I’m sitting in the Drexler Auditorium of the Buck Institute, where I’ve been working over the last six months. Today we’re being treated to an off-schedule “Special Institute Lecture” by Harvard’s Gregory Verdine. These are my notes about the talk; below, I’m paraphrasing Verdine’s words, not writing my own.
To fix it you have to find it: Repairing oxidative damage to DNA.
Mitochondrial metabolism generates oxygen radicals, which damage DNA and increase the risk of mutation. The primary oxidative adduct of guanine, 8-oxoG, differs by only two atoms from the original guanine, but this small difference is still enough to change the residue’s base-pairing characteristics (i.e., from G=C to 8-oxoG=A). 8-oxoG is repaired by the enzyme Ogg1, which displaces the damaged residue by covalently bonding to the DNA backbone.
Ogg1 has a tough job: oxoG-C base pairs are perfectly stable, and from the outside they look just like G-C pairs, so the detection of rare lesions within the genome poses a tremendous challenge. In crystallographic studies that exploited a catalytically dead Ogg1 enzyme (which can recognize but not cleave DNA), Verdine’s lab has shown that the binding of Ogg1 at a G-C base pair results in the extrusion of G or oxoG to the exterior of the double helix, setting the stage for repair — but how does Ogg1 find the lesion site in the first place? To answer this question, Verdine’s group visualized single molecules of Ogg1 diffusing in one dimension along a double helix. They observed that Ogg1 moves so quickly that it can’t be checking every G-C base pair along its path. Instead, Ogg1 (and other lesion-repair proteins) may exploit subtle rearrangements in the DNA backbones near lesion sites. The enzyme amplifies these local structural changes into substantial conformational changes, leading to base extrusion and starting the process of repair.
We want a new drug: Synthetic biologicals as novel pharmaceuticals
Small-molecule drugs have “good geography,” in the sense that they can cross cell membranes. However, they’re limited, in that they can only target proteins that engulf them (e.g., in hydrophobic pockets or active sites). Proteins, on the other hand, have much more diverse function, but terrible geography — they simply can’t get into cells, and they’re therefore useless for intracellular targets. Both classes of drug can attack (generously) only ~10% of prospective targets. Therefore, we need an entirely new class of drug: synthetic biologics like stapled peptides and RIPtides, which combine the bioavailability of small molecules with the functional diversity of proteins.
Stapled peptides are essentially the interaction domains of proteins, conformationally restrained in such a way that they still retain the active structure. (Think of a protein as a delivery system for an interaction domain, in which the non-interacting portions serve primarily to hold the ID in place.) An interaction domain alone would be too floppy to have a biological effect; conversely, the intact protein has the desired function but can’t cross the membrane. Solution: replace the main body of the protein with a hydrocarbon “staple” that keeps the interactive domain in the active conformation, without substantially increasing its size. Surprisingly, stapled peptides are taken up by cells via an energy-dependent active transport process, one upshot of which is that they don’t need to be uncharged and hydrophobic in order to cross the membrane. Drugs of this kind have already been used in animal studies to suppress leukemia by activating apoptotic factors in tumor cells.
Declaring open season on transcription factors
A brief concluding note: Transcription factors are among the most well-validated prospective targets, but they have historically been outside the scope of drug developers. TFs function primarily by protein-protein interactions that aren’t amenable to interference by small-molecule drugs. Recently, however, Verdine and others have been able to use synthetic biologicals to interfere with a specific oncogenic transcription factors.
My own comments
OK, so, not a lot of specific about either aging or cancer, but the idea of a novel class of pharmaceuticals that could be used to attack the “missing 80%” of validated prospective drug targets is still very exciting.
Ouroboros 
Pills that give you a decade or two more of active life—a good market hole for drug companies to dig more bucks from. But would a real breakthrough in technology or drugs (following one in science) be allowed to eventually find itself as a product in the public market? I’m new to this blog: has there been such speculation here before? Is such speculation within its scope?
I would see his argument as purely phiosophical…
Yes, small molecules require a protein target to wrap around them, hydrophobic pockets etc., but why is that a disadvantage? Invariably those hydrophobic pockets are exactly where the active site of the protein (enzyme) is located! It could only be considered a disadvantage if there’s something special about your target protein which makes the 3D space important for its activity inaccessible to small molecules.
IMHO, the advantages (if any) of going to a peptide-based drug are far outweighed by a number of issues which make them not “druggable” in the pharmaceutical sense. This includes difficulty of manufacture on a large scale (including things such as sterility, purity), long-term stability, bio-availability (oral vs. IV), and metabolism (peptidases). Other than immunoglobulin-based therapies, there are really not that many protein/peptide based drugs in the marketplace today. At least from the perspective of “big-pharma”, small molecules will be king for quite some time to come. Novel approaches such as fragment-based design strongly suggest that there are a lot of possible molecules still to be made and tested. Purely from a “see no evil, hear no evil” viewpoint, why restrict the chemical space for your potential drug, by limiting yourself to such a small set of molecules?
Thanks for your comments, Virgil.
Exactly.
The advantage of stapled peptides is that many proteins don’t have active sites. Transcription factors and regulatory proteins, many of which are on the long list of validated drug targets (i.e., proteins where knockdowns or dominant negatives have a desired effect), usually don’t have a hydrophobic pocket that binds a substrate — instead, the interaction with relevant factors usually takes place on the surface. Many more proteins have active sites that are so generic that they can’t be drugged — e.g., Ras, which is a GTPase, but which after 20 years still has no bioavailable small-molecule inhibitor.
So, for proteins with druggable active sites, stapled peptides aren’t an advantage. But for the (large number of) proteins that simply don’t work that way, peptide mimetics and related approaches hold promise.
This is exactly Verdine’s argument in favor of peptide-based drugs.
The short answer is that it’s not a small set of molecules; the combinatorial space of peptides is astronomical. Consider a 10-residue alpha helix; even if only half the positions can be substituted, that’s still 10 trillion molecules (and that’s if we limit ourselves to the 20 canonical amino acids, which there’s no reason to do).
Beyond that, peptides can be combinatorially synthesized much more straightforwardly than drugs, since the addition of a different residue can be accomplished with a standardized chemistry.
Regarding the other objections: There are already protein-based drugs in wide use (e.g. the monoclonal-antibody-derived drugs like rituximab and herceptin”), so I think the sterility, purity and other problems have been solved well enough. It’s worth mentioning that these currently used drugs are made in workhorse microbes, presenting a sterility and purity issue that isn’t attached to chemically synthesized peptides.
I do concur that it’s likely to be a long time before any such alternative paradigm for drugs is adopted widely, so we’re in agreement that for the time being small molecules are king. But after hearing Verdine’s talk, I suspect this isn’t going to last forever.
In closing, a word of caution. I heard one talk about this, and did a less than perfectly thorough job of recording Verdine’s arguments; I’m not an expert and I’d hate for anyone to reach a conclusion based on my attempts to share or defend the idea.
For those who are interested, I’d recommend checking out the publications on the Verdine lab website (PDFs are available). Here are two reviews I find particularly helpful:
The Challenge of Drugging Undruggable Targets in Cancer: Lessons Learned from Targeting BCL-2 Family Members, Verdine & Walensky (here’s the PDF)
Specific peptides for the therapeutic targeting of oncogenes, Privé & Melnick
“Ogg1 has a tough job: oxoG-C base pairs are perfectly stable,”?
Can Ogg1 recognize 8-oxoG=A? or 8-oxoG=anything? ie is the deformation in the backbone due only to the 8-oxoG or is there any relation to what it is pairing with? To carry it a step further, is ogg1 actually responsible for the G=C to T=A mutations when they are incorporated (ie repaired by BER)?