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Kirsch P, Stein SC, Berwanger A, Rinkes J, Jakob V, Schulz TF, Empting M. Hit-to-lead optimization of a latency-associated nuclear antigen inhibitor against Kaposi’s sarcoma-associated herpesvirus infections. Eur J Med Chem 2020; 202:112525. [DOI: 10.1016/j.ejmech.2020.112525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/25/2020] [Accepted: 05/30/2020] [Indexed: 12/15/2022]
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Kirsch P, Jakob V, Oberhausen K, Stein SC, Cucarro I, Schulz TF, Empting M. Fragment-Based Discovery of a Qualified Hit Targeting the Latency-Associated Nuclear Antigen of the Oncogenic Kaposi's Sarcoma-Associated Herpesvirus/Human Herpesvirus 8. J Med Chem 2019; 62:3924-3939. [PMID: 30888817 DOI: 10.1021/acs.jmedchem.8b01827] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The latency-associated nuclear antigen (LANA) is required for latent replication and persistence of Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8. It acts via replicating and tethering the virus episome to the host chromatin and exerts other functions. We conceived a new approach for the discovery of antiviral drugs to inhibit the interaction between LANA and the viral genome. We applied a biophysical screening cascade and identified the first LANA binders from small, structurally diverse compound libraries. Starting from a fragment-sized scaffold, we generated optimized hits via fragment growing using a dedicated fluorescence-polarization-based assay as the structure-activity-relationship driver. We improved compound potency to the double-digit micromolar range. Importantly, we qualified the resulting hit through orthogonal methods employing EMSA, STD-NMR, and MST methodologies. This optimized hit provides an ideal starting point for subsequent hit-to-lead campaigns providing evident target-binding, suitable ligand efficiencies, and favorable physicochemical properties.
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Affiliation(s)
- Philine Kirsch
- Department of Drug Design and Optimization (DDOP) , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Pharmacy , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , 66123 Saarbrücken , Germany
| | - Valentin Jakob
- Department of Drug Design and Optimization (DDOP) , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Pharmacy , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany
| | - Kevin Oberhausen
- Department of Drug Design and Optimization (DDOP) , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Pharmacy , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany
| | - Saskia C Stein
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , 66123 Saarbrücken , Germany.,Institute of Virology , Hannover Medical School , Carl-Neuberg-Strasse 1 , 30625 Hannover , Germany
| | - Ivano Cucarro
- Department of Drug Design and Optimization (DDOP) , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Pharmacy , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany
| | - Thomas F Schulz
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , 66123 Saarbrücken , Germany.,Institute of Virology , Hannover Medical School , Carl-Neuberg-Strasse 1 , 30625 Hannover , Germany
| | - Martin Empting
- Department of Drug Design and Optimization (DDOP) , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Pharmacy , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , 66123 Saarbrücken , Germany
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Sanchez-Weatherby J, Moraes I. Crystal Dehydration in Membrane Protein Crystallography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:73-89. [PMID: 27553236 PMCID: PMC6126552 DOI: 10.1007/978-3-319-35072-1_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Crystal dehydration has been successfully implemented to facilitate the structural solution of a number of soluble and membrane protein structures over the years. This chapter will present the currently available tools to undertake controlled crystal dehydration, focusing on some successful membrane protein cases. Also discussed here will be some practical considerations regarding membrane protein crystals and the relationship between different techniques in order to help researchers to select the most suitable technique for their projects.
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Affiliation(s)
| | - Isabel Moraes
- Membrane Protein Laboratory, Diamond Light Source/Imperial College London, Harwell Campus, Didcot, Oxfordshire UK
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The 3D structure of Kaposi sarcoma herpesvirus LANA C-terminal domain bound to DNA. Proc Natl Acad Sci U S A 2015; 112:6694-9. [PMID: 25947153 DOI: 10.1073/pnas.1421804112] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kaposi sarcoma herpesvirus (KSHV) persists as a latent nuclear episome in dividing host cells. This episome is tethered to host chromatin to ensure proper segregation during mitosis. For duplication of the latent genome, the cellular replication machinery is recruited. Both of these functions rely on the constitutively expressed latency-associated nuclear antigen (LANA) of the virus. Here, we report the crystal structure of the KSHV LANA DNA-binding domain (DBD) in complex with its high-affinity viral target DNA, LANA binding site 1 (LBS1), at 2.9 Å resolution. In contrast to homologous proteins such as Epstein-Barr virus nuclear antigen 1 (EBNA-1) of the related γ-herpesvirus Epstein-Barr virus, specific DNA recognition by LANA is highly asymmetric. In addition to solving the crystal structure, we found that apart from the two known LANA binding sites, LBS1 and LBS2, LANA also binds to a novel site, denoted LBS3. All three sites are located in a region of the KSHV terminal repeat subunit previously recognized as a minimal replicator. Moreover, we show that the LANA DBD can coat DNA of arbitrary sequence by virtue of a characteristic lysine patch, which is absent in EBNA-1 of the Epstein-Barr virus. Likely, these higher-order assemblies involve the self-association of LANA into supermolecular spirals. One such spiral assembly was solved as a crystal structure of 3.7 Å resolution in the absence of DNA. On the basis of our data, we propose a model for the controlled nucleation of higher-order LANA oligomers that might contribute to the characteristic subnuclear KSHV microdomains ("LANA speckles"), a hallmark of KSHV latency.
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