Research Overview
Mechanism and Structure-based Studies to Develop More Effective Therapeutics for AIDS
HIV-1 reverse transcriptase (RT) converts viral RNA into viral DNA, enabling its integration into the host genome. As such, RT is a key target for antiretroviral therapy. There are two main classes of RT inhibitors: Nucleoside Reverse Transcriptase Inhibitors (NRTIs), which competitively inhibit RT activity, and Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs), which allosterically inhibit RT by altering its conformation. Unfortunately, drug resistance arises across all classes of HIV-1 viral protein inhibitors. To address this, we are investigating the mechanisms of HIV-1 RT function and resistance, with the goal of informing the development of more effective therapeutic agents for the treatment of AIDS.
Targeting Epigenetic Proteins as Promising Anticancer and Anti-neurodegenerative Therapeutics
DNMT3B is a master regulator of gene expression by catalyzing de novo DNA CpG methylation using the co-factor S-adenosylmethionine (SAM). Therefore, targeting abnormal DNMT3B function is a promising strategy for cancer treatment. We are employing structure-guided and computer-based approaches with the aid of a high-resolution ESI-TOF mass spectrometry to develop inhibitors for this protein.
SETDB1, or ESET, is a histone H3K9 mono-, di- and tri-methyltransferase whose dysregulation results in tumorigenesis and neurodegenerative diseases. SETDB1 has an insertion of 350 amino acids in the middle of the SET domain including a ubiquitinated Lys867 essential for the enzyme activity, which leads to the unique bifurcated SET domain among all the SET domain-containing methyltransferases. The function of the insertion is unclear, and its structure is beyond the capability of current AI predictions. It is important to understand the structure and function of this one-of-a-kind SET domain protein in order to explore its full therapeutic potential. We use cryo-EM to study the structure of this enzyme and employ mass spectrometry to measure enzyme kinetics and inhibition to circumvent the tritium radioactivity quantification methods used conventionally for methyltransferases.
LINE-1 Reverse Transcripase as a Novel Anticancer Target
LINE-1 (Long Interspersed Nuclear Element-1) is a type of retrotransposon, which is often referred to as a “jumping gene,” that can copy and insert itself into different genomic locations via an RNA intermediate. L1 elements are typically epigenetically silenced during cell differentiation; however, their reactivation is strongly associated with the acquisition of oncogenic phenotypes, driven by insertional mutagenesis and/or gene expression reprogramming.
The ORF2 protein (ORF2p), which harbors both reverse transcriptase and endonuclease activities encoded by LINE-1, plays a crucial role in retrotransposition and is considered a promising target for anti-cancer drug development.
Our research focuses on discovering the allosteric binding site of ORF2p and investigating how non-nucleoside reverse transcriptase inhibitors (NNRTIs) bind to this site to inhibit its function, using an integrated approach combining structural biology, biochemistry, and structure-based drug screening.
Fragment-Based Drug Design
Fragment-based drug development (FBDD) is a cost-effective way to sample a broad chemical space. Compared to traditional FBDD where hit identification and cocrystal structure acquisition are separated, the high throughput crystallography conducted at the NSLSII 17-ID-1 @ BNL combines fragment library screening and structure acquisition in one shot. The datasets analyses and hit identification are automated through software pipelines for more efficient drug development.