Author: michaelchimenti

Posted on

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.

Posted on

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

Posted on

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).

Posted on

Importance of list comprehensions in Python

A beginner to python programming is usually taught to use for loops to do a lot things. The temptation  is to bust out a for loop whenever you need to modify a list or string object, but this quickly leads to complex “loops within loops” code architectures that are hard to read (by humans), even though they may work OK.

A simple example:

>>>test_list = [2,4,6,8]

>>>for x in test_list:

…     new_list.append(x  + 1)

>>>new_list

[3,5,7,9]

A better approach is to take advantage of Python’s built-in list comprehension expressions, with the form ‘x for x in y’.

Example:

>>>new_list = [x+2 for x in test_list]

>>>new_list

[4,6,8,10]

This can be expanded to include conditionals, for example:

>>>stripped_list = [line.strip() for line in line_list if line !=””]

You can also loop over multiple elements like this:

>>>seq1=’abc’

>>>seq2=(1,2,3)

>>>[(x,y) for x in seq1 for y in seq2]

[(‘a’,1),(‘a’,2),(‘a’,3),(‘b’,1),(‘b’,2)….(‘c’,3)]

Posted on

Practical Fragments: Natural Products as Fragments

There’s an interesting post at Practical Fragments regarding how natural products have been assembled into a small fragment library for screening and lead selection.   Natural products appear to have some advantages over synthetic fragments, including their “3D-ness” and the fact that they were screened by evolution to be protein-binders.