The Finn Research Laboratory - Research
 
At the core of our efforts is an appreciation for the mechanisms of chemical reactivity and the power of molecular biology to create useful tools for chemists, chemical biologists, and materials scientists. Below you will find brief descriptions of our current projects and links to representative papers in those areas.
Combining Molecular Biology with Chemistry: Viruses as Molecular Building Blocks

About 10 years ago, we helped pioneer the use of organic chemistry techniques to modify virus particles, and we have parlayed those capabilities into a wide variety of applications.  Our most commonly used particles are currently the capsid and . The former is expressed in large quantities in E. coli cells as a non-infectious virus-like particle, whereas the latter is grown in pea plants. Both particles are highly stable toward extremes of pH, temperature, solvent composition, and reagents, allowing them to be modified by a variety of chemical reactions.

Virus particles are many times larger than almost all products of synthetic chemistry, and many times smaller than most cells. But they are not so large as to be out of reach of chemical techniques, and they are large enough to present surfaces of biologically relevant size to cells and tissues.Combining organic chemistry and molecular biology to create and modify these particles is extraordinarily powerful. Viruses are also highly regular structures, presenting multiple copies of identical functionality on their external sand internal surfaces.

Dendrimers, polymers, metal; nanoparticles, and cells all have some of these qualities, but viruses are unique: no other entities of comparable dimensions are available with structures known and controllable to atomic resolution. Such well-defined polyvalency is crucial to the biological function of viruses and of critical importance to our efforts to use them in many different applications. Shown here are CPMV particles with inserted cysteine residues (red dots) providing attachment points in different patterns.

At the present time, research is on going in the following areas:

Chemical Fundamentals: New methods of , including the use of enhancing particle stability; learning the chemistry of new viruses particles.

Polyvalent Presentation to Biology: Attachment of biologically active compounds, from to and exploration of their . This work includes the display of , peptides, and drug molecules, and with cellular receptors and tissues. At the right is a representation of a cryo-EM reconstruction of transferrin molecules attached to the surface of the Q particle, making a nanostructure that is taken up by cancer cells with remarkable efficiency. Especially important in current projects is the display of  on the surfaces of virus-like particles, in order to bring new functions and attachment points to these scaffolds.

Immunology: Virus particles are naturally immunogenic and have been used for many years as antigens or carriers for antigenic molecules. To this field we have added the idea that benefit in similar ways from being displayed on , and we are exploring a variety of systems with immunology collaborators. Our emphasis is on anti-cancer and anti-bacterial vaccine development.
Catalysis: We have developed a practical method for the preparation of Q virus-like
particles . When packaged in this way, the enzymes are highly active when their substrates and products can diffuse through the capsid shell, and are protected from denaturating and hydrolysis by proteases. This technology, represented in cartoon form at the right, is quite general, which creates opportunities for interesting reaction cascades and therapeutic applications.
Nanoparticle Assemblies and Materials Science:  The marriage of biological nanoparticles with aqueous-compatible methods of polymer synthesis allows us to prepare highly monodisperse particles with . One can also attach moieties to virus particles that mediate their into higher-order structures. Our goals in include applications to immunological shielding, light harvesting, catalysis, and molecular sensing.
Selection and Evolution: Creation of virus libraries selection for function, retaining the property of high expression yields. 

Our collaborators, with whom we greatly enjoy working, include:
(UCSD) – virus targeting to cells and tissues
(Scripps) – anti-HIV vaccine development
(Michigan State) and (UC Irvine)
– vaccines against tumor-associated carbohydrate antigens
(Technische Universität Munich) – cell targeting with integrin-binding ligands
(Scripps) – polyvalent probes of immune cell binding
(Scripps) – anti-bacterial immune response, vaccine development
(Scripps)

Synthetic Methods and Click Chemistry

As originally defined by Kolb, Finn, and Sharpless, click chemistry involves the use of only the most reliable, general, high-yielding, and byproduct-free organic reactions for the construction of compounds with desired function. Its central hypothesis is that most, if not all, chemical functions can be attained by many different compounds among the nearly limitless possibilities of three-dimensional structural space. If you restrict yourself as much as possible to using only the best reactions, more diversity will be accessible, since your reactions work with a wider variety of pieces. One stands a better chance, therefore, of finding functional molecules this way, although they will not look like the compounds made by nature for the same purpose. To appreciate the possibilities, synthetic chemists might ask themselves “what if every bond connection worked flawlessly, regardless of the structure of the connecting pieces?” Others, non-practitioners of the synthetic arts, might wonder what would be possible if molecules of any desired shape or pattern of functional group display were available without much trouble? We are not yet close to such ideals, but the concept is powerful and enabling.

Click reactions usually use high-energy (“spring-loaded”) reagents with well-defined reaction pathways, giving rise to selective bond-forming events of wide scope. Examples include the nucleophilic trapping of strained-ring electrophiles (epoxide, aziridines, aziridinium ions, episulfonium ions), certain limited forms of carbonyl reactivity (aldehydes + hydrazines or hydroxylamines, for example), and several types of cycloaddition reactions. Our efforts using click chemistry include three basic processes.

Cu-catalyzed Azide-Alkyne Cycloaddition: 
This process,by Valery Fokin, Barry Sharpless, and colleagues for solution phase reactions (and by Morten Meldal and colleagues for ), has contributed dramatically to applications in materials science, chemical biology, medicinal chemistry, and many other fields. We have studied its mechanism and developed catalysts for use in demanding cases of . New improvements continue to emerge as we use the reaction with virus particles and other.

Versatile Electrophiles for Bioconjugation and Release: The 7-oxanorbornadienes derived from Diels-Alder cycloaddition of furans and electron-deficient alkynes are an easily synthesized class of compounds that serve as highly reactive electrophiles and interesting cleavable linkages.
In our,we showed them to be about as reactive as maleimides toward conjugate addition of thiols, yet more stable toward deactivation in aqueous solution and able to undergo triggered retro-Diels-Alder cleavage. We are continuing to develop this system and to explore its use in drug delivery and materials science.

Reversible Organic Linkages based on Anchimeric Assistance:
Another highly reliable reaction pattern is the substitution reaction triggered by internal nucleophiles giving rise to high-energy cyclic intermediates. An old example of this type of anchimeric assistance with particularly favorable properties wasby us and the Sharpless laboratory several years ago. Our group is carrying this forward by exploring the of the method and applying it to the synthesis of functional polymers and surfaces.

Medicinal Chemistry

Enzyme Inhibitors: Using techniques of , organic synthesis, and , we are developing small molecule agents against a panel of important medicinal targets. These include thefor control of nicotine addiction, drug transport enzymes for malaria treatment, for AIDS treatment, for autoimmune diseases, and . In addition, we have several projects ongoing with collaborators at Pfizer. These programs provide excellent training for group members in organic synthesis, experience with the principles and applications of medicinal chemistry, and contacts with outstanding laboratories in both industry and academia.  The latter include Professors , , , , , and at Scripps, Professor at UCSD, and Professor and colleagues at Scripps Florida.

  Materials Science
The branch of chemistry most heavily dependent on reactions which meet the click chemistry standard is polymer synthesis. Indeed, the reliability of polymerization reactions and the rich functions of the products were among the original inspirations for the click chemistry concept. The identification of each new click reaction immediately enables the synthesis of novel materials. With each of the synthetic methods described above, we are making new and functional polymeric materials with interesting applications.

These include (shown here are graduate students
Adrian Accurso and Vu Hong demonstrating the strength of one of Adrian’s adhesive formulations), hydrogels for slow release of drug molecules, and biodegradable materials for drug delivery.
Analytical Methods

The binding of two molecules in solution invariably changes the structure, conformation, and solvation states of the solutes. These factors contribute to the overall refractive index of the solution, and therefore binding events always change refractive index. Some years ago, of Vanderbilt University realized this fact and built an instrument capable of detecting changes in refractive index with the necessary sensitivity. The technique, known as backscattering interferometry (BSI), requires a simple laser-based optical train and is done at room temperature using small amounts of analytes in a microfluidic channel. We collaborate with the Bornhop group to further develop and apply this technique to biomolecular interactions such as binding, complexation and the binding of to their ligands or inhibitors. BSI is a label-free technique that works with all sizes of molecules under a wide variety of conditions, including serum, cell lysates, and crude membrane preparations. In conjunction with the Bornhop group, we have built a BSI instrument in our laboratory at Scripps. Research is ongoing into the fundamental aspects of the BSI technique as well as in applications to many of the projects described above.