Research Overview

The overarching research objective of our laboratory is to delineate the chemical basis of the molecular recognition events employed by biomolecules to drive important biological processes. We are interested in how perturbation of molecular recognition, by natural and synthetic ligands, can be used to understand the molecular basis of biological processes. In the pursuit of our research, we find inspiration in the fact that the basic molecular recognition principles in globular RNAs and proteins are one and the same. In this line of thought, one of the primary research focuses of our laboratory is the use of common molecular template to design new ligands for RNA and protein targets. Histone deacetylases and ribosomes are the current targets in this project. The ligands that have resulted from these studies have been used to probe the molecular basis of the function of their respective targets. Also, many elicit practical and desirable bioactivities including anti-tumor and anti-infective activities. Furthermore, our laboratory is involved in an interdisciplinary collaboration with the El-Sayed’s group on the design of new organic ligand conjugated gold nanoparticles (AuNPs) for cell selective delivery. Individual research project in our laboratory involves a unique blend of the tools of synthetic organic chemistry, computational chemistry, biochemistry and molecular biology. Enumerated below are specific interrelated research projects that are currently underway:

(1) Nonpeptide macrocyclic histone deacetylase inhibitors (HDACi)

HDACi are useful molecular probes of histone deacetylase (HDAC) function and an emerging class of novel anti-cancer drugs. Several HDACi have been identified in the literature including suberoylanilide hydroxamic acid (SAHA) and FK228 (romidepsin), both approved by the FDA for the treatment of cutaneous T cell lymphoma. However, the majority of these compounds non-selectively inhibit the deacetylase activity of class I and II HDACs. At the fore of HDAC drug development is the identification of isoform-selective HDACi with the potential for enhanced potency and reduced side effects. However, these efforts have been so far modestly successful. Premised on an original proposal that targeted HDAC inhibition is a viable alternative for isoform-selective HDAC inhibition, we are working on the design, synthesis and characterization of new HDACi endowed with tissue/organ selective distribution profiles. Toward this end, we have focused on macrolides templates, such as azithromycin (AZ), clarithromycin (CL) and TE-802, which have been shown in preclinical and clinical (AZ & CL) studies to have tissue selective distribution profiles. We envisioned that the macrolide templates could engage in productive interactions with large hydrophobic patches at the outer rim of HDACs, thereby enabling proper presentation of an appropriately placed zinc binding group (ZBG) to the catalytic zinc ion for optimum HDAC activity inhibition. HDACi based on these macrocyclic templates should possess targeted anticancer activity due to selective tissue distribution conferred by the appended macrolide moiety.

Using a combination of the tools of synthetic organic chemistry, computational chemistry and cell based assays; we have identified over two-dozen macrocyclic HDACi, derived from AZ, CL and TE-802, which elicit selective and potent anti-proliferative activity against various human cancer cell lines. These compounds have improved enzyme inhibition potency and isoform-selectivity. Computational analyses enabled us to have an understanding of the roles of the interaction between the HDAC enzymes outer rim and the inhibitors’ macrocyclic templates that are responsible for enhanced affinity and isoform selectivity. We found that the macrocyclic templates of these HDACi adopt multiple, yet productive docked postures. In the pursuit of this project, we have also introduced into the literature new HDACi SAR.

Another shortcoming of current HDACi is the broadness of their biological responses which could compromise their efficacy and therefore constitute a major obstacle to their long-term clinical use. An understanding of the structural attributes that confer a specific biological response to HDACi is vital. Toward this end, we are investigating the effects of our HDACi on the viability of many transformed human cell lines and two representative examples of rapidly proliferative pathogenic eukaryotes – Plasmodium falciparum and Leismania donovani, the causative parasites of human malaria and leishmaniasis respectively. These studies have furnished important information regarding specific structural attributes that confer (enhance) a specific biological response to these HDACi. To investigate the tissue distribution profiles of our macrocyclic HDACi, we have developed a facile screening method that uses C-14 tag to follow the fate of the macrocyclic HDACi in healthy mice Balb/c mice. Using this facile screening method, we have identified two lead compounds as promising candidates that are selectively accumulated in the lungs.

As part of our future plans, we will expand our investigation to include other macrolide skeletons and systematically probe the effects of macrolide-type, ZBG and the linker group on compounds’ anti-HDAC activity. We will also extend this concept to design HDACi derived from other small molecule endowed with organ selective distribution. Additionally, we will advance the two lead compounds that we have identified into in vivo efficacy studies using a mouse orthotopic lung cancer model. This research is currently funded by an RO1 grant with Prof. Oyelere as the sole PI.

(2) Bio-inspired approaches to targeted delivery of gold nanoparticles.

In line with our interest in targeted delivery of small molecules, another direction of our program is targeted delivery of supramolecular architectures, specifically plasmonic AuNPs. Our efforts in this area, in collaboration with the El-sayed group, focused on the use of small molecules to achieve selective delivery of AuNPs. We published our first observation on the use of the nucleus localizing peptide from simian virus (SV40, NLS Peptide) in Bioconjugate Chemistry in July 2007. This article is among one of the most-accessed articles published in Bioconjugate Chem. in the 3rd quarter of 2007 (Source: http://pubs.acs.org/journals /bcches/promo/most/most_accessed/index.html) and one of the Editor selected paper in imaging representing high quality, peer reviewed research published in the journal.

In a follow-up study, we have discovered that we could achieve a selective targeting and destruction of cancer cells using a multifunctional vector approach. Relatedly, we have discovered that small molecules that target surface receptors, over-expressed on some tumors, could facilely facilitate selective uptake of appropriately appended AuNPs. Specifically, we have demonstrated that tamoxifen, through its interaction with estrogen receptor alpha (ERα), facilitated a selective uptake of tamoxifen functionalized AuNPs into MCF-7, a hormone positive human breast cancer cell line. This suggests that membrane ERα is an active participant in the genomic effects of estrogen receptors in addition to its widely accepted nongenomic roles. Supported by a program grant from the NIH [Oyelere Co-PI with PIs Mostafa A. El-Sayed & Dong M. Shin (Emory)], we are now designing AuNPs that target macrophage cells, prostate and head and neck tumors. Additionally, we are engineering AuNPs capable of self clearance from tissues/organs after photothermal and or similar treatments.

(3) Nucleic acid-small molecule interaction.

Our laboratory’s interests in nucleic acid biochemistry range from the elucidation of the molecular basis of their interaction with their ligands and the development of enabling chemistries for facile derivatization of nucleic acid analogs. We have initiated related studies aimed at understanding the molecular principles of the recognition of RNA structural motifs by small molecules and peptides.

In a recent publication, we showed that anthracyclines preferentially bind to the GU wobble pair in ferritin iron-responsive elements (IREs) RNAs. IREs serve as the main control mechanism for iron metabolism in the cell via their interaction with the Iron Regulatory Proteins (IRPs). This is an important model system to investigate because such an undertaking may have implication on the mechanism of aberration of intracellular iron homeostatis upon anthracycline exposure. In a related study, we have shown that anthracyclines preferentially bind to GT mismatch sites on DNA hairpins. These studies suggest that the noncanonical base pairs may serve as ubiquitous recognition sites for anthracycline.

The major thrust of our current work in nucleic acid biochemistry is to gain an understanding of how the ribosome, the largest naturally occurring ribozyme so far known, distinguishes between some peptide sequences while facilitating unhindered passage of the vast majority of peptides through the peptide exit tunnel. An atomic level description of such specific nascent peptide-exit tunnel interactions is still in its infancy. The availability of molecular probes that allow for precise placement of any peptide sequence within a defined region of the peptide exit tunnel would enrich our knowledge of the roles of this crucial ribosome segment in translation. We have designed such probes and initial biochemical analyses have revealed that these compounds avidly bind to the ribosome. Efforts are under way to obtain structural information on the interaction of these probes with the ribosome. We anticipate that our approach will provide a general means to directly interrogate the nascent peptide-exit tunnel interactions. Our work on nucleic acid-ligand interaction is currently funded in part through a NASA centre grant on which Prof. Oyelere is a co-PI (PI: L. D. Williams).