Baek Kim, PhD
Director, Center for Drug Discovery
Research Projects in Progress
(A) Enzymology of HIV-1 reverse transcriptase: Molecular evolution, mutagenesis and cell tropism of lentiviruses
HIV-1 reverse transcriptase is the most error-prone DNA polymerases among known replication DNA polymerases. Our research primarily focuses on mechanistic and structural understanding of the error-prone active site of HIV-1 RT. Other RTs with high fidelity such as MuLV RT are also studied, in order to identify molecular elements that contribute to the fidelity difference between HIV-1 and oncoretroviral RTs. For this study we employ both pre-steady and steady state kinetic analyses as well as other well established fidelity assays such as M13 lacZα forward mutation assay and gel-based misincorporation assay. Next, we also focus on the contribution of RT fidelity to HIV-1 genomic mutagenesis, evolution and escape using various virological methodologies. Finally, we recently showed that HIV-1 RT also incorporates rNTPs during DNA synthesis in macrophages, but not in T cells. The effect of rNTP incorporation on HIV-1 replication kinetics, genomic mutagenesis and cell tropism are under active investigation. Our observation has also led us to identify 3’ deoxy rN compounds a new class of anti-HIV drugs, which uniquely block HIV-1 replication in nondividing target cell types such as macrophages and microglia. This study is currently being supported by NIH R01 AI049781. Recently our study on dNTP pools in macrophages was recognized by three publications in Nature, which reported a new anti-HIV host factor, SAMDH1, and our follow-up study proving that SAMHD1 is responsible for the poor dNTP pool in macrophages was recently published in Nature Immunology (see press coverage in BBC).
(B) HIV-1 and macrophage reservoirs: HIV-1 infected macrophages are long-living viral reservoirs that persistently produce viral particles. We reported that HIV-1 infection proactively regulates the PI3K/Akt cell survival pathway using viral Tat protein. This observation enabled us to explore PI3K and Akt inhibitors, which were already developed for cancer drugs, for their effect on antagonizing the long-term survival phenotype of HIV-1 infected macrophages. Medicinal chemistry and cell signaling are two major research interests in this project. This research activity includes collaborations with Dr. Stephen Dewhurst and Dr. Vicente Planelles (University of Utah). This study is currently being funded by NIH R01 AI077401.
(C) Enzymology and fidelity of avian influenza virus RNA polymerases: We are examining the enzymatic fidelity and mechanisms of avian and H5N1 influenza RNA polymerases, and the role of the polymerase in viral evolution and host adaptation. We are also exploring the endonuclease activity of the PA subunit of the influenza virus RNA polymerase. As part of this work, we have established the first high-throughput assay platform that uses the full length PA protein for small molecule screening and early-phase drug discovery. This project is a part of a NIH contract awarded through the NIH CEIRS network, as part of the University of Rochester’s New York Influenza Center of Excellence (NYICE; Co-PI, NIH HHSN26620077778C).
(D) Recombination and HIV-1 evolution: Research activities on identifying molecular determinants of lentiviral recombination. These studies focus on the roles of RT processivity, viral cis-acting sequences (secondary structures) and RT polymerase kinetics in viral recombination frequency. These research activities include collaborations with Dr. Robert A. Bambara (Co-PI, NIH GM049573)