Community-based Gene Annotation

Gene annotation is essential for the advance of research in Malaria. Thus, we believe that allowing the users of the Malaria community in TSL to input (in a structured manner) their collective knowledge of a protein/gene can only benefit basic research towards drug discovery against Malaria. The aim of this project is to provide such tools in a flexible manner so they can be extended to different genomes in the future. When the project will be open (sometime in early 2006), all TSL registered users will be able to annotate genes/proteins from the malaria genome.

To contribute to the project you need to register with TSL.

Gene Cards for the Malaria genome

Gene annotation is essential for the advance of research in Malaria. However, the annotation of genes is collected in several databases and sometimes (more than desired), associating the entries of different databases is no trivial. The aim of this project is to provide a tool that collects information from different databases for all genes in a genome and presents a summarized version of the collected information, which includes all relevant links to the original sources. Eventually, as the projects advances, we plan to maintain a wiki version of the Gene Cards so that users can modify its content. The Sali group at UCSF has collected data from several annotated sources of the Malaria genome. As of September 2005, the Malaria genome had 5,270 ORFs. The used sources were:

• NCBI at http://www.ncbi.nlm.nih.gov/
• BioMart at http://www.biomart.org/
• ModBase at http://www.salilab.org/modbase

You will be able to search the database from this page after the project is released in early 2006.

Gene Wiki Programmers Needed

TDI and TSL are in need of volunteers for the tools development within the Malaria community. You can read about the projects themselves here. So, what we need? Basically, we seek programmers with an interest of being part of a new community for BioMedical research. You would be applying your skills to develop tools that that should help advance the research of drug discovery for neglected diseases. This is something that you will feel good about! Gives good Karma!! The skills we are looking for in a volunteer in those projects are: - JavaScripting (in particular bookmarklets) - PHP programmer - MySql database experience - Familiarity developing Wiki-based tools a strong plus. - Familiarity with Drupal a strong plus - Familiarity with Trac a strong plus - Familiarity with Subversion a strong plus If you see that you would like to join, please do so by posting a comment to this entry! Thanks! marc

Malaria Gene Basket

Gene annotation is essential for the advance of research in Malaria. Thus, we believe that allowing the users of the Malaria community in TSL automatically "annotate" each gene/protein in the malaria genome, can only benefit basic research towards drug discovery against Malaria. The aim of this project is to provide such tools in a flexible manner so they can be extended to different genomes in the future. As seen in other social communities for photos or bookmarks., TSL registered users will be able to save gene cards in their baskets and associate pieces of information or tags to entries in the basket. This will allow a semi-automatic association of data to particular genes in their baskets. The mechanism will take advantage of the use of bookmarklets so that the user can add information to its basket with just one click on their browser. For example, a user may be browsing the literature at PubMed and find an interesting article, with just one click the system should be able to propose and association between the article and any of the genes in his/her basket.

Target Selection for Structural Genomics of Malaria

Structural genomics aims to structurally characterize most protein sequences by an efficient combination of experiment and modeling. Central to the success of these efforts is effective target selection. There are a variety of target selection schemes, ranging from focusing on only novel folds to selecting all proteins in a model genome. Many of the target selection strategies of the Structural Genomic Consortiums are biologically based, providing a set of protein targets that are key actors in an interesting biological process. This project aims to provide a flexible tool for general target selection (in this case of Structural Genomics) based on collective knowledge. TDI registered users can vote for genes/proteins that may be promissing candidates for structural determination. The aim of the project is to generate a list of target proteins, which structure may help the advance of drug discovery for malaria. Dr. Raymond Hui, from the Structural Genomics Consortium in Toronto, and Dr Marc A. Marti-Renom, a computational bioligist, from UCSF, will analyze the gene the community voted on to have the highest potential. Results from that analysis will be posted here as well as open-access databases such as PlasmoDB. To contribute to the project you need to login with TSL. We intend to release this project in the early month of 2006.

A list of what's needed in the OSDD Malaria project

Main: Comment/Analysis on Initial Bioactivity Data
We have some excellent first results. What to do next?
 
Resynthesis of TCMDC-123812 and TCMDC-123794 (ELN)
Need: advice on oxidation of pyrrole-3-carbaldehydes - here. Through a work-around, these syntheses are complete, but we could still ue advice on the step above.
 
General Analog Synthesis Planning
Need: Advice from med chemists on what to alter first - here.
 
Biological Evaluation of Initial Leads
Need: Advice on what kinds of biological evaluation are most desirable to validate the initial GSK leads - here.
 
Where Else Can we Access This Series?
Need: People with stocks of analogous compounds (i.e. members of the arylpyrrole series) to submit those compounds for screening. First possibility seen here.

Analog Synthesis - Variation of the Aryl Ring

Open source is most powerful when people participate by creating. Open science is no different, and in the case of lab-based sciences, that means actually doing experiments. For the open source drug discovery for malaria project we need people to make molecules. In fact a lot of people need to make molecules. We have our first offer (November 2011).
 
Sanjay Batra at the Medicinal and Process Chemistry Division of the Central Drug Research Institute in Lucknow, India, has offered to ask a student to make some molecules as part of the current push to validate the GSK aryl pyrroles (thanks to Saman Habib for putting us in touch by email - Saman is going to be leading the Indian OSDD Malaria project that is starting in 2012). This opening post describes where we are, and what I think needs to be made next (though the post may change over time as the project changes).

 
Below are the compounds sent last week (Nov 24 2011) for biological evaluation. Included are the original TCAMS compounds, some “near neighbour” compounds, and a range of pro-drug possibilities (i.e., if the TCAMS compounds are actually prodrugs, given that that ester is unlikely to survive for long). Most were made by Paul Ylioja, and some by the undergraduate student Paul was mentoring, Laura White, who posted a nice report of what she did here. The compound codes will allow you to find the procedures in the ELNs.

 
According to wisdom received from the GSK Tres Cantos and MMV guys, we should be doing a broad and shallow SAR search, which is to say we ought to be picking several points of variation in the TCAMS structures and making a small number of changes in each position rather than exhaustively changing one position. The rationale there is that we need to see that the potency varies when we change things, otherwise there are a bunch of other hit series we can look at.
 
I think that means the best thing for Sanjay’s lab to do is to finish off making variations in the aniline of the arylpyrrole synthesis – i.e. vary the fluorine:
 

 
We’ve done some of this – converting the F to H, Me and CF3. Not all of these have been taken all the way through to the end yet. Our undergrad student Zoe is working with Paul Ylioja to make a 3,5-CF3 variant. But I think it’s important we change the position of the F, that we change the Ph ring to, for example, a pyridine, and we bulk out the ring with something like two methyls. I also think the biphenyl would be a good one to try (i.e., use 4-phenylaniline). Which compounds are made depends on which starting materials are available. I think we need 3-4 diverse anilines taken through to the end, so 8 final compounds. Whether intermediates should be saved for screening depends on whether the "prodrug" compounds sent for evaluation above look promising.

 
The pyrrole esters would then need to be hydrolysed, and coupled with the TCAMS R' groups according to procedures Paul has nicely worked out. Typical procedures are given as red URLs above, but generally the chemistry can be browsed at the ELN.
 
It would help a great deal if Sanjay was able to use the same lab book that we are using, i.e., to start an account on Labtrove and start a separate blog on this page called something like “CDRI Synthesis of Aniline Variants” where the experiments would be posted (we can create this if it's not easy/obvious). Crucially, this is an open science project, so all data must be deposited – check out the Six Laws. Our labs will be geographically separated, so we must have full access to each others’ data. This also means that readers of the project can have faith in what we’re doing because they can check the raw data.
 
I hope this project idea sounds good as a starter, Sanjay, and your students are happy!
 
Biological evaluation of compounds would happen either here in Australia, or better in India, if we are able to establish a willing venue for that. I suspect that will be no problem, but is not currently sorted out. The assays for the compounds made need to be similar to the ones being done elsewhere, and the same control compounds should be used. The controls should probably include one of the original TCAMS hits, and we could provide that compound if and when it's needed.

 
Note if you’re reading this and want to take part by making some molecules, please say. You're both welcome and needed, provided you subscribe to the Six Laws. There’s so much to do, we can’t do it all on our own. Similarly, if you’re a medicinal chemist who just can’t help themselves, and think we’re approaching this all wrong/right, please feel free to say why. Discussion can happen here. Project status will be most up to date on the wiki. You can tweet the project. Or you can catch up with some of us on Google+, which is a pretty useful addition to the project tools and gets us away from private email, which is generally useless for an open project.

Availability of TCMDC-123812 and TCMDC-123794

We're starting open source drug discovery for malaria. We have to start somewhere: in this case a couple of known compounds that showed good activity and have plenty of possibilities for modification - compounds contained in the open deposition of malaria data from 2010, originating from GSK's Tres Cantos lab.

Before getting too excited about these leads, we must validate them, meaning we need to obtain samples and screen. Paul Ylioja is currently making these compounds, and the chemistry is going very well, helped in part by his pyrrole wizardry. Please analyze and comment on the lab book, particularly if you're a synthetic organic chemist.

SciFinder and Google searches on the SMILES/InChIs for these structures throw up very little, but it turns out they are commercially available from a number of suppliers (Paul first spotted this). We corresponded with Felix Calderon at GSK Tres Cantos, who said that, indeed, these compounds had been bought in from the Enamine library. Tres Cantos have stock of these compounds in Madrid, and have kindly offered to look into them further if needed. Potential evaluation will be dealt with in another post elsewhere.
 
Given we will be wanting to modify the structures, we need to be able to synthesize them rather than buy them.

But I wonder why these compounds were made in the first place?

Biological Evaluation of Arylpyrrole Series

New Stuff:
Online lab book hosting bioactivity data is here.
First set of compounds have been evaluated (Jan 2012) - here.
Background:
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.

Druggability of the Arylpyrrole leads (TCMDC-123794 etc)

Project is starting with a couple of leads from the GSK Tres Cantos set. There is a newly-published analysis of the druggability of the compounds in the original data set. The arylpyrrole series is listed as one of the most promising (though the Aryl-F is missing in the published paper - presume that is a clerical error).
 
Tres Cantos are appealing for collaborators to work with them on these compounds, which is an excellent idea. That's what we're doing, except that the project hosted here is open source, meaning anyone can see what we're doing and guide the direction of the project.
 
The initial phase is the resynthesis of these leads and their validation. We will soon be moving to analog synthesis. The obvious first question for the community of medicinal chemists is: what should we change?
 
My gut feeling was to verify the need for the aryl-F and the methyls on the pyrrole. Paul Willis' gut feeling was that ester. Gut feelings and half-formed thoughts enormously welcome as comments below.
 

Known Near Neighbours of Initial Tres Cantos Leads

We're starting with the resynthesis of two leads from the GSK Tres Cantos dataset. The obvious question is: are there other, related structures in the dataset that might give us information on what to change next?

Paul Willis from MMV did a quick "near neighbour" search (25 Aug 2011), particularly with an eye to getting rid of the ester in the lead structures. Structures below. As he said: "The first compound is a ketone analogue of the ester lineage – it’s a singleton and not an ideal group from a drug discovery perspective but indicates other groups may be tolerated.  The next set is the entire cluster output of another near neighbor I spotted – all have replacements for the ester group (again not especially drug like but possible indication that wide variation possible at this position) and interestingly some contain variations on the 4-F-Ph"

Cc1ccc(cc1)n2c(cc(c2C)C(=O)CN3C(=O)C(NC3=O)Cc4ccccc4)C
Cc1cc(c(n1c2ccc(cc2)Cl)C)C=C3C(=O)N(C(=Nc4ccccc4)S3)C5CCCC5
Cc1ccnc(c1)n2c(cc(c2C)C=C3C(=O)N(C(=Nc4ccccc4)S3)Cc5ccco5)C
Cc1cc(cc(c1)n2c(cc(c2C)C=C3C(=O)NC(=Nc4ccc(cc4)Cl)S3)C)C
CCOC(=O)c1ccc(cc1)n2c(cc(c2C)C=C3C(=O)N(C(=Nc4ccccc4)S3)C5CCCC5)C
CCn1c(cc(c1C)C=C2C(=O)NC(=Nc3ccccc3)S2)C

Questions:

1) Are there other structures that are "similar" in the GSK set - searchable at Chembl.

2) What do these structures tell us about what to change next in the lead compounds?

3) Importantly, can we gain access to analogous structures that have been evaluated but not reported?

Interestingly this includes compounds that are related to the TC hits above but which were perhaps assayed against other targets.

Data for the above compounds will be posted to the wiki page. Discussion of them can more easily happen in comments below.

Proposed resynthesis strategy for TCMDC-123812 and TCMDC-123794

Below is a proposed synthesis strategy to the two members of the TCMDC aryl pyrrole series. Please comment, give your thoughts and improvements.
Experimental attempts are documented on an electonic lab notebook found here: malaria.ourexperiment.org/tcmdc_ap/

A semi-quantitative cell-based phenotypic assay for determining the lysosomal accumulation of small molecule antimalarials

One of the reasons why scientists in the past have not been able to develop small molecule drugs targeted to subcellular organelles is the lack of suitable assays to monitor the absolute concentration of small molecules within those organelles.  Although measuring the absolute concentration of small molecules within organelles is still very difficult experimentally, the availability of large chemical libraries of small molecules have permitted the use of semi-quantitative (or qualitative) experimental readouts, to test the validity of mathematical models predicting subcellular distribution of small molecules.  In this context, Nan Zheng, a second year PhD graduate student that recently joined the lab, is interested in developing a bioassay to report the accumulation of small molecules in lysosomes.  Such an assay would allow validating the results of cell-based molecular transport simulations as they pertain to the lysosomal accumulation of small drug-like molecules, such as falcipain-2 inhibitors being developed as antimalarial agents (falcipain-2 is a resident lysosomal enzyme).

In the past, it had been observed that small lysosomotropic molecules (such as the antimalarial drug chloroquine) induce a vacuolation phenotype in cells that are incubated with drug.  This vacuolation phenotype is the result of the osmotic swelling and expansion of the lysosomal compartment, as a result of the accumulation of the drug molecules in the organelle.  Back in 1974, Charles DeDuve described this phenomenom, and attributed it to an ion trapping mechanism. According to this mechanism, the lumen of the lysosome is acidic (pH 5) in relation to the cytosol (pH 7.4).  Weakly basic molecules (such as molecules containing amine functionality) exist mostly in neutral form in the cytosol, while in the lysosomes they exist mostly in protonated, charged form.  Because the protonated charged form of the molecule is largely membrane impermeant while the neutral form is membrane permeant, the pH gradient across the lysosomal membrane results in a chemical potential that drives the accumulation of the weakly basic molecule in the lumen of the lysosome.

While one may expect that most weakly basic molecules would tend to accumulate in lysosomes, one would also expect them to do so to different extents based on differences in the ionization constants and membrane permeability of the different ionic species.  But, perhaps most importantly,  pH gradient across the lysosomal membrane is a generated by the lysosomal H+ATPase, a protein that uses ATP hydrolysis to pump protons from the cytosol into the lysosomal lumen.  Thus, the lysosomal accumulation of small molecules should also be highly sensitive to the metabolic status of the cell.  If a small molecule accumulates in mitochondria or other organelles in a non-specific fashion (in addition to accumulating in lysosomes), it will compromise the metabolic status of the cell in a manner that decreases the production of ATP, ultimately leading to the dissipation of the lysosomal pH gradient. In this manner, only those molecules that selectively accumulate in lysosomes –while not accumulating in other organelles- should be able to induce lysosomal vacuolation phenotype.   Accordingly, the goal of Nan’s project will be to fine-tune our molecular transport simulators so as to be able to rank molecules in terms of their ability to induce lysosomal swelling, considering not only the ion trapping mechanism, but also the selectivity of the molecules for accumulating in lysosomes vs. other organelles.

Development of Falcipain-2 Inhibitors as Antimalarial Agents

The development of falcipain-2 inhibitors as antimalarial agents is a collaborative Open Science project that we are joining.  Our research group studies the development of small molecule chemotherapeutic agents that are targeted to specific sites-of-action, at a microscopic level.  Falcipain-2 is a lysosomal enzyme of Plasmodium, the parasite that causes malaria.  Therefore, the ability to identify small molecule falcipain-2 inhibitors that accumulate in the lysosomes of the parasite while not accumulating in other parts of the human body is key if the chemotherapeutic agents under development are going to have potent antimalarial activity in vivo, with minimal side effects. 

 Remarkably, the design of small molecule drugs targeted to microscopic sites of action (ie. specific organelles) within cells is in its infancy.  Although the importance of the site of action in the context of drug design and development should be obvious, current rational design strategies used in the pharmaceutical industry focus on optimizing a drug's mechanism of action (ie. the binding of a drug to its specific molecular target and its inhibitory activity), because little is known about how to direct small molecule to the site of action.  In our research group, we are developing cell-based molecular transport simulations, which allow prediction of how the chemical structure of small molecules lead to differential accumulation in various organelles of the cell.  Therefore, one of the goals of this project is to combine results of such simulation, with data about target binding and target inhibitory activity, to determine which small molecule drug candidate is most likely to be effective and non-toxic in a cellular (and ultimately and organismic) context.

The student in charge of this project will be Jason Baik, a second year PhD student in the department of pharmaceutical sciences at the University of Michigan College of Pharmacy.  As part of this project, Jason will be keeping a blog instead of the usual laboratory notebook. 

Mathematical Modeling of Cellular Pharmacokinetics: Cell-Based Molecular Transport Simulators

Every single protein encoded by a genome -human or otherwise- is localized to some microccopic subcellular compartment or organelle. In the case of the malaria parasite, the parasite generally inhibits the red blood cells in the ciruclation.  Within the red blood cells, the parasite thrives by feeding on hemoglobin, which constitutes the bulk of the protein mass of the red blood cell.  To digest the hemoglobin, the parasite relies on lysosomes, a digestive organelle that contains proteases that chop the large hemoglobin molecules into smaller peptides and ultimately amno acids that can be incorporated into the parasite's own metabolism to help it grow, reproduce and infect other cells.  So, how does one design a small molecule that is absorbed by the body, enters the blood without being metabolized, ultimately accumulating in the parasites lysosome without accumulating in other parts of the body?

 To enable design of such a drug, one of the graduate students in my lab -Xinyuan Zhang- has developed a new type of computational tool referred to as a cell based molecular transport simulator.  Her work was recently published in a peer-reviewed research journal: 

Xinyuan Zhang, Kerby Shedden, Gus Rosania. (2006). A cell-based molecular transport simulator for pharmacokinetic prediction and cheminformatic exploration. Molecular Pharmaceutics; 3(6) pp 704 - 716.

For orally administered drug products, dissolution of drug molecules in the gastrointestinal tract followed by transport across the epithelial cell monolayer lining the lumen of the intestine can exert a major influence on systemic drug concentration and activity.  This research project will involve building computational models to simulate biochemical reactions and diffusion of small drug-like molecules inside and across intestinal epithelial cells. These cells form the barrier between the lumen of the intestine and the inside of the human body. Acting as a gateway, intestinal epithelial cells exert a major influence on drug absorption into the body, and are a key determinant of drug concentration in the blood.

For mathematical modeling, passive and active transport of drug molecules can be described in fundamental biophysical terms, using several well-known differential equations. For example, Fick’s equation and Nernst-Planck equation can be used to calculate the rate of transmembrane drug transport based on the pKa of functional groups on the drug molecule, and the octanol:water partition coefficients of the different ionic species that the drug molecule can exist in, as a function of the local pH microenvironment. Michaelis-Menten’s equation can be used to capture the effect of transmembrane transport proteins (such as P-glycoprotein) as well as the effect of drug metabolizing enzymes, on local drug concentrations and distributions within any given subcellular compartment.

To model drug transport within and across cells, we  consider the individual subcellular compartments that are delimited by membranes (ie. apical and basolateral compartment; cytosolic compartment; mitochondrial compartment; lysosomal compartments; etc). Each compartment has a characteristic pH, and the membrane delimiting each compartment possesses its own transmembrane electrical potential. Accordingly, we will use coupled sets of the aforementioned differential equations to describe how the different subcellular compartments selectively accumulate different drug concentrations through time, as well as the rate at which drug molecules are transported across cells (the drug’s transcellular permeability) –all in the presence of a transcellular drug concentration gradient to mimic intestinal absorption.  To test and improve the model, the computational results are being related to published experimental measurements, as well as measurements we perform in the lab.

Complementary to in vivo and in vitro models used in drug discovery today, the cell-based molecular transport simulations we aim to develop are promising new tools to facilitate pharmaceutical discovery and development. Nevertheless, computational models are inexpensive, flexible and scalable, and they can be continually improved upon by future generation of scientists.   Indeed, with the aid of computational simulations of drug transport such as the one we are developing, we expect that one day, drugs may be designed, optimized and ultimately approved for clinical use computationally - in terms of their site of action- as much as the drugs today are designed, optimized and approved experimentally, in terms of their mechanism of action.

Histone acetyltransferase inhibitors

Histone acetyltransferases (HATs) and HAT inhibitors
The significance of studying HATs is underscored by an abundance of genetic studies that implicate them in having a role in disease (for reviews, see (10), (6), and (16)).  Consistent with this, some histone deacetylase (HDAC) inhibitors display anti-tumor activity and are being evaluated in clinical trials (8).  In addition to regulating transcription, HATs have crucial functions in modulating other DNA processes (7).  Histone acetylation machinery may also be a viable target for novel anti-infectives (5).
The impact of the various HATs on cellular physiology and disease would greatly benefit from the identification of specific pharmacological inhibitors, but very few have been described to date (11).  Two natural products, anacardic acid and garcinol (a polyprenylated benzophenone), are reported to inhibit both p300/CBP and PCAF in a 5-10 mM range in vitro (1, 2).  In contrast, curcumin displays activity against p300/CBP, but not PCAF (3).  Subsequent studies suggest that anacardic acid may be a broad-spectrum HAT inhibitor, as it also interferes with the MYST HAT Tip60 (13).  Isothiazolones were identified in a high-throughput screen as inhibitors of PCAF and p300 (12), but like the aforementioned compounds, activity against GCN5 was not determined.  Moreover, isothiazolones are strongly reactive with thiol groups and hence are likely to have substantial nonspecific effects.  Two small molecule inhibitors of GCN5 that have been documented include a butyrolactone (4) and MC1626 (2-methyl-3-carbethoxyquinoline) (9).  However, in our hands, the butyrolactone and MC1626 exhibit no inhibition of recombinant yeast GCN5 in a standard in vitro HAT assay (Sullivan, unpublished).  As a positive control, parallel HAT assays showed anacardic acid does inhibit yeast GCN5.
Two reports describe systems that can be used in high-throughput format to identify potential HAT inhibitors (14, 15).
We are interested in acquiring HAT inhibitors, especially those that appear to be selective for distinct types of HATs (i.e. GCN5, MYST).  Not only would these serve as valuable probes to study histone acetylation in eukaryotic cells, they may also hold promise as novel drugs to combat parasitic disease.
References

1.         Balasubramanyam, K., M. Altaf, R. A. Varier, V. Swaminathan, A. Ravindran, P. P. Sadhale, and T. K. Kundu. 2004. Polyisoprenylated benzophenone, garcinol, a natural histone acetyltransferase inhibitor, represses chromatin transcription and alters global gene expression. J Biol Chem 279:33716-26.

2.         Balasubramanyam, K., V. Swaminathan, A. Ranganathan, and T. K. Kundu. 2003. Small molecule modulators of histone acetyltransferase p300. J Biol Chem 278:19134-40.

3.         Balasubramanyam, K., R. A. Varier, M. Altaf, V. Swaminathan, N. B. Siddappa, U. Ranga, and T. K. Kundu. 2004. Curcumin, a novel p300/CREB-binding protein-specific inhibitor of acetyltransferase, represses the acetylation of histone/nonhistone proteins and histone acetyltransferase-dependent chromatin transcription. J Biol Chem 279:51163-71.

4.         Biel, M., A. Kretsovali, E. Karatzali, J. Papamatheakis, and A. Giannis. 2004. Design, synthesis, and biological evaluation of a small-molecule inhibitor of the histone acetyltransferase Gcn5. Angew Chem Int Ed Engl 43:3974-6.

5.         Darkin-Rattray, S. J., A. M. Gurnett, R. W. Myers, P. M. Dulski, T. M. Crumley, J. J. Allocco, C. Cannova, P. T. Meinke, S. L. Colletti, M. A. Bednarek, S. B. Singh, M. A. Goetz, A. W. Dombrowski, J. D. Polishook, and D. M. Schmatz. 1996. Apicidin: a novel antiprotozoal agent that inhibits parasite histone deacetylase. Proc Natl Acad Sci U S A 93:13143-7.

6.         Davis, P. K., and R. K. Brackmann. 2003. Chromatin remodeling and cancer. Cancer Biol Ther 2:22-9.

7.         Hasan, S., and M. O. Hottiger. 2002. Histone acetyl transferases: a role in DNA repair and DNA replication. J Mol Med 80:463-74.

8.         Kristeleit, R., L. Stimson, P. Workman, and W. Aherne. 2004. Histone modification enzymes: novel targets for cancer drugs. Expert Opin Emerg Drugs 9:135-54.

9.         Ornaghi, P., D. Rotili, G. Sbardella, A. Mai, and P. Filetici. 2005. A novel Gcn5p inhibitor represses cell growth, gene transcription and histone acetylation in budding yeast. Biochem Pharmacol 70:911-7.

10.       Roth, S. Y., J. M. Denu, and C. D. Allis. 2001. Histone acetyltransferases. Annu Rev Biochem 70:81-120.

11.       Schafer, S., and M. Jung. 2005. Chromatin modifications as targets for new anticancer drugs. Arch Pharm (Weinheim) 338:347-57.

12.       Stimson, L., M. G. Rowlands, Y. M. Newbatt, N. F. Smith, F. I. Raynaud, P. Rogers, V. Bavetsias, S. Gorsuch, M. Jarman, A. Bannister, T. Kouzarides, E. McDonald, P. Workman, and G. W. Aherne. 2005. Isothiazolones as inhibitors of PCAF and p300 histone acetyltransferase activity. Mol Cancer Ther 4:1521-32.

13.       Sun, Y., X. Jiang, S. Chen, and B. D. Price. 2006. Inhibition of histone acetyltransferase activity by anacardic acid sensitizes tumor cells to ionizing radiation. FEBS Lett 580:4353-6.

14.       Turlais, F., A. Hardcastle, M. Rowlands, Y. Newbatt, A. Bannister, T. Kouzarides, P. Workman, and G. W. Aherne. 2001. High-throughput screening for identification of small molecule inhibitors of histone acetyltransferases using scintillating microplates (FlashPlate). Anal Biochem 298:62-8.

15.       Wynne Aherne, G., M. G. Rowlands, L. Stimson, and P. Workman. 2002. Assays for the identification and evaluation of histone acetyltransferase inhibitors. Methods 26:245-53.

16.       Yang, X. J. 2004. The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases. Nucleic Acids Res 32:959-976.