Open Source Drug Discovery for Malaria

25 Jul
Published by MatTodd

We're starting a new project – open source drug discovery for malaria. Initially the participants are my group at the University of Sydney and the Medicines for Malaria Venture (MMV), but naturally as an open project we need to expand beyond this. If you're reading this, you can join us. Check here for what's needed at the moment.

 
In brief the idea is this: we start with some known compounds released into the public domain as part of the 2010 deposition of data by GSK Tres Cantos and others. These lead compounds, selected by a team at MMV, will first be resynthesised and their activity confirmed. The initial funding we have received from MMV is intended to achieve this.
 
MMV have also committed funding to a “Linkage grant” we have submitted to the Australian Research Council for funding. We will hear whether we have been successful later in 2011, but those funds would then allow us to progress to a full medicinal chemistry/drug discovery project. i.e. the synthesis of analogs, and prosecution of a hit to lead campaign.
 
We'll initially be working with MMV, GSK Tres Cantos, and the OSDD project based at Lucknow in India, who are also applying for funds from the Indian agency CSIR, to start up a malaria project. This core must grow. If you have an interest in drug discovery, chemistry, biology, bioinformatics, toxicology, clinical trials, and so on, please get on board – this project will be an interesting test case of how all these disparate fields can get together. Open projects mean you can showcase your expertise/tools/software without any IP worries.
 
We (my group and MMV) are starting this project off, and we're super excited to lead it when we are able. But we do not “own” the project. If you would like to join in, understand that you can, at any level. With one proviso – that by taking part you understand that whatever you do needs to be recontributed back to the project in full. Please do not even think about participating if you're not completely clear about the need, and spectacular benefits, of sharing all your data and ideas in public.
 
More will come soon – there's a lot to say about a project like this. For now, a word about the general structure. There are several components, as far as I can see:
 
1)   The Synaptic Leap site can be a good place for overall project discussion and coordination. We're hoping to change it around a little to make it easier to comment and post.
2)   We'll use a wiki as a place to describe the project status. We've started this here. Chemists: you can see the structures of the first two molecules we'll go after here.
3)   The raw synthetic data will be hosted on publicly available electronic lab notebooks. Every experiment, every spectrum. Screening data will hosted publicly elsewhere when we start to acquire them. If you want to make molecules as part of the project, it would be great if you used the same lab book, but it's not essential.
4)   We'll try to start up a web presence for updates and feeds – the Twitter feed is active already.
 
Taking a look at what we're about to start here is both exciting and alarming. I'll try to post about this elsewhere, to keep this first post short. But here are some basic principles:
 
1)   First law: All data are open and all ideas are shared
2)   Second Law: Anyone can take part at any level of the project
3)   Third Law: There will be no patents
4)   Fourth Law: Suggestions are the best form of criticism
5)   Fifth Law: Public discussion is much more valuable than private email
6)   Sixth Law: The project is bigger than, and is not owned by, any given lab. The aim is to find a good drug for malaria, by whatever means, as quickly as possible.
 
 
 

Comments

Just to clarify, ideas are Open too, right?

MatTodd's picture

Yes. You know, that's really one of the key aspects to me of open research. Sharing open data is good, and sharing lab books is an excellent idea, but if you don't share what you need, or what you're currently thinking, then people will rightly think that they can't influence the current direction of the project. Our recent posts on some of the malaria stuff are guided by this idea. The advice we need is about current problems we might have, sure, but it's also about bigger picture things, such as which analogs ought we to be making, and what kinds of biological data are needed for drug development guys to be convinced that we are working on a promising lead?
 
(Still need to do that Open Tox prediction on our two leads, though. I stalled on it. You don't want to run it, by any chance? ;))

excellent steps in the right direction - I'll give some friends/collaborators the heads-up to see if we cant get this ball rolling a little fast.

Hello all,

This is clearly a good initiative and I think that it is in collaboration with the OSDDm project of Council of Scientific and Industrial Research (CSIR) and CDRI, India . You all can collaborate.

Here are a few links :

https://sites.google.com/a/osdd.net/malaria/
http://portal.osdd.jnu.ac.in/tags/osddm
www.osdd.net

Regards,
Anurag

MatTodd's picture

Yes certainly - we've already started this collaboration. See this link. We need more interactions and people to combine. Anyone can be part of the worldwide project provided that all data and ideas are freely shared. That necessitates public electronic laboratory notebooks and no patents.