmann (Ruhr University Bochum). They started by solving the NMR structure of the N-terminal domain of PEX14 from T. brucei, the organism that causes sleeping sickness. Previous work had shown that PEX5 binds to this domain, with two aromatic side chains of PEX5 binding in adjacent hydrophobic pockets. With this information in hand, the team performed a virtual screen of several million (non-fragment-sized) molecules. Eight of the best-scoring hits were tested, and four showed binding in an NMR assay, with compound 1 having the highest affinity.

Next, the researchers screened a library of 1500 fragments (each at 1 mM in pools of 5) using 1H, 15N HMQC NMR. This led to 12 hits with affinities better than 2 mM. Strikingly, all of these fragments contained fused bicylic aromatic ring systems, three of which were substituted naphthyls. Appending these onto compound 1 led to compound 4, with low micromolar affinity. Introducing an amine to interact with a glutamic acid residue in PEX14 led to compound 5, with high nanomolar affinity. This compound also showed activity against several species of pathogenic Trypanosoma. Further tweaking led to a molecule with activity in a mouse model of infection.

This example of fragment-assisted drug discovery (FADD) is reminiscent of other cases (described here, here, and here) in which fragments were used to replace elements of a previously identified molecule. While it is possible that traditional medicinal chemistry could have achieved the same result, fragments probably helped winnow down the number of molecules to be synthesized. It is also nice to see this technology applied to understudied diseases. 

17 July 2017

Native mass spectrometry revisited

Native electrospray ionization mass spectrometry (ESI-MS) is one of the less-commonly used fragment finding methods. The technique relies on gently ionizing a protein-fragment complex without causing denaturation; bound fragments reveal themselves as shifts in mass. The technique is truly label-free, and can use very small amounts of protein and fragments. In practice the technique can work really well, reasonably well, or quite poorly. Two new papers shed light on factors that influence success.

The first paper, by Kevin Pagel (Freie Universität Berlin), Benno Kuropka (Bayer), and collaborators, examines four different cancer-related proteins. Let me say up-front that that the paper is remiss in not disclosing the chemical structures of any of the fragments, so in a very real sense this work is not reproducible. It is a shame the editors of ChemMedChem were not more demanding. That said, there is some useful information here.

Most of the focus is on the protein MTH1, screened at 10 µM concentration with 100 µM of each fragment. This was not a naïve screen; the fragments were previously identified from a thermal shift assay (TSA): 24 stabilized the protein, 4 destabilized it, and 5 had no effect. Remarkably, all of the fragments showed complexes in ESI-MS ranging between 6 – 66%, even those that had no effect in the TSA! Choosing an (admittedly arbitrary) 20% cutoff weeded out most of the false positives: 16 of the 24 stabilizers passed, while none of the destabilizers or neutral molecules did.

The best hit by ESI-MS also gave the strongest thermal shift, and a titration curve revealed an impressive dissociation constant of 1.7 µM. However, even at high concentrations of fragment the amount of bound complex did not exceed 70%, meaning that interpretation of single-dose experiments (for example, from a primary screen) could be problematic.

The results were similar for the protein KDM5B: 8 of 9 stabilizing fragments were hits by ESI-MS, as were two of 7 destabilizing fragments. Note that fragments that destabilize proteins can still be tight binders, as illustrated here.

For two additional proteins, however, ESI-MS was disappointing. For BRPF1, ESI-MS didn’t find any of the 11 hits from TSA, while for UHRF1 it found only a single hit – though this hit was not one of the 10 stabilizers identified by TSA. One could argue that the TSA hits were false positives were it not for the fact that, in the case of BRPF1, 6 of them were confirmed by crystallography.

The second paper, in Angew. Chem., comes from Chris Abell and coworkers at the University of Cambridge, and focuses on the protein EthR, a potential target for tuberculosis that we’ve previously discussed.

EthR binds to DNA, so rather than look for direct binding of fragments to EthR the researchers instead looked for fragments that could disrupt the EthR-DNA complex. A small library of 73 fragments was tested (at 0.5 mM each, in 2% DMSO), yielding 8 hits. The same library was screened under the same conditions using differential scanning fluorimetry (DSF), yielding 7 hits, 4 of which had also been identified using ESI-MS. All 11 of these molecules were then tested under the same conditions in an SPR assay to see if they could disrupt the interaction between EthR and chip-bound DNA. The 7 best SPR hits were all fragments that had been identified by ESI-MS. Moreover, two fragments – one identified solely by ESI-MS and one identified by both ESI-MS and DSF – were characterized bound to EthR crystallographically, and these represent new chemotypes for this target.

So what are we to make of all this? In common with other techniques, ESI-MS works well for some targets and less well for others. The problem is that it is not clear what distinguishes the two classes of targets. If you have access to the equipment and expertise you might consider adding ESI-MS to your screening cascade. But if you can only afford to buy one instrument for fragment screening, you’d probably be better off investing in NMR or SPR.

10 July 2017

Reagents as covalent fragments

Covalent drugs are a thing these days: as long as you can get selectivity, there’s nothing like a covalent bond to juice up affinity for a target. Screening for covalent fragments is thus a reasonable approach, and multiple researchers have assembled libraries of fragments containing either irreversible or reversible covalent “warheads”. The latest example, by Marion Lanier, Mark Hixon, and collaborators at Takeda, appears in J. Med. Chem.

Boronic acids can form reversible covalent bonds with the side chains of serines or threonines in proteins, with a predilection for the highly reactive active-site residues found in hydrolytic enzymes. Indeed, three approved drugs – bortezomib, tavaborole, and ixazomib – contain boronic acids.

When medicinal chemists think of boronic acids, they probably think of them as reagents for the Suzuki coupling, a useful method for forming carbon-carbon bonds. Because the reaction is so popular, some 6000 boronic acids are commercially available, many of them fragment-sized. Thus, the researchers assembled a set of 650 into a boronic acid library (BAL).

To determine whether this BAL would be useful, the researchers screened it against autotaxin, a phospholipase with anti-cancer and anti-inflammatory potential. Fragments were tested at 100 µM in a functional assay, with hits retested in 11-point dose-response curves. This yielded a whopping 51 molecules with IC50 values better than 10 µM, some as good as 200 nM.

The researchers also screened autotaxin against a set of 1750 non-boronic acid containing fragments, this time at 500 µM. Not surprisingly, hits tended to be significantly weaker despite the similar sizes of the fragments. The BAL fragments had average ligand efficiencies of 0.61 kcal mol-1 per heavy atom, while the conventional fragments averaged a lower but still respectable 0.41. Some of the BAL fragments were also crystallized bound to autotaxin, revealing that they do in fact form bonds with the catalytic threonine. 

This is a nice paper, though I do wish that the researchers had tried to calculate the inherent reactivities of the boronic acids to determine how these differences affected their affinities for the protein, as has been done for other warheads such as aryl acrylamides. Also, it would be interesting to see how a docking program such as DOCKovalent performs against this target with the same set of fragments. Hopefully we’ll see these questions addressed in the future. In the meantime, expect to see commercial vendors start offering libraries of boronic acid fragments.

03 July 2017

Fragment events in 2017 and 2018

The year is halfway behind us, but there are still a couple upcoming fragment-based events, and next year is already taking shape.


July 23-28: Australia is coming into its own as a destination for fragment experts, many of whom will be participating in the Royal Australian Chemical Institute's Centenary Congress in Melbourne. The entire event should be huge - think ACS with wombats - so if you've been looking for yet another reason to travel Down Under, this is it.

September 25-29: CHI's Discovery on Target in Boston includes an Inaugural Lead Generation Strategies track (September 26-27), and it looks like fragments will play a major role - as well they should!


January 28 - February 1: The First Alpine Winter Conference on Medicinal and Synthetic Chemistry will take place in St. Anton am Alberg, Austria. This looks like a fun event and includes a section on FBDD.

April 2-6: CHI’s Thirteenth Annual Fragment-Based Drug Discovery, the longest-running fragment event, will be held in San Diego. You can read impressions of this year's meeting here, last year's meeting here; the 2015 meeting herehere, and here; the 2014 meeting here and here; the 2013 meeting here and here; the 2012 meeting here; the 2011 meeting here; and 2010 here.

June 13-15: Although not exclusively fragment-focused, the fifth NovAliX Conference on Biophysics in Drug Discovery will have lots of relevant talks, and will be held for the first time in Boston. You can read my impressions of the recent Strasbourg event here and Teddy's impressions of the 2013 event herehere, and here.

October 7-10: Finally, FBLD 2018 returns to San Diego, where it was born back in 2008. This will mark the seventh in an illustrious series of conferences organized by scientists for scientists. You can read impressions of FBLD 2016, FBLD 2014,  FBLD 2012FBLD 2010, and FBLD 2009.

Know of anything else? Add it to the comments or let us know!

26 June 2017

Fragments vs BCL6, two ways

Disrupting protein-protein interactions (PPIs) tends to be challenging: interfaces are often large and flat, with few deep pockets in which small molecules can bind. Also, much like unhappy families, PPIs are usually dissimilar, meaning that HTS collections yield fewer, less attractive hits. Both of these challenges are well-addressed by fragments, and indeed last year saw the approval of venetoclax, which targets a PPI. Two new papers in J. Med. Chem. report inhibitors of another PPI.

B-Cell lymphoma 6 (BCL6) binds to other proteins to regulate gene expression. As its name suggests, it was identified in diffuse large B-cell lymphoma (DLBCL), and is thus an interesting anticancer target. Also, structures of the protein in complex with a peptide suggested that it may not be impossible to find small molecule inhibitors. Yusuke Kamada and colleagues at Takeda set out to do just this.

An SPR-based screen of 1494 fragments, each at 1 mM, identified 64 hits which confirmed in dose-response titrations. However, only seven compounds confirmed in an STD-NMR experiment. Of these, compound 1 was characterized crystallographically bound in the peptide groove.

A few tweaks to the fragment led to compound 4, with improved potency. Meanwhile, an HTS screen had identified the very weak compound 5, and crystallography showed that it bound at the same site as compound 4. Merging the two molecules led to compound 7, with mid-nanomolar biochemical potency and low micromolar activity in a cell-based assay. This is a classic case of fragment-assisted drug discovery (FADD), and a good illustration of how FBLD and HTS can be complementary.

The second paper, by William McCoull and a large team of collaborators from AstraZeneca and Pharmaron, goes somewhat further. The researchers conducted an SPR-based screen of 3500 fragments along with a virtual screen. Both found hits, and led to molecules with the same core as compound A2. Crystallography revealed that these also bind in the peptide groove, and combining elements of both molecules while tweaking the properties led to compound A5, with improved affinity.

The next step was growing compound A5 to try to make a hydrogen bond interaction with the protein. That led to compound A8, with submicromolar affinity. A crystal structure of a related compound bound to BCL6 revealed that two chemically distant portions of the molecule were in close proximity, suggesting a macrocyclization strategy similar to what we described last week. This proved highly successful, improving the affinity by more than two orders of magnitude for compound A11. NMR studies of the linear and cyclized compounds revealed that the conformation of the latter was indeed closer to that seen in the crystal structure.

The medicinal chemistry continues extensively from here. In particular, compound A11 showed some activity against the kinase CK2, but this could be engineered out. Multiple additional changes were explored, with many compounds showing low nanomolar activity in a biochemical assay and some showing high nanomolar activity in a cell-based assay. Unfortunately, none were very effective at inhibiting the proliferation of lymphoma cell lines. The authors state, “we conclude that the BCL6 hypothesis as a means of treatment for DLBCL is still unproven and we have elected not to progress this series of BCL6 inhibitors further into development.”

This makes sense, though I wouldn’t abandon all hope. For two other PPIs, BCL2 and MCL1, robust cell activity required picomolar affinity in a biochemical assay. Whether this level of potency is achievable for BCL6 remains an open question.

19 June 2017

Fragments vs BRD4, two ways

Bromodomains, epigenetic targets that recognize acetylated lysine residues, have received considerable attention from the fragment community. (I devoted all of last July to the topic, and covered it more recently here.) Of the dozens of bromodomain-containing proteins, the four BET-family members have been highly studied, and the second bromodomain of BRD4 (BRD4-BRDII) in particular has been implicated in cancer and inflammation. In two new papers, researchers from AbbVie describe inhibitors of this target.

In the first Bioorg. Med. Chem. Lett. paper, George Sheppard and colleagues briefly describe a protein-detected (13C-HSQC) NMR screen of BRD4 in which the methyl groups of isoleucine, leucine, valine, and methionine were 13C-labeled. About 18,000 fragments were screened in pools of 30, and hits were then tested individually in NMR and time-resolved fluorescence resonance energy transfer (TR-FRET) assays. Despite extensive work on this target by multiple groups, these screens were able to identify several new fragments, such as the related compounds 1 and 2.

Crystallography of each fragment bound to BRD4 revealed that they bind in the acetyl lysine recognition site and make contacts with the conserved asparagine residue as well as a nearby water molecule. Merging the fragments led to compound 5, with a slight increase in affinity.

Comparison with other BRD4 inhibitors suggested a growth strategy, leading to compound 15, with nanomolar activity in the TR-FRET assay and two cell-based assays. The compound was orally bioavailable but had relatively high clearance, so further medicinal chemistry focused on changing the original core. This ultimately led to compound 38, with improved oral bioavailability, lower clearance, good selectivity against non-BET bromodomains, and activity in a mouse xenograft assay.

The second paper, by Le Wang, John Pratt, and colleagues in J. Med. Chem., starts with a different fragment from the original screen, compound A1. This molecule was even weaker than the fragments described above, but crystallography confirmed that it binds in the same acetyl lysine binding pocket.

Again, comparison with known inhibitors provided ideas for fragment growing, rapidly leading to compound A11. Further medicinal chemistry – which is extensively described in the paper – led to compound A30a, which bears considerable resemblance to the series reported in the previous paper.

Crystal structures of compounds bound to the protein suggested that it might be possible to make a macrocycle, which would in theory increase the affinity by locking the molecule in a low energy conformation. This proved to be synthetically challenging but ultimately worthwhile in the form of compound A74b. (Incidentally, this is the first case I can recall where a fragment led to a macrocycle. It won’t be the last.) Not only was this molecule more potent than the open form, it also showed excellent oral bioavailability and pharmacokinetics, good selectivity against non-BET bromodomains, and even better activity in a mouse xenograft model. 

One lesson from these papers is that fragments can generate new ideas even for heavily pursued targets. A second is that, as we saw in the recent poll, crystallographic information can be critical for advancing fragments to leads. The discovery of new moieties along with clear data on their binding modes can be a powerful combination for creative medicinal chemists.

12 June 2017

Fourth NovAliX Biophysics in Drug Discovery Conference

NovAliX held its fourth Biophysics in Drug Discovery meeting last week in the beautiful city of Strasbourg. This was my first time attending, and although Teddy’s recounting of the first meeting (here, here and here) had given me high expectations they were easily exceeded. With 134 participants from 13 countries, most of whom stayed for the full time, the event felt like a Gordon Research Conference, with lots of lively discussions over excellent food and drink. Rather than trying to summarize all 30+ talks and nearly as many posters, I’ll just provide a few impressions. Conference Chairman Jean-Paul Renaud posted a 2 minute video overview here.

Factors that drive success in FBLD were a theme of Jenny Sandmark (AstraZeneca). She discussed several projects in which fragments were able to generate useful chemical matter, including one (Complement Factor B) where HTS and DNA-encoded libraries both came up short. In the case of neutrophil elastase, SAR on HTS hits was making rapid progress, but chemistry to explore the S1 pocket was difficult. A directed NMR screen of 800 fragments did not yield anything better, but it did save considerable synthetic effort and was thus judged a success.

Tweaking experimental conditions was often essential to get informative results: soaking crystals of neutrophil elastase with fragments dissolved in DMSO produced no hits, while dissolving the fragments in water did. With crystals of Factor XIa, glycerol – not fragments – bound in the active site. Fortunately the researchers recognized this and were able to use a different cryoprotectant.

Glyn Williams (Astex) has been doing FBLD since the earliest days, and discussed some of the lessons learned. Although the current Astex fragment library consists of about 1800 compounds, some 8000 fragments have been evaluated over the years. Small fragments in particular can be quite volatile, so Astex stores its library at -80 °C under nitrogen. Researchers also do rigorous quality control (QC) and maintain “fragment CVs”, which summarize analytical and screening data for each molecule. Astex is heavily invested in synthesizing novel fragments to explore specific regions of chemical space, and this means being constantly on guard for risks such as redox cyclers.

Understanding the enemy is always useful, so Martin Redhead (UCB) has constructed a library of bad actors – including PAINS, chelators, and metals – to stress-test his assays. But even robust assays show plenty of false positives. A screen of 20,000 molecules against a protein-protein interaction revealed 105 stabilizers, only 3 of which turned out to be real, but four times as many inhibitors, none of which were legitimate. Some of the stabilizers could subsequently be modified to inhibitors, and Martin suggested that screening for stabilizers initially could be a general way of improving signal to noise.

NMR is uniquely capable of providing extensive QC information about both proteins and ligands, and Alvar Gossert (ETH) discussed how a “validation cross” confirming both integrity and binding can improve confidence. Alvar also discussed using dynamic nuclear polarization to reduce the number of spectra required to assign a protein from five collected over two weeks to one obtained in under three days. This requires a specialized setup involving a second magnet, but it does appear powerful. Another unusual NMR configuration was described by Ad Bax (NIH), who is studying protein folding by rapidly (< 1 msec) increasing the pressure of a sample to 2500 bar – the equivalent energy of “discharging a small handgun into your NMR.”

Plenty of more accessible technologies were also described, including some interesting new commercial offerings. Matyas Vegh (Creoptix) discussed using waveguide interferometry to study protein-ligand interactions. This is similar to surface plasmon resonance (SPR) but with higher sensitivity and lower bulk effect. Their new four-channel instrument can be temperature controlled from 4-45 °C and is capable of accurately measuring kinetics even for weak binders, such as the 2.79 s-1 off-rate for the binding of methylsulfonamide (MW = 95 Da, Kd = 419 µM) to carbonic anhydrase II. And Sven Malik (Sierra Sensors) described a sensitive new SPR instrument with 8 channels, each with 4 spots, capable of running 384 samples in under 3 hours.

Several talks or posters highlighted an instrument from Biodesy which is capable of studying sub-Ångström conformational changes in dye-labeled, surface-immobilized proteins using second harmonic generation. Their plate-based instrument can measure 20,000 samples per week. Elizabeth Vo (UCSF) is using this to study the protein K-Ras, and has identified a number of active fragments which are being further characterized using orthogonal methods. It will be fun to see how these compare with previously reported K-Ras binders.

Finally, the keynote lecture was delivered by Jean-Pierre Changeux (Collège de France and Institut Pasteur), who described some of the highlights – many of them quite recent – from a career that spans nearly six decades. Jean-Pierre literally invented the model for allostery at a time when the three dimensional structures of only two proteins were known; today the Protein Data Bank contains more than 130,000 structures, and at least 90 marketed drugs are known to work through allosteric mechanisms. It is humbling to be reminded of how far we've come, yet how little we still know.

Strasbourg is a wonderful city, but with today’s travel budgets it can be difficult to access for some researchers, so next year the conference will head to Boston (June 12-15), returning to Strasbourg in 2019 before moving on to Kyoto in 2020. Hope to see you there!

05 June 2017

Poll results: what structural information is needed to optimize fragments

Our latest poll asked “how much structural information do you need to begin optimizing a fragment?” Over the past few weeks we received 143 responses, and the results are shown here.
Just over a third of you said that you wouldn’t work on a project without a crystal structure, while nearly a quarter said you’d settle for an NMR-based model. In other words, more than half of you demanded fairly detailed structural data to embark on a fragment optimization campaign.

But consistent with continuing improvements in modeling, almost a fifth said that a computational model would be just fine.

And perhaps most surprisingly, fully one quarter of you said that SAR alone would be sufficient to begin optimizing a fragment. Presumably this is driven at least somewhat by internal successes, and I look forward to seeing these disclosed in meetings and publications.

All of these approaches are rapidly developing, and it will be fun to revisit this poll in a few years to see whether crystallography maintains its lead, or whether lower resolution methods gain dominance.

In the meantime, are there other topics you’d like to see polled?