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Intrinsically disordered proteins (IDPs) are a class of proteins that do not adopt a stable secondary or tertiary structure under physiological conditions in vitro, but still have biological functions. Many IDPs are implicated in cancer, neurodegenerative diseases, and diabetes, which makes them attractive drug targets. Are there any successful examples of that? Are there any drugs which disrupt protein-protein interactions (as one of the protein being IDP)?

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IDPs are indeed attractive drug targets and there are ongoing efforts to develop drug molecules that block interactions between a disordered and a structured protein. According to this relatively recent paper, however, these efforts have not brought a drug on the market, yet.

A few promising studies have shown drug-like molecules that inhibit protein-protein interactions based on intrinsic disorder of one of the partners and target:

  • oncogenic fusion protein EWS-FLI1 and RNA helicase A. A small molecule has been found that targets the disordered region of EWS-FLI1, blocks the interaction with the helicase and inhibits growth of Ewing's sarcoma.

  • p53 tumor supressor and its interactor Mdm2. Mdm2, by binding to an intrinsically disordered region of p53, targets p53 for ubiquitination and also causes it to be transported out of the nucleus. Promising small molecules have been found that associate with Mdm2 and thereby block its interaction with p53.

  • c-Myc oncoprotein and the interaction with its partner Max protein. This study demonstrates two small molecules that bind to c-Myc and stabilize its disordered conformation, which inhibits its interaction with the Max protein.

The challenge in targeting protein-protein interactions for therapies stems largely from the fact, that the protein-protein contact surfaces are much larger than those involved in protein–small-molecule interactions (1,500–3,000 Å2 and (300–1,000 Å2, respectively) [2]. They are often flat and have no defined binding pocket. Also, IDPs often don't bind natural small ligands, that could act as starting points in developing drugs.

You may find this paper helpful:

Metallo SJ, Intrinsically disordered proteins are potential drug targets, Curr Opin Chem Biol. 2010 14(4): 481–488.

BTW: for a comprehensive, manually curated list of disordered proteins and regions, please check the Database of Protein Disorder.

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Thanks for your answer and the references. I will definitely look them up. I already read the Metallo, SJ paper, which is an excellent paper! What concerns me the most though, is that all IDPs can interact with multiple small molecules or other proteins, so they cannot be specifically targeted. That's why I am very interested whether specific interactions have been discovered. –  Gergana Vandova Jan 15 '12 at 21:38
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I have been working on this problem for quite some time now and believe me getting specific binding is a real issue with IDRs. Also, since these regions dont form core structure of the protein, the residues are less conserved (more prone to mutations). So in case of evolving drug-resistance contributing proteins this become a bottleneck.

I have done some work on IDPs as potential drug target: Unraveling the potential of intrinsically disordered proteins as drug targets: application to Mycobacterium tuberculosis.

But the concept has been taken well by even the conventional structural biologists.

As the paper suggests, my work is focused on Mycobacterium tuberculosis. Multiple Drug resistance (MDR) and extremely drug resistance (XDR) form of TB have added to the tuberculosis loads not only in the developing but also developed nations. The drug resistance has been associated with proteins (mostly those involved in transport and metabolism) which have helped the pathogen grow resistant to first line of drugs or more. I refer such proteins as "Drug resistance associated proteins".

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Thanks for your answer. I will definitely read your paper. I also saw a list of your papers on linked in. I am particularly interested in the protein-protein interactions. By the way, what do you mean by "drug-resistance contributing proteins"? –  Gergana Vandova Feb 7 '12 at 19:54
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