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Dr. Terry Burke



Dr. Terry Burke
Bioorganic Chemistry
301-846-5906

Postdoctoral positions are available for highly talented and motivated synthetic/medicinal chemists to join the Burke laboratory. Ideal candidates will have an interest/experience in peptide/peptide mimetic chemistry and preference will be given to candidates who are also capable of performing hands-on biological assays. Applicants must be near completion or have recently completed a Ph.D. Interested candidates should contact Dr. Terrence Burke directly at burkete@mail.nih.gov and include CV, research summary and statement of expectations.

Research Summary

Development of HIV Integrase Inhibitors

FDA-approved inhibitors of HIV-1 IN belong to a class of drugs called ' integrase strand transfer inhibitors' (INSTIs), due to their ability to preferentially block the enzyme's strand transfer (ST) reaction as compared to the enzymes 3'-processing (3'-P) reaction. Unfortunately, mutant forms of IN arise that lead to clinical resistance against these INSTIs. This adds impetus to a continuing need to develop next-generation agents that have the ability to retain high antiviral efficacy against emerging strains of INSTI-resistant virus. Utilizing our laboratory's design and synthetic capabilities, we have teamed with pharmacologists (Dr. Yves Pommier, NCI), virologists (Dr. Hughes, NCI) and structural biologists (Dr. Cherepanov, the Francis Crick Institute, UK) to develop new INSTIs. In collaboration with Dr. Cherepanov we have obtained co-crystal structures of our best inhibitors bound to the prototype foamy virus (PFV) intasome (multimeric integrase with DNA substrate and metal cofactor). Using a single-round replication assay, Dr. Hughes has evaluated DTG and BIC, the leading second-generation FDA-approved INSTIs and a collection of our best inhibitors against a broad panel of INSTI-resistant mutants. Two of our inhibitors showed superior antiviral profiles than DTG and BIC across the panel of mutants. Our collaboration has recently been extended to include the Salk Institute laboratory of Dr. Dmitry Lyumkis, the NIDDK laboratory of Dr. Robert Craigie to obtain cryo-EM structures of our inhibitors bound to the catalytic site of HIV IN with DNA substrate and metal cofactor. To date, a number of high-resolution cryo-EM structures have been solved. Finally, a collaboration has been initiated with the Imperial College London laboratory of Dr. Goedele Maertens to examine a diverse selection of our IN inhibitors against human T-cell leukemia virus type 1 (HTLV-1) and a number of our synthetic constructs show significant potency against this target.

Development of Plk1 Polo-box Domain-binding Inhibitors

The Plk1 plays a central role in cell division and upregulation of Plk1 activity appears to be closely associated with aggressiveness and poor prognosis of several cancers. Targeting Plk1 may permit induction of cancer cell-selective mitotic block and apoptotic cell death in Plk1-addicted cancers. However, a potential limitation of inhibitors directed at the Plk1 kinase domain (KD) may arise from a lack of specificity due to the high degree of similarity in the ATP binding clefts among kinases, particularly among other members of the Plk family (Plk1-5). Improving Plk1 specificity is one of the most pressing concerns to address to accomplish better clinical outcomes with less toxicological problems. In addition to its catalytic KD, Plk1 also contains a non-catalytic polo-box domain (PBD), which binds to the enzyme’s physiological substrates and localizes the enzyme to discrete locations within the kinetochore. Unlike ATP-competitive inhibitors, whose specificities must be obtained against more than 500 other cellular kinases, PBD inhibitors target a structurally unique domain found in only four proteins (Plk1-3 and Plk5). Inhibition of Plk1 PBD function alone is sufficient for effectively imposing mitotic arrest and apoptotic cell death in cancer cells but not in normal cells and inhibitors of PBD-binding interactions may serve as a target-restricted strategy for developing anti-Plk1 therapeutics. Starting from the 5-mer phosphopeptide 'PLHSpT and in collaboration with the NCI laboratory of Dr. Kyung Lee and the MIT laboratory of Dr. Michael Yaffe, we initially identified peptidic inhibitors that showed from 1000- to more than 10,000-fold improved PBD-binding affinity. X-ray co-crystal structures of these peptides bound to Plk1 PBD indicated unanticipated modes of binding that take advantage of a 'cryptic' binding channel that is not present in the non-liganded PBD or engaged by the parent pentamer phosphopeptide. The cryptic pocket is accessed by means of a phenylalkyl moiety attached to the N(pi) nitrogen of the His imidazole ring. Subsequently, we have optimized these PBD-ligand interactions using an oxime ligation-based strategy. Most recently, we have utilized on-resin azide-alkyne cycloaddition reactions to introduce 1,2,3-triazole functionality into potent lead Plk1 PBD inhibitors. The triazole rings were intended either to induce conformational constraint or to serve as His mimetics. Certain of these new ligands retain the high Plk1 PBD-binding affinity of the parent peptide, while having enhanced selectivity for the PBD of Plk1 relative to the PBDs of Plk2 and Plk3. It is of note that certain peptides exhibit significantly greater than anticipated reduced affinities in full-length Plk1 ELISA assays relative to values obtained with the isolated PBD (160-fold in one case and 480-fold in a second case). The larger differences may indicate a reduced ability of these triazole-containing peptides to effectively relieve auto-inhibition arising from interdomain interactions between the KD and PBD or to engage the PBD cryptic pocket in the full-length construct. This may potentially indicate significant latitude in the structural interactions of the KD and PBD in full-length Plk1.

Development of Tdp1 Inhibitors

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) removes DNA 3′ end-blocking lesions generated by chain-terminating nucleosides and alkylating agents, and by base oxidation both in the nuclear and mitochondrial genomes. Combination therapy with Tdp1 inhibitors may potentially synergize with topoisomerase inhibitors (TOP1) to enhance selectivity and potency against cancer cells. In collaboration with the NCI laboratories of Dr. David Waugh and Dr. Yves Pommier, a crystallographic fragment screening campaign was performed against the catalytic domain of Tdp1 to identify new lead compounds for the construction of Tdp1 inhibitors. Crystal structures identified two fragments that bind to the TdpP1 active site and exhibit measurable inhibitory activity against Tdp1. The binding mode of these fragments is in a similar position in the TDP1 active site as seen in prior crystal structures of Tdp1 with bound vanadate, a transition state mimic. Using structural insights into fragment binding, we prepared several fragment derivatives, some of which exhibited significantly higher Tdp1 inhibitory potencies than the parent fragments. In a separate effort, in collaboration with the NCI laboratory of Dr. Jay Schneekloth, we have performed a Tdp1 small molecule microarray screen of over 20,000 drug-like molecules to identify new Tdp1-binding motifs. In collaboration with the laboratories of Drs. Pommier and Waugh, we are currently in the process of optimizing these initial leads.

Development of Antibody – Drug Conjugates

Antibody-drug conjugates (ADCs) constitute an important and emerging class of therapeutics. Our laboratory has a long-standing collaboration with the laboratory of Dr. Christoph Rader (Scripps Florida) to develop ADCs. This capitalizes on our expertise in small molecule and peptide mimetic chemistry. Aspects of our approach employ monoclonal antibodies and antibody Fc fragments harboring a single C-terminal selenocysteine residue (Fc-Sec). In other work, we use the 'catalytic antibody' h38C2 to effect selective covalent conjugation using azetidinone, beta-diketone and most recently, heteroaryl methylsulfonyl-containing drug payloads. We are also contributing to the development of a platform of chemically programmed bispecific antibodies (biAbs). These endow target cell-binding small molecules with the ability to recruit and redirect cytotoxic T cells to eliminate cancer cells. In parallel, we are using chimeric antigen receptor ('CAR')-engineered T cells that include the hapten-binding site of h38C2.

Research Tools

  1. ICM Browser®: Tools for Visualizing Protein Structures
    This software can be downloaded free-of-charge from the Molsoft L.L.C. web site.
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PublicationsPatents
1 - 5 of 342 results

1)  Métifiot M, Johnson BC, Kiselev E, Marler L, Zhao XZ, Burke TR, Marchand C, Hughes SH, Pommier Y.
Selectivity for strand-transfer over 3'-processing and susceptibility to clinical resistance of HIV-1 integrase inhibitors are driven by key enzyme-DNA interactions in the active site.
Nucleic Acids Res. 44: 6896-906, 2016. In Press. [Journal]

2)  Hogan Megan, Bahta Medhanit, Tsuji Kohei, Nguyen Trung X, Cherry Scott, Lountos George T, Tropea Joseph E, Zhao Bryan M, Zhao Xue Zhi, Waugh David S, Burke Terrence R, Ulrich Robert G.
Targeting Protein-Protein Interactions of Tyrosine Phosphatases with Microarrayed Fragment Libraries Displayed on Phosphopeptide Substrate Scaffolds.
ACS Comb Sci. 21: 158-170, 2019. [Journal]

3)  Zhao Xue Zhi, Tsuji Kohei, Hymel David, Burke Terrence R.
Development of Highly Selective 1,2,3-Triazole-containing Peptidic Polo-like Kinase 1 Polo-box Domain-binding Inhibitors.
Molecules. 24, 2019. [Journal]

4)  Lountos George, Zhao Xue Zhi, Kieselev Evgeny, Tropea Joseph, Needle Danielle, Pommier Yves, Burke Terrence, Waugh David.
Identification of ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening.
Nuclei Acids Res. 1: 1, 2019. [Journal]

5)  Smith Steven J, Zhao Xue Zhi, Burke Terrence R, Hughes Stephen H.
HIV-1 Integrase Inhibitors That Are Broadly Effective against Drug-Resistant Mutants.
Antimicrob. Agents Chemother. 62, 2018. [Journal]

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