THE SUBCELLULAR DRUG TRANSPORT LABORATORY: Cellular pharmacokinetic analysis of antimalarials

Published by Gus Rosania on 18 December 2007 - 4:38am

THE SUBCELLULAR DRUG TRANSPORT LABORATORY (click hereto visit our lab website)


OurResearch Group studies the microscopic transport properties of small drug-like molecules inside cells. As an overarching hypothesis, we propose that a drug's microscopic distribution within cellular organelles is a major determinant of drug efficacy and toxicity, as important as its macroscopic distribution in the organs of the body. Experimentally, we use high throughput microscopic imaging instruments to capture the local distribution and dynamics of small molecules inside cells. For image data analysis, we are developing innovative computational tools and statistical strategies, combining cheminformatics and machine vision to relate the chemical structure of small molecules of varying chemical structures to their subcellular distribution. We are also developing biochemical analysis methods to study the microdistribution and cellular pharmacokinetics of small drug-like molecules. Lastly, with the information gained through experiments, we build mathematical models that are used to simulate drug transport and distribution in single cells and higher order cellular organizations, based on biophysical principles governing molecular transport phenomena at the cellular level.



We envision a day when drugs will be designed, optimized and ultimately approved for clinical use in terms of their site of action, as much as drugs today are designed, optimized and approved based on their molecular mechanism of action. Complementary to in vivo and in vitro models used in drug discovery today, in silico models (such as cell-based molecular transport simulations we use in our experiments) can be applied to pharmaceutical discovery and development. Indeed, computer simulations of drug distribution in biological systems remain largely unexplored as a tool for screening drug candidates. Nevertheless, computers are becoming increasingly fast, reliable and inexpensive research tools. For drug design, we are exploring cell-based molecular transport simulations as a way to probe the role of microscopic drug transport as a determinant of drug. absorption, distribution, metabolism and excretion. Within virtual environments, cell-based molecular transport simulations make it possible to observe and manipulate the distribution of large numbers of drug candidates inside cells, in a manner that is practically impossible to perform experimentally. Weare already exploring how cell-based molecular transport simulations can be used, for example, to analyze the most desirable physicochemical features of molecules targeting extracellular domains of cell surface receptors, imparting maximal tissue penetration while minimizing intracellular accumulation in non-target sites. Furthermore, by making modeling and simulation toolsavailable for free and disseminating them via the internet, our ultimate aim is to help educate the next generation of pharmaceutical scientists and medicinal chemists throughout the world, as much as it is to facilitate the practical development of drugs against diseases neglected by the pharmaceutical industry, such as parasitic infections.



We were introduced toThe Synaptic Leap by Rajarshi Guha from Indiana University and Jean-Claude Bradley fromDrexel University, with whom we will startto collaborate in the development of falcipain-2 inhibitors. Effectivelyour goalwill beto become part of this Open Science project, so that others can learnto use the computational tools we are developing,and help us develop new computationaltools.As part of this open science project, we realize thatscientific progress often relies on making many mistakes before achieving some success. Accordingly, all the results we post should be consideredtentativeor preliminary.Nevertheless, as weproceed with ourwork, wewill be ableto provide the antimalarial drug development communitywith crucial guidance in the pharmaceutical sciences, that should facilitate selection of antimalarial drug candidateswith optimal pharmaceutical properties, for clinical development.For example, we will be performing computational analysis ofthe absorption, distribution, metabolism, excretion properties of thealibrary ofcandidate antimalarial agents under development,using cell-based molecular transport simulations to analyzethe intracellular distribution of small drug-like molecules in the target cells (the malaria parasite), as well as off-target cells (the cells of the humanbody). One goal will beto identifya subset ofmolecules that accumulate maximally in the subcellular compartment in which the drug target is localized --in the case of falcipain-2, the parasite's lysosomes.Anothergoal will be toidentify those molecules that have the highest transcellular permeability in intestinal epithelial cells, so that they can be administered via the oral route.Yet another goal will beto identify those molecules that show lowest intracellular accumulation in off-target cells, which should minimize metabolism and off-target toxicity, while maximizing the concentration of drug in the blood. As we proceed with our analysis,we willintegrate our results with results from our collaborators (ie. docking studies, biochemical screening assays, parasite cytotoxicity assays, and other bioaassays)to assist in the prioritization ofantimalarial drug candidates for advancement into clinical trials. Beyond falcipain-2 inhibitors, lysosomes are a key subcellular target of antimalarial drugs of widespread clinical use, such as chloroquine. Therefore, theincreased understanding weobtain from thisresearch project should be broadly applicable to the development of future generations of lysosome-targeted antimalarial agents.


jcbradley's picture

Gus - it is a real pleasure to start this collaboration with you! Hopefully you'll attract additional collaborators by posting your projects on the Synaptic Leap.

MatTodd's picture


Great to have these projects posted here. I took a quick tour of your grad students' online notebooks, and it made me ask the general question - how is it best to represent all these data? If a lab book will eventually contain a few hundred experiments, is a blog a good place to store that, or is there some other way of storing/sharing the information? I guess we would want to maximise searchability and image content without overloading the students with technical requirements or doing that. Do you/your students find the process of posting data to a blog intuitive/useful, or does the process currently get in the way/take too long, owing to technical limitations of the presentation format?

JC will also have thoughts on this. I know that there are a lot of commercial electronic notebook products (I've never used them, but observed a few), yet we are sticking with fairly standard blogs/wikis. Do you/JC have any advice for students thinking about starting their own online notebooks?


jcbradley's picture

Mat - I think Gus is doing the right thing in having his students record their results on the wiki. Later on, things can be re-organized and linked in new ways as people report having trouble finding specific information. By far the biggest obstacle is simply getting info into some public system.

Reminds me of some aspects of my university research. I am investigating delivery using pulsating electromagnetic fields.