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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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Recent Advances in Protein-Protein Interactions. Int J Mol Sci 2023; 24:ijms24021282. [PMID: 36674795 PMCID: PMC9864157 DOI: 10.3390/ijms24021282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Protein-protein interactions (PPIs) lead to formation of complexes and aggregates between a pair or multiple protein molecules [...].
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Association of Polymorphisms in NHEJ Pathway Genes with HIV-1 Infection and AIDS Progression in a Northern Chinese MSM Population. DISEASE MARKERS 2022; 2022:5126867. [PMID: 36312587 PMCID: PMC9605847 DOI: 10.1155/2022/5126867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 10/07/2022] [Indexed: 11/17/2022]
Abstract
Background and Aims Men who have sex with men (MSM) are at high risk of HIV infection. The nonhomologous end joining (NHEJ) pathway is the main way of double-stranded DNA break (DSB) repair in the higher eukaryotes and can repair the DSB timely at any time in cell cycle. It is also indicated that the NHEJ pathway is associated with HIV-1 infection since the DSB in host genome DNA occurs in the process of HIV-1 integration. The aim of the present investigation was to evaluate associations of single-nucleotide polymorphisms (SNPs) in NHEJ pathway genes with susceptibility to HIV-1 infection and AIDS progression among MSM residing in northern China. Methods A total of 481 HIV-1 seropositive men and 493 HIV-1 seronegative men were included in this case-control study. Genotyping of 22 SNPs in NHEJ pathway genes was performed using the SNPscan™ Kit. Results Positive associations were observed between XRCC6 rs132770 and XRCC4 rs1056503 genotypes and the susceptibility to HIV-1 infection. In gene-gene interaction analysis, significant SNP-SNP interactions of XRCC6 and XRCC4 genetic variations were found to play a potential role in the risk of HIV-1 infection. In stratified analysis, XRCC5 rs16855458 was significantly associated with CD4+ T cell counts in AIDS patients, whereas LIG4 rs1805388 was linked to the clinical phases of AIDS patients. Conclusions NHEJ gene polymorphisms can be considered to be risk factors of HIV-1 infection and AIDS progression in the northern Chinese MSM population.
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Complex Relationships between HIV-1 Integrase and Its Cellular Partners. Int J Mol Sci 2022; 23:ijms232012341. [PMID: 36293197 PMCID: PMC9603942 DOI: 10.3390/ijms232012341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
RNA viruses, in pursuit of genome miniaturization, tend to employ cellular proteins to facilitate their replication. HIV-1, one of the most well-studied retroviruses, is not an exception. There is numerous evidence that the exploitation of cellular machinery relies on nucleic acid-protein and protein-protein interactions. Apart from Vpr, Vif, and Nef proteins that are known to regulate cellular functioning via interaction with cell components, another viral protein, integrase, appears to be crucial for proper virus-cell dialog at different stages of the viral life cycle. The goal of this review is to summarize and systematize existing data on known cellular partners of HIV-1 integrase and their role in the HIV-1 life cycle.
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