Drug Discovery : Targets


Rhinovirus-C Peptide for Development of Vaccines and Antivirals

UW–Madison researchers have identified novel immunogenic peptides from RV-C that are useful targets for therapeutic antibodies.

Recent advances in microscopy enabled the researchers to determine (with atomic resolution) the structure of an RV-C strain, both in its full, infectious form and as native empty particles. The structures highlighted immunogenic surfaces that could be used to design antivirals or vaccines against RV-C.

New Target for Diagnosing, Treating Neurodegenerative Diseases

UW–Madison researchers have demonstrated that neurofilament tangles lead to subsequent degeneration and death of motor neurons in ALS patients. They also discovered that these tangles are caused by the reduced expression of a type of neurofilament mRNA. Thus, neurofilament regulation appears to be a promising target for drug screening and gene therapy.

The researchers conducted their studies using motor neurons derived from ALS patients.

Increasing Red Blood Cell Production

UW–Madison researchers have developed a method for increasing the production of red blood cells by knocking down certain components of the exosome (a protein complex inside cells that degrades RNA). Specifically, the new method uses an siRNA, ribozyme or other inhibitory nucleic acid molecule to decrease the expression of Exosc8, Exosc9, Dis3, Dis3L or Exosc10.

Knocking down these exosome components boosts genes and proteins that promote red blood cell development.

New Peptide-Mimicking Compounds for Anti-Cancer PET Imaging

UW–Madison and USF researchers have developed a new class of RGD mimetic compounds called γ-AApeptides that specifically target tumor integrin αvβ3 and resist being degraded. The γ-AApeptide tracers mimic the structural and functional properties of natural peptide-based tracers but with significantly improved stability.

New Antimicrobials for Treating Bacterial Infection and Contamination

UW–Madison researchers have developed a lead compound and synthetic analogs that represent a new class of antimicrobial weapons.

The researchers identified a new family of small molecules from a high-throughput screen that are inhibitors of bacterial cell division. These compounds are toxic to a range of Gram-negative bacteria, including Escherichia coli, Caulobacter crescentus, Vibrio cholera, Shigella boydii and Acinetobacter baumannii. Compound treatment blocks the assembly and maturation of the divisome in bacteria and leads to the incomplete constriction of the cell division plane. The division process resumes once the compound is washed away.

Novel Candidates for an Improved Tuberculosis Vaccine

UW-Madison researchers have developed four candidates for a live attenuated TB vaccine.  They disrupted regions of the M. tuberculosis genome that are associated with pathogenicity and identified viable but attenuated mutants with disruptions in the ctpV, rv0990c, rv0971c or rv0348 genes.  These mutants may be useful for eliciting an immune response against tuberculosis.

Novel UGM Inhibitors for the Treatment of Tuberculosis and Other Microbial Infections

UW-Madison researchers have identifed a set of novel small molecule inhibitors of UGM that may be useful in the treatment of tuberculosis and other diseases caused by microbial infections. They synthesized a library of 2-aminothiazole derivatives and used a high throughput, fluorescence polarization screen to identify these inhibitors.

The molecules inhibit the growth of microorganisms that depend on UGM to incorporate Galf residues. They also attenuate the virulence of pathogenic microorganisms, such as M. tuberculosis, M. smegmatis and Klebsiella pneumoniae, that rely on UGM.

Novel Poly(A) Polymerases that Interact with Nuclear Phosphoinositide Signaling Molecules

UW-Madison researchers have identified novel PAPs that interact with phosphoinositide signaling molecules. These new PAPs, called phosphatidylinositol phosphate (PIP)-PAPs, provide a new nuclear regulatory mechanism, and therefore a new means of controlling and regulating protein expression. Unlike known PAPs, the activity of these PIP-PAPs may be directly modulated by components of phosphatidylinositol-based signaling pathways, which play crucial roles in the regulation of cell processes at the plasma membrane and in the nucleus.

The first of these PIP-PAPs to be identified is the Speckle Targeted PIP kinase alpha Regulated (Star)-PAP. Altering the expression of Star-PAP affects a set of over 300 genes, many of which encode proteins that are important in oxidative stress pathways that modulate diseases, including neuronal disease, cardiovascular disease, stroke and pulmonary disease.

HPV-Positive Biomarkers for Cervical and Head and Neck Cancers

UW-Madison researchers have identified three potential biomarkers that are specific for HPV-positive cancers in cervical and head and neck tumors: testicular cell adhesion molecule 1 (TCAM1), synaptonemal complex protein 2 (SYCP2) and stromal antigen 3 (STAG3).  These biomarkers can be used to detect cervical or head and neck cancer.  TCAM1 and SYCP2 also can be used to detect precancerous lesions.

TCAM1, SYCP2 and STAG3 are testis-specific human genes.  The inventors have shown that mRNA from these genes is expressed in HPV-positive head and neck and cervical cancers but cannot be detected in normal somatic tissues or HPV-negative head and neck cancers.

Additionally, the TCAM1 protein likely is expressed on the cell surface, which would make it an accessible, easily-assayed biomarker for HPV-positive cells in cancers and precancerous lesions.  TCAM1 also may provide a useful target for therapies against HPV-positive cancers and precancerous lesions.

Novel Antimicrobial Compounds

UW-Madison researchers have developed a method for identifying potential antibiotic compounds that block the association of bacterial SSB with a target protein. The inventors determined—for the first time—the high-resolution structure of the E. coli SSB segment bound to Exonuclease I, a target protein. They used this structure to develop a rapid fluorescence polarization method for measuring SSB-Exonuclease I binding in solution. This method was then used to identify small molecules that inhibit the interaction between bacterial SSB and its target proteins.

Because of the importance of protein interactions with SSB for bacterial viability and the high conservation of the SSB protein binding sequence across bacterial species, these molecules have potent broad spectrum antibacterial properties. Because the SSB peptide sequence is not found in human and other eukaryotic SSBs, these small molecules are also likely to be non-toxic to human cell lines. Together, these features make these compounds excellent candidates for novel, broad spectrum antibiotics.

Treating Cancer by Inhibiting the Interaction of MAGE Protein with KAP-1

UW-Madison researchers have developed a method of treating cancer by interfering with the binding of MAGE proteins to KAP-1. The method involves administering a substance, such as a monoclonal antibody, to cancerous cells that express the MAGE protein. The substance inhibits the formation of the MAGE/KAP-1 complex, for example, by blocking the binding of MAGE to KAP-1. Alternatively, the antibody binds to the complex and interferes with its function. This invention also includes a method of screening for a substance that inhibits the formation of the MAGE/KAP-1 complex. 

Stem Cell Marker for Breast Cancer

UW-Madison researchers have discovered that the low density lipoprotein receptor related protein LRP5 is a cell surface marker for somatic mammary stem cells and mammary tumor stem cells. LRP5 helps initiate signaling by the Wnt family of secreted lipoproteins. Wnt signaling plays a significant role in normal mammary gland development and is also the most common source of tumor initiation for human epithelial tissue. Adult female mice that lack LRP5 lack ductal stem cells in their breast tissue, showing that although the loss of Wnt signaling does not affect breast tissue grossly, it dramatically changes the growth potential of the tissue. Inhibiting LRP5 greatly interferes with the ability of ectopic Wnt signaling to initiate and maintain tumors.

Global Regulator of Morphogenesis and Pathogenicity in Dimorphic Fungi

UW-Madison researchers have identified strains of dimorphic fungi that are useful in vaccine development because they do not become virulent, along with a method of identifying compounds that prevent dimorphic fungi from becoming virulent. The researchers discovered that the fungal histidine kinase is responsible for the transformation of these organisms into virulent yeast. Knocking out or otherwise inactivating the histidine kinase gene results in a fungal strain that does not become virulent.

To determine if a test compound may be useful as an anti-fungal therapeutic, it is exposed to the fungal histidine kinase. Because histidine kinases play a key role in the ability of many fungi to sense and respond to environmental changes, compounds that reduce the activity of the kinase may be used to prevent or treat infection with pathogenic fungi, including dimorphic fungi.

Protein Inhibitor of Ran Activity

UW-Madison researchers have identified a specific inhibitor of Ran activity. They discovered that the encephalomyocarditis virus leader protein, a small protein with no measurable enzymatic activity, binds directly and specifically to Ran. Expression of this leader protein in human cells inhibits Ran activity, blocking nuclear export of cellular mRNAs and leading to reduced translational activity.

Vaccine Candidates Against Johne's Disease

A UW-Madison researcher has developed potential vaccine candidates for Johne’s disease. The disease is caused by the slow-growing bacterium Mycobacterium avium subspecies paratuberculosis, or M. paratuberculosis. The inventor identified several Mycobacterium strain-specific genes that may contribute to the pathogenicity of M. paratuberculosis. These genes could be used to design vaccines against pathogenic subspecies of M. avium, including M. paratuberculosis. In a recent study, vaccine preparations based on these sequences helped protect rodents against infection with M. paratuberculosis.

Production of Packaged DNA Sequence

UW-Madison researchers have developed a method for packaging the full papillomaviral genome into HPV virions in transfected mammalian cells, making easy and efficient generation of infectious HPV possible for the first time. A DNA sequence containing a full-length or nearly full-length papillomaviral genome is selected and preferably cloned and amplified in an appropriate plasmid. The genome sequence is then isolated from the plasmid and recircularized before it is co-transfected with an HPV capsid sequence into a suitable mammalian cell. Finally, the resulting infectious viral particles are purified. Either the papillomaviral genome or the HPV capsid sequence may be modified before packaging.

Synthetic Cofactor Analogs of S-Adenosylmethionine as Ligatable Probes of Biological Methylation

UW-Madison researchers have developed compounds and methods for specifically labeling the substrates of SAM-dependent methyltransferases. The methods use SAM analogs that have been modified at the C5` position so the analog is transferred by the methyltransferase to a methylation site in a substrate, such as a peptide or nucleic acid. Once anchored to the substrate, these cofactor analogs allow for the addition of a detectable and/or isolable label. The label may contain various moieties that aid in determining the methylation state of the substrate. The SAM analogs can also be used with nucleic acid methyltransferases to allow for the rapid identification of specific DNA or RNA residues that are typically methylated.

Method for Preventing or Treating Cardiac Hypertrophy

UW-Madison researchers have developed a method for preventing or treating cardiac hypertrophy. Contrary to what was previously thought, the researchers discovered that inhibiting the retinoic acid (RA) signaling pathway reduces cardiac hypertrophy and benefits cardiomyopathy patients. To prevent or treat cardiac hypertrophy, the level of retinol-binding protein (RBP), retinoids, or an affiliated signaling pathway is reduced or inhibited through dietary, genetic, protein-based and/or pharmacologic approaches.

Stearoyl-CoA Desaturase 4 Gene

UW-Madison researchers have developed a fourth SCD gene in mice that is expressed mainly in heart tissue. They identified and characterized a cDNA corresponding to mouse SCD4, which synthesizes most of the monounsaturated fatty acids in the heart. Studies suggest that SCD4 is regulated by leptin and carbohydrates. In addition to the SCD4 gene and protein, the researchers also have developed antibodies to SCD4 and genetic constructs, cells and transgenic animals containing the SCD4 gene.

Assay to Detect Viral Uncoating

UW-Madison researchers have developed a cell-free system for studying the viral uncoating mechanism. This system uses a sub group of avian sarcoma and leucosis virus (ASLV-A) as a model retrovirus. The TVA receptor for ASLV-A is incorporated into the human cell line 293. After ASLV-A enters the 293 cells and accumulates in the cell’s endosomes, the cells are lysed. The virus-containing endosomes are isolated under conditions of high pH, which block entry of the virus into the cytosol, providing a cell-free system for studying uncoating. Conditions can then be altered to determine the effect of various agents on viral uncoating and other post viral envelope-endosome fusion events. Experiments have shown that the viral nucleic acid released from the endosomes is competent for reverse transcription, and that viral DNA synthesis is dependent on cellular factors contained in the S100 or S10 fraction of the 293 cell line.

Compositions and Methods for Regulating mRNA Transcription and Translation

This technology provides novel nucleic acid constructs encoding the cardiovirus 2A polypeptide operably linked to a promoter. When expressed in mammalian cells, in the absence of any other viral proteins or genes, protein 2A localizes to the nucleolus, binds to ribosomes, and inhibits cap-dependent mRNA translation, effectively preventing the translation of anything that is not a viral protein. Because cardiovirus protein 2A does not inhibit cap-independent IRES-driven mRNA translation, the result is a net increase in IRES-dependent protein expression relative to cap-dependent protein expression.

Macrolide Analogs and Methods for Analyzing Them

A UW-Madison researcher has developed methods of identifying macrolide analogs capable of unregulated inhibition of actin filament dynamics. For the methods, F-actin is contacted with a candidate macrolide analog to determine if the candidate compound inhibits actin filament dynamics. The candidate compound should be able to sever F-actin and cap the resulting F-actin positive and negative ends to prevent subsequent G-actin incorporation. In addition, the severing and capping activities should be independent of physiological cues. Several macrolide analogs were identified using these methods.

Sterol Carrier Protein-2 from the Mosquito, Aedes aegypti

UW-Madison researchers have developed polypeptides and polynucleotides from AeSCP-2, a sterol carrier protein that can transport cholesterol in mosquitoes. AeSCP-2 is developmentally regulated and highly expressed in the gut. These AeSCP-2 sequences may be used in the discovery and development of insecticides.

Methods for Identifying Agents That Regulate Chromosomal Stability, Gene Activation and Aging

UW-Madison researchers have developed compositions and methods for identifying agents that affect chromosomal stability and aging. They identified a novel acetyl-ADP ribose compound, O-acetyl-ADP ribose, as the primary product of the histone deacetylase reaction catalyzed by SIR2 proteins. This compound plays a pivotal role in cell cycle control. O-acetyl-ADP ribose and antibodies that specifically recognize it, along with methods for quantifying it, can be used to screen for agents that inhibit or enhance histone and non-histone deacetylation, and may therefore modulate age-related disease, such as diabetes and cancer.

Estrogen-Related Receptor Gamma, a Breast Cancer Biomarker and Target for Treatment

UW-Madison researchers have developed methods for using ERR-gamma as both a breast cancer biomarker and a target for treatment. As a biomarker, it provides a method of determining a patient’s breast cancer prognosis. Expression levels of ERR-gamma are analyzed along with the status of other genes related to breast cancer to help breast cancer patients and their doctors make treatment choices. A high level of ERR-gamma in breast cancer cells indicates good prognosis and a high likelihood of being sensitive to hormonal blockade therapy such as tamoxifen therapy. The receptor also provides a target for treating breast cancer, which involves decreasing the activity of ERR-gamma in breast cancer cells.

Common Variants of the Sodium Channel Alpha Subunits

UW-Madison researchers have identified four groups of SCN5A variants that represent the most common SCN5A variants in humans. The researchers found that none of the three previously known SCN5A clones represented a common sequence for SCN5A. The new SCN5A variants, on the other hand, have been observed in hundreds of individuals. Thus, they provide the true reference or background sequences for evaluating the normal functions of the sodium channel. They are also the true reference sequences against which the effects of various SCN5A mutations should be judged.

The researchers have put the four full constructs into appropriate expression vectors. They also have created mammalian cell lines that stably express each of the channels.

Marker Sequences for Liver and Other Cancers

UW-Madison researchers have identified polypeptides whose expression is upregulated in liver tumor cells and cells from pre-neoplastic foci in liver tissue. These polypeptides may be overexpressed in tumor and pre-neoplastic cells in general; the researchers have so far demonstrated their overexpression in human breast, colon and kidney cancer cell lines, in addition to liver tumors.

Liver Tumor Marker Sequences

UW-Madison researchers have developed novel polypeptides and nucleic acids that are differentially expressed in liver tumors relative to normal liver tissues. The researchers initially isolated these sequences by using representational difference analysis (RDA), and then cloned the entire coding region of the genes. One polypeptide they identified is CRG-L1, which includes seven putative transmembrane domains. CRG-L1 is over-expressed in liver tumors, but expressed at fairly low levels in normal liver tissues.

Receptor For Bacillus anthracis Toxin

UW-Madison researchers have now provided the structure and sequence of the anthrax toxin receptor. The complete receptor includes an extracellular domain, a transmembrane domain and a cytoplasmic domain that can vary in length.

Identification of the sequence of the anthrax toxin receptor (ATR) will enable the detection and quantification of ATR mRNA and protein in a sample, and will also allow the generation of transgenic and knockout animals. This should lead to methods for treating human and non-human animals suffering from anthrax. For example, the inventors have demonstrated the therapeutic effectiveness of this invention by showing in tissue culture models that a soluble form of the receptor can block anthrax toxin by acting like a decoy.

Method for Preventing Superoxide Damage to Cells and Oxygen-Labile Proteins

UW-Madison researchers have developed a method of protecting cells and oxygen-labile enzymes from oxidative damage. YggX is a protein identified from Salmonella enterica serovar Typhimurium. Elevated levels of the YggX protein increase the resistance of Salmonella enterica to superoxide stress and reduce damage to its DNA. Also, when high levels of this protein are present in the cell, enzymes that are normally susceptible to oxidative damage remain active. Engineering cells to overexpress the YggX protein or its homolog renders the cells more resistant to oxidative damage. The YggX protein or its homolog could also be used to protect an oxygen-labile protein from superoxide damage by co-expressing YggX with the oxygen-labile protein.

Plasmid DNA from Yersinia pestis, the Causative Agent for Bubonic Plague

UW-Madison researchers have developed the complete DNA sequence of three virulence plasmids, pPCP1, pMT1 and pCD1, from Y. pestis. The open reading frames (ORFs), or protein coding regions, of the plasmids have been determined. The plasmid pPCP1 contains genes encoding plasminogen activator/coagulase and pesticin, a toxin that inhibits the growth of closely related bacteria. In the plasmid pMT1, 115 of the potential ORFs likely encode proteins, including seven new potential virulence factors. The plasmid pCD1 encodes a complex virulence property called the low calcium response (LCR). The sequence information will enable diagnostic, prophylactic, and therapeutic tools to be developed for use in combating Y. pestis.

Methods and Materials for Assaying Non-SCD1 Isoforms

UW-Madison researchers have developed useful tools for the discovery of SCD inhibitors. The invention consists of cDNAs for murine SCD2 and SCD3 and human SCD5, along with a stable mammalian cell line and yeast strain that express human SCD5. In addition, the invention includes SCD2, and SCD3 knockout and transgenic mice, as well as the targeting constructs used to generate the SCD1 and SCD3 transgenic mice.

Mouse Strains and Cells Useful to Investigate Tissue-Specific Roles of Stearoyl-CoA Desaturase Isoforms

A UW–Madison researcher has developed several mouse strains and cells useful in the study of SCDs.  To understand the tissue-specific role of SCD1 and other SCD isoforms in disorders such as obesity, diabetes, cancer, inflammation, atherosclerosis and metabolism, the researcher generated mice with tissue-specific knockouts of SCDs.  He also developed transgenic mice in which SCDs can be overexpressed in specific tissues.

Method to Screen for Novel Antibiotics

UW-Madison researchers have developed an indicator strain of Bacillus subtilis, which can detect potential antibiotic compounds that inhibit cell wall biosynthesis. This reporter strain includes the vancomycin-inducible VanA operon, which is responsible for a major form of inducible resistance to glycopeptide antibiotics, operably linked to a reporter gene.

To screen compounds for efficacy as antibiotics, a test compound is exposed to the strain. The effects of the compound on the indicator strain’s growth, as well as the presence or absence of the reporter gene product are observed. If the reporter gene product is present and growth of the indicator bacterial strain is inhibited or reduced, then the compound likely inhibits bacterial wall synthesis and is a potential, new antibiotic compound.