1
|
Le BT, Chen S, Veedu RN. Rational Design of Chimeric Antisense Oligonucleotides on a Mixed PO-PS Backbone for Splice-Switching Applications. Biomolecules 2024; 14:883. [PMID: 39062597 PMCID: PMC11274656 DOI: 10.3390/biom14070883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 07/15/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024] Open
Abstract
Synthetic antisense oligonucleotides (ASOs) are emerging as an attractive platform to treat various diseases. By specifically binding to a target mRNA transcript through Watson-Crick base pairing, ASOs can alter gene expression in a desirable fashion to either rescue loss of function or downregulate pathogenic protein expression. To be clinically relevant, ASOs are generally synthesized using modified analogs to enhance resistance to enzymatic degradation and pharmacokinetic and dynamic properties. Phosphorothioate (PS) belongs to the first generation of modified analogs and has played a vital role in the majority of approved ASO drugs, mainly based on the RNase H mechanism. In contrast to RNase H-dependent ASOs that bind and cleave target mature mRNA, splice-switching oligonucleotides (SSOs) mainly bind and alter precursor mRNA splicing in the cell nucleus. To date, only one approved SSO (Nusinersen) possesses a PS backbone. Typically, the synthesis of PS oligonucleotides generates two types of stereoisomers that could potentially impact the ASO's pharmaco-properties. This can be limited by introducing the naturally occurring phosphodiester (PO) linkage to the ASO sequence. In this study, towards fine-tuning the current strategy in designing SSOs, we reported the design, synthesis, and evaluation of several stereo-random SSOs on a mixed PO-PS backbone for their binding affinity, biological potency, and nuclease stability. Based on the results, we propose that a combination of PO and PS linkages could represent a promising approach toward limiting undesirable stereoisomers while not largely compromising the efficacy of SSOs.
Collapse
Affiliation(s)
- Bao T. Le
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (B.T.L.); (S.C.)
- ProGenis Pharmaceuticals Pty Ltd., Bentley, WA 6102, Australia
| | - Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (B.T.L.); (S.C.)
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (B.T.L.); (S.C.)
- ProGenis Pharmaceuticals Pty Ltd., Bentley, WA 6102, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| |
Collapse
|
2
|
Rigal S, Casas B, Kanebratt KP, Wennberg Huldt C, Magnusson LU, Müllers E, Karlsson F, Clausen M, Hansson SF, Leonard L, Cairns J, Jansson Löfmark R, Ämmälä C, Marx U, Gennemark P, Cedersund G, Andersson TB, Vilén LK. Normoglycemia and physiological cortisone level maintain glucose homeostasis in a pancreas-liver microphysiological system. Commun Biol 2024; 7:877. [PMID: 39025915 PMCID: PMC11258270 DOI: 10.1038/s42003-024-06514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 06/26/2024] [Indexed: 07/20/2024] Open
Abstract
Current research on metabolic disorders and diabetes relies on animal models because multi-organ diseases cannot be well studied with standard in vitro assays. Here, we have connected cell models of key metabolic organs, the pancreas and liver, on a microfluidic chip to enable diabetes research in a human-based in vitro system. Aided by mechanistic mathematical modeling, we demonstrate that hyperglycemia and high cortisone concentration induce glucose dysregulation in the pancreas-liver microphysiological system (MPS), mimicking a diabetic phenotype seen in patients with glucocorticoid-induced diabetes. In this diseased condition, the pancreas-liver MPS displays beta-cell dysfunction, steatosis, elevated ketone-body secretion, increased glycogen storage, and upregulated gluconeogenic gene expression. Conversely, a physiological culture condition maintains glucose tolerance and beta-cell function. This method was reproducible in two laboratories and was effective in multiple pancreatic islet donors. The model also provides a platform to identify new therapeutic proteins, as demonstrated with a combined transcriptome and proteome analysis.
Collapse
Affiliation(s)
| | - Belén Casas
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Kajsa P Kanebratt
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Charlotte Wennberg Huldt
- Bioscience Metabolism, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lisa U Magnusson
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Erik Müllers
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Karlsson
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Maryam Clausen
- Translational Genomics, Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Sara F Hansson
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Louise Leonard
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan Cairns
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Rasmus Jansson Löfmark
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Carina Ämmälä
- Bioscience Metabolism, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Peter Gennemark
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Gunnar Cedersund
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden
- Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Tommy B Andersson
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Liisa K Vilén
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
- Division of Pharmaceutical Biosciences, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
3
|
Delibegović M, Dall'Angelo S, Dekeryte R. Protein tyrosine phosphatase 1B in metabolic diseases and drug development. Nat Rev Endocrinol 2024; 20:366-378. [PMID: 38519567 DOI: 10.1038/s41574-024-00965-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2024] [Indexed: 03/25/2024]
Abstract
Protein tyrosine phosphatase 1B (PTP1B), a non-transmembrane phosphatase, has a major role in a variety of signalling pathways, including direct negative regulation of classic insulin and leptin signalling pathways, and is implicated in the pathogenesis of several cardiometabolic diseases and cancers. As such, PTP1B has been a therapeutic target for over two decades, with PTP1B inhibitors identified either from natural sources or developed throughout the years. Some of these inhibitors have reached phase I and/or II clinical trials in humans for the treatment of type 2 diabetes mellitus, obesity and/or metastatic breast cancer. In this Review, we summarize the cellular processes and regulation of PTP1B, discuss evidence from in vivo preclinical and human studies of the association between PTP1B and different disorders, and discuss outcomes of clinical trials. We outline challenges associated with the targeting of this phosphatase (which was, until the past few years, viewed as difficult to target), the current state of the field of PTP1B inhibitors (and dual phosphatase inhibitors) and future directions for manipulating the activity of this key metabolic enzyme.
Collapse
Affiliation(s)
- Mirela Delibegović
- Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK.
| | - Sergio Dall'Angelo
- Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK
| | - Ruta Dekeryte
- Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK
| |
Collapse
|
4
|
Li Y, Chen S, Rahimizadeh K, Zhang Z, Veedu RN. Inhibition of survivin by 2'- O-methyl phosphorothioate-modified steric-blocking antisense oligonucleotides. RSC Adv 2024; 14:13336-13341. [PMID: 38660533 PMCID: PMC11040434 DOI: 10.1039/d4ra01925c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Chemically modified antisense oligonucleotide (ASO) has been established as a successful therapeutic strategy for treating various human diseases. To date, ten ASO drugs, which are capable of either inducing mRNA degradation via RNase H recruitment (fomivirsen, mipomersen, inotersen, volanesorsen and tofersen) or splice modulation (eteplirsen, nusinersen, golodirsen, viltolarsen and casimersen), have been approved by the regulatory agencies for market entry. Nonetheless, none of these approved drugs are prescribed as cancer therapy. Towards this, we have developed steric-blocking ASOs targeting BIRC5 - a well-validated oncogene. Initial screening was performed by transfection of HepG2 cells with seven BIRC5 exon-2 targeting, uniformly 2'-OMe-PS modified ASOs at 400 nM respectively, leading to the identification of two best-performing candidates ASO-2 and ASO-7 in reducing the production of BIRC5 mRNA. Subsequent dose-response assay was conducted via transfection of HepG2 cells by different concentrations (400, 200, 100, 50, 25 nM) of ASO-2 and ASO-7 respectively, showing that both ASOs consistently and efficiently inhibited BIRC5 mRNA expression in a dose-dependent manner. Furthermore, western blot analysis confirmed that ASO-7 could significantly repress survivin production on protein level. Based on our preliminary results, we believe that ASO-7 could be a useful BIRC5 inhibitor for both research purpose and therapeutic development.
Collapse
Affiliation(s)
- Yalin Li
- School of Food and Biological Engineering, Henan University of Animal Husbandry and Economy Zhengzhou 450018 China
| | - Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University Murdoch 6150 Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science Nedlands WA 6009 Australia
| | - Kamal Rahimizadeh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University Murdoch 6150 Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science Nedlands WA 6009 Australia
| | - Zhen Zhang
- School of Food and Biological Engineering, Henan University of Animal Husbandry and Economy Zhengzhou 450018 China
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University Murdoch 6150 Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science Nedlands WA 6009 Australia
| |
Collapse
|
5
|
Chen S, Heendeniya SN, Le BT, Rahimizadeh K, Rabiee N, Zahra QUA, Veedu RN. Splice-Modulating Antisense Oligonucleotides as Therapeutics for Inherited Metabolic Diseases. BioDrugs 2024; 38:177-203. [PMID: 38252341 PMCID: PMC10912209 DOI: 10.1007/s40259-024-00644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2024] [Indexed: 01/23/2024]
Abstract
The last decade (2013-2023) has seen unprecedented successes in the clinical translation of therapeutic antisense oligonucleotides (ASOs). Eight such molecules have been granted marketing approval by the United States Food and Drug Administration (US FDA) during the decade, after the first ASO drug, fomivirsen, was approved much earlier, in 1998. Splice-modulating ASOs have also been developed for the therapy of inborn errors of metabolism (IEMs), due to their ability to redirect aberrant splicing caused by mutations, thus recovering the expression of normal transcripts, and correcting the deficiency of functional proteins. The feasibility of treating IEM patients with splice-switching ASOs has been supported by FDA permission (2018) of the first "N-of-1" study of milasen, an investigational ASO drug for Batten disease. Although for IEM, owing to the rarity of individual disease and/or pathogenic mutation, only a low number of patients may be treated by ASOs that specifically suppress the aberrant splicing pattern of mutant precursor mRNA (pre-mRNA), splice-switching ASOs represent superior individualized molecular therapeutics for IEM. In this work, we first summarize the ASO technology with respect to its mechanisms of action, chemical modifications of nucleotides, and rational design of modified oligonucleotides; following that, we precisely provide a review of the current understanding of developing splice-modulating ASO-based therapeutics for IEM. In the concluding section, we suggest potential ways to improve and/or optimize the development of ASOs targeting IEM.
Collapse
Affiliation(s)
- Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Saumya Nishanga Heendeniya
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Bao T Le
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
- ProGenis Pharmaceuticals Pty Ltd, Bentley, WA, 6102, Australia
| | - Kamal Rahimizadeh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Navid Rabiee
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Qurat Ul Ain Zahra
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA, 6009, Australia.
- ProGenis Pharmaceuticals Pty Ltd, Bentley, WA, 6102, Australia.
| |
Collapse
|
6
|
Yang K, Xiao Y, Zhong L, Zhang W, Wang P, Ren Y, Shi L. p53-regulated lncRNAs in cancers: from proliferation and metastasis to therapy. Cancer Gene Ther 2023; 30:1456-1470. [PMID: 37679529 DOI: 10.1038/s41417-023-00662-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been identified as master gene regulators through various mechanisms such as transcription, translation, protein modification and RNA-protein complexes. LncRNA dysregulation is frequently associated with a variety of biological functions and human diseases including cancer. The p53 network is a key tumor-suppressive mechanism that transcriptionally activates target genes to suppress cellular proliferation in human malignancies. Recent research indicates that lncRNAs play an important role in the p53 signaling pathway. In this review, we summarize the current knowledge of lncRNAs in p53-relevant functions and provide an overview of how these altered lncRNAs contribute to tumor initiation and progression. We also discuss the association between lncRNA and up- or downstream genes of p53. These findings imply that lncRNAs can help identify cellular vulnerabilities that may prove to be promising potential biomarkers and therapeutic targets for cancer treatment.
Collapse
Affiliation(s)
- Kaixin Yang
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Yinan Xiao
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Linghui Zhong
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Wenyang Zhang
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Peng Wang
- College of Animal Science and Technology, Hebei North University, Zhangjiakou, 075131, People's Republic of China
| | - Yaru Ren
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Lei Shi
- RNA Oncology Group, School of Public Health, Lanzhou University, Lanzhou, 730000, People's Republic of China.
| |
Collapse
|
7
|
Mehta M, Raguraman R, Ramesh R, Munshi A. RNA binding proteins (RBPs) and their role in DNA damage and radiation response in cancer. Adv Drug Deliv Rev 2022; 191:114569. [PMID: 36252617 PMCID: PMC10411638 DOI: 10.1016/j.addr.2022.114569] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 01/24/2023]
Abstract
Traditionally majority of eukaryotic gene expression is influenced by transcriptional and post-transcriptional events. Alterations in the expression of proteins that act post-transcriptionally can affect cellular signaling and homeostasis. RNA binding proteins (RBPs) are a family of proteins that specifically bind to RNAs and are involved in post-transcriptional regulation of gene expression and important cellular processes such as cell differentiation and metabolism. Deregulation of RNA-RBP interactions and any changes in RBP expression or function can lead to various diseases including cancer. In cancer cells, RBPs play an important role in regulating the expression of tumor suppressors and oncoproteins involved in various cell-signaling pathways. Several RBPs such as HuR, AUF1, RBM38, LIN28, RBM24, tristetrapolin family and Musashi play critical roles in various types of cancers and their aberrant expression in cancer cells makes them an attractive therapeutic target for cancer treatment. In this review we provide an overview of i). RBPs involved in cancer progression and their mechanism of action ii). the role of RBPs, including HuR, in breast cancer progression and DNA damage response and iii). explore RBPs with emphasis on HuR as therapeutic target for breast cancer therapy.
Collapse
Affiliation(s)
- Meghna Mehta
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajeswari Raguraman
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Anupama Munshi
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA.
| |
Collapse
|
8
|
Li C, Zhang G, Mohapatra S, Callahan AJ, Loas A, Gómez‐Bombarelli R, Pentelute BL. Machine Learning Guides Peptide Nucleic Acid Flow Synthesis and Sequence Design. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201988. [PMID: 36270977 PMCID: PMC9731686 DOI: 10.1002/advs.202201988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Peptide nucleic acids (PNAs) are potential antisense therapies for genetic, acquired, and viral diseases. Efficiently selecting candidate PNA sequences for synthesis and evaluation from a genome containing hundreds to thousands of options can be challenging. To facilitate this process, this work leverages machine learning (ML) algorithms and automated synthesis technology to predict PNA synthesis efficiency and guide rational PNA sequence design. The training data is collected from individual fluorenylmethyloxycarbonyl (Fmoc) deprotection reactions performed on a fully automated PNA synthesizer. The optimized ML model allows for 93% prediction accuracy and 0.97 Pearson's r. The predicted synthesis scores are validated to be correlated with the experimental high-performance liquid chromatography (HPLC) crude purities (correlation coefficient R2 = 0.95). Furthermore, a general applicability of ML is demonstrated through designing synthetically accessible antisense PNA sequences from 102 315 predicted candidates targeting exon 44 of the human dystrophin gene, SARS-CoV-2, HIV, as well as selected genes associated with cardiovascular diseases, type II diabetes, and various cancers. Collectively, ML provides an accurate prediction of PNA synthesis quality and serves as a useful computational tool for informing PNA sequence design.
Collapse
Affiliation(s)
- Chengxi Li
- Department of ChemistryMassachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
- College of Chemical and Biological EngineeringZhejiang UniversityNo.866 Yuhangtang RoadHangzhouZhejiang310030P. R. China
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterNo.733 Jianshe San Road, Xiaoshan DistrictHangzhouZhejiang311200P. R. China
| | - Genwei Zhang
- Department of ChemistryMassachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
| | - Somesh Mohapatra
- Department of Materials Science and EngineeringMassachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
| | - Alex J. Callahan
- Department of ChemistryMassachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
| | - Andrei Loas
- Department of ChemistryMassachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
| | - Rafael Gómez‐Bombarelli
- Department of Materials Science and EngineeringMassachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
| | - Bradley L. Pentelute
- Department of ChemistryMassachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
- The Koch Institute for Integrative Cancer ResearchMassachusetts Institute of Technology500 Main StreetCambridgeMA02142USA
- Center for Environmental Health SciencesMassachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
- Broad Institute of MIT and Harvard415 Main StreetCambridgeMA02142USA
| |
Collapse
|
9
|
Engineered Extracellular Vesicles in Treatment of Type 1 Diabetes Mellitus: A Prospective Review. Biomedicines 2022; 10:biomedicines10123042. [PMID: 36551798 PMCID: PMC9775549 DOI: 10.3390/biomedicines10123042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
Insulin replacement is an available treatment for autoimmune type 1 diabetes mellitus (T1DM). There are multiple limitations in the treatment of autoimmune diseases such as T1DM by immunosuppression using drugs and chemicals. The advent of extracellular vesicle (EV)-based therapies for the treatment of various diseases has attracted much attention to the field of bio-nanomedicine. Tolerogenic nanoparticles can induce immune tolerance, especially in autoimmune diseases. EVs can deliver cargo to specific cells without restrictions. Accordingly, EVs can be used to deliver tolerogenic nanoparticles, including iron oxide-peptide-major histocompatibility complex, polyethylene glycol-silver-2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester, and carboxylated poly (lactic-co-glycolic acid) nanoparticles coupled with or encapsulating an antigen, to effectively treat autoimmune T1DM. The present work highlights the advances in exosome-based delivery of tolerogenic nanoparticles for the treatment of autoimmune T1DM.
Collapse
|
10
|
Kulkarni A, Muralidharan C, May SC, Tersey SA, Mirmira RG. Inside the β Cell: Molecular Stress Response Pathways in Diabetes Pathogenesis. Endocrinology 2022; 164:6783239. [PMID: 36317483 PMCID: PMC9667558 DOI: 10.1210/endocr/bqac184] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Indexed: 11/05/2022]
Abstract
The pathogeneses of the 2 major forms of diabetes, type 1 and type 2, differ with respect to their major molecular insults (loss of immune tolerance and onset of tissue insulin resistance, respectively). However, evidence suggests that dysfunction and/or death of insulin-producing β-cells is common to virtually all forms of diabetes. Although the mechanisms underlying β-cell dysfunction remain incompletely characterized, recent years have witnessed major advances in our understanding of the molecular pathways that contribute to the demise of the β-cell. Cellular and environmental factors contribute to β-cell dysfunction/loss through the activation of molecular pathways that exacerbate endoplasmic reticulum stress, the integrated stress response, oxidative stress, and impaired autophagy. Whereas many of these stress responsive pathways are interconnected, their individual contributions to glucose homeostasis and β-cell health have been elucidated through the development and interrogation of animal models. In these studies, genetic models and pharmacological compounds have enabled the identification of genes and proteins specifically involved in β-cell dysfunction during diabetes pathogenesis. Here, we review the critical stress response pathways that are activated in β cells in the context of the animal models.
Collapse
Affiliation(s)
| | | | - Sarah C May
- Kovler Diabetes Center and Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
| | - Sarah A Tersey
- Kovler Diabetes Center and Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
| | - Raghavendra G Mirmira
- Correspondence: Raghavendra G. Mirmira, MD, PhD, Kovler Diabetes Center and Department of Medicine, The University of Chicago, 900 E 57th St, KCBD 8132, Chicago, IL 60637, USA.
| |
Collapse
|
11
|
Raguraman P, Balachandran AA, Chen S, Diermeier SD, Veedu RN. Antisense Oligonucleotide-Mediated Splice Switching: Potential Therapeutic Approach for Cancer Mitigation. Cancers (Basel) 2021; 13:5555. [PMID: 34771719 PMCID: PMC8583451 DOI: 10.3390/cancers13215555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 12/13/2022] Open
Abstract
Splicing is an essential process wherein precursor messenger RNA (pre-mRNA) is reshaped into mature mRNA. In alternative splicing, exons of any pre-mRNA get rearranged to form mRNA variants and subsequently protein isoforms, which are distinct both by structure and function. On the other hand, aberrant splicing is the cause of many disorders, including cancer. In the past few decades, developments in the understanding of the underlying biological basis for cancer progression and therapeutic resistance have identified many oncogenes as well as carcinogenic splice variants of essential genes. These transcripts are involved in various cellular processes, such as apoptosis, cell signaling and proliferation. Strategies to inhibit these carcinogenic isoforms at the mRNA level are promising. Antisense oligonucleotides (AOs) have been developed to inhibit the production of alternatively spliced carcinogenic isoforms through splice modulation or mRNA degradation. AOs can also be used to induce splice switching, where the expression of an oncogenic protein can be inhibited by the induction of a premature stop codon. In general, AOs are modified chemically to increase their stability and binding affinity. One of the major concerns with AOs is efficient delivery. Strategies for the delivery of AOs are constantly being evolved to facilitate the entry of AOs into cells. In this review, the different chemical modifications employed and delivery strategies applied are discussed. In addition to that various AOs in clinical trials and their efficacy are discussed herein with a focus on six distinct studies that use AO-mediated exon skipping as a therapeutic strategy to combat cancer.
Collapse
Affiliation(s)
- Prithi Raguraman
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (P.R.); (A.A.B.); (S.C.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Akilandeswari Ashwini Balachandran
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (P.R.); (A.A.B.); (S.C.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (P.R.); (A.A.B.); (S.C.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Sarah D. Diermeier
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand;
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (P.R.); (A.A.B.); (S.C.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| |
Collapse
|
12
|
Xu W, Kannan S, Verma CS, Nacro K. Update on the Development of MNK Inhibitors as Therapeutic Agents. J Med Chem 2021; 65:983-1007. [PMID: 34533957 DOI: 10.1021/acs.jmedchem.1c00368] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mitogen-activated protein kinase-interacting kinases 1 and 2 (MNK1/2) represent a central class of enzymes that are activated by extracellular signal-regulated kinase (ERK) or p38 mitogen-activated protein (MAP) kinases. MNK1 and MNK2 coordinate cellular signaling, control production of inflammatory chemokines, and regulate cell proliferation and survival. MNK1/2 are referred to as serine/threonine kinases as they phosphorylate serine or threonine residues on their substrates. Upon activation, MNK1/2 phosphorylate eukaryotic translation initiation factor 4E (eIF4E) at Ser209, which in turn initiates ribosome assembly and protein translation. Deleterious overexpression of MNK1/2 and/or eIF4E have been reported in several diseases including cancers, neurological disorders, autism, and inflammation. Recently, there have been intense efforts toward the development of potent and selective inhibitors of MNK1/2 in both academia and industry. Herein, we review the current understanding of the structural and biological aspects of MNK1/2 and provide an update of pharmacological inhibitors of MNK1/2 including candidates in clinical trials.
Collapse
Affiliation(s)
- Weijun Xu
- Experimental Drug Development Centre (EDDC), A*STAR, 10 Biopolis Road, Chromos #05-01, 138670, Singapore
| | | | - Chandra S Verma
- Bioinformatics Institute (BII), A*STAR, 30 Biopolis Street, #07-01 Matrix, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Kassoum Nacro
- Experimental Drug Development Centre (EDDC), A*STAR, 10 Biopolis Road, Chromos #05-01, 138670, Singapore
| |
Collapse
|
13
|
Knerr L, Prakash TP, Lee R, Drury Iii WJ, Nikan M, Fu W, Pirie E, Maria LD, Valeur E, Hayen A, Ölwegård-Halvarsson M, Broddefalk J, Ämmälä C, Østergaard ME, Meuller J, Sundström L, Andersson P, Janzén D, Jansson-Löfmark R, Seth PP, Andersson S. Glucagon Like Peptide 1 Receptor Agonists for Targeted Delivery of Antisense Oligonucleotides to Pancreatic Beta Cell. J Am Chem Soc 2021; 143:3416-3429. [PMID: 33626278 DOI: 10.1021/jacs.0c12043] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The extra hepatic delivery of antisense oligonucleotides (ASOs) remains a challenge and hampers the widespread application of this powerful class of therapeutic agents. In that regard, pancreatic beta cells are a particularly attractive but challenging cell type because of their pivotal role in diabetes and the fact that they are refractory to uptake of unconjugated ASOs. To circumvent this, we have expanded our understanding of the structure activity relationship of ASOs conjugated to Glucagon Like Peptide 1 Receptor (GLP1R) agonist peptide ligands. We demonstrate the key role of the linker chemistry and its optimization to design maleimide based conjugates with improved in vivo efficacy. In addition, truncation studies and scoping of a diverse set of GLP1R agonists proved fruitful to identify additional targeting ligands efficacious in vivo including native hGLP1(7-36)NH2. Variation of the carrier peptide also shed some light on the dramatic impact of subtle sequence differences on the corresponding ASO conjugate performance in vivo, an area which clearly warrant further investigations. We have confirmed the remarkable potential of GLP1R agonist conjugation for the delivery of ASOs to pancreatic beta cell by effectively knocking down islet amyloid polypeptide (IAPP) mRNA, a potential proapoptotic target, in mice.
Collapse
Affiliation(s)
- Laurent Knerr
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Richard Lee
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - William J Drury Iii
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mehran Nikan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Wuxia Fu
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Elaine Pirie
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Eric Valeur
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ahlke Hayen
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Maria Ölwegård-Halvarsson
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Johan Broddefalk
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Carina Ämmälä
- Bioscience, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Michael E Østergaard
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Johan Meuller
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Linda Sundström
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Patrik Andersson
- Respiratory and Immunology Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - David Janzén
- DMPK, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Rasmus Jansson-Löfmark
- DMPK, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Shalini Andersson
- Research and early Development, Discovery Sciences,, AstraZeneca, Gothenburg, Sweden
| |
Collapse
|