WO2003093512A1 - Methods and compositions for the modification of nucleic acids - Google Patents
Methods and compositions for the modification of nucleic acids Download PDFInfo
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- WO2003093512A1 WO2003093512A1 PCT/US2003/014363 US0314363W WO03093512A1 WO 2003093512 A1 WO2003093512 A1 WO 2003093512A1 US 0314363 W US0314363 W US 0314363W WO 03093512 A1 WO03093512 A1 WO 03093512A1
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- biological composition
- compound
- nucleic acid
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- IBQQMFFTQYTEEJ-UHFFFAOYSA-N CS(OCCN(Cc1ccccc1)Cc1ccccc1)(=O)=O Chemical compound CS(OCCN(Cc1ccccc1)Cc1ccccc1)(=O)=O IBQQMFFTQYTEEJ-UHFFFAOYSA-N 0.000 description 2
- JHTQHOGTBDMULK-UHFFFAOYSA-N CC(C)C1NC1 Chemical compound CC(C)C1NC1 JHTQHOGTBDMULK-UHFFFAOYSA-N 0.000 description 1
- YOTPPDHDYCNUSG-UHFFFAOYSA-N NCC(CN)CN1CC1 Chemical compound NCC(CN)CN1CC1 YOTPPDHDYCNUSG-UHFFFAOYSA-N 0.000 description 1
Classifications
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D203/00—Heterocyclic compounds containing three-membered rings with one nitrogen atom as the only ring hetero atom
- C07D203/04—Heterocyclic compounds containing three-membered rings with one nitrogen atom as the only ring hetero atom not condensed with other rings
- C07D203/06—Heterocyclic compounds containing three-membered rings with one nitrogen atom as the only ring hetero atom not condensed with other rings having no double bonds between ring members or between ring members and non-ring members
- C07D203/08—Heterocyclic compounds containing three-membered rings with one nitrogen atom as the only ring hetero atom not condensed with other rings having no double bonds between ring members or between ring members and non-ring members with only hydrogen atoms, hydrocarbon or substituted hydrocarbon radicals, directly attached to the ring nitrogen atom
- C07D203/12—Radicals substituted by nitrogen atoms not forming part of a nitro radical
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
- A61P31/04—Antibacterial agents
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
- A61P31/12—Antivirals
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P33/00—Antiparasitic agents
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N7/00—Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
- C12N2750/00011—Details
- C12N2750/14011—Parvoviridae
- C12N2750/14311—Parvovirus, e.g. minute virus of mice
- C12N2750/14361—Methods of inactivation or attenuation
- C12N2750/14363—Methods of inactivation or attenuation by chemical treatment
Definitions
- This invention relates to methods and compositions for the modification of nucleic acids.
- blood transfusion Following traumatic injury (or during surgery), an organism may require a blood transfusion to prevent death due to blood loss. In humans and certain domesticated animals, blood transfusion has enabled the survival of injured individuals who would otherwise have died from blood loss.
- Blood proteins include antibodies, complement proteins, and proteins involved in the blood clotting cascade, i addition, each of the different types of blood cells plays a unique role in maintaining the health of the organism.
- Red blood cells for instance, are essential for the transport of oxygen and carbon dioxide gases to and from the cells of a multicellular organism.
- Another type of blood cell, a platelet is involved in initiating blood clotting; thrombocytopenia patients have a platelet deficiency and are prone to bleeding disorders. It is desirable to identify agents capable of inactivating microorganisms that are found in biological compositions. For blood transfusions, there is the danger of transmitting blood- borne viruses from donor blood to a recipient.
- viral diseases e.g., hepatitis A, B, and C, acquired immunodeficiency syndrome, and cytomegalovirus infections
- Screening donor blood for viral markers can help reduce the transmission of viruses to recipients, but many screening methods are directed to only a few discrete viruses and are therefore incomplete or less than 100% sensitive.
- Bacterial infections also pose a significant risk for transfusion recipients. Storage conditions may allow contaminating bacteria to multiply, causing sepsis in the transfusion recipients. Ensuring safe products produced from or including biological compositions is rendered difficult because any effective treatment should inactivate a broad spectrum of cell-free and cell-associated viruses and bacteria without inducing toxicity or carcinogenicity.
- manufacture of maximally safe and effective killed vaccines for human or veterinary use requires methods that completely and reliably render live microorganisms, e.g., viruses, bacteria and parasites, noninfectious.
- the invention features methods and compositions for the modification of nucleic acids.
- methods and compositions are useful for inactivating microorganisms, such as viruses, bacteria, or parasites, in biological compositions for in vitro or in vivos use.
- the invention features a method for modifying nucleic acid molecules in a biological composition.
- This method includes the step of contacting the biological composition with an aziridino inactivating compound that has the fo ⁇ nula (I):
- each Ri is, independently, selected from the group consisting of H, C 2 - 4 alkenyl, phenyl, and benzyl, wherein the contacting is performed under conditions and for a period of time sufficient to modify at least some nucleic acid molecules in the biological composition.
- the compound is 1-aziridinepropanamine or 1- aziridinebutanamine (compounds 1 and 2, respectively):
- the invention features another method for modifying nucleic acid molecules in a biological composition, this method including the step of contacting the biological composition with an aziridino inactivating compound having the formula:
- each i is, independently, selected from the group consisting of H, C ⁇ _ 4 alkyl, C . alkenyl, phenyl, and benzyl, provided that at least one Ri is phenyl or benzyl, wherein contacting is performed under conditions and for a period of time sufficient to modify at least some of the nucleic acid molecules in the biological composition.
- Exemplary aziridino inactivating compounds that fall within formula (II) are 3- phenyl-1-aziridinepropanamine, N,N-dibenzyl-l-aziridineethanamine, and N-benzyl-N-ethyl- 1-aziridineethanamine, and 2-benzyl-l-aziridineethanamine (compounds 3, 4, 5, and 6, respectively).
- the invention features still another method for modifying nucleic acid molecules in a biological composition, this method including the step of contacting the biological composition with an aziridino inactivating compound having the formula:
- Ri is selected from the group consisting of H, C ⁇ - 4 alkyl, C - 4 alkenyl, phenyl, and benzyl, wherein contacting is performed under conditions and for a period of time sufficient to modify at least some of the nucleic acid molecules in the biological composition.
- Exemplary compounds that satisfy formula (III) are 1,1 '-[iminobis(dimethylene)]bis aziridine and l,r-[iminobis(trimethylene)]bis aziridine (compounds 8 and 9, respectively).
- the invention features still another method for modifying nucleic acid molecules in a biological composition, this method including the step of contacting the biological composition with an aziridino inactivating compound having the formula:
- Ri is a C ⁇ - 4 alkyl and R 2 and R 3 is each, independently, H or a C 1 - 4 alkyl and wherein contacting is performed under conditions and for a period of time sufficient to modify at least some of the nucleic acid molecules in the biological composition.
- An exemplary compound of formula (IV) is:
- the invention features still another method for modifying nucleic acid molecules in a biological composition, this method including the step of contacting the biological composition with one of the following aziridino inactivating compounds:
- the invention features yet another method for modifying nucleic acid molecules in a biological composition, this method including the step of contacting the biological composition with a aziridino inactivating compound having the formula:
- An exemplary compound of formula (V) is:
- substituted forms of compounds of formula (I) may have the following formula:
- each Ri is, independently, selected from the group consisting of H, C 2 . 4 alkenyl, phenyl, and benzyl.
- X is Cl, Br, F, or I
- Nitrogen mustards are strong electrophiles and alkylate nucleophilic groups of nucleic bases either directly or through intermediate conversion into the respective aziridines.
- these substituted compounds may be employed as aziridino inactivating compounds to modify nucleic acids and/or inactivate microorganisms in biological compositions.
- the inactivating compounds of the present invention are protonated (i.e., positively charged) on one or more nitrogens at physiological pH.
- protonated compounds of formula (I) (II), and (III) have the following respective formulas:
- each Ri is, independently, selected from the group consisting of H, C 2 . 4 alkenyl, phenyl, and benzyl, and X is a pharmaceutically acceptable counter-ion (e.g., sulfate, nitrate, halide, tosylate, phosphate, and the like).
- X is a pharmaceutically acceptable counter-ion (e.g., sulfate, nitrate, halide, tosylate, phosphate, and the like).
- Ri can also be C ⁇ - alkyl.
- Compounds falling within formula (VIII) also have at least one Ri that is phenyl or benzyl.
- the compounds of the invention described herein also include isomers such as diastereomers and enantiomers, mixtures of isomers, including racemic mixtures, solvates, and polymorphs thereof.
- the modification of the nucleic acid molecules or microorganism inactivation is achieved while the non-nucleic acid components e.g., cells or biopolymers, such as proteins, carbohydrates or lipids, also present in the biological composition, are not substantially modified in their functionality.
- the modification of the nucleic acid molecules is achieved while preserving the structure and function of non-nucleic acid components, e.g.
- biopolymers such as proteins
- the extent of this biopolymer modification can be determined by means known in the art including, for example, isoelectric focusing, polyacrylamide gel electrophoresis, HPLC, and other forms of chromatography with detection by autoradiography or a suitable method.
- Modification of cellular function would be an effect on the metabolic or mechanical integrity of the cellular product. Modification of cellular function can be determined by monitoring, using known methods, metabolic parameters, including the ability of cells to generate substrates used for the maintenance of cell function, such as ATP.
- Mechanical integrity as used herein, relates to the maintenance of the deformability of the cell membrane structure.
- a decrease in mechanical integrity will result in an increased propensity for cell lysis (e.g., hemolysis for red blood cells) which is detectable using known methods.
- Substantial changes in cellular function will diminish the therapeutic utility of the cellular product. For example in the case of red cells, a substantial change would result in less than 75% of blood cells remaining in circulation 24 hours after infusion.
- the nucleic acid molecules that are modified are those of a microorganism, resulting in the inactivation of microorganism (i.e., the inability of the microorganism to replicate).
- Microorganisms that are inactivated according to the methods of the invention include, for example, viruses, bacteria, or parasites that are cell-contained or cell-free.
- Viruses inactivated by the methods and compounds of the invention include DNA and RNA viruses or viroids. Viruses inactivated by the methods of the invention include both enveloped or non-enveloped viruses. In a preferred embodiment, the viruses to be inactivated are infectious vertebrate viruses. In a particularly preferred embodiment the viruses to be inactivated are infectious human viruses.
- viruses include: poxviruses, herpes viruses, adenoviruses, papovaviruses, parvoviruses, reoviruses, orbiviruses, picornaviruses, rotaviruses, alphaviruses, rubiviruses, influenza virus e.g., including type A and B, flaviviruses, coronaviruses, paramyxo viruses, morbilliviruses, pneumoviruses, rhabdoviruses, lyssaviruses, orthmyxoviruses, bunyaviruses, phleboviruses, nairoviruses, hepadnaviruses, hepatitis A virus, hepatitis B virus, hepatitis C virus, arenaviruses, retroviruses including human immunodeficiency virus, enteroviruses, rhinoviruses and/or the filoviruses.
- TTV is an additional
- the methods and compounds of the invention can be used to inactivate infectious bacteria including, but not limited to Gram-negative or Gram-positive bacteria.
- Exemplary Gram-positive bacteria inactivated by the compounds and methods of the invention include, but are not limited to Pasteurella species, Staphylococci species, and Streptococcus species.
- Gram-negative bacteria inactivated by the compounds and methods of the invention include, but are not limited to, Escherichia coli, Pseudomonas species, and Salmonella species.
- Specific examples of infectious bacteria inactivated by the compounds and methods of the invention include but are not limited to: Helicobacter pylori, Borellia burgdorferi, Legionella pneumophila, Mycobacteria species (e.g., M.
- tuberculosis M. avium, M. intracellulare, M. kansaii, M. gordonae), Bacillus cereus, Staphylococcus aureus, Staphylococcus epidermidis, Neisseria gonorrhoeae, Neisseria meningitidis, Listeria monocytogenes, Streptococcus pyogenes (Group A Streptococcus), Streptococcus agalactiae (Group B Streptococcus), Streptococcus viridans (viridans group), Streptococcus faecalis, Streptococcus bovis, Streptococcus (anaerobic species), Streptococcus pneumoniae, pathogenic Campylobacter species, Enterococcus species, Haemophilus influenzae, Bacillus anthracis, Corynebacterium diphtheriae, Corynebacterium diphthe
- Pseudomonas putida Additional exemplary bacteria are Bartonella spp., Tropheryma whippelii, Mycoplasma, e.g. My coplasma pneumoniae and Chlamydophila, e.g. Chlamydophila pneumoniae.
- Bacteria inactivated by the compositions and methods of the invention can be included in killed vaccines.
- Examples of parasites inactivated by the methods and compositions of the invention are as follow: blood-borne and/or tissues parasites such as Plasmodium, Babesia microti, Babesia divergens, Leishmania tropica, Leishmania, Leishmania braziliensis, Leishmania donovani, Trypanosoma gambiense and Tiypanosoma rhodesiense (African sleeping sickness), Trypanosoma cruzi (Chagas' disease), and Toxoplasma gondii.
- blood-borne and/or tissues parasites such as Plasmodium, Babesia microti, Babesia divergens, Leishmania tropica, Leishmania, Leishmania braziliensis, Leishmania donovani, Trypanosoma gambiense and Tiypanosoma rhodesiense (African sleeping sickness), Trypanosoma cruzi (Chagas' disease), and Toxoplasma gondii.
- Parasites inactivated by the compositions and methods of the invention can be included in killed vaccines.
- compositions and methods of the invention reduce the number of infectious microorganisms in the inactivating compound contacted biological composition relative to the number of microorganisms in biological composition prior to the inactivation step, hi some embodiments, the number of infectious microorganisms in the inactivating compound contacted biological composition is reduced at least 1 log, preferably at least 2 logs, preferably at least 3 logs, or more preferably at least 4 logs relative to the number of microorganisms in biological composition prior to the inactivation step.
- the number of infectious microorganisms in the inactivating compound contacted biological composition is reduced at least 5 logs, more preferably at least 6 logs, more preferably at least 7 logs, more preferably at least 8 logs, and more preferably at least 9 logs relative to the number of microorganisms in the biological composition prior to the inactivation step. It is possible that the number of infectious microorganisms in the inactivating compound contacted biological composition is reduced at least 10, 11, 12, 13, 14, or even 15 logs.
- the biological composition is blood, a red blood cell comprising composition, a red blood cell concentrate, a platelet concentrate, blood plasma, a platelet-rich plasma, a placental extract, a cell culture product or culture medium, a product of fermentation, or an ascites fluid.
- the biological composition is serum, a blood cell protein, a blood plasma concentrate, a blood plasma protein fraction, a purified or partially purified blood protein or other component, a supernatant or a precipitate from any fractionation of the plasma, a purified or partially purified blood component (e.g., proteins or lipids), colostrum, milk, urine, saliva, a cell lysate, cryoprecipitate, cryosupernatant, or portion or derivative thereof, compositions containing proteins induced in blood cells, and compositions containing products produced in cell culture by normal or transformed cells (e.g., via recombinant DNA or monoclonal antibody technology), hi preferred embodiments of the invention, the biological compositions are derived from vertebrates.
- the biological compositions are derived from mammals. In additional preferred embodiments of the invention, the biological compositions are derived from humans. In particularly preferred embodiments of the invention, the biological composition is a purified human enucleated cell composition, particularly a purified red blood cell composition.
- the method of the first, second, third, fourth, fifth, or sixth aspect can also include the step of transfusing the inactivating compound-contacted biological composition into a mammal such as a human.
- At least some of said inactivating compound may be removed prior to transfusion, e.g., by washing or solid phase removal, hi addition to (or instead of) removing the inactivating compound, the inactivating compound can be quenched with a quenching agent after the contacting step.
- the quenching agent can be soluble or bound to a solid support which may subsequently be removed.
- the inactivated microorganisms produced by one of the foregoing methods may be harvested and used as an immunogen for the purpose of vaccinating an animal (e.g., a human) against that microorganism.
- the method of the first, second, third, fourth, fifth, or sixth aspect can also be considered a method for making a vaccine or an immunogen for administration to a human or other animal.
- Compositions containing inactivated microorganisms, optionally including one or more adjuvants, also are provided.
- the compositions are vaccine compositions.
- the invention features a purified compound having the formula:
- each Ri is, independently, selected from the group consisting of H, Ci- 4 alkyl, C 2 . 4 alkenyl, phenyl, and benzyl, provided that at least one i is phenyl or benzyl.
- Inactivating compounds that fall within formula (II) include, for example, 3 -phenyl- 1- aziridinepropanamine, N,N-dibenzyl-l-aziridineethanamine, and N-benzyl-N-ethyl-1- aziridineethanamine, and 2-benzyl-l-aziridineethanamine (compounds 3, 4, 5, and 6, respectively), depicted above.
- the invention features a purified compound selected from:
- the compounds and methods of this invention can be used to inactivate microorganisms including viruses, bacteria or parasites, particularly blood-transmitted viruses, bacteria or parasites, in cell- or protein-containing compositions in various contexts, e.g., in the hospital, laboratory, as part of a kit. Since cell compositions also include a variety of proteins, the method of microorganism inactivation described herein is also applicable to protein fractions such as blood plasma protein fractions or purified blood products, including, but not limited to, fractions containing clotting factors (such as factor VIII and factor IX), serum albumin or immunoglobulins. The microorganism inactivation may be accomplished by treating a protein fraction or purified protein with a compound of the invention, as described herein.
- more than one inactivating aziridino compound may be contacted with the biological composition.
- the methods and compositions of the invention can be combined with still other modes of inactivating viruses.
- the compounds and methods of the present invention can be used in the Solvent/Detergent procedure described by Budowsky et al., U.S. Patent No. 6,369,048, incorporated herein by reference.
- certain processes used in the preparation of medical products e.g., chromatography in buffers of low pH, or storage of red blood cells in acidic solutions containing calcium chelating agents
- a blood product decontaminated by the methods and compositions of the invention.
- purified is meant a preparation or composition that contains, by volume or weight, at least 50%, more preferably, at least 70%, more preferably at least 85%, even more preferably at least 95%, and most preferably, at least 98% of the indicated component.
- a purified preparation of red blood cells contains at least 50% by volume red blood cells, while purified 3-phenyl-l-aziridinepropanamine is at least 50% by weight 3-phenyl-l- aziridinepropanamine.
- nucleic acid is meant both DNA and RNA, both single and double stranded.
- modifying means to substantially eliminate the template activity of DNA or RNA, for example, by destroying the ability to replicate, or to transcribe or translate a message.
- the inhibition of translation of an RNA molecule can be determined by measuring the amount of protein encoded by a definitive amount of RNA produced in a suitable in vitro or in vivo translation system.
- inactivating when referring to a microorganism, means eliminating its ability to propagate.
- bacteria or parasites the term means reducing the number of living bacteria or parasites capable of replicating or reproducing.
- viruses the term means diminishing or eliminating the number of infectious viral particles measured as a decrease in the infectious titer or number of infectious virus particles per milliliter. Such a decrease in infectious virus particles is determined by assays well known to a person of ordinary skill in the art.
- Microorganism inactivating conditions refers to the conditions under wliich microorganisms incubated with a compound of this invention are inactivated. Variables include, for example, time of treatment, pH, temperature, salt composition, ionic strength and concentration of the inactivating compound so as to inactivate the microorganisms to the desired extent.
- inactivate at least some of the microorganisms is meant that the number of infectious microorganisms is reduced at least 1 log, preferably at least 2 logs, preferably at least 3 logs, or more preferably at least 4 logs relative to the number of microorganisms in biological composition prior to the inactivation step.
- the number of infectious microorganisms in the inactivating compound contacted biological composition is reduced at least 5 logs, more preferably at least 6 logs, more preferably at least 7 logs, more preferably at least 8 logs, and still more preferably at least 9 logs relative to the number of microorganisms in the biological composition prior to the inactivation step. It is possible that the number of infectious microorganisms in the inactivating compound contacted biological composition is reduced at least 10, 11, 12, 13, 14, or even 15 logs.
- nucleic acid molecules modify at least some of the nucleic acid molecules
- modify at least some of the nucleic acid molecules is meant that at least 50% of the nucleic acid molecules in the treated biological composition are modified, preferably at least 70%, preferably at least 80%, still more preferably at least 90%, still more preferably at least 95%, still more preferably at least 99% of the nucleic acid molecules in the treated biological composition are modified.
- Methods to detect nucleic acid modification include the detection of covalent chemical adducts using either mass spectrometry or radiolabeled aziridino compounds.
- An alternative method to detect nucleic acid modification is to employ molecular science techniques of PCR in which the nucleic acid molecule is evaluated for its ability to be replicated by polymerase enzymes. The presence of nucleic acid damage can result in the loss of ability of the nucleic acid molecule to be replicated if the appropriate primers are employed.
- biological composition a composition containing cells or proteins.
- Cell-containing compositions include, for example, blood, red blood cell concentrates, platelet concentrates, blood plasma, platelet-rich plasma, placental extracts, cell culture product or culture medium, products of fermentation, and ascites fluid.
- Biological compositions may also be cell-free.
- Protein-containing biological compositions include, for example, serum, blood cell proteins, blood plasma concentrate, blood plasma protein fractions, purified or partially purified blood proteins or other components, a supernatant or a precipitate from any fractionation of the plasma, purified or partially purified blood components (e.g., proteins or lipids), colostrum, milk, urine, saliva, a cell lysate, cryoprecipitate, cryosupernatant, or portion or derivative thereof, compositions containing proteins induced in blood cells, and compositions containing products produced in cell culture by normal or transformed cells (e.g., via recombinant DNA or monoclonal antibody technology).
- the biological compositions are derived from vertebrates.
- the biological compositions are derived from mammals.
- the biological compositions are derived from humans, hi particularly preferred embodiments of the invention, the biological compositions are purified human enucleated cells, particularly purified red blood cells.
- an “enucleated cell” is meant a cell which, when mature, lacks a nucleus.
- enucleated cells are platelets and red blood cells.
- a solution that does not quench an inactivating compound is meant a solution that does not contain a quenching agent (e.g., a thiophosphate or a thiosulfate).
- a quenching agent e.g., a thiophosphate or a thiosulfate.
- a quenching agent when contacted with a compound, renders the contacted inactivating compound unreactive.
- Exemplary solutions that do not react with a compound of the invention are unbuffered saline and water.
- quenching agent a compound that when contacted with a compound of the invention, is capable of rendering the contacted compound unreactive.
- quenching agents are thiophosphate or a thiosulfate, or a compound containing a thiophosphate or a thiosulfate.
- the invention features compositions and methods to modify nucleic acids in biological compositions by contacting the composition with an inactivating aziridino compound.
- the methods and compositions of the invention can be used to modify nucleic acid molecules of microorganisms in a biological composition, resulting in microorganism inactivation, by contacting the composition with an inactivating aziridino compound of the invention, under microorganism inactivating conditions.
- An inactivating aziridino compounds of the invention may have one of the following four formulas:
- each Ri is, independently, selected from the group consisting of H, C 2 - 4 alkenyl, phenyl, and benzyl.
- Ri can also be C1- 4 alkyl.
- Compounds falling within formula (II) have at least one Ri that is phenyl or benzyl.
- An aziridino inactivating compound of the invention may also have the following structures:
- Ri is a - alkyl and R 2 and R 3 is each, independently, H or a C1- 4 alkyl.
- aziridino inactivating compounds of the invention may have one of the following structures:
- Nucleic acid molecules can be modified by contacting the composition comprising the nucleic acid or microorganism comprising nucleic acid with about 0.00001 to about 0.250 M, preferably about 0.0001 to about 0.015 M of an inactivating aziridino compound of the invention in a solution having an ionic strength of about 0.01 M to about 0.5 M, at apH of about 4.5 to 8.5, preferably about 6.0 to 8.0, preferably about 6.5 to about 7.5, at a temperature of about 4°C to about 60°C, preferably 4°C to about 30°C, for a time sufficient to modify the nucleic acid to the desired extent.
- the reaction time range from about 1 minute to about 500 hours and can be, for example, about 1 minute, about 1 hour, about six hours, about twelve hours, about 24 hours, about forty-eight hours or about one hundred and forty-eight hours.
- the salts used can be any of those normally used in biochemical applications, including sodium, potassium, acetate, and so on.
- the practitioner can adjust the pH of the solution using many buffers customarily used in the art to handle biopolymers or cells, such as acetate, HEPES, MOPS, and so forth.
- the practitioner can also adjust factors such as concentration of the reactants, temperature, and time of incubation.
- reaction rate, the ionic strength of the reaction solution, temperature and concentration of aziridino inactivating compound are interdependent.
- increasing the concentration of the aziridino inactivating compound, reaction temperature and/or reducing the ionic strength results in a shorter reaction time to achieve the desired extent of nucleic acid modification or microorganism inactivation.
- increasing the reaction temperature allows the practitioner to decrease the concentration of aziridino inactivating compound, reaction time and/or to increase the ionic strength to achieve the desired degree of nucleic acid modification or microorganism inactivation.
- increasing the concentration of aziridino inactivating compound allows the practitioner to reduce the reaction temperature, reaction time and/or increase the ionic strength to achieve the desired degree of nucleic acid modification or microorganism inactivation.
- increasing the ionic strength of the reaction solution results in a longer reaction time, increased concentration of aziridino inactivating compound or increased temperature to achieve the desired degree of nucleic acid modification or microorganism inactivation.
- Aziridino inactivating compounds of the invention are suitable, for example, for use in the treatment of a red blood cell preparation in order to inactivate microorganisms (e.g., viruses, bacteria, and/or parasites) contaminating the red blood cell preparation, while leaving the red blood cells suitable for use in a therapeutic setting (e.g., for use in transfusion).
- microorganisms e.g., viruses, bacteria, and/or parasites
- One method to remove aziridino compound from a cell containing biological composition is to subject the cells to repeated washings with an appropriate washing solution as described in co-pending U.S. patent application serial number 10/055,143, which is herein incorporated by reference in its entirety.
- aziridino inactivating compounds can be removed from biologic mixtures using standard laboratory methodologies including dialysis, diafiltration, size exclusion chromatography, affinity chromatography and also by the use of resins which have an affinity for aziridino compounds due to either electrostatic or covalent chemical reactions.
- the resins can be presented to the biologic mixture in the free form or as part of a filter matrix.
- the quenching agent and quenched inactivating compound may be removed from a biological composition by bonding the quenching agent to a nucleophile, e.g., a thiosulfate or thiophosphate group, to a second moiety (the separation moiety) which supplies particular properties to the quenching agent, such that the quenching agent can be completely and reliably separated, along with the quenched inactivating compound, from the biological composition.
- a nucleophile e.g., a thiosulfate or thiophosphate group
- the separation moiety which supplies particular properties to the quenching agent, such that the quenching agent can be completely and reliably separated, along with the quenched inactivating compound, from the biological composition.
- These modified quenching compounds can react with and quench electrophiles such as the inactivating compounds described herein. Methods of quenching are described in co-pending application U.S.S.N. 09/260,375 and U.S. Pat.
- This method has the added advantage that it is compatible with methods to remove solvent and detergent from protein-containing preparations that are virally-inactivated by the Solvent/Detergent procedure described by Budowsky et al., U.S. Patent No. 6,369,048, incorporated above by reference in its entirety.
- the Solvent/Detergent method of virus activation is compatible with the inactivation of microorganisms by compounds such as those described herein. Thus, one can perform two methods of inactivation in sequence or simultaneously. Alternatively, the inactivation of microorganisms through the use of the methods of the invention, followed by quenching and removal of the quenching agent and inactivating compound using the methods described herein, can be performed without the use of the Solvent/Detergent method. It is also advantageous that the quenching agent be easily detectable in order to monitor its removal. This can be fulfilled, for example, with the addition of thymidine, which is readily detected by its absorbance of 260 nm light.
- a thiophosphodiester e.g.,
- the substituent may be, for example, a linear, branched, or cyclic saturated or unsaturated hydrocarbon with one to forty carbons, a benzyl group, a polycyclic aromatic group, an unsubstituted alkyl group, or an alkyl group substituted with hydroxyl, amino, azido, or cyano groups.
- Polythiophosphate moieties i.e., moieties having two or more adjacent phosphate groups
- GDP guanosine diphosphate
- GTP guanosine triphosphate
- one or more of the phosphate groups is a thiophosphate group
- one or both phosphate groups may be thiophosphate groups, hi the case of guanosine triphosphate, one, two, or all three of the phosphate groups maybe thiophosphate groups.
- GDP or GTP may be attached to the separation moiety, for example, at the 2' or the 3' hydroxyl group or to the heterocyclic base.
- the quenching systems of the invention can be used as follows.
- An inactivating compound such as 1-aziridinepropanamine
- a biological composition under microorganism inactivating conditions as described herein.
- quenching agent e.g., a compound containing one or more thiosulfate or thiophosphate moieties attached to a separation moiety.
- quenching agent e.g., a compound containing one or more thiosulfate or thiophosphate moieties attached to a separation moiety.
- the biological composition and the quenching agent are allowed to remain in contact for the desired time.
- An excess of thiosulfate or thiophosphate groups per equivalent of inactivating compound is generally used.
- the thiosulfate or thiophosphate moieties react with the highly reactive moieties of the inactivating compounds or their haloderivative salts, and become covalently linked to these compounds.
- the coupled thiosulfate or thiophosphate moieties are removed from the biological composition, therefore, the quenched inactivating compounds are removed as well.
- the end result is a biological composition that is substantially free of infectious microorganisms (e.g., viruses), quenched inactivating compounds, and quenching agent.
- Killed vaccines can be made by contacting a virus or other microorganism with an inactivating compound under microorganism-inactivating conditions.
- the microorganism- inactivating conditions may be selected from the methods described herein, hi one example, virus at a titer of about 10 to 10 units per mL is incubated with inactivating agent at about pH 6.5 to about pH 7.5, in a solution having an ionic strength of less than about 0.5 M at about 4°C to about 40°C.
- the time of treatment i.e., the end point of inactivation depends on the structure and composition of the particular virus, temperature of incubation, ionic strength, and the number of protonizable or positively charged groups in the inactivating agents.
- incubation time could be as little as a few seconds, and also can be about 1 hour, 5 hours, 50 hours, 100 hours 300 hours or 500 hours.
- the killed virus can be used directly in vaccine formulations, or lyophilized in individual or multiple dose containers for subsequent mixture with the pharmaceutically acceptable carrier. Methods of preparing vaccines are well known in the art.
- the vaccines of this invention are useful in the prevention of animal or human disease. Vaccines capable of conferring the desired degree of immunity will, of course, contain an amount of inactivated microorganism effective to evoke an immune response.
- the sample of microorganism is incubated with the aziridino inactivating agents of this invention in amounts and under such conditions to inactivate the microorganism while retaining immunogenicity.
- the vaccine can be administered in or with an adjuvant, i.e., a substance that potentiates an immune response when used in conjunction with an antigen.
- the vaccine can be given in an immunization dose.
- An immunization dose is an amount of an antigen or immunogen needed to produce or enhance an immune response. The amount will vary with the animal and immunogen or antigen or adjuvant but will generally be less than about 1000 ⁇ g per dose.
- the immunization dose is easily determined by methods well known to those skilled in the art, such as by conducting statistically valid host animal immunization and challenge studies.
- the particular dosage of the vaccine to be administered to a subject will depend on a variety of considerations including the nature of the microorganism, the schedule of administration, the age and physical characteristics of the subject, and so forth. Proper dosages may be established using clinical approaches familiar to the medicinal arts.
- N-benzyl-2-(ethylamino)ethanol (5.38 g; 0.03 moles) was dissolved and 8.4 mL (0.06 moles) triethylamine in 100 mL dichloromethane.
- the reaction mixture was chilled in an ice bath for 0.5 hr.
- Methanesulfonyl chloride (4.7 mL; 0.06 moles) was dissolved in 11 mL dichloromethane and added dropwise to the reaction mixture over ⁇ 10 min.
- the reaction mixture was allowed to warm to room temperature over 4 hr, then poured on a column of 101.4 g silica gel (60-200 mesh) and eluted with hexanes, followed by 10% EtOAc:hexanes.
- Scheme 7 Referring to Scheme 7, aziridine (1.3 mL; 0.025 moles), potassium carbonate (3.49 g; 0.025 moles), and 91 mL acetonitrile were mixed together and chilled in an ice bath for 0.5 hr. l-Methanesulfonyl-3-aza-3-benzylpentane (3.1 g; 0.012 moles) was dissolved in 13 mL acetonitrile and added dropwise over 15 min, stirred at room temperature overnight, and refluxed for 3 hr. The reaction mixture was filtered and the filtrate concentrated on a rotary evaporator under reduced pressure (6 mm).
- N,N-Dibenzyl-l-aziridineethanamine was prepared as follows.
- N,N-dibenzylethanolamine (9.65 g; 0.04 moles) and triethylamine (6.1 mL; 0.044 moles) were dissolved in 90 mL dichloromethane.
- methanesulfonyl chloride 3.4 mL; 0.044 moles
- the addition was exothermic.
- the reaction was stirred at room temperature for 4 hr.
- the reaction mixture was then chromatographed on 122.4 g silica gel (60-200 mesh), eluting with hexanes then 20% EtOAc:hexanes.
- Scheme 12 Referring to Scheme 12, a mixture of 10.3 g (0.079 moles) cinnamonitrile, 24.1 g (0.56 moles) aziridine, 5.5 mL (0.39 moles) triethylamine, and 3.0 g (0.02 moles) DBU was refluxed for 76 hr. The reaction mixture was concentrated on a rotary evaporator. The residue was chromatographed on silica gel eluting with hexanes, then 50% EtOAc:hexanes. The appropriate fractions were concentrated to yield 13.4 g 3-phenyl-l- aziridinepropanenitrile as an oil. 98% yield.
- N-[3-(l-aziridinyl)propyl]-l,4-butanediamine was prepared as follows.
- Example 8 Synthesis of l,l'-[iminobis(trimethylene)]bis aziridine 1,1 '-[iminobis(trimethylene)]bis aziridine was prepared as follows.
- Example 9 Inactivation of Escherichia coli by 1-aziridinepropanamine The ability of 1-aziridinepropanamine to inactivate E. coli is demonstrated in the following assay.
- E. coli stationary phase culture prepared by overnight growing in LB media at 37°C is spiked to a concentration of 10° to IO 7 cfu/ml in low ionic strength medium (LISM: 4.3% Dextrose (239 mM), 12.5 mM Na-phosphate pH 7.1-7.2, osmolality: 285-290 mOsm). The E. coli culture is divided into four 10 mL aliquots in 50 mL culture flasks.
- a 1-aziridinepropanamine 20x stock solution is prepared immediately before use by addition of a specified quantity of the compound, prepared as described above, to a 0.32 M NaH 2 PO 4 solution.
- the freshly prepared 1-aziridinepropanamine 20x stock solution (pH 7.5 to 7.6) is kept on ice until it is added to two flasks, to a final concentration of 12 mM.
- One control flask, having no 1-aziridinepropanamine, and a flask having 12 mM 1-aziridinepropanamine are incubated at 37°C for ten hours.
- Another control flask, having no 1-aziridinepropanamine, and a flask having 12 mM 1-aziridinepropanamine are incubated at 22°C for ten hours.
- One milliliter aliquots are taken sterilely from the control and treated flasks every two hours, serially diluted with phosphate buffered saline (PBS) and are plated on LB agar plates. The plates are incubated for 48 hrs at 37°C and bacterial colonies are counted. The limit of detection is 10° cfu/mL.
- PBS phosphate buffered saline
- Example 10 Inactivation of Yersinia enter ocolitica by 1-aziridinepropanamine and 1- aziridinebutanamine
- Yersinia enterocolitica stationary phase culture prepared by overnight growing in LB media at 37°C is spiked to a final concentration of 10 to 10 cfii/ml in low ionic strength medium (LISM: 4.3% Dextrose (239 mM), 12.5 mM Na-phosphate pH 7.1-7.2, osmolality: 285-290 mOsm).
- the Yersinia enterocolitica stationary phase culture is divided into three 10 mL aliquots in 50 mL culture flasks.
- 1-aziridinepropanamine prepared as described above and freshly diluted in 0.32 M NaH 2 PO 4 , is added as a 20x stock (pH 7.5 to 7.6) to a final concentration of 12 mM to one of the flasks.
- 1-aziridinebutanamine prepared as described above and freshly diluted in 0.38 M NaH 2 P0 4 , is added to a final concentration of 12 mM to another flasks.
- a control flask, having no 1-aziridinepropanamine or 1-aziridinebutanamine, a tube having 12 mM 1-aziridinepropanamine and a flask having 12 mM 1- aziridinebutanamine are incubated at 22°C for six hours.
- Example 11 Inactivation of porcine parvo virus by 1-aziridinepropanamine.
- 1-aziridinepropanamine is prepared as described above.
- a 20x stock solution is prepared by diluting 1-aziridinepropanamine into 0.32 M NaH 2 PO (final pH of 20x stock 7.5-7.6), and kept on ice, immediately prior to use.
- PPV is prepared according to conventional procedures including purification and determination of infectivity and stability. Aliquots of the viral stock are added to tubes of thawed fresh frozen plasma ("FP") to result in a concentration of 10° - 10 7 TCID 5 o/ml. Aliquots of the stock 1-aziridinepropanamine solution are added, to a final concentration of 6 mM, to the tubes of PPV in FP , except that no 1-aziridinepropanamine is added to the control tubes. The tubes are incubated at 22°C and aliquots are taken sterilely from each reaction tube and control at 1 hour, 3 hours, and 6 hours.
- FP thawed fresh frozen plasma
- the aliquots are serially diluted in a microtiter plate for a total of 8 microtiter wells. 25 ⁇ l of each dilution is incubated for 6 days with PT-1 cells (porcine testicle cells) in microtiter plates. The wells are checked for a cytopathic effect. The limit of detection is > 5 TCTDso/mL.
- the presence of 6 mM 1-aziridinepropanamine in FP incubated at 22°C for 1 hour, 3 hours and 6 hours, resulted in less than a 2 log, more than a 2 log, and about a 3 log PPV reduction, respectively, compared to the positive control at the same time point.
- Example 12 Inactivation of porcine parvo virus by l,l'-[iminobis(trimethylene)]bis aziridine.
- l,l'-[iminobis(trimethylene)]bis aziridine The ability of l,l'-[iminobis(trimethylene)]bis aziridine to inactivate PPV is demonstrated in the following assay.
- l,r-[iminobis(trimethylene)]bis aziridine is prepared as described above and a 20x stock solution prepared immediately prior to us by diluting 1,1 '-[iminobis(trimethylene)]bis aziridine into 0.5 M NaH 2 PO (final pH of 20x stock 7.4), and kept on ice.
- PPV is prepared according to conventional procedures including purification and determination of infectivity and stability.
- Aliquots of the viral stock are added to tubes of thawed fresh frozen plasma ("FP") and red blood cell concentrate (“RBCC”) to result in a concentration of 10 6 TCID 5 o/mL.
- Aliquots of the l,l'-[iminobis(trimethylene)]bis aziridine 20x stock solution are added, to a final concentration of 12 mM, to the tubes of PPV in FP and RBCC except that no l,r-[iminobis(trimethylene)]bis aziridine is added to the control tubes.
- the tubes are incubated at 22°C and aliquots are taken sterilely from each reaction tube and control at 1 hour, 3 hours, and 6 hours.
- the aliquots are serially diluted in a microtiter plate for a total of 8 microtiter wells. Twenty- five microliters of each dilution is incubated for 6 days with PT-1 cells (described above) in microtiter plates. The wells are checked for a cytopathic effect. The limit of detection is > 5 TCID 5 o/ml. The presence 12 mM 1,1 '-[iminobis(trimethylene)]bis aziridine in FP, incubated at
- Example 13 Inactivation of encephalomyocarditis virus by 1-ethylaziridine
- 1-ethylaziridine to inactivate encephalomyocarditis virus (“EMCV") is demonstrated in the following assay.
- 1-ethylaziridine is prepared as described above.
- a 20x stock solution is prepared by diluting 1-ethylaziridine in 0.18 M NaH 2 PO (final pH of 20x stock 7.1-7.3), and kept on ice, immediately prior to use.
- EMCV is prepared according to conventional procedures including purification and determination of infectivity and stability.
- An aliquot of the viral stock is added to a tube of 12.5 mM sodium phosphate, pH 7.2, to arrive at a concentration of 10° - IO 7 TCID 5 o/mL.
- An aliquot of the stock 1-ethylaziridine is added, to a final concentration of 12 mM, to the tube of EMCV and sodium phosphate. No 1-ethylaziridine is added to the control tube.
- the tubes are incubated at 37°C and aliquots are taken sterilely from the reaction tube and control 4 hours.
- the aliquots are serially diluted in a microtiter plate for a total of 8 microtiter wells. Twenty- five microliters of each dilution is incubated for 6 days with African green monkey kidney cells in microtiter plates. The wells are checked for a cytopathic effect. The limit of detection is > 5 TCID 5 o/mL.
Abstract
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CA002484940A CA2484940A1 (en) | 2002-05-06 | 2003-05-06 | Methods and compositions for the modification of nucleic acids |
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WO2005002570A1 (en) * | 2003-06-27 | 2005-01-13 | V.I. Technologies, Inc. | Use of an aziridino compound to selectively inactivate parasites in biological compositions |
CN112342144A (en) * | 2020-09-28 | 2021-02-09 | 江西农业大学 | Aspergillus flavus strain and application thereof |
CN112996545A (en) * | 2018-07-27 | 2021-06-18 | 萨塔制药公司 | Methods for pathogen, microbial and parasitic inactivation |
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US6093564A (en) * | 1997-10-03 | 2000-07-25 | V.I. Technologies, Inc. | Methods and compositions for the selective modification of nucleic acids |
US6352695B1 (en) * | 1997-10-03 | 2002-03-05 | V.I. Technologies, Inc. | Methods and compositions for the selective modification of nucleic acids |
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JP2002535389A (en) * | 1999-01-29 | 2002-10-22 | ブイ.アイ. テクノロジーズ インク. | Synthesis of ethyleneimine dimer |
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US6093564A (en) * | 1997-10-03 | 2000-07-25 | V.I. Technologies, Inc. | Methods and compositions for the selective modification of nucleic acids |
US6352695B1 (en) * | 1997-10-03 | 2002-03-05 | V.I. Technologies, Inc. | Methods and compositions for the selective modification of nucleic acids |
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Cited By (5)
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WO2005002570A1 (en) * | 2003-06-27 | 2005-01-13 | V.I. Technologies, Inc. | Use of an aziridino compound to selectively inactivate parasites in biological compositions |
CN112996545A (en) * | 2018-07-27 | 2021-06-18 | 萨塔制药公司 | Methods for pathogen, microbial and parasitic inactivation |
EP3829656A4 (en) * | 2018-07-27 | 2022-03-16 | Zata Pharmaceuticals Inc. | Method for pathogens, microorganisms, and parasites inactivation |
CN112342144A (en) * | 2020-09-28 | 2021-02-09 | 江西农业大学 | Aspergillus flavus strain and application thereof |
CN112342144B (en) * | 2020-09-28 | 2023-02-14 | 江西农业大学 | Aspergillus flavus strain and application thereof |
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