1
|
Elebeedy D, Elkhatib WF, Kandeil A, Ghanem A, Kutkat O, Alnajjar R, Saleh MA, Abd El Maksoud AI, Badawy I, Al-Karmalawy AA. Anti-SARS-CoV-2 activities of tanshinone IIA, carnosic acid, rosmarinic acid, salvianolic acid, baicalein, and glycyrrhetinic acid between computational and in vitro insights. RSC Adv 2021; 11:29267-29286. [PMID: 35492070 PMCID: PMC9040650 DOI: 10.1039/d1ra05268c] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/18/2021] [Indexed: 02/05/2023] Open
Abstract
Six compounds namely, tanshinone IIA (1), carnosic acid (2), rosmarinic acid (3), salvianolic acid B (4), baicalein (5), and glycyrrhetinic acid (6) were screened for their anti-SARS-CoV-2 activities against both the spike (S) and main protease (Mpro) receptors using molecular docking studies. Molecular docking recommended the superior affinities of both salvianolic acid B (4) and glycyrrhetinic acid (6) as the common results from the previously published computational articles. On the other hand, their actual anti-SARS-CoV-2 activities were tested in vitro using plaque reduction assay to calculate their IC50 values after measuring their CC50 values using MTT assay on Vero E6 cells. Surprisingly, tanshinone IIA (1) was the most promising member with IC50 equals 4.08 ng μl-1. Also, both carnosic acid (2) and rosmarinic acid (3) showed promising IC50 values of 15.37 and 25.47 ng μl-1, respectively. However, salvianolic acid (4) showed a weak anti-SARS-CoV-2 activity with an IC50 value equals 58.29 ng μl-1. Furthermore, molecular dynamics simulations for 100 ns were performed for the most active compound from the computational point of view (salvianolic acid 4), besides, the most active one biologically (tanshinone IIA 1) on both the S and Mpro complexes of them (four different molecular dynamics processes) to confirm the docking results and give more insights regarding the stability of both compounds inside the SARS-CoV-2 mentioned receptors, respectively. Also, to understand the mechanism of action for the tested compounds towards SARS-CoV-2 inhibition it was necessary to examine the mode of action for the most two promising compounds, tanshinone IIA (1) and carnosic acid (2). Both compounds (1 and 2) showed very promising virucidal activity with a most prominent inhibitory effect on viral adsorption rather than its replication. This recommended the predicted activity of the two compounds against the S protein of SARS-CoV-2 rather than its Mpro protein. Our results could be very promising to rearrange the previously mentioned compounds based on their actual inhibitory activities towards SARS-CoV-2 and to search for the reasons behind the great differences between their in silico and in vitro results against SARS-CoV-2. Finally, we recommend further advanced preclinical and clinical studies especially for tanshinone IIA (1) to be rapidly applied in COVID-19 management either alone or in combination with carnosic acid (2), rosmarinic acid (3), and/or salvianolic acid (4).
Collapse
Affiliation(s)
- Dalia Elebeedy
- College of Biotechnology, Misr University for Science and Technology (MUST) 6th of October City Egypt
| | - Walid F Elkhatib
- Microbiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, African Union Organization St. Abbassia Cairo 11566 Egypt.,Department of Microbiology & Immunology, Faculty of Pharmacy, Galala University New Galala city, Suez Egypt
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre Giza 12622 Egypt
| | - Aml Ghanem
- Department of Molecular Biology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City Sadat City Egypt
| | - Omnia Kutkat
- Center of Scientific Excellence for Influenza Viruses, National Research Centre Giza 12622 Egypt
| | - Radwan Alnajjar
- Department of Chemistry, Faculty of Science, University of Benghazi Benghazi Libya.,Department of Chemistry, University of Cape Town Rondebosch 7701 South Africa
| | - Marwa A Saleh
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University Nasr City Cairo Egypt
| | - Ahmed I Abd El Maksoud
- Industrial Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City Sadat City Egypt
| | - Ingy Badawy
- College of Biotechnology, Misr University for Science and Technology (MUST) 6th of October City Egypt
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
| |
Collapse
|
2
|
Morcillo-Parra MÁ, Beltran G, Mas A, Torija MJ. Determination of melatonin by a whole cell bioassay in fermented beverages. Sci Rep 2019; 9:9120. [PMID: 31235891 PMCID: PMC6591416 DOI: 10.1038/s41598-019-45645-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/12/2019] [Indexed: 11/09/2022] Open
Abstract
Melatonin is a bioactive compound that is present in fermented beverages, such as wine and beer, at concentrations ranging from picograms to nanograms per mL of product. The purpose of this study was to optimize a novel fluorescent bioassay for detecting melatonin based on a cell line that contains the human melatonin receptor 1B gene and to compare these results with LC-MS/MS as a reference method. Conditions that could affect cell growth and detection (cell number per well, stimulation time, presence or absence of fetal bovine serum and adhesion of cells) were tested in the TANGO® cell line. Food matrices (wine and grape must) could not be directly used for the cell line due to low response. Therefore, for the determination of melatonin in food samples, an extraction procedure was required before conducting the assay. We demonstrated an improvement in melatonin determination by the cell-based bioassay due to increased sensitivity and specificity and improved quantification in complex matrices. Therefore, this method is a good alternative to determine melatonin content in some food samples, especially for those containing very low melatonin levels.
Collapse
Affiliation(s)
| | - Gemma Beltran
- Departament de Bioquimica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Albert Mas
- Departament de Bioquimica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - María-Jesús Torija
- Departament de Bioquimica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain.
| |
Collapse
|
3
|
NMR-Fragment Based Virtual Screening: A Brief Overview. Molecules 2018; 23:molecules23020233. [PMID: 29370102 PMCID: PMC6017141 DOI: 10.3390/molecules23020233] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 01/23/2023] Open
Abstract
Fragment-based drug discovery (FBDD) using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.
Collapse
|
4
|
Melnikov F, Hsieh JH, Sipes NS, Anastas PT. Channel Interactions and Robust Inference for Ratiometric β-lactamase Assay Data: a Tox21 Library Analysis. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2018; 6:3233-3241. [PMID: 32461840 PMCID: PMC7252516 DOI: 10.1021/acssuschemeng.7b03394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ratiometric β-lactamase (BLA) reporters are widely used to study transcriptional responses in a high-throughput screening (HTS) format. Typically, a ratio readout (background/target fluorescence) is used for toxicity assessment and structure-activity modeling efforts from BLA HTS data. This ratio readout may be confounded by channel-specific artifacts. To maximize the utility of BLA HTS data, we analyzed the relationship between individual channels and ratio readouts after fitting 10,000 chemical titration series screened in seven BLA stress-response assays from the Tox21 initiative. Similar to previous observations, we found that activity classifications based on BLA ratio readout alone are confounded by interference patterns for up to 85% (50 % on average) of active chemicals. Most Tox21 analyses adjust for this issue by evaluating target and ratio readout direction. In addition, we found that the potency and efficacy estimates derived from the ratio readouts may not represent the target channel effects and thus complicates chemical activity comparison. From these analyses we recommend a simpler approach using a direct evaluation of the target and background channels as well as the respective noise levels when using BLA data for toxicity assessment. This approach eliminates the channel interference issues and allows for straightforward chemical assessment and comparisons.
Collapse
Affiliation(s)
- Fjodor Melnikov
- School of Forestry and Environmental Studies, Yale University, New Haven, CT 06520, United States
| | - Jui-Hua Hsieh
- Kelly Government Solutions, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - Nisha S Sipes
- National Toxicology Program / National Institute of Environmental Health Sciences (NIEHS), 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - Paul T Anastas
- School of Forestry and Environmental Studies, Yale University, New Haven, CT 06520, United States
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06520, United States
| |
Collapse
|
5
|
Sato-Nishiwaki M, Aida Y, Abe S, Shibata Y, Kimura T, Yamauchi K, Kishi H, Igarashi A, Inoue S, Sato M, Nakajima O, Kubota I. Reduced number and morphofunctional change of alveolar macrophages in MafB gene-targeted mice. PLoS One 2013; 8:e73963. [PMID: 24040127 PMCID: PMC3765310 DOI: 10.1371/journal.pone.0073963] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 07/25/2013] [Indexed: 01/19/2023] Open
Abstract
Alveolar macrophages (AMs) play an important role in the pathogenesis of chronic obstructive pulmonary disease (COPD). We previously demonstrated that the transcription factor, MafB, increased in the AMs of mice exposed to cigarette smoke, and in those of human patients with COPD. The aim of this study was to evaluate the role of MafB in AMs using newly established transgenic (TG) mice that specifically express dominant negative (DN) MafB in macrophages under the control of macrophage scavenger receptor (MSR) enhancer-promoter. We performed cell differential analyses in bronchoalveolar lavage cells, morphological analyses with electron microscopy, and flow cytometry-based analyses of surface markers and a phagocytic capacity assay in macrophages. AM number in the TG mice was significantly decreased compared with wild-type (WT) mice. Morphologically, the high electron density area in the nucleus increased, the shape of pseudopods on the AMs was altered, and actin filament was less localized in the pseudopods of AMs of TG mice, compared with WT mice. The expression of surface markers, F4/80 and CD11b, on peritoneal macrophages in TG mice was reduced compared with WT mice, while those on AMs remained unchanged. Phagocytic capacity was decreased in AMs from TG mice, compared with WT mice. In conclusion, MafB regulates the phenotype of macrophages with respect to the number of alveolar macrophages, the nuclear compartment, cellular shape, surface marker expression, and phagocytic function. MSR-DN MafB TG mice may present a useful model to clarify the precise role of MafB in macrophages.
Collapse
MESH Headings
- Animals
- Antigens, Surface/metabolism
- Apoptosis
- Bronchoalveolar Lavage Fluid/cytology
- Gene Expression Regulation
- Genes, Dominant
- Humans
- Immunophenotyping
- Macrophages, Alveolar/immunology
- Macrophages, Alveolar/metabolism
- Macrophages, Alveolar/ultrastructure
- Macrophages, Peritoneal/immunology
- Macrophages, Peritoneal/metabolism
- MafB Transcription Factor/genetics
- MafB Transcription Factor/metabolism
- Mice
- Mice, Transgenic
- Phagocytosis/immunology
- Promoter Regions, Genetic
- Receptors, Fc/metabolism
- Receptors, Scavenger/genetics
- Spleen/immunology
- Spleen/metabolism
Collapse
Affiliation(s)
- Michiko Sato-Nishiwaki
- Department of Cardiology, Pulmonology and Nephrology, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
| | - Yasuko Aida
- Department of Cardiology, Pulmonology and Nephrology, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
| | - Shuichi Abe
- Department of Cardiology, Pulmonology and Nephrology, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
| | - Yoko Shibata
- Department of Cardiology, Pulmonology and Nephrology, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
- * E-mail:
| | - Tomomi Kimura
- Department of Cardiology, Pulmonology and Nephrology, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
| | - Keiko Yamauchi
- Department of Cardiology, Pulmonology and Nephrology, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
| | - Hiroyuki Kishi
- Department of Cardiology, Pulmonology and Nephrology, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
| | - Akira Igarashi
- Department of Cardiology, Pulmonology and Nephrology, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
| | - Sumito Inoue
- Department of Cardiology, Pulmonology and Nephrology, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
| | - Masamichi Sato
- Department of Cardiology, Pulmonology and Nephrology, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
| | - Osamu Nakajima
- Research Laboratory for Molecular Genetics, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
| | - Isao Kubota
- Department of Cardiology, Pulmonology and Nephrology, School of Medicine, Yamagata University, Yamagata City, Yamagata, Japan
| |
Collapse
|
6
|
Holler TP, Parkinson T, Pryde DC. Targeting the non-structural proteins of hepatitis C virus: beyond hepatitis C virus protease and polymerase. Expert Opin Drug Discov 2013; 4:293-314. [PMID: 23489127 DOI: 10.1517/17460440902762802] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Chronic hepatitis C virus (HCV) infection is a main cause of cirrhosis of the liver and hepatocellular carcinoma. The standard of care is a combination of pegylated interferon with ribavirin, a regimen that has undesirable side effects and is frequently ineffective. Compounds targeting HCV protease and polymerase are in late-stage clinical trials and have been extensively reviewed elsewhere. OBJECTIVE To review and evaluate the progress towards finding novel HCV antivirals targeting HCV proteins beyond the already precedented NS3 protease and NS5B polymerase. METHODS Searches of CAplus and Medline databases were combined with information from key conferences. This review focuses on NS2/3 serine protease, NS3 helicase activity and the non-structural proteins 4A, 4B and 5A. CONCLUSIONS Use of the replicon model of HCV replication and biochemical assays of specific targets has allowed screening of vast libraries of compounds, but resulted in clinical candidates from only NS4A and NS5A. The field is hindered by a lack of good chemical matter that inhibits the remaining enzymes from HCV, and a lack of understanding of the functions of non-structural proteins 4A, 4B and 5A in the replication of HCV.
Collapse
Affiliation(s)
- Tod P Holler
- Associate Research Fellow Pfizer Global Research and Development, Antiviral Biology, Ramsgate Road, Sandwich, Kent CT13 9NJ, UK +44 130 464 6387 ; +44 130 465 1819 ;
| | | | | |
Collapse
|
7
|
Abstract
Current HCV therapy presents many side effects, is inadequate in treating all patients infected with the disease, and it is likely that future therapy will involve the specific targeting of multiple viral enzymes. The HCV NS2/3 protease is a dimeric autocatalytic protease that cleaves the viral polyprotein between NS2 and NS3. NS2/3 cleavage has been shown to be absolutely required for genome replication and viral infectivity in a chimpanzee and, therefore, NS2/3 has been suggested to be a promising target for future HCV drug development. This article focuses on the characterization of NS2/3 processing, the methods developed and progress achieved towards the generation of NS2/3 cleavage inhibitors. The challenges involved in developing active site inhibitors of this enzyme, as well as alternative approaches to inhibiting HCV replication through the NS2/3 and NS2 proteins, are also discussed.
Collapse
Affiliation(s)
- Sarah Welbourn
- Goodman Cancer Centre & Department of Biochemistry, McGill University, Montréal, Québec, Canada, H3A 1A3
| | - Arnim Pause
- Goodman Cancer Centre & Department of Biochemistry, McGill University, Cancer Pavilion, room 618, 1160 av. des Pins Ouest, Montréal, Québec, Canada, H3A 1A3
| |
Collapse
|
8
|
Brownlee C. James Inglese: uniting biology and chemistry in high throughput. ACS Chem Biol 2008; 3:394-8. [PMID: 18642797 DOI: 10.1021/cb8001599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Osak B, Fitzgerald LR. A beta-lactamase reporter assay for monitoring the activation of the smoothened pathway. Assay Drug Dev Technol 2008; 5:785-92. [PMID: 18052850 DOI: 10.1089/adt.2007.088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The seven-transmembrane protein Smoothened (Smo) mediates the cellular response to the Hedgehog protein signal and is involved in cell growth and differentiation during embryonic development. Stimulation of the Smo pathway is directly implicated in tissue maintenance and repair, but overactivation of Smo could lead to tumorigenesis. We developed a robust and sensitive functional cell-based assay that measures the activity of endogenous Smo using a beta-lactamase transcriptional readout. This is the first Smo reporter assay that utilizes beta-lactamase reporter technology. This assay type has distinct advantages over other reporter technologies and can be used in a high-throughput mode to search for therapeutically relevant downstream Smo target effectors.
Collapse
Affiliation(s)
- Bella Osak
- Mechanistic and Target Biology, Pfizer, Ann Arbor, MI, USA
| | | |
Collapse
|
10
|
Inglese J, Johnson RL, Simeonov A, Xia M, Zheng W, Austin CP, Auld DS. High-throughput screening assays for the identification of chemical probes. Nat Chem Biol 2007; 3:466-79. [PMID: 17637779 DOI: 10.1038/nchembio.2007.17] [Citation(s) in RCA: 431] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
High-throughput screening (HTS) assays enable the testing of large numbers of chemical substances for activity in diverse areas of biology. The biological responses measured in HTS assays span isolated biochemical systems containing purified receptors or enzymes to signal transduction pathways and complex networks functioning in cellular environments. This Review addresses factors that need to be considered when implementing assays for HTS and is aimed particularly at investigators new to this field. We discuss assay design strategies, the major detection technologies and examples of HTS assays for common target classes, cellular pathways and simple cellular phenotypes. We conclude with special considerations for configuring sensitive, robust, informative and economically feasible HTS assays.
Collapse
MESH Headings
- Animals
- Catalysis
- Chemistry, Pharmaceutical/instrumentation
- Chemistry, Pharmaceutical/methods
- Drug Design
- Drug Evaluation, Preclinical/instrumentation
- Drug Evaluation, Preclinical/methods
- Enzymes/chemistry
- Humans
- Ions
- Kinetics
- Models, Biological
- Models, Chemical
- Receptors, G-Protein-Coupled/metabolism
- Signal Transduction
- Technology, Pharmaceutical/instrumentation
- Technology, Pharmaceutical/methods
- Transcription, Genetic
Collapse
Affiliation(s)
- James Inglese
- US National Institutes of Health Chemical Genomics Center, National Institutes of Health, 9800 Medical Center Drive, Bethesda, Maryland 20892-3370, USA.
| | | | | | | | | | | | | |
Collapse
|
11
|
Machiya JI, Shibata Y, Yamauchi K, Hirama N, Wada T, Inoue S, Abe S, Takabatake N, Sata M, Kubota I. Enhanced Expression of MafB Inhibits Macrophage Apoptosis Induced by Cigarette Smoke Exposure. Am J Respir Cell Mol Biol 2007; 36:418-26. [PMID: 17079784 DOI: 10.1165/rcmb.2006-0248oc] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In the lungs of smokers, oxidative stress rises due to increase of free radicals and oxidants, including lipid peroxide (LPO). The functions of alveolar macrophages (AMs) are altered in such an environment, and their survival is prolonged against toxicities of cigarette smoke (CS) by an unknown mechanism. Whereas functions of AMs are potentially regulated by various transcriptional factors, their expressions and roles in smoking individuals have not been elucidated. Therefore, we investigated their expressions using murine model of CS exposure. Eight-week-old male B6C3F1 mice were whole-bodily exposed to CS (2 cigarettes/mouse/day, 5 d/wk) for 6 mo. Development of pulmonary emphysema in 6-mo CS-exposed mice was confirmed by a morphometric analysis. Among the transcriptional factors investigated, only MafB was upregulated in AMs from CS-exposed mice. DNA binding capacity of MafB for Maf recognition element was also increased in AMs from those mice. LPO was increased significantly in the lungs of CS-exposed mice. Because the end product of LPO, 4-hydroxy-2-nonenal, enhanced MafB expression and its transcriptional activity in a cultured macrophage cell line, LPO-related oxidative stress was suggested to be involved in the mechanism of MafB expression in CS-exposed lung. Furthermore, we established a macrophage cell line that can overexpress MafB and thereby clarify the role of MafB. Forced expression of MafB heightened cell viability and attenuated the occurrence of apoptosis in cells treated with CS-extract. These results suggest that enhanced MafB expression by oxidative stress inhibits AM cell death and prolongs their survival in the CS-exposed lung.
Collapse
Affiliation(s)
- Jun-Ichi Machiya
- Department of Cardiology, Pulmonology, and Nephrology, Yamagata University School of Medicine, 2-2-2 Iida-Nishi, Yamagata 990-9585, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Suo Z, Abdullah MAF. Unique Composite Active Site of the Hepatitis C Virus NS2-3 Protease: a New Opportunity for Antiviral Drug Design. ChemMedChem 2007; 2:283-4. [PMID: 17266160 DOI: 10.1002/cmdc.200600285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zucai Suo
- Department of Biochemistry, The Ohio State University, 484 W. 12th Ave., Biological Sciences Building, Columbus, OH 43210, USA.
| | | |
Collapse
|
13
|
Qureshi SA. β-Lactamase: an ideal reporter system for monitoring gene expression in live eukaryotic cells. Biotechniques 2007; 42:91-6. [PMID: 17269490 DOI: 10.2144/000112292] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To gain insightful information about the mechanisms through which genes are activated and repressed requires gene reporter systems that are sensitive, robust, and cost-effective. Although numerous reporter gene technologies are commercially available, none are as sophisticated and user-friendly as β-lactamase (BLA) when it comes to studying gene expression in live cells. This article presents an overview of the BLA technology and describes how it can be exploited for studying rare events such as homologous recombination in somatic cells and be used to deliver any DNA sequence of choice anywhere within the genome.
Collapse
Affiliation(s)
- Sohail A Qureshi
- Department of Biological & Biomedical Sciences, The Aga Khan University Hospital, Karachi, Pakistan.
| |
Collapse
|
14
|
Niles WD, Coassin PJ. Piezo- and solenoid valve-based liquid dispensing for miniaturized assays. Assay Drug Dev Technol 2005; 3:189-202. [PMID: 15871693 DOI: 10.1089/adt.2005.3.189] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Miniaturization of biological assays requires dispensing liquids in the submicroliter range of volumes. Accuracy and reproducibility of dispensing this range depend on both the dispenser and the receptacle in which the assay is constructed. Miniaturization technologies developed by Aurora Discovery, Inc. (San Diego, CA) include high-density multiwell plates for assay samples and reagent storage, as well as piezo-based and solenoid valve-based liquid dispensers. Some basic principles of small-volume dispensing by jetting are described to provide context for dispenser design and function. Performance of the latest instruments incorporating these dispensing devices is presented.
Collapse
|
15
|
Ferrer M, Maiolo J, Kratz P, Jackowski JL, Murphy DJ, Delagrave S, Inglese J. Directed evolution of PDZ variants to generate high-affinity detection reagents. Protein Eng Des Sel 2005; 18:165-73. [PMID: 15820976 DOI: 10.1093/protein/gzi018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
High-throughput protease assays are used to identify new protease inhibitors which have the potential to become valuable therapeutic products. Antibodies are of great utility as affinity reagents to detect proteolysis products in protease assays, but isolating and producing such antibodies is unreliable, slow and costly. It has been shown previously that PDZ domains can also be used to detect proteolysis products in high-throughput homogeneous assays but their limited natural repertoire restricts their use to only a few peptides. Here we show that directed evolution is an efficient way to create new PDZ domains for detection of protease activity. We report the first use of phage display to alter the specificity of a PDZ domain, yielding three variants with up to 25-fold increased affinity for a peptide cleavage product of HIV protease. Three distinct roles are assigned to the amino acid substitutions found in the selected variants of the NHERF PDZ domain: specific 'beta1-beta3' interaction with ligand residue -1, interactions with ligand residues -4 to -7 and improvement in phage display efficiency. The variants, having affinities as high as 620 nM, display improvements in assay sensitivity of over 5-fold while requiring smaller amounts of reagents. The approach demonstrated here leads the way to highly sensitive reagents for drug discovery that can be isolated more reliably and produced less expensively.
Collapse
Affiliation(s)
- Marc Ferrer
- Department of Automated Biotechnology, Merck and Co., Inc., 502-503 Louise Lane, North Wales, PA 19454, USA
| | | | | | | | | | | | | |
Collapse
|
16
|
Walker MP, Yao N, Hong Z. Promising candidates for the treatment of chronic hepatitis C. Expert Opin Investig Drugs 2003; 12:1269-80. [PMID: 12882616 DOI: 10.1517/13543784.12.8.1269] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Chronic hepatitis C virus (HCV) infection is the cause of an emerging global pandemic of chronic liver disease. Current pegylated IFN-alpha/ribavirin combination therapies are merely 54 - 56% efficacious and are often poorly tolerated. Popular strategies to improve upon existing therapies include efforts to decrease the dosing regime, improve the safety profile and specifically target the liver, the site of HCV replication. A clear goal of novel therapies is to significantly improve the therapeutic response for HCV-infected patients. One popular scheme to accomplish this is to directly target the viral enzymes involved in HCV RNA replication. While peptidomimetics have been pursued as potent and specific inhibitors of the serine protease, nucleoside analogues and non-nucleoside small molecules have been explored as RNA-dependent RNA polymerase inhibitors with promising potential. Advances in the understanding of HCV replication at the molecular level that stem from the use of the subgenomic replicon system, in vitro enzyme assays and from co-crystallographic structure solutions of the replication enzymes with novel inhibitors have propelled these compounds into clinical development. As these candidates are developed further, there is great hope for a cure for all those chronically infected with HCV.
Collapse
Affiliation(s)
- Michelle P Walker
- Drug Discovery, Ribapharm, Inc., 3300 Hyland Avenue, Costa Mesa, CA 92626, USA
| | | | | |
Collapse
|
17
|
Narjes F, Koch U, Steinkühler C. Recent developments in the discovery of hepatitis C virus serine protease inhibitors--towards a new class of antiviral agents? Expert Opin Investig Drugs 2003; 12:153-63. [PMID: 12556211 DOI: 10.1517/13543784.12.2.153] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hepatitis C virus (HCV) infection is an epidemic disease and a significant worldwide health problem. Despite impressive improvements in the efficacy of the standard, interferon-based therapies, at present, the virus can not be eradicated in the majority of infected individuals. The last decade has witnessed a burst in our understanding of the molecular biology of HCV infection and lead to the identification of essential features of the viral genome that are being targeted for the development of specific antiviral agents. The non-structural protein 3 of the HCV genome harbours a serine protease domain that is essential for viral replication. This enzyme has been studied in great detail and the wealth of structural and functional data are presently nurturing drug development efforts. The peculiar active site structure of the enzyme imposes considerable obstacles to the development of small molecule inhibitors. However, the combination of creativity with the powerful tools of modern drug discovery has led to impressive progress in this field over the past few years and, as a result, the first compounds are now entering clinical trials.
Collapse
Affiliation(s)
- Frank Narjes
- Instituto di Ricerche di Biologia Molecolare-Merck Research Laboratories Rome,Via Pontina Km 30,600,00040 Pomezia, Italy
| | | | | |
Collapse
|
18
|
Abstract
A myriad of new therapies for treating hepatitis C are in various stages of preclinical and clinical development. As reviewed here, these include nucleic acid-based approaches (antisense and ribozymes), small molecule inhibitors of essential hepatitis C virus (HCV)-encoded enzymes (protease, helicase, and polymerase), immune modulation, and immunotherapy. As more details of the HCV lifecycle are elucidated, new targets and approaches will be discovered. Drug development is difficult, expensive, and always agonizingly slow for patients in need and their physicians. Nonetheless, a broad effort has been mounted for HCV, and substantial progress has been achieved. The prospects for new HCV treatments are bright.
Collapse
Affiliation(s)
- Raffaele De Francesco
- Istituto di Ricerche di Biologia Molecolare P. Angeletti, Via Pontina KM 30,600, 00040 Pomezia, Rome, Italy.
| | | |
Collapse
|
19
|
Walker MP, Appleby TC, Zhong W, Lau JYN, Hong Z. Hepatitis C virus therapies: current treatments, targets and future perspectives. Antivir Chem Chemother 2003; 14:1-21. [PMID: 12790512 DOI: 10.1177/095632020301400101] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Chronic hepatitis C virus (HCV) infection is the cause of an emerging global epidemic of chronic liver disease. Current combination therapies are at best 80% efficacious and are often poorly tolerated. Strategies to improve the therapeutic response include the development of novel interferons, nucleoside analogues with reduced haemolysis compared with ribavirin and inosine 5'-monophosphate dehydrogenase inhibitors. Compounds in preclinical or early clinical trials include small molecules that inhibit virus-specific enzymes (such as the serine proteases, RNA polymerase and helicase) or interfere with translation (including anti-sense molecules, iRNA and ribozymes). Advances in understanding HCV replication, obtaining a sub-genomic replicon and contriving potential small animal models, in addition to solving crystallographic structures for the replication enzymes, have improved prospects for developing novel therapies. This review summarizes current and evolving treatments for chronic hepatitis C infection. In addition, progress in HCV targets and drug discovery tools valuable in the search for novel anti-HCV agents is detailed.
Collapse
|
20
|
Tan SL, Pause A, Shi Y, Sonenberg N. Hepatitis C therapeutics: current status and emerging strategies. Nat Rev Drug Discov 2002; 1:867-81. [PMID: 12415247 DOI: 10.1038/nrd937] [Citation(s) in RCA: 168] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chronic infection with hepatitis C virus (HCV) is an emerging global epidemic. The development of effective HCV antiviral therapeutics continues to be a daunting challenge owing to the absence of adequate animal models and tissue-culture systems for analysis and propagation of the virus. Despite these obstacles, inhibitors of the replicative elements of HCV, immune modulators and non-specific hepatoprotective agents are being pursued and exciting progress has been made. Successful therapeutic intervention of HCV will probably require combination approaches and new approaches, including host drug discovery targets.
Collapse
Affiliation(s)
- Seng-Lai Tan
- Infectious Diseases Research, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
| | | | | | | |
Collapse
|