students in lab using microscope

Research Programs

The Institute’s current Fellows research initiatives include:

Inhibitors of parasitic mitogen-activated protein kinases (MAPKs) as potential anti-parasitic therapeutics and the mechanism of HIV Nef protein activation of host p38 MAPK and induction of Fas ligand.

  • Dr. John Siekierka, Institute Director, Chemistry and Biochemistry
  • Dr. Ronald Goldberg, Associate Fellow

We are focused on the development of small molecule inhibitors of parasite mitogen-activated protein kinases (MAP kinases) as potential therapeutic agents. Research is currently underway on a Leishmania MAPK and a MAPK found in the parasitic nematode, Brugia malayiLeishmania, the causative agent of Leishmaniasis, is second only to malaria in terms of global morbidity. Brugia malayi is the causative agent of Lymphatic filariasis or elephantiasis, a serious debilitating disease endemic in Southeast Asia and Indonesia. Our laboratory also conducts research on HIV viral protein interactions with host p38 MAP kinase leading to evasion of virally-infected T-cell from immune surveillance.

Dr. Ronald Goldberg has joined Dr. Siekierka’s laboratory as Associate Sokol Institute Fellow. Dr. Goldberg has over 20 years of experience in pharmaceutical research and most recently was laboratory director at Novartis. Dr. Goldberg’s expertise is in Inflammatory Diseases, assay development and high-throughput screening.

Predicting drug-target relationships for dihydrofolate reductase (DHFR) homologs through phylogenetic analysis.

  • Dr. Nina Goodey, Chemistry and Biochemistry
  • Dr. Katherine Herbert, Computer Science

The goal of this project is to discover and exploit homology relationships between DHFRs from various organisms and to predict novel drug-DHFR interactions in pathogenic organisms through the creation of a new computational toolkit called “DrugTree”. We are using the enzyme dihydrofolate reductase as a model system to predict which existing drugs that have already been found to successfully inhibit this enzyme in one organism can be used to inhibit the same enzyme in another organism, thereby leading to new therapeutic uses for know drugs. While these tools will be applicable to other enzyme systems, dihydrofolate reductase is both an important target and a good model system. This enzyme is a validated drug target for treatment of various parasitic diseases such as malaria, trypanosomiasis (African sleeping sickness), Changa’s disease, and tuberculosis.

Binding of ICER (Inducible cAMP Early Repressor) to Its Own Promoter as a Mode of Cooperative Regulation.

  • Dr. Hans Schelvis, Chemistry and Biochemistry
  • Dr. Carlos Molina, Biology and Molecular Biology

Inducible cAMP Early Repressor (ICER) is a regulator of cAMP signaling in the cell. ICER can be found in normal cells but it is not present in tumor cells. The growth of these tumor cells is attentuated when ICER protein is artificially reintroduced in these cells. Therefore it is hypothesized that ICER manipulation could potentially be used as a new therapy for the treatment of cancer. Although much is known about the physiological role of ICER, little is known about the regulation of the gene. We are studying one aspect of ICER regulation, negative autoregulation of ICER by binding to its own regulatory sequences. In other words, how the ICER protein can turn off its own production in the cell, when its concentration in the cell becomes too high.

Design of Photoprobes to Study a Heme-GAPDH Complex.

  • Dr. David Konas, Chemistry and Biochemistry

Heme proteins play essential roles in biochemical processes including electron transfer, signal transduction, and oxygen storage. Insertion of heme into apo-proteins is a post-translational event, which is complicated by the fact that free heme is toxic within cells. Despite its importance, very little is currently known the mechanisms of intracellular heme transport or heme insertion in mammals. Nitric oxide (NO) blocks heme insertion into a broad range of heme proteins, and its action with respect to inducible nitric oxide synthase heme insertion involves nitrosylation of a GAPDH cysteine residue. Thus, GAPDH is identified as a cytosolic protein involved in regulating heme insertion. New photoaffinity-based probes are being designed for synthesis and use in obtaining structural information about the GAPDH-heme complex.

Multifunctional Poly-Amidoamine Dendrimers as Nanocarriers to Deliver Non-Polar Anticancer Drug Molecules into Human Breast Cancer Cells.

  • Dr. Shifeng Hou, Chemistry and Biochemistry

The use of nanotechnology as alternative treatment options for a variety of diseases is steadily increasing. The nanomaterial based drug delivery system involves the use of man-made, nano-sized (typically one billionths of a meter in size) particles called nanoparticles. Nanocarriers for drug delivery can generate new dosage forms that are easier to administer, more pleasant for the patient to take, and confer a competitive advantage in the marketplace. Dendrimers, a particular type of nanoparticle, are precisely engineered to carry molecules that are enclosed in their structure and can be used as vehicles to specifically deliver drugs only to affected cells while sparing healthy cells. Our work focused on the use of dendrimers to deliver non-water soluble drug molecules, mainly triptolide, a natural anticancer agent, to induce apoptosis in MCF-7 human breast cancer cells. In our protocols, the dendrimer will encapsulate the non-water soluble drug into its hydrophobic core and enable the drug to solubilize in water. This can overcome the problem of poor solubility of drug in water, which will significantly decrease the treatment dosage, minimize the side effects, and increase the delivery capacities. Some achievements in our studies are as follows: (i) to our knowledge, we are the first to have encapsulated triptolide into dendrimers. A series of dendrimers (poly-amidoamine) with hydrophobic cores of various alkyl lengths (C2, C4, C6, and C12) were used as drug carriers to load relatively insoluble triptolide into dendrimers. Briefly, triptolide and the dendrimer were dissolved in methanol, the solutions were mixed, and then the dendrimer was separated from triptolide; (ii) the dendrimers encapsulated with triptolide were characterized using UV, NMR, and HPLC-MS. We will introduce dendrimers into MCF-7 cells and then release triptolide in subcellular locations via a controlled concentration-time delivery profile; and (iii) magnetic nanoparticles were introduced into dendrimer cores. The magnetic force will enable delivery of dendrimer triptolide complexes directly to cancer cells in vivo. Our findings will foster the development of novel treatments against breast cancer.

Effects of Changed Body Composition & Energy Expenditures from Alterations in Physical Activity Levels.

  • Dr. Diana Thomas, Mathematical Sciences

Although many obesity interventions include physical activity, the specific changes in body composition and energy expenditures as a result of alterations in physical activity is not well understood. We examined how transitions in physical activity from intense athletic training to off-training periods impact body composition, resting energy expenditure, duration and intensity of vigorous physical activity, activity energy expenditures, sedentary periods, and sleep duration. ) This is an ongoing longitudinal study in young male college hockey players (n=10, ages 18 to 22) who underwent an intense period of training followed by an off-season period. Body composition was assessed once during the intense training period followed by another off- season measurement by dual energy X-ray aborpiometry at a Bone Density laboratory. Simultaneous measurements of resting energy expenditures (REE) were performed using indirect calorimetry. Subjects wore the Sense Wear armband (Body Media, Pittsburgh, PA) continuously for a duration of 3 days in a baseline period, intense training period, and off season period. The armband recorded sleep duration, total energy expenditures, bouts of vigorous physical activity, and sedentary periods. Energy intake was approximated by summing total energy expenditures with changed body composition energy stores. We observed that REE was higher than expected as predicted by the Mifflin resting metabolic rate equation and the Livingston-Kohlstadt equation. We confirmed previous results that highly trained individuals have higher REE than expected even after adjusting for body composition.

Fast Ligand?GPCR Docking Program Using Chemscore and Parallelized Tribe Particle Swarm Optimization.

  • Dr. Wenwei Xiong, Biology and Molecular Biology

We report the progress of a computational study on ligand binding with G Protein-Coupled Receptor (GPCR). A fast parallel program has been developed for virtual molecular docking that takes the full advantage of state-of-the-art multicore cluster computers. Using Message Passing Interface standard (MPI), the parallel program performs automatic docking between a target protein and a huge number of small molecules by distributing tasks to multiple cores. Using the efficient optimal-site search algorithm tribe-PSO (tribe Particle Swarm Optimization) and scoring function chemscore, the parallel program tries docking as many ligands as allowed by the cluster with the target GPCR to find those ligands with lowest affinity binding energy. These ligands sifted through by the program will be the first-round candidates for new lead compounds interacting with the GPCR. The completed program may find its use in assisting in cost-effective drug design processes.