The rise of fragment-based drug discovery has largely depended on the success of structural biology. FBDD began in earnest with NMR techniques in the mid 1990s, soon followed by high-throughput crystallography techniques in the early part of this century. In an article published online in Current Opinion in Structural Biology, Christopher Murray of Astex and Tom Blundell of the University of Cambridge discuss this reliance on structure.
The review describes several cases where structural biology played pivotal roles in advancing fragments to leads or drug candidates. Many have been discussed in Practical Fragments, including AT7519 and AT9283 from Astex, the JAK-2 program from SGX, DG-051 from deCODE, HSP90 inhibitors from Vernalis/Novartis and Evotec, Schering-Plough’s BACE inhibitors, and Plexxikon's indeglitazar.
The researchers also discuss the potential of fragment methods for generating inhibitors of antimicrobial targets, such as enzymes in the organisms that cause tuberculosis and sleeping sickness. In these cases too, structural biology played critical roles.
Structural biology is so important, the authors conclude, that “it is only through the expert use of structure-based drug design that FBDD can be expected to fulfill its promise of delivering candidates with the improved physical properties (lower molecular weight and lipophilicity) which it is hoped will lead to reduced attrition in clinical trials.”
But is dependence on structure truly inevitable? The authors themselves highlight one case in which a new antimicrobial agent with animal efficacy was developed using fragment-based methods in the absence of direct structural information. If this success could be generalized, it would open the potential of fragment methods to a much wider range of practitioners.
26 July 2010
21 July 2010
Virtual phosphate fragments
Phosphate groups are handy little things: easy for enzymes to put on and take off, they pack a lot of charge in a small volume, thereby providing plenty of binding energy for electrostatic interactions. Not surprisingly, they are ubiquitous in biology. Unfortunately, the same things that make them attractive for an organism make them problematic for drugs: they are easily removed, and their highly negative charge gives molecules containing phosphates a real problem getting across membranes. What’s a chemist to do?
This was the dilemma faced by Ruth Brenk, Ian Gilbert, and colleagues at the University of Dundee. They were interested in inhibiting the enzyme 6-phosphogluconate dehydrogenase (6PGDH) from the parasite that causes sleeping sickness. (See here for previous work from the same group using fragment methods to discover inhibitors against a different enzyme from the same organism.) The enzyme 6PGDH, as its name suggests, binds phosphate-containing substrates and has a very polar active site. Nanomolar inhibitors have been reported in the literature, but these contain phosphates and are not active in cell assays.
As reported in a recent issue of Bioorganic and Medicinal Chemistry, the researchers computationally filtered a set of commercially available compounds to find those that were less than 320 Da and were negatively charged, thereby potentially mimicking a phosphate. They then used DOCK 3.5.54 to see which of the resulting 64,000 molecules might bind in the active site of 6PGDH, resulting in 5836 possible hits. Subsequent triaging led to the purchase of 71 compounds. These were tested for inhibition of the enzyme at 200 micromolar concentration. Ten of these compounds inhibited the enzyme more than 80% at this concentration, of which 3 gave clean IC50 curves. These three molecules are all 5-membered carboxylic-acid-containing heterocycles, and although the IC50s are modest (ranging from 28 to 45 micromolar), they have good ligand efficiencies (up to 0.66 (kcal/mol)/atom). A computational search for analogs resulted in a few more active molecules with similar properties.
Whether these fragments can be advanced remains to be seen. The calculated solubilites, Log P, total polar surface area, and intestinal absorption parameters are more attractive than previous inhibitors, but the history of phosphate mimics is not encouraging. Most prominently, the protein PTP-1B, which recognizes phosphotyrosine residues, was once one of the hottest drug targets around, spawning a cottage industry of groups developing phosphotyrosine mimetics. Fragment methods were particularly effective, and numerous potent small molecules were published. But none of them were sufficiently drug-like, and to my knowledge none are in the clinic. Still, it is worth trying: 6PGHD may be more druggable, and approaches like this are likely to provide an answer.
This was the dilemma faced by Ruth Brenk, Ian Gilbert, and colleagues at the University of Dundee. They were interested in inhibiting the enzyme 6-phosphogluconate dehydrogenase (6PGDH) from the parasite that causes sleeping sickness. (See here for previous work from the same group using fragment methods to discover inhibitors against a different enzyme from the same organism.) The enzyme 6PGDH, as its name suggests, binds phosphate-containing substrates and has a very polar active site. Nanomolar inhibitors have been reported in the literature, but these contain phosphates and are not active in cell assays.
As reported in a recent issue of Bioorganic and Medicinal Chemistry, the researchers computationally filtered a set of commercially available compounds to find those that were less than 320 Da and were negatively charged, thereby potentially mimicking a phosphate. They then used DOCK 3.5.54 to see which of the resulting 64,000 molecules might bind in the active site of 6PGDH, resulting in 5836 possible hits. Subsequent triaging led to the purchase of 71 compounds. These were tested for inhibition of the enzyme at 200 micromolar concentration. Ten of these compounds inhibited the enzyme more than 80% at this concentration, of which 3 gave clean IC50 curves. These three molecules are all 5-membered carboxylic-acid-containing heterocycles, and although the IC50s are modest (ranging from 28 to 45 micromolar), they have good ligand efficiencies (up to 0.66 (kcal/mol)/atom). A computational search for analogs resulted in a few more active molecules with similar properties.
Whether these fragments can be advanced remains to be seen. The calculated solubilites, Log P, total polar surface area, and intestinal absorption parameters are more attractive than previous inhibitors, but the history of phosphate mimics is not encouraging. Most prominently, the protein PTP-1B, which recognizes phosphotyrosine residues, was once one of the hottest drug targets around, spawning a cottage industry of groups developing phosphotyrosine mimetics. Fragment methods were particularly effective, and numerous potent small molecules were published. But none of them were sufficiently drug-like, and to my knowledge none are in the clinic. Still, it is worth trying: 6PGHD may be more druggable, and approaches like this are likely to provide an answer.
17 July 2010
ANCHORing fragments
Protein-protein interactions are intriguing though challenging targets for lead discovery, and fragment-based approaches have often been used to tackle them (for example here, here and here). One of the difficulties is trying to figure out which of the often many residues in a large contact surface are really important. To make this easier, Lidio Meireles, Alexander Dömling, and Carlos Camacho at University of Pittsburgh have unveiled a free web-based tool, described in a recent issue of Nucleic Acids Research.
The tool, called ANCHOR, is both a server and a database of protein-protein interactions. The database contains over 30,000 entries taken from the protein data bank (PDB). Each of these entries has been analyzed computationally. ANCHOR examines bound and free (as computationally isolated from the complex) forms of each protein, focusing on side chains that, depending on protein state, are either buried within the partner protein or exposed to solvent. The change in solvent-accessible surface area is calculated for every residue in the protein-protein contact area. ANCHOR also estimates each residue’s contribution to the binding free energy, using both electrostatic and solvation terms in the calculation.
While the absolute numbers should probably be taken with a grain of salt, the relative values could help identify “anchoring” residues most likely to be useful as initial fragments. This means you can enter a pdb number and rapidly find the residues likely to be most important. You can also do more complex queries across the entire database, for example searching for buried tryptophan residues for oncology targets. If your protein is not already in the database, you also have the option of uploading a structure for custom analysis.
What makes ANCHOR particularly appealing is its powerful graphical interface, which shows which residues are selected and allows significant customization. The whole system is quite intuitive and easy to use. Try it on your favorite protein-protein interaction and tell us what you think!
The tool, called ANCHOR, is both a server and a database of protein-protein interactions. The database contains over 30,000 entries taken from the protein data bank (PDB). Each of these entries has been analyzed computationally. ANCHOR examines bound and free (as computationally isolated from the complex) forms of each protein, focusing on side chains that, depending on protein state, are either buried within the partner protein or exposed to solvent. The change in solvent-accessible surface area is calculated for every residue in the protein-protein contact area. ANCHOR also estimates each residue’s contribution to the binding free energy, using both electrostatic and solvation terms in the calculation.
While the absolute numbers should probably be taken with a grain of salt, the relative values could help identify “anchoring” residues most likely to be useful as initial fragments. This means you can enter a pdb number and rapidly find the residues likely to be most important. You can also do more complex queries across the entire database, for example searching for buried tryptophan residues for oncology targets. If your protein is not already in the database, you also have the option of uploading a structure for custom analysis.
What makes ANCHOR particularly appealing is its powerful graphical interface, which shows which residues are selected and allows significant customization. The whole system is quite intuitive and easy to use. Try it on your favorite protein-protein interaction and tell us what you think!
11 July 2010
So Long, and Thanks for all the Fish
I am writing this to say thank you to everyone who reads this blog, and those who have contributed to this blog. When Dan and I started this, it was after meeting at a FBDD conference in San Diego. We decided that this field needed something like this. There are now LinkedIn groups, Facebook groups, other blogs about FBDD (all linked to the right). As many of you know, my current position does not involve FBDD. FBDD has been a passion of mine since I got involved in 2001. I appreciate my boss at the time Mike Shapiro for giving me the chance to set up and lead the FBDD efforts at Lilly. It was a fantastic experience and very successful. I also want to thank Mike for co-editing the book with me (please buy a copy, every copy earns me something close to three cents ;-)). I want to acknowledge all the great friends I have made through the years, including Dan who has picked up the onus of publishing this blog and has done and will continue to do a fantastic job.
I have always said that research carries a two year shelf-life. It's been almost two years since the book came out, that means I am done. I have nothing new to add to the field (and probably haven't for longer than two years). This means no more embarassing questions when I give talks on FBDD about what I doing now (which is nothing in FBDD). It is exciting to follow the field, but it is also really tough not being a part of it.
I wish you all the best of luck and ask that you don't be strangers. I will be speaking on NMR in the upcoming months, and am always happy to add more NMR speaking engagements (hint hint).
I have always said that research carries a two year shelf-life. It's been almost two years since the book came out, that means I am done. I have nothing new to add to the field (and probably haven't for longer than two years). This means no more embarassing questions when I give talks on FBDD about what I doing now (which is nothing in FBDD). It is exciting to follow the field, but it is also really tough not being a part of it.
I wish you all the best of luck and ask that you don't be strangers. I will be speaking on NMR in the upcoming months, and am always happy to add more NMR speaking engagements (hint hint).
Subscribe to:
Posts (Atom)
Subscribe To
Posts
All Comments