1
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Yanovich A, Vepreva A, Malkova K, Kantin G, Dar’in D. Entry to new spiroheterocycles via tandem Rh(II)-catalyzed O-H insertion/base-promoted cyclization involving diazoarylidene succinimides. Beilstein J Org Chem 2024; 20:561-569. [PMID: 38505240 PMCID: PMC10949003 DOI: 10.3762/bjoc.20.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024] Open
Abstract
A facile approach to novel medicinally relevant spiro heterocyclic scaffolds (namely furan-2(5H)-ones, tetrahydrofurans and pyrans spiro-conjugated with the succinimide ring) has been developed. The protocol consists of Rh(II)-catalyzed insertion of heterocyclic carbenes derived from diazoarylidene succinimides (DAS) into the O-H bond of propiolic/allenic acids or brominated alcohols, followed by base-promoted cyclization to afford the target spirocyclic compounds in good to high yields.
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Affiliation(s)
- Alexander Yanovich
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskiy pr., Peterhof, Saint Petersburg 198504, Russian Federation
| | - Anastasia Vepreva
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskiy pr., Peterhof, Saint Petersburg 198504, Russian Federation
| | - Ksenia Malkova
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskiy pr., Peterhof, Saint Petersburg 198504, Russian Federation
| | - Grigory Kantin
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskiy pr., Peterhof, Saint Petersburg 198504, Russian Federation
| | - Dmitry Dar’in
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskiy pr., Peterhof, Saint Petersburg 198504, Russian Federation
- Saint Petersburg Research Institute of Phthisiopulmonology, 2-4 Ligovsky pr., Saint Petersburg 191036, Russian Federation
- Department of Medicinal Chemistry, Institute of Chemistry, Saint Petersburg State University, 26 Universitetskiy pr., Peterhof 198504, Russian Federation
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2
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Dar'in D, Kantin G, Glushakova D, Sharoyko V, Krasavin M. Diazo Tetramic Acids Provide Access to Natural-Like Spirocyclic Δ α,β-Butenolides through Rh(II)-Catalyzed O-H Insertion/Base-Promoted Cyclization. J Org Chem 2023. [PMID: 36603207 DOI: 10.1021/acs.joc.2c02600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
3-Diazotetramic acids were found to be valid substrates for the recently discovered approach toward natural-like Δα,β-spirobutenolides via Rh(II)-catalyzed O-H insertion into propiolic acids followed by base-promoted intramolecular Michael addition. The target Δα,β-spirobutenolides were obtained in generally high yields and, in the case of chiral 5-monosubstituted 3-diazotetramic acids, high diastereoselectivity. The synthesis of Δα,β-spirobutenolides that we report here was virtually insensitive to the structure of the propiolic acids though it was somewhat sensitive to the structure of the 3-diazotetramic acids, thereby demonstrating quite a large scope. Thus, a new class of α-diazocarbonyl compounds suitable for the realization of the approach outlined above was identified.
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Affiliation(s)
- Dmitry Dar'in
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetsky prospekt, Peterhof 198504 Russia
| | - Grigory Kantin
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetsky prospekt, Peterhof 198504 Russia
| | - Daria Glushakova
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetsky prospekt, Peterhof 198504 Russia
| | - Vladimir Sharoyko
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetsky prospekt, Peterhof 198504 Russia
- The Pavlov First Medical University, 6-8 Lva Tolstogo ulitsa, Saint Petersburg 197022, Russia
| | - Mikhail Krasavin
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetsky prospekt, Peterhof 198504 Russia
- Immanuel Kant Baltic Federal University, 14 Aleksandra Nevskogo ulitsa, Kaliningrad 236041, Russia
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3
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Kar A, Rana G, Chanda R, Jana U. Iron( iii)-catalyzed synthesis of indole–xanthydrol hybrid through oxidative cycloisomerization/hydroxylation reaction. Org Biomol Chem 2022; 20:8545-8553. [DOI: 10.1039/d2ob01727j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Iron(iii)-catalyzed synthesis of indole–xanthydrol hybrid through oxidative cycloisomerization/hydroxylation reaction.
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Affiliation(s)
- Abhishek Kar
- Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Gopal Rana
- Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Rupsa Chanda
- Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Umasish Jana
- Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
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4
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Wang R, Wei Y, Wang M, Yan P, Jiang H, Du Z. Interaction of Natural Compounds in Licorice and Turmeric with HIV-NCp7 Zinc Finger Domain: Potential Relevance to the Mechanism of Antiviral Activity. Molecules 2021; 26:molecules26123563. [PMID: 34200973 PMCID: PMC8230585 DOI: 10.3390/molecules26123563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/28/2021] [Accepted: 06/09/2021] [Indexed: 01/10/2023] Open
Abstract
Nucleocapsid proteins (NCp) are zinc finger (ZF) proteins, and they play a central role in HIV virus replication, mainly by interacting with nucleic acids. Therefore, they are potential targets for anti-HIV therapy. Natural products have been shown to be able to inhibit HIV, such as turmeric and licorice, which is widely used in traditional Chinese medicine. Liquiritin (LQ), isoliquiritin (ILQ), glycyrrhizic acid (GL), glycyrrhetinic acid (GA) and curcumin (CUR), which were the major active components, were herein chosen to study their interactions with HIV-NCp7 C-terminal zinc finger, aiming to find the potential active compounds and reveal the mechanism involved. The stacking interaction between NCp7 tryptophan and natural compounds was evaluated by fluorescence. To elucidate the binding mode, mass spectrometry was used to characterize the reaction mixture between zinc finger proteins and active compounds. Subsequently, circular dichroism (CD) spectroscopy and molecular docking were used to validate and reveal the binding mode from a structural perspective. The results showed that ILQ has the strongest binding ability among the tested compounds, followed by curcumin, and the interaction between ILQ and the NCp7 zinc finger peptide was mediated by a noncovalent interaction. This study provided a scientific basis for the antiviral activity of turmeric and licorice.
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Affiliation(s)
- Runjing Wang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
- Ningxia Pharmaceutical Inspection and Research Institute, Yinchuan 750001, China
| | - Yinyu Wei
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
| | - Meiqin Wang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
| | - Pan Yan
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
| | - Hongliang Jiang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
| | - Zhifeng Du
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
- Correspondence:
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5
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Dar'in D, Kantin G, Chupakhin E, Sharoyko V, Krasavin M. Natural-Like Spirocyclic Δ α,β -Butenolides Obtained from Diazo Homophthalimides. Chemistry 2021; 27:8221-8227. [PMID: 33848018 DOI: 10.1002/chem.202100880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Indexed: 01/07/2023]
Abstract
α-Diazo homophotalimides were reacted with various propiolic acids on Rh2 (esp)2 catalysis. The resulting propiolate esters were transformed into novel, heterocyclic Δα,β -spirobutenolides in good to excellent product yields. The approach represents a fundamentally novel entry into natural-like Δα,β -spirobutenolides present in many biologically active natural products as well as fully synthetic compounds endowed with diverse biological activities. The Δα,β -spirobutenolides thus obtained were shown to inhibit thioredoxin reductase, a selenocysteine enzyme target for cancer. Moreover, for the best compound in the series (TrxR IC50 1.49±0.08 μM), by using MALDI-TOF mass-spectrometry it was shown that it selectively binds selenocysteine in the presence of a 10-fold excess of cysteine. This validates the new compound as a promising lead for anticancer therapy development.
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Affiliation(s)
- Dmitry Dar'in
- Chair of Natural Products Chemistry, Saint Petersburg State University, Saint-Petersburg, 199034, Russian Federation
| | - Grigory Kantin
- Chair of Natural Products Chemistry, Saint Petersburg State University, Saint-Petersburg, 199034, Russian Federation
| | - Evgeny Chupakhin
- Chair of Natural Products Chemistry, Saint Petersburg State University, Saint-Petersburg, 199034, Russian Federation.,Immanuel Kant Baltic Federal University, Kaliningrad, 236041, Russian Federation
| | - Vladimir Sharoyko
- Chair of Natural Products Chemistry, Saint Petersburg State University, Saint-Petersburg, 199034, Russian Federation.,Laboratory for Cell Biotechnology, Saint Petersburg State Institute of Technology (University), Saint Petersburg, 190013, Russian Federation
| | - Mikhail Krasavin
- Chair of Natural Products Chemistry, Saint Petersburg State University, Saint-Petersburg, 199034, Russian Federation.,Immanuel Kant Baltic Federal University, Kaliningrad, 236041, Russian Federation
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6
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Le HT, Jo H, Oh S, Jung J, Kim YG, Kang C, Kim TW. Endoplasmic Reticulum Targeting Reactive Oxygen Species Sensor Based on Dihydrofluorescein: Application of Endoplasmic Reticulum Stress. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hoa Thi Le
- Department of Applied Chemistry, College of Applied Sciences Kyung Hee University Gyeonggi‐do 449‐701 Republic of Korea
| | - Hye‐Ryeong Jo
- Graduate School of East‐West Medical Science Kyung Hee University Gyeonggi‐do 449‐701 Republic of Korea
| | - Se‐Yun Oh
- Graduate School of East‐West Medical Science Kyung Hee University Gyeonggi‐do 449‐701 Republic of Korea
| | - Jinwook Jung
- Graduate School of East‐West Medical Science Kyung Hee University Gyeonggi‐do 449‐701 Republic of Korea
| | - Young Gi Kim
- Graduate School of East‐West Medical Science Kyung Hee University Gyeonggi‐do 449‐701 Republic of Korea
| | - Chulhun Kang
- Graduate School of East‐West Medical Science Kyung Hee University Gyeonggi‐do 449‐701 Republic of Korea
| | - Tae Woo Kim
- Graduate School of East‐West Medical Science Kyung Hee University Gyeonggi‐do 449‐701 Republic of Korea
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7
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Monette A, Mouland AJ. Zinc and Copper Ions Differentially Regulate Prion-Like Phase Separation Dynamics of Pan-Virus Nucleocapsid Biomolecular Condensates. Viruses 2020; 12:E1179. [PMID: 33081049 PMCID: PMC7589941 DOI: 10.3390/v12101179] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 02/08/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) is a rapidly growing research focus due to numerous demonstrations that many cellular proteins phase-separate to form biomolecular condensates (BMCs) that nucleate membraneless organelles (MLOs). A growing repertoire of mechanisms supporting BMC formation, composition, dynamics, and functions are becoming elucidated. BMCs are now appreciated as required for several steps of gene regulation, while their deregulation promotes pathological aggregates, such as stress granules (SGs) and insoluble irreversible plaques that are hallmarks of neurodegenerative diseases. Treatment of BMC-related diseases will greatly benefit from identification of therapeutics preventing pathological aggregates while sparing BMCs required for cellular functions. Numerous viruses that block SG assembly also utilize or engineer BMCs for their replication. While BMC formation first depends on prion-like disordered protein domains (PrLDs), metal ion-controlled RNA-binding domains (RBDs) also orchestrate their formation. Virus replication and viral genomic RNA (vRNA) packaging dynamics involving nucleocapsid (NC) proteins and their orthologs rely on Zinc (Zn) availability, while virus morphology and infectivity are negatively influenced by excess Copper (Cu). While virus infections modify physiological metal homeostasis towards an increased copper to zinc ratio (Cu/Zn), how and why they do this remains elusive. Following our recent finding that pan-retroviruses employ Zn for NC-mediated LLPS for virus assembly, we present a pan-virus bioinformatics and literature meta-analysis study identifying metal-based mechanisms linking virus-induced BMCs to neurodegenerative disease processes. We discover that conserved degree and placement of PrLDs juxtaposing metal-regulated RBDs are associated with disease-causing prion-like proteins and are common features of viral proteins responsible for virus capsid assembly and structure. Virus infections both modulate gene expression of metalloproteins and interfere with metal homeostasis, representing an additional virus strategy impeding physiological and cellular antiviral responses. Our analyses reveal that metal-coordinated virus NC protein PrLDs initiate LLPS that nucleate pan-virus assembly and contribute to their persistence as cell-free infectious aerosol droplets. Virus aerosol droplets and insoluble neurological disease aggregates should be eliminated by physiological or environmental metals that outcompete PrLD-bound metals. While environmental metals can control virus spreading via aerosol droplets, therapeutic interference with metals or metalloproteins represent additional attractive avenues against pan-virus infection and virus-exacerbated neurological diseases.
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Affiliation(s)
- Anne Monette
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Andrew J. Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
- Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
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8
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Monette A, Niu M, Chen L, Rao S, Gorelick RJ, Mouland AJ. Pan-retroviral Nucleocapsid-Mediated Phase Separation Regulates Genomic RNA Positioning and Trafficking. Cell Rep 2020; 31:107520. [PMID: 32320662 PMCID: PMC8965748 DOI: 10.1016/j.celrep.2020.03.084] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/12/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023] Open
Abstract
The duality of liquid-liquid phase separation (LLPS) of cellular components into membraneless organelles defines the nucleation of both normal and disease processes including stress granule (SG) assembly. From mounting evidence of LLPS utility by viruses, we discover that HIV-1 nucleocapsid (NC) protein condenses into zinc-finger (ZnF)-dependent LLPSs that are dynamically influenced by cytosolic factors. ZnF-dependent and Zinc (Zn2+)-chelation-sensitive NC-LLPS are formed in live cells. NC-Zn2+ ejection reverses the HIV-1 blockade on SG assembly, inhibits NC-SG assembly, disrupts NC/Gag-genomic RNA (vRNA) ribonucleoprotein complexes, and causes nuclear sequestration of NC and the vRNA, inhibiting Gag expression and virus release. NC ZnF mutagenesis eliminates the HIV-1 blockade of SG assembly and repositions vRNA to SGs. We find that NC-mediated, Zn2+-coordinated phase separation is conserved among diverse retrovirus subfamilies, illustrating that this exquisitely evolved Zn2+-dependent feature of virus replication represents a critical target for pan-antiretroviral therapies. Monette et al. discover a high degree of conservation of zinc-finger embedded, intrinsically disordered prion-like domains across retrovirus Gag proteins. These domains within the Gag Nucleocapsid regulate the formation of zinc-dependent liquid-liquid phase condensates and stress granules in HIV-1-expressing cells to induce repositioning of the viral genomic RNA.
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Affiliation(s)
- Anne Monette
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada.
| | - Meijuan Niu
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Lois Chen
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Shringar Rao
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Biochemistry, Erasmus University Medical Center, Ee634, PO Box 2040, 3000CA Rotterdam, the Netherlands
| | - Robert James Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Andrew John Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada; Department of Medicine, McGill University, Montréal, QC H3G 2M1, Canada.
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9
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Zhang C, Zhang H, Huang LS, Zhu S, Xu Y, Zhang XQ, Schooley RT, Yang X, Huang Z, An J. Virtual Screening, Biological Evaluation, and 3D-QSAR Studies of New HIV-1 Entry Inhibitors That Function via the CD4 Primary Receptor. Molecules 2018; 23:molecules23113036. [PMID: 30463393 PMCID: PMC6278378 DOI: 10.3390/molecules23113036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 02/07/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is responsible for the majority of HIV infections worldwide, and we still lack a cure for this infection. Blocking the interaction of HIV-1 and its primary receptor CD4 is one strategy for identifying new anti-HIV-1 entry inhibitors. Here we report the discovery of a novel ligand that can inhibit HIV-1 entry and infection via CD4. Biological and computational analyses of this inhibitor and its analogs, using bioactivity evaluation, Rule of Five (RO5), comparative molecular field analysis (CoMFA)/comparative molecular similarity index analysis (CoMSIA) models, and three-dimensional quantitative structure-activity relationship (3D-QSAR), singled out compound 3 as a promising lead molecule for the further development of therapeutics targeting HIV-1 entry. Our study demonstrates an effective approach for employing structure-based, rational drug design techniques to identify novel antiviral compounds with interesting biological activities.
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Affiliation(s)
- Chaozai Zhang
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China.
| | - Huijun Zhang
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
- School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Lina S Huang
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
- College of Arts and Sciences, Cornell University, Ithaca, NY 14853, USA.
| | - Siyu Zhu
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
- School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Yan Xu
- School of Life Sciences, Tsinghua University, Beijing 100084, China.
- Nobel Institute of Biomedicine, Zhuhai 519000, Guangdong, China.
| | - Xing-Quan Zhang
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
| | - Robert T Schooley
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
| | - Xiaohong Yang
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China.
| | - Ziwei Huang
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
- School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Jing An
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
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10
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Shvadchak V, Zgheib S, Basta B, Humbert N, Langedijk J, Morris MC, Ciaco S, Maskri O, Darlix JL, Mauffret O, Fossé P, Réal E, Mély Y. Rationally Designed Peptides as Efficient Inhibitors of Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein. Biochemistry 2018; 57:4562-4573. [PMID: 30019894 DOI: 10.1021/acs.biochem.8b00527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to its essential roles in the viral replication cycle and to its highly conserved sequence, the nucleocapsid protein (NCp7) of the human immunodeficiency virus type 1 is a target of choice for inhibiting replication of the virus. Most NCp7 inhibitors identified so far are small molecules. A small number of short peptides also act as NCp7 inhibitors by competing with its nucleic acid (NA) binding and chaperone activities but exhibit antiviral activity only at relatively high concentrations. In this work, in order to obtain more potent NCp7 competitors, we designed a library of longer peptides (10-17 amino acids) whose sequences include most of the NCp7 structural determinants responsible for its specific NA binding and destabilizing activities. Using an in vitro assay, the most active peptide (pE) was found to inhibit the NCp7 destabilizing activity, with a 50% inhibitory concentration in the nanomolar range, by competing with NCp7 for binding to its NA substrates. Formulated with a cell-penetrating peptide (CPP), pE was found to accumulate into HeLa cells, with low cytotoxicity. However, either formulated with a CPP or overexpressed in cells, pE did not show any antiviral activity. In vitro competition experiments revealed that its poor antiviral activity may be partly due to its sequestration by cellular RNAs. The selected peptide pE therefore appears to be a useful tool for investigating NCp7 properties and functions in vitro, but further work will be needed to design pE-derived peptides with antiviral activity.
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Affiliation(s)
- Volodymyr Shvadchak
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Sarwat Zgheib
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Beata Basta
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Nicolas Humbert
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | | | - May C Morris
- Institut des biomolécules Max Mousseron, CNRS, UMR 5247 , Université de Montpellier Faculté de Pharmacie , 15 av Charles Flahault 34093 Montpellier , France
| | - Stefano Ciaco
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Ouerdia Maskri
- LBPA, ENS Paris Saclay, CNRS , Université Paris-Saclay , 94235 , Cachan Cedex , France
| | - Jean-Luc Darlix
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Olivier Mauffret
- LBPA, ENS Paris Saclay, CNRS , Université Paris-Saclay , 94235 , Cachan Cedex , France
| | - Philippe Fossé
- LBPA, ENS Paris Saclay, CNRS , Université Paris-Saclay , 94235 , Cachan Cedex , France
| | - Eléonore Réal
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Yves Mély
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
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11
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Mori M, Kovalenko L, Malancona S, Saladini F, De Forni D, Pires M, Humbert N, Real E, Botzanowski T, Cianférani S, Giannini A, Dasso Lang MC, Cugia G, Poddesu B, Lori F, Zazzi M, Harper S, Summa V, Mely Y, Botta M. Structure-Based Identification of HIV-1 Nucleocapsid Protein Inhibitors Active against Wild-Type and Drug-Resistant HIV-1 Strains. ACS Chem Biol 2018; 13:253-266. [PMID: 29235845 DOI: 10.1021/acschembio.7b00907] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
HIV/AIDS is still one of the leading causes of death worldwide. Current drugs that target the canonical steps of the HIV-1 life cycle are efficient in blocking viral replication but are unable to eradicate HIV-1 from infected patients. Moreover, drug resistance (DR) is often associated with the clinical use of these molecules, thus raising the need for novel drug candidates as well as novel putative drug targets. In this respect, pharmacological inhibition of the highly conserved and multifunctional nucleocapsid protein (NC) of HIV-1 is considered a promising alternative to current drugs, particularly to overcome DR. Here, using a multidisciplinary approach combining in silico screening, fluorescence-based molecular assays, and cellular antiviral assays, we identified nordihydroguaiaretic acid (6), as a novel natural product inhibitor of NC. By using NMR, mass spectrometry, fluorescence spectroscopy, and molecular modeling, 6 was found to act through a dual mechanism of action never highlighted before for NC inhibitors (NCIs). First, the molecule recognizes and binds NC noncovalently, which results in the inhibition of the nucleic acid chaperone properties of NC. In a second step, chemical oxidation of 6 induces a potent chemical inactivation of the protein. Overall, 6 inhibits NC and the replication of wild-type and drug-resistant HIV-1 strains in the low micromolar range with moderate cytotoxicity that makes it a profitable tool compound as well as a good starting point for the development of pharmacologically relevant NCIs.
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Affiliation(s)
- Mattia Mori
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Lesia Kovalenko
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
- Department
of Chemistry, Kyiv National Taras Shevchenko University, 01033 Kyiv, Ukraine
| | - Savina Malancona
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Francesco Saladini
- Department
of Medical Biotechnologies, University of Siena, Viale Mario Bracci,
16, 50100 Siena, Italy
| | | | - Manuel Pires
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Nicolas Humbert
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Eleonore Real
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Thomas Botzanowski
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Alessia Giannini
- Department
of Medical Biotechnologies, University of Siena, Viale Mario Bracci,
16, 50100 Siena, Italy
| | - Maria Chiara Dasso Lang
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Giulia Cugia
- ViroStatics S.r.l, Viale Umberto
I 46, 07100 Sassari, Italy
| | | | - Franco Lori
- ViroStatics S.r.l, Viale Umberto
I 46, 07100 Sassari, Italy
| | - Maurizio Zazzi
- Department
of Medical Biotechnologies, University of Siena, Viale Mario Bracci,
16, 50100 Siena, Italy
| | - Steven Harper
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Vincenzo Summa
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Yves Mely
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Maurizio Botta
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
- Sbarro
Institute for Cancer Research and Molecular Medicine, Center for Biotechnology,
College of Science and Technology, Temple University, BioLife Science
Bldg., Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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12
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Iraci N, Tabarrini O, Santi C, Sancineto L. NCp7: targeting a multitask protein for next-generation anti-HIV drug development part 2. Noncovalent inhibitors and nucleic acid binders. Drug Discov Today 2018; 23:687-695. [PMID: 29326078 DOI: 10.1016/j.drudis.2018.01.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 10/25/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023]
Abstract
Nucleocapsid protein 7 (NCp7) represents a viable target not yet reached by the currently available antiretrovirals. It is a small and highly basic protein, which is essential for multiple stages of the viral replicative cycle, with its structure preserved in all viral strains, including clinical isolates. NCp7 can be inhibited covalently, noncovalently and by shielding the nucleic acid (NA) substrates of its chaperone activity. Although covalent NCp7 inhibitors have already been detailed in the first part of this review series, the focus here is based on noncovalent and NA-binder inhibitors and on the analysis of the NCp7 3D structure to deliver fruitful insights for future drug design strategies.
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Affiliation(s)
- Nunzio Iraci
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Claudio Santi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Luca Sancineto
- Department of Heterorganic Chemistry, Centre of Molecular and Macromulecular Studies, Lodz, Poland.
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13
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Hadpech S, Nangola S, Chupradit K, Fanhchaksai K, Furnon W, Urvoas A, Valerio-Lepiniec M, Minard P, Boulanger P, Hong SS, Tayapiwatana C. Alpha-helicoidal HEAT-like Repeat Proteins (αRep) Selected as Interactors of HIV-1 Nucleocapsid Negatively Interfere with Viral Genome Packaging and Virus Maturation. Sci Rep 2017; 7:16335. [PMID: 29180782 PMCID: PMC5703948 DOI: 10.1038/s41598-017-16451-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/13/2017] [Indexed: 12/21/2022] Open
Abstract
A new generation of artificial proteins, derived from alpha-helicoidal HEAT-like repeat protein scaffolds (αRep), was previously characterized as an effective source of intracellular interfering proteins. In this work, a phage-displayed library of αRep was screened on a region of HIV-1 Gag polyprotein encompassing the C-terminal domain of the capsid, the SP1 linker and the nucleocapsid. This region is known to be essential for the late steps of HIV-1 life cycle, Gag oligomerization, viral genome packaging and the last cleavage step of Gag, leading to mature, infectious virions. Two strong αRep binders were isolated from the screen, αRep4E3 (32 kDa; 7 internal repeats) and αRep9A8 (28 kDa; 6 internal repeats). Their antiviral activity against HIV-1 was evaluated in VLP-producer cells and in human SupT1 cells challenged with HIV-1. Both αRep4E3 and αRep9A8 showed a modest but significant antiviral effects in all bioassays and cell systems tested. They did not prevent the proviral integration reaction, but negatively interfered with late steps of the HIV-1 life cycle: αRep4E3 blocked the viral genome packaging, whereas αRep9A8 altered both virus maturation and genome packaging. Interestingly, SupT1 cells stably expressing αRep9A8 acquired long-term resistance to HIV-1, implying that αRep proteins can act as antiviral restriction-like factors.
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Affiliation(s)
- Sudarat Hadpech
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Faculty of Pharmaceutical Science, Burapha University, Muang District, Chonburi Province, 20131, Thailand.,University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Sawitree Nangola
- Division of Clinical Immunology and Transfusion Sciences, School of Allied Health Sciences, University of Phayao, Phayao, 56000, Thailand
| | - Koollawat Chupradit
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Kanda Fanhchaksai
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Wilhelm Furnon
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Pierre Boulanger
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Saw-See Hong
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France. .,Institut National de la Santé et de la Recherche Médicale, 101, rue de Tolbiac, 75654, Paris Cedex 13, France.
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
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14
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de Paiva REF, Du Z, Peterson EJ, Corbi PP, Farrell NP. Probing the HIV-1 NCp7 Nucleocapsid Protein with Site-Specific Gold(I)–Phosphine Complexes. Inorg Chem 2017; 56:12308-12318. [DOI: 10.1021/acs.inorgchem.7b01762] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raphael E. F. de Paiva
- Institute of Chemistry, University of Campinas − UNICAMP, P.O. Box 6154, 13083-970 Campinas-SP, Brazil
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
| | - Zhifeng Du
- Institute of Chemistry, University of Campinas − UNICAMP, P.O. Box 6154, 13083-970 Campinas-SP, Brazil
| | - Erica J. Peterson
- Institute of Chemistry, University of Campinas − UNICAMP, P.O. Box 6154, 13083-970 Campinas-SP, Brazil
| | - Pedro P. Corbi
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
| | - Nicholas P. Farrell
- Institute of Chemistry, University of Campinas − UNICAMP, P.O. Box 6154, 13083-970 Campinas-SP, Brazil
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15
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Yıldız T, Küçük HB. An organocatalytic method for the synthesis of some novel xanthene derivatives by the intramolecular Friedel–Crafts reaction. RSC Adv 2017. [DOI: 10.1039/c6ra27094h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An efficient organocatalytic method for the synthesis of new substituted 9-arylxanthenes (2a–2u) starting from diarylcarbinol compounds with an arenoxy group (1a–1u) has been developed using the intramolecular Friedel–Crafts reaction.
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Affiliation(s)
- Tülay Yıldız
- Istanbul University
- Faculty of Engineering, Department of Chemistry
- Istanbul
- Turkey
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16
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Spell SR, Mangrum JB, Peterson EJ, Fabris D, Ptak R, Farrell NP. Au(iii) compounds as HIV nucleocapsid protein (NCp7)-nucleic acid antagonists. Chem Commun (Camb) 2016; 53:91-94. [PMID: 27858001 PMCID: PMC7086404 DOI: 10.1039/c6cc07970a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The HIV nucleocapsid NCp7-SL2 RNA interaction is interrupted in the presence of a formally substitution-inert gold(dien)-nucleobase/N-heterocycle AuN4 compound where the N-heterocycle serves the dual purposes of a template for "non-covalent" molecular recognition of the essential tryptophan of the protein, mimicking the natural reaction and subsequent "fixation" by Au-Cys bond formation providing a chemotype for a new distinct class of nucleocapsid-nucleic acid antagonist.
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Affiliation(s)
- Sarah R Spell
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
| | - John B Mangrum
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Erica J Peterson
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
| | - Daniele Fabris
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Roger Ptak
- Southern Research Institute, 431 Aviation Way, Frederick, Maryland 21701, USA
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
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17
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Bernardes VHF, Qu Y, Du Z, Beaton J, Vargas MD, Farrell NP. Interaction of the HIV NCp7 Protein with Platinum(II) and Gold(III) Complexes Containing Tridentate Ligands. Inorg Chem 2016; 55:11396-11407. [PMID: 27934299 DOI: 10.1021/acs.inorgchem.6b01925] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human immunodeficiency virus (HIV) nucleocapsid protein (NCp7) plays significant roles in the virus life cycle and has been targeted by compounds that could lead to its denaturation or block its interaction with viral RNA. Herein, we describe the interactions of platinum(II) and gold(III) complexes with NCp7 and how the reactivity/affinity of potential inhibitors can be modulated by judicious choice of ligands. The interactions of [MCl(N3)]n+ (M = Pt2+ (n = 1) and Au3+ (n = 2); N3 = tridentate chelate ligands: bis(2-pyridylmethyl)methylamine (Mebpma, L1) and bis(2-pyridylmethyl)amine (bpma, L2) with the C-terminal zinc finger of NCp7 (ZF2) were investigated by electrospray ionization-mass spectroscopy (ESI-MS). Mass spectra from the incubation of [MCl(Mebpma)]n+ complexes (PtL1 and AuL1) with ZF2 indicated that they were more reactive than the previously studied diethylenetriamine-containing analogues [MCl(dien)]n+. The initial product of reaction of PtL1 with ZF2 results in loss of all ligands and release of zinc to give the platinated apopeptide {PtF} (F = apopeptide). This is in contrast to the incubation with [PtCl(dien)]+, in which {Pt(dien)}-peptide adducts are observed. Incubation of the Au3+ complex AuL1 with ZF2 gave AuxFn+ species (x = 1, 2, 4, F = apopeptide) again with loss of all ligands. Furthermore, the formally substitution-inert analogues [Pt(N3)L]2+ (L = 4-methylpyridine (4-pic), 4-dimethylaminopyridine (dmap), and 9-ethylguanine (9-EtGua)) were prepared to examine stacking interactions with N-acetyltryptophan (N-AcTrp), the Trp-containing ZF2, and the "full" two-finger NCp7 itself using fluorescence quenching titration. Use of bpma and Mebpma gave slightly higher affinity than analogous [Pt(dien)L)]2+ complexes. The dmap-containing complexes (PtL1a and PtL2a) had the greatest association constants (Ka) for N-AcTrp and ZF2 peptide. The complex PtL1a had the highest Ka when compared with other known Pt2+ analogues: [Pt(dien)(9-EtGua)]2+ < [Pt(bpma)(9-EtGua)]2+ < [Pt(dien)(dmap)]2+< PtL2a < PtL1a. A Ka value of ca. 40.6 ± 1.0 × 103 M-1 was obtained for the full NCp7 peptide with PtL1a. In addition, the mass spectrum of the interaction between ZF2 and PtL1a confirms formation of a 1:1 PtL1a/ZF2 adduct. The reactivity of selected complexes with sulfur-containing amino acid N-acetylcysteine (N-AcCys) was also investigated by 195Pt and 1H NMR spectroscopy and ESI-MS. The precursor compounds [PtCl(N3)]+ PtL1 and PtL2 reacted readily, whereas their [Pt(N3)L]2+ analogues PtL1a and PtL2a were inert to substitution.
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Affiliation(s)
- Victor H F Bernardes
- Chemistry Institute, Fluminense Federal University , Campus Valonguinho, CEP 24020-141, Niterói-RJ, Brazil.,Department of Chemistry, Virginia Commonwealth University , 1001 W. Main St., Richmond, Virginia 23284-2006, United States
| | - Yun Qu
- Department of Chemistry, Virginia Commonwealth University , 1001 W. Main St., Richmond, Virginia 23284-2006, United States
| | - Zhifeng Du
- Department of Chemistry, Virginia Commonwealth University , 1001 W. Main St., Richmond, Virginia 23284-2006, United States
| | - James Beaton
- Department of Chemistry, Virginia Commonwealth University , 1001 W. Main St., Richmond, Virginia 23284-2006, United States
| | - Maria D Vargas
- Chemistry Institute, Fluminense Federal University , Campus Valonguinho, CEP 24020-141, Niterói-RJ, Brazil
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University , 1001 W. Main St., Richmond, Virginia 23284-2006, United States
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18
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Tsotsoros SD, Lutz PB, Daniel AG, Peterson EJ, de Paiva REF, Rivera E, Qu Y, Bayse CA, Farrell NP. Enhancement of the physicochemical properties of [Pt(dien)(nucleobase)] 2+ for HIVNCp7 targeting. Chem Sci 2016; 8:1269-1281. [PMID: 28451269 PMCID: PMC5369524 DOI: 10.1039/c6sc03445d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/06/2016] [Indexed: 12/31/2022] Open
Abstract
Physicochemical properties of coordination compounds can be exploited for molecular recognition of biomolecules. The inherent π-π stacking properties of [Pt(chelate)(N-donor)]2+ ([PtN4]) complexes were modulated by systematic variation of the chelate (diethylenetriamine and substituted derivatives) and N-donor (nucleobase or nucleoside) in the formally substitution-inert PtN4 coordination sphere. Approaches to target the HIV nucleocapsid protein HIVNCp7 are summarized building on (i) assessment of stacking interactions with simple tryptophan or tryptophan derivatives to (ii) the tryptophan-containing C-terminal zinc finger and (iii) to the full two-zinc finger peptide and its interactions with RNA and DNA. The xanthosine nucleoside was identified as having significantly enhanced stacking capability over guanosine. Correlation of the LUMO energies of the modified nucleobases with the DFT π-stacking energies shows that frontier orbital energies of the individual monomers can be used as a first estimate of the π-stacking strength to Trp. Cellular accumulation studies showed no significant correlation with lipophilicity of the compounds, but all compounds had very low cytotoxicity suggesting the potential for antiviral selectivity. The conceptual similarities between nucleobase alkylation and platination validates the design of formally substitution-inert coordination complexes as weak Lewis acid electrophiles for selective peptide targeting.
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Affiliation(s)
- S D Tsotsoros
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA .
| | - P B Lutz
- Department of Science , Technology and Mathematics , Regent University , Virginia Beach , Virginia 23464 , USA.,Department of Chemistry and Biochemistry , Old Dominion University , Norfolk , VA 23529 , USA .
| | - A G Daniel
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA .
| | - E J Peterson
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA . .,Massey Cancer Center , Virginia Commonwealth University , Richmond , VA , USA
| | - R E F de Paiva
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA .
| | - E Rivera
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA .
| | - Y Qu
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA .
| | - C A Bayse
- Department of Chemistry and Biochemistry , Old Dominion University , Norfolk , VA 23529 , USA .
| | - N P Farrell
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA . .,Massey Cancer Center , Virginia Commonwealth University , Richmond , VA , USA
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19
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Kim MJ, Kim SH, Park JA, Yu KL, Jang SI, Kim BS, Lee ES, You JC. Identification and characterization of a new type of inhibitor against the human immunodeficiency virus type-1 nucleocapsid protein. Retrovirology 2015; 12:90. [PMID: 26545586 PMCID: PMC4636002 DOI: 10.1186/s12977-015-0218-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 10/22/2015] [Indexed: 01/18/2023] Open
Abstract
Background The human immunodeficiency virus type-1 (HIV-1) nucleocapsid protein (NC) is an essential and multifunctional protein involved in multiple stages of the viral life cycle such as reverse transcription, integration of proviral DNA, and especially genome RNA packaging. For this reason, it has been considered as an attractive target for the development of new anti-HIV drugs. Although a number of inhibitors of NC have been reported thus far, the search for NC-specific and functional inhibitor(s) with a good antiviral activity continues. Results In this study, we report the identification of A1752, a small molecule with inhibitory action against HIV-1 NC, which shows a strong antiviral efficacy and an IC50 around 1 μM. A1752 binds directly to HIV-1 NC, thereby inhibiting specific chaperone functions of NC including Psi RNA dimerization and complementary trans-activation response element (cTAR) DNA destabilization, and it also disrupts the proper Gag processing. Further analysis of the mechanisms of action of A1752 also showed that it generates noninfectious viral particles with defects in uncoating and reverse transcription in the infected cells. Conclusions These results demonstrate that A1752 is a specific and functional inhibitor of NC with a novel mode of action and good antiviral efficacy. Thus, this agent provides a new type of anti-HIV NC inhibitor candidate for further drug development. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0218-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Seon Hee Kim
- Avixgen Inc., Seoul, 137-701, Korea. .,National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul, 137-701, Korea.
| | | | - Kyung Lee Yu
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul, 137-701, Korea.
| | - Soo In Jang
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul, 137-701, Korea.
| | | | - Eun Soo Lee
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul, 137-701, Korea.
| | - Ji Chang You
- Avixgen Inc., Seoul, 137-701, Korea. .,National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul, 137-701, Korea.
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20
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Sosic A, Cappellini M, Sinigaglia L, Jacquet R, Deffieux D, Fabris D, Quideau S, Gatto B. Polyphenolic C-glucosidic ellagitannins present in oak-aged wine inhibit HIV-1 nucleocapsid protein. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.01.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Retrospective on the all-in-one retroviral nucleocapsid protein. Virus Res 2014; 193:2-15. [PMID: 24907482 PMCID: PMC7114435 DOI: 10.1016/j.virusres.2014.05.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/11/2014] [Accepted: 05/11/2014] [Indexed: 01/08/2023]
Abstract
This retrospective reviews 30 years of research on the retroviral nucleocapsid protein (NC) focusing on HIV-1 NC. Originally considered as a non-specific nucleic-acid binding protein, NC has seminal functions in virus replication. Indeed NC turns out to be a all-in-one viral protein that chaperones viral DNA synthesis and integration, and virus formation. As a chaperone NC provides assistance to genetic recombination thus allowing the virus to escape the immune response and antiretroviral therapies against HIV-1.
This review aims at briefly presenting a retrospect on the retroviral nucleocapsid protein (NC), from an unspecific nucleic acid binding protein (NABP) to an all-in-one viral protein with multiple key functions in the early and late phases of the retrovirus replication cycle, notably reverse transcription of the genomic RNA and viral DNA integration into the host genome, and selection of the genomic RNA together with the initial steps of virus morphogenesis. In this context we will discuss the notion that NC protein has a flexible conformation and is thus a member of the growing family of intrinsically disordered proteins (IDPs) where disorder may account, at least in part, for its function as a nucleic acid (NA) chaperone and possibly as a protein chaperone vis-à-vis the viral DNA polymerase during reverse transcription. Lastly, we will briefly review the development of new anti-retroviral/AIDS compounds targeting HIV-1 NC because it represents an ideal target due to its multiple roles in the early and late phases of virus replication and its high degree of conservation.
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22
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Ouyang W, Okaine S, McPike MP, Lin Y, Borer PN. Probing the RNA Binding Surface of the HIV-1 Nucleocapsid Protein by Site-Directed Mutagenesis. Biochemistry 2013; 52:3358-68. [DOI: 10.1021/bi400125z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Wei Ouyang
- Graduate
Program in Structural Biology, Biochemistry, and Biophysics and ‡Department of
Chemistry, Syracuse University, Syracuse, New York 13244-4100, United States
| | - Stephen Okaine
- Graduate
Program in Structural Biology, Biochemistry, and Biophysics and ‡Department of
Chemistry, Syracuse University, Syracuse, New York 13244-4100, United States
| | - Mark P. McPike
- Graduate
Program in Structural Biology, Biochemistry, and Biophysics and ‡Department of
Chemistry, Syracuse University, Syracuse, New York 13244-4100, United States
| | - Yong Lin
- Graduate
Program in Structural Biology, Biochemistry, and Biophysics and ‡Department of
Chemistry, Syracuse University, Syracuse, New York 13244-4100, United States
| | - Philip N. Borer
- Graduate
Program in Structural Biology, Biochemistry, and Biophysics and ‡Department of
Chemistry, Syracuse University, Syracuse, New York 13244-4100, United States
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23
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Breuer S, Chang MW, Yuan J, Torbett BE. Identification of HIV-1 inhibitors targeting the nucleocapsid protein. J Med Chem 2012; 55:4968-77. [PMID: 22587465 DOI: 10.1021/jm201442t] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The HIV-1 nucleocapsid (NC) is a RNA/DNA binding protein encoded within the Gag polyprotein, which is critical for the selection and chaperoning of viral genomic RNA during virion assembly. RNA/DNA binding occurs through a highly conserved zinc-knuckle motif present in NC. Given the necessity of NC-viral RNA/DNA interaction for viral replication, identification of compounds that disrupt the NC-RNA/DNA interaction may have value as an antiviral strategy. To identify small molecules that disrupt NC-viral RNA/DNA binding, a high-throughput fluorescence polarization assay was developed and a library of 14,400 diverse, druglike compounds was screened. Compounds that disrupted NC binding to a fluorescence-labeled DNA tracer were next evaluated by differential scanning fluorimetry to identify compounds that must bind to NC or Gag to impart their effects. Two compounds were identified that inhibited NC-DNA interaction, specifically bound NC with nanomolar affinity, and showed modest anti-HIV-1 activity in ex vivo cell assays.
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Affiliation(s)
- Sebastian Breuer
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Mori M, Schult-Dietrich P, Szafarowicz B, Humbert N, Debaene F, Sanglier-Cianferani S, Dietrich U, Mély Y, Botta M. Use of virtual screening for discovering antiretroviral compounds interacting with the HIV-1 nucleocapsid protein. Virus Res 2012; 169:377-87. [PMID: 22634301 DOI: 10.1016/j.virusres.2012.05.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/14/2012] [Accepted: 05/16/2012] [Indexed: 12/16/2022]
Abstract
The HIV-1 nucleocapsid protein (NC) is considered as an emerging drug target for the therapy of AIDS. Several studies have highlighted the crucial role of NC within the viral replication cycle. However, although NC inhibition has provided in vitro and in vivo antiretroviral activity, drug-candidates which interfere with NC functions are still missing in the therapeutic arsenal against HIV. Based on previous studies, where the dynamic behavior of NC and its ligand binding properties have been investigated by means of computational methods, here we used a virtual screening protocol for discovering novel antiretroviral compounds which interact with NC. The antiretroviral activity of virtual hits was tested in vitro, whereas biophysical studies elucidated the direct interaction of most active compounds with NC(11-55), a peptide corresponding to the zinc finger domain of NC. Two novel antiretroviral small molecules capable of interacting with NC are presented here.
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Affiliation(s)
- Mattia Mori
- Università di Roma La Sapienza, Dipartimento di Chimica e Tecnologie del Farmaco, piazzale A. Moro 5, I-00185 Roma, Italy
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25
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Manna SK, Parai MK, Panda G. An efficient synthesis of 6H,7H-chromeno[4,3-b]chromenes and 6,7-dihydrothio chromeno[3,2-c]chromenes as 9-substituted xanthene like analogs. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.08.127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Flexible nature and specific functions of the HIV-1 nucleocapsid protein. J Mol Biol 2011; 410:565-81. [PMID: 21762801 DOI: 10.1016/j.jmb.2011.03.037] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/14/2011] [Accepted: 03/17/2011] [Indexed: 01/04/2023]
Abstract
One salient feature of reverse transcription in retroviruses, notably in the human immunodeficiency virus type 1, is that it requires the homologous nucleocapsid (NC) protein acting as a chaperoning partner of the genomic RNA template and the reverse transcriptase, from the initiation to the completion of viral DNA synthesis. This short review on the NC protein of human immunodeficiency virus type 1 aims at briefly presenting the flexible nature of NC protein, how it interacts with nucleic acids via its invariant zinc fingers and flanking basic residues, and the possible mechanisms that account for its multiple functions in the early steps of virus replication, notably in the obligatory strand transfer reactions during viral DNA synthesis by the reverse transcriptase enzyme.
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Quintal SM, dePaula QA, Farrell NP. Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences. Metallomics 2011; 3:121-39. [PMID: 21253649 DOI: 10.1039/c0mt00070a] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Zinc finger reactions with inorganic ions and coordination compounds are as diverse as the zinc fingers themselves. Use of metal ions such as Co(2+) and Cd(2+) has given structural, thermodynamic and kinetic information on zinc fingers and zinc-finger-DNA/RNA interactions. It is a general truism that alteration of the coordination sphere in the finger environment will disrupt the recognition with DNA/RNA and this has implications for mechanism of toxicity and carcinogenesis of metal ions. Structural zinc fingers are susceptible to electrophilic attack and the recognition that the coordination sphere of inorganic compounds may be modulated for control of electrophilic attack on zinc fingers raises the possibility of systematic studies of zinc fingers as drug targets using inorganic chemistry. Some inorganic compounds such as those of As(III) and Au(I) may exert their biological effects through inactivation of zinc fingers and novel approaches to specifically attack the zinc-bound ligands using Co(III)-Schiff bases and Platinum(II)-Nucleobase compounds have been proposed. The genomic importance of zinc fingers suggests that the "coordination chemistry" of zinc fingers themselves is ripe for exploration to design new targets for medicinal inorganic chemistry.
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Affiliation(s)
- Susana M Quintal
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main St., Richmond, VA 23284-2006, USA
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Blackiston D, Shomrat T, Nicolas CL, Granata C, Levin M. A second-generation device for automated training and quantitative behavior analyses of molecularly-tractable model organisms. PLoS One 2010; 5:e14370. [PMID: 21179424 PMCID: PMC3003703 DOI: 10.1371/journal.pone.0014370] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 11/23/2010] [Indexed: 11/18/2022] Open
Abstract
A deep understanding of cognitive processes requires functional, quantitative analyses of the steps leading from genetics and the development of nervous system structure to behavior. Molecularly-tractable model systems such as Xenopus laevis and planaria offer an unprecedented opportunity to dissect the mechanisms determining the complex structure of the brain and CNS. A standardized platform that facilitated quantitative analysis of behavior would make a significant impact on evolutionary ethology, neuropharmacology, and cognitive science. While some animal tracking systems exist, the available systems do not allow automated training (feedback to individual subjects in real time, which is necessary for operant conditioning assays). The lack of standardization in the field, and the numerous technical challenges that face the development of a versatile system with the necessary capabilities, comprise a significant barrier keeping molecular developmental biology labs from integrating behavior analysis endpoints into their pharmacological and genetic perturbations. Here we report the development of a second-generation system that is a highly flexible, powerful machine vision and environmental control platform. In order to enable multidisciplinary studies aimed at understanding the roles of genes in brain function and behavior, and aid other laboratories that do not have the facilities to undergo complex engineering development, we describe the device and the problems that it overcomes. We also present sample data using frog tadpoles and flatworms to illustrate its use. Having solved significant engineering challenges in its construction, the resulting design is a relatively inexpensive instrument of wide relevance for several fields, and will accelerate interdisciplinary discovery in pharmacology, neurobiology, regenerative medicine, and cognitive science.
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Affiliation(s)
- Douglas Blackiston
- Biology Department and Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts, United States of America
- Department of Regenerative and Developmental Biology, Forsyth Institute, Boston, Massachusetts, United States of America
| | - Tal Shomrat
- Biology Department and Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts, United States of America
| | - Cindy L. Nicolas
- Biology Department and Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts, United States of America
| | - Christopher Granata
- Boston Engineering Corporation, Waltham, Massachusetts, United States of America
| | - Michael Levin
- Biology Department and Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts, United States of America
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Goldschmidt V, Miller Jenkins LM, de Rocquigny H, Darlix JL, Mély Y. The nucleocapsid protein of HIV-1 as a promising therapeutic target for antiviral drugs. ACTA ACUST UNITED AC 2010. [DOI: 10.2217/hiv.10.3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The nucleocapsid protein (NCp7) is a major HIV-1 structural protein that plays key roles in viral replication, mainly through its conserved zinc fingers that direct specific interactions with the viral nucleic acids. Owing to its high degree of conservation and critical functions, NCp7 represents a target of choice for drugs that can potentially complement HAART, thus possibly impairing the circulation of drug-resistant HIV-1 strains. Zinc ejectors showing potent antiretroviral activity were developed, but early generations suffered from limited selectively and significant toxicity. Compounds with improved selectivity have been developed and are being explored as topical microbicide candidates. Several classes of molecules inhibiting the interaction of NCp7 with the viral nucleic acids have also been developed. Although small molecules would be more suited for drug development, most molecules selected by screening showed limited antiretroviral activity. Peptides and RNA aptamers appear to be more promising, but the mechanism of their antiretroviral activity remains elusive. Substantial and more concerted efforts are needed to further develop anti-HIV drugs targeting NCp7 and bring them to the clinic.
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Affiliation(s)
- Valérie Goldschmidt
- Laboratoire de Biophotonique et Pharmacologie, UMR-CNRS 7213, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Cedex, France
| | - Lisa M Miller Jenkins
- Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hugues de Rocquigny
- Laboratoire de Biophotonique et Pharmacologie, UMR-CNRS 7213, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Cedex, France
| | - Jean-Luc Darlix
- LaboRetro, Unité de Virologie Humaine INSERM 758, Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR-CNRS 7213, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Cedex, France
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30
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Small molecule inhibitors of HIV RT Ribonuclease H. Bioorg Med Chem Lett 2009; 20:398-402. [PMID: 19939680 DOI: 10.1016/j.bmcl.2009.10.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 10/07/2009] [Accepted: 10/09/2009] [Indexed: 11/21/2022]
Abstract
Two classes of compounds, thiocarbamates 1 and triazoles 2, have been identified as HIV RT RNase H inhibitors using a novel FRET-based HTS assay. The potent analogs in each series exhibited selectivity and were active in cell-based assays. In addition, saturable, 1:1 stoichiometric binding to target was established and time of addition studies were consistent with inhibition of RT-mediated HIV replication.
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Waybright TJ, Britt JR, McCloud TG. Overcoming Problems of Compound Storage in DMSO: Solvent and Process Alternatives. ACTA ACUST UNITED AC 2009; 14:708-15. [DOI: 10.1177/1087057109335670] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The common practice of preparing storage libraries of compounds in 100% DMSO solution well in advance of bioassay brings with it difficulties that affect the accuracy of the data obtained. This publication presents a series of studies done on a subset of compounds that are difficult to bioassay because they precipitate from DMSO solution. These compounds are members of a frequently used, diverse compound library of the sort commonly used in the high-throughput screening (HTS) environment. Experiments were performed to determine the concentration of drug in solution above the precipitate, observe the time course and effect of various mixtures of solvents upon precipitation, measure the viscosity of cosolvents to determine compatibility with HTS, determine water absorption rates for various solvent combinations, and investigate resolubilization techniques to ensure proper drug solution for HTS. Recommendations are made on how to best maximize the probability that problem compounds will remain in solution, be accurately transferred during assay plate production, and, as a result, be accurately bioassayed at the specified molar concentration. ( Journal of Biomolecular Screening 2009:708-715)
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Affiliation(s)
- Timothy J. Waybright
- Laboratory of Proteomics and Analytical Technologies, Advanced Technologies Program, SAIC-Frederick, Inc., Frederick, Maryland
| | - John R. Britt
- Natural Products Support Group, Applied/Developmental Research Support Program, SAIC-Frederick, Inc., Frederick, Maryland
| | - Thomas G. McCloud
- Natural Products Support Group, Applied/Developmental Research Support Program, SAIC-Frederick, Inc., Frederick, Maryland,
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33
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Identification by high throughput screening of small compounds inhibiting the nucleic acid destabilization activity of the HIV-1 nucleocapsid protein. Biochimie 2009; 91:916-23. [PMID: 19401213 DOI: 10.1016/j.biochi.2009.04.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 04/15/2009] [Indexed: 11/22/2022]
Abstract
Due to its highly conserved zinc fingers and its nucleic acid chaperone properties which are critical for HIV-1 replication, the nucleocapsid protein (NC) constitutes a major target in AIDS therapy. Different families of molecules targeting NC zinc fingers and/or inhibiting the binding of NC with its target nucleic acids have been developed. However, their limited specificity and their cellular toxicity prompted us to develop a screening assay to target molecules able to inhibit NC chaperone properties, and more specifically the initial NC-promoted destabilization of the nucleic acid secondary structure. Since this destabilization is critically dependent on the properly folded fingers, the developed assay is thought to be highly specific. The assay was based on the use of cTAR DNA, a stem-loop sequence complementary to the transactivation response element, doubly labelled at its 5' and 3' ends by a rhodamine 6G fluorophore and a fluorescence quencher, respectively. Addition of NC(12-55), a peptide corresponding to the zinc finger domain of NC, to this doubly-labelled cTAR, led to a partial melting of the cTAR stem, which increases the distance between the two labels and thus, restores the rhodamine 6G fluorescence. Thus, positive hits were detected through the decrease of rhodamine 6G fluorescence. An "in-house" chemical library of 4800 molecules was screened and five compounds with IC(50) values in the micromolar range have been selected. The hits were shown by mass spectrometry and fluorescence anisotropy titration to prevent binding of NC(12-55) to cTAR through direct interaction with the NC folded fingers, but without promoting zinc ejection. These non-zinc ejecting NC binders are a new series of anti-NC molecules that could be used to rationally design molecules with potential anti-viral activities.
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34
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Almaraz E, de Paula QA, Liu Q, Reibenspies JH, Darensbourg MY, Farrell NP. Thiolate Bridging and Metal Exchange in Adducts of a Zinc Finger Model and PtII Complexes: Biomimetic Studies of Protein/Pt/DNA Interactions. J Am Chem Soc 2008; 130:6272-80. [DOI: 10.1021/ja711254q] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elky Almaraz
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, and Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, 23284-2006
| | - Queite A. de Paula
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, and Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, 23284-2006
| | - Qin Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, and Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, 23284-2006
| | - Joseph H. Reibenspies
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, and Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, 23284-2006
| | - Marcetta Y. Darensbourg
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, and Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, 23284-2006
| | - Nicholas P. Farrell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, and Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, 23284-2006
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35
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36
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Darlix JL, Garrido JL, Morellet N, Mély Y, de Rocquigny H. Properties, functions, and drug targeting of the multifunctional nucleocapsid protein of the human immunodeficiency virus. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2007; 55:299-346. [PMID: 17586319 DOI: 10.1016/s1054-3589(07)55009-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Jean-Luc Darlix
- LaboRetro, Unité INSERM de Virologie Humaine, IFR128, ENS Sciences de Lyon 46 allée d'Italie, Lyon, France
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37
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Cruceanu M, Stephen AG, Beuning PJ, Gorelick RJ, Fisher RJ, Williams MC. Single DNA molecule stretching measures the activity of chemicals that target the HIV-1 nucleocapsid protein. Anal Biochem 2006; 358:159-70. [PMID: 17034752 PMCID: PMC1661600 DOI: 10.1016/j.ab.2006.08.037] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Revised: 08/10/2006] [Accepted: 08/25/2006] [Indexed: 11/25/2022]
Abstract
We develop a biophysical method for investigating chemical compounds that target the nucleic acid chaperone activity of HIV-1 nucleocapsid protein (NCp7). We used an optical tweezers instrument to stretch single lambda-DNA molecules through the helix-coil transition in the presence of NCp7 and various chemical compounds. The change in the helix-coil transition width induced by wild-type NCp7 and its zinc finger variants correlates with in vitro nucleic acid chaperone activity measurements and in vivo assays. The compound-NC interaction measured here reduces NCp7's capability to alter the transition width. Purified compounds from the NCI Diversity set, 119889, 119911, and 119913 reduce the chaperone activity of 5 nM NC in aqueous solution at 10, 25, and 100 nM concentrations respectively. Similarly, gallein reduced the activity of 4 nM NC at 100 nM concentration. Further analysis allows us to dissect the impact of each compound on both sequence-specific and non-sequence-specific DNA binding of NC, two of the main components of NC's nucleic acid chaperone activity. These results suggest that DNA stretching experiments can be used to screen chemical compounds targeting NC proteins and to further explore the mechanisms by which these compounds interact with NC and alter its nucleic acid chaperone activity.
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Affiliation(s)
| | - Andrew G. Stephen
- Protein Chemistry Laboratory, SAIC Frederick, Inc., NCI at Frederick, Frederick, Maryland 2170, USA
| | - Penny J. Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, 102 Hurtig Hall, Boston, MA 02115, USA
| | - Robert J. Gorelick
- AIDS Vaccine Program, SAIC Frederick, Inc., NCI at Frederick, Frederick, Maryland 21702, USA
| | - Robert J. Fisher
- Protein Chemistry Laboratory, SAIC Frederick, Inc., NCI at Frederick, Frederick, Maryland 2170, USA
| | - Mark C. Williams
- Department of Physics and
- Center for Interdisciplinary Research on Complex Systems, Northeastern University, 111 Dana Research Center, Boston, Massachusetts 02115, USA
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38
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Anzellotti AI, Liu Q, Bloemink MJ, Scarsdale JN, Farrell N. Targeting retroviral Zn finger-DNA interactions: a small-molecule approach using the electrophilic nature of trans-platinum-nucleobase compounds. ACTA ACUST UNITED AC 2006; 13:539-48. [PMID: 16720275 DOI: 10.1016/j.chembiol.2006.04.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Revised: 03/30/2006] [Accepted: 04/03/2006] [Indexed: 11/29/2022]
Abstract
Noncovalent interactions are ubiquitous in ternary systems involving metal ions, DNA/RNA, and proteins and represent a structural motif for design of selective inhibitors of biological function. This contribution shows that small molecules containing platinated purine nucleobases mimic the natural DNA(RNA)-tryptophan recognition interaction of zinc finger peptides, specifically the C-terminal finger of HIV NCp7 protein. Interaction with platinum results in Zn ejection from the peptide accompanied by loss of tertiary structure. Targeting the NCp7-DNA interaction for drug design represents a conceptual advance over electrophiles designed for chemical attack on the zinc finger alone. These results demonstrate examples of a new platinum structural class targeting specific biological processes, distinct from the bifunctional DNA-DNA binding of cytotoxic agents like cisplatin. The results confirm the validity of a chemical biological approach for metallodrug design for selective ternary DNA(RNA)-protein interactions.
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Affiliation(s)
- Atilio I Anzellotti
- Department of Chemistry, Virginia Commonwealth University, PO Box 842006, Richmond, Virginia 23284, USA
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39
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Yang Y, Escobedo JO, Wong L, Schowalter CM, Touchy MC, Jiao L, Crowe WE, Fronczek FR, Strongin RM. A convenient preparation of xanthene dyes. J Org Chem 2006; 70:6907-12. [PMID: 16095313 PMCID: PMC3376412 DOI: 10.1021/jo051002a] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A facile synthetic route utilizing readily available reagents affords a series of regioisomerically pure xanthene dye derivatives. Advantages include relatively mild conditions and good to excellent yields. Nonpolar, highly crystalline intermediates are isolable by standard chromatographic techniques. The intermediates are in the requisite xanthene oxidation state, thus avoiding the need for relatively inefficient oxidation chemistry and/or harsh conditions. During the course of this work, a new boron-mediated 1,2-aryl migration reaction was discovered.
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40
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Yang QE, Stephen AG, Adelsberger JW, Roberts PE, Zhu W, Currens MJ, Feng Y, Crise BJ, Gorelick RJ, Rein AR, Fisher RJ, Shoemaker RH, Sei S. Discovery of small-molecule human immunodeficiency virus type 1 entry inhibitors that target the gp120-binding domain of CD4. J Virol 2005; 79:6122-33. [PMID: 15857997 PMCID: PMC1091715 DOI: 10.1128/jvi.79.10.6122-6133.2005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The interaction between human immunodeficiency virus type 1 (HIV-1) gp120 and the CD4 receptor is highly specific and involves relatively small contact surfaces on both proteins according to crystal structure analysis. This molecularly conserved interaction presents an excellent opportunity for antiviral targeting. Here we report a group of pentavalent antimony-containing small molecule compounds, NSC 13778 (molecular weight, 319) and its analogs, which exert a potent anti-HIV activity. These compounds block the entry of X4-, R5-, and X4/R5-tropic HIV-1 strains into CD4(+) cells but show little or no activity in CD4-negative cells or against vesicular stomatitis virus-G pseudotyped virions. The compounds compete with gp120 for binding to CD4: either immobilized on a solid phase (soluble CD4) or on the T-cell surface (native CD4 receptor) as determined by a competitive gp120 capture enzyme-linked immunosorbent assay or flow cytometry. NSC 13778 binds to an N-terminal two-domain CD4 protein, D1/D2 CD4, immobilized on a surface plasmon resonance sensor chip, and dose dependently reduces the emission intensity of intrinsic tryptophan fluorescence of D1/D2 CD4, which contains two of the three tryptophan residues in the gp120-binding domain. Furthermore, T cells incubated with the compounds alone show decreased reactivity to anti-CD4 monoclonal antibodies known to recognize the gp120-binding site. In contrast to gp120-binders that inhibit gp120-CD4 interaction by binding to gp120, these compounds appear to disrupt gp120-CD4 contact by targeting the specific gp120-binding domain of CD4. NSC 13778 may represent a prototype of a new class of HIV-1 entry inhibitors that can break into the gp120-CD4 interface and mask the gp120-binding site on the CD4 molecules, effectively repelling incoming virions.
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Affiliation(s)
- Quan-En Yang
- Laboratory of Antiviral Drug Mechanisms, Screening Technologies Branch, Developmental Therapeutics Program, SAIC-Frederick, NCI-Frederick, Bldg. 439, P.O. Box B, Frederick, MD 21702, USA
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41
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Rich RL, Myszka DG. A survey of the year 2002 commercial optical biosensor literature. J Mol Recognit 2004; 16:351-82. [PMID: 14732928 DOI: 10.1002/jmr.649] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have compiled 819 articles published in the year 2002 that involved commercial optical biosensor technology. The literature demonstrates that the technology's application continues to increase as biosensors are contributing to diverse scientific fields and are used to examine interactions ranging in size from small molecules to whole cells. Also, the variety of available commercial biosensor platforms is increasing and the expertise of users is improving. In this review, we use the literature to focus on the basic types of biosensor experiments, including kinetics, equilibrium analysis, solution competition, active concentration determination and screening. In addition, using examples of particularly well-performed analyses, we illustrate the high information content available in the primary response data and emphasize the impact of including figures in publications to support the results of biosensor analyses.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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42
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Novac O, Guenier AS, Pelletier J. Inhibitors of protein synthesis identified by a high throughput multiplexed translation screen. Nucleic Acids Res 2004; 32:902-15. [PMID: 14769948 PMCID: PMC373382 DOI: 10.1093/nar/gkh235] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The use of small molecule inhibitors of cellular processes is a powerful approach to understanding gene function that complements the genetic approach. We have designed a high throughput screen to identify new inhibitors of eukaryotic protein synthesis. We used a bicistronic mRNA reporter to multiplex our assay and simultaneously screen for inhibitors of cap-dependent initiation, internal initiation and translation elongation/termination. Functional screening of >90 000 compounds in an in vitro translation reaction identified 36 inhibitors, 14 of which are known inhibitors of translation and 18 of which are nucleic acid-binding ligands. Our results indicate that intercalators constitute a large class of protein synthesis inhibitors. Four non-intercalating compounds were identified, three of which block elongation and one of which inhibits initiation. The novel inhibitor of initiation affects 5' end-mediated initiation, as well as translation initiated from picornaviral IRESs, but does not significantly affect internal initiation from the hepatitis C virus 5'-untranslated region. This compound should be useful for delineating differences in mechanism of initiation among IRESs.
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Affiliation(s)
- Olivia Novac
- Department of Biochemistry, McGill Cancer Center, 3655 Promenade Sir William Osler, McIntyre Medical Sciences Building, McGill University, Montreal, Quebec H3G 1Y6, Canada
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43
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Khandogin J, Musier-Forsyth K, York DM. Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods. J Mol Biol 2003; 330:993-1004. [PMID: 12860122 DOI: 10.1016/s0022-2836(03)00658-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) plays several important roles in the viral life-cycle and presents an attractive target for rational drug design. Here, the macromolecular reactivity of NC and its binding to RNA is characterized through determination of electrostatic and chemical descriptors derived from linear-scaling quantum calculations in solution. The computational results offer a rationale for the experimentally observed susceptibility of the Cys49 thiolate toward small-molecule electrophilic agents, and support the recently proposed stepwise protonation mechanism of the C-terminal Zn-coordination complex. The distinctive binding mode of NC to SL2 and SL3 stem-loops of the HIV-1 genomic RNA packaging signal is studied on the basis of protein side-chain contributions to the electrostatic binding energies. These results indicate the importance of several basic residues in the 3(10) helical region and the N-terminal zinc finger, and rationalize the presence of several evolutionarily conserved residues in NC. The combined reactivity and RNA-binding study provides new insights that may contribute toward the structure-based design of anti-HIV therapies.
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Affiliation(s)
- Jana Khandogin
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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