Improve your docked poses with receptor flexibility

I have noticed that rigid docking methods, even when run with high-precision force fields, don’t always capture the correct poses for your true positives.  Sometimes a hit will be docked somewhere other than into the site that you specified because the algorithm could not fit the molecule into the rigid receptor.  This will cause true positives to be buried at the bottom of your ranked list.

You may want to try introducing receptor flexibility to improve the poses of your true positives.  There are two main ways to do this:  scale down the Van der Waals interactions to mimic flexibility (i.e., make the receptor atoms “squishy”) or use induced-fit docking (IFD) methods.  I have found that while setting a lower threshold for VdW scaling can rescue false negatives (poorly docked true binders), at least in one case, it does not improve the overall ranking of all of the true positives.  So it is not a panacea.

Induced fit methods work by mutating away several side chains in the binding pocket, docking a compound, mutating the side chains back, and energy minimizing the structure.  Then the compound is re-docked to the minimized structure using a high-precision algorithm.  There are two main applications for IFD: (1) improving the pose of a true positive that cannot be docked correctly by rigid docking and (2) rescuing false negatives.

My experience has been that IFD improves the docking scores of true positives and false positives by about the same amount, so the value of running the method on an entire library remains unclear.  However, there is much value in running IFD on a true hit where you are not sure the rigid pose is optimal.  Often, the improvement in the shape complementarity and number of interactions will be dramatic.

Also, you can use the alternative receptor conformations generated by IFD to a true positive to rescreen your library with faster rigid docking methods.  If you are screening on a prospective basis, this approach could help you identify other chemotypes that may bind well but are missed in a first pass rigid docking screen.

Why isn’t pharma making blockbuster antibiotics?

It seems intuitive that there would be a large market for new, highly-effective antibiotics.  Doctors are warning publicly about the waning effectiveness of today’s antibiotics owing to over-prescription and increased drug resistance.

The linked article even mentions that a course of action could be to provide government incentives to the industry to make new antibiotics.  But where the market creates a profit potential, why would government incentives be necessary in the first place?

I had never heard a suitable explanation for this situation until recently, in a conversation, the following theory was advanced:  if new wonder drugs are developed, they will be “held back” by doctors seeking to establish last-line-of-defense antibiotics, and will therefore not be heavily prescribed, dramatically limiting profitability.

Does the above explanation make sense?  Is there more to the story?  Share your thoughts in the comments below.




Rethinking drug action: activating an ion channel to treat Cystic Fibrosis

In my first “Rethinking Drug Action” post, I described how researchers are seeking activators of PARK9, a protein that is mutated in Parkinson’s Disease.  In a similar manner, Ivacaftor, a new drug for Cystic Fibrosis (CF), shifts the paradigm from treating CF symptoms to therapeutic treatment of the underlying cause of the disease: defects in the activity of the CFTR ion channel owing to genetic loss-of-function mutation.

The molecular structure of Ivacaftor (Kalydeco).
The molecular structure of Ivacaftor (Kalydeco).

In this case the mutation is the rare G551D variant (4-5% of all CF patients) that makes CFTR non-responsive to ATP-dependent channel opening.  The more common delta-F508 CFTR mutation is thought to prevent membrane expression of CFTR through misfolding, and indeed, clinical trials showed that ivacaftor alone had no effect on patients with this mutation.

Ivacaftor, a new drug for Cystic Fibrosis (CF), shifts the paradigm from treating CF symptoms to therapeutic treatment of the underlying cause of the disease

However, for patients with the G551D mutant, where CFTR does reach the membrane but is less active than WT, the drug is very efficacious.  In a clinical trial, patients who received ivacaftor were 55% less likely to experience pulmonary exacerbation (defined as a worsening of lung function owing to infection or inflammation) after 48 weeks on the drug.  Other markers of CF were also improved during this period.

The exact mechanism of action of ivacaftor is not known. Interestingly, however, ivacaftor enhances spontaneous ATP-independent activity of both G551D-CFTR and WT-CFTR to a similar magnitude.  In a recent PNAS paper, researchers propose that ivacaftor affects both WT and G551D in the same way, namely by shifting the equilibrium from the closed (C2) state towards the open2 (O2) state, in essence, “wedging” CFTR open.

Proposed mechanism of CFTR gating from the PNAS paper cited below.  Ivacaftor is thought to stabilize the O2 form over the C2 form.
Proposed mechanism of CFTR gating from the PNAS paper cited above. Ivacaftor is thought to stabilize the O2 form over the C2 form.

In the same paper, the researchers propose that the CFTR transmembrane domains (TMD) may be the site of binding for the drug.  In support of this, they note that the drug is relatively hydrophobic and is measured to increase gate opening times regardless of whether it is applied from the cytoplasmic or extracellular side, suggestion membrane permeation and binding to the TMDs.

In a clinical trial, patients who received ivacaftor were 55% less likely to experience pulmonary exacerbation

More studies are needed to prove this mechanism, but it will be very interesting to see how this paradigm-shifting new drug works on the molecular level.  In addition, other compounds are in development that aim to enhance the folding and membrane expression of the more common DF508 mutation.  Perhaps combination therapy with new compounds for DF508 and ivacaftor together will aid those CF patients who currently are not helped by ivacaftor alone.

Why are many drugs aromatic heterocycles?

To the non-specialist in medicinal chemistry (like myself), the abundance of drugs that contain aromatic ring moieties, usually with heteroatoms like N, is somewhat surprising. In fact, in 2012, the top 4 out of 5 drugs by sales contain such groups. 

There are at least a few good reasons why these types of compounds appear so often:

1 Heterocyclic systems are easier to prepare synthetically than all-carbon based aromatic systems and they are easier to modify later.

2  Scaffolds with heterocycles allow the easy introduction of H-bond donors and acceptors to fine-tune the properties of the compound, like binding affinity, solubility, and resistance to metabolism in vivo.

3 Can “template hop” easily off of aromatic ring scaffolds to evolve new IP with the same functionality as a known drug (e.g., Viagra to Levitra).

Can synthetic chemistry specialists give more reasons?  (Post in the comments!) 

Source:  Jordan, A, Roughley, S.  “Drug discovery chemistry: a primer for the non-specialist.”  Drug Disc Today, 14. 2009

Antifungals and the urgent need for biofilm-specific drugs

Last year I had the opportunity to help write a business plan for a startup company that is taking on a very difficult challenge: finding novel antifungal treatments that target the biofilm, rather than free-living, form of fungal infections.

This is important because recent estimates by the NIH indicate that biofilms are responsible for over 80% of all microbial (bacterial and fungal) infections. For both structural and genetic reasons, biofilms are inherently resistant to antimicrobial therapy and host immune defenses.

Systemic biofilm infections are most frequently seeded from biofilms formed on mucosal surfaces or implanted medical devices, such as catheters. In fact, biofilm-based infections on catheters are the most serious and prevalent life-threatening consequence of biofilms, resulting in systemic invasive infections.

Existing antifungal drugs aim to kill C. albicans, a major fungal pathogen of humans, but they have significant disadvantages:

1) Inefficient at eradicating C. albicans existing in the resistant biofilm-form.

2) Disrupt the intricate microbial balance within the gastrointestinal tract, allowing for other microorganisms to flourish.

3) Can cause nephrotoxicity in the dosages required to have some effect on the biofilm.

Current treatments for fungal biofilm-based infections are ineffective at destroying the biofilm reservoir, and novel therapeutics specifically designed to target the biofilm are desperately needed to treat these prevalent infections.

In a ground-breaking 2012 Cell paper, Nobile and colleagues identified the transcriptional network controlling the process of C. Albicans biofilm formation.  It consists of six transcriptional regulators and over 1,000 target genes (40 of which are predicted to be highly druggable).