Molecular Interaction Discussion Group

(originally written for the Mount Sinai Grad School Newletter)

If you were one of those people who thought that chemistry was a terrible bore I would fervently urge you, in light of the truly mind boggling advances being made, to reconsider. In the past year, through a biweekly seminar called the Molecular Interactions Discussion Group and through the Department of Structural and Chemical Biology, Sinai has been visited by numerous chemists who have described their work. Of course these talks have the obligate explanation of the chemistry itself – the reaction mechanism, the synthetic logic, reaction efficiencies, etc. – but with that you will be treated to a view of the capabilities of the modern chemist and the structure-of-thought of the chemistry that will certainly change the future of biology. I’d like to highlight a few of the projects as examples and mention how, here at Sinai, you might engage this if you are so inclined.

Forward Chemical Genetics and Development of Fluorescent Chemical Inhibitors

In one of his slides, Dr. Young Tae Chan (NYU: edit:moved to Singapore) shows a graduate student, gloved, masked and goggled, pulling some 96- well plates from the microwave. Next is a picture of the plates under UV light - here and there a well is red or turquoise, green or yellow; each of them glows brightly. Armed with chemical savvy and a microwave, Dr. Chang has literally constructed a combinatorial library of fluorescent molecules, and he uses them ambitiously. By placing his compounds on cells he can immediately identify if they bind to something specifically by the sub-cellular localization. By bathing/feeding model organisms (c. elegans, drosophila, zebrafish) these compounds and watching for a phenotype, Dr. Chang can identify inhibitors to fundamental biological pathways. He can then localize and identify the target quite easily (the molecules glow). He discovers modulators to fundamental pathways and in doing so simultaneously develops chemical inhibitors for these proteins. Did he mention that he also has developed several candidates of RNA-specific dyes - a property for which there is only a single (poorly-constructed, in his opinion) commercial product?

Customizable Synthesis of Peptide-like Molecules of Virtually Unlimited Size (and chemical variability)

A peptide and peptide- analogue chemist, Dr. Kent Kirshenbaum (NYU) uses high throughput synthesis and rational-design to tailor-make peptide and peptide-like molecules. He can choose from side-chain molecules that far exceed the diversity of those present in natural systems and he can also use molecules that will allow him to branch other molecules off of them, enabling him an enviable ability to synthesize molecules of a nearly unlimited combination of size/shape/pH/electric properties. And what does he do with these? He showed us two of his creations. The first folds to resemble a porphyrin molecule suggesting heavy-metal binding. Indeed it binds gadolinium quite nicely and is being developed for use as a gadolinium-delivery-agent, used in MRI to increase contrast (resolution) of the images. The second was a molecule with lipophilic and hydrophilic portions with well placed aromatic residues (needed for coordinating RNA). This ungainly thing can deliver short RNA molecules and efficiently transfect them into a variety of cell types. He also makes much longer polymers for the development of collagen-like fibers for artificial tissue engineering. What does he advise biologists? “The sky is the limit. What are the properties you want in a molecule? Chances are, we can make it.”

Structure-Based Ligand Design

John Koh (U.Del). A synthetic and computational chemist, John combines molecular modeling and synthesis to make some very useful compounds. He works on hormone receptors and can take from the literature the most common mutations of, say, the Androgen Receptor amongst prostate cancer patients who have developed resistance to a particular anti-androgen drug. In these patients, the drug that was supposed to prevent binding of the normal ligand is kicked out because of these mutations. The malignancy is now in danger of growing because persistent administration of the drug has selected for cells containing the mutation, and they are no longer responsive to the drug. Very well. John will model the mutated proteins, conduct molecular dynamic experiments on them including the virtual docking of virtual compounds into the ligand-binding site. He will take the top hits, synthesize them (and variants), and develop compounds that will bind mutant but not Wild Type receptor. By genotyping the malignancy, one can now utilize a drug that interferes with AR signaling only in the tumor! And if it is a different mutation? No problem, there is a different, equally specific, drug in the wings. This sort of structure-based ligand design is the basis of pharmaco-genetics and few people seem to do it as smoothly as Dr. Koh.

Control Ion Channels with Light

Neuroscientists would love to be able to control the opening or closing of channels and [Dirk Trauner] ( of UC Berkeley is making it possible. All of us remember cis-trans conformations from organic chemistry and Dirk exploits a chemical moiety that is sensitive to light to exploit that type of conformational change and use it as a molecular switch. His light-switch prefers the trans-form in the absence of UV light but will switch over (>90% efficiency) to the cis- conformation at a specific wavelength (320nm). This photo-activated switch can be tethered to an engineered cysteine near the ligand- binding pocket and, in a light-sensitive fashion, allow the ligand to bind. Presto! the channel opens. The tool is immediate, reversible, stable, and quick – the switch can be turned on and off as rapidly as 50HZ, reaching the timescale of the ligand bind-release kinetics. In a stunning follow up, this molecular magician used non-engineered tissues (and a different channel type) to demonstrate that he could take tissue from a normal rat and, using a similar technique, induce light- sensitivity in neurons that are not light-responsive. He casually mentioned that… “perhaps there might be some implication for allowing light-sensitivity in individuals whose rods and cones have been destroyed.” Unbelievable.

Although there are even more visiting chemists and more designer molecules with cool tricks – prion-sequestration drugs; synthetic transcriptional modulators; splicing and/or light-activated proteins – I think I should mention that there are some in-house possibilities for incorporating some of the chemical tools these investigators use in our own work/study. Firstly, there is a class run given by the NYU chemistry department, BioOrganicChemistry, which concerns itself with the behavior, shapes, and manipulations/mimicry of proteins, DNA and RNA. If you want just a taste, there are several interesting lectures on similar topics that are part of the BSBB Core III module (Ask when Dr. Arora will be speaking). Also, you are also most welcome to come to the “Molecular Interactions Discussion Group;” talks are usually every other Tuesday at 6:00PM and there is food afterwards.

Lastly, a small plug for our own chemical-biology screening facility. On the 16th floor of the East Building we have a few big machines. For the most part they are robotic arms but they have the ability to read all sorts of light characteristics from plates – florescence emission, polarization, refraction index, etc. – and they are hooked up to a refrigerator housing aliquots of several thousand small molecules covering all of the major organic-chemical motifs found in drugs. You can arrange to use this facility in an assay to screen cellular or in-vitro interactions of your system of interest, anything fitting in a cell-culture plate or a 96 well plate. Hopefully you would be able to discover a good candidate inhibitor of your protein of interest.A website is forthcoming; in the meantime, you can get in touch with Dr. Ming-Ming Zhou to set up a screen.

Chemistry is indeed merging with biology and where the two subjects meet are interesting new fields. The talks mentioned above represent the bleeding edge of some of these fields and, in the name of interdisciplinary cross-talk, it can be very useful to plug into these talks. Hopefully we’ll see some more of you there in the coming months!