1
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Mukhametova LI, Zherdev DO, Kuznetsov AN, Yudina ON, Tsvetkov YE, Eremin SA, Krylov VB, Nifantiev NE. Fluorescence-Polarization-Based Assaying of Lysozyme with Chitooligosaccharide Tracers. Biomolecules 2024; 14:170. [PMID: 38397407 PMCID: PMC10886901 DOI: 10.3390/biom14020170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Lysozyme is a well-known enzyme found in many biological fluids which plays an important role in the antibacterial protection of humans and animals. Lysozyme assays are used for the diagnosis of a number of diseases and utilized in immunohistochemistry, genetic and cellular engineering studies. The assaying methods are divided into two categories measuring either the concentration of lysozyme as a protein or its activity as an enzyme. While the first category of methods traditionally uses an enzyme-linked immunosorbent assay (ELISA), the methods for the determination of the enzymatic activity of lysozyme use either live bacteria, which is rather inconvenient, or natural peptidoglycans of high heterogeneity and variability, which leads to the low reproducibility of the assay results. In this work, we propose the use of a chemically synthesized substrate of a strictly defined structure to measure in a single experiment both the concentration of lysozyme as a protein and its enzymatic activity by means of the fluorescence polarization (FP) method. Chito-oligosaccharides of different chain lengths were fluorescently labeled and tested leading to the selection of the pentasaccharide as the optimal size tracer and the further optimization of the assay conditions for the accurate (detection limit 0.3 μM) and rapid (<30 min) determination of human lysozyme. The proposed protocol was applied to assay human lysozyme in tear samples and resulted in good correlation with the reference assay. The use of synthetic fluorescently labeled tracer, in contrast to natural peptidoglycan, in FP analysis allows for the development of a reproducible method for the determination of lysozyme activity.
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Affiliation(s)
- Liliya I. Mukhametova
- Faculty of Chemistry, M.V. Lomonosov Moscow State University, Leninsky Gory 1/3, 119991 Moscow, Russia; (L.I.M.); (S.A.E.)
| | - Dmitry O. Zherdev
- Faculty of Chemistry, M.V. Lomonosov Moscow State University, Leninsky Gory 1/3, 119991 Moscow, Russia; (L.I.M.); (S.A.E.)
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia (Y.E.T.)
| | - Anton N. Kuznetsov
- Laboratory of Synthetic Glycovaccines, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia;
| | - Olga N. Yudina
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia (Y.E.T.)
| | - Yury E. Tsvetkov
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia (Y.E.T.)
| | - Sergei A. Eremin
- Faculty of Chemistry, M.V. Lomonosov Moscow State University, Leninsky Gory 1/3, 119991 Moscow, Russia; (L.I.M.); (S.A.E.)
| | - Vadim B. Krylov
- Laboratory of Synthetic Glycovaccines, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia;
| | - Nikolay E. Nifantiev
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia (Y.E.T.)
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2
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Hua L, Wang D, Wang K, Wang Y, Gu J, Zhang Q, You Q, Wang L. Design of Tracers in Fluorescence Polarization Assay for Extensive Application in Small Molecule Drug Discovery. J Med Chem 2023; 66:10934-10958. [PMID: 37561645 DOI: 10.1021/acs.jmedchem.3c00881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Development of fluorescence polarization (FP) assays, especially in a competitive manner, is a potent and mature tool for measuring the binding affinities of small molecules. This approach is suitable for high-throughput screening (HTS) for initial ligands and is also applicable for further study of the structure-activity relationships (SARs) of candidate compounds for drug discovery. Buffer and tracer, especially rational design of the tracer, play a vital role in an FP assay system. In this perspective, we provided different kinds of approaches for tracer design based on successful cases in recent years. We classified these tracers by different types of ligands in tracers, including peptide, nucleic acid, natural product, and small molecule. To make this technology accessible for more targets, we briefly described the basic theory and workflow, followed by highlighting the design and application of typical FP tracers from a perspective of medicinal chemistry.
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Affiliation(s)
- Liwen Hua
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Danni Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Keran Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jinying Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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3
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Slavish PJ, Cuypers MG, Rimmer MA, Abdolvahabi A, Jeevan T, Kumar G, Jarusiewicz JA, Vaithiyalingam S, Jones JC, Bowling JJ, Price JE, DuBois RM, Min J, Webby RJ, Rankovic Z, White SW. Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential. Eur J Med Chem 2023; 247:115035. [PMID: 36603507 DOI: 10.1016/j.ejmech.2022.115035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Influenza is one of the leading causes of disease-related mortalities worldwide. Several strategies have been implemented during the past decades to hinder the replication cycle of influenza viruses, all of which have resulted in the emergence of resistant virus strains. The most recent example is baloxavir marboxil, where a single mutation in the active site of the target endonuclease domain of the RNA-dependent-RNA polymerase renders the recent FDA approved compound ∼1000-fold less effective. Raltegravir is a first-in-class HIV inhibitor that shows modest activity to the endonuclease. Here, we have used structure-guided approaches to create rationally designed derivative molecules that efficiently engage the endonuclease active site. The design strategy was driven by our previously published structures of endonuclease-substrate complexes, which allowed us to target functionally conserved residues and reduce the likelihood of resistance mutations. We succeeded in developing low nanomolar equipotent inhibitors of both wild-type and baloxavir-resistant endonuclease. We also developed macrocyclic versions of these inhibitors that engage the active site in the same manner as their 'open' counterparts but with reduced affinity. Structural analyses provide clear avenues for how to increase the affinity of these cyclic compounds.
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Affiliation(s)
- Peter J Slavish
- Departments of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Maxime G Cuypers
- Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mary Ashley Rimmer
- Departments of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Alireza Abdolvahabi
- Departments of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Trushar Jeevan
- Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Gyanendra Kumar
- Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jamie A Jarusiewicz
- Departments of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | | | - Jeremy C Jones
- Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - John J Bowling
- Departments of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jeanine E Price
- Departments of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Rebecca M DuBois
- Baskin School of Engineering, University of California at Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jaeki Min
- Departments of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Richard J Webby
- Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Zoran Rankovic
- Departments of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Stephen W White
- Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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4
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Gorbunova IA, Shadrin VM, Pulina NA, Novikova VV, Dubrovina SS, Shipilovskikh DA, Shipilovskikh SA. Synthesis and Antibacterial Activity of 4-Oxo-2-thienylaminobut-2-enoic Acids. RUSS J GEN CHEM+ 2023. [DOI: 10.1134/s1070363223010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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5
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Stokes R, Kohlbrand AJ, Seo H, Sankaran B, Karges J, Cohen SM. Carboxylic Acid Isostere Derivatives of Hydroxypyridinones as Core Scaffolds for Influenza Endonuclease Inhibitors. ACS Med Chem Lett 2022; 14:75-82. [PMID: 36655124 PMCID: PMC9841593 DOI: 10.1021/acsmedchemlett.2c00434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
Among the most important influenza virus targets is the RNA-dependent RNA polymerase acidic N-terminal (PAN) endonuclease, which is a critical component of the viral replication machinery. To inhibit the activity of this metalloenzyme, small-molecule inhibitors employ metal-binding pharmacophores (MBPs) that coordinate to the dinuclear Mn2+ active site. In this study, several metal-binding isosteres (MBIs) were examined where the carboxylic acid moiety of a hydroxypyridinone MBP is replaced with other groups to modulate the physicochemical properties of the compound. MBIs were evaluated for their ability to inhibit PAN using a FRET-based enzymatic assay, and their mode of binding in PAN was determined using X-ray crystallography.
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Affiliation(s)
- Ryjul
W. Stokes
- Department
of Chemistry and Biochemistry, University
of California, La Jolla, California 92093, United States
| | - Alysia J. Kohlbrand
- Department
of Chemistry and Biochemistry, University
of California, La Jolla, California 92093, United States
| | - Hyeonglim Seo
- Department
of Chemistry and Biochemistry, University
of California, La Jolla, California 92093, United States
| | - Banumathi Sankaran
- The
Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Johannes Karges
- Department
of Chemistry and Biochemistry, University
of California, La Jolla, California 92093, United States
| | - Seth M. Cohen
- Department
of Chemistry and Biochemistry, University
of California, La Jolla, California 92093, United States,
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6
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Exo-III enzyme based colorimetric small extracellular vesicles (sEVs) detection via G-quadruplex-based signal quenching strategy. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Sharavyeva YO, Siutkina AI, Chashchina SV, Novikova VV, Makhmudov RR, Shipilovskikh SA. Synthesis, analgesic and antimicrobial activity of substituted 2-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-ylamino)-4-oxo-4-phenylbut-2-enoates. Russ Chem Bull 2022. [DOI: 10.1007/s11172-022-3445-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Synthesis and anti-inflammatory activity of N′-substituted 2-[2-(diarylmethylene)hydrazinyl]-5,5-dimethyl-4-oxohex-2-enehydrazides. Russ Chem Bull 2022. [DOI: 10.1007/s11172-022-3439-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Hou L, Zhang Y, Ju H, Cherukupalli S, Jia R, Zhang J, Huang B, Loregian A, Liu X, Zhan P. Contemporary medicinal chemistry strategies for the discovery and optimization of influenza inhibitors targeting vRNP constituent proteins. Acta Pharm Sin B 2022; 12:1805-1824. [PMID: 35847499 PMCID: PMC9279641 DOI: 10.1016/j.apsb.2021.11.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/02/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Influenza is an acute respiratory infectious disease caused by the influenza virus, affecting people globally and causing significant social and economic losses. Due to the inevitable limitations of vaccines and approved drugs, there is an urgent need to discover new anti-influenza drugs with different mechanisms. The viral ribonucleoprotein complex (vRNP) plays an essential role in the life cycle of influenza viruses, representing an attractive target for drug design. In recent years, the functional area of constituent proteins in vRNP are widely used as targets for drug discovery, especially the PA endonuclease active site, the RNA-binding site of PB1, the cap-binding site of PB2 and the nuclear export signal of NP protein. Encouragingly, the PA inhibitor baloxavir has been marketed in Japan and the United States, and several drug candidates have also entered clinical trials, such as favipiravir. This article reviews the compositions and functions of the influenza virus vRNP and the research progress on vRNP inhibitors, and discusses the representative drug discovery and optimization strategies pursued.
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10
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Targeted inhibition of the endonuclease activity of influenza polymerase acidic proteins. Future Med Chem 2022; 14:571-586. [PMID: 35213253 DOI: 10.4155/fmc-2021-0264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Influenza is a type of acute respiratory virus infection caused by the influenza virus that occurs in epidemics worldwide every year. Due to the increasing incidence of influenza virus resistance to existing drugs, researchers are looking for novel antiviral drugs with new mechanisms. The endonuclease activity of polymerase acidic protein is essential in the process of influenza virus reproduction, and inhibiting it could prevent the virus from replicating. There are relatively few drugs that act on this protein, and only baloxavir marboxil has been approved for clinical use. In this article, the structure and function of influenza virus polymerase acidic protein endonuclease, mechanism of action of polymerase acidic endonuclease inhibitors and the research progress of inhibitors are reviewed.
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11
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Denisova EI, Lipin DV, Parkhoma KY, Devyatkin IO, Shipilovskikh DA, Chashchina SV, Makhmudov RR, Igidov NM, Shipilovskikh SA. Synthesis, Intramolecular Cyclization, and Antinociceptive Activity of Substituted 2-[2-(4-Nitrobenzoyl)hydrazinylidene]-4-oxobut-2-enoic Acids. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1070428021120083] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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12
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Siutkina AI, Chashchina SV, Makhmudov RR, Kizimova IA, Shipilovskikh SA, Igidov NM. Synthesis and Biological Activity of Substituted 2-[2-(Diphenylmethylene)hydrazinyl]-5,5-dimethyl-4-oxohex-2-enoates. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1070428021110105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Kasprzyk R, Jemielity J. Enzymatic Assays to Explore Viral mRNA Capping Machinery. Chembiochem 2021; 22:3236-3253. [PMID: 34291555 PMCID: PMC8426721 DOI: 10.1002/cbic.202100291] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/21/2021] [Indexed: 12/25/2022]
Abstract
In eukaryotes, mRNA is modified by the addition of the 7-methylguanosine (m7 G) 5' cap to protect mRNA from premature degradation, thereby enhancing translation and enabling differentiation between self (endogenous) and non-self RNAs (e. g., viral ones). Viruses often develop their own mRNA capping pathways to augment the expression of their proteins and escape host innate immune response. Insights into this capping system may provide new ideas for therapeutic interventions and facilitate drug discovery, e. g., against viruses that cause pandemic outbreaks, such as beta-coronaviruses SARS-CoV (2002), MARS-CoV (2012), and the most recent SARS-CoV-2. Thus, proper methods for the screening of large compound libraries are required to identify lead structures that could serve as a basis for rational antiviral drug design. This review summarizes the methods that allow the monitoring of the activity and inhibition of enzymes involved in mRNA capping.
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Affiliation(s)
- Renata Kasprzyk
- Centre of New TechnologiesUniversity of WarsawBanacha 2c02-097WarsawPoland
- College of Inter-Faculty Individual Studies inMathematics and Natural SciencesUniversity of WarsawBanacha 2c02-097WarsawPoland
| | - Jacek Jemielity
- Centre of New TechnologiesUniversity of WarsawBanacha 2c02-097WarsawPoland
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14
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Rogolino D, Naesens L, Bartoli J, Carcelli M, De Luca L, Pelosi G, Stokes RW, Van Berwaer R, Vittorio S, Stevaert A, Cohen SM. Exploration of the 2,3-dihydroisoindole pharmacophore for inhibition of the influenza virus PA endonuclease. Bioorg Chem 2021; 116:105388. [PMID: 34670331 DOI: 10.1016/j.bioorg.2021.105388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/09/2021] [Accepted: 09/25/2021] [Indexed: 11/19/2022]
Abstract
Seasonal influenza A and B viruses represent a global concern. Antiviral drugs are crucial to treat severe influenza in high-risk patients and prevent virus spread in case of a pandemic. The emergence of viruses showing drug resistance, in particular for the recently licensed polymerase inhibitor baloxavir marboxil, drives the need for developing alternative antivirals. The endonuclease activity residing in the N-terminal domain of the polymerase acidic protein (PAN) is crucial for viral RNA synthesis and a validated target for drug design. Its function can be impaired by molecules bearing a metal-binding pharmacophore (MBP) able to coordinate the two divalent metal ions in the active site. In the present work, the 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one scaffold is explored for the inhibition of influenza virus PA endonuclease. The structure-activity relationship was analysed by modifying the substituents on the lipophilic moiety linked to the MBP. The new compounds exhibited nanomolar inhibitory activity in a FRET-based enzymatic assay, and a few compounds (15-17, 21) offered inhibition in the micromolar range, in a cell-based influenza virus polymerase assay. When investigated against a panel of PA-mutant forms, compound 17 was shown to retain full activity against the baloxavir-resistant I38T mutant. This was corroborated by docking studies providing insight into the binding mode of this novel class of PA inhibitors.
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Affiliation(s)
- Dominga Rogolino
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici) Parma Unit, 43124 Parma, Italy.
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium.
| | - Jennifer Bartoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici) Parma Unit, 43124 Parma, Italy
| | - Mauro Carcelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici) Parma Unit, 43124 Parma, Italy
| | - Laura De Luca
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali, Polo Universitario SS. Annunziata, Università di Messina, Viale Palatucci 13, Messina I-98168, Italy
| | - Giorgio Pelosi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici) Parma Unit, 43124 Parma, Italy
| | - Ryjul W Stokes
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States
| | - Ria Van Berwaer
- Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Serena Vittorio
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali, Polo Universitario SS. Annunziata, Università di Messina, Viale Palatucci 13, Messina I-98168, Italy
| | - Annelies Stevaert
- Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States
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15
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Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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16
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Gorbunova IA, Shipilovskikh DA, Rubtsov AE, Shipilovskikh SA. Synthesis and Intramolecular Cyclization of Substituted 4-(Het)aryl-4-oxo-2-thienylaminobut-2-enoic Acids Containing Nitrile Group in the Thiophene Ring. RUSS J GEN CHEM+ 2021. [DOI: 10.1134/s1070363221090048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Gao C, Che B, Dai H. A new G-triplex-based strategy for sensitivity enhancement of the detection of endonuclease activity and inhibition. RSC Adv 2021; 11:28008-28013. [PMID: 35480740 PMCID: PMC9037997 DOI: 10.1039/d1ra04203c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/14/2021] [Indexed: 01/09/2023] Open
Abstract
EcoRI is an important biomacromolecule in live cells and protects bacterial cells against foreign DNA. In this work, we developed a simple and convenient G-triplex (G3) (5′-TGGGAAGGGAGGGAATTCCCT-3′)-based colorimetric assay for the rapid and selective detection of EcoRI activity and inhibition. The sequence specifically responds to EcoRI in the presence of K+ and hemin to form a G-triplex/hemin complex. Taking advantage of G-triplex, EcoRI activity was investigated under the optimized conditions. The absorption intensity ratio displayed a linear relationship against the concentration of EcoRI in the range 0 to 100 U mL−1, and the detection limit was 5.7 U mL−1. Furthermore, G3 showed good selectivity, and the ability to be used to screen for EcoRI inhibitors, indicating its potential in detection and analysis applications. A new G-triplex-based probe was developed for detecting EcoRI activity and inhibition. The probe showed good selectivity towards EcoRI. The assay was colorimetric and can be monitored by the naked eye.![]()
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Affiliation(s)
- Congcong Gao
- Beijing Institute for Drug Control, MNPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Medicine), MNPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing Key Laboratory of Analysis and Evaluation on Chinese Medicine Beijing 102206 China
| | - Baoquan Che
- Beijing Institute for Drug Control, MNPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Medicine), MNPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing Key Laboratory of Analysis and Evaluation on Chinese Medicine Beijing 102206 China
| | - Hong Dai
- Beijing Institute for Drug Control, MNPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Medicine), MNPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing Key Laboratory of Analysis and Evaluation on Chinese Medicine Beijing 102206 China
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18
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Zima V, Radilová K, Kožíšek M, Albiñana CB, Karlukova E, Brynda J, Fanfrlík J, Flieger M, Hodek J, Weber J, Majer P, Konvalinka J, Machara A. Unraveling the anti-influenza effect of flavonoids: Experimental validation of luteolin and its congeners as potent influenza endonuclease inhibitors. Eur J Med Chem 2020; 208:112754. [PMID: 32883638 DOI: 10.1016/j.ejmech.2020.112754] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/20/2020] [Accepted: 08/09/2020] [Indexed: 01/27/2023]
Abstract
The biological effects of flavonoids on mammal cells are diverse, ranging from scavenging free radicals and anti-cancer activity to anti-influenza activity. Despite appreciable effort to understand the anti-influenza activity of flavonoids, there is no clear consensus about their precise mode-of-action at a cellular level. Here, we report the development and validation of a screening assay based on AlphaScreen technology and illustrate its application for determination of the inhibitory potency of a large set of polyols against PA N-terminal domain (PA-Nter) of influenza RNA-dependent RNA polymerase featuring endonuclease activity. The most potent inhibitors we identified were luteolin with an IC50 of 72 ± 2 nM and its 8-C-glucoside orientin with an IC50 of 43 ± 2 nM. Submicromolar inhibitors were also evaluated by an in vitro endonuclease activity assay using single-stranded DNA, and the results were in full agreement with data from the competitive AlphaScreen assay. Using X-ray crystallography, we analyzed structures of the PA-Nter in complex with luteolin at 2.0 Å resolution and quambalarine B at 2.5 Å resolution, which clearly revealed the binding pose of these polyols coordinated to two manganese ions in the endonuclease active site. Using two distinct assays along with the structural work, we have presumably identified and characterized the molecular mode-of-action of flavonoids in influenza-infected cells.
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Affiliation(s)
- Václav Zima
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 00, Prague 2, Czech Republic; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Kateřina Radilová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic; First Faculty of Medicine, Charles University, Kateřinská 1660, 121 08, Prague 2, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic.
| | - Carlos Berenguer Albiñana
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 00, Prague 2, Czech Republic; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Elena Karlukova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic; Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 140 00, Prague 4, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Miroslav Flieger
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 140 00, Prague 4, Czech Republic
| | - Jan Hodek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 128 00, Prague 2, Czech Republic
| | - Aleš Machara
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 00, Prague 2, Czech Republic; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic.
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19
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Shipilovskikh SA, Rubtsov AE. Synthesis of New Substituted 3-(Thien-2-yl)imino-3H-furan-2-ones. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220060031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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20
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Pham T, Nguyen HL, Phan-Toai T, Nguyen H. Investigation of Binding Affinity between Potential Antiviral Agents and PB2 Protein of Influenza A: Non-equilibrium Molecular Dynamics Simulation Approach. Int J Med Sci 2020; 17:2031-2039. [PMID: 32788882 PMCID: PMC7415388 DOI: 10.7150/ijms.46231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 07/09/2020] [Indexed: 11/30/2022] Open
Abstract
The PB2 protein of the influenza virus RNA polymerase is a major virulence determinant of influenza viruses. It binds to the cap structure at the 5' end of host mRNA to generate short capped RNA fragments that are used as primers for viral transcription named cap-snatching. A large number of the compounds were shown to bind the minimal cap-binding domain of PB2 to inhibit the cap-snatching machinery. However, their binding in the context of an extended form of the PB2 protein has remained elusive. A previous study reported some promising compounds including azaindole and hydroxymethyl azaindole, which were analyzed here to predict binding affinity to PB2 protein using the steered molecular dynamics (SMD) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods. The results show that the rupture force (Fmax) value of three complexes is in agreement with the binding free energy value (ΔGbind) estimated by the MM-PBSA method, whereas for the non-equilibrium pulling work (Wpull) value a small difference between A_PB2-4 and A_PB2-12 was observed. The binding affinity results indicate the A_PB2-12 complex is more favorable than the A_PB2-4 and A_PB2-16 complexes, which means the inhibitor (12) has the potential to be further developed as anti-influenza agents in the treatment of influenza A.
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Affiliation(s)
- Tri Pham
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam.,VNUHCM-University of Technology, Ho Chi Minh City, Vietnam
| | - Hoang Linh Nguyen
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam.,VNUHCM-University of Technology, Ho Chi Minh City, Vietnam
| | - Tuyn Phan-Toai
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Hung Nguyen
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
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21
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Jiménez-Cruz JC, Guzmán-Mejía R, Juaristi E, Sánchez-Antonio O, García-Revilla MA, González-Campos JB, Aviña-Verduzco J. Preparation of aromatic γ-hydroxyketones by means of Heck coupling of aryl halides and 2,3-dihydrofuran, catalyzed by a palladium( ii) glycine complex under microwave irradiation. NEW J CHEM 2020. [DOI: 10.1039/d0nj02630a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The synthesis of phenyl-γ-hydroxyketones through Heck coupling and subsequent opening of the tetrahydrofuran ring by the nucleophilic attack of a water molecule catalyzed by PdCl2·Gly2 under microwave irradiation.
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Affiliation(s)
- Juan C. Jiménez-Cruz
- Instituto de Investigaciones Químico Biológicas
- Universidad Michoacana de San Nicolás de Hidalgo
- 58030 Morelia
- Mexico
| | - Ramón Guzmán-Mejía
- Instituto de Investigaciones Químico Biológicas
- Universidad Michoacana de San Nicolás de Hidalgo
- 58030 Morelia
- Mexico
| | - Eusebio Juaristi
- Departamento de Química
- Centro de Investigación y de Estudios Avanzados
- Avenida Instituto Politécnico
- 07360 Ciudad de México
- Mexico
| | - Omar Sánchez-Antonio
- Departamento de Química
- Centro de Investigación y de Estudios Avanzados
- Avenida Instituto Politécnico
- 07360 Ciudad de México
- Mexico
| | | | - J. Betzabe González-Campos
- Instituto de Investigaciones Químico Biológicas
- Universidad Michoacana de San Nicolás de Hidalgo
- 58030 Morelia
- Mexico
| | - Judit Aviña-Verduzco
- Instituto de Investigaciones Químico Biológicas
- Universidad Michoacana de San Nicolás de Hidalgo
- 58030 Morelia
- Mexico
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22
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Credille CV, Morrison CN, Stokes RW, Dick BL, Feng Y, Sun J, Chen Y, Cohen SM. SAR Exploration of Tight-Binding Inhibitors of Influenza Virus PA Endonuclease. J Med Chem 2019; 62:9438-9449. [PMID: 31536340 DOI: 10.1021/acs.jmedchem.9b00747] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Significant efforts have been reported on the development of influenza antivirals including inhibitors of the RNA-dependent RNA polymerase PA N-terminal (PAN) endonuclease. Based on recently identified, highly active metal-binding pharmacophores (MBPs) for PAN endonuclease inhibition, a fragment-based drug development campaign was pursued. Guided by coordination chemistry and structure-based drug design, MBP scaffolds were elaborated to improve activity and selectivity. Structure-activity relationships were established and used to generate inhibitors of influenza endonuclease with tight-binding affinities. The activity of these inhibitors was analyzed using a fluorescence-quenching-based nuclease activity assay, and binding was validated using differential scanning fluorometry. Lead compounds were found to be highly selective for PAN endonuclease against several related dinuclear and mononuclear metalloenzymes. Combining principles of bioinorganic and medicinal chemistry in this study has resulted in some of the most active in vitro influenza PAN endonuclease inhibitors with high ligand efficiencies.
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Affiliation(s)
- Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Ryjul W Stokes
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Yifan Feng
- State Key Laboratory of Medicinal Chemical Biology , Nankai University , No. 94 Weijin Road , Nankai District, Tianjin , 300071 , P. R. China
| | - Jiaxing Sun
- State Key Laboratory of Medicinal Chemical Biology , Nankai University , No. 94 Weijin Road , Nankai District, Tianjin , 300071 , P. R. China
| | - Yao Chen
- State Key Laboratory of Medicinal Chemical Biology , Nankai University , No. 94 Weijin Road , Nankai District, Tianjin , 300071 , P. R. China
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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23
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Zhang J, Hu Y, Musharrafieh R, Yin H, Wang J. Focusing on the Influenza Virus Polymerase Complex: Recent Progress in Drug Discovery and Assay Development. Curr Med Chem 2019; 26:2243-2263. [PMID: 29984646 DOI: 10.2174/0929867325666180706112940] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 03/27/2018] [Accepted: 05/06/2018] [Indexed: 12/17/2022]
Abstract
Influenza viruses are severe human pathogens that pose persistent threat to public health. Each year more people die of influenza virus infection than that of breast cancer. Due to the limited efficacy associated with current influenza vaccines, as well as emerging drug resistance from small molecule antiviral drugs, there is a clear need to develop new antivirals with novel mechanisms of action. The influenza virus polymerase complex has become a promising target for the development of the next-generation of antivirals for several reasons. Firstly, the influenza virus polymerase, which forms a heterotrimeric complex that consists of PA, PB1, and PB2 subunits, is highly conserved. Secondly, both individual polymerase subunit (PA, PB1, and PB2) and inter-subunit interactions (PA-PB1, PB1- PB2) represent promising drug targets. Lastly, growing insight into the structure and function of the polymerase complex has spearheaded the structure-guided design of new polymerase inhibitors. In this review, we highlight recent progress in drug discovery and assay development targeting the influenza virus polymerase complex and discuss their therapeutic potentials.
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Affiliation(s)
- Jiantao Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Rami Musharrafieh
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Hang Yin
- Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States.,BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
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24
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Yang J, Huang Y, Liu S. Investigational antiviral therapies for the treatment of influenza. Expert Opin Investig Drugs 2019; 28:481-488. [PMID: 31018720 DOI: 10.1080/13543784.2019.1606210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Influenza viral ribonucleoprotein complexes (vRNPs) play a key role in viral transcription and replication; hence, the recent development of novel anti-influenza drugs targeting vRNPs has garnered widespread interest. AREAS COVERED We discuss the function of the constituents of vRNPs and summarize those vRNPs-targeted synthetic drugs that are in preclinical and early clinical development. EXPERT OPINION vRNPs contain high-value drug targets; such targets include the subunits PA, PB1, PB2, and NP. Developing a new generation of antiviral therapies with strategies that utilize existing drugs, natural compounds originated from new resources and novel drug combinations may open up new therapeutic approaches to influenza.
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Affiliation(s)
- Jie Yang
- a Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences , Southern Medical University , Guangzhou , China
| | - Yingna Huang
- a Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences , Southern Medical University , Guangzhou , China
| | - Shuwen Liu
- a Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences , Southern Medical University , Guangzhou , China.,b State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology , Southern Medical University , Guangzhou , China
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25
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Zhou Z, Liu T, Zhang J, Zhan P, Liu X. Influenza A virus polymerase: an attractive target for next-generation anti-influenza therapeutics. Drug Discov Today 2018; 23:503-518. [PMID: 29339107 DOI: 10.1016/j.drudis.2018.01.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/31/2017] [Accepted: 01/05/2018] [Indexed: 12/20/2022]
Abstract
The influenza RNA-dependent RNA polymerase (RdRP) is conserved among different types of influenza virus, playing an important part in transcription and replication. In this regard, influenza RdRP is an attractive target for novel anti-influenza drug discovery. Herein, we will introduce the structural and functional information of influenza polymerase; and an overview of inhibitors targeting the PA endonuclease and PB2 cap-binding site is provided, along with the approaches utilized for identification of these inhibitors. The protein-protein interactions (PPIs) of the three polymerase subunits: PA, PB1 and PB2, are described based on the published crystal structures, and inhibitors targeting the PA-PB1 interaction are introduced briefly.
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Affiliation(s)
- Zhongxia Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Tao Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, China.
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26
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Binding affinity of the L-742,001 inhibitor to the endonuclease domain of A/H1N1/PA influenza virus variants: Molecular simulation approaches. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2017.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Protein-Structure Assisted Optimization of 4,5-Dihydroxypyrimidine-6-Carboxamide Inhibitors of Influenza Virus Endonuclease. Sci Rep 2017; 7:17139. [PMID: 29215062 PMCID: PMC5719402 DOI: 10.1038/s41598-017-17419-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/24/2017] [Indexed: 01/11/2023] Open
Abstract
Influenza is a serious hazard to human health that causes hundreds of thousands of deaths annually. Though vaccines and current therapeutics can blunt some of the perilous impact of this viral infection, new treatments are needed due to the constantly evolving nature of this virus. Recently, our growing understanding of an essential influenza viral protein, PA, has led to the development of focused libraries of new small molecules that specifically target the active site of the PA influenza endonuclease, which we report here. Our overarching approach has been to proactively develop lead inhibitors that are less likely to rapidly develop clinical resistance by optimizing inhibitors that retain activity against induced resistant mutants. Here, we report details behind the discovery of new potent inhibitors of wild type and resistant mutant endonucleases along with their high-resolution co-crystal structure-activity relationships. These results add to our understanding of nuclease protein targets and potentially serve as starting points for a new therapeutic approach to the treatment of influenza.
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28
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Xing W, Barauskas O, Kirschberg T, Niedziela-Majka A, Clarke M, Birkus G, Weissburg P, Liu X, Schultz BE, Sakowicz R, Kwon H, Feng JY. Biochemical characterization of recombinant influenza A polymerase heterotrimer complex: Endonuclease activity and evaluation of inhibitors. PLoS One 2017; 12:e0181969. [PMID: 28809961 PMCID: PMC5557545 DOI: 10.1371/journal.pone.0181969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/10/2017] [Indexed: 12/23/2022] Open
Abstract
Influenza polymerase is a heterotrimer composed of polymerase acidic protein A (PA) and basic proteins 1 (PB1) and 2 (PB2). The endonuclease active site, located in the PA subunit, cleaves host mRNA to prime viral mRNA transcription, and is essential for viral replication. To date, the human influenza A endonuclease activity has only been studied on the truncated active-site containing N-terminal domain of PA (PAN) or full-length PA in the absence of PB1 or PB2. In this study, we characterized the endonuclease activity of recombinant proteins of influenza A/PR8 containing full length PA, PA/PB1 dimer, and PA/PB1/PB2 trimer, observing 8.3-, 265-, and 142-fold higher activity than PAN, respectively. Using the PA/PB1/PB2 trimer, we developed a robust endonuclease assay with a synthetic fluorogenic RNA substrate. The observed Km (150 ± 11 nM) and kcat [(1.4 ± 0.2) x 10-3s-1] values were consistent with previous reports using virion-derived replication complex. Two known influenza endonuclease phenylbutanoic acid inhibitors showed IC50 values of 10–20 nM, demonstrating the utility of this system for future high throughput screening.
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Affiliation(s)
- Weimei Xing
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Ona Barauskas
- Gilead Sciences, Inc., Foster City, California, United States of America
| | | | | | - Michael Clarke
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Gabriel Birkus
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Perry Weissburg
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Xiaohong Liu
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Brian E. Schultz
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Roman Sakowicz
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - HyockJoo Kwon
- Gilead Sciences, Inc., Foster City, California, United States of America
- * E-mail: (HJK); (JYF)
| | - Joy Y. Feng
- Gilead Sciences, Inc., Foster City, California, United States of America
- * E-mail: (HJK); (JYF)
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29
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An electrochemiluminescence biosensor for endonuclease EcoRI detection. Biosens Bioelectron 2017; 89:585-591. [DOI: 10.1016/j.bios.2016.01.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 01/11/2016] [Accepted: 01/28/2016] [Indexed: 10/22/2022]
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30
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Wu X, Wu X, Sun Q, Zhang C, Yang S, Li L, Jia Z. Progress of small molecular inhibitors in the development of anti-influenza virus agents. Am J Cancer Res 2017; 7:826-845. [PMID: 28382157 PMCID: PMC5381247 DOI: 10.7150/thno.17071] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/18/2016] [Indexed: 02/05/2023] Open
Abstract
The influenza pandemic is a major threat to human health, and highly aggressive strains such as H1N1, H5N1 and H7N9 have emphasized the need for therapeutic strategies to combat these pathogens. Influenza anti-viral agents, especially active small molecular inhibitors play important roles in controlling pandemics while vaccines are developed. Currently, only a few drugs, which function as influenza neuraminidase (NA) inhibitors and M2 ion channel protein inhibitors, are approved in clinical. However, the acquired resistance against current anti-influenza drugs and the emerging mutations of influenza virus itself remain the major challenging unmet medical needs for influenza treatment. It is highly desirable to identify novel anti-influenza agents. This paper reviews the progress of small molecular inhibitors act as antiviral agents, which include hemagglutinin (HA) inhibitors, RNA-dependent RNA polymerase (RdRp) inhibitors, NA inhibitors and M2 ion channel protein inhibitors etc. Moreover, we also summarize new, recently reported potential targets and discuss strategies for the development of new anti-influenza virus drugs.
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31
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Kaushik S, Prokop Z, Damborsky J, Chaloupkova R. Kinetics of binding of fluorescent ligands to enzymes with engineered access tunnels. FEBS J 2016; 284:134-148. [DOI: 10.1111/febs.13957] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/30/2016] [Accepted: 11/04/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Shubhangi Kaushik
- Loschmidt Laboratories Department of Experimental Biology Research Centre for Toxic Compounds in the Environment (RECETOX) Masaryk University Brno Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories Department of Experimental Biology Research Centre for Toxic Compounds in the Environment (RECETOX) Masaryk University Brno Czech Republic
- International Clinical Research Center St. Anne's University Hospital Brno Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories Department of Experimental Biology Research Centre for Toxic Compounds in the Environment (RECETOX) Masaryk University Brno Czech Republic
- International Clinical Research Center St. Anne's University Hospital Brno Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories Department of Experimental Biology Research Centre for Toxic Compounds in the Environment (RECETOX) Masaryk University Brno Czech Republic
- International Clinical Research Center St. Anne's University Hospital Brno Czech Republic
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32
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Jones JC, Marathe BM, Lerner C, Kreis L, Gasser R, Pascua PNQ, Najera I, Govorkova EA. A Novel Endonuclease Inhibitor Exhibits Broad-Spectrum Anti-Influenza Virus Activity In Vitro. Antimicrob Agents Chemother 2016; 60:5504-14. [PMID: 27381402 PMCID: PMC4997863 DOI: 10.1128/aac.00888-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/27/2016] [Indexed: 11/20/2022] Open
Abstract
Antiviral drugs are important in preventing and controlling influenza, particularly when vaccines are ineffective or unavailable. A single class of antiviral drugs, the neuraminidase inhibitors (NAIs), is recommended for treating influenza. The limited therapeutic options and the potential risk of antiviral resistance are driving the search for additional small-molecule inhibitors that act on influenza virus proteins. The acid polymerase (PA) of influenza viruses is a promising target for new antivirals because of its essential role in initiating virus transcription. Here, we characterized a novel compound, RO-7, identified as a putative PA endonuclease inhibitor. RO-7 was effective when added before the cessation of genome replication, reduced polymerase activity in cell-free systems, and decreased relative amounts of viral mRNA and genomic RNA during influenza virus infection. RO-7 specifically inhibited the ability of the PA endonuclease domain to cleave a nucleic acid substrate. RO-7 also inhibited influenza A viruses (seasonal and 2009 pandemic H1N1 and seasonal H3N2) and B viruses (Yamagata and Victoria lineages), zoonotic viruses (H5N1, H7N9, and H9N2), and NAI-resistant variants in plaque reduction, yield reduction, and cell viability assays in Madin-Darby canine kidney (MDCK) cells with nanomolar to submicromolar 50% effective concentrations (EC50s), low toxicity, and favorable selective indices. RO-7 also inhibited influenza virus replication in primary normal human bronchial epithelial cells. Overall, RO-7 exhibits broad-spectrum activity against influenza A and B viruses in multiple in vitro assays, supporting its further characterization and development as a potential antiviral agent for treating influenza.
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Affiliation(s)
- Jeremy C Jones
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Bindumadhav M Marathe
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | | | | | - Philippe Noriel Q Pascua
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Elena A Govorkova
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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33
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Stevaert A, Naesens L. The Influenza Virus Polymerase Complex: An Update on Its Structure, Functions, and Significance for Antiviral Drug Design. Med Res Rev 2016; 36:1127-1173. [PMID: 27569399 PMCID: PMC5108440 DOI: 10.1002/med.21401] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/18/2016] [Accepted: 06/24/2016] [Indexed: 12/11/2022]
Abstract
Influenza viruses cause seasonal epidemics and pandemic outbreaks associated with significant morbidity and mortality, and a huge cost. Since resistance to the existing anti‐influenza drugs is rising, innovative inhibitors with a different mode of action are urgently needed. The influenza polymerase complex is widely recognized as a key drug target, given its critical role in virus replication and high degree of conservation among influenza A (of human or zoonotic origin) and B viruses. We here review the major progress that has been made in recent years in unravelling the structure and functions of this protein complex, enabling structure‐aided drug design toward the core regions of the PA endonuclease, PB1 polymerase, or cap‐binding PB2 subunit. Alternatively, inhibitors may target a protein–protein interaction site, a cellular factor involved in viral RNA synthesis, the viral RNA itself, or the nucleoprotein component of the viral ribonucleoprotein. The latest advances made for these diverse pharmacological targets have yielded agents in advanced (i.e., favipiravir and VX‐787) or early clinical testing, besides several experimental inhibitors in various stages of development, which are all covered here.
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Affiliation(s)
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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34
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Roch FF, Hinterkörner G, Menke J, Tang GQ, Cusack S, Butzendobler B, Buschmann H, Datta K, Wolkerstorfer A. An RNA Hybridization Assay for Screening Influenza A Virus Polymerase Inhibitors Using the Entire Ribonucleoprotein Complex. Assay Drug Dev Technol 2016; 13:488-506. [PMID: 26461433 DOI: 10.1089/adt.2015.668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Novel antiviral drugs, which are less prone to resistance development, are desirable alternatives to the currently approved drugs for the treatment of potentially serious influenza virus infections. The viral polymerase is highly conserved and serves as an attractive target for antiviral drugs since potent inhibitors would directly stop viral replication at an early stage. Recent structural studies on the functional domains of the heterotrimeric influenza polymerase, which comprises subunits PA, PB1, and PB2, opened the way to a structure-based approach for optimizing inhibitors of viral replication. These strategies, however, are limited by the use of isolated protein fragments instead of employing the entire ribonucleoprotein complex (RNP), which represents the functional form of the influenza polymerase in infected cells. In this study, we have established a screening assay for efficient and reliable analysis of potential influenza polymerase inhibitors of various molecular targets such as monoselective polymerase inhibitors targeting the endonuclease site, the cap-binding domain, and the polymerase active site, respectively. By utilizing whole viral RNPs and a radioactivity-free endpoint detection with the capability for efficient compound screening while offering high-content information on potential inhibitors to drive medicinal chemistry program in a reliable manner, this biochemical assay provides significant advantages over the currently available conventional assays. We propose that this assay can eventually be adapted for coinstantaneous analysis and subsequent optimization of two or more different chemical scaffold classes targeting multiple active sites within the polymerase complex, thus enabling the evaluation of drug combinations and characterization of molecules with dual functionality.
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Affiliation(s)
| | | | - John Menke
- 2 Virology Discovery, Hoffmann-La Roche, Inc. , Nutley, New Jersey
| | - Guo-Qing Tang
- 2 Virology Discovery, Hoffmann-La Roche, Inc. , Nutley, New Jersey
| | - Stephen Cusack
- 3 Grenoble Outstation, European Molecular Biology Laboratory , Grenoble, France
| | | | | | - Kausiki Datta
- 2 Virology Discovery, Hoffmann-La Roche, Inc. , Nutley, New Jersey
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35
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Abstract
The influenza virus is responsible for millions of cases of severe illness annually. Yearly variance in the effectiveness of vaccination, coupled with emerging drug resistance, necessitates the development of new drugs to treat influenza infections. One attractive target is the RNA-dependent RNA polymerase PA subunit. Herein we report the development of inhibitors of influenza PA endonuclease derived from lead compounds identified from a metal-binding pharmacophore (MBP) library screen. Pyromeconic acid and derivatives thereof were found to be potent inhibitors of endonuclease. Guided by modeling and previously reported structural data, several sublibraries of molecules were elaborated from the MBP hits. Structure-activity relationships were established, and more potent molecules were designed and synthesized using fragment growth and fragment merging strategies. This approach ultimately resulted in the development of a lead compound with an IC50 value of 14 nM, which displayed an EC50 value of 2.1 μM against H1N1 influenza virus in MDCK cells.
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Affiliation(s)
- Cy V Credille
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Yao Chen
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
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36
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Yuan S, Chu H, Zhang K, Ye J, Singh K, Kao RYT, Chow BKC, Zhou J, Zheng BJ. A novel small-molecule compound disrupts influenza A virus PB2 cap-binding and inhibits viral replication. J Antimicrob Chemother 2016; 71:2489-97. [PMID: 27272726 DOI: 10.1093/jac/dkw194] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/22/2016] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES The conserved residues 318-483 in the PB2 subunit of influenza A polymerase is an independently folded cap-binding domain (PB2cap) that exhibits a distinct binding mode from other host cap-binding proteins, which suggests that PB2cap might be an ideal drug target. This study aimed to identify a new class of anti-influenza inhibitors that specifically disrupts the interaction between PB2cap and host cap structures. METHODS An innovative fluorescence polarization assay was established for primary screening, followed by cap-binding inhibitory activity, antiviral efficacy and cytotoxicity evaluations of the selected compounds. The best compound was characterized by multi-cycle virus growth assay, cross-protection test, synergism evaluation, mini-replicon assay, binding affinity analysis, docking simulation and mouse study. RESULTS Several PB2 cap-binding inhibitors were discovered. The compound 7-(4-hydroxy-2-oxo-2H-chromen-3-yl)-6H,7H,8H-chromeno[3',4':5,6]pyrano[3,2-c]chromene-6,8-dione, designated PB2-39, was identified as a potent inhibitor of replication of multiple subtypes of influenza A virus, including H1N1, H3N2, H5N1, H7N7, H7N9 and H9N2 in vitro and H1N1, H5N1 and H7N9 in vivo. Combinational treatment with the influenza virus release inhibitor zanamivir and PB2-39 exerted a synergistic anti-influenza effect. Mechanistic experiments supported that PB2-39 suppressed viral polymerase activity. Docking and binding affinity analyses demonstrated that PB2-39 interacted with the PB2 cap-binding pocket, suggesting its role as a cap-binding competitor. CONCLUSIONS Our study provides new insights for the strategic development of novel cap-binding inhibitors of influenza A viruses.
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Affiliation(s)
- Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Hin Chu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ke Zhang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jiahui Ye
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kailash Singh
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China
| | - Richard Y T Kao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Billy K C Chow
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China
| | - Jie Zhou
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Bo-Jian Zheng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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37
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Hall MD, Yasgar A, Peryea T, Braisted JC, Jadhav A, Simeonov A, Coussens NP. Fluorescence polarization assays in high-throughput screening and drug discovery: a review. Methods Appl Fluoresc 2016; 4:022001. [PMID: 28809163 DOI: 10.1088/2050-6120/4/2/022001] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The sensitivity of fluorescence polarization (FP) and fluorescence anisotropy (FA) to molecular weight changes has enabled the interrogation of diverse biological mechanisms, ranging from molecular interactions to enzymatic activity. Assays based on FP/FA technology have been widely utilized in high-throughput screening (HTS) and drug discovery due to the homogenous format, robust performance and relative insensitivity to some types of interferences, such as inner filter effects. Advancements in assay design, fluorescent probes, and technology have enabled the application of FP assays to increasingly complex biological processes. Herein we discuss different types of FP/FA assays developed for HTS, with examples to emphasize the diversity of applicable targets. Furthermore, trends in target and fluorophore selection, as well as assay type and format, are examined using annotated HTS assays within the PubChem database. Finally, practical considerations for the successful development and implementation of FP/FA assays for HTS are provided based on experience at our center and examples from the literature, including strategies for flagging interference compounds among a list of hits.
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Affiliation(s)
- Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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38
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Fudo S, Yamamoto N, Nukaga M, Odagiri T, Tashiro M, Hoshino T. Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit. Biochemistry 2016; 55:2646-60. [PMID: 27088785 DOI: 10.1021/acs.biochem.5b01087] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Influenza viruses are global threat to humans, and the development of new antiviral agents are still demanded to prepare for pandemics and to overcome the emerging resistance to the current drugs. Influenza polymerase acidic protein N-terminal domain (PAN) has endonuclease activity and is one of the appropriate targets for novel antiviral agents. First, we performed X-ray cocrystal analysis on the complex structures of PAN with two endonuclease inhibitors. The protein crystallization and the inhibitor soaking were done at pH 5.8. The binding modes of the two inhibitors were different from a common binding mode previously reported for the other influenza virus endonuclease inhibitors. We additionally clarified the complex structures of PAN with the same two endonuclease inhibitors at pH 7.0. In one of the crystal structures, an additional inhibitor molecule, which chelated to the two metal ions in the active site, was observed. On the basis of the crystal structures at pH 7.0, we carried out 100 ns molecular dynamics (MD) simulations for both of the complexes. The analysis of simulation results suggested that the binding mode of each inhibitor to PAN was stable in spite of the partial deviation of the simulation structure from the crystal one. Furthermore, crystal structure analysis and MD simulation were performed for PAN in complex with an inhibitor, which was already reported to have a high compound potency for comparison. The findings on the presence of multiple binding sites at around the PAN substrate-binding pocket will provide a hint for enhancing the binding affinity of inhibitors.
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Affiliation(s)
- Satoshi Fudo
- Graduate School of Pharmaceutical Sciences, Chiba University , 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Norio Yamamoto
- Graduate School of Medicine, Juntendo University , 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.,Influenza Virus Research Center, National Institute of Infectious Diseases , 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Michiyoshi Nukaga
- Faculty of Pharmaceutical Sciences, Josai International University , 1 Gumyo, Togane-shi Chiba 283-8555, Japan
| | - Takato Odagiri
- Influenza Virus Research Center, National Institute of Infectious Diseases , 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Masato Tashiro
- Influenza Virus Research Center, National Institute of Infectious Diseases , 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University , 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
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39
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Abstract
This viewpoint describes the results obtained from matched molecular pair analyses and quantum mechanics calculations that show unsaturated rings found in drug-like molecules may be replaced with their saturated counterparts without losing potency even if they are engaged in stacking interactions with the side chains of aromatic residues.
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Affiliation(s)
- Hakan Gunaydin
- Department of Structural Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Michael D. Bartberger
- Department of Molecular Engineering, Therapeutic Discovery, One Amgen Center Drive, Thousand Oaks, California 91320, United States
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40
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Identification and characterization of influenza variants resistant to a viral endonuclease inhibitor. Proc Natl Acad Sci U S A 2016; 113:3669-74. [PMID: 26976575 DOI: 10.1073/pnas.1519772113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The influenza endonuclease is an essential subdomain of the viral RNA polymerase. It processes host pre-mRNAs to serve as primers for viral mRNA and is an attractive target for antiinfluenza drug discovery. Compound L-742,001 is a prototypical endonuclease inhibitor, and we found that repeated passaging of influenza virus in the presence of this drug did not lead to the development of resistant mutant strains. Reduced sensitivity to L-742,001 could only be induced by creating point mutations via a random mutagenesis strategy. These mutations mapped to the endonuclease active site where they can directly impact inhibitor binding. Engineered viruses containing the mutations showed resistance to L-742,001 both in vitro and in vivo, with only a modest reduction in fitness. Introduction of the mutations into a second virus also increased its resistance to the inhibitor. Using the isolated wild-type and mutant endonuclease domains, we used kinetics, inhibitor binding and crystallography to characterize how the two most significant mutations elicit resistance to L-742,001. These studies lay the foundation for the development of a new class of influenza therapeutics with reduced potential for the development of clinical endonuclease inhibitor-resistant influenza strains.
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41
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Yuan S, Chu H, Singh K, Zhao H, Zhang K, Kao RYT, Chow BKC, Zhou J, Zheng BJ. A novel small-molecule inhibitor of influenza A virus acts by suppressing PA endonuclease activity of the viral polymerase. Sci Rep 2016; 6:22880. [PMID: 26956222 PMCID: PMC4783701 DOI: 10.1038/srep22880] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 02/23/2016] [Indexed: 12/17/2022] Open
Abstract
The RNA-dependent RNA polymerase of influenza A virus comprises conserved and independently-folded subdomains with defined functionalities. The N-terminal domain of the PA subunit (PAN) harbors the endonuclease function so that it can serve as a desired target for drug discovery. To identify a class of anti-influenza inhibitors that impedes PAN endonuclease activity, a screening approach that integrated the fluorescence resonance energy transfer based endonuclease inhibitory assay with the DNA gel-based endonuclease inhibitory assay was conducted, followed by the evaluation of antiviral efficacies and potential cytotoxicity of the primary hits in vitro and in vivo. A small-molecule compound ANA-0 was identified as a potent inhibitor against the replication of multiple subtypes of influenza A virus, including H1N1, H3N2, H5N1, H7N7, H7N9 and H9N2, in cell cultures. Combinational treatment of zanamivir and ANA-0 exerted synergistic anti-influenza effect in vitro. Intranasal administration of ANA-0 protected mice from lethal challenge and reduced lung viral loads in H1N1 virus infected BALB/c mice. In summary, ANA-0 shows potential to be developed to novel anti-influenza agents.
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Affiliation(s)
- Shuofeng Yuan
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Hin Chu
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Kailash Singh
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Hanjun Zhao
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Ke Zhang
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Richard Y T Kao
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Billy K C Chow
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Jie Zhou
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Bo-Jian Zheng
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
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Shirayama R, Shoji M, Sriwilaijaroen N, Hiramatsu H, Suzuki Y, Kuzuhara T. Inhibition of PA endonuclease activity of influenza virus RNA polymerase by Kampo medicines. Drug Discov Ther 2016; 10:109-13. [DOI: 10.5582/ddt.2016.01010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Riku Shirayama
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University
| | - Masaki Shoji
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University
| | - Nongluk Sriwilaijaroen
- Faculty of Medicine, Thammasat University (Rangsit Campus)
- College of Life and Health Sciences, Chubu University
| | | | - Yasuo Suzuki
- College of Life and Health Sciences, Chubu University
| | - Takashi Kuzuhara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University
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43
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Dobb KS, Kaye SJ, Beckmann N, Thain JL, Stateva L, Birch M, Oliver JD. Characterisation of the Candida albicans Phosphopantetheinyl Transferase Ppt2 as a Potential Antifungal Drug Target. PLoS One 2015; 10:e0143770. [PMID: 26606674 PMCID: PMC4659657 DOI: 10.1371/journal.pone.0143770] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/09/2015] [Indexed: 01/14/2023] Open
Abstract
Antifungal drugs acting via new mechanisms of action are urgently needed to combat the increasing numbers of severe fungal infections caused by pathogens such as Candida albicans. The phosphopantetheinyl transferase of Aspergillus fumigatus, encoded by the essential gene pptB, has previously been identified as a potential antifungal target. This study investigated the function of its orthologue in C. albicans, PPT2/C1_09480W by placing one allele under the control of the regulatable MET3 promoter, and deleting the remaining allele. The phenotypes of this conditional null mutant showed that, as in A. fumigatus, the gene PPT2 is essential for growth in C. albicans, thus fulfilling one aspect of an efficient antifungal target. The catalytic activity of Ppt2 as a phosphopantetheinyl transferase and the acyl carrier protein Acp1 as a substrate were demonstrated in a fluorescence transfer assay, using recombinant Ppt2 and Acp1 produced and purified from E.coli. A fluorescence polarisation assay amenable to high-throughput screening was also developed. Therefore we have identified Ppt2 as a broad-spectrum novel antifungal target and developed tools to identify inhibitors as potentially new antifungal compounds.
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Affiliation(s)
| | - Sarah J. Kaye
- F2G Ltd., Lankro Way, Eccles, Manchester, M30 0LX, United Kingdom
| | - Nicola Beckmann
- F2G Ltd., Lankro Way, Eccles, Manchester, M30 0LX, United Kingdom
| | - John L. Thain
- F2G Ltd., Lankro Way, Eccles, Manchester, M30 0LX, United Kingdom
| | - Lubomira Stateva
- Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Mike Birch
- F2G Ltd., Lankro Way, Eccles, Manchester, M30 0LX, United Kingdom
| | - Jason D. Oliver
- F2G Ltd., Lankro Way, Eccles, Manchester, M30 0LX, United Kingdom
- * E-mail:
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44
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Pala N, Stevaert A, Dallocchio R, Dessì A, Rogolino D, Carcelli M, Sanna V, Sechi M, Naesens L. Virtual Screening and Biological Validation of Novel Influenza Virus PA Endonuclease Inhibitors. ACS Med Chem Lett 2015; 6:866-71. [PMID: 26288686 DOI: 10.1021/acsmedchemlett.5b00109] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 06/18/2015] [Indexed: 01/01/2023] Open
Abstract
The influenza virus RNA-dependent RNA polymerase complex (RdRp), a heterotrimeric protein complex responsible for viral RNA transcription and replication, represents a primary target for antiviral drug development. One particularly attractive approach is interference with the endonucleolytic "cap-snatching" reaction by the RdRp subunit PA, more precisely by inhibiting its metal-dependent catalytic activity which resides in the N-terminal part of PA (PA-Nter). Almost all PA inhibitors (PAIs) thus far discovered bear pharmacophoric fragments with chelating motifs able to bind the bivalent metal ions in the catalytic core of PA-Nter. More recently, the availability of crystallographic structures of PA-Nter has enabled rational design of original PAIs with improved binding properties and antiviral potency. We here present a coupled pharmacophore/docking virtual screening approach that allowed us to identify PAIs with interesting inhibitory activity in a PA-Nter enzymatic assay. Moreover, antiviral activity in the low micromolar range was observed in cell-based influenza virus assays.
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Affiliation(s)
- Nicolino Pala
- Dipartimento
di Chimica e Farmacia, Università di Sassari, Via Vienna
2, 07100 Sassari, Italy
| | - Annelies Stevaert
- Rega
Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Roberto Dallocchio
- Istituto
di Chimica Biomolecolare, CNR−Consiglio Nazionale delle Ricerche, Sassari, 07100 Li Punti Italy
| | - Alessandro Dessì
- Istituto
di Chimica Biomolecolare, CNR−Consiglio Nazionale delle Ricerche, Sassari, 07100 Li Punti Italy
| | - Dominga Rogolino
- Dipartimento
di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Mauro Carcelli
- Dipartimento
di Chimica, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Vanna Sanna
- Dipartimento
di Chimica e Farmacia, Università di Sassari, Via Vienna
2, 07100 Sassari, Italy
| | - Mario Sechi
- Dipartimento
di Chimica e Farmacia, Università di Sassari, Via Vienna
2, 07100 Sassari, Italy
| | - Lieve Naesens
- Rega
Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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45
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Zhang H, Wu Q, Berezin MY. Fluorescence anisotropy (polarization): from drug screening to precision medicine. Expert Opin Drug Discov 2015; 10:1145-61. [PMID: 26289575 DOI: 10.1517/17460441.2015.1075001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Fluorescence anisotropy (FA) is one of the major established methods accepted by industry and regulatory agencies for understanding the mechanisms of drug action and selecting drug candidates utilizing a high-throughput format. AREAS COVERED This review covers the basics of FA and complementary methods, such as fluorescence lifetime anisotropy and their roles in the drug discovery process. The authors highlight the factors affecting FA readouts, fluorophore selection and instrumentation. Furthermore, the authors describe the recent development of a successful, commercially valuable FA assay for long QT syndrome drug toxicity to illustrate the role that FA can play in the early stages of drug discovery. EXPERT OPINION Despite the success in drug discovery, the FA-based technique experiences competitive pressure from other homogeneous assays. That being said, FA is an established yet rapidly developing technique, recognized by academic institutions, the pharmaceutical industry and regulatory agencies across the globe. The technical problems encountered in working with small molecules in homogeneous assays are largely solved, and new challenges come from more complex biological molecules and nanoparticles. With that, FA will remain one of the major work-horse techniques leading to precision (personalized) medicine.
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Affiliation(s)
- Hairong Zhang
- a 1 Washington University School of Medicine, Department of Radiology , St. Louis 63110, USA
| | - Qian Wu
- a 1 Washington University School of Medicine, Department of Radiology , St. Louis 63110, USA
| | - Mikhail Y Berezin
- a 1 Washington University School of Medicine, Department of Radiology , St. Louis 63110, USA.,b 2 Washington University School of Medicine, Institute of Materials Science and Engineering, Department of Radiology , 510 S. Kingshighway, Barnard Bldg, 6th floor, 6604A, St. Louis, MO, USA +1 314 747 0701 ; +1 314 747 5191 ;
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46
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Structural and computational study on inhibitory compounds for endonuclease activity of influenza virus polymerase. Bioorg Med Chem 2015; 23:5466-75. [PMID: 26252962 DOI: 10.1016/j.bmc.2015.07.046] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 07/21/2015] [Accepted: 07/24/2015] [Indexed: 11/21/2022]
Abstract
Seasonal epidemics and occasional pandemics caused by influenza viruses are global threats to humans. Since the efficacy of currently approved drugs is limited by the emerging resistance of the viruses, the development of new antiviral drugs is still demanded. Endonuclease activity, which lies in the influenza polymerase acidic protein N-terminal domain (PA(N)), is a potent target for novel antiviral agents. Here, we report the identification of some novel inhibitors for PA(N) endonuclease activity. The binding mode of one of the inhibitory compounds to PA(N) was investigated in detail by means of X-ray crystal structure analysis and molecular dynamics (MD) simulation. It was observed in the crystal structure that three molecules of the same kind of inhibitor were bound to one PA(N). One of the three molecules is located at the active site and makes a chelation to metal ions. Another molecule is positioned at the space adjacent to the metal-chelated site. The other molecule is located at a site slightly apart from the metal-chelated site, causing a conformational change of Arg124. The last binding site was not observed in previous crystallographic studies. Hence, the stability of inhibitor binding was examined by performing 100-ns MD simulation. During the MD simulation, the three inhibitor molecules fluctuated at the respective binding sites at different amplitudes, while all of the molecules maintained interactions with the protein. Molecular mechanics/generalized Born surface area (MM/GBSA) analysis suggested that the molecule in the last binding site has a higher affinity than the others. Structural information obtained in this study will provide a hint for designing and developing novel potent agents against influenza viruses.
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47
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Closa F, Gosse C, Jullien L, Lemarchand A. Identification of two-step chemical mechanisms using small temperature oscillations and a single tagged species. J Chem Phys 2015; 142:174108. [PMID: 25956091 DOI: 10.1063/1.4919632] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In order to identify two-step chemical mechanisms, we propose a method based on a small temperature modulation and on the analysis of the concentration oscillations of a single tagged species involved in the first step. The thermokinetic parameters of the first reaction step are first determined. Then, we build test functions that are constant only if the chemical system actually possesses some assumed two-step mechanism. Next, if the test functions plotted using experimental data are actually even, the mechanism is attributed and the obtained constant values provide the rate constants and enthalpy of reaction of the second step. The advantage of the protocol is to use the first step as a probe reaction to reveal the dynamics of the second step, which can hence be relieved of any tagging. The protocol is anticipated to apply to many mechanisms of biological relevance. As far as ligand binding is considered, our approach can address receptor conformational changes or dimerization as well as competition with or modulation by a second partner. The method can also be used to screen libraries of untagged compounds, relying on a tracer whose concentration can be spectroscopically monitored.
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Affiliation(s)
- F Closa
- Sorbonne Universités, UPMC Univ. Paris 06, Laboratoire de Physique Théorique de la Matière Condensée, 4 place Jussieu, case courrier 121, 75252 Paris Cedex 05, France
| | - C Gosse
- Laboratoire de Photonique et de Nanostructures, LPN-CNRS, route de Nozay, 91460 Marcoussis, France
| | - L Jullien
- Department of Chemistry, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005 Paris, France
| | - A Lemarchand
- Sorbonne Universités, UPMC Univ. Paris 06, Laboratoire de Physique Théorique de la Matière Condensée, 4 place Jussieu, case courrier 121, 75252 Paris Cedex 05, France
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Stevaert A, Nurra S, Pala N, Carcelli M, Rogolino D, Shepard C, Domaoal RA, Kim B, Alfonso-Prieto M, Marras SAE, Sechi M, Naesens L. An integrated biological approach to guide the development of metal-chelating inhibitors of influenza virus PA endonuclease. Mol Pharmacol 2015; 87:323-37. [PMID: 25477342 PMCID: PMC11037440 DOI: 10.1124/mol.114.095588] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/04/2014] [Indexed: 04/26/2024] Open
Abstract
The influenza virus PA endonuclease, which cleaves capped cellular pre-mRNAs to prime viral mRNA synthesis, is a promising target for novel anti-influenza virus therapeutics. The catalytic center of this enzyme resides in the N-terminal part of PA (PA-Nter) and contains two (or possibly one or three) Mg(2+) or Mn(2+) ions, which are critical for its catalytic function. There is great interest in PA inhibitors that are optimally designed to occupy the active site and chelate the metal ions. We focused here on a series of β-diketo acid (DKA) and DKA-bioisosteric compounds containing different scaffolds, and determined their structure-activity relationship in an enzymatic assay with PA-Nter, in order to build a three-dimensional pharmacophore model. In addition, we developed a molecular beacon (MB)-based PA-Nter assay that enabled us to compare the inhibition of Mn(2+) versus Mg(2+), the latter probably being the biologically relevant cofactor. This real-time MB assay allowed us to measure the enzyme kinetics of PA-Nter or perform high-throughput screening. Several DKA derivatives were found to cause strong inhibition of PA-Nter, with IC50 values comparable to that of the prototype L-742,001 (i.e., below 2 μM). Among the different compounds tested, L-742,001 appeared unique in having equal activity against either Mg(2+) or Mn(2+). Three compounds ( 10: , with a pyrrole scaffold, and 40: and 41: , with an indole scaffold) exhibited moderate antiviral activity in cell culture (EC99 values 64-95 μM) and were proven to affect viral RNA synthesis. Our approach of integrating complementary enzymatic, cellular, and mechanistic assays should guide ongoing development of improved influenza virus PA inhibitors.
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Affiliation(s)
- Annelies Stevaert
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Salvatore Nurra
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Nicolino Pala
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Mauro Carcelli
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Dominga Rogolino
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Caitlin Shepard
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Robert A Domaoal
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Baek Kim
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Mercedes Alfonso-Prieto
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Salvatore A E Marras
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Mario Sechi
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
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49
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Chen E, Swift RV, Alderson N, Feher VA, Feng GS, Amaro RE. Computation-guided discovery of influenza endonuclease inhibitors. ACS Med Chem Lett 2014; 5:61-64. [PMID: 24490002 DOI: 10.1021/ml4003474] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Influenza is a global human health threat, and there is an immediate need for new antiviral therapies to circumvent the limitations of vaccination and current small molecule therapies. During viral transcription, influenza incorporates the 5'-end of the host cell's mRNA in a process that requires the influenza endonuclease. Based on recently published endonuclease crystalized structures, a three-dimensional pharmacophore was developed and used to virtually screen 450,000 compounds for influenza endonuclease inhibitors. Of 264 compounds tested in a FRET-based endonuclease-inhibition assay, 16 inhibitors (IC50 <50 μM) that span 5 molecular classes novel to this endonuclease were found (6.1% hit rate). To determine cytotoxicity and antiviral activity, subsequent cellular assays were performed. Two compounds suppress viral replication with negligible cell toxicity.
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Affiliation(s)
- Eric Chen
- Department of Chemistry & Biochemistry and ‡Department of Pathology, University of California San Diego, La Jolla, California 92093, United States
| | - Robert V. Swift
- Department of Chemistry & Biochemistry and ‡Department of Pathology, University of California San Diego, La Jolla, California 92093, United States
| | - Nazilla Alderson
- Department of Chemistry & Biochemistry and ‡Department of Pathology, University of California San Diego, La Jolla, California 92093, United States
| | - Victoria A. Feher
- Department of Chemistry & Biochemistry and ‡Department of Pathology, University of California San Diego, La Jolla, California 92093, United States
| | - Gen-Sheng Feng
- Department of Chemistry & Biochemistry and ‡Department of Pathology, University of California San Diego, La Jolla, California 92093, United States
| | - Rommie E. Amaro
- Department of Chemistry & Biochemistry and ‡Department of Pathology, University of California San Diego, La Jolla, California 92093, United States
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50
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Yan Z, Zhang L, Fu H, Wang Z, Lin J. Design of the influenza virus inhibitors targeting the PA endonuclease using 3D-QSAR modeling, side-chain hopping, and docking. Bioorg Med Chem Lett 2013; 24:539-47. [PMID: 24365156 DOI: 10.1016/j.bmcl.2013.12.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/02/2013] [Accepted: 12/06/2013] [Indexed: 11/26/2022]
Abstract
With the emergence of drug resistance and the structural determination of the PA N-terminal domain (PAN), influenza endonucleases have become an attractive target for antiviral therapies for influenza infection. Here, we combined 3D-QSAR with side-chain hopping and molecular docking to produce novel structures as endonuclease inhibitors. First, a new molecular library was generated with side-chain hopping on an existing template molecule, L-742001, using an in-house fragment library that targets bivalent-cation-binding proteins. Then, the best 3D-QSAR model (AAAHR.500), with q(2)=0.76 and r(2)=0.97 from phase modeling, was constructed from 23 endonuclease inhibitors and validated with 17 test compounds. The AAAHR.500 model was then used to select effective candidates from the new molecular library. Combining 3D-QSAR with docking using Glide and Autodock, 13 compounds were considered the most likely candidate inhibitors. Docking studies showed that the binding modes of these compounds were consistent with the crystal structures of known inhibitors. These compounds could serve as potential endonuclease inhibitors for further biological activity tests.
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Affiliation(s)
- Zhihui Yan
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin 300457, China
| | - Lijie Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin 300457, China
| | - Haiyang Fu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin 300457, China
| | - Zhonghua Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin 300457, China.
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