- Bio Sciences
- Bio-med Eng.
- Bio-med Sci.
- Chemical Eng.
- Computer Sci.
Dr. Bassaganya-Riera, in collaboration with Dr. Hontecillas, directs the Nutritional Immunology and Molecular Medicine Laboratory(www.nimml.org), a cutting-edge research laboratory that conducts translational research aimed at developing novel therapeutic and preventive approaches for modulating immune and inflammatory responses. The NIMML combines computational modeling, bioinformatics approaches, immunology experimentation, and pre-clinical and clinical studies to better understand the mechanisms of immune regulation and inflammation at mucosal surfaces and ultimately accelerate the development of novel treatments for inflammatory, infectious and immune-mediated diseases. The NIMML has received over $12 million over the last five years to conduct basic and translational research in inflammation and immunity.
Development of Novel Therapies for Gut Inflammatory Diseases. Inflammation is at the core of most human diseases, including chronic, infectious and immune-mediated. In the gut, chronic immune-mediated diseases such as inflammatory bowel disease (IBD) are initiated and maintained by defective immunoregulation. Current therapies against IBD are modestly successful and with significant side effects. Interestingly, about one third of current pharmaceuticals have a natural origin. The NIMML reported for the first time that the botanical compound abscisic acid (ABA) exerts potent anti-inflammatory effects in mouse models of gut inflammation. Our group and others provided evidence in support of a role of lanthionine synthetase component C-like protein 2 (LANCL2) as a putative novel target for the binding and signaling of ABA. LANCL2 has emerged as a promising new therapeutic target against inflammation. We are actively screening compound libraries for their ability to bind to LANCL2 and suppress inflammation. We have recently discovered thatthe bis(benzimidazoyl)terephthalanilides class of anti-inflammatory compounds can also bind to LANCL2 and elicit anti-inflammatory effects. We are currently planning ADME, pharmacokinetic/pharmacodynamic and toxicology studies to develop and improve the oral delivery of this and other classes of compounds.
Development of Novel Vaccines and Immune Therapeutics for gut Infectious Diseases. I am also the Principal Investigator of the Center for Modeling Immunity to Enteric Pathogens (www.modelingimmunity.org) a NIAID-funded $10.6 million Center of the Modeling Immunity for Biodefense program. As a part of this program we will develop novel vaccines and immune therapeutics. Our group has the expertise, tools and know-how of bioinformatics and immunology and a demonstrated track record in pre-clinical and clinical research and product development.
In 2008, Dr. Bassaganya-Riera founded BioTherapeutics, Inc, (http://biotherapeuticsinc.com) a biotechnology company focusing on development of novel anti-inflammatory and anti-diabetic compounds that target the novel LANCL2 pathway.
My research group is fascinated by how our cells make energy. Our research is primarily focused on mitochondria, intracellular organelles responsible for generating most of the body’s energy from food. Dysfunctional mitochondria have been implicated across a number of diseases. We are interested to understand how and why mitochondria become dysfunctional, and then develop therapies that can improve/restore mitochondrial bioenergetics. We primarily study heart disease, although over the last 10 years we have researched mitochondria across many different tissues and pathologies. Our specific approaches include mitochondrial respiration screening assays, high resolution respirometry, and fluorescence imaging.
Development of novel therapies for heart disease: In heart disease and following a heart attack, mitochondrial energy production declines and production of reactive oxygen species goes up. Dr. Brown is co-PI on an NIH R01 grant to study the molecular underpinnings that cause this bioenergetic demise during myocardial infarction. We are particularly interested in how small peptides that target mitochondrial membranes may improve bioenergetics by ‘clustering’ the electron transport chain proteins together.
Development of therapies for Complex I diseases: In both genetic mitochondrial disease as well as common acquired diseases, complex I of the electron transport chain can become impaired. We are helping to develop several coenzyme-Q mimetics that appear to effectively ‘bypass’ dysfunctional components of complex I. These studies include partnerships with several collaborators in industry and NIH small business grants.
The research in my lab involves the application of computational molecular modeling to relate the structure and dynamics of molecular systems to function. Systems currently under investigation include the amyloid beta-peptide that is associated with Alzheimer’s disease and peroxisome proliferator-activated receptor that is associated with inflammation, diabetes, and obesity. We also are initiating projects involving G-protein coupled receptors (GPCRs), and irisin, a recently discovered protein with hormone-like properties. Finally, we are using computational methods to design enzymes, with our strategy being to alter the substrate specificity of existing enzymes.
- Li, M., Liu, P., Wiley, J.D., Ojani, R., Bevan, D.R., Li, J., and Zhu, J. (2014) A Steroid Receptor Coactivator Acts as the DNA-binding Partner of the Methoprene-tolerant Protein in Regulating Juvenile Hormone-Responsive Genes. Mol. Cell. Endocrinol. 394: 47-58.
- Fisher, A.K., Freedman, B.G., Bevan, D.R., and Senger, R.S. (2014) A Review of Metabolic and Enzymatic Engineering Strategies for Designing and Optimizing Performance of Microbial Cell Factories. Comput. Struct. Biotechnol. J. 11: 91-99.
- Yen, J.Y., Tanniche, I., Fisher, A.K., Gillaspy, G.E., Bevan, D.R., and Senger, R.S. (2015) Designing Metabolic Engineering Strategies with Genome-scale Metabolic Flux Modeling. Adv. Genom. Genet. 5, in press.
- Lewis, S.N., Garcia, Z., Hontecillas, R., Bassaganya-Riera, J., and Bevan, D.R. (2015) Pharmacophore Modeling Improves Virtual Screening for Novel Peroxisome Proliferator-Activated Receptor-gamma Ligands. J. Comput.-Aided Mol. Des., in press.
- Lemkul, J.A., Lewis, S.N., Bassaganya-Riera, J., and Bevan, D.R. (2015) Phosphorylation of PPARgamma Affects the Collective Motions of the PPARgamma-RXRalpha-DNA Complex. PLoS One, in press.
Research Drug addiction is a chronic relapsing disorder driven by molecular changes that occur in the brain in response to habitual drug use, and currently available pharmacotherapies have shown only limited efficacy reducing drug use and relapse in addicts. There exists a critical need to identify novel treatments from a more chemically diverse target pool in order to develop effective therapeutics. Accordingly, Dr. Buczynski’s research objective is to identify the novel molecular changes caused by drug exposure and validate their functional role in neurological disorders. This work integrates advanced mass spectrometry platforms with a wide range of techniques including chemical biology, molecular biology, in vivo microdialysis, and behavioral pharmacology. Ultimately, his research program aims to discover novel therapeutics to facilitate new treatments for addiction.
Medicinal chemistry research in the Carlier group is oriented towards the diseases of the central nervous system (CNS). Major depression is a complex and often debilitating disease, and roughly 30% of all those diagnosed are refractory (resistant) to treatment with current antidepressant drugs. Furthermore, even in cases where current therapies are effective, symptomatic relief ensues only 4-6 weeks after the start of drug therapy. Current antidepressants work by inhibiting synaptic reuptake of serotonin (SSRI) or both serotonin and norepinephrine (SNRI). Several lines of evidence suggest that triple reuptake inhibitors (TRI), which would add a dopamine reuptake inhibition component, and might offer faster onset of action and relief to SSRI- and SNRI-refractory patients.1,2 In collaboration with the Mayo Clinic, we developed several examples of TRIs,3-6 and in 2009-2010 with support from AstraZeneca, we explored further development of this concept. Mayo and Virginia Tech have recently obtained the rights to all the compounds developed during this industrial collaboration and we are poised to continue this research.
Alzheimer’s disease (AD) is a progressive neurodegenerative disease that begins with memory loss, leads to troubling emotional and behavioral changes, and eventual death. It is extremely distressing to patients and their caregivers, and exacts a huge economic toll in the US. At present there are no effective disease-modifying treatments. Inhibition of the APP-processing enzyme b-secretase is considered to be a promising therapeutic approach, and in collaboration with Georgetown University, we developed inhibitors of this enzyme.7 Another area of active investigation is multifunctional molecules based on the chinese natural product Huperzine A. Like the natural product that inspired it, bis(12)-hupyridone inhibits acetylcholinesterase (AChE) and thus increases synaptic concentrations of the neurotransmitter acetylcholine. However, unlike Huperzine A, bis(12)-hupyridone also reduces oxidative stress-induced apoptosis and promotes neuronal differentiation.8,9 These properties could slow the neurodegeneration associated with AD.
Inhibition of acetylcholinesterase lies at the heart of our malaria research. Development of therapeutic drugs to treat infection by the malaria parasite is critically important, but our current focus is the vector of the parasite, the malaria mosquito Anopheles gambiae. Whereas mild central inhibition of AChE improves learning and memory, significant systemic inhibition is toxic and consitutes the mode of action of several agricultural insecticides. Our goal is to develop AChE inhibitors that potently inhibit mosquito AChE, and show very little affinity to human AChE. Such highly species selective enzyme inhibitors could constitute a new class of human-safe mosquitocides and could be applied to bednets.10
(1) Skolnick, P.; Basile, A. S. Drug Discovery Today: Therapeutic Strategies 2006, 3, 489-494.
(2) Millan, M. J. Neurotherapeutics 2009, 6, 53-77.
(3) Carlier, P. R.; Lo, M. M.-C.; Lo, P. C.-K.; Richelson, E.; Tatsumi, M.; Reynolds, I. J.; Sharma, T. A. Bioorg. Med. Chem. Lett. 1998, 8, 487-492.
(4) Shaw, A. M.; Boules, M. M.; Williams, K.; Robinson, J.; Carlier, P. R.; Richelson, E. Biological Psychiatry 2006, 59, 61S-61S.
(5) Shaw, A. M.; Boules, M.; Zhang, Y.; Williams, K.; Robinson, J.; Carlier, P. R.; Richelson, E. Eur. J. Pharmacol. 2007, 555, 30-36.
(6) Liang, Y. Q.; Shaw, A. M.; Boules, M.; Briody, S.; Robinson, J.; Oliveros, A.; Blazar, E.; Williams, K.; Zhang, Y.; Carlier, P. R.; Richelson, E. J. Pharmacol. Exp. Ther. 2008, 327, 573-583.
(7) Monceaux, C. J.; Hirata-Fukae, C.; Lam, P. C. H.; Totrov, M. M.; Matsuoka, Y.; Carlier, P. R. Bioorg. Med. Chem. Lett. 2011, 21, 3992-3996.
(8) Cui, W.; Li, W.; Zhao, Y.; Mak, S.; Gao, Y.; Luo, J.; Zhang, H.; Liu, Y.; Carlier, P. R.; Rong, J.; Han, Y. Brain Res. 2011, 1394, 14-23.
(9) Cui, W.; Cui, G. Z.; Li, W. M.; Zhang, Z. J.; Hu, S. Q.; Mak, S. H.; Zhang, H.; Carlier, P. R.; Choi, C. L.; Wong, Y. T.; Lee, S. M. Y.; Han, Y. F. Brain Res. 2011, 1401, 10-17.
(10) “Species-Selective Insecticidal Carbamates for Mosquito Control” Paul R. Carlier, Jeffrey R. Bloomquist, Sally L. Paulson, Eric A. Wong, U.S. Patent Application No.: 12/209,301. Date Filed: September 12, 2008
Spontaneous wiring and rewiring of circuits in our brain are largely regulated by the chemical messenger glutamate induced activation of complicated proteins known as NMDA receptors. We identify chemical tools to understand the complexity and to reduce disease burden of anomalies.
Bioelectromechanical Systems is a cross disciplinary field that combines engineering and science from the nano to the macro level. In our laboratory, we have developed technology for tissue viability detection, picoliter sample management, and imaging for molecular medicine. Using electrical feedback to perform complex procedures in biotechnology with precision and control, we have established robust methods for single cell analysis, selective cell concentration, and cancer therapy.
Dr. Davis received her Bachelor of Science degree in Animal Science and her Doctor of Veterinary Medicine from Virginia Tech. She then did an internship at Mississippi State University in Equine Medicine and Surgery. From there, she completed a residency in Equine Internal Medicine at North Carolina State University, during which time she received a Master’s degree in Specialized Veterinary Medicine and achieved board certification as a specialist in Large Animal Internal Medicine. Following this, she completed a PhD program and residency in Clinical Pharmacology. She also received board certification as a specialist in Veterinary Clinical Pharmacology. Dr. Davis spent 10 years as faculty at North Carolina State University’s College of Veterinary Medicine in Equine Internal Medicine and Clinical Pharmacology. She has recently moved backed to Blacksburg and is currently an Associate Professor of Clinical Pharmacology at the VMCVM. Her research area of interest involves pharmacokinetics/pharmacodynamics of therapeutic and investigational drugs, drug release from novel pharmaceutical forms, and drug stability/strength in compounded formulations.
Our main research goal is the development of drug-containing nanoparticles (typically 50-500 nm in diameter) with well-defined size distributions, drug compositions, and drug release kinetics. The formation of submicron drug particles with well-defined particle size distributions and biocompatibility is important for drug delivery applications. The size distribution affects the kinetics of drug release and, along with biocompatibility, can be controlled by complexation with polymers with tailored structures and molecular weights. Both insoluble, hydrophobic drugs as well as charged, water-soluble drugs are currently under study. The particles are typically stabilized with polymers – synthesized by collaborators at Virginia Tech – that can form attached or extended brushes which provide biocompatibility. Particle systems currently under investigation include:
1. Polymer nanoparticles complexed with water-insoluble and also water-soluble drugs along with superparamagnetic magnetite nanoparticles for enhanced magnetic resonance imaging – These particles have the potential for use as theranostic systems that combine drug delivery and an imaging functionality.
2. Polysaccharide-based nanoparticles that can incorporate water-insoluble, hydrophobic drugs for oral delivery – Our objective is to form nanoparticles of drugs combined with polymers designed to improve delivery of insoluble drugs and make it possible for drugs to be delivered orally that currently cannot be delivered at all or require intravenous (IV) delivery. Oral administration of drugs is by far the most preferred mode of delivery for delivery of drugs for illnesses such as hypertension and high cholesterol. However, many drugs, such as those used to treat diseases such as tuberculosis and cancer, cannot currently be delivered by oral means and thus require intravenous (IV) delivery. Other drugs, such as those used to treat HIV, are delivery orally but with poor efficiency. In many cases, these drugs have poor water solubility which partly accounts for the poor oral delivery and also greatly complicates IV delivery. We are studying polysaccharides which are very promising for oral drug delivery due to their affinity for complexing with a variety of drugs which can suppress crystallization of the drugs, their relatively high glass transition temperatures, and their biocompatibility. We employ a high-speed precipitation process that can produce drug-polymer particles with tunable sizes in the range of 50-200 nanometers (nm) needed for optimal drug solubility. Due to the high area/volume of these particles, significant increases in mass transfer rates are possible. Reducing particle diameter from 1 micron to 50 nm increases the specific area and can increase the drug mass transfer rate by 400-fold.
Engineering, Science, and Mechanics
VT Carilion Research Institute
The problem of poor aqueous solubility is a major cause of poor drug bioavailability, and thus of drug candidate failure. Modern methods of drug discovery are creating lead compounds with a strong tendency to be hydrophobic, in many cases highly crystalline, and thus poorly soluble in water. Our labs seeks to create drug delivery systems based on amorphous solid dispersions in polysaccharide derivative matrices that eliminate drug crystallinity and thus can strongly enhance aqueous solubility by removing the need to overcome the heat of fusion of the drug. We work to elucidate the design criteria for such polysaccharide derivatives, develop efficient methods for their synthesis and characterization, and interrogate their ability to form effective amorphous solid dispersions that enhance water solubility of important therapeutic molecules, including antivirals, antibiotics, and anticancer drugs.
Marion Ehrich is a professor at Virginia-Maryland Regional College of Veterinary Medicine in Blacksburg, VA, and at Virginia Tech Carilion School of Medicine in Roanoke. In addition to the teaching pharmacology and toxicology to veterinary, medical and graduate students, her professional responsibilities include service in the Veterinary Medical Teaching Hospital Pharmacy and in the Toxicology Diagnostic Laboratory. Dr. Ehrich has a B.S. in pharmacy from South Dakota State University, a M.S. in pharmacology/toxicology from the University of Chicago, and a Ph.D. in pharmacology/toxicology from the University of Connecticut at Storrs. She has been teaching at VMRCVM since 1980, the year in which she became a member of the Society of Toxicology and a Diplomate of the American Board of Toxicology. Teaching at the new medical school began in 2010. She was elected a fellow of the Academy of Toxicological Sciences in 1999. Dr. Ehrich’s primary research activities are associated with the comparative neurotoxicities of antiesterase pesticides, with both in vivo and in vitro models used for study. Dr. Ehrich was the 2003-2004 President of the Society of Toxicology, and received their Merit Award in 2010. She served as Treasurer for the Board of Directors of the American Board of Toxicology (1985-89) and as Secretary for the Society of Toxicology (1992-94). She has also chaired SOT’s Education Committee (1990-92), SOT’s Regulatory Affairs and Legislative Action Committee (1997-98), and the Toxicology Education Foundation (2000-2001). In addition, she served on the Executive Board of the Council for Scientific Society Presidents and the National Research Council’s Committee on Toxicology, and currently serves on the USP Committee on Toxicology. She is on editorial boards NeuroToxicology, In Vitro Toxicology, and Journal of Applied Toxicology and is an associate editor for the International Journal of Toxicology. In addition, she has received teaching awards both at the local and national level.
Drug Discovery in the Etzkorn Group
Pin1 is a key regulator of the cell cycle that has been identified as a target for anti-cancer therapeutics. We synthesize Pin1 catalytic site inhibitors, and WW domain ligands. Other targets are the kinases upstream of Pin1, and the downstream phosphatases that add more layers to the complex regulation of the cell cycle. We have designed peptide mimics to stabilize the collagen triple helix conformation necessary for the unique structural properties of collagen. Collagen peptide mimics will be incorporated into biomaterials for potential use in joint replacement, cellular matrix, or drug delivery applications.
Our design process begins with 3D structures available for many proteins and uses chemical intuition together with molecular modeling. Synthesis efforts focus on control of stereochemistry, and combinatorial libraries. Our compounds are assayed for enzyme inhibition, binding activity, structure, and dynamics by: NMR, mass spectrometry, circular dichroism, fluorescence, and/or X-ray crystallography.
1. Mayfield, J. E.; Fan, S.; Wei, S.; Zhang, M.; Li, B.; Ellington, A. D.; Etzkorn, F. A.; Zhang, Y. J. Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II, ACS Chem Biol 2015, 10, 2405 doi: 10.1021/acschembio.5b00296, http://www.ncbi.nlm.nih.gov/pubmed/26332362.
2. Etzkorn, F. A.; Zhao, S. Stereospecific phosphorylation by the central mitotic kinase Cdk1-cyclin B, ACS Chem Biol 2015, 10, 952 doi: 10.1021/cb500815b, http://www.ncbi.nlm.nih.gov/pubmed/25603287.
3. Chen, X. R.; Fan, S. A.; Ware, R. I.; Etzkorn, F. A. Stereochemical control in the Still-Wittig rearrangement synthesis of (Z)-alkene cyclohexyl inhibitors of Pin1, PLoS One 2015, 10, e0139543 doi: 10.1371/journal.pone.0139543.
4. Park, J. M.; Hu, J. H.; Milshteyn, A.; Zhang, P. W.; Moore, C. G.; Park, S.; Datko, M. C.; Domingo, R. D.; Reyes, C. M.; Wang, X. J.; Etzkorn, F. A.; Xiao, B.; Szumlinski, K. K.; Kern, D.; Linden, D. J.; Worley, P. F. A prolyl-isomerase mediates dopamine-dependent plasticity and cocaine motor sensitization, CELL 2013, 154, 637 doi: 10.1016/j.cell.2013.07.001, http://www.ncbi.nlm.nih.gov/pubmed/23911326.
5. Mercedes-Camacho, A. Y.; Mullins, A. B.; Mason, M. D.; Xu, G. G.; Mahoney, B. J.; Wang, X.; Peng, J. W.; Etzkorn, F. A. Kinetic isotope effects support the twisted amide mechanism of Pin1 peptidyl-prolyl isomerase, Biochemistry 2013, 52, 7707 doi: 10.1021/bi400700b, http://www.ncbi.nlm.nih.gov/pubmed/24116866.
6. Zhang, M.; Wang, X. J.; Chen, X.; Bowman, M. E.; Luo, Y.; Noel, J. P.; Ellington, A. D.; Etzkorn, F. A.; Zhang, Y. Structural and kinetic analysis of prolyl-isomerization/phosphorylation cross-talk in the CTD code, ACS Chem. Biol. 2012, 7, 1462 doi: 10.1021/cb3000887, http://www.ncbi.nlm.nih.gov/pubmed/22670809.
7. Xu, G. G.; Slebodnick, C.; Etzkorn, F. A. Cyclohexyl ketone inhibitors of Pin1 dock in a trans-diaxial cyclohexane conformation, PLoS One 2012, 7, e44226 doi: 10.1371/journal.pone.0044226, http://www.ncbi.nlm.nih.gov/pubmed/23028504.
8. Tarrant, M. K.; Rho, H.-S.; Xie, Z.; Jiang, Y. L.; Gross, C.; Culhane, J. C.; Yan, G.; Qian, J.; Ichikawa, Y.; Matsuoka, T.; Zachara, N.; Etzkorn, F. A.; Hart, G. W.; Jeong, J. S.; Blackshaw, S.; Zhu, H.; Cole, P. A. Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis, Nat. Chem. Biol. 2012, 8, 262 doi: 10.1038/nchembio.771.
9. Xu, G. G.; Zhang, Y.; Mercedes-Camacho, A. Y.; Etzkorn, F. A. A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state, Biochemistry 2011, 50, 9545 doi: 10.1021/bi201055c, http://www.ncbi.nlm.nih.gov/pubmed/21980916.
10. Namanja, A. T.; Wang, X. J.; Xu, B.; Mercedes-Camacho, A. Y.; Wilson, K. A.; Etzkorn, F. A.; Peng, J. W. Stereospecific gating of functional motions in Pin1, Proc. Nat. Acad. Sci. USA 2011, 108, 12289 doi: 10.1073/pnas.1019382108, http://www.ncbi.nlm.nih.gov/pubmed/21746900.
11. Xu, G. G.; Etzkorn, F. A. Convergent synthesis of alpha-ketoamide inhibitors of Pin1, Organic Letters 2010, 12, 696 doi: 10.1021/ol9027013, http://www.ncbi.nlm.nih.gov/pubmed/20102178.
12. Namanja, A. T.; Wang, X. J.; Xu, B.; Mercedes-Camacho, A. Y.; Wilson, B. D.; Wilson, K. A.; Etzkorn, F. A.; Peng, J. W. Toward Flexibility-Activity Relationships by NMR Spectroscopy: Dynamics of Pin1 Ligands, J. Am. Chem. Soc. 2010, 132, 5607 doi: 10.1021/ja9096779.
13. Mercedes-Camacho, A. Y.; Etzkorn, F. A. Enzyme-linked enzyme-binding assay for Pin1 WW domain ligands, Anal. Biochem. 2010, 402, 77 doi: 10.1016/j.ab.2010.03.018.
14. Xu, G. G.; Etzkorn, F. A. Pin1 as an anticancer drug target, Drug News Perspect 2009, 22, 399 doi: 10.1358/dnp.2009.22.7.1381751, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19890497
15. Nachman, R. J.; Kim, Y. J.; Wang, X. J.; Etzkorn, F. A.; Kaczmarek, K.; Zabrocki, J.; Adams, M. E. Potent activity of a PK/PBAN analog with an (E)-alkene, trans-Pro mimic identifies the Pro orientation and core conformation during interaction with HevPBANR-C receptor, Bioorg Med Chem 2009, 17, 4216 doi: S0968-0896(09)00252-1 [pii] 10.1016/j.bmc.2009.03.036, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19356938
In collaboration with Dr. Richard Gandour, Department of Chemistry at Virginia Tech, a series of dendritic amphiphiles has been synthesized and their antimicrobial activities measured against a representative panel of microbial pathogens. A number of the compounds have strong, promising antimicrobial activities against such pathogens as Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), Mycobacterium spp., and Candida albicans. Research to synthesize derivatives with higher activities continues with funds provided by a new Georgetown University-Virginia Tech drug discovery program.
In 1993, Dr. Falkinham and two others founded Dominion BioSciences, Inc. It is a biotechnology development company focusing on development of novel products for the agricultural market. Their first product, a cockroach-insecticide based on inhibition of uric acid metabolism is on sale. Their second product is a broad spectrum antifungal compound produced by a non-obligate Predator soil bacterium. The fungicide has activity against fungal pathogens of bananas, papaya, pineapple, wheat, rice, grapes, tomatoes, and ornamental plants. Product development is being continued in partnership with an established producer of crop protection chemicals.
With a grant from International Cooperative Biodiversity Group (ICBG) program of the Fogarty Center of NIH, Dr. Falkinham and his students are collaborating with natural product chemists from Research Triangle Institute (Dr. Nicholas H. Oberlies) and Jordan University of Science and Technology (Dr. Feras Q. Alali), to detect, isolate and identify novel chemotherapeutic agents. The focus of the investigations is non-obligate predatory bacteria that grow on other microorganisms (or in common laboratory media), that produce antimicrobial compounds. Predator bacteria have not been systematically investigated as sources of antibiotics, although current studies document the cost effectiveness of their high frequency production of novel antibiotics.
The goal of our project is to advance the frontiers of biology, chemistry and nanometer-scale technology to better understand processes that lead to disease development, progression, and treatment. Our interdisciplinary group encompasses a broad spectrum of competence, ranging from pure chemistry and molecular biologists to several applied disciplines thus providing a unique opportunity to create a unified research program devoted to translational-based research.
Summary of Proposed Research Plan:The emerging field of chronotherapy, in which treatments for various diseases are administered at times of the day most likely to yield the greatest efficacy, will rely on deciphering the regulatory systems to which all circadian components connect, and most importantly, on understanding the structural complexity that determines the specificity of their interactions.
In recent years, a family of antidepressants, addictive drugs and antiproliferative agents (all known as “ligands”) were used to regulate the expression of therapeutically relevant circadian-controlled genes by directly targeting a key regulatory protein complex named Clock/Bmal1. However, there is no evidence of how binding specificity among these molecules is achieved in a biologically relevant setting nor structural characterization of pharmacologically-relevant inhibitor binding sites in the Clock/Bmal1 complex. Moreover, the strength (affinity) and mode of their association (i.e. cooperativity, one molecule helps the other one to bind) have not been explored, the regulatory mechanisms (what each protein does in the complex) are largely unknown, and correlations between in vitro specificity and in vivo selectivity (the ligand exclusively binds to one complex among the hundreds in the cell) remain elusive. We propose to use a multidisciplinary approach that includes x-ray crystallography, biophysical studies and in vivo analysis of complex-ligand interactions to address these fundamental problems. The long-term goal of this proposal is to use structural information of the circadian molecules-ligand complex to design modified small molecule ligands with improved potency, selectivity, specificity and stability properties over first generation drugs. To achieve this goal, we envision strong collaborative efforts with other laboratories on campus as well as partnership with biotech companies. By consolidating links with industrial partners, we will be able to optimize the transfer of new findings and technology from the research laboratory into opportunities for improvement therapeutic treatments through the use of nanodevices.
Lipid-bilayer-coated nanoparticles for drug delivery and antimicrobial dendritic amphiphiles.
Two key issues for drug delivery are (1) enabling the delivery of known active agents and (2) enhancing the delivery of novel agents. Many superior agents are not drugs because their physiochemical properties prevent facile transport and targeting. New drug delivery vehicles are needed to enable delivering these known agents. Any novel synthetic agents should be designed a priori with drug-like properties, especially water-solubility. The Gandour lab addresses both challenges.
Engineering drug delivery vehicles for specific drugs and target organs reamins a key challenge for future medicine. Lipid-bilayer-coated nanoparticles (Nps) can be tailored to meet this challenge. A strategy for design and construction of complex functional Nps (Figure 1) for drug-delivery applications is under development in collaboration with Professor Alan Esker and three outside collaborators, who are developing molecular modeling algorithms to simulate assembling these Nps. To achieve the ultimate goal—lipid-bilayer-coated Nps containing multiple agents, the basic nanoarchitecture must be constructed first. The synthesis involves two steps—the coating of metal oxide Nps with linkers and the fusing of linker-coated Nps with liposomes. Attaching linkers to Nps to give stable linker-coated Nps is the first goal. Constructing stable lipid-bilayer-coated Nps is the second goal. Both goals depend on the chemical structure of the linker; therefore, a small library of linkers is being synthesized to define the structure–property space. Differential scanning calorimetry (DSC) and quartz crystal microbalance with dissipation monitoring (QCM-D) will be used to characterize these Nps.
Four objectives are to: i) screen a linker library to assay their ability to insert into lipid bilayers by utilizing multilamellar vesicles (DSC), ii) characterize linker-coated planar metal oxide surfaces and liposome fusion onto linker modified planar metal oxide surfaces to create tethered lipid bilayers (QCM-D), iii) study linker-coated Nps interactions with supported and tethered phospholipid bilayers (QCM-D), and iv) probe interactions between tethered lipid-bilayer-coated Nps and supported and tethered lipid bilayers on planar surfaces (QCM-D). Completing these studies will confirm the structure and utility of these Nps, and set the stage for developing strategies for loading these Nps with multiple drugs.
A second key challenge is developing water-soluble antimicrobial agents. Several members of our library of dendritic amphiphiles (Figure 2) have shown excellent activity against bacteria, fungi, and mycobacteria. The high species- and compound-selectivities suggest a specific mechanism of action for each microbe, which appears to be unrelated to membrane disruption. Mechanistic studies are underway to probe the activity of the one promising anti-Staphylococcal agent, 5(18) (Figure 3). The minimal inhibitory concentration (MIC) of 1.1 μg/mL is slightly better than that (2.2 μg/mL) of vancomycin, the drug of last resort in Staphylococcal infections.
VT Carilion Research Institute
Rob Gourdie is Professor and the Commonwealth Research Commercialization Fund Eminent Scholar, at the VTCRI; Director of the Center for Cardiovascular and Regenerative Biology VTCRI; Director of Emergency Medicine Research, Carilion Clinic; and Professor at the Virginia Tech Wake Forest University School of Biomedical Engineering and Sciences (quite a list!) His web research description is copied below. The research of the Gourdie lab is on the subunit proteins of gap junctions—connexins. This work encompasses both basic and practical /translational aspects. In basic research the cellular and molecular mechanisms of the carboxyl terminal domain of Cx43 in regulating gap junction remodeling and electrical conduction in the normal and arrhythmic heart are under study. In more practically oriented work, Cx43 assignments in wound healing, scarring, and regeneration are under intensive research. The lab is developing a platform of drugs targeting Cx43 function. The first candidate is a mimetic of the carboxyl terminus of Cx43(aCT1). Based on our results in skin and heart, we have been granted three patents in regenerative medicine. The lab currently has another five patents pending on small molecules and stem cell technologies. One of our technologies is now in phase II clinical trials, which is expected to be completed in November 2012.
Virginia Bioinformatics Institute
Drug Discovery and Biodiversity Conservation in Madagascar
Natural products have provided over a third of currently used pharmaceuticals, and the tropical rain forests of the world represent a great and largely untapped source of new natural products; examples of some of the compounds isolated in the Kingston group are shown below. Regrettably these forests are disappearing at a rapid rate as they are logged for timber or conversion to agricultural purposes. We have joined with conservation, industrial, and botanical groups to develop a model program for drug discovery and biodiversity conservation in Madagascar. Plants, marine organisms, and microbial species are collected in Madagascar and screened for bioactivity at Virginia Tech, and those with anticancer activity or CNS activity are studied in our laboratories. We have also helped to set up a malaria screening facility in Madagascar, and we are working to isolate antimalarial compounds in collaboration with our Malagasy colleagues. Any royalties from the resulting drugs will be shared with Madagascar as an economic incentive to maintain their tropical forests. The new bioactive compounds below have all been isolated from plants collected in this program. We are partnered with Eisai Inc. in this work, and any compounds with significant anticancer activity will be offered to Eisai for development.
Chemistry and Drug Delivery of Paclitaxel
The complex diterpenoid natural product taxol is an exciting anti-cancer drug that is currently in clinical use against ovarian and breast cancer. It does have some significant side-effects, and we are working with CytImmune Sciences Inc. to develop a gold nanoparticle approach to drug delivery. Preliminary results are encouraging, and one of the agents we have helped develop is approximately twentyfold more potent than paclitaxel itself. This project blends synthesis and biological studies to improve on one of the most important new anti-cancer natural products of the past 30 years.
Biochemistry of the human malaria parasite Plasmodium falciparum
Malaria is one of the most devastating infectious diseases in the world today. The objective of my research is to understand how the human malaria parasite Plasmodium falciparum thrives in its host red blood cell. We employ biochemical and cell biological approaches to study:
- endocytosis and catabolism of erythrocyte hemoglobin by the parasite
- lipid catabolism and utilization of host lipid species for fatty acid scavenging
- protein sorting and trafficking to the parasite’s vacuole and specialized apical secretory organelles
- mechanisms of action of anti-malarial compounds
Research in our group is focused on elucidating the molecular mechanisms of breast cancer cell cycle via proteomics and holistic, systems biology approaches. Most cancers exhibit some, if not all, of eight major characteristics: cancer cells evade apoptosis, are able to proliferate in the absence of growth factors, ignore inhibitory factors, recruit their own blood supply, avoid immune destruction, display deregulated cell energetics, become immortal and are able to metastasize. Our laboratory is using ER+ and HER2+ breast cancer cells to investigate the molecular mechanisms that enable cancer cells to bypass tightly regulated molecular checkpoints such as the G1/S restriction point, proliferate in an unrestrained manner, metastasize and hijack normal biological function. The mass spectrometry and proteomic technologies that we developed in our laboratory have enabled, so far, the identification of over 4000 breast cancer proteins, with representative protein clusters being mapped to all hallmarks of cancer. Differential protein expression analysis of the G1 and S cell cycle stages of breast cancer cells has revealed functional protein clusters that uncover new relationships between co-regulated protein networks with essential roles in transcription activation/repression, signaling and cell cycle control. Originators of proliferation, as possible drivers through the G1/S transition point in cancerous cell states, were found to be decisively abundant.
By providing novel insights into the functional categories that drive cancer cells into division, the data points to a broad range of potential therapeutic targets that concurrently affect the cell cycle signaling and transcriptional/translational machinery. The identified proteins can be used alone, or in combination, as target molecules for developing novel anti-cancer drugs and therapies, or as biomarker sets for cancer detection and diagnosis. We are pursuing the expansion of these projects with studies that will provide a better understanding of the functional implications of drug delivery and impact on signaling pathways that control cell proliferation.
Programming of Innate Immune Memory in Chronic Inflammatory Diseases
Our research group reveals a striking association between skewed innate immunity and the pathogenesis of inflammatory diseases. We first systematically documented the novel “memory” of innate immune response and its underlying immunological mechanisms. Conventionally, it was thought that only acquired immunity has memory, and that innate immunity only serves as a rudimentary first-line of defense with no memory. However, both basic and clinical studies allude to the notion that innate immunity also has memory. This is classically represented by the paradigm of “priming” and “tolerance” manifested in innate monocytes and macrophages when challenged with sequential dosages of inflammatory mediators such as microbial lipopolysaccharide (LPS), hormones, or cytokines. This bears critical relevance in human health and diseases. For example, Pre-conditioned innate immune systems by low dosages of microbial products may elicit a more robust defense toward subsequent infection. On the other hand, innate systems challenged with overwhelming dosages of microbial products or cytokines would try to dampen host responses in order to prevent excessive collateral inflammatory damages to the host. In terms of “sterile” inflammatory conditions without live microbes, priming and tolerance of innate immunity also determine the fate of inflammation such as acute “resolving” inflammation, versus chronic “non-resolving” inflammation. Non-resolving inflammation is the key culprit underlying the pathogenesis of human inflammatory diseases such as sepsis, atherosclerosis, fibrosis, diabetes, cancer and Alzheimer’s disease. Our research will continue to define the dynamic circuitries responsible for the programming of innate leukocytes. Potential drug targets will be identified for the treatment of chronic diseases. Promising compounds that may intervene or re-program innate memory will be tested.
Human Nutrition, Foods and Exercise
The Macromolecules/Biotechnology Interface:
The National Academy of Science has identified biomaterials and bioinspired materials as a “new and rapidly developing” subfield of science with the “goal of creating new materials of technical importance.” The increasing demand for transformative biomaterials solutions for improved quality and quantity of life has catalyzed interdisciplinary materials research programs and technological innovation in our research group. Our current research focuses on the design, performance, and societal implications of novel biomaterials for gene and drug delivery, which provides cutting-edge research opportunities and significant impact on global health, while also providing sufficient breadth for the alignment of universities and international organizations. The development of efficient, nontoxic materials for the delivery of therapeutic nucleic acids and drugs is a fundamental and important problem in biotechnology research. For example, while many drugs are available to control cardiovascular disease (a leading global health problem), drug toxicity and lack of specificity leads to serious side effects. Delivery vehicles have the potential to minimize side effects while maximizing medicinal efficacy, yet fundamental studies on biomaterials-based delivery systems are severely lacking.
Successful drug and gene delivery is governed by complex transport processes (Figure 2) that span a wide range of length scales from the vascular to the molecular and nanometer levels. Thus, understanding how the biomaterials chemistry (i.e., size, shape, charge, hydrophilicity) governs the transport, binding and drug/gene release rate is central to advancing this field. Our research team focuses on the development and study of water-soluble polycations, particularly segmented block copolymer structures, for the binding, encapsulation, and delivery of anionic drugs and nucleic acids into cultured cells.We are currently examing structure-property effects of incorporating different cationic groups into these structures such as histidine-mimics and quaternary ammonium and phosphonium groups, and investigate the influence of nucleobase substitution in vector design, which may lead to novel binding strategies.
Macromolecular and Supramolecular Chemistry
We focus on expanding the study and therapeutic use of hydrogen sulfide (H2S) as a signaling gas. Despite its reputation as a foul-smelling and toxic pollutant, H2S is a vital biological signaling agent, and it is of interest as a therapeutic, most notably in cardiovascular disease but in many other areas of medicine as well. The majority of biological studies on this gasotransmitter have been carried out with systemically administered small molecule H2S donors, which have little tissue specificity and the potential for off-target effects. We address these shortcoming using H2S-releasing materials, which can offer localized H2S delivery with tunable kinetics. Our platforms include small molecules, soluble polymers, and peptide-based gels designed to release therapeutically relevant concentrations of H2S with controllable kinetics.
Group website: https://matsonlab.com/
VT Carilion Research Institute
We are developing computational methods that are often used in
virtual screening and scoring approaches utilized in computer aided drug
design. The ultimate goal is to be able to predict, with high accuracy, the
thermodynamics of protein-ligand binding. At the most detailed, atomistic
level, accurate models of water becomes critical for the accuracy of the
over-all calculation; our group has developed several such models that have
become popular in the community, this effort continues.
We are also working on predictive models of chromatin (DNA)
compaction in living cells; the hope is that the fundamental understanding will eventually lead to completely novel therapeutic approaches.
We are also interested in how small
RNA fragments can be compacted, with an eye towards developing better
packaging strategies for siRNA payloads.
Medicinal Chemistry/Drug Discovery
According to the American Cancer Society, cancer ranks second as a leading cause of death in the US, accounting for nearly 600,000 lives lost in 2007. It is not surprising that the financial and emotional cost of cancer treatment is tremendous: $35 billion/year (medical) plus $65 billion/year (nonmedical). Lung cancer, followed by prostate and breast cancers, claims the most lives. The lifetime risk of developing cancer is 1 in 2 for men and 1 in 3 for women. Therefore, new drugs that combat different types of cancer are urgently needed.
Potential targets for anti-cancer therapy are sphingosine kinases, which are enzymes that attach a phosphate group to sphingosine (Sph). When sphingosine is phosphorylated, it becomes a signaling molecule (sphingosine-1-phosphate, S1P) that tells the cells to grow. By controlling the formation of this signaling molecule, growth in some cells can be halted. Cancer is essentially uncontrolled cell growth and molecules that can inhibit this process have potential as anticancer agents.
Sphingosine kinases (SphK1, SphK2) are the master regulators of the balance between the pro-survival sphingolipid, sphingosine-1-phosphate (S1P) and the pro-apoptotic sphingolipids, sphingosine and ceramide (Figure 1). SphKs, in particular SphK1, are overexpressed in a variety of tumor types (lung, ovary, liver, colon, etc.) and clinical evidence for their role in disease progression and reduced survival has been documented in cancers of breast and stomach as well as in astrocytomas. Because of its key role in sphingolipid metabolism, SphK is an attractive target for anticancer drugs. However, the field has suffered from the paucity of SphK inhibitors with the selectivity and drug-like properties needed to validate these enzymes as therapeutic targets. Our group has developed small molecule inhibitors of SphK—the current goal is to improve their selectivity and pharmacokinetic properties by further structure-activity relationship studies.
More than 15% of carcinomas can be attributed to known infectious agents such as bacteria and viruses. Fusobacterium nucleatum is a Gram-‐negative bacterium that is significantly overrepresented in the colonic tissue of patients with colorectal cancer. We are working at the interface of chemistry and biology to determine the role of the microbiome in cancer using: Chemical biology, X-‐ray crystallography, Biochemistry, Molecular genetics, Enzymology, and Cell biology.
We are interested in understanding the mechanism and regulation of enzymesimportant for virulence in several human pathogens. Currently we are focusing on enzyme drug targets from Mycobacterium tuberculosis, Aspergillus fumigatus, Leishmania major, and Trypanosoma cruzi, the causative agents of tuberculosis, aspergillosis, leishmaniasis, and Chagas disease, respectively. Together these human pathogens are responsible for more than 2 M deaths every year. Our research includes, dissecting the contributions of substrate binding and protein-protein interactions to catalysis, determining the structure of the transition state and the mechanism of substrate selectivity. Our drug discovery approach includes rational drug design andin silico computational inhibitor screening. In addition, we have also developed and implemented high-throughput screening assays to screen small molecule libraries for inhibitors of enzyme drug targets. The following projects are currently being developed in the laboratory.
1) Mechanism of hydroxylation of siderophores in microbial pathogens. During infection many human pathogens produce and secrete low molecular weight peptidic metabolites called, siderophores. The role of siderophores is to scavenge ferric iron from the host in order for the bacteria to proliferate. We are interested in the biosynthesis of the siderophores produced by the human pathogens Mycobacterium tuberculosis, Aspergillus fumigatus, andYersinia pestis. Specifically, we are targeting the enzymes that hydroxylate the siderophores to form a hydroxamate moiety, which is essential for iron binding. Our objective is to provide a detailed understanding of the chemical and kinetic mechanisms, determine the 3-dimensional structure, and identify inhibitors for this novel family of enzymes.
2) UDP-Galactopyranose mutase reaction. Galactofuranose (Galf) is an important component the cell surface of several pathogenic bacteria, protozoan, fungi and mycobacterium. Galf is not present in humans, making its biosynthetic pathway a target for new antibiotics. Galf is produced from the transformation of UDP-galactopyranose to UDP-galactofuranose by the flavin-containing enzyme, UDP-glactopyranose mutase (UGM). We are interested in understanding the role of the flavin cofactor in catalysis, determining the 3-dimensional structure and to identify inhibitors against the UGM from the human pathogens: M. tuberculosis, L. major, T. cruzi and A. fumigatus.
Dr. Harald Sontheimer researches the biology of glial cells, the brain’s most abundant cell type. He is credited with making foundational discoveries on the functional properties of glial cells in the brain, including the localization and mechanisms of a range of receptors and ion channels that were previously thought to exist only on nerve cells.
Currently, Dr. Sontheimer studies the molecular structure and activity of glial cells in health, cancer, and other diseases. He and his research team work to understand the mechanisms underpinning the functions of glial cells, and how these functions may fault.
Targeted drug delivery for intracellular pathogens – In the last few decades, the emergence of drug resistant strains of Salmonella sp., Brucella sp., Mycobacterium sp., etc. representing intracellular bacterial pathogens is manifesting into a global health problem thereby raising new pharmaceutical challenges and necessitating the development of an efficient and cost effective novel agent. My laboratory is aiming to achieve site specific targeted drug delivery with increased bioavailability of antimicrobials/drugs using nanoparticles as carriers. Our ultimate goal is to design and develop novel nanoparticle based drugs by incorporating biological, engineering and chemical manufacturing principles for therapeutic application of chronic infectious diseases i.e., tuberculosis, brucellosis and salmonellosis. In addition, I also believe that development of nanoparticle based targeted drug delivery system may provide new therapeutic opportunities for the use of vast array of unstable, toxic, and insoluble antimicrobials (sitting on the shelves of drug companies), with minimum or no deleterious side effects.
VT Carilion Research Institute
Laboratory for Integrative Tumor Ecology
The tumor microenvironment is a dynamic and heterogeneous tissue ecosystem. Appropriate cell-tissue interactions suppress the development of malignant tumors, while altered architecture and cues can promote malignancy, as well as reduce the efficacy of anti-tumor therapies. We believe that genetic studies only provide a partial picture, and that effective cancer treatment and improved patient prognosis will result from an improved understanding of the role of cell-microenvironment interactions in driving the evolution and therapy response of individual patient tumors. To this end, the Verbridge LITE lab has integrated tissue engineering and biomaterials advances with microfabrication approaches to build experimental, in vitro, yet physiologically relevant models of heterogeneous, vascularized tumor tissues. We are leveraging these platforms, in combination with mathematical modeling, to study the dynamics underlying cellular invasion and therapy response in brain tumors, focusing on glioblastoma (GBM), which is the most common and deadly primary brain malignancy.
Material Science and Engineering
The major theme of research in Dr. Xu’s laboratory focuses on biochemical, molecular, structural, and functional studies on cell surface receptor-ligand molecular recognition,protein-protein interaction, receptor signaling, and novel ligand/receptor target discovery and engineering that are relevant to human chronic diseases such as diabetes and obesity. His lab is also interested in studying molecular and structural basis of host-pathogen interactions such as mechanisms of pathogen evasion of host immune defense. Currently his lab has the following ongoing pilot projects:
(1) How omega-3 fatty acids, such as DHA and EPA, the major ingredients in fish oil, bind to G protein-coupled receptor 120 (GPR120) and exert potent anti-inflammatory and anti-diabetic effects.
(2) Discovery of novel ligand on pancreatic beta cells for immunoreceptor NKp46, whose activation may lead to insulitis and type I diabetes.
(3) Mechanistic studies of natural products from plants that exert anti-diabetic and antiinflammatory
(4) Molecular and structural basis of viral proteins counteracting host defense.
Bio-nanoparticle mediated drug delivery for cancer treatment
Cancers impact people from all walks of life. The advance of science has brought several drugs to the market and those drugs can be very effective in killing cancerous cells and eradicating cancer tissues. However, those drugs do not differentiate rapidly dividing cancerous cells from normal cells and thus are commonly accompanied by severe side effects. Our research is to develop drug delivery systems that can deliver drugs to targeted tissues with minimal basal release and thus minimal side effects. We focus on developing bio-nanoparticle assembly processes, testing the drug loading capacity of different particles and the drug release profiles, and the delivery of the bio-nanoparticles in cultured cells.