Welcome one and all. ‘They’ call me Saj (M. Saj Sajid) and I have joined The Synaptic Leap to take over the responsible task of Malaria Community Leader from our previous overseer, Marc A. Marti-Renom. Currently, I co-direct the Biochemistry and Molecular Biology Core of the Sandler Center for Basic Research in Parasitic Diseases, at the University of California San Francisco. I am involved in a number of related projects looking at proteases as drug targets in parasitic organisms, and have a particular interest in the malaria parasite, Plasmodium.
Even with huge advances in biomedical science, malaria eradication has eluded mankind. (See WHO and CDC sites for malaria background). This lack of effective control, the appearance of drug resistant strains of malaria in the field along with the enormous mortality and socioeconomic loss have been the driving forces to search for novel malariacides and anti-malaria immunotherapies. Worldwide, malaria prevalence is 300-500 million cases annually. This preventable scourge causes 1-2 million deaths per year, mainly confined to Africa and to children less than 5 years of age; representing 10% of all deaths in Africa and 30 to 50% of all hospital admissions. To put this number into perspective, the children in Africa that die every day due to infection with malaria would fill 7 Jumbo jets and a moderate infection consumes an equivalent amount of protein as there is in a burger (remember this the next you grab some fast food!). These numbers clearly illustrate the pressing need for effective control, cure and prophylaxis for malaria. (See the excellent overview on the economic loss due to malaria by Gallup and Sach). In addition to children, high-risk groups include pregnant women and non-immune travelers such the armed forces, labourers and refugees. Once infected, the individual becomes feverish and drowsy, vomiting and shivering may also occur, accompanied by anemia. There is also an increased susceptibility to infection by other diseases, and malaria has been linked with impaired cognitive development in children and therefore educational achievement. Pregnant women are particularly susceptible to severe malaria and are more likely to deliver underweight babies. There is a strong correlation between malaria prevalence and poverty, and poor countries are further burdened by the inability of infected individuals to work and care for their families. For a long time malaria has been a neglected disease of developing countries, however, there has been a recent global drive to eliminate this devastating disease.
Although some pharmaceutical companies have an interest in malaria (for example GSK and Novartis), the vast majority of malaria research is carried out in hundreds of academic and clinical labs worldwide. Malaria research has had substantial increases in funding over the years (for example the Bill and Melinda Gates Foundation and the Global Fund), and even large multinational coalitions have also been formed to ‘Roll Back Malaria’. Nonetheless, there is still a lack of novel anti-malaria immuno and chemotherapies on the market, mainly due to the huge expense of taking a potential drug through the chemotherapy validation process. The vast chasm that exists between academic target validation, lead compound optimization and clinical trials has been tackled by a number of non-profit based organizations such as MMV and One World Health. Moreover, the enormous global expertise in malaria that has accumulated over the years is spread into discrete laboratories, where valuable information is not easily available to the malaria community. However, this collective knowledge can now be usefully disseminated by tapping into an Open Source based global malaria resource - and here is where the TSL comes in.
I hope to encourage as many malariologists (and general scientists) to visit TSL in the hope that the malaria community will start to perceive TSL as an invaluable resource in all aspects of malaria research – whether it be issues relating to basic wet lab science, informatics, epidemiology or novel drug target selection and validation. For TSL to be truly ‘usable’ it will need a small amount of input by many, and I envisage that once we have gathered momentum, the TSL will grow in leaps and bounds. I encourage you all to login (this will only take a few minutes) and surf TSL; start to think of TSL as a portal to hundreds of scientists globally that all have a common interest, the eradication of malaria. Tell your colleagues and friends (and your friend’s friends!) about the TSL. Remember, as the number of TSL users increases so will the collective power of this Open Source Collaboration.
Go to our current projects page for a list of projects in process. From there, you may learn more about these projects and learn how you can participate. Or, you may "add a child page" (see the link at the bottom) to initiate and describe your own open research project for malaria.
If you're still in the brainstorming phase of starting a project, write a blog article to discuss your ideas with other scientists around the world also studying malaria. Working together, we can direct the research towards the most promising ideas.
You can also help shape and direct other malaria research ideas by reading and commenting on other community posts.
To assist you with your malaria research we have pulled together a research tools page for malaria as well as an RSS news feeds for malaria. If you know of a useful tool that we don't have on the list, add a comment for others to see.
In the time it has taken you to read this page, 5 to 6 children have died of malaria.
The Malaria genome is largely unexplored (~65% of ORF are annotated as hypothetical proteins). We intend to provide the Malaria community with tools to use, analyze and annotate the known data about all proteins in the Malaria genome. We believe that “collective knowledge” can contribute to a large efforts which could not be accomplished by the individuals alone. The use of open source methods and the tools to initiate research collaborations within the Malaria community, will help towards identifying the most promising targets and compounds for drug discovery against Malaria.
All malaria projects currently in process should be created as child pages to this page. See the "add child" link at the bottom if you want to initiate a new open research project for malaria.
Proteins that have a GPI glycolipid modification are acknowledged to be key in the lifecycle of Plasmodium; for example the involvement of the GPI-anchored MSP1 on merozoites in erythrocyte invasion. The enzyme that transfers the preformed GPI to the proteins such as MSP1 is named GPI:protein transamidase, however, studying this enzyme biochemically has been arduous, due to the following hurdles. Firstly, the GPI:protein transamidase functions as a subunit in multidomain complex, some components of which maybe membrane associated, and there are no reports of functional recombinant reconstitution of this complex. Secondly, there are no convenient and sensitive transamidase assays available that are amenable to medium/high throughput studies, even though large small molecule cysteine peptidase inhibitor libraries exist and can be used to studying this enzyme. Any input/thoughts on how to overcome the aforementioned obstacles in studying the Plasmodium GPI:protein transamidase would be most welcome. Please peruse the attached file.
See the attached document for an overall concept of our Gene Wiki idea.
Please login and add comments on your thoughts on this project. Type of feedback we're looking for:
The more comments the better - even if they're negative. I want some online brainstorming.
Cheers!
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 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:
You will be able to search the database from this page after the project is released in early 2006.
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
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.
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.
THE SUBCELLULAR DRUG TRANSPORT LABORATORY (click here to visit our lab website)
Our Research 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.
OUR VISION
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. We are 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 tools available 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.
WHAT WE WILL PROVIDE TO THE MALARIA RESEARCH COMMUNITY
We were introduced to The Synaptic Leap by Rajarshi Guha from Indiana University and Jean-Claude Bradley from Drexel University, with whom we will start to collaborate in the development of falcipain-2 inhibitors. Effectively our goal will be to become part of this Open Science project, so that others can learn to use the computational tools we are developing, and help us develop new computational tools. As part of this open science project, we realize that scientific progress often relies on making many mistakes before achieving some success. Accordingly, all the results we post should be considered tentative or preliminary. Nevertheless, as we proceed with our work, we will be able to provide the antimalarial drug development community with crucial guidance in the pharmaceutical sciences, that should facilitate selection of antimalarial drug candidates with optimal pharmaceutical properties, for clinical development. For example, we will be performing computational analysis of the absorption, distribution, metabolism, excretion properties of the a library of candidate antimalarial agents under development, using cell-based molecular transport simulations to analyze the intracellular distribution of small drug-like molecules in the target cells (the malaria parasite), as well as off-target cells (the cells of the human body). One goal will be to identify a subset of molecules that accumulate maximally in the subcellular compartment in which the drug target is localized --in the case of falcipain-2, the parasite's lysosomes. Another goal will be to identify 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 be to 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 will integrate our results with results from our collaborators (ie. docking studies, biochemical screening assays, parasite cytotoxicity assays, and other bioaassays) to assist in the prioritization of antimalarial 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, the increased understanding we obtain from this research project should be broadly applicable to the development of future generations of lysosome-targeted antimalarial agents.
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.
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.
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.
All projects that are complete should be registered as a child of this book page.
The functional characterization of protein sequences is central to problems in biology. This task is usually facilitated by an accurate three-dimensional (3D) structure of the protein of interest. In the absence of an experimentally determined structure, comparative or homology modeling can provide a useful 3D model for a protein that is related to at least one known structure. The Sali group at UCSF has used the ModPipe software to build models for as many as possible ORFs in the Malaria genome. This has resulted in 10,743 three-dimensional models of 3,321 genes in the malaria genome (63% of all annotated ORF). To visualize the result of this project, you can visit the Gene Card project page. Alternatively, models can also be directly accessed in the ModBase database by selecting the tdi_malaria set of models. The data generated by ModPipe and deposited either in this site or the ModBase database is freely available for non-commercial propouses.
Welcome, I am Bill Sullivan, the online leader for The Synaptic Leap’s Toxoplasma research community. You can find out more about my work at the laboratory web site.
Toxoplasma gondii is a protozoan (single-celled) parasite that has permanently infected tens of millions of people in the world. A normal immune response typically controls infection promptly, but the parasite persists as a latent cyst within host tissues. Tissue cysts can form in brain, heart, and skeletal muscle tissue. If immunity should become compromised due to disease (such as AIDS) or immunosuppressive therapies (e.g., cancer chemotherapy or organ transplantation), the acute stage of infection may recrudesce. Thus, Toxoplasma is a significant opportunisitc pathogen. However, there are instances when Toxoplasma threatens normal, healthy individuals as well. For example, Toxoplasma can cause abortion or congenital birth defects; this may occur if a woman becomes infected for the first time during pregnancy. Additionally, emerging studies have demonstrated intriguing alterations in host organism behavior upon infection, or correlations with neurological disorders such as schizophrenia.
Toxoplasma infection may be picked up from cats (the definitive host) or contaminated food/water. People at significant risk (HIV+ or pregnant individuals) should cook meat thoroughly, wash vegetables, and avoid cat litter boxes and gardening.
If you're studying Toxoplasma, I encourage you to make all or portions of your project open. Invite others to help or add their thoughts to your project. Simply create a "child page" to our current project page to begin. Or if you're still in the brainstorming phase, post a blog and invite others you know working in the field to participate online.
Create a "child page" to add a new project about Toxoplasma.
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.