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Anisenko A, Galkin S, Mikhaylov AA, Khrenova MG, Agapkina Y, Korolev S, Garkul L, Shirokova V, Ikonnikova VA, Korlyukov A, Dorovatovskii P, Baranov M, Gottikh M. KuINins as a New Class of HIV-1 Inhibitors That Block Post-Integration DNA Repair. Int J Mol Sci 2023; 24:17354. [PMID: 38139188 PMCID: PMC10744174 DOI: 10.3390/ijms242417354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Integration of HIV-1 genomic cDNA results in the formation of single-strand breaks in cellular DNA, which must be repaired for efficient viral replication. Post-integration DNA repair mainly depends on the formation of the HIV-1 integrase complex with the Ku70 protein, which promotes DNA-PK assembly at sites of integration and its activation. Here, we have developed a first-class inhibitor of the integrase-Ku70 complex formation that inhibits HIV-1 replication in cell culture by acting at the stage of post-integration DNA repair. This inhibitor, named s17, does not affect the main cellular function of Ku70, namely its participation in the repair of double-strand DNA breaks through the non-homologous end-joining pathway. Using a molecular dynamics approach, we have constructed a model for the interaction of s17 with Ku70. According to this model, the interaction of two phenyl radicals of s17 with the L76 residue of Ku70 is important for this interaction. The requirement of two phenyl radicals in the structure of s17 for its inhibitory properties was confirmed using a set of s17 derivatives. We propose to stimulate compounds that inhibit post-integration repair by disrupting the integrase binding to Ku70 KuINins.
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Affiliation(s)
- Andrey Anisenko
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (M.G.K.); (Y.A.); (S.K.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (L.G.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Simon Galkin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (L.G.)
| | - Andrey A. Mikhaylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia (V.S.); (V.A.I.); (M.B.)
| | - Maria G. Khrenova
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (M.G.K.); (Y.A.); (S.K.)
- Federal Research Centre of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Yulia Agapkina
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (M.G.K.); (Y.A.); (S.K.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Sergey Korolev
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (M.G.K.); (Y.A.); (S.K.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Lidia Garkul
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (L.G.)
| | - Vasilissa Shirokova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia (V.S.); (V.A.I.); (M.B.)
- Higher Chemical College, D.I. Mendeleev University of Chemical Technology of Russia, 125047 Moscow, Russia
| | - Viktoria A. Ikonnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia (V.S.); (V.A.I.); (M.B.)
- Higher Chemical College, D.I. Mendeleev University of Chemical Technology of Russia, 125047 Moscow, Russia
| | - Alexander Korlyukov
- Nesmeyanov Institute of Organoelement Compounds, 119334 Moscow, Russia;
- Institute of Translational Medicine and Institute of Pharmacy and Medicinal Chemistry, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | | | - Mikhail Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia (V.S.); (V.A.I.); (M.B.)
- Institute of Translational Medicine and Institute of Pharmacy and Medicinal Chemistry, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Marina Gottikh
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (L.G.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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Petri L, Egyed A, Bajusz D, Imre T, Hetényi A, Martinek T, Ábrányi-Balogh P, Keserű GM. An electrophilic warhead library for mapping the reactivity and accessibility of tractable cysteines in protein kinases. Eur J Med Chem 2020; 207:112836. [PMID: 32971426 DOI: 10.1016/j.ejmech.2020.112836] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022]
Abstract
Targeted covalent inhibitors represent a viable strategy to block protein kinases involved in different disease pathologies. Although a number of computational protocols have been published for identifying druggable cysteines, experimental approaches are limited for mapping the reactivity and accessibility of these residues. Here, we present a ligand based approach using a toolbox of fragment-sized molecules with identical scaffold but equipped with diverse covalent warheads. Our library represents a unique opportunity for the efficient integration of warhead-optimization and target-validation into the covalent drug development process. Screening this probe kit against multiple kinases could experimentally characterize the accessibility and reactivity of the targeted cysteines and helped to identify suitable warheads for designed covalent inhibitors. The usefulness of this approach has been confirmed retrospectively on Janus kinase 3 (JAK3). Furthermore, representing a prospective validation, we identified Maternal embryonic leucine zipper kinase (MELK), as a tractable covalent target. Covalently labelling and biochemical inhibition of MELK would suggest an alternative covalent strategy for MELK inhibitor programs.
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Affiliation(s)
- László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary
| | - Attila Egyed
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary
| | - Tímea Imre
- MS Metabolomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary
| | - Anasztázia Hetényi
- Department of Medicinal Chemistry, University of Szeged, Dóm Tér 8, H-6720, Szeged, Hungary
| | - Tamás Martinek
- Department of Medicinal Chemistry, University of Szeged, Dóm Tér 8, H-6720, Szeged, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary.
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Bezgin DA, Ershov OV, Ievlev MY, Belikov MY, Bardasov IN. Aqueous-Phase Synthesis and Solid-Phase Fluorescence of 3-(Methoxyphenyl)-2-cyanoacrylamides. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1070428018070217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Narendar Reddy T, Raktani B, Perla R, Ravinder M, Vaidya JR, Babu NJ. An efficient catalyst-free one-pot synthesis of primary amides from the aldehydes of the Baylis–Hillman reaction. NEW J CHEM 2017. [DOI: 10.1039/c7nj01965c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Herein, a facile and efficient method for the preparation of allyl amides from the aldehydes of Baylis–Hillman adducts has been developed using a hydroxylamine/methanol system under a catalyst-free condition.
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Affiliation(s)
- Thatikonda Narendar Reddy
- Crop Protection Chemicals Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- AcSIR
| | - Bikshapathi Raktani
- Crop Protection Chemicals Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- AcSIR
| | - Ramesh Perla
- Natural Products Chemistry Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
| | - Mettu Ravinder
- Crop Protection Chemicals Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- AcSIR
| | - Jayathirtha Rao Vaidya
- Crop Protection Chemicals Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- AcSIR
| | - N. Jagadeesh Babu
- Centre for X-ray Crystallography
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
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