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Conway PJ, Dao J, Kovalskyy D, Mahadevan D, Dray E. Polyploidy in Cancer: Causal Mechanisms, Cancer-Specific Consequences, and Emerging Treatments. Mol Cancer Ther 2024; 23:638-647. [PMID: 38315992 DOI: 10.1158/1535-7163.mct-23-0578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/19/2023] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
Drug resistance is the major determinant for metastatic disease and fatalities, across all cancers. Depending on the tissue of origin and the therapeutic course, a variety of biological mechanisms can support and sustain drug resistance. Although genetic mutations and gene silencing through epigenetic mechanisms are major culprits in targeted therapy, drug efflux and polyploidization are more global mechanisms that prevail in a broad range of pathologies, in response to a variety of treatments. There is an unmet need to identify patients at risk for polyploidy, understand the mechanisms underlying polyploidization, and to develop strategies to predict, limit, and reverse polyploidy thus enhancing efficacy of standard-of-care therapy that improve better outcomes. This literature review provides an overview of polyploidy in cancer and offers perspective on patient monitoring and actionable therapy.
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Affiliation(s)
- Patrick J Conway
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas
- Department of Molecular Immunology & Microbiology, University of Texas Health San Antonio, San Antonio, Texas
| | - Jonathan Dao
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, Texas
| | - Dmytro Kovalskyy
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, Texas
| | - Daruka Mahadevan
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas
- Department of Molecular Immunology & Microbiology, University of Texas Health San Antonio, San Antonio, Texas
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Eloise Dray
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, Texas
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
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2
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Chernii S, Losytskyy M, Tretyakova I, Kharchuk M, Vakarov S, Kovalskyy D, Gerasymchyk Y, Pekhnyo V, Chernii V, Kovalska V. Inhibition of heat-induced protein aggregation by zirconium phthalocyanines. Proteins 2023. [PMID: 36732896 DOI: 10.1002/prot.26475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
Specific proteins found in food sources tend to aggregate into fibrils under heat treatment; studying these aggregation processes and developing tools to control protein heat-induced aggregation is an active area of research. Phthalocyanine complexes are known to exhibit antiprionic and anti-fibrillogenic activity. Thus, the anti-fibrillogenic effect of a series of Zr phthalocyanines with different out-of-plane coordinated ligands, namely positively charged (PcZrLys2 ), negatively charged (PcZrCitr2 ), and group able to form disulfide bridges (PcZrS2 ), on the heat-induced aggregation of such proteins as BLG, insulin, and lysozyme was studied. The inhibition of reaction activity up to about 90% was observed in the presence of these compounds for all proteins. The effective concentration of the inhibitor was calculated for the compound with the highest activity (PcZrS2 ) to be 10.6 ± 3.6 and 7.3 ± 1.2 μM/L, respectively. Fluorescence spectroscopy studies demonstrated similar binding constants of three phthalocyanines binding with BLG globule. This is consistent with the results of molecular dynamics simulation, which imply the interaction of the globule with the tetrapyrrole macrocycle of phthalocyanine, leading to the globule stabilization. At the same time, TEM shows that in the presence of phthalocyanine PcZrS2 , thinner and longer fibrils were formed compared to control in all three proteins (BLG, insulin, and lysozyme). Thus, we can conclude that phthalocyanine PcZrS2 affects the amyloid aggregation's general mechanism, which is typical for proteins of different structures. Therefore, the phthalocyanine PcZrS2 is proposed as an anti-amyloidogenic agent suppressing heat-induced aggregation of proteins of different structures, making it potentially suitable for application in the food industry.
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Affiliation(s)
- Svitlana Chernii
- Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine.,V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU, Kyiv, Ukraine
| | - Mykhaylo Losytskyy
- Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine.,Faculty of Physics, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Iryna Tretyakova
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU, Kyiv, Ukraine
| | - Maksym Kharchuk
- Danylo Zabolotny Institute of Microbiology and Virology, NASU, Kyiv, Ukraine
| | - Serhii Vakarov
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU, Kyiv, Ukraine
| | - Dmytro Kovalskyy
- Greehey Children Cancer Research Institute, The University of Texas Health Science Center, San Antonio, Texas, USA
| | - Yuriy Gerasymchyk
- Institute of Low Temperature and Structure Research, PAS, Wrocław, Poland
| | - Vasyl Pekhnyo
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU, Kyiv, Ukraine
| | - Viktor Chernii
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU, Kyiv, Ukraine
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3
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Kamdem N, Roske Y, Kovalskyy D, Platonov M, Balinskyi O, Kreuchwig A, Saupe J, Fang L, Diehl A, Schmieder P, Krause G, Rademann J, Heinemann U, Birchmeier W, Oschkinat H. Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling. Magn Reson (Gott) 2021; 2:355-374. [PMID: 37904770 PMCID: PMC10539800 DOI: 10.5194/mr-2-355-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/28/2021] [Indexed: 11/01/2023]
Abstract
Dishevelled (Dvl) proteins are important regulators of the Wnt signalling pathway, interacting through their PDZ domains with the Wnt receptor Frizzled. Blocking the Dvl PDZ-Frizzled interaction represents a potential approach for cancer treatment, which stimulated the identification of small-molecule inhibitors, among them the anti-inflammatory drug Sulindac and Ky-02327. Aiming to develop tighter binding compounds without side effects, we investigated structure-activity relationships of sulfonamides. X-ray crystallography showed high complementarity of anthranilic acid derivatives in the GLGF loop cavity and space for ligand growth towards the PDZ surface. Our best binding compound inhibits Wnt signalling in a dose-dependent manner as demonstrated by TOP-GFP assays (IC50 ∼ 50 µ M ) and Western blotting of β -catenin levels. Real-time PCR showed reduction in the expression of Wnt-specific genes. Our compound interacted with Dvl-1 PDZ (KD = 2.4 µ M ) stronger than Ky-02327 and may be developed into a lead compound interfering with the Wnt pathway.
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Affiliation(s)
- Nestor Kamdem
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Dmytro Kovalskyy
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- ChemBio Ctr, Taras Shevchenko National University of Kyiv, 62 Volodymyrska, Kyiv 01033, Ukraine
| | - Maxim O. Platonov
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- ChemBio Ctr, Taras Shevchenko National University of Kyiv, 62 Volodymyrska, Kyiv 01033, Ukraine
| | - Oleksii Balinskyi
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- ChemBio Ctr, Taras Shevchenko National University of Kyiv, 62 Volodymyrska, Kyiv 01033, Ukraine
| | - Annika Kreuchwig
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Jörn Saupe
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Liang Fang
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Anne Diehl
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Gerd Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Jörg Rademann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Pharmazie, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
| | - Udo Heinemann
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Walter Birchmeier
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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4
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Leblanc R, Kashyap R, Barral K, Egea-Jimenez AL, Kovalskyy D, Feracci M, Garcia M, Derviaux C, Betzi S, Ghossoub R, Platonov M, Roche P, Morelli X, Hoffer L, Zimmermann P. Pharmacological inhibition of syntenin PDZ2 domain impairs breast cancer cell activities and exosome loading with syndecan and EpCAM cargo. J Extracell Vesicles 2020; 10:e12039. [PMID: 33343836 PMCID: PMC7737769 DOI: 10.1002/jev2.12039] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 11/02/2020] [Accepted: 11/14/2020] [Indexed: 12/17/2022] Open
Abstract
Exosomes support cell-to-cell communication in physiology and disease, including cancer. We currently lack tools, such as small chemicals, capable of modifying exosome composition and activity in a specific manner. Building on our previous understanding of how syntenin, and its PDZ partner syndecan (SDC), impact on exosome composition we optimized a small chemical compound targeting the PDZ2 domain of syntenin. In vitro , in tests on MCF-7 breast carcinoma cells, this compound is non-toxic and impairs cell proliferation, migration and primary sphere formation. It does not affect the size or the number of secreted particles, yet it decreases the amounts of exosomal syntenin, ALIX and SDC4 while leaving other exosomal markers unaffected. Interestingly, it also blocks the sorting of EpCAM, a bona fide target used for carcinoma exosome immunocapture. Our study highlights the first characterization of a small pharmacological inhibitor of the syntenin-exosomal pathway, of potential interest for exosome research and oncology.
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Affiliation(s)
- R Leblanc
- Equipe labellisée Ligue 2018 Centre de Recherche en Cancérologie de Marseille (CRCM) Aix-Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes Marseille France
| | - R Kashyap
- Equipe labellisée Ligue 2018 Centre de Recherche en Cancérologie de Marseille (CRCM) Aix-Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes Marseille France
| | - K Barral
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - A L Egea-Jimenez
- Equipe labellisée Ligue 2018 Centre de Recherche en Cancérologie de Marseille (CRCM) Aix-Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes Marseille France
| | - D Kovalskyy
- Enamine Ltd. Kyiv Ukraine.,Taras Shevchenko National University of Kyiv Kyiv Ukraine
| | - M Feracci
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - M Garcia
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - C Derviaux
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - S Betzi
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - R Ghossoub
- Equipe labellisée Ligue 2018 Centre de Recherche en Cancérologie de Marseille (CRCM) Aix-Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes Marseille France
| | - M Platonov
- Enamine Ltd. Kyiv Ukraine.,Institute of Molecular Biology and Genetics National Academy of Sciences of Ukraine Kyiv Ukraine
| | - P Roche
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - X Morelli
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - L Hoffer
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - Pascale Zimmermann
- Equipe labellisée Ligue 2018 Centre de Recherche en Cancérologie de Marseille (CRCM) Aix-Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes Marseille France.,Department of Human Genetics K. U. Leuven Leuven Belgium
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5
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Viswanathan T, Arya S, Chan SH, Qi S, Dai N, Misra A, Park JG, Oladunni F, Kovalskyy D, Hromas RA, Martinez-Sobrido L, Gupta YK. Structural basis of RNA cap modification by SARS-CoV-2. Nat Commun 2020; 11:3718. [PMID: 32709886 PMCID: PMC7381649 DOI: 10.1038/s41467-020-17496-8] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/04/2020] [Indexed: 02/06/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused millions of infections worldwide. In SARS coronaviruses, the non-structural protein 16 (nsp16), in conjunction with nsp10, methylates the 5'-end of virally encoded mRNAs to mimic cellular mRNAs, thus protecting the virus from host innate immune restriction. We report here the high-resolution structure of a ternary complex of SARS-CoV-2 nsp16 and nsp10 in the presence of cognate RNA substrate analogue and methyl donor, S-adenosyl methionine (SAM). The nsp16/nsp10 heterodimer is captured in the act of 2'-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. We observe large conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state. This induced fit model provides mechanistic insights into the 2'-O methylation of the viral mRNA cap. We also discover a distant (25 Å) ligand-binding site unique to SARS-CoV-2, which can alternatively be targeted, in addition to RNA cap and SAM pockets, for antiviral development.
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Affiliation(s)
- Thiruselvam Viswanathan
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Shailee Arya
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Siu-Hong Chan
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Shan Qi
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Nan Dai
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Anurag Misra
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Jun-Gyu Park
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Fatai Oladunni
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Dmytro Kovalskyy
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Robert A Hromas
- Division of Hematology and Oncology, Department of Medicine, University of Texas Health at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | | | - Yogesh K Gupta
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA.
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
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6
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Yan H, Fernandez M, Wang J, Wu S, Wang R, Lou Z, Moroney JB, Rivera CE, Taylor JR, Gan H, Zan H, Kovalskyy D, Liu D, Casali P, Xu Z. Correction: B Cell Endosomal RAB7 Promotes TRAF6 K63 Polyubiquitination and NF-κB Activation for Antibody Class-Switching. J Immunol 2020; 204:3058. [PMID: 32277056 DOI: 10.4049/jimmunol.2000342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Lin X, Ammosova T, Choy MS, Pietzsch CA, Ivanov A, Ahmad A, Saygideğer Y, Kumari N, Kovalskyy D, Üren A, Peti W, Bukreyev A, Nekhai S. Targeting the Non-catalytic RVxF Site of Protein Phosphatase-1 With Small Molecules for Ebola Virus Inhibition. Front Microbiol 2019; 10:2145. [PMID: 31572348 PMCID: PMC6753193 DOI: 10.3389/fmicb.2019.02145] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/30/2019] [Indexed: 12/17/2022] Open
Abstract
Ebola virus (EBOV) is a non-segmented negative-sense RNA virus that causes a severe human disease. The ongoing EBOV outbreak in the Eastern part of Democratic Republic of the Congo has resulted to date in over 2500 confirmed cases including over 1500 deaths. Difficulties with vaccine administration indicate the necessity for development of new general drugs and therapeutic strategies against EBOV. Host Ser/Thr protein phosphatases, particularly PP1 and PP2A, facilitate EBOV transcription by dephosphorylating the EBOV VP30 protein and switching activity of the polymerase complex toward replication. Previously, we developed small molecule 1E7-03 that targeted host protein phosphatase-1 (PP1) and induces phosphorylation of EBOV VP30 protein thus shifting transcription-replication balance and inhibiting EBOV replication. Here, we developed a new EBOV inhibitor, 1E7-07, that potently inhibits EBOV replication and displays significantly improved metabolic stability when compared to previously described 1E7-03. Proteome analysis of VP30 shows that 1E7-07 increases its phosphorylation on Thr-119 and Ser-124 over 3-fold with p < 0.001, which likely contributes to EBOV inhibition. We analyzed 1E7-07 binding to PP1 using a mass spectrometry-based protein painting approach. Combined with computational docking, protein painting shows that 1E7-07 binds to several PP1 sites including the RVxF site, C-terminal groove and NIPP1-helix binding pocket. Further analysis using surface plasmon resonance and a split NanoBiT system demonstrates that 1E7-07 binds primarily to the RVxF site. Together, detailed analysis of 1E7-07 binding to PP1 and identification of the RVxF site as the main binding site opens up an opportunity for future development of PP1-targeting EBOV inhibitors.
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Affiliation(s)
- Xionghao Lin
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
- College of Dentistry, Howard University, Washington, DC, United States
| | - Tatiana Ammosova
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
- Department of Medicine, College of Medicine, Howard University, Washington, DC, United States
- Yakut Science Centre of Complex Medical Problems, Yakutsk, Russia
| | - Meng S. Choy
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - Colette A. Pietzsch
- Department of Pathology, Department of Microbiology and Immunology, and Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Andrey Ivanov
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
| | - Asrar Ahmad
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
| | - Yasemin Saygideğer
- Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Namita Kumari
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
| | - Dmytro Kovalskyy
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX, United States
| | - Aykut Üren
- Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - Alexander Bukreyev
- Department of Pathology, Department of Microbiology and Immunology, and Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Sergei Nekhai
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
- Department of Medicine, College of Medicine, Howard University, Washington, DC, United States
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8
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Pinto DO, Scott TA, DeMarino C, Pleet ML, Vo TT, Saifuddin M, Kovalskyy D, Erickson J, Cowen M, Barclay RA, Zeng C, Weinberg MS, Kashanchi F. Effect of transcription inhibition and generation of suppressive viral non-coding RNAs. Retrovirology 2019; 16:13. [PMID: 31036006 PMCID: PMC6489247 DOI: 10.1186/s12977-019-0475-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 04/20/2019] [Indexed: 01/03/2023] Open
Abstract
Background HIV-1 patients receiving combination antiretroviral therapy (cART) survive infection but require life-long adherence at high expense. In chronic cART-treated patients with undetectable viral titers, cell-associated viral RNA is still detectable, pointing to low-level viral transcriptional leakiness. To date, there are no FDA-approved drugs against HIV-1 transcription. We have previously shown that F07#13, a third generation Tat peptide mimetic with competitive activity against Cdk9/T1-Tat binding sites, inhibits HIV-1 transcription in vitro and in vivo. Results Here, we demonstrate that increasing concentrations of F07#13 (0.01, 0.1, 1 µM) cause a decrease in Tat levels in a dose-dependent manner by inhibiting the Cdk9/T1-Tat complex formation and subsequent ubiquitin-mediated Tat sequestration and degradation. Our data indicate that complexes I and IV contain distinct patterns of ubiquitinated Tat and that transcriptional inhibition induced by F07#13 causes an overall reduction in Tat levels. This reduction may be triggered by F07#13 but ultimately is mediated by TAR-gag viral RNAs that bind suppressive transcription factors (similar to 7SK, NRON, HOTAIR, and Xist lncRNAs) to enhance transcriptional gene silencing and latency. These RNAs complex with PRC2, Sin3A, and Cul4B, resulting in epigenetic modifications. Finally, we observed an F07#13-mediated decrease of viral burden by targeting the R region of the long terminal repeat (HIV-1 promoter region, LTR), promoting both paused polymerases and increased efficiency of CRISPR/Cas9 editing in infected cells. This implies that gene editing may be best performed under a repressed transcriptional state. Conclusions Collectively, our results indicate that F07#13, which can terminate RNA Polymerase II at distinct sites, can generate scaffold RNAs, which may assemble into specific sets of “RNA Machines” that contribute to gene regulation. It remains to be seen whether these effects can also be seen in various clades that have varying promoter strength, mutant LTRs, and in patient samples. Electronic supplementary material The online version of this article (10.1186/s12977-019-0475-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel O Pinto
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Tristan A Scott
- Center for Gene Therapy, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Michelle L Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Thy T Vo
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Mohammed Saifuddin
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Dmytro Kovalskyy
- Protein Engineering Department, Institute of Molecular Biology and Genetics, UAS, Kiev, Ukraine
| | - James Erickson
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Maria Cowen
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Robert A Barclay
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Chen Zeng
- Department of Physics, The George Washington University, Washington, DC, USA
| | - Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.,Wits/SA MRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA. .,Laboratory of Molecular Virology, George Mason University, Discovery Hall Room 182, 10900 University Blvd., Manassas, VA, 20110, USA.
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9
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Rugel A, Tarpley RS, Lopez A, Menard T, Guzman MA, Taylor AB, Cao X, Kovalskyy D, Chevalier FD, Anderson TJC, Hart PJ, LoVerde PT, McHardy SF. Design, Synthesis, and Characterization of Novel Small Molecules as Broad Range Antischistosomal Agents. ACS Med Chem Lett 2018; 9:967-973. [PMID: 30344901 DOI: 10.1021/acsmedchemlett.8b00257] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 09/14/2018] [Indexed: 12/26/2022] Open
Abstract
Schistosomiasis is a major human parasitic disease afflicting more than 250 million people, historically treated with chemotherapies praziquantel or oxamniquine. Since oxamniquine is species-specific, killing Schistosoma mansoni but not other schistosome species (S. haematobium or S. japonicum) and evidence for drug resistant strains is growing, research efforts have focused on identifying novel approaches. Guided by data from X-ray crystallographic studies and Schistosoma worm killing assays on oxamniquine, our structure-based drug design approach produced a robust structure-activity relationship (SAR) program that identified several new lead compounds with effective worm killing. These studies culminated in the discovery of compound 12a, which demonstrated broad-species activity in killing S. mansoni (75%), S. haematobium (40%), and S. japonicum (83%).
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Affiliation(s)
| | - Reid S. Tarpley
- Center for Innovative
Drug Discovery, University of Texas at San Antonio, Department of Chemistry, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Ambrosio Lopez
- Center for Innovative
Drug Discovery, University of Texas at San Antonio, Department of Chemistry, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Travis Menard
- Center for Innovative
Drug Discovery, University of Texas at San Antonio, Department of Chemistry, One UTSA Circle, San Antonio, Texas 78249, United States
| | | | - Alexander B. Taylor
- X-ray Crystallography Core Laboratory,Institutional Research Cores, UT Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | | | | | - Frédéric D. Chevalier
- Texas BioMedical Research Institute, 7620 NW Loop 410, San Antonio, Texas 78227-5301, United States
| | - Timothy J. C. Anderson
- Texas BioMedical Research Institute, 7620 NW Loop 410, San Antonio, Texas 78227-5301, United States
| | - P. John Hart
- X-ray Crystallography Core Laboratory,Institutional Research Cores, UT Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229, United States
| | | | - Stanton F. McHardy
- Center for Innovative
Drug Discovery, University of Texas at San Antonio, Department of Chemistry, One UTSA Circle, San Antonio, Texas 78249, United States
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10
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Opp S, Fricke T, Shepard C, Kovalskyy D, Bhattacharya A, Herkules F, Ivanov DN, Kim B, Valle-Casuso J, Diaz-Griffero F. The small-molecule 3G11 inhibits HIV-1 reverse transcription. Chem Biol Drug Des 2016; 89:608-618. [PMID: 27748043 DOI: 10.1111/cbdd.12886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/10/2016] [Accepted: 10/09/2016] [Indexed: 12/20/2022]
Abstract
The small-molecule 6-(tert-butyl)-4-phenyl-4-(trifluoromethyl)-1H,3H-1,3,5-triazin-2-one (3G11) inhibits HIV-1 replication in the human T cell line MT-2. Here, we showed that 3G11 specifically and potently blocks HIV-1 infection. By contrast, 3G11 did not block other retroviruses such as HIV-2, simian immunodeficiency virus (SIVmac ), bovine immunodeficiency virus, feline immunodeficiency virus, equine infectious anemia virus, N-tropic murine leukemia virus, B-tropic murine leukemia virus, and Moloney murine leukemia virus. Analysis of DNA metabolism by real-time PCR revealed that 3G11 blocks the formation of HIV-1 late reverse transcripts during infection prior to the first-strand transfer step. In agreement, an in vitro assay revealed that 3G11 blocks the enzymatic activity of HIV-1 reverse transcriptase as strong as nevirapine. Docking of 3G11 to the HIV-1 reverse transcriptase enzyme suggested a direct interaction between residue L100 and 3G11. In agreement, an HIV-1 virus bearing the reverse transcriptase change L100I renders HIV-1 resistant to 3G11, which suggested that the reverse transcriptase enzyme is the viral determinant for HIV-1 sensitivity to 3G11. Although NMR experiments revealed that 3G11 binds to the HIV-1 capsid, functional experiments suggested that capsid is not the viral determinant for sensitivity to 3G11. Overall, we described a novel non-nucleoside reverse transcription inhibitor that blocks HIV-1 infection.
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Affiliation(s)
- Silvana Opp
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Thomas Fricke
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Caitlin Shepard
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Dmytro Kovalskyy
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX, USA
| | - Akash Bhattacharya
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX, USA
| | - Frank Herkules
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX, USA
| | - Dmitri N Ivanov
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX, USA
| | - Baek Kim
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Jose Valle-Casuso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
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11
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Rajamanickam S, Panneerdoss S, Gorthi A, Timilsina S, Onyeagucha B, Kovalskyy D, Ivanov D, Hanes MA, Vadlamudi RK, Chen Y, Bishop AJ, Arbiser JL, Rao MK. Inhibition of FoxM1-Mediated DNA Repair by Imipramine Blue Suppresses Breast Cancer Growth and Metastasis. Clin Cancer Res 2016; 22:3524-36. [PMID: 26927663 DOI: 10.1158/1078-0432.ccr-15-2535] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/17/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE The approaches aimed at inhibiting the ability of cancer cells to repair DNA strand breaks have emerged as promising targets for treating cancers. Here, we assessed the potential of imipramine blue (IB), a novel analogue of antidepressant imipramine, to suppress breast cancer growth and metastasis by inhibiting the ability of breast cancer cells to repair DNA strand breaks by homologous recombination (HR). EXPERIMENTAL DESIGN The effect of IB on breast cancer growth and metastasis was assessed in vitro as well as in preclinical mouse models. Besides, the therapeutic efficacy and safety of IB was determined in ex vivo explants from breast cancer patients. The mechanism of action of IB was evaluated by performing gene-expression, drug-protein interaction, cell-cycle, and DNA repair studies. RESULTS We show that the systemic delivery of IB using nanoparticle-based delivery approach suppressed breast cancer growth and metastasis without inducing toxicity in preclinical mouse models. Using ex vivo explants from breast cancer patients, we demonstrated that IB inhibited breast cancer growth without affecting normal mammary epithelial cells. Furthermore, our mechanistic studies revealed that IB may interact and inhibit the activity of proto-oncogene FoxM1 and associated signaling that play critical roles in HR-mediated DNA repair. CONCLUSIONS These findings highlight the potential of IB to be applied as a safe regimen for treating breast cancer patients. Given that FoxM1 is an established therapeutic target for several cancers, the identification of a compound that inhibits FoxM1- and FoxM1-mediated DNA repair has immense translational potential for treating many aggressive cancers. Clin Cancer Res; 22(14); 3524-36. ©2016 AACR.
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Affiliation(s)
- Subapriya Rajamanickam
- Department of Cell and Structure Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas. Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Subbarayalu Panneerdoss
- Department of Cell and Structure Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas. Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Aparna Gorthi
- Department of Cell and Structure Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas. Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Santosh Timilsina
- Department of Cell and Structure Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas. Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Benjamin Onyeagucha
- Department of Cell and Structure Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas. Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Dmytro Kovalskyy
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Dmitri Ivanov
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Martha A Hanes
- Department of Laboratory Animal Resources, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Ratna K Vadlamudi
- Department of Obstetrics and Gynecology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas. Department of Epidemiology and Statistics, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Alexander J Bishop
- Department of Cell and Structure Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas. Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Jack L Arbiser
- Emory School of Medicine, Atlanta, Georgia. Veterans Administration Medical Center, Atlanta, Georgia
| | - Manjeet K Rao
- Department of Cell and Structure Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas. Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas.
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12
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Tyagi M, Iordanskiy S, Ammosova T, Kumari N, Smith K, Breuer D, Ilatovskiy AV, Kont YS, Ivanov A, Üren A, Kovalskyy D, Petukhov M, Kashanchi F, Nekhai S. Reactivation of latent HIV-1 provirus via targeting protein phosphatase-1. Retrovirology 2015; 12:63. [PMID: 26178009 PMCID: PMC4504130 DOI: 10.1186/s12977-015-0190-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 07/09/2015] [Indexed: 11/23/2022] Open
Abstract
Background HIV-1 escapes antiretroviral drugs by integrating into the host DNA and forming a latent transcriptionally silent HIV-1 provirus. This provirus presents the major hurdle in HIV-1 eradication and cure. Transcriptional activation, which is prerequisite for reactivation and the eradication of latent proviruses, is impaired in latently infected T cells due to the lack of host transcription factors, primarily NF-κB and P-TEFb (CDK9/cyclin T1). We and others previously showed that protein phosphatase-1 (PP1) regulates HIV-1 transcription by modulating CDK9 phosphorylation. Recently we have developed a panel of small molecular compounds targeting a non-catalytic site of PP1. Results Here we generated a new class of sulfonamide-containing compounds that activated HIV-1 in acute and latently infected cells. Among the tested molecules, a small molecule activator of PP1 (SMAPP1) induced both HIV-1 replication and reactivation of latent HIV-1 in chronically infected cultured and primary cells. In vitro, SMAPP1 interacted with PP1 and increased PP1 activity toward a recombinant substrate. Treatment with SMAPP1 increased phosphorylation of CDK9’s Ser90 and Thr186 residues, but not Ser175. Proteomic analysis showed upregulation of P-TEFb and PP1 related proteins, including PP1 regulatory subunit Sds22 in SMAPP1-treated T cells. Docking analysis identified a PP1 binding site for SMAPP1 located within the C-terminal binding pocket of PP1. Conclusion We identified a novel class of PP1-targeting compounds that reactivate latent HIV-1 provirus by targeting PP1, increasing CDK9 phosphorylation and enhancing HIV transcription. This compound represents a novel candidate for anti-HIV-1 therapeutics aiming at eradication of latent HIV-1 reservoirs.
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Affiliation(s)
- Mudit Tyagi
- Department of Medicine, The George Washington University, Washington, DC, 2003, USA.
| | - Sergey Iordanskiy
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA.
| | - Tatyana Ammosova
- Center for Sickle Cell Disease, Howard University, 1840 7th Street, N.W. HURB1, Suite 202, Washington, DC, 20059, USA. .,Department of Medicine, Howard University, Washington, DC, 20059, USA. .,Yakut Science Center for Complex Medical Problems, Yakutsk, 677019, Russia.
| | - Namita Kumari
- Center for Sickle Cell Disease, Howard University, 1840 7th Street, N.W. HURB1, Suite 202, Washington, DC, 20059, USA.
| | - Kahli Smith
- Center for Sickle Cell Disease, Howard University, 1840 7th Street, N.W. HURB1, Suite 202, Washington, DC, 20059, USA.
| | - Denitra Breuer
- Center for Sickle Cell Disease, Howard University, 1840 7th Street, N.W. HURB1, Suite 202, Washington, DC, 20059, USA.
| | - Andrey V Ilatovskiy
- Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina, Russia. .,Instiute of Nanobiotechnologies, St. Petersburg State Polytechnical University, St. Petersburg, Russia.
| | | | - Andrey Ivanov
- Center for Sickle Cell Disease, Howard University, 1840 7th Street, N.W. HURB1, Suite 202, Washington, DC, 20059, USA.
| | - Aykut Üren
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA.
| | - Dmytro Kovalskyy
- Department of Biochemistry and Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
| | - Michael Petukhov
- Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina, Russia. .,Instiute of Nanobiotechnologies, St. Petersburg State Polytechnical University, St. Petersburg, Russia.
| | - Fatah Kashanchi
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA.
| | - Sergei Nekhai
- Center for Sickle Cell Disease, Howard University, 1840 7th Street, N.W. HURB1, Suite 202, Washington, DC, 20059, USA. .,Department of Medicine, Howard University, Washington, DC, 20059, USA.
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13
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Ammosova T, Platonov M, Ivanov A, Kont YS, Kumari N, Kehn-Hall K, Jerebtsova M, Kulkarni AA, Uren A, Kovalskyy D, Nekhai S. 1E7-03, a low MW compound targeting host protein phosphatase-1, inhibits HIV-1 transcription. Br J Pharmacol 2015; 171:5059-75. [PMID: 25073485 DOI: 10.1111/bph.12863] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/07/2014] [Accepted: 06/14/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND AND PURPOSE HIV-1 transcription is activated by the Tat protein which recruits the cyclin-dependent kinase CDK9/cyclin T1 to TAR RNA. Tat binds to protein phosphatase-1 (PP1) through the Q(35) VCF(38) sequence and translocates PP1 to the nucleus. PP1 dephosphorylates CDK9 and activates HIV-1 transcription. We have synthesized a low MW compound 1H4, that targets PP1 and prevents HIV-1 Tat interaction with PP1 and inhibits HIV-1 gene transcription. Here, we report our further work with the 1H4-derived compounds and analysis of their mechanism of action. EXPERIMENTAL APPROACH Using the 1H4-PP1 complex as a model, we iteratively designed and synthesized follow-up libraries that were analysed for the inhibition of HIV-1 transcription and toxicity. We also confirmed the mechanism of action of the PP1-targeting molecules by determining the affinity of binding of these molecules to PP1, by analysing their effects on PP1 activity, disruption of PP1 binding to Tat and shuttling of PP1 to the nucleus. KEY RESULTS We identified a tetrahydroquinoline derivative, compound 7, which disrupted the interaction of Tat with PP1. We further optimized compound 7 and obtained compound 7c, renamed 1E7-03, which inhibited HIV-1 with low IC50 (fivefold lower than the previously reported compound, 1H4), showed no cytotoxicity and displayed a plasma half-life greater than 8 h in mice. 1E7-03 bound to PP1 in vitro and prevented shuttling of PP1 into the nucleus. CONCLUSIONS AND IMPLICATIONS Our study shows that low MW compounds that functionally mimic the PP1-binding RVxF peptide can inhibit HIV-1 transcription by deregulating PP1.
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Affiliation(s)
- Tatyana Ammosova
- Center for Sickle Cell Disease, Department of Medicine, Howard University, Washington, DC, USA
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14
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Smith KA, Lin X, Bolshakov O, Griffin J, Niu X, Kovalskyy D, Ivanov A, Jerebtsova M, Taylor RE, Akala E, Nekhai S. Activation of HIV-1 with Nanoparticle-Packaged Small-Molecule Protein Phosphatase-1-Targeting Compound. Sci Pharm 2015; 83:535-48. [PMID: 26839837 PMCID: PMC4727795 DOI: 10.3797/scipharm.1502-01] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/22/2015] [Indexed: 11/22/2022] Open
Abstract
Complete eradication of HIV-1 infection is impeded by the existence of latent HIV-1 reservoirs in which the integrated HIV-1 provirus is transcriptionally inactive. Activation of HIV-1 transcription requires the viral Tat protein and host cell factors, including protein phosphatase-1 (PP1). We previously developed a library of small compounds that targeted PP1 and identified a compound, SMAPP1, which induced HIV-1 transcription. However, this compound has a limited bioavailability in vivo and may not be able to reach HIV-1-infected cells and induce HIV-1 transcription in patients. We packaged SMAPP1 in polymeric polyethylene glycol polymethyl methacrylate nanoparticles and analyzed its release and the effect on HIV-1 transcription in a cell culture. SMAPP1 was efficiently packaged in the nanoparticles and released during a 120-hr period. Treatment of the HIV-1-infected cells with the SMAPP1-loaded nanoparticles induced HIV-1 transcription. Thus, nanoparticles loaded with HIV-1-targeting compounds might be useful for future anti-HIV-1 therapeutics.
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Affiliation(s)
- Kahli A Smith
- Center for Sickle Cell Disease, Howard University, Washington DC 20059, USA; Department of Pharmacology, Howard University, Washington DC 20059, USA
| | - Xionghao Lin
- Center for Sickle Cell Disease, Howard University, Washington DC 20059, USA
| | - Oleg Bolshakov
- Department of Pharmaceutical Sciences, Howard University, Washington DC 20059, USA
| | - James Griffin
- College of Engineering, Howard University, Washington DC 20059, USA
| | - Xiaomei Niu
- Center for Sickle Cell Disease, Howard University, Washington DC 20059, USA
| | - Dmytro Kovalskyy
- Department of Biochemistry, School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr., San Antonio TX 78229, USA; Enamine LLC, Princeton Corporate Plaza, 7 Deer Park Drive, Ste. M-3 Monmouth Jct., NJ 08852, USA
| | - Andrey Ivanov
- Center for Sickle Cell Disease, Howard University, Washington DC 20059, USA
| | - Marina Jerebtsova
- Department of Microbiology, College of Medicine, Howard University, Washington DC 20059, USA
| | - Robert E Taylor
- Department of Pharmacology, Howard University, Washington DC 20059, USA
| | - Emmanuel Akala
- Department of Pharmaceutical Sciences, Howard University, Washington DC 20059, USA
| | - Sergei Nekhai
- Center for Sickle Cell Disease, Howard University, Washington DC 20059, USA; Department of Pharmacology, Howard University, Washington DC 20059, USA; Department of Microbiology, College of Medicine, Howard University, Washington DC 20059, USA; Department of Medicine, Howard University, Washington DC 20059, USA
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15
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Buta A, Maximyuk O, Kovalskyy D, Sukach V, Vovk M, Ievglevskyi O, Isaeva E, Isaev D, Savotchenko A, Krishtal O. Novel Potent Orthosteric Antagonist of ASIC1a Prevents NMDAR-Dependent LTP Induction. J Med Chem 2015; 58:4449-61. [PMID: 25974655 DOI: 10.1021/jm5017329] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Acid sensing ion channels 1a (ASIC1a) are of crucial importance in numerous physiological and pathological processes in the brain. Here we demonstrate that novel 2-oxo-2H-chromene-3-carboxamidine derivative 5b, designed with molecular modeling approach, inhibits ASIC1a currents with an apparent IC50 of 27 nM when measured at pH 6.7. Acidification to 5.0 decreases the inhibition efficacy by up to 3 orders of magnitude. The 5b molecule not only shifts pH dependence of ASIC1a activation but also inhibits its maximal evoked response. These findings suggest that compound 5b binds to pH sensor of ASIC1a acting as orthosteric noncompetitive antagonist. At 100 nM, compound 5b completely inhibits induction of long-term potentiation (LTP) in CA3-CA1 but not in MF-CA3 synapses. These findings support the knockout data indicating the crucial modulatory role of ASIC1a channels in the NMDAR-dependent LTP and introduce a novel type of ASIC1a antagonists.
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Affiliation(s)
- Andriy Buta
- †Bogomoletz Institute of Physiology of NAS Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine.,§State Key Laboratory for Molecular and Cellular Biology, 4 Bogomoletz Str., 01024 Kyiv, Ukraine
| | - Oleksandr Maximyuk
- †Bogomoletz Institute of Physiology of NAS Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine.,§State Key Laboratory for Molecular and Cellular Biology, 4 Bogomoletz Str., 01024 Kyiv, Ukraine
| | - Dmytro Kovalskyy
- ∥ChemBio Center, Taras Shevchenko University of Kyiv, 67 Chervonotkatska Str., 02094 Kyiv, Ukraine
| | - Volodymyr Sukach
- ‡Institute of Organic Chemistry of NAS Ukraine, 5 Murmanska Str., 02660 Kyiv, Ukraine
| | - Mykhailo Vovk
- ‡Institute of Organic Chemistry of NAS Ukraine, 5 Murmanska Str., 02660 Kyiv, Ukraine
| | - Oleksandr Ievglevskyi
- †Bogomoletz Institute of Physiology of NAS Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine
| | - Elena Isaeva
- †Bogomoletz Institute of Physiology of NAS Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine
| | - Dmytro Isaev
- †Bogomoletz Institute of Physiology of NAS Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine
| | - Alina Savotchenko
- †Bogomoletz Institute of Physiology of NAS Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine
| | - Oleg Krishtal
- †Bogomoletz Institute of Physiology of NAS Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine.,§State Key Laboratory for Molecular and Cellular Biology, 4 Bogomoletz Str., 01024 Kyiv, Ukraine
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16
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Ilinykh PA, Tigabu B, Ivanov A, Ammosova T, Obukhov Y, Garron T, Kumari N, Kovalskyy D, Platonov MO, Naumchik VS, Freiberg AN, Nekhai S, Bukreyev A. Role of protein phosphatase 1 in dephosphorylation of Ebola virus VP30 protein and its targeting for the inhibition of viral transcription. J Biol Chem 2014; 289:22723-22738. [PMID: 24936058 DOI: 10.1074/jbc.m114.575050] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The filovirus Ebola (EBOV) causes the most severe hemorrhagic fever known. The EBOV RNA-dependent polymerase complex includes a filovirus-specific VP30, which is critical for the transcriptional but not replication activity of EBOV polymerase; to support transcription, VP30 must be in a dephosphorylated form. Here we show that EBOV VP30 is phosphorylated not only at the N-terminal serine clusters identified previously but also at the threonine residues at positions 143 and 146. We also show that host cell protein phosphatase 1 (PP1) controls VP30 dephosphorylation because expression of a PP1-binding peptide cdNIPP1 increased VP30 phosphorylation. Moreover, targeting PP1 mRNA by shRNA resulted in the overexpression of SIPP1, a cytoplasm-shuttling regulatory subunit of PP1, and increased EBOV transcription, suggesting that cytoplasmic accumulation of PP1 induces EBOV transcription. Furthermore, we developed a small molecule compound, 1E7-03, that targeted a non-catalytic site of PP1 and increased VP30 dephosphorylation. The compound inhibited the transcription but increased replication of the viral genome and completely suppressed replication of EBOV in cultured cells. Finally, mutations of Thr(143) and Thr(146) of VP30 significantly inhibited EBOV transcription and strongly induced VP30 phosphorylation in the N-terminal Ser residues 29-46, suggesting a novel mechanism of regulation of VP30 phosphorylation. Our findings suggest that targeting PP1 with small molecules is a feasible approach to achieve dysregulation of the EBOV polymerase activity. This novel approach may be used for the development of antivirals against EBOV and other filovirus species.
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Affiliation(s)
- Philipp A Ilinykh
- Departments of Pathology and University of Texas Medical Branch at Galveston, Galveston, Texas 77555; Galveston National Laboratory, Galveston, Texas 77555
| | - Bersabeh Tigabu
- Departments of Pathology and University of Texas Medical Branch at Galveston, Galveston, Texas 77555; Galveston National Laboratory, Galveston, Texas 77555
| | - Andrey Ivanov
- Center for Sickle Cell Disease and Howard University, Washington, D. C. 20059
| | - Tatiana Ammosova
- Center for Sickle Cell Disease and Howard University, Washington, D. C. 20059; Departments of Medicine and Howard University, Washington, D. C. 20059
| | - Yuri Obukhov
- Center for Sickle Cell Disease and Howard University, Washington, D. C. 20059
| | - Tania Garron
- Departments of Pathology and University of Texas Medical Branch at Galveston, Galveston, Texas 77555; Galveston National Laboratory, Galveston, Texas 77555,; Departments of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
| | - Namita Kumari
- Center for Sickle Cell Disease and Howard University, Washington, D. C. 20059
| | - Dmytro Kovalskyy
- Kiev National Taras Shevchenko University, Kiev 01601, Ukraine, and; Enamine Ltd., Kiev 01103, Ukraine
| | - Maxim O Platonov
- Kiev National Taras Shevchenko University, Kiev 01601, Ukraine, and; Enamine Ltd., Kiev 01103, Ukraine
| | - Vasiliy S Naumchik
- Kiev National Taras Shevchenko University, Kiev 01601, Ukraine, and; Enamine Ltd., Kiev 01103, Ukraine
| | - Alexander N Freiberg
- Departments of Pathology and University of Texas Medical Branch at Galveston, Galveston, Texas 77555; Galveston National Laboratory, Galveston, Texas 77555
| | - Sergei Nekhai
- Galveston National Laboratory, Galveston, Texas 77555,; Departments of Medicine and Howard University, Washington, D. C. 20059; Departments of Microbiology, Howard University, Washington, D. C. 20059,.
| | - Alexander Bukreyev
- Departments of Pathology and University of Texas Medical Branch at Galveston, Galveston, Texas 77555; Galveston National Laboratory, Galveston, Texas 77555,; Departments of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555,.
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Francisco LE, Kovalskyy D, Biris N, Wang Z, Taylor A, Hart PJ, Ivanov D. Small Molecule Inhibitors of Interaction between ERCC1 and XPA. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Duffy MR, Parker AL, Kalkman ER, White K, Kovalskyy D, Kelly SM, Baker AH. Identification of novel small molecule inhibitors of adenovirus gene transfer using a high throughput screening approach. J Control Release 2013; 170:132-40. [DOI: 10.1016/j.jconrel.2013.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/04/2013] [Accepted: 05/13/2013] [Indexed: 10/26/2022]
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Van Duyne R, Guendel I, Jaworski E, Sampey G, Klase Z, Chen H, Zeng C, Kovalskyy D, El Kouni MH, Lepene B, Patanarut A, Nekhai S, Price DH, Kashanchi F. Effect of mimetic CDK9 inhibitors on HIV-1-activated transcription. J Mol Biol 2012; 425:812-29. [PMID: 23247501 DOI: 10.1016/j.jmb.2012.12.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 12/04/2012] [Accepted: 12/05/2012] [Indexed: 02/04/2023]
Abstract
Potent anti-retroviral therapy has transformed HIV-1 infection into a chronic manageable disease; however, drug resistance remains a common problem that limits the effectiveness and clinical benefits of this type of treatment. The discovery of viral reservoirs in the body, in which HIV-1 may persist, has helped to explain why therapeutic eradication of HIV-1 has proved so difficult. In the current study, we utilized a combination of structure-based analysis of cyclin/CDK complexes with our previously published Tat peptide derivatives. We modeled the Tat peptide inhibitors with CDKs and found a particular pocket that showed the most stable binding site (Cavity 1) using in silico analysis. Furthermore, we were able to find peptide mimetics that bound to similar regions using in silico searches of a chemical library, followed by cell-based biological assays. Using these methods, we obtained the first-generation mimetic drugs and tested these compounds on HIV-1 long terminal repeat-activated transcription. Using biological assays followed by similar in silico analysis to find second-generation drugs resembling the original mimetic, we found the new targets of Cavity 1 and Cavity 2 regions on CDK9. We examined the second-generation mimetic against various viral isolates and observed a generalized suppression of most HIV-1 isolates. Finally, the drug inhibited viral replication in humanized mouse models of Rag2(-/-)γc(-/-) with no toxicity to the animals at tested concentrations. Our results suggest that it may be possible to model peptide inhibitors into available crystal structures and further find drug mimetics using in silico analysis.
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Affiliation(s)
- Rachel Van Duyne
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA 20110, USA
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20
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Ammosova T, Platonov M, Yedavalli VRK, Obukhov Y, Gordeuk VR, Jeang KT, Kovalskyy D, Nekhai S. Small molecules targeted to a non-catalytic "RVxF" binding site of protein phosphatase-1 inhibit HIV-1. PLoS One 2012; 7:e39481. [PMID: 22768081 PMCID: PMC3387161 DOI: 10.1371/journal.pone.0039481] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 05/22/2012] [Indexed: 11/18/2022] Open
Abstract
HIV-1 Tat protein recruits host cell factors including CDK9/cyclin T1 to HIV-1 TAR RNA and thereby induces HIV-1 transcription. An interaction with host Ser/Thr protein phosphatase-1 (PP1) is critical for this function of Tat. PP1 binds to a Tat sequence, Q35VCF38, which resembles the PP1-binding “RVxF” motif present on PP1-binding regulatory subunits. We showed that expression of PP1 binding peptide, a central domain of Nuclear Inhibitor of PP1, disrupted the interaction of HIV-1 Tat with PP1 and inhibited HIV-1 transcription and replication. Here, we report small molecule compounds that target the “RVxF”-binding cavity of PP1 to disrupt the interaction of PP1 with Tat and inhibit HIV-1 replication. Using the crystal structure of PP1, we virtually screened 300,000 compounds and identified 262 small molecules that were predicted to bind the “RVxF”-accommodating cavity of PP1. These compounds were then assayed for inhibition of HIV-1 transcription in CEM T cells. One of the compounds, 1H4, inhibited HIV-1 transcription and replication at non-cytotoxic concentrations. 1H4 prevented PP1-mediated dephosphorylation of a substrate peptide containing an RVxF sequence in vitro. 1H4 also disrupted the association of PP1 with Tat in cultured cells without having an effect on the interaction of PP1 with the cellular regulators, NIPP1 and PNUTS, or on the cellular proteome. Finally, 1H4 prevented the translocation of PP1 to the nucleus. Taken together, our study shows that HIV- inhibition can be achieved through using small molecules to target a non-catalytic site of PP1. This proof-of-principle study can serve as a starting point for the development of novel antiviral drugs that target the interface of HIV-1 viral proteins with their host partners.
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Affiliation(s)
- Tatiana Ammosova
- Center for Sickle Cell Disease, Howard University, Washington, D.C., United States of America
- RCMI Proteomics Core Facility, Howard University, Washington, D.C., United States of America
- Department of Medicine, Howard University, Washington, D.C., United States of America
| | - Maxim Platonov
- ChemBio Center, National Taras Shevchenko University, Kiev, Ukraine
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Venkat R. K. Yedavalli
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yuri Obukhov
- RCMI Proteomics Core Facility, Howard University, Washington, D.C., United States of America
| | - Victor R. Gordeuk
- Center for Sickle Cell Disease, Howard University, Washington, D.C., United States of America
- Sickle Cell Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Kuan-Teh Jeang
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dmytro Kovalskyy
- ChemBio Center, National Taras Shevchenko University, Kiev, Ukraine
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Sergei Nekhai
- Center for Sickle Cell Disease, Howard University, Washington, D.C., United States of America
- RCMI Proteomics Core Facility, Howard University, Washington, D.C., United States of America
- Department of Medicine, Howard University, Washington, D.C., United States of America
- * E-mail:
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Kovalskyy D, Dubyna V, Mark AE, Kornelyuk A. A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: The role of Na+ ions in stabilizing the active site. Proteins 2004; 58:450-8. [DOI: 10.1002/prot.20304] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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