Research Areas for Medicinal Chemistry
Faculty Research Areas
Heparan Sulfate Proteoglycans: Biosynthesis, Structures and Functions
In the post-genomics era, it is now accepted that complex glycoconjugates such as proteoglycan regulate numerous patho-physiological processes in all living species. They carry enormous structural information in terms of sulfation, epimerization, domain organization, chain length, number of chains and type of chains along with their core proteins. Production of proteoglycans with such high complexity occurs in template-independent fashion seamlessly, yet our understanding of their biosynthesis, structures and functions is somewhat incomplete and imperfect. We are developing a wide variety of chemical biology tools to define the biosynthetic pathways of heparan sulfate and related glycosaminoglycans (GAG) such as chondroitin sulfate and dermatan sulfate.
Chemical probes for visualizing PTP activity
Protein tyrosine phosphatases (PTPs) play critical roles in cellular signaling, regulating tyrosine phosphorylation through hydrolysis of the tyrosine phosphate in a temporally, spatially and regioselectively controlled manner. In contrast to their counterparts, the protein tyrosine kinases (PTKs), the substrate selectivity, biological regulation and specific roles of PTPs are relatively poorly understood. However, aberrant phosphotyrosine-dependent cellular signaling plays an important role in many human diseases, including cancer, diabetes and autoimmunity. PTK-targeted drugs have hit the market with considerable success as anticancer agents, but no PTP-targeted drugs have been developed to date. In this project, our aim is to develop novel PTP-targeted chemical probes that can be used to elucidate the biological roles of PTPs and can serve as lead compounds in the development of PTP-targeted therapeutics. For example, we designed the phosphocoumaryl amino acid pCAP as a fluorogenic phosphotyrosine mimic. This probe has been invaluable in allowing us to profile the substrate selectivity of PTPs, perform several high-throughput screens to identify novel PTP inhibitors, and visualize PTP activity both directly in cells and in cell lysates through polyacrylamide gel electrophoresis. Current work includes characterizing and optimizing the new inhibitors we have discovered and developing novel activity-based probes for PTPs.
Understanding the biological action of metal-based drugs
While the majority of drug molecules are organic compounds, several very successful drugs contain metal ions. Certainly the most well-know (and well-studied) example is cisplatin, a platinum containing anticancer agent, but other examples include auranofin, a gold-containing antiarthritic agent; Pepto-BismolÂ®, a bismuth-containing treatment for gastrointestinal problems; and imaging agents such as magnevist (a gadolinium-based MRI contrast agent) and cardiolyte (a technetium-based radioimaging agent). In our lab, we have been studying the ability of auranofin and auranofin analogs to inhibit enzyme activity as one possible mechanism of action in the body. Au(I)-based compounds such as auranofin inhibit thiol-dependent enzymes, and we have demonstrated that, by tuning the ligands bound to the Au(I) ion, we can tune the selectivity and potency of the Au(I)-mediated inhibition. The relative potencies and selectivities of the new complexes hold up not only in vitro but also in vivo.
Designing redox sensors
A recent area of emphasis for our lab is the development of fluorogenic chemical probes that can be used to image the production of redox active species in vivo. Our first efforts in this field are aimed at developing hydrogen peroxide sensors that can be delivered to a specific subcellular location (i.e. the cell surface, the cytosol, the mitochondria, etc.) and at developing hydrogen sulfide sensors based on fluorogenic organometallic compounds.
The long-term goal of our research is design and development of digital therapeutics (mobile medical apps and videogames) which integrate non-pharmacological interventions with pharmaceutical drugs. Since mobile apps and videogames have become FDA-approved software as medical device, we aim to develop drug-device combination products targeting a specific chronic disease at both molecular and behavioral levels.
Why do we focus on developing digital therapeutics? Because:
They can mitigate limitations of pharmaceutical drugs (adverse effects, non-adherence, drug-resistance, affordability, shortages)
Mobile app-based treatments can improve sustainability of health care by delivering self-care and promoting prevention of chronic medical conditions
Digital transformation in medicine and health care has been happening.
Our research has advanced development of neuropeptide-based drug leads for the treatments of epilepsy and pain. This collaborative project with Prof. Steve White and Prof. Cameron Metcalf yielded several galanin-based lead compounds such as NAX 505-5, NAX 409-9 and NAX 810-2 (a candidate for Investigational New Drug (IND) for the treatment of epilepsy). Noteworthy, our galanin-based compounds also exhibit analgesic properties, offering opportunities to develop first-in-class therapies for inflammatory and chronic pain.
The people in our lab use and develop molecular dynamics, free energy simulation, and trajectory analysis methodologies in applications aimed at better understanding biomolecular structure, dynamics and interactions. A strong focus of our funded efforts centers on the reliable representation of nucleic acid systems (DNA and RNA) in solution. For example, we helped solved the NMR structure of the drug-bound Hepatitis C virus IRES structure shown on the left. Based on this (and related structures), we can now apply CADD methods and simulation to better understand and design potential new Hepatitis C therapeutics. In addition, large efforts are underway to better characterize RNA structure and force fields through simulation of a large number of commonly observed RNA structural motifs and a large variety of NMR and crystal structures. We are also involved with international collaborative efforts to understand DNA structure, for example through the ABC consortium and long simulations of DNA...
Critical to reliable representation of the structure, dynamics and interactions is not only trying to simulation the biomolecules in their native solution environment but to also both critically assess and validate the simulation results with experiment. Our group focuses on both brute-force and enhanced sampling/ensemble-based simulation using available high performance computational resources at the University of Utah (www.chpc.utah.edu) and elsewhere. Outside resources include large allocations of computer time from Blue Waters, XSEDE (www.xsede.org), on the Anton machine at PSC and from other sources. With these resources we also are able to expose and overcome limitations in the methods and force fields...
Beyond nucleic acids, we are also interested in various coiled-coils, enzymes and cytochrome P450's. A key emphasis is on improving stability or understanding how ligands alter receptor structure upon binding. Also, in addition to continued development of the ptraj/cpptraj tools within the AmberTools suite for analysis of MD trajectories, we are exploring methods to mine more information from the simulation data and means to more broadly disseminate the MD results.
RNA Structural Biology
My laboratory is involved in the study of nucleic acid and protein structure using high-field NMR spectroscopy. We have recently developed a structure-based drug design program focused on discovering and optimizing small molecules that interact with biomedically relevant RNA targets. NMR spectroscopy is uniquely suited to solving the 3D structures of RNA domains in complex with inhibitor molecules, and NMR also is a unique tool for identifying lead compounds that only interact weakly with macromolecules. The University of Utah has an outstanding biomolecular NMR facility with 500, and 600 MHz instruments locally, and access to 800 and 900 MHz instruments at the University of Colorado.
Hepatitis C virus (HCV) infection is a major cause of liver cancer in the US and liver disease associated with HCV accounts for the majority of liver transplants. In the developing world, a high percentage of HIV patients are also co-infected with HCV, presenting a particularly challenging health problem. The 5’ untranslated region of the HCV RNA genome contains a large structured domain that serves as an IRES (internal ribosme entry site) that enables 5’ cap independent RNA translation. The IRES of HCV is an attractive therapeutic target since it is crucial for HCV replication. The RNA has a well-defined structure, raising the possibility for developing targeted therapeutics against HCV.
Our laboratory has solved the structure of a functionally important domain of the HCV IRES RNA in complex with an inhibitor of viral replication. Current research in the laboratory involves using NMR to screen for additional inhibitors that bind this target. We are also using NMR for a structure-based drug design initiative aimed at developing next-generation inhibitors with improved potency. The structure based design project is multi-disciplinary, with a computational chemistry component in collaboration with the Cheatham laboratory, and a synthetic chemistry initiative in collaboration with the Rainier laboratory.
Left) Superposition of NMR structures for a domain of the hepatitis C virus internal ribosomal entry site RNA complexed with an inhibitor. Right) Correlation of experimental CH residual dipolar coupling NMR restraints. Open circles are calculated values of the free RNA plotted against the experimental RDC values of the complex, showing that the free RNA does not fit the experimental data, while closed circles are for the inhibited structure indicating a good fit with experiment.
The eukaryotic genome is regulated by a variety of epigenetic mechanisms that establish and maintain proper gene expression profiles to control cell identity and fate. One of these vital mechanisms is accomplished by chromatin, which is the packaging medium for genomic DNA. The chromatin polymer consists of individual nucleosomes in which the DNA is wrapped around an octamer of the canonical histone proteins H2A, H2B, H3, and H4. The histone proteins are highly post-translationally modified, and these modifications (PTMs) have an impact on the local chromatin environment through both direct biophysical perturbations and recruitment of downstream effectors. Different PTM chemotypes (e.g., methylation, acetylation, ADP-ribosylation) at different sites within the histones act as dynamic signals to delineate specific chromatin states. Thus, far from being a passive scaffold for the genome, chromatin actively controls access to the underlying genetic material to aid in regulating transcription, translation, and repair. Importantly, when histone PTMs and other epigenetic factors are disrupted, these processes are misregulated leading to diseases such as cancer and developmental disorders.
Our lab and others are trying to understand how the deposition, removal, and recognition of these PTMs are regulated and what downstream effects these PTMs have on DNA-mediated processes. In particular, our focus is studying how metabolism is linked to genomic regulation via the metabolites that fuel chromatin dynamics. We seek to elucidate mechanisms by which the metabolic state of the cell (e.g., acetyl-CoA level) is reported to the genome via chromatin (e.g., histone acetylation) to lead to changes in DNA transcription, translation, or repair. To do so, my lab will utilize a range of techniques across organic chemistry, peptide/protein chemistry, biochemistry, and molecular and cell biology.
Some project areas include 1) biochemical and in cell characterization of mechanisms by which the histone deacetylases called sirtuins sense and report on cellular metabolism, 2) development of fluorescent sensors for metabolites and histone post-translational modifications (PTMs) for obtaining detailed metabolite/PTM profiles in live cells, 3) investigation of NAD+ and ATP dynamics during the DNA damage response, and 4) characterization of mechanisms for the subnuclear localization of metabolic enzymes and development of strategies to target this localization.
DNA-encoded libraries: Streamlining drug discovery
One of the key steps in developing a new drug is to identify molecules that bind to a putative therapeutic target. However, there is a near-unlimited number of possible molecules and to identify the right one is a formidable challenge.
One approach to achieve this goal is to tag compounds with DNA strands whose sequence encodes for the structure of each compounds. In this way it is possible to use target proteins immobilized on surfaces as baits to fish for compounds that bind to this protein. Sequencing the attached DNA codes then allows to identify the corresponding molecules. In fact, this approach provides a semi-quantitative estimation of the target affinity of each compound in the library.
Such DNA-encoded libraries are nowadays used routinely in drug discovery at pharmaceutical companies. However, the prospect of this method remains largely untapped in academic medicinal chemistry efforts because of the costs associated with generating large library platforms and the validation of multiple hit compounds. We aim to overcome this problem by generating libraries that are structurally designed with specific protein families in mind. In this way, we can achieve consistent screening success at a fraction of the costs of large one-fit-all DNA-encoded library platforms.
Using such libraries, we were able to discover high potency hit compounds for several enzymes with speed and cost-efficiency unachievable by conventional methods. In parallel, we aim to further our understanding of how to synthesize and design such library and to develop algorithms for extracting important structural data from such library screens.
Dissociative Bioorthogonal Chemistry: Activating drugs and probes on demand
Reactions between non-biological reagents that occur readily in biological systems without being disturbed by it are called bioorthogonal. Numerous bioorthogonal reactions have been developed with a focus on reactions that link two molecules together. Although less well established, bioorthogonal reactions that dissociate and release a molecule could find widespread applications in molecular tools for biological research, the development of diagnostics, and the design of innovative therapeutics.
A key focus of the Franzini group is the development of such reactions that can release molecules inside cells or living organisms. Reactions thus discovered will then be applied to the development of tools to study cellular processes and new targeted therapeutics for cancer therapy.
Marine microbiology and marine biotechnology
Marine Invertebrate symbioses: Well known for in-depth studies of marine invertebrate symbioses, particularly the association between the bryozoan Bugula neritina and its symbiont Endobugula sertula, which produces the anticancer bryostatins to protect the bryozoan’s offspring from predation. Due in large part to our work, this is now the best-understood example of a marine chemical defense symbiosis. More recently, demonstrated that shipworm symbionts, in addition to their known nutritional role, also contribute bioactive secondary metabolites to the association.
Iron acquisition by marine bacteria: Long term collaboration with Alison Butler of UC Santa Barbara on siderophores, molecules used in iron binding and transport, in marine bacteria. Established the prevalence of a new class of amphiphilic siderophores typical in marine bacteria.
The main focus of our research group is the study of marine natural products and their biological activities. In particular our group has extensively studied the chemistry of marine invertebrates such as sponges and ascidians. These organisms have proven to be a prolific source of diverse chemical structures with potential anticancer use.
Our research focuses on the isolation and structure determination of compounds from marine invertebrates, the detection of their effects on biological systems, and the characterization of their mode of action and structural determinants contributing to their biological activity. Our emphasis on organisms from tropical reefs is based on the hypothesis that competitive environments select for potent biological activities. Reefs are highly diverse ecosystems that are subject to a variety of selective mechanisms such as predation, fouling by microorganisms, and limited benthic substrates for settlement of sessile organisms. A common strategy for competing in such environments adopted by several organisms that are structurally vulnerable to these pressures is the production or accumulation of chemicals that can be used defensively or offensively.
Although the human body and its pathogens are foreign to a typical marine community, many of the biological pathways implicated in diseases such as cancer, infection, and autoimmune disorders are similar enough to those of competitors in tropical reefs that high potency of biological activity is frequently found in marine natural products. While the ecological roles of most marine natural products are unknown, the high potency and selectivity observed in marine natural products and the observation that structure-activity relationships are often highly optimized in marine natural products suggests that acquiring and maintaining high potency in these systems is a dominant selective pressure acting on their biosynthetic pathways. Add in the fact that marine invertebrates often host diverse and complex microbial communities where invasive disruption on a short time scale is a distinct possibility and that sponges and, to a lesser extent, ascidians have long evolutionary histories among the metazoans and it is no wonder that such potent compounds are to be found in these organisms.
The three main research areas for the Prestwich lab are:
(i) New reagents for phosphoinositide and lysophospholipid signaling in cell biology and cancer treatment.
(ii) Biomaterials for cell therapy, wound repair, cartilage repair, tissue engineering, scar-free healing, and xenograft models.
(iii) Sulfated glycosaminoglycan analogues as inflammation modulators for clinical use.
A recent presentations on the application of clinically-targeted hyaluronic acid derivatives in 3-D cell culture, bioprinting, cell therapy, xenograft models, and anti-inflammatory drugs can be viewed on the BioTime website at www.biotimeinc.com. An overview of the anti-inflammatory glycosaminoglycan projects can be found on the GlycoMira website at www.glycomira.com.
The mission of our laboratory is to understand the origin of chemical diversity, and to apply that diversity to drug discovery and the synthetic biology of new materials to serve human health.
We are funded by National Institutes of Health, Department of Defense, National Oceanic and Atmospheric Administration, National Science Foundation, and others.
Current projects include:
Biosynthesis of natural products in marine animals
RiPP biosynthesis and synthetic biology
Discovery of non-opioid drugs to treat pain
New treatments for infectious diseases
Specialized small molecules produced in nature and often possess a variety of biological activities that can be used toward improving our quality of life. These molecules possess exquisite chemical diversity and are often an inspiration for the development of new pharmaceutical agents. Research in the Winter lab is focused on 1) Elucidating the biosynthetic blueprint that nature uses for assembling secondary metabolites in bacteria and fungi, 2) Manipulating and reprograming biosynthetic systems for the generation of new compounds with enhanced bioactivity, and 3) Exploring the functional roles these molecules serve the producing organism, as well as their impact on the environment. To address these topics, we apply a multifaceted approach in our studies and implement research techniques from molecular genetics, biochemistry, chemistry, bioinformatics, structural biology and bioengineering.
Discovery and development of anti-microbial and anti-cancer agents
As secondary metabolites continue to be an inspiration for drug discovery programs, new chemical entities and molecules possessing novel modes of action are in high demand. Biological pressures can influence the chemical diversity of secondary metabolites and it has been shown that marine-derived microorganisms often produce molecules not observed in their terrestrial counterparts. These microorganisms serve as an ideal resource for drug discovery efforts and for the characterization of novel biosynthetic enzymes. We are specifically interested in marine-derived fungi that produce molecules with anti-microbial and anti-cancer properties. By identifying the corresponding biosynthetic clusters, we can 1) Interrogate the strategies that nature uses for synthesizing and installing unique functional groups responsible for the observed biological activity and 2) Use this information to incorporate new chemical features into existing molecular scaffolds and enhance their inherent biological activities.
In their host organisms, secondary metabolites are assembled and modified by specialized machinery. Often times, the complex structures or chemical modifications instated by these molecular assembly lines are difficult to replicate using traditional synthetic methods, which pose significant challenges when developing pharmaceutical agents or derivatives for testing in biological assays. We aim to develop alternative approaches for producing these otherwise inaccessible molecules or derivatives by 1) Reprogramming the biosynthetic machinery for the production of therapeutic agents with increased biological activities and 2) Develop the individual enzymes that carry out complicated reactions into renewable and environmentally friendly biocatalysts for the chemoenzymatic synthesis or derivatization of new chemical entities.
In addition to studying biologically active molecules, we are also interested in identifying virulence factors in fungi. Many fungi produce mycotoxins which are hazardous to human and animal health and can have devastating effects on food supplies. We are interested in 1) identifying and characterizing mycotoxin-producing clusters from fungal plant pathogens and 2) using this information for the development of antifungal and mycotoxin-detoxifying agents.