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Wang R, Wang X, Xie S, Zhang Y, Ji D, Zhang X, Cui C, Jiang J, Tan W. Molecular elements: novel approaches for molecular building. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220024. [PMID: 36633277 PMCID: PMC9835600 DOI: 10.1098/rstb.2022.0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Classically, a molecular element (ME) is a pure substance composed of two or more atoms of the same element. However, MEs, in the context of this review, can be any molecules as elements bonded together into the backbone of synthetic oligonucleotides (ONs) with designed sequences and functions, including natural A, T, C, G, U, and unnatural bases. The use of MEs can facilitate the synthesis of designer molecules and smart materials. In particular, we discuss the landmarks associated with DNA structure and related technologies, as well as the extensive application of ONs, the ideal type of molecules for intervention therapy aimed at correcting disease-causing genetic errors (indels). It is herein concluded that the discovery of ON therapeutics and the fabrication of designer molecules or nanostructures depend on the ME concept that we previously published. Accordingly, ME will be our focal point as we discuss related research directions and perspectives in making molecules and materials. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Ruowen Wang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Xueqiang Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Sitao Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Yanyan Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Dingkun Ji
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
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Hofmeister A, Jahn-Hofmann K, Brunner B, Helms M, Metz-Weidmann C, Krack A, Kurz M, Heubel C, Scheidler S. Small Interfering RNAs Containing Dioxane- and Morpholino-Derived Nucleotide Analogues Show Improved Off-Target Profiles and Chirality-Dependent In Vivo Knock-Down. J Med Chem 2022; 65:13736-13752. [PMID: 36223135 DOI: 10.1021/acs.jmedchem.2c00873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To expand the applicability of recently developed dioxane- and morpholino-based nucleotide analogues, their seed region destabilizing properties in small interfering RNAs (siRNAs) were investigated in order to improve potential off-target profiles. For this purpose, the corresponding adenosine analogues were synthesized in two diastereomeric series as building blocks for the automated oligonucleotide synthesis. The obtained nucleotide precursors were integrated at position 7 of an siRNA antisense strand, targeting transthyretin messenger RNA. Evaluation of the melting temperatures revealed significant differences in the obtained duplex stabilities between the two diastereomeric series, while the influence of the central scaffold was small. All siRNAs containing these novel nucleotide structures showed improved off-target profiles in vitro compared to their parent sequence with the common 2'-OMe-modified adenosine at the same position. In contrast, in vivo potencies were highly dependent on the chirality within the six-membered nucleotide scaffolds and showed high mRNA downregulations for the (2R,6R)-configured diastereomers.
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Affiliation(s)
- Armin Hofmeister
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | | | - Bodo Brunner
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Mike Helms
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | | | - Arne Krack
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Michael Kurz
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Christoph Heubel
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Sabine Scheidler
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
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Hofmeister A, Jahn-Hofmann K, Brunner B, Helms MW, Metz-Weidmann C, Krack A, Kurz M, Li Z, Weitzenberg MM, Pflimlin E, Plettenburg O, Scheidler S. Syntheses of Morpholine-Based Nucleotide Analogs for Hepatic siRNA Targeting and Stabilization. J Med Chem 2021; 64:6838-6855. [PMID: 33950677 DOI: 10.1021/acs.jmedchem.1c00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A morpholine-based nucleotide analog was developed as a building block for hepatic siRNA targeting and stabilization. Attachment of an asialoglycoprotein-binding GalNAc ligand at the morpholine nitrogen was realized with different linkers. The obtained morpholino GalNAc scaffolds were coupled to the sense strand of a transthyretin-targeting siRNA and tested for their knockdown potency in vitro and in vivo. A clear structure-activity relationship was developed with regard to the linker type and length as well as the attachment site of the morpholino GalNAc moieties at the siRNA sense strand. Further, simple alkylation of the morpholine nitrogen led to a nucleotide analog, which increased siRNA stability, when used as a double 3'-overhang at the sense strand sequence. Combination of the best morpholino GalNAc building blocks as targeting nucleotides with an optimized stabilizing alkyl-substituted morpholine as 3'-overhangs resulted in siRNAs without any phosphorothioate stabilization in the sense strand and clearly improved the duration of action in vivo.
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Affiliation(s)
- Armin Hofmeister
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | | | - Bodo Brunner
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | - Mike W Helms
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | | | - Arne Krack
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | - Michael Kurz
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | - Ziyu Li
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
| | - Merle M Weitzenberg
- Institute of Organic Chemistry, Center of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Hannover 30167, Germany.,Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Institute of Medicinal Chemistry (IMC), Neuherberg 85764, Germany
| | | | - Oliver Plettenburg
- Institute of Organic Chemistry, Center of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Hannover 30167, Germany.,Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Institute of Medicinal Chemistry (IMC), Neuherberg 85764, Germany
| | - Sabine Scheidler
- Sanofi R&D, Industrial Park Hoechst, G838, Frankfurt am Main 65926, Germany
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The Protective A673T Mutation of Amyloid Precursor Protein (APP) in Alzheimer's Disease. Mol Neurobiol 2021; 58:4038-4050. [PMID: 33914267 DOI: 10.1007/s12035-021-02385-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/05/2021] [Indexed: 10/21/2022]
Abstract
Alzheimer's disease is a progressive neurodegenerative disorder characterized by extracellular amyloid beta peptides and neurofibrillary tangles consisted of intracellular hyperphosphorylated Tau in the hippocampus and cerebral cortex. Most of the mutations in key genes that code for amyloid precursor protein can lead to significant accumulation of these peptides in the brain and cause Alzheimer's disease. Moreover, some point mutations in amyloid precursor protein can cause familial Alzheimer's disease, such as Swedish mutation (KM670/671NL) and A673V mutation. However, recent studies have found that the A673T mutation in amyloid precursor protein gene can protect against Alzheimer's disease, even if it is located next to the Swedish mutation (KM670/671NL) and at the same site as A673V mutation, which are pathogenic. It makes us curious about the protective A673T mutation. Here, we summarize the most recent insights of A673T mutation, focus on their roles in protective mechanisms against Alzheimer's disease, and discuss their involvement in future treatment.
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Patisiran in hATTR Amyloidosis: Six-Month Latency Period before Efficacy. Brain Sci 2021; 11:brainsci11040515. [PMID: 33921571 PMCID: PMC8073153 DOI: 10.3390/brainsci11040515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 01/29/2023] Open
Abstract
Hereditary amyloidosis associated with mutations in the transthyretin gene (hATTR) is a progressive devastating disease, with a fatal outcome occurring within 10years after onset. In recent years, TTR gene silencing therapy appeared as a promising therapeutic strategy, showing evidence that disease progression can be slowed and perhaps reversed. We report here 18 subjects affected by hATTR amyloidosis treated with patisiran, a small interfering RNA acting as TTR silencer, and evaluated with a PND score, the NIS and NIS-LL scale, and a Norfolk QOL-DN questionnaire at baseline and then every 6 months. A global clinical stabilizationwas observed for the majority of the patients, with mild-moderate improvements in some cases, even in advanced disease stage (PND score > 2). Analysis of NIS, NIS-LL and Norfolk QOL-DN results, and PND score variation suggest the possible presence of a 6-month latency period prior to benefit of treatment.
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Perlini S, Mussinelli R, Salinaro F. New effective treatment options reinforce disease awareness: the case of transthyretin cardiac amyloidosis. Eur J Heart Fail 2021; 23:290-292. [PMID: 33527646 DOI: 10.1002/ejhf.2111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/27/2021] [Indexed: 11/07/2022] Open
Affiliation(s)
- Stefano Perlini
- Emergency Medicine, Vascular and Metabolic Disease Unit, Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation, University of Pavia, Pavia, Italy.,Amyloidosis Research and Treatment Center, IRCCS Policlinico San Matteo Foundation, University of Pavia, Pavia, Italy
| | - Roberta Mussinelli
- Amyloidosis Research and Treatment Center, IRCCS Policlinico San Matteo Foundation, University of Pavia, Pavia, Italy
| | - Francesco Salinaro
- Emergency Medicine, Vascular and Metabolic Disease Unit, Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation, University of Pavia, Pavia, Italy
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Kubo T, Nishimura Y, Sato Y, Yanagihara K, Seyama T. Sixteen Different Types of Lipid-Conjugated siRNAs Containing Saturated and Unsaturated Fatty Acids and Exhibiting Enhanced RNAi Potency. ACS Chem Biol 2021; 16:150-164. [PMID: 33346648 DOI: 10.1021/acschembio.0c00847] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SiRNAs are strong gene-silencing agents that function in a target sequence-specific manner. Although siRNAs might one day be used in therapy for intractable diseases such as cancers, a number of problems with siRNAs must first be overcome. In this study, we developed 16 different types of lipid-conjugated siRNAs (lipid-siRNAs) that could effectively inhibit the expression of target genes. We determined the hybridization properties, cellular uptake efficacies, and RNAi potencies of the resulting lipid-siRNAs. The lipid-siRNAs exhibited a mild interaction with Lipofectamine RNAiMAX (LFRNAi) as a transfection reagent, and a high membrane permeability was observed in all lipid-siRNAs-LFRNAi complexes; the conjugate siRNAs composed of 16-18 carbon chains as fatty acids showed an especially good cellular uptake efficacy. The in vitro RNAi effect of lipid-siRNAs targeted to a β-catenin gene exhibited a strong RNAi potency compared with those of unmodified siRNAs. In particular, the conjugate siRNAs composed of 16-18 carbon chains as fatty acids showed excellent RNAi potencies with prolonged effectivities. Interestingly, the RNAi potencies of conjugate siRNAs containing 18 carbon chains with a trans-form (elaidic acid and trans-vaccenic acid) were inferior to those of the carbon chains with a cis-form (oleic acid and cis-vaccenic acid). These lipid-siRNAs can solve the many problems hindering the clinical application of siRNAs.
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Affiliation(s)
| | | | | | - Kazuyoshi Yanagihara
- Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Chiba 277-8577, Japan
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AL Qtaish N, Gallego I, Villate-Beitia I, Sainz-Ramos M, López-Méndez TB, Grijalvo S, Eritja R, Soto-Sánchez C, Martínez-Navarrete G, Fernández E, Puras G, Pedraz JL. Niosome-Based Approach for In Situ Gene Delivery to Retina and Brain Cortex as Immune-Privileged Tissues. Pharmaceutics 2020; 12:pharmaceutics12030198. [PMID: 32106545 PMCID: PMC7150807 DOI: 10.3390/pharmaceutics12030198] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 01/02/2023] Open
Abstract
Non-viral vectors have emerged as a promising alternative to viral gene delivery systems due to their safer profile. Among non-viral vectors, recently, niosomes have shown favorable properties for gene delivery, including low toxicity, high stability, and easy production. The three main components of niosome formulations include a cationic lipid that is responsible for the electrostatic interactions with the negatively charged genetic material, a non-ionic surfactant that enhances the long-term stability of the niosome, and a helper component that can be added to improve its physicochemical properties and biological performance. This review is aimed at providing recent information about niosome-based non-viral vectors for gene delivery purposes. Specially, we will discuss the composition, preparation methods, physicochemical properties, and biological evaluation of niosomes and corresponding nioplexes that result from the addition of the genetic material onto their cationic surface. Next, we will focus on the in situ application of such niosomes to deliver the genetic material into immune-privileged tissues such as the brain cortex and the retina. Finally, as future perspectives, non-invasive administration routes and different targeting strategies will be discussed.
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Affiliation(s)
- Nuseibah AL Qtaish
- NanoBioCel group, University of the Basque Country (UPV/EHU), E-01006 Vitoria-Gasteiz, Spain; (N.A.Q.); (I.G.); (I.V.-B.); (M.S.-R.); (T.B.L.-M.)
- Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-01006 Vitoria-Gasteiz, Spain
| | - Idoia Gallego
- NanoBioCel group, University of the Basque Country (UPV/EHU), E-01006 Vitoria-Gasteiz, Spain; (N.A.Q.); (I.G.); (I.V.-B.); (M.S.-R.); (T.B.L.-M.)
- Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-01006 Vitoria-Gasteiz, Spain
| | - Ilia Villate-Beitia
- NanoBioCel group, University of the Basque Country (UPV/EHU), E-01006 Vitoria-Gasteiz, Spain; (N.A.Q.); (I.G.); (I.V.-B.); (M.S.-R.); (T.B.L.-M.)
- Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-01006 Vitoria-Gasteiz, Spain
| | - Myriam Sainz-Ramos
- NanoBioCel group, University of the Basque Country (UPV/EHU), E-01006 Vitoria-Gasteiz, Spain; (N.A.Q.); (I.G.); (I.V.-B.); (M.S.-R.); (T.B.L.-M.)
- Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-01006 Vitoria-Gasteiz, Spain
| | - Tania Belén López-Méndez
- NanoBioCel group, University of the Basque Country (UPV/EHU), E-01006 Vitoria-Gasteiz, Spain; (N.A.Q.); (I.G.); (I.V.-B.); (M.S.-R.); (T.B.L.-M.)
- Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-01006 Vitoria-Gasteiz, Spain
| | - Santiago Grijalvo
- Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain; (S.G.); (R.E.)
- Institute for Advanced Chemistry of Catalonia, (IQAC-CSIC), E-08034 Barcelona, Spain
| | - Ramón Eritja
- Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain; (S.G.); (R.E.)
- Institute for Advanced Chemistry of Catalonia, (IQAC-CSIC), E-08034 Barcelona, Spain
| | - Cristina Soto-Sánchez
- Neuroprothesis and Neuroengineering Research Group, Miguel Hernández University, E-03202 Elche, Spain; (C.S.-S.); (G.M.-N.); (E.F.)
| | - Gema Martínez-Navarrete
- Neuroprothesis and Neuroengineering Research Group, Miguel Hernández University, E-03202 Elche, Spain; (C.S.-S.); (G.M.-N.); (E.F.)
- Networking Research Centre for Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-03202 Elche, Spain
| | - Eduardo Fernández
- Neuroprothesis and Neuroengineering Research Group, Miguel Hernández University, E-03202 Elche, Spain; (C.S.-S.); (G.M.-N.); (E.F.)
- Networking Research Centre for Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-03202 Elche, Spain
| | - Gustavo Puras
- NanoBioCel group, University of the Basque Country (UPV/EHU), E-01006 Vitoria-Gasteiz, Spain; (N.A.Q.); (I.G.); (I.V.-B.); (M.S.-R.); (T.B.L.-M.)
- Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-01006 Vitoria-Gasteiz, Spain
- Correspondence: (G.P.); (J.L.P.); Tel.: +34-945014536 (G.P.); +34-945013091 (J.L.P.)
| | - José Luis Pedraz
- NanoBioCel group, University of the Basque Country (UPV/EHU), E-01006 Vitoria-Gasteiz, Spain; (N.A.Q.); (I.G.); (I.V.-B.); (M.S.-R.); (T.B.L.-M.)
- Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-01006 Vitoria-Gasteiz, Spain
- Correspondence: (G.P.); (J.L.P.); Tel.: +34-945014536 (G.P.); +34-945013091 (J.L.P.)
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