WO1999051776A1 - Procede a haut rendement de criblage d'activite antivirale - Google Patents

Procede a haut rendement de criblage d'activite antivirale Download PDF

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Publication number
WO1999051776A1
WO1999051776A1 PCT/US1999/007551 US9907551W WO9951776A1 WO 1999051776 A1 WO1999051776 A1 WO 1999051776A1 US 9907551 W US9907551 W US 9907551W WO 9951776 A1 WO9951776 A1 WO 9951776A1
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Prior art keywords
cells
viral
well
microtiter plate
compound
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PCT/US1999/007551
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English (en)
Inventor
Susan M. Halliday
Robert W. Buckheit, Jr.
Luke A. Pallansch
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Southern Research Institute
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Priority to AU34744/99A priority Critical patent/AU3474499A/en
Publication of WO1999051776A1 publication Critical patent/WO1999051776A1/fr

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701Specific hybridization probes
    • C12Q1/706Specific hybridization probes for hepatitis
    • C12Q1/707Specific hybridization probes for hepatitis non-A, non-B Hepatitis, excluding hepatitis D

Definitions

  • the present invention relates to a high-throughput method for screening potentially active compounds for antiviral activity. More particularly, the invention relates to an jLn vitro antiviral screening method employing virus-producing cell lines.
  • the antiviral activities of a number of drugs have been discovered by screening procedures using cell cultures infected with the virus.
  • Various formats and end points of detection have been used in such screening methods. For example, activity against cytotoxic viruses may be assessed by determining the ability of a compound to inhibit virus- induced cell death.
  • Other methods measure the effect of a putative antiviral drug on the rate of production virus particles by infected cells.
  • the effect of compounds on expression of viral genes may be used as an indication of antiviral activity.
  • antiviral screening methods should be robust, sensitive, fast and capable of accommodating large numbers of samples simultaneously.
  • experimental drugs often are available only in small quantities.
  • a successful screening method therefore advantageously uses small cell culture volumes and sensitive detection methods.
  • the standard 96-well microtiter plate format is preferred for these types of procedures.
  • a necessary component of such antiviral screening methods is a cell culture that can be cultivated efficiently in vitro and which can be infected with either the virus of interest or a related virus that simulates the in vivo viral infection for which a treatment is sought. Viral replication in the infected cell line should mimic that which occurs in vivo .
  • chronically infected cell lines i.e., those in which the viral genome is stably introduced into the cells.
  • Such cell lines should either produce virus continuously or viral production should be inducible, so that antiviral activity can be determined at one or more stages of the viral replication cycle.
  • HBV infection is widespread, with over two million individuals chronically infected. HBV infection causes both acute and chronic liver disease and has been linked to liver cancer.
  • Current therapies include treatment with interferons and certain nucleoside analogs; however, neither of these treatments is entirely effective. Accordingly, a substantial need exists for new and more effective anti-HBV drugs.
  • the procedures described in these publications involve cultivating the infected cells in the presence of the compound being tested. The cells were grown to confluency and the putative antiviral compound was added in ten consecutive daily doses. Samples of culture medium were taken at day zero (before drug addition) and after three, six, and ten days of treatment. The samples were analyzed by a slot-blot hybridization technique for extra-cellular (virion) HBV DNA. Results were reported as the concentration which induced a ninety percent decrease in the level of HBV DNA (EC 90 ) . While the procedures described in these publications represent an advance over prior HBV screening methods, they still suffer from certain disadvantages. Most significantly, the relative insensitivity of the hybridization technique used for detecting viral DNA requires that relatively high culture volumes and cell densities be employed.
  • a method for simultaneously screening a plurality of compounds for antiviral activity against a virus involves the steps of:
  • cultivating cells which are capable of expressing viral genes, in culture medium in wells of a microtiter plate, each well containing a culture volume of from about 50 ⁇ l to about 250 ⁇ l;
  • the small culture volumes permit the screening assay to be performed in a microtiter plate format and permit the use of very small amounts of test compounds.
  • a microtiter plate format By using the microtiter plate format, numerous compounds can be tested simultaneously to provide a high-throughput screening method.
  • Figure 1 is a representative microtiter plate layout for testing compounds in accordance with the method of the present invention.
  • Figure 2 is a microtiter plate layout used for determining a drug dose response curve in accordance with a method according to the present invention.
  • the screening method described herein may be applied to a wide variety of viruses. Any virus for which an infected or producer cell line can be cultivated in vitro and which expresses viral genes can be employed in this method.
  • the cells employed in the screening method express at least those viral genes that are associated with the phase of viral replication that is a target for therapeutic interference.
  • viral gene expression, packaging and release of viral particles into the medium in which the cells are cultured simulates that which occurs in infected cells in vivo in the natural host.
  • Activity against both DNA and RNA viruses can be determined by the present screening methods.
  • viruses include, for example, hepadnaviruses, members of the herpesvirus family, retroviruses, rhabdoviruses, bunyaviruses, flaviviruses, togaviruses, baculoviruses, and the like.
  • the screening method of this invention will be further illustrated and described in detail by reference to a method for screening for activity against the hepadnavirus, HBV.
  • the HepG2-2.2.15 cell line described by Sells et al . may advantageously be utilized in the present method for screening compounds for activity against HBV.
  • a cell line transformed with the HBV genome under control of an inducible promoter may be used.
  • cells may be grown to a desired cell density and then expression of the HBV genes may be induced by adding a compound that induces expression or by replacing media containing a compound that represses expression with repressor-free media.
  • a cell line containing the HBV genome under control of an inducible promoter is described by Ladner et al . , Antimicrobial Agents and Chemotherapy r August 1997, 1715-1720.
  • the cells may be cultured by techniques well known to those skilled in the art.
  • the cells are cultivated in a nutrient medium that supports cell viability and growth. While the medium may vary, depending upon the particular cells employed. Suitable media include Dulbecco's modified Eagle's medium (“DMEM”) or Roswell Park Memorial Institute medium (RPMI-1640) supplemented with 10% fetal bovine serum.
  • DMEM Dulbecco's modified Eagle's medium
  • RPMI-1640 Roswell Park Memorial Institute medium
  • Culture plates are advantageously maintained in humidified incubation chambers at 37 °C in an atmosphere containing 5% carbon dioxide.
  • Cell-containing media are added to the wells of a microtiter plate.
  • a preferred format for carrying out the screening method of this invention utilizes a conventional 96-well microtiter plate. Each well contains less than about 200 ⁇ l, preferably less than about 100 ⁇ l of culture medium, e.g., from about 50 ⁇ l to about 200 ⁇ l, preferably from about 50 ⁇ l to about 100 ⁇ l of culture medium.
  • the cells are cultivated to a desired cell density.
  • the cells be grown to a confluent monolayer on the bottom of the plate. Further growth to higher cell densities is usually unnecessary in the present method.
  • the compounds to be tested are added to the microtiter plate wells. It is preferred that each compound being tested be added to a plurality of wells at different concentrations. It is usually desired the compound be added in dilutions that include a useful dose-response curve. If concentrations are selected appropriately, the results of the method can be expressed as the concentration of the compound which is effective in inhibiting a certain percentage of viral replication, e.g., the EC 90 . It is also preferred that blank wells, which contain cells and media but do not contain test compound, are included as controls. Positive controls, i.e., compounds which are known to inhibit viral replication, also may be included.
  • a wide variety of different types of potential antiviral agents may be tested in the method of this invention.
  • chemical agents such as nucleoside analogs, biological agents such as peptides, proteins or antibodies, natural agents, such as extracts of plants, bacteria and fungi, and many other types of agents may be tested.
  • the culture medium is removed from each well and is replaced with culture medium containing the test compound. Cultivation typically spans several days, and it is preferred that culture medium containing test compound be replaced on a periodic, e.g., daily, basis.
  • the present method permits the use of test compound concentrations in the micromolar range and below.
  • concentrations generally range from about 1 nanomolar to about 5 millimolar. Concentrations can be adjusted after initial results to obtain a useable dose-response curve.
  • the culture medium of each well is analyzed by a quantitative nucleic acid application procedure. A nucleic acid sequence that is indicative of replication of the virus is selected for amplification.
  • the nucleic acid sequence may, for example, be a sequence from a gene encoding a core protein, a viral enzyme, such as polymerase, kinase, or protease, an envelope or transmembrane protein, or any other component indicative of viral replication.
  • the nucleic acid amplification technique may be any method that specifically amplifies the nucleic acid of interest, including polymerase chain reaction ("PCR"), ligase chain reaction (“LCR”) or nucleic acid specific base amplification (“NASBA”).
  • PCR is the preferred amplification procedure.
  • the primers used for the amplification are selected so as to amplify a unique segment of a viral gene that is indicative of viral replication.
  • the amplification primers generally comprise from 8 to about 50, preferably from about 10 to 30 nucleotides.
  • the primers are chosen to amplify a segment containing from about 25 to about 500, preferably from about 50 to about 150 nucleotides.
  • the primers are selected such that the primer template complex has a melting point of about 50°C. Software that assists in primer design is commercially available.
  • the quantitative nucleic acid amplification technique is preferably a technique which involves monitoring the progress of the nucleic acid amplifications by use of an oligonucleotide probe 10
  • the quencher molecule substantially quenches any fluorescence from the reporter molecule when the oligonucleotide probe is a single-stranded form, and the reporter is substantially unquenched whenever the oligonucleotide is a double- stranded form hybridized to the target.
  • This type of probe is sometimes referred to as "TaqMan" probe. Quantitative PCR by this technique is described in U.S. patent 5,538,848 which issued on July 23, 1996 to Livak et al., the disclosure of which is incorporated herein by reference. Related probes and quantitative amplification procedures are described in U.S.
  • Example This example describes the use of the HBV producer cell line, HepG2-2.2.15 described by Sells et al. supra for determining the anti-HBV activity of test compounds .
  • the cells are plated in 96-well microtiter plates at an initial density of 2.5xl0 3 cells/lOO ⁇ l in DMEM medium supplemented with 10% fetal bovine serum.
  • the 96-well plates are pre- coated with collagen prior to cell plating.
  • the exterior wells are filled with complete medium to help minimize sample evaporation.
  • the confluent monolayer of HepG2- 2.2.15 cells is washed and the medium is replaced by complete medium containing various concentrations of test compound. See Figure 1 as a representative plate 12
  • the culture medium is replaced with fresh medium containing the appropriate diluted drug.
  • the cell culture supernatant is collected and clarified by centrifugation using a Sorvall RT-6000D centrifuge, at 1000 RPM for five minutes.
  • the clarified supernatants are then treated with 0.75 ⁇ g/ml Pronase for 30 minutes at 37°C to inactivate proteases and with DNAse for 60 minutes at 37°C to degrade unencapsidated DNA.
  • the supernatants then are heated to 95°C for 30 minutes to inactivate the DNAse.
  • Virion-associated HBV DNA present in the cell culture supernatants is amplified by PCR using primers derived from HBV strain AYW.
  • the sequences of the forward and reverse primers are: Forward primer: 5 ' -CCA AAT GCC CCT ATC CTA TCA-3'
  • Reverse primer 5 ' -GAG GCG AGG GAG TTC TTC TTC TA-3'
  • the PCR-amplified HBV DNA is detected in real time (i.e., at each PCR thermocycle step) by monitoring increases in florescence signals that result from an exonucleolytic degradation of a quenched fluorescent probe molecule following hybridization of the probe to the amplified HBV DNA.
  • the probe used is of the TaqMan design and is complementary to DNA sequences present in the HBV DNA region amplified. Its sequence is: 5'-FAM-CG GAA ACT ACT GTT GTT AGA CGA CGA GGC AG-TAMRA-
  • FAM 6-carboxyfluorescein phosphoramidite
  • TAMRA 6-carboxytetramethylrhodamine
  • clarified supernatent (3 microliters) is analyzed directly, without DNA extraction, in a 50 microliter PCR reaction, using standard PCR reagents and conditions.
  • the plate layout used for determining a drug dose response curve is provided in Figure 2.
  • a standard curve is simultaneously generated for several log dilutions of a purified 1.2 kbp HBV ayw subgenomic fragment. The standard curve ranges from lxlO 6 to lxlO 1 nominal copy equivalence for PCR reaction.

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  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
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  • Wood Science & Technology (AREA)
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  • Proteomics, Peptides & Aminoacids (AREA)
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Abstract

La présente invention concerne un procédé de criblage de l'activité antivirale de composés qui comprend la culture de cellules aptes à exprimer des gènes viraux lors de leur culture dans des puits de plaque à microtitration en présence de composés tests, et la détection du taux d'expression de gène viral à l'aide d'une technique quantitative d'amplification d'acide nucléique.
PCT/US1999/007551 1998-04-07 1999-04-07 Procede a haut rendement de criblage d'activite antivirale WO1999051776A1 (fr)

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AU34744/99A AU3474499A (en) 1998-04-07 1999-04-07 High-throughput method for screening for antiviral activity

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US60/080,894 1998-04-07

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Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002033128A2 (fr) * 2000-10-18 2002-04-25 Pharmasset Limited Quantification simultanee d'acides nucleiques dans des cellules infectees
EP1256803A1 (fr) * 2001-05-07 2002-11-13 Crucell Holland B.V. Méthodes pour l'identification des composés antiviraux
AU2007240180B2 (en) * 2000-10-18 2011-07-28 Pharmasset Inc Simultaneous quantification of nucleic acids in diseased cells

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5070010A (en) * 1989-10-30 1991-12-03 Hoffman-La Roche Inc. Method for determining anti-viral transactivating activity
US5541058A (en) * 1993-09-09 1996-07-30 Kreider; John W. In vitro assay system for testing the effectiveness of anti-papilloma viral agents
US5610050A (en) * 1990-04-20 1997-03-11 The General Hospital Corporation Methods of preventing viral replication
WO1997027319A1 (fr) * 1996-01-29 1997-07-31 Virologic, Inc. Compositions et procedes pour determiner la sensibilite et la resistance vis-a-vis de medicaments antiviraux et criblage de medicaments antiviraux
WO1997040193A2 (fr) * 1996-04-19 1997-10-30 Innogenetics N.V. Procede de typage et de detection du virus de l'hepatite b (hbv)
US5723319A (en) * 1995-06-05 1998-03-03 Avid Therapeutics, Inc. Cultured cell line that inducibly expresses the hepatitis B virus genome, and uses thereof for screening antiviral substances

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5070010A (en) * 1989-10-30 1991-12-03 Hoffman-La Roche Inc. Method for determining anti-viral transactivating activity
US5610050A (en) * 1990-04-20 1997-03-11 The General Hospital Corporation Methods of preventing viral replication
US5541058A (en) * 1993-09-09 1996-07-30 Kreider; John W. In vitro assay system for testing the effectiveness of anti-papilloma viral agents
US5723319A (en) * 1995-06-05 1998-03-03 Avid Therapeutics, Inc. Cultured cell line that inducibly expresses the hepatitis B virus genome, and uses thereof for screening antiviral substances
WO1997027319A1 (fr) * 1996-01-29 1997-07-31 Virologic, Inc. Compositions et procedes pour determiner la sensibilite et la resistance vis-a-vis de medicaments antiviraux et criblage de medicaments antiviraux
WO1997040193A2 (fr) * 1996-04-19 1997-10-30 Innogenetics N.V. Procede de typage et de detection du virus de l'hepatite b (hbv)

Non-Patent Citations (3)

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Title
HALLIDAY ET AL.: "DEVELOPMENT OF A MODERATE THROUGHPUT ASSAY USING TaqMan PCR TECHNOLOGY TO IDENTIFY INHIBITORS OF HEPATITIS B VIRUS", ANTIVIRAL RESEARCH, vol. 37, no. 3, March 1998 (1998-03-01), pages A66/96, XP002113789 *
JURINKE C ET AL: "Detection of hepatitis B virus DNA in serum samples via nested PCR and MALDI-TOF mass spectrometry", GENETIC ANALYSIS: BIOMOLECULAR ENGINEERING, vol. 13, no. 3, 1 September 1996 (1996-09-01), pages 67-71, XP004070185, ISSN: 1050-3862 *
MORRIS ET AL.: "RAPID REVERSE TRANSCRIPTION-PCR DETECTION OF HEPATITIS C VIRUS RNA IN SERUM BY USING THE TaqMan FLUOROGENIC DETECTION SYSTEM", J.CLIN.MICROBIOL., vol. 34, no. 12, 1996, pages 2933 - 2936, XP002113780 *

Cited By (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002033128A2 (fr) * 2000-10-18 2002-04-25 Pharmasset Limited Quantification simultanee d'acides nucleiques dans des cellules infectees
WO2002033128A3 (fr) * 2000-10-18 2003-08-21 Pharmasset Ltd Quantification simultanee d'acides nucleiques dans des cellules infectees
EP2180064A2 (fr) * 2000-10-18 2010-04-28 Pharmasset, Inc. Quantification multiplexe d'acides nucléiques dans des cellules malades
US7718790B2 (en) 2000-10-18 2010-05-18 Pharmasset, Inc. Kit for assessing mitochondrial toxicity
EP2180064A3 (fr) * 2000-10-18 2010-08-11 Pharmasset, Inc. Quantification multiplex d'acides nucléiques dans des cellules malades
US7919247B2 (en) 2000-10-18 2011-04-05 Pharmasset, Inc. Simultaneous quantification of nucleic acids in diseased cells
AU2007240180B2 (en) * 2000-10-18 2011-07-28 Pharmasset Inc Simultaneous quantification of nucleic acids in diseased cells
EP1256803A1 (fr) * 2001-05-07 2002-11-13 Crucell Holland B.V. Méthodes pour l'identification des composés antiviraux
WO2002090982A1 (fr) * 2001-05-07 2002-11-14 Crucell Holland B.V. Methodes d'identification de composes antiviraux
US7163787B2 (en) 2001-05-07 2007-01-16 Crucell Holland B.V. Methods for the identification of antiviral compounds

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