rmoretti Staff Lv 1
We’re excited to announce the start of another round of small molecule design puzzles.
We are again looking at molecules which can bind E3 ligases to be used in the future design of PROTAC drugs. This time, we’re focusing on KLHDC2 (Kelch domain-containing protein 2). KLHDC2 is an excellent target for PROTAC binders, as it’s expressed in a wide variety of tissues (so useful for a range of degradation targets) and is conserved across species (useful for early testing in animal models). It’s also a rather tight binder to its target ligand, whose structure in complex with the protein is known. However, we currently only have peptide binders for this protein. Peptides are problematic for potential drugs, as they’re easily broken down by your body, and can have issues getting into cells.
That’s where you come in. In this puzzle series, we’re giving you the structure of the peptide in complex with the KLHDC2 protein. We’re hoping you can rebuild this molecule to preserve the nice binding interactions, while simultaneously making it less like a peptide.
As with the previous VHL design round, we’re working with collaborators at Boehringer Ingelheim (BI), who have volunteered to evaluate the compounds which players design, and synthesize those molecules which look promising. BI also has an existing collaboration with researchers at Oxford University, who have signed up to test the synthesized compounds in their KLHDC2 binding assays.
To help you along, here’s some considerations to keep in mind:
Carboxylate interaction: The core of the interaction between the ligand and the protein is the hydrogen bonding and electrostatic (charge) interactions between the end carboxylate group and a pair of arginines and a serine in the protein. We recommend you keep that interaction (and the carboxylate structure) intact.
Hydrogen bonds to the ligand carboxylate
Hydrophobic interaction: Experiments indicate a large amount of binding energy comes from the interaction of the methionine sidechain with a hydrophobic pocket. We’d like you to maintain that hydrophobic interaction. The thioether (sulfur) in methionine isn’t ideal from a drug perspective, but you should be able to replace it with some other hydrophobic group.
The hydrophobic pocket, with pocket residues highlighted in red.
Amides: The standard amide backbone of a protein is a liability for drugs. See if you can replace those amides while keeping the hydrogen bonds and other hydrophilic interactions they make. Note it’s mostly the standard alpha amino acid backbone which is a problem. Amides in other contexts have fewer issues in drugs.
An example of an amide backbone
Drug properties: We want to improve the efflux and membrane permeability properties of the molecule (how well the drug is taken up and moves around the body). Metrics such as TPSA, clogP, hydrogen bond donors and hydrogen bond acceptors are helpful proxies on how the drug will behave in the body. Keep an eye on these objectives, and make sure they stay in range. It’s tricky, because these metrics are a balancing act. Keep the good binding to the protein while threading the needle of the multiple properties.
Torsion Quality: One of the significant issues we saw with the VHL results was rotatable bonds which were in a strained position. The new Torsion Quality objective is a good way to keep track of how strained the rotatable bonds are. We’ve updated things such that wiggling should help, but there’s also a new “Tweak Ligand” tool which should allow you to rotate bonds into a better position. Of course, if you reduce the number of rotatable bonds, they can’t be strained.
The display from the Torsion Quality objective, and the Tweak Ligand tool
Atom number and bad groups: We want to make sure we stay within the “typical” range of number of atoms for each element for drugs, to make sure that synthesis is easy. Also, to work well as a drug, we need to avoid certain groups. Either because they’re too unstable to actually be synthesized, because they’ll react or fall apart as soon as they enter the body, or because they are toxic or otherwise complicate the drug development process. (Note that groups which are bad in open chains may be perfectly fine when present in the context of rings.)
Gallery of selected bad groups.
We realize that’s a lot of objectives to keep track of, but we’re hopeful Foldit players are up to the task of balancing all these objectives and coming up with novel molecules which will still bind the protein well.
All participants and game sponsors of current and future small molecule design games commit to complying with the Foldit Terms of Service including those pertaining to intellectual property. All compounds created as part of the collaboration puzzles will be made publicly available. Experimental results from testing the molecules will also be released publicly.