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Daniel S. Pilch, Ph.D.

Associate Professor
Phone: (732) 235-3352


Research Interest:

Antimicrobial and anticancer drug design and development, antibiotics, drug resistance, drug-maromolecule interactions, protein and nucleic acid structure and function, biothermodynamics, molecular-biophysics


Research Description:

The research conducted in my laboratory incorporates a multi-disciplinary approach toward investigating the following three programs of research:
Development of G-Quadruplex-Stabilizing Anticancer Drugs
The stabilization of G-quadruplex DNA structures represents a new strategy for the treatment of cancer. G-quadruplex structures have been identified in G-rich regions of telomeres as well as the promoter regions of several oncogenes (including c-myc and K-RAS). The principle mechanism by which telomeric structure and function is maintained in cells is through the actions of an enzyme termed telomerase. Compounds that stabilize telomeric quadruplex DNA can inhibit both telomerase activity and telomeric DNA binding proteins, thereby inducing cell cycle arrest, apoptosis, and senescence. Stabilization of G-quadruplex structures in oncogene promoters results in decreased expression of the oncogenes. The primary goal of this research program is to develop new classes G-quadruplex stabilizing anticancer agents. Toward this goal, we have identified the macrocyclic polyoxazoles as a promising new class of compounds that exhibit a high degree of selectivity for the G-quadruplex nucleic acid form. They induce both rapid apoptosis and cell cycle arrest in a broad range of cancer cells. We have recently developed a series of computational, spectroscopic, calorimetric, and cellular assays for defining the quantitative structure-activity relationships of these compounds. These assays facilitate preclinical characterizations by enabling the selection of lead compounds for examination of in vivo antitumor activities in mouse xenograft models.
Development of New Antibiotics with Novel Mechanisms of Action
Antibiotic resistance has emerged into a major public health problem throughout the world. Resistance has now been documented in most significant bacterial pathogens and is prevalent in both nosocomial and community settings. One of the more significant and therapeutically challenging manifestations of the resistance problem has been the emergence of multidrug resistance in Gram-positive bacterial pathogens. Multidrug-resistant (MDR) Gram-positive pathogens of particular concern are methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE). Overcoming the alarming rise in resistance that has developed among Gram-positive bacteria requires new antibiotics that exhibit novel mechanisms of action, as well as the abilities to circumvent known resistance pathways. This research program is currently focused on the development of a novel class of antibiotics that target an essential bacterial cell division protein, termed FtsZ. FtsZ is an appealing target for antimicrobial compounds because (i) it is essential for bacterial viability, (ii) it is highly conserved among significant bacterial pathogens, and (iii) it is absent in humans. This drug development program incorporates a multi-disciplinary approach that includes structure-guided design, synthesis, mechanism-based in vitro studies, and in vivo evaluation in animal models of infection.

Molecular Determinants of Drug-RNA Recognition
RNA can fold into a variety of different structures and/or conformations that can serve as specific recognition elements for drugs. Targeting these structural RNA elements in a site-specific manner offers the potential for modulating the biological function of the targeted RNA. To date, little is known about the molecular driving forces that dictate, control, and stabilize drug-RNA interactions. The primary goal of this research program is to define the rules that govern the affinities and specificities of drugs for their RNA targets. Specifically, we are defining the relative contributions of van der Waals, hydrogen-bonding, and electrostatic interactions to the binding affinities and specificities of RNA-directed drugs. We also are evaluating how the presence and sequence of loops and bulges in the host RNA modulate drug recognition. The information gleaned from our studies will enhance our understanding of how specific drug-RNA interactions are translated into biological endpoints (e.g., bactericidal and antiviral activities), and will facilitate our abilities to overcome known resistance mechanisms. Currently, our studies are focused on targeting various bacterial, viral, and group I intron RNA sequences with neomycin- and kanamycin-class aminoglycosides. We have demonstrated that aminoglycosides can inhibit the RNase H activity of the HIV-1 reverse transcriptase (RT) enzyme by targeting specific viral RNA‚ÄĘDNA hybrid structures. This inhibitory effect should have antiviral ramifications, since the RNase H activity of the HIV-1 RT enzyme is essential to the replication of the virus. In addition, we have developed a fluorescence-based assay for detecting and characterizing drug-RNA interactions, as well as associated conformational changes. This assay opens the door not only to the characterization of the conformation and dynamics of drug-RNA complexes, but also to the development of high-throughput screening methodologies.