Biological Evaluation of Arylpyrrole Series

Published by MatTodd on 27 August 2011 - 12:51pm

New Stuff:
Online lab book hosting bioactivity data is here.
First set of compounds have been evaluated (Jan 2012) - here.
Initial phase of this project is to validate the biological activity of the two Tres Cantos leads. The promise of these compounds (and others) is discussed in a paper linked here.

Original activity data for the two compounds are here and here.

For this initial phase, the question is: What kind of biological (re)evaluation is needed? (not toxicology, just activity)

For experiments, Tres Cantos (Felix Calderon) kindly offered to re-evaluate these compounds. We also have links with other labs who have expressed an interest in this project (the Eskitis Institute in Queensland or Stuart Ralph's lab in Melbourne). Question is, what data are we looking for?

In our original proposal for this project, we assumed the following assays would be needed in general. Are all these needed for validation of the current two compounds, or only later during analog evaluation?

1) A primary whole cell parasite assay covering a sensitive and resistant falciparum strain (3D7, Dd2 and W2mef). (Screening for activity would use an image based anti-malarial HTS assay incorporating DAPI or SYBR-Green dyes to monitor parasite growth: asexual and, potentially, gametocytes.

2) Assay for information on the selectivity between drug resistant and sensitive falciparum strains, as well as possible cytotoxicity on mammalian cell lines (typically HepG2 or HEK293 cells), to check for a high therapeutic ratio.

3) For compounds that inhibit growth selectively, IC50s should be determined using serial dilutions of inhibitor in 48 and 96 h assays, which will allow us to screen for promising cell-permeable inhibitors and to discern immediate and delayed parasite death – suggesting whether inhibition is of cytosolic- or apicoplast-based targets.

In our correspondence with Felix, he said the following:

1) The antimalarial activity of these compounds is not affected by the presence or absence of folate in the culture medium, implying they are not inhibitors of the folate biosynthesis pathway. Is this of general significance since it steers clear of well-established resistance mechanisms? (review)

2) The compounds are neither bc1 nor DHODH inhibitors. Why is this important?

3) Felix would be happy to determine the IC50 for these compounds in the standard hypoxanthine incorporation assay (48 h). Determination in the original Tres Cantos dataset was measured at 72 h using the LDH assays. Is this difference in assay significant/desirable?

These questions are intentionally naive, because though there are many options, we need a consensus on what people will be looking for in validation of the existing compounds, and why.


MatTodd's picture

(We've started a G+ page, but there seems no way as yet for anyone to make posts, and there also seems to be no notification mechanism for posts.)
The first compounds are (Nov 17 2011) on their way to GSK Tres Cantos. The compounds are also going to be evaluated by Stuart Ralph's lab. He said (by email on November 10th, approved reposting):
"We are certainly happy to help out with drug assays as soon as possible. I have a couple of people who will be doing assays in the next 2 months. Am I correct in understanding from the link below that there are seven compounds for testing in the immediate term? We could turn that initial batch around in a couple of weeks to get IC50s at least."
This is great. On the advice from Paul Willis at MMV, we ought to be including a standard in assays so we can compare between different evaluations. That probably means assaying these analogs against known antmalarials, and then in future also using one of the TCAMS compounds as a further standard. As we test more compounds, at different sites, controls will be very important.
Currently: discussing assay types with Vicky Avery and the guys at GSK, and have asked whether I can share the current email correspondence. I'm trying to shift all correspondence to open platforms (the projects Fifth Law), but this is never easy in science where email is dominant.

For the ToxBank project (, we are looking for Open Data for dose-response studies... we're developing an Open Source platform for this, based on OpenTox. Our GitHub repositories are available at:

Please let us know when the full dose-response data becomes available! Our software will handle both metadata, extracted data, and the original raw data. Such demo data will be very beneficial for our development!

Grtz, Egon