The first of two conferences in 2010 exclusively devoted to fragment-based drug discovery concluded in San Diego this week, and I thought I’d jot down some observations while my memories are still fresh.
The pre-conference short courses were quite successful (and I’m hopefully only slightly biased by the fact that Teddy and I were both instructors). Participants included folks with considerable experience in fragments, which allowed good discussion.
One talk from the conference that stands out in my mind was by Sandy Farmer of Boehringer Ingelheim. BI is a relative late-comer to fragment-based methods, really only starting in late 2004. Sandy described how fragment efforts are run in parallel with HTS. They use an intentionally modest fragment library of 2000 diverse compounds; increasing the size of this library tended to overwhelm downstream efforts. Fragments are confirmed using multiple assays, including SPR and size-exclusion chromatography coupled with mass spectrometry, with crystallography playing a pivotal role in determining which fragments to advance. Part of the challenge at BI has been getting chemists to accept FBS, or “faith-based synthesis,” particularly where initial fragments have low affinities. A focus on ligand efficiency helps, as do organizational strategies such as establishing a dedicated group of chemists focused on fragment projects.
Often at conferences you hear about success stories, but sometimes the continuing challenges are more instructive, as when Ravi Kurumbail at Pfizer discussed his efforts to discover drug-like inhibitors of the serine protease Factor XIa. One of the sobering findings was that, although a functional assay of 2500 fragments yielded a 6.5% hit rate, adding 0.01% detergent eliminated activity and revealed most ‘hits’ as false positives. Even one crystallographically characterized fragment with an apparent IC50 of 75 micromolar turned out to be an artifact after subsequent analysis – a reminder to always be vigilant at higher concentrations.
But back to success stories: Daniel Wyss gave an update on the BACE program from Merck (legacy Schering-Plough, which has run more than 30 fragment screens on various targets). We highlighted a couple publications resulting from this effort earlier this year. It turns out there are now three molecules from this program in early clinical trials – a clear indication of the importance of this target and the utility of fragment screening.
Finally, Rick Artis, formerly of Plexxikon (now Elan) gave an update on the PLX4032 Raf kinase program. This project demonstrates the potential for fragment-based efforts to move quickly: it was started in February 2005, the clinical candidate was identified in January 2006, the IND was filed in September, and the first patient was dosed in November of that year. The molecule has continued to move at warp speed through the clinic: it is now partnered with Roche in Phase III testing for metastatic melanoma, and was recently profiled in the New York Times. This lengthy but excellent article is well worth reading for a bit of perspective when life in the lab gets you down.
These are just a few of many nice talks and breakout discussions. I know that at least some readers of this blog were there – what were your impressions?
30 April 2010
25 April 2010
Hot spots for fragments
Although most people try to advance fragments to more potent molecules, some have taken the reverse approach: starting with potent binders and deconstructing them into fragments (see for example here, here, and here). A recent, thorough example in J. Med. Chem. shows how isolated fragments do not necessarily bind in the same manner as they do in fully elaborated molecules.
In this paper, Isabelle Krimm and colleagues at the Université de Lyon in France applied “fragment-based deconstruction” to inhibitors of the anti-cancer target Bcl-xL. This protein is one of the great success stories in fragment-based drug discovery: ABT-263, which is in multiple clinical trials, was discovered by researchers at Abbott using SAR-by-NMR. In that work, fragments were identified binding near each other on the protein (site 1 and site 2) and subsequently linked together. Very extensive medicinal chemistry eventually led to the picomolar inhibitor now in clinical testing.
Krimm and colleagues dissected 9 inhibitors of Bcl-2, including ABT-263, into 22 different fragments and studied their binding by NMR. They first used ligand-observed NMR (WaterLOGSY and saturation transfer difference, or STD) and found that 19 fragments interacted with the protein. When they then turned to protein-observed NMR (proton-15N heteronuclear single quantum correlation, or HSQC), only 13 fragments caused changes to the spectra of Bcl-xL, suggesting that the other six bound too weakly to detect. In fact, the most potent fragment has an affinity of just 2.7 mM, so it is not surprising that some of the fragments were undetectable.
The nice thing about protein-observed NMR is that it can provide insight into where on the protein the fragments bind, and in this case the researchers found that 12 of the 13 fragments that caused NMR shifts in the protein bind to site 1, despite the fact that structures and modeling suggest that some of these fragments should be binding in other sub-sites. (The 13th fragment appears to bind to multiple sites on the protein surface.) In other words, the binding modes of the isolated fragments are not the same as the binding modes of the fragments when assembled.
The authors conclude that fragments “will interact with their preferred binding site, which can be different from the site they occupy when they are included in the larger molecule.”
Interestingly, one of the fragments studied by Krimm (2,3-dihydroxynapthalene) was also tested at Abbott, but found to bind in site 2. The reason? In the Abbott study, this fragment (and a number of others) were tested in the presence of a fragment that binds to site 1. It seems that site 1 is a thermodynamic sink, or hot spot. Unless this site is filled, other fragments will bind there, even if they could also bind elsewhere on the protein. The implication is that, if you want to find fragments that bind to a new site on your protein, it may be worth screening in the presence of a fragment known to bind to an existing site.
In this paper, Isabelle Krimm and colleagues at the Université de Lyon in France applied “fragment-based deconstruction” to inhibitors of the anti-cancer target Bcl-xL. This protein is one of the great success stories in fragment-based drug discovery: ABT-263, which is in multiple clinical trials, was discovered by researchers at Abbott using SAR-by-NMR. In that work, fragments were identified binding near each other on the protein (site 1 and site 2) and subsequently linked together. Very extensive medicinal chemistry eventually led to the picomolar inhibitor now in clinical testing.
Krimm and colleagues dissected 9 inhibitors of Bcl-2, including ABT-263, into 22 different fragments and studied their binding by NMR. They first used ligand-observed NMR (WaterLOGSY and saturation transfer difference, or STD) and found that 19 fragments interacted with the protein. When they then turned to protein-observed NMR (proton-15N heteronuclear single quantum correlation, or HSQC), only 13 fragments caused changes to the spectra of Bcl-xL, suggesting that the other six bound too weakly to detect. In fact, the most potent fragment has an affinity of just 2.7 mM, so it is not surprising that some of the fragments were undetectable.
The nice thing about protein-observed NMR is that it can provide insight into where on the protein the fragments bind, and in this case the researchers found that 12 of the 13 fragments that caused NMR shifts in the protein bind to site 1, despite the fact that structures and modeling suggest that some of these fragments should be binding in other sub-sites. (The 13th fragment appears to bind to multiple sites on the protein surface.) In other words, the binding modes of the isolated fragments are not the same as the binding modes of the fragments when assembled.
The authors conclude that fragments “will interact with their preferred binding site, which can be different from the site they occupy when they are included in the larger molecule.”
Interestingly, one of the fragments studied by Krimm (2,3-dihydroxynapthalene) was also tested at Abbott, but found to bind in site 2. The reason? In the Abbott study, this fragment (and a number of others) were tested in the presence of a fragment that binds to site 1. It seems that site 1 is a thermodynamic sink, or hot spot. Unless this site is filled, other fragments will bind there, even if they could also bind elsewhere on the protein. The implication is that, if you want to find fragments that bind to a new site on your protein, it may be worth screening in the presence of a fragment known to bind to an existing site.
11 April 2010
Getting misled by NMR: ILOE artifacts
We’ve pointed out potential pitfalls with crystallography (here, here, and here) as well as with biochemical screening, but NMR has escaped attention– until now.
NMR has of course been a mainstay of fragment discovery methods since the original SAR by NMR paper. There have been plenty of developments since, but one that is particularly intriguing relies on the “interligand nuclear Overhauser effect,” or ILOE. In the “SAR by ILOE” approach, a 2D NMR experiment is used to detect when two small molecule ligands bind to a protein next to one another. There are some attractive features of this method. First, only ligands that bind in relatively close proximity to each other will generate a signal, thereby allowing researchers to identify fragments close enough to allow productive linking. Second, the technique can be applied to proteins that are too large to study by other NMR methods. In fact, it can be used even in the complete absence of structure. So what’s the problem?
In a new paper in J. Am. Chem. Soc., Chris Abell and colleagues at the University of Cambridge applied the approach to pantothenate synthetase (PtS) from M. tuberculosis. They previously did rigorous fragment screening followed by both linking and growing on this enzyme, which we discussed last year. Initial NMR experiments with compounds 1 and 2 (see figure) in the presence of PtS showed strong ILOE signals; the problem was that signals were seen between all the protons of compound 1 and all the protons of compound 2. This suggests non-specific binding: if the two molecules were binding next to each other in a single orientation you would expect that some protons from compound 1 would be closer to some protons in compound 2 than others, and there would thus be differences in signal intensities.
Adding a methyl group to compound 1 to give compound 4 didn’t help. In fact, there were ILOE signals from both the methyl groups of compound 4 to all the aromatic protons of compound 2, again suggesting non-specific binding. Even more damning, adding the substrates ATP and pantoate failed to significantly diminish the ILOE signals as expected; because crystallography showed these fragments bind in the active site, they should have been readily displaced by substrates.
Reasoning that the hydrophobic nature of compound 4 might be causing it to aggregate at high concentrations, the researchers appended a carboxyl group to give compound 5. NMR experiments with this compound in the presence of compound 2 and the protein now revealed specific ILOE signals between the 2-methyl group of compound 5 and H2 of compound 2. Moreover, this signal could be competed by adding ATP and pantoate.
Happily, linking these two fragments together resulted in compound 6, which bound to the enzyme three orders of magnitude more tightly than either of the starting fragments. The compound was also well-behaved mechanistically, showing competitive inhibition with ATP, and a crystal structure revealed that it binds as expected given the structures of the individual fragments.
Overall then this is a success story. However, it does suggest that the ILOE method may be more prone to aggregation artifacts than other biophysical methods. In particular, had the researchers not been able to do competition experiments (if, for example, they did not have another small molecule inhibitor available) they would have had a harder time sorting things out. Also, the researchers actually had crystal structures of both compounds 1 and 2 bound to PtS, so it is not clear how valuable the ILOE data really were for linking. Still, the potential advantages of an NMR-based method that doesn’t require structure are appealing. Hopefully we will see more applications of SAR-by-ILOE, now that people are more aware of the dangers.
NMR has of course been a mainstay of fragment discovery methods since the original SAR by NMR paper. There have been plenty of developments since, but one that is particularly intriguing relies on the “interligand nuclear Overhauser effect,” or ILOE. In the “SAR by ILOE” approach, a 2D NMR experiment is used to detect when two small molecule ligands bind to a protein next to one another. There are some attractive features of this method. First, only ligands that bind in relatively close proximity to each other will generate a signal, thereby allowing researchers to identify fragments close enough to allow productive linking. Second, the technique can be applied to proteins that are too large to study by other NMR methods. In fact, it can be used even in the complete absence of structure. So what’s the problem?
In a new paper in J. Am. Chem. Soc., Chris Abell and colleagues at the University of Cambridge applied the approach to pantothenate synthetase (PtS) from M. tuberculosis. They previously did rigorous fragment screening followed by both linking and growing on this enzyme, which we discussed last year. Initial NMR experiments with compounds 1 and 2 (see figure) in the presence of PtS showed strong ILOE signals; the problem was that signals were seen between all the protons of compound 1 and all the protons of compound 2. This suggests non-specific binding: if the two molecules were binding next to each other in a single orientation you would expect that some protons from compound 1 would be closer to some protons in compound 2 than others, and there would thus be differences in signal intensities.
Adding a methyl group to compound 1 to give compound 4 didn’t help. In fact, there were ILOE signals from both the methyl groups of compound 4 to all the aromatic protons of compound 2, again suggesting non-specific binding. Even more damning, adding the substrates ATP and pantoate failed to significantly diminish the ILOE signals as expected; because crystallography showed these fragments bind in the active site, they should have been readily displaced by substrates.
Reasoning that the hydrophobic nature of compound 4 might be causing it to aggregate at high concentrations, the researchers appended a carboxyl group to give compound 5. NMR experiments with this compound in the presence of compound 2 and the protein now revealed specific ILOE signals between the 2-methyl group of compound 5 and H2 of compound 2. Moreover, this signal could be competed by adding ATP and pantoate.
Happily, linking these two fragments together resulted in compound 6, which bound to the enzyme three orders of magnitude more tightly than either of the starting fragments. The compound was also well-behaved mechanistically, showing competitive inhibition with ATP, and a crystal structure revealed that it binds as expected given the structures of the individual fragments.
Overall then this is a success story. However, it does suggest that the ILOE method may be more prone to aggregation artifacts than other biophysical methods. In particular, had the researchers not been able to do competition experiments (if, for example, they did not have another small molecule inhibitor available) they would have had a harder time sorting things out. Also, the researchers actually had crystal structures of both compounds 1 and 2 bound to PtS, so it is not clear how valuable the ILOE data really were for linking. Still, the potential advantages of an NMR-based method that doesn’t require structure are appealing. Hopefully we will see more applications of SAR-by-ILOE, now that people are more aware of the dangers.
01 April 2010
The Rule of 1
Everyone is familiar with the Rule of 5, Lipinski’s famous set of guidelines for orally active small molecule drugs. Most folks working with fragments are also familiar with the Rule of 3, proposed by Astex researchers to guide fragment selection so as to avoid starting with something too large. On the assumption that if small is good, tiny is superlative, scientists at Lilliput Pharmaceuticals have proposed the Rule of 1:
By limiting themselves to molecules with less than 8 heavy atoms, Lilliput reckons it can purchase or synthesize just about every stable molecule; according to Reymond’s GDB database there are only a few tens of thousands of possibilities. “The rules of 5 and 3 are for the lily-livered,” says CEO I. M. Lyttle, Jr. “We aim for total coverage of chemical space.” Of course, finding fragments this small is bound to be a challenge, but anything they detect is likely to have killer ligand efficiency.
MW < 100 Daltons
<= 1 Hydrogen bond donor
<= 1 Hydrogen bond acceptor
ClogP <= 1
By limiting themselves to molecules with less than 8 heavy atoms, Lilliput reckons it can purchase or synthesize just about every stable molecule; according to Reymond’s GDB database there are only a few tens of thousands of possibilities. “The rules of 5 and 3 are for the lily-livered,” says CEO I. M. Lyttle, Jr. “We aim for total coverage of chemical space.” Of course, finding fragments this small is bound to be a challenge, but anything they detect is likely to have killer ligand efficiency.