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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: Impact of stereopure chimeric backbone chemistries on the potency and durability of gene silencing by RNA interference.

Liu, Wei / Iwamoto, Naoki / Marappan, Subramanian / Luu, Khoa / Tripathi, Snehlata / Purcell-Estabrook, Erin / Shelke, Juili Dilip / Shah, Himali / Lamattina, Anthony / Pan, Qianli / Schrand, Brett / Favaloro, Frank / Bedekar, Mugdha / Chatterjee, Arindom / Desai, Jigar / Kawamoto, Tomomi / Lu, Genliang / Metterville, Jake / Samaraweera, Milinda /

Prakasha, Priyanka Shiva / Yang, Hailin / Yin, Yuan / Yu, Hui / Giangrande, Paloma H / Byrne, Michael / Kandasamy, Pachamuthu / Vargeese, Chandra

Nucleic acids research

2023 Volume 51, Issue 9, Page(s) 4126–4147

Abstract: Herein, we report the systematic investigation of stereopure phosphorothioate (PS) and phosphoryl guanidine (PN) linkages on siRNA-mediated silencing. The incorporation of appropriately positioned and configured stereopure PS and PN linkages to N- ... ...

Abstract	Herein, we report the systematic investigation of stereopure phosphorothioate (PS) and phosphoryl guanidine (PN) linkages on siRNA-mediated silencing. The incorporation of appropriately positioned and configured stereopure PS and PN linkages to N-acetylgalactosamine (GalNAc)-conjugated siRNAs based on multiple targets (Ttr and HSD17B13) increased potency and durability of mRNA silencing in mouse hepatocytes in vivo compared with reference molecules based on clinically proven formats. The observation that the same modification pattern had beneficial effects on unrelated transcripts suggests that it may be generalizable. The effect of stereopure PN modification on silencing is modulated by 2'-ribose modifications in the vicinity, particularly on the nucleoside 3' to the linkage. These benefits corresponded with both an increase in thermal instability at the 5'-end of the antisense strand and improved Argonaute 2 (Ago2) loading. Application of one of our most effective designs to generate a GalNAc-siRNA targeting human HSD17B13 led to ∼80% silencing that persisted for at least 14 weeks after administration of a single 3 mg/kg subcutaneous dose in transgenic mice. The judicious use of stereopure PN linkages improved the silencing profile of GalNAc-siRNAs without disrupting endogenous RNA interference pathways and without elevating serum biomarkers for liver dysfunction, suggesting they may be suitable for therapeutic application.
MeSH term(s)	Animals ; Humans ; Mice ; Gene Silencing ; Mice, Transgenic ; RNA Interference ; RNA, Messenger/genetics ; RNA, Small Interfering/genetics
Chemical Substances	RNA, Messenger ; RNA, Small Interfering
Language	English
Publishing date	2023-04-18
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/gkad268
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Article: A diversity oriented synthesis of 3'-O-modified nucleoside triphosphates for DNA 'sequencing by synthesis'.

Lu, Genliang / Burgess, Kevin

Bioorganic & medicinal chemistry letters

2006 Volume 16, Issue 15, Page(s) 3902–3905

Abstract: The nucleoside triphosphates 1, containing a photochemically cleavable group, and 2, having one that may be cleaved via palladium catalysis, were prepared as a prelude to investigating sequencing of DNA via sequencing by synthesis. ...

Abstract	The nucleoside triphosphates 1, containing a photochemically cleavable group, and 2, having one that may be cleaved via palladium catalysis, were prepared as a prelude to investigating sequencing of DNA via sequencing by synthesis.
MeSH term(s)	Nucleotides/chemical synthesis ; Sequence Analysis, DNA/methods
Chemical Substances	Nucleotides
Language	English
Publishing date	2006-08-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2006.05.035
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Article: Mechanism of stereoinduction in asymmetric synthesis of highly functionalized 1,2-dihydroquinolines and 2H-1-benzopyrans via nonracemic palladacycles with a metal-bonded stereogenic carbon.

Lu, Genliang / Malinakova, Helena C

The Journal of organic chemistry

2004 Volume 69, Issue 14, Page(s) 4701–4715

Abstract: To establish the synthetic utility of palladacycles, a stable racemic benzannulated azapalladacycle featuring a palladium-bonded sp(3)-hybridized stereogenic carbon was prepared and converted into a series of racemic 2,3,4-trisubstituted 1,2- ... ...

Abstract	To establish the synthetic utility of palladacycles, a stable racemic benzannulated azapalladacycle featuring a palladium-bonded sp(3)-hybridized stereogenic carbon was prepared and converted into a series of racemic 2,3,4-trisubstituted 1,2-dihydroquinolines via a regioselective insertion of activated alkynes (RCCCOOEt). Analogous diastereomerically enriched azapalladacyle (92% de) and oxapalladacycle (64% de) were synthesized from arylpalladium(II) iodo complexes possessing a nonracemic spectator ligand ((1R,2R)-N,N,N',N'-tetramethyl-1,2-diaminocyclohexane) via an intramolecular displacement of the iodide by an ester enolate. Absolute configurations of the metal-bonded stereocenters in the diastereomerically enriched palladacycles were unequivocally assigned, and the efficiency of stereoinduction was systematically studied. On the basis of these experiments, a plausible mechanism for the transfer of chirality from the nonracemic auxiliary ligand to the palladium-bonded stereogenic carbon was proposed. A restricted rotation about the palladium-aryl bond in arylpalladium(II) iodo complexes giving rise to atropisomers, as well as the nature of the leaving group (iodide or acetate), were found to play a crucial role in the chirality transfer process. Diastereomerically enriched palladacycles underwent a ligand exchange with triphenylphosphine followed by regioselective insertion of unsymmetrical alkynes to afford nonracemic 1,2-dihydroquinolines (six examples) in excellent 80-91% ee and 2H-1-benzopyrans (four examples) in 32-56% ee.
Language	English
Publishing date	2004-07-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	123490-0
ISSN	1520-6904 ; 0022-3263
ISSN (online)	1520-6904
ISSN	0022-3263
DOI	10.1021/jo040148r
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Article: Regio- and diastereoselective insertion of allenes into stable oxapalladacycles with a metal-bonded stereogenic carbon. preparation of contiguously substituted 3,4-dihydro-2H-1-benzopyrans.

Lu, Genliang / Malinakova, Helena C

The Journal of organic chemistry

2004 Volume 69, Issue 24, Page(s) 8266–8279

Abstract: Insertion of monosubstituted allenes into stable oxapalladacycle I was studied. The aim of this work was to define steric and electronic parameters of allenes that would allow for a regio- and diastereoselective synthesis of 2,3-disubstituted 3,4-dihydro- ...

Abstract	Insertion of monosubstituted allenes into stable oxapalladacycle I was studied. The aim of this work was to define steric and electronic parameters of allenes that would allow for a regio- and diastereoselective synthesis of 2,3-disubstituted 3,4-dihydro-2H-1-benzopyrans, which could not be prepared via related catalytic protocols. Allenes with electron-donating alkyl substituents R sterically unencumbered at the C-3 and C-4 carbons reacted with palladacycles I to afford benzopyrans IV in good yields (45-81%), exclusively as cis diastereomers. Less than 10% of the regioisomeric benzopyrans V was detected in the crude reaction mixtures. Methoxy 1,2-propadiene afforded benzopyran IV in 98% yield as the trans diastereomer in 92% de. In contrast, allenes with electron-withdrawing substituents yielded benzopyrans V with an E double bond exclusively. Nonracemic palladacycles featuring a palladium-bonded stereogenic carbon as the only element of asymmetry underwent the allene insertion with 63-93% retention of the stereochemical information, providing benzopyrans IV or V in 40-47% ee. These results demonstrated that O-bonded palladium enolates did not operate as predominant intermediates in the insertion process. The study highlights the configurational stability of carbon-bonded palladium ester enolates, especially notable in systems lacking chiral nonracemic auxiliary ligands.
MeSH term(s)	Alkadienes/chemistry ; Benzopyrans/chemical synthesis ; Carbon/chemistry ; Catalysis ; Cyclization ; Molecular Conformation ; Organometallic Compounds/chemical synthesis ; Organometallic Compounds/chemistry ; Palladium/chemistry ; Stereoisomerism
Chemical Substances	Alkadienes ; Benzopyrans ; Organometallic Compounds ; Palladium (5TWQ1V240M) ; Carbon (7440-44-0)
Language	English
Publishing date	2004-11-26
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	123490-0
ISSN	1520-6904 ; 0022-3263
ISSN (online)	1520-6904
ISSN	0022-3263
DOI	10.1021/jo0486847
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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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Article: An iterative route to "decorated" ethylene glycol-based linkers.

Lu, Genliang / Lam, Sang / Burgess, Kevin

Chemical communications (Cambridge, England)

2006 , Issue 15, Page(s) 1652–1654

Abstract: Iterative copper-catalyzed cycloadditions of azides to alkynes were used to join functionalized triethylene glycol molecules to give "linkers" of defined lengths equipped with several different end-group functionalities. ...

Abstract	Iterative copper-catalyzed cycloadditions of azides to alkynes were used to join functionalized triethylene glycol molecules to give "linkers" of defined lengths equipped with several different end-group functionalities.
MeSH term(s)	Alkynes/chemistry ; Azides/chemistry ; Catalysis ; Copper/chemistry ; Cross-Linking Reagents/chemistry ; Ethylene Glycol/chemistry
Chemical Substances	Alkynes ; Azides ; Cross-Linking Reagents ; Copper (789U1901C5) ; Ethylene Glycol (FC72KVT52F)
Language	English
Publishing date	2006-04-21
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/b518061a
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Article: An iterative route to “decorated” ethylene glycol-based linkers

Lu, Genliang / Lam, Sang / Burgess, Kevin

Chemical communications. 2006 Mar. 31, , no. 15

2006

Abstract: Iterative copper-catalyzed cycloadditions of azides to alkynes were used to join functionalized triethylene glycol molecules to give “linkers” of defined lengths equipped with several different end-group functionalities. ...

Abstract	Iterative copper-catalyzed cycloadditions of azides to alkynes were used to join functionalized triethylene glycol molecules to give “linkers” of defined lengths equipped with several different end-group functionalities.
Keywords	alkynes ; azides ; catalytic activity ; cycloaddition reactions ; ethylene ; triethylene glycol
Language	English
Dates of publication	2006-0331
Size	p. 1652-1654.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/b518061a
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Article ; Online: Control of phosphorothioate stereochemistry substantially increases the efficacy of antisense oligonucleotides.

Iwamoto, Naoki / Butler, David C D / Svrzikapa, Nenad / Mohapatra, Susovan / Zlatev, Ivan / Sah, Dinah W Y / Meena / Standley, Stephany M / Lu, Genliang / Apponi, Luciano H / Frank-Kamenetsky, Maria / Zhang, Jason Jingxin / Vargeese, Chandra / Verdine, Gregory L

Nature biotechnology

2017 Volume 35, Issue 9, Page(s) 845–851

Abstract: Whereas stereochemical purity in drugs has become the standard for small molecules, stereoisomeric mixtures containing as many as a half million components persist in antisense oligonucleotide (ASO) therapeutics because it has been feasible neither to ... ...

Abstract	Whereas stereochemical purity in drugs has become the standard for small molecules, stereoisomeric mixtures containing as many as a half million components persist in antisense oligonucleotide (ASO) therapeutics because it has been feasible neither to separate the individual stereoisomers, nor to synthesize stereochemically pure ASOs. Here we report the development of a scalable synthetic process that yields therapeutic ASOs having high stereochemical and chemical purity. Using this method, we synthesized rationally designed stereopure components of mipomersen, a drug comprising 524,288 stereoisomers. We demonstrate that phosphorothioate (PS) stereochemistry substantially affects the pharmacologic properties of ASOs. We report that Sp-configured PS linkages are stabilized relative to Rp, providing stereochemical protection from pharmacologic inactivation of the drug. Further, we elucidated a triplet stereochemical code in the stereopure ASOs, 3'-SpSpRp, that promotes target RNA cleavage by RNase H1 in vitro and provides a more durable response in mice than stereorandom ASOs.
MeSH term(s)	Animals ; Drug Stability ; Female ; Genetic Therapy/methods ; Humans ; Hydrophobic and Hydrophilic Interactions ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Oligonucleotides ; Oligonucleotides, Antisense/chemistry ; Oligonucleotides, Antisense/pharmacokinetics ; Oligonucleotides, Antisense/therapeutic use ; Phosphorothioate Oligonucleotides/chemistry ; Rats ; Rats, Sprague-Dawley ; Ribonuclease H/metabolism ; Stereoisomerism
Chemical Substances	Oligonucleotides ; Oligonucleotides, Antisense ; Phosphorothioate Oligonucleotides ; mipomersen (9GJ8S4GU0M) ; Ribonuclease H (EC 3.1.26.4) ; ribonuclease HI (EC 3.1.26.4)
Language	English
Publishing date	2017-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/nbt.3948
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Article ; Online: Universal peptidomimetics.

Ko, Eunhwa / Liu, Jing / Perez, Lisa M / Lu, Genliang / Schaefer, Amber / Burgess, Kevin

Journal of the American Chemical Society

2010 Volume 133, Issue 3, Page(s) 462–477

Abstract: This paper concerns peptidomimetic scaffolds that can present side chains in conformations resembling those of amino acids in secondary structures without incurring excessive entropic or enthalpic penalties. Compounds of this type are referred to here as ...

Abstract	This paper concerns peptidomimetic scaffolds that can present side chains in conformations resembling those of amino acids in secondary structures without incurring excessive entropic or enthalpic penalties. Compounds of this type are referred to here as minimalist mimics. The core hypothesis of this paper is that small sets of such scaffolds can be designed to analogue local pairs of amino acids (including noncontiguous ones) in any secondary structure; i.e., they are universal peptidomimetics. To illustrate this concept, we designed a set of four peptidomimetic scaffolds. Libraries based on them were made bearing side chains corresponding to many of the protein-derived amino acids. Modeling experiments were performed to give an indication of kinetic and thermodynamic accessibilities of conformations that can mimic secondary structures. Together, peptidomimetics based on these four scaffolds can adopt conformations that resemble almost any combination of local amino acid side chains in any secondary structure. Universal peptidomimetics of this kind are likely to be most useful in the design of libraries for high-throughput screening against diverse targets. Consequently, data arising from submission of these molecules to the NIH Molecular Libraries Small Molecule Repository (MLSMR) are outlined.
MeSH term(s)	Kinetics ; Models, Molecular ; Peptidomimetics ; Protein Structure, Secondary ; Quantum Theory ; Thermodynamics
Chemical Substances	Peptidomimetics
Language	English
Publishing date	2010-12-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/ja1071916
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