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Article ; Online: Quantitative Measurement of Cytosolic and Nuclear Penetration of Oligonucleotide Therapeutics.

Deprey, Kirsten / Batistatou, Nefeli / Debets, Marjoke F / Godfrey, Jack / VanderWall, Kirstin B / Miles, Rebecca R / Shehaj, Livia / Guo, Jiaxing / Andreucci, Amy / Kandasamy, Pachamuthu / Lu, Genliang / Shimizu, Mamoru / Vargeese, Chandra / Kritzer, Joshua A

ACS chemical biology

2022 Volume 17, Issue 2, Page(s) 348–360

Abstract: A major obstacle in the development of effective oligonucleotide therapeutics is a lack of understanding about their cytosolic and nuclear penetration. To address this problem, we have applied the chloroalkane penetration assay (CAPA) to oligonucleotide ... ...

Abstract	A major obstacle in the development of effective oligonucleotide therapeutics is a lack of understanding about their cytosolic and nuclear penetration. To address this problem, we have applied the chloroalkane penetration assay (CAPA) to oligonucleotide therapeutics. CAPA was used to quantitate cytosolic delivery of antisense oligonucleotides (ASOs) and siRNAs and to explore the effects of a wide variety of commonly used chemical modifications and their patterning. We evaluated potential artifacts by exploring the effects of serum, comparing activity data and CAPA data, and assessing the impact of the chloroalkane tag and its linker chemistry. We also used viral transduction to expand CAPA to the nuclear compartment in epithelial and neuronal cell lines. Using this enhanced method, we measured a 48-h time course of nuclear penetration for a panel of chemically diverse modified RNAs. Moving forward, CAPA will be a useful tool for deconvoluting the complex processes of endosomal uptake, escape into the cytosol, and subcellular trafficking of oligonucleotide therapeutics in therapeutically relevant cell types.
MeSH term(s)	Cell Nucleus ; Cytosol/metabolism ; Oligonucleotides/metabolism ; Oligonucleotides, Antisense/metabolism ; RNA, Small Interfering/metabolism
Chemical Substances	Oligonucleotides ; Oligonucleotides, Antisense ; RNA, Small Interfering
Language	English
Publishing date	2022-01-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.1c00830
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Article ; Online: Theoretical simulation of Kelvin probe force microscopy for Si surfaces by taking account of chemical forces.

Tsukada, Masaru / Masago, Akira / Shimizu, Mamoru

Journal of physics. Condensed matter : an Institute of Physics journal

2012 Volume 24, Issue 8, Page(s) 84002

Abstract: A new method of theoretical simulation for Kelvin probe force microscopy (KPFM) imaging on semiconductor or metal samples is proposed. The method is based on a partitioned real space (PR) density functional based tight binding (DFTB) calculation of the ... ...

Abstract	A new method of theoretical simulation for Kelvin probe force microscopy (KPFM) imaging on semiconductor or metal samples is proposed. The method is based on a partitioned real space (PR) density functional based tight binding (DFTB) calculation of the electronic states to determine the multi-pole electro-static force, which is augmented with the chemical force obtained by a perturbation treatment of the orbital hybridization. With the PR-DFTB method, the change of the total energy is calculated together with the induced charge distribution in the tip and the sample by their approach under an applied bias voltage, and the KPFM images, namely the patterns of local contact potential difference (LCPD) distribution, are obtained with the minimum condition of the interaction force. However, since the interaction force is due to electro-static multi-poles, the spatial resolution of the KPFM images obtained by PR-DFTB is limited to the nano-scale range and an atom-scale resolution cannot be attained. By introducing an additional chemical force, i.e., the force due to the orbital hybridization, we succeeded in reproducing atom-scale resolution of KPFM images. Case studies are performed for clean and impurity embedded Si surfaces with Si tip models.
Language	English
Publishing date	2012-02-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1472968-4
ISSN	1361-648X ; 0953-8984
ISSN (online)	1361-648X
ISSN	0953-8984
DOI	10.1088/0953-8984/24/8/084002
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Article ; Online: A Potential of an Anti-HTLV-I gp46 Neutralizing Monoclonal Antibody (LAT-27) for Passive Immunization against Both Horizontal and Mother-to-Child Vertical Infection with Human T Cell Leukemia Virus Type-I.

Fujii, Hideki / Shimizu, Mamoru / Miyagi, Takuya / Kunihiro, Marie / Tanaka, Reiko / Takahashi, Yoshiaki / Tanaka, Yuetsu

Viruses

2016 Volume 8, Issue 2

Abstract: Although the number of human T-cell leukemia virus type-I (HTLV-I)-infected individuals in the world has been estimated at over 10 million, no prophylaxis vaccines against HTLV-I infection are available. In this study, we took a new approach for ... ...

Abstract	Although the number of human T-cell leukemia virus type-I (HTLV-I)-infected individuals in the world has been estimated at over 10 million, no prophylaxis vaccines against HTLV-I infection are available. In this study, we took a new approach for establishing the basis of protective vaccines against HTLV-I. We show here the potential of a passively administered HTLV-I neutralizing monoclonal antibody of rat origin (LAT-27) that recognizes epitopes consisting of the HTLV-I gp46 amino acids 191-196. LAT-27 completely blocked HTLV-I infection in vitro at a minimum concentration of 5 μg/mL. Neonatal rats born to mother rats pre-infused with LAT-27 were shown to have acquired a large quantity of LAT-27, and these newborns showed complete resistance against intraperitoneal infection with HTLV-I. On the other hand, when humanized immunodeficient mice were pre-infused intravenously with humanized LAT-27 (hu-LAT-27), all the mice completely resisted HTLV-I infection. These results indicate that hu-LAT-27 may have a potential for passive immunization against both horizontal and mother-to-child vertical infection with HTLV-I.
MeSH term(s)	Adult ; Animals ; Antibodies, Monoclonal/administration & dosage ; Antibodies, Monoclonal/immunology ; Disease Transmission, Infectious/prevention & control ; Female ; Gene Products, env/genetics ; Gene Products, env/immunology ; HTLV-I Infections/immunology ; HTLV-I Infections/prevention & control ; HTLV-I Infections/transmission ; HTLV-I Infections/virology ; Human T-lymphotropic virus 1/genetics ; Human T-lymphotropic virus 1/immunology ; Human T-lymphotropic virus 1/physiology ; Humans ; Immunization, Passive ; Infant ; Infectious Disease Transmission, Vertical/prevention & control ; Male ; Mice ; Rats ; Rats, Inbred F344 ; Rats, Sprague-Dawley ; Retroviridae Proteins, Oncogenic/genetics ; Retroviridae Proteins, Oncogenic/immunology
Chemical Substances	Antibodies, Monoclonal ; Gene Products, env ; Retroviridae Proteins, Oncogenic ; gp46 protein, Human T-cell leukemia virus type I
Language	English
Publishing date	2016-02-03
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v8020041
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Article: Convenient method for the preparation of carbamates, carbonates, and thiocarbonates.

Shimizu, Mamoru / Sodeoka, Mikiko

Organic letters

2007 Volume 9, Issue 25, Page(s) 5231–5234

Abstract: A convenient, rapid, and efficient method for the preparation of carbamates from amines with 1-alkoxycarbonyl-3-nitro-1,2,4-triazole transfer reagents is reported. Reactions of newly synthesized stable crystalline reagents with alkyl amines were ... ...

Abstract	A convenient, rapid, and efficient method for the preparation of carbamates from amines with 1-alkoxycarbonyl-3-nitro-1,2,4-triazole transfer reagents is reported. Reactions of newly synthesized stable crystalline reagents with alkyl amines were completed in a few minutes without any additional base, and highly pure carbamates were obtained without chromatographic purification. These highly active reagents are also useful for the selective protection of nucleobases and preparation of carbonates and thiocarbonates.
MeSH term(s)	Alcohols/chemistry ; Amines/chemistry ; Carbamates/chemical synthesis ; Carbamates/chemistry ; Carbonates/chemical synthesis ; Carbonates/chemistry ; Crystallography, X-Ray ; Models, Molecular ; Molecular Structure ; Sulfhydryl Compounds/chemistry
Chemical Substances	Alcohols ; Amines ; Carbamates ; Carbonates ; Sulfhydryl Compounds
Language	English
Publishing date	2007-12-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1523-7060
ISSN	1523-7060
DOI	10.1021/ol7024108
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Article ; Online: Solid-phase synthesis of oligodeoxyribonucleotides without base protection utilizing O-selective reaction of oxazaphospholidine derivatives.

Oka, Natsuhisa / Maizuru, Yukihiro / Shimizu, Mamoru / Wada, Takeshi

Nucleosides, nucleotides & nucleic acids

2010 Volume 29, Issue 2, Page(s) 144–154

Abstract: A study on the development of a novel method to synthesize oligodeoxyribonucleotides without base protection is described. We found that nucleoside 3'-O-oxazaphospholidine derivatives exclusively react with the hydroxy group of nucleosides in the ... ...

Abstract	A study on the development of a novel method to synthesize oligodeoxyribonucleotides without base protection is described. We found that nucleoside 3'-O-oxazaphospholidine derivatives exclusively react with the hydroxy group of nucleosides in the presence of unprotected nucleobase amino groups. Since the O-chemoselectivity of the oxazaphospholidine derivatives is likely due to their ring structure, which allows the regeneration of the oxazaphospholidine derivatives from the corresponding base phosphitylation adducts via an intramolecular recyclization, the method is expected to be compatible with any kinds of acidic activators.
MeSH term(s)	Anion Exchange Resins/chemistry ; Chemistry, Organic/methods ; Chromatography, High Pressure Liquid ; Cytosine/chemistry ; Magnetic Resonance Spectroscopy ; Oligodeoxyribonucleotides/chemical synthesis ; Oligodeoxyribonucleotides/chemistry ; Oxazoles/chemistry
Chemical Substances	Anion Exchange Resins ; Oligodeoxyribonucleotides ; Oxazoles ; Cytosine (8J337D1HZY)
Language	English
Publishing date	2010-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2008956-9
ISSN	1532-2335 ; 1525-7770
ISSN (online)	1532-2335
ISSN	1525-7770
DOI	10.1080/15257771003612839
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Zs.A 3870: Show issues

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Article ; Online: Solid-phase synthesis of backbone-modified DNA analogs by the boranophosphotriester method using new protecting groups for nucleobases.

Kawanaka, Toshihide / Shimizu, Mamoru / Shintani, Noriko / Wada, Takeshi

Bioorganic & medicinal chemistry letters

2008 Volume 18, Issue 13, Page(s) 3783–3786

Abstract: Backbone-modified DNA analogs were synthesized in good yields by the boranophosphotriester method on a solid support. The oligodeoxyribonucleoside boranophosphates, protected with 2-(azidomethyl)benzoyl groups for nucleobases, were converted into DNA and ...

Abstract	Backbone-modified DNA analogs were synthesized in good yields by the boranophosphotriester method on a solid support. The oligodeoxyribonucleoside boranophosphates, protected with 2-(azidomethyl)benzoyl groups for nucleobases, were converted into DNA and its backbone-modified analogs via the corresponding H-phosphonate intermediates. A new protecting group for the O6 position of 2'-deoxyguanosine, 4-azidobenzyl (ABn) group, was also developed. The ABn group can be quickly removed by treatment with MePPh2 and H2O in the presence of 2-mercaptoethanol.
MeSH term(s)	Boranes/chemistry ; Chemistry, Pharmaceutical/methods ; Chromatography, High Pressure Liquid ; DNA/chemistry ; DNA/metabolism ; Drug Design ; Esters/chemistry ; Guanine/chemistry ; Mercaptoethanol/chemistry ; Models, Chemical ; Molecular Biology/methods ; Molecular Conformation ; Oligodeoxyribonucleotides/chemistry ; Oligonucleotides/chemistry ; Organophosphonates/chemistry ; Phosphates/chemistry
Chemical Substances	Boranes ; Esters ; Oligodeoxyribonucleotides ; Oligonucleotides ; Organophosphonates ; Phosphates ; boranophosphate ; Guanine (5Z93L87A1R) ; Mercaptoethanol (60-24-2) ; DNA (9007-49-2)
Language	English
Publishing date	2008-07-01
Publishing country	England
Document type	Journal Article
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2008.05.053
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Zs.A 3203: Show issues

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Article ; Online: Impact of guanidine-containing backbone linkages on stereopure antisense oligonucleotides in the CNS.

Kandasamy, Pachamuthu / Liu, Yuanjing / Aduda, Vincent / Akare, Sandheep / Alam, Rowshon / Andreucci, Amy / Boulay, David / Bowman, Keith / Byrne, Michael / Cannon, Megan / Chivatakarn, Onanong / Shelke, Juili Dilip / Iwamoto, Naoki / Kawamoto, Tomomi / Kumarasamy, Jayakanthan / Lamore, Sarah / Lemaitre, Muriel / Lin, Xuena / Longo, Kenneth /

Looby, Richard / Marappan, Subramanian / Metterville, Jake / Mohapatra, Susovan / Newman, Bridget / Paik, Ik-Hyeon / Patil, Saurabh / Purcell-Estabrook, Erin / Shimizu, Mamoru / Shum, Pochi / Standley, Stephany / Taborn, Kris / Tripathi, Snehlata / Yang, Hailin / Yin, Yuan / Zhao, Xiansi / Dale, Elena / Vargeese, Chandra

Nucleic acids research

2022 Volume 50, Issue 10, Page(s) 5401–5423

Abstract: Attaining sufficient tissue exposure at the site of action to achieve the desired pharmacodynamic effect on a target is an important determinant for any drug discovery program, and this can be particularly challenging for oligonucleotides in deep tissues ...

Abstract	Attaining sufficient tissue exposure at the site of action to achieve the desired pharmacodynamic effect on a target is an important determinant for any drug discovery program, and this can be particularly challenging for oligonucleotides in deep tissues of the CNS. Herein, we report the synthesis and impact of stereopure phosphoryl guanidine-containing backbone linkages (PN linkages) to oligonucleotides acting through an RNase H-mediated mechanism, using Malat1 and C9orf72 as benchmarks. We found that the incorporation of various types of PN linkages to a stereopure oligonucleotide backbone can increase potency of silencing in cultured neurons under free-uptake conditions 10-fold compared with similarly modified stereopure phosphorothioate (PS) and phosphodiester (PO)-based molecules. One of these backbone types, called PN-1, also yielded profound silencing benefits throughout the mouse brain and spinal cord at low doses, improving both the potency and durability of response, especially in difficult to reach brain tissues. Given these benefits in preclinical models, the incorporation of PN linkages into stereopure oligonucleotides with chimeric backbone modifications has the potential to render regions of the brain beyond the spinal cord more accessible to oligonucleotides and, consequently, may also expand the scope of neurological indications amenable to oligonucleotide therapeutics.
MeSH term(s)	Animals ; Cells, Cultured ; Central Nervous System ; Guanidine/chemistry ; Mice ; Neurons/drug effects ; Oligonucleotides, Antisense/chemistry ; Oligonucleotides, Antisense/pharmacology ; Phosphorothioate Oligonucleotides ; Ribonuclease H/metabolism
Chemical Substances	Oligonucleotides, Antisense ; Phosphorothioate Oligonucleotides ; Ribonuclease H (EC 3.1.26.4) ; Guanidine (JU58VJ6Y3B)
Language	English
Publishing date	2022-01-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac037
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Zs.A 1067: Show issues

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Article ; Online: Endogenous ADAR-mediated RNA editing in non-human primates using stereopure chemically modified oligonucleotides.

Monian, Prashant / Shivalila, Chikdu / Lu, Genliang / Shimizu, Mamoru / Boulay, David / Bussow, Karley / Byrne, Michael / Bezigian, Adam / Chatterjee, Arindom / Chew, David / Desai, Jigar / Favaloro, Frank / Godfrey, Jack / Hoss, Andrew / Iwamoto, Naoki / Kawamoto, Tomomi / Kumarasamy, Jayakanthan / Lamattina, Anthony / Lindsey, Amber /

Liu, Fangjun / Looby, Richard / Marappan, Subramanian / Metterville, Jake / Murphy, Ronelle / Rossi, Jeff / Pu, Tom / Bhattarai, Bijay / Standley, Stephany / Tripathi, Snehlata / Yang, Hailin / Yin, Yuan / Yu, Hui / Zhou, Cong / Apponi, Luciano H / Kandasamy, Pachamuthu / Vargeese, Chandra

Nature biotechnology

2022 Volume 40, Issue 7, Page(s) 1093–1102

Abstract: Technologies that recruit and direct the activity of endogenous RNA-editing enzymes to specific cellular RNAs have therapeutic potential, but translating them from cell culture into animal models has been challenging. Here we describe short, chemically ... ...

Abstract	Technologies that recruit and direct the activity of endogenous RNA-editing enzymes to specific cellular RNAs have therapeutic potential, but translating them from cell culture into animal models has been challenging. Here we describe short, chemically modified oligonucleotides called AIMers that direct efficient and specific A-to-I editing of endogenous transcripts by endogenous adenosine deaminases acting on RNA (ADAR) enzymes, including the ubiquitously and constitutively expressed ADAR1 p110 isoform. We show that fully chemically modified AIMers with chimeric backbones containing stereopure phosphorothioate and nitrogen-containing linkages based on phosphoryl guanidine enhanced potency and editing efficiency 100-fold compared with those with uniformly phosphorothioate-modified backbones in vitro. In vivo, AIMers targeted to hepatocytes with N-acetylgalactosamine achieve up to 50% editing with no bystander editing of the endogenous ACTB transcript in non-human primate liver, with editing persisting for at least one month. These results support further investigation of the therapeutic potential of stereopure AIMers.
MeSH term(s)	Animals ; Oligonucleotides ; Primates/genetics ; Primates/metabolism ; RNA ; RNA Editing/genetics ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism
Chemical Substances	Oligonucleotides ; RNA-Binding Proteins ; RNA (63231-63-0)
Language	English
Publishing date	2022-03-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-022-01225-1
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Zs.A 2167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 137: Show issues
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Article: Solid-phase synthesis of oligodeoxyribonucleoside boranophosphates by the boranophosphotriester method.

Shimizu, Mamoru / Saigo, Kazuhiko / Wada, Takeshi

The Journal of organic chemistry

2006 Volume 71, Issue 11, Page(s) 4262–4269

Abstract: Oligodeoxyribonucleoside boranophosphates (BH3-ODNs), containing four kinds of nucleobases, were synthesized by the solid-phase boranophosphotriester method. The 2'-deoxyribonucleoside 3'-boranophosphate monomers having 2-cyanoethyl (CE) groups as the ... ...

Abstract	Oligodeoxyribonucleoside boranophosphates (BH3-ODNs), containing four kinds of nucleobases, were synthesized by the solid-phase boranophosphotriester method. The 2'-deoxyribonucleoside 3'-boranophosphate monomers having 2-cyanoethyl (CE) groups as the phosphorus protecting groups were synthesized in good yields. A new condensing reagent, 1,3-dimethyl-2-(3-nitro-1,2,4-triazol-1-yl)-2-pyrrolidin-1-yl-1,3,2-diazaphospholidinium hexafluorophosphate, was found to be highly effective for the condensation reaction on the solid support. We also found that 1,8-bis(N,N-dimethylamino)naphthalene could accelerate the condensation reaction without causing beta-elimination of the CE groups from the boranophosphate triesters. The internucleotidic CE groups were selectively removed by treatment with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) under anhydrous conditions. The acetylation of the terminal 5'-hydroxy group was found to be effective to suppress the decomposition of the BH3-ODNs during the DBU treatment on the solid support. Under optimized conditions for the solid-phase synthesis and the deprotection reactions, BH3-ODNs (4mers and 12mers) containing four kinds of nucleobases were synthesized in good yields. The hybridization properties of the BH3-ODN 12mers with the complementary native DNAs and RNAs were determined by the thermal denaturing studies. In contrast to the low thermal melting (Tm) value of the duplex composed of T((PB)T)11 and native dA12 (12.8 degrees C), the duplex consisting of d(C(PB)A(PB)G(PB)T)3 and d(ACTG)3 showed a higher Tm value (44.7 degrees C) under high-salt conditions. Furthermore, d(C(PB)A(PB)G(PB)T)3 formed a more stable duplex with the complementary RNA, r(ACUG)3 with a Tm value of 50.5 degrees C. Thus, we first demonstrated that the binding affinity of BH3-ODN to a complementary DNA or RNA is dramatically increased, owing to the inclusion of the four kinds of nucleobases.
MeSH term(s)	Boranes/chemistry ; Molecular Structure ; Oligodeoxyribonucleotides/chemistry ; Phosphates/chemistry
Chemical Substances	Boranes ; Oligodeoxyribonucleotides ; Phosphates ; boranophosphate
Language	English
Publishing date	2006-05-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	123490-0
ISSN	1520-6904 ; 0022-3263
ISSN (online)	1520-6904
ISSN	0022-3263
DOI	10.1021/jo0603779
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Zs.A 4473: Show issues

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Article ; Online: A novel method for the synthesis of DNA and its analogs by the use of BH3 as a protecting group for phosphonic acid.

Kawanaka, Toshihide / Shimizu, Mamoru / Saigo, Kazuhiko / Wada, Takeshi

Nucleic acids symposium series (2004)

2005 , Issue 49, Page(s) 27–28

Abstract: Recently, we have developed a novel reaction for the transformation of boranophosphate diesters to the corresponding H-phosphonate diesters in the presence of trityl cation under acidic conditions. In this study, DNA and backbone-modified DNA analogs ... ...

Abstract	Recently, we have developed a novel reaction for the transformation of boranophosphate diesters to the corresponding H-phosphonate diesters in the presence of trityl cation under acidic conditions. In this study, DNA and backbone-modified DNA analogs were synthesized in good yields upon applying this reaction. We report the transformation of boranophosphate DNAs, fully protected with 2-azidomethylbenzoyl groups, to various backbone-modified DNA analogs via the H-phosphonate intermediates in solution and on a solid support.
MeSH term(s)	Biochemistry/methods ; Boranes/chemistry ; DNA/chemical synthesis ; DNA/chemistry ; Organophosphonates/chemistry ; Phosphates/chemistry
Chemical Substances	Boranes ; Organophosphonates ; Phosphates ; boranophosphate ; DNA (9007-49-2)
Language	English
Publishing date	2005
Publishing country	England
Document type	Journal Article
ZDB-ID	2205588-5
ISSN	1746-8272 ; 1362-4962 ; 0305-1048 ; 0261-3166
ISSN (online)	1746-8272 ; 1362-4962
ISSN	0305-1048 ; 0261-3166
DOI	10.1093/nass/49.1.27
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