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Nagasawa R, Onizuka K, Komatsu KR, Miyashita E, Murase H, Ojima K, Ishikawa S, Ozawa M, Saito H, Nagatsugi F. Large-scale analysis of small molecule-RNA interactions using multiplexed RNA structure libraries. Commun Chem 2024; 7:98. [PMID: 38693284 DOI: 10.1038/s42004-024-01181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 04/17/2024] [Indexed: 05/03/2024] Open
Abstract
The large-scale analysis of small-molecule binding to diverse RNA structures is key to understanding the required interaction properties and selectivity for developing RNA-binding molecules toward RNA-targeted therapies. Here, we report a new system for performing the large-scale analysis of small molecule-RNA interactions using a multiplexed pull-down assay with RNA structure libraries. The system profiled the RNA-binding landscapes of G-clamp and thiazole orange derivatives, which recognizes an unpaired guanine base and are good probes for fluorescent indicator displacement (FID) assays, respectively. We discuss the binding preferences of these molecules based on their large-scale affinity profiles. In addition, we selected combinations of fluorescent indicators and different ranks of RNA based on the information and screened for RNA-binding molecules using FID. RNAs with high- and intermediate-rank RNA provided reliable results. Our system provides fundamental information about small molecule-RNA interactions and facilitates the discovery of novel RNA-binding molecules.
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Affiliation(s)
- Ryosuke Nagasawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Miyagi, 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Miyagi, 980-8578, Japan.
- Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Miyagi, 980-8577, Japan.
| | - Kaoru R Komatsu
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Emi Miyashita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Hirotaka Murase
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
| | - Kanna Ojima
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Miyagi, 980-8578, Japan
| | - Shunya Ishikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Miyagi, 980-8578, Japan
| | - Mamiko Ozawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
| | - Hirohide Saito
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan.
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Miyagi, 980-8578, Japan.
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2
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Tong H, Yang T, Xu S, Li X, Liu L, Zhou G, Yang S, Yin S, Li XJ, Li S. Huntington's Disease: Complex Pathogenesis and Therapeutic Strategies. Int J Mol Sci 2024; 25:3845. [PMID: 38612657 PMCID: PMC11011923 DOI: 10.3390/ijms25073845] [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: 02/19/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Huntington's disease (HD) arises from the abnormal expansion of CAG repeats in the huntingtin gene (HTT), resulting in the production of the mutant huntingtin protein (mHTT) with a polyglutamine stretch in its N-terminus. The pathogenic mechanisms underlying HD are complex and not yet fully elucidated. However, mHTT forms aggregates and accumulates abnormally in neuronal nuclei and processes, leading to disruptions in multiple cellular functions. Although there is currently no effective curative treatment for HD, significant progress has been made in developing various therapeutic strategies to treat HD. In addition to drugs targeting the neuronal toxicity of mHTT, gene therapy approaches that aim to reduce the expression of the mutant HTT gene hold great promise for effective HD therapy. This review provides an overview of current HD treatments, discusses different therapeutic strategies, and aims to facilitate future therapeutic advancements in the field.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-Human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China; (H.T.); (T.Y.); (S.X.); (X.L.); (L.L.); (G.Z.); (S.Y.); (S.Y.)
| | - Shihua Li
- Guangdong Key Laboratory of Non-Human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China; (H.T.); (T.Y.); (S.X.); (X.L.); (L.L.); (G.Z.); (S.Y.); (S.Y.)
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3
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Kaur J, Sharma A, Mundlia P, Sood V, Pandey A, Singh G, Barnwal RP. RNA-Small-Molecule Interaction: Challenging the "Undruggable" Tag. J Med Chem 2024. [PMID: 38498010 DOI: 10.1021/acs.jmedchem.3c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases. A deeper understanding of RNA biology reveals that RNA molecules can adopt a variety of structures, carrying defined binding pockets that can accommodate small-molecule drugs. Due to its functional diversity and structural complexity, RNA can be perceived as a prospective target for therapeutic intervention. This perspective highlights the proof of concept of RNA-small-molecule interactions, exemplified by targeting of various transcripts with functional modulators. The advent of RNA-oriented knowledge would help expedite drug discovery.
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Affiliation(s)
- Jaskirat Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
| | - Poonam Mundlia
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
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4
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Ishigami Y, Wong MS, Martí-Gómez C, Ayaz A, Kooshkbaghi M, Hanson SM, McCandlish DM, Krainer AR, Kinney JB. Specificity, synergy, and mechanisms of splice-modifying drugs. Nat Commun 2024; 15:1880. [PMID: 38424098 PMCID: PMC10904865 DOI: 10.1038/s41467-024-46090-5] [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: 02/22/2023] [Accepted: 02/10/2024] [Indexed: 03/02/2024] Open
Abstract
Drugs that target pre-mRNA splicing hold great therapeutic potential, but the quantitative understanding of how these drugs work is limited. Here we introduce mechanistically interpretable quantitative models for the sequence-specific and concentration-dependent behavior of splice-modifying drugs. Using massively parallel splicing assays, RNA-seq experiments, and precision dose-response curves, we obtain quantitative models for two small-molecule drugs, risdiplam and branaplam, developed for treating spinal muscular atrophy. The results quantitatively characterize the specificities of risdiplam and branaplam for 5' splice site sequences, suggest that branaplam recognizes 5' splice sites via two distinct interaction modes, and contradict the prevailing two-site hypothesis for risdiplam activity at SMN2 exon 7. The results also show that anomalous single-drug cooperativity, as well as multi-drug synergy, are widespread among small-molecule drugs and antisense-oligonucleotide drugs that promote exon inclusion. Our quantitative models thus clarify the mechanisms of existing treatments and provide a basis for the rational development of new therapies.
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Affiliation(s)
- Yuma Ishigami
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Mandy S Wong
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Beam Therapeutics, Cambridge, MA, 02142, USA
| | | | - Andalus Ayaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Mahdi Kooshkbaghi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- The Estée Lauder Companies, New York, NY, 10153, USA
| | | | | | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
| | - Justin B Kinney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
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5
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Audic F. Gene therapy in spinal muscular atrophy. Arch Pediatr 2023; 30:8S12-8S17. [PMID: 38043977 DOI: 10.1016/s0929-693x(23)00222-1] [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] [Indexed: 12/05/2023]
Abstract
Infantile SMA is a neuromuscular disease caused by the motor neuron degeneration, depending on the age of appearance of clinical signs and the evolution of the disease, three types of decreasing severity have been defined. SMA is caused by mutations or deletions of the SMN1 gene and disease. Various therapies aimed at increasing SMN protein levels have been developed. Gene therapy is part of the therapeutic arsenal now available for the treatment of SMA under certain conditions. It uses the scAAV9 vector carrying a functional copy of SMN1 to restore SMN protein expression at the cellular level. Because the adeno-associated virus genome is maintained as it is an episome, a single intravenous administration is sufficient to producing a long-lasting therapeutic effect. The effectiveness of gene replacement therapy in patients with SMA has been demonstrated in various studies. It is now clear that treatment as early as possible provides better clinical results. However, this treatment must be carried out in a suitable medical environment, with close monitoring initially due to potentially serious side effects. In France, this treatment has been available since 2019. A national committee of experts involved in the treatment of pediatric SMA patients has established that pediatric patients with SMA decide on the indications for disease-modifying therapies (DMT) in children. The French Spinal Muscular Atrophy Registry (SMA France Registry) was established in January 2020. The registry includes all patients with genetically confirmed SMN1-related SMA. All patients treated with GT are systematically included in the registry. As of July 21, 2023: 72 patients with SMA have been treated with GT in France since June 2019. The arrival of new treatments reveals new clinical phenotypes of SMA which constitute a new management challenge. Treatment as early as possible is also a very important factor for a favorable outcome and calls for presymptomatic screening. However, the arrival of these new treatments, extremely expensive raises other socio-economic questions. © 2023 Published by Elsevier Masson SAS on behalf of French Society of Pediatrics.
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Affiliation(s)
- Frédérique Audic
- Centre de Référence des Maladies Neuromusculaires de l'enfant PACARARE, Service de Neuropédiatrie, Hôpital Timone Enfants, 264 rue Saint Pierre, 14 13385 Marseille Cedex 5, France.
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6
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Liu L, Malagu K, Haughan AF, Khetarpal V, Stott AJ, Esmieu W, Vater HD, Webster SJ, Van de Poël AJ, Clissold C, Cosgrove B, Sutton B, Spencer JA, Breccia P, Gancia E, Bonomo S, Ladduwahetty T, Lazari O, Patel H, Atton HC, Clifton S, Mota DM, Magnani D, O'Neill A, Stebbeds M, Macabuag N, Todd D, Herva ME, Mitchell P, Visser M, Compte Sancerni S, Grand Moursel L, da Silva M, Kritikou E, Heikkinen TT, Bolkvadze T, Fodale V, Spadafora D, Daldin M, Bresciani A, Mangette JE, Doherty EM, Lee MR, Herbst T, Monteagudo E, Macdonald D, Plotnikov NV, Chambers M, McAllister G, Muňoz-Sanjuan I, Dominguez C. Identification and Optimization of RNA-Splicing Modulators as Huntingtin Protein-Lowering Agents for the Treatment of Huntington's Disease. J Med Chem 2023; 66:13205-13246. [PMID: 37712656 DOI: 10.1021/acs.jmedchem.3c01173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Huntington's disease (HD) is caused by an expanded CAG trinucleotide repeat in exon 1 of the huntingtin (HTT) gene. We report the design of a series of HTT pre-mRNA splicing modulators that lower huntingtin (HTT) protein, including the toxic mutant huntingtin (mHTT), by promoting insertion of a pseudoexon containing a premature termination codon at the exon 49-50 junction. The resulting transcript undergoes nonsense-mediated decay, leading to a reduction of HTT mRNA transcripts and protein levels. The starting benzamide core was modified to pyrazine amide and further optimized to give a potent, CNS-penetrant, and orally bioavailable HTT-splicing modulator 27. This compound reduced canonical splicing of the HTT RNA exon 49-50 and demonstrated significant HTT-lowering in both human HD stem cells and mouse BACHD models. Compound 27 is a structurally diverse HTT-splicing modulator that may help understand the mechanism of adverse effects such as peripheral neuropathy associated with branaplam.
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Affiliation(s)
- Longbin Liu
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Karine Malagu
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Alan F Haughan
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Vinod Khetarpal
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Andrew J Stott
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - William Esmieu
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Huw D Vater
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Stephen J Webster
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Amanda J Van de Poël
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Cole Clissold
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Brett Cosgrove
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Benjamin Sutton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Jonathan A Spencer
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Perla Breccia
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Emanuela Gancia
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Silvia Bonomo
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Tammy Ladduwahetty
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Ovadia Lazari
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Hiral Patel
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Helen C Atton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Steve Clifton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Daniel M Mota
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Dario Magnani
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Amy O'Neill
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Marta Stebbeds
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Natsuko Macabuag
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Daniel Todd
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Maria E Herva
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Philip Mitchell
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Mijke Visser
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | | | | | - Marta da Silva
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | - Eva Kritikou
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | | | | | | | | | | | | | | | - Elizabeth M Doherty
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Matthew R Lee
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Todd Herbst
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Edith Monteagudo
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Douglas Macdonald
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Nikolay V Plotnikov
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Mark Chambers
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - George McAllister
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Ignacio Muňoz-Sanjuan
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Celia Dominguez
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
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Ponomarev AS, Chulpanova DS, Yanygina LM, Solovyeva VV, Rizvanov AA. Emerging Gene Therapy Approaches in the Management of Spinal Muscular Atrophy (SMA): An Overview of Clinical Trials and Patent Landscape. Int J Mol Sci 2023; 24:13743. [PMID: 37762045 PMCID: PMC10530942 DOI: 10.3390/ijms241813743] [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: 06/30/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a rare autosomal recessive neuromuscular disease that is characterized by progressive muscle atrophy (degeneration), including skeletal muscles in charge of the ability to move. SMA is caused by defects in the SMN1 gene (Survival of Motor Neuron 1) which encodes a protein crucial for the survival and functionality of neuron cells called motor neurons. Decreased level of functioning SMN protein leads to progressive degeneration of alpha-motor neurons performing muscular motility. Over the past decade, many strategies directed for SMN-level-restoration emerged, such as gene replacement therapy (GRT), CRISPR/Cas9-based gene editing, usage of antisense oligonucleotides and small-molecule modulators, and all have been showing their perspectives in SMA therapy. In this review, modern SMA therapy strategies are described, making it a valuable resource for researchers, clinicians and everyone interested in the progress of therapy of this serious disorder.
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Affiliation(s)
| | | | | | | | - Albert A. Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (A.S.P.); (D.S.C.); (L.M.Y.); (V.V.S.)
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8
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Li Q, Kang C. Targeting RNA-binding proteins with small molecules: Perspectives, pitfalls and bifunctional molecules. FEBS Lett 2023; 597:2031-2047. [PMID: 37519019 DOI: 10.1002/1873-3468.14710] [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: 03/01/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
RNA-binding proteins (RBPs) play vital roles in organisms through binding with RNAs to regulate their functions. Small molecules affecting the function of RBPs have been developed, providing new avenues for drug discovery. Herein, we describe the perspectives on developing small molecule regulators of RBPs. The following types of small molecule modulators are of great interest in drug discovery: small molecules binding to RBPs to affect interactions with RNA molecules, bifunctional molecules binding to RNA or RBP to influence their interactions, and other types of molecules that affect the stability of RNA or RBPs. Moreover, we emphasize that the bifunctional molecules may play important roles in small molecule development to overcome the challenges encountered in the process of drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore, Singapore
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9
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Wicks SL, Morgan BS, Wilson AW, Hargrove AE. Probing Bioactive Chemical Space to Discover RNA-Targeted Small Molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551350. [PMID: 37577658 PMCID: PMC10418101 DOI: 10.1101/2023.07.31.551350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Small molecules have become increasingly recognized as invaluable tools to study RNA structure and function and to develop RNA-targeted therapeutics. To rationally design RNA-targeting ligands, a comprehensive understanding and explicit testing of small molecule properties that govern molecular recognition is crucial. To date, most studies have primarily evaluated properties of small molecules that bind RNA in vitro, with little to no assessment of properties that are distinct to selective and bioactive RNA-targeted ligands. Therefore, we curated an RNA-focused library, termed the Duke RNA-Targeted Library (DRTL), that was biased towards the physicochemical and structural properties of biologically active and non-ribosomal RNA-targeted small molecules. The DRTL represents one of the largest academic RNA-focused small molecule libraries curated to date with more than 800 small molecules. These ligands were selected using computational approaches that measure similarity to known bioactive RNA ligands and that diversify the molecules within this space. We evaluated DRTL binding in vitro to a panel of four RNAs using two optimized fluorescent indicator displacement assays, and we successfully identified multiple small molecule hits, including several novel scaffolds for RNA. The DRTL has and will continue to provide insights into biologically relevant RNA chemical space, such as the identification of additional RNA-privileged scaffolds and validation of RNA-privileged molecular features. Future DRTL screening will focus on expanding both the targets and assays used, and we welcome collaboration from the scientific community. We envision that the DRTL will be a valuable resource for the discovery of RNA-targeted chemical probes and therapeutic leads.
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Affiliation(s)
- Sarah L. Wicks
- Department of Chemistry; Duke University; 124 Science Drive; Durham, NC 27708
| | - Brittany S. Morgan
- Department of Chemistry & Biochemistry; University of Notre Dame; 123 McCourtney Hall Notre Dame, IN 46556
| | - Alexander W. Wilson
- Department of Chemistry; Duke University; 124 Science Drive; Durham, NC 27708
| | - Amanda E. Hargrove
- Department of Chemistry; Duke University; 124 Science Drive; Durham, NC 27708
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10
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Ottesen EW, Singh NN, Luo D, Kaas B, Gillette B, Seo J, Jorgensen H, Singh RN. Diverse targets of SMN2-directed splicing-modulating small molecule therapeutics for spinal muscular atrophy. Nucleic Acids Res 2023; 51:5948-5980. [PMID: 37026480 PMCID: PMC10325915 DOI: 10.1093/nar/gkad259] [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: 09/07/2021] [Revised: 03/13/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
Designing an RNA-interacting molecule that displays high therapeutic efficacy while retaining specificity within a broad concentration range remains a challenging task. Risdiplam is an FDA-approved small molecule for the treatment of spinal muscular atrophy (SMA), the leading genetic cause of infant mortality. Branaplam is another small molecule which has undergone clinical trials. The therapeutic merit of both compounds is based on their ability to restore body-wide inclusion of Survival Motor Neuron 2 (SMN2) exon 7 upon oral administration. Here we compare the transcriptome-wide off-target effects of these compounds in SMA patient cells. We captured concentration-dependent compound-specific changes, including aberrant expression of genes associated with DNA replication, cell cycle, RNA metabolism, cell signaling and metabolic pathways. Both compounds triggered massive perturbations of splicing events, inducing off-target exon inclusion, exon skipping, intron retention, intron removal and alternative splice site usage. Our results of minigenes expressed in HeLa cells provide mechanistic insights into how these molecules targeted towards a single gene produce different off-target effects. We show the advantages of combined treatments with low doses of risdiplam and branaplam. Our findings are instructive for devising better dosing regimens as well as for developing the next generation of small molecule therapeutics aimed at splicing modulation.
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Affiliation(s)
- Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Diou Luo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Bailey Kaas
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Benjamin J Gillette
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Joonbae Seo
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Hannah J Jorgensen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
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Abstract
An analysis of 156 published clinical candidates from the Journal of Medicinal Chemistry between 2018 and 2021 was conducted to identify lead generation strategies most frequently employed leading to drug candidates. As in a previous publication, the most frequent lead generation strategies resulting in clinical candidates were from known compounds (59%) followed by random screening approaches (21%). The remainder of the approaches included directed screening, fragment screening, DNA-encoded library screening (DEL), and virtual screening. An analysis of similarity was also conducted based on Tanimoto-MCS and revealed most clinical candidates were distant from their original hits; however, most shared a key pharmacophore that translated from hit-to-clinical candidate. An examination of frequency of oxygen, nitrogen, fluorine, chlorine, and sulfur incorporation in clinical candidates was also conducted. The three most similar and least similar hit-to-clinical pairs from random screening were examined to provide perspective on changes that occur that lead to successful clinical candidates.
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Affiliation(s)
- Dean G Brown
- Jnana Therapeutics, One Design Center Pl Suite 19-400, Boston, Massachusetts 02210, United States
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12
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Zhang L, Xie X, Djokovic N, Nikolic K, Kosenkov D, Abendroth F, Vázquez O. Reversible Control of RNA Splicing by Photoswitchable Small Molecules. J Am Chem Soc 2023. [PMID: 37276581 DOI: 10.1021/jacs.3c03275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Dynamics are intrinsic to both RNA function and structure. Yet, the available means to precisely provide RNA-based processes with spatiotemporal resolution are scarce. Here, our work pioneers a reversible approach to regulate RNA splicing within primary patient-derived cells by synthetic photoswitches. Our small molecule enables conditional real-time control at mRNA and protein levels. NMR experiments, together with theoretical calculations, photochemical characterization, fluorescence polarization measurements, and living cell-based assays, confirmed light-dependent exon inclusion as well as an increase in the target functional protein. Therefore, we first demonstrated the potential of photopharmacology modulation in splicing, tweaking the current optochemical toolkit. The timeliness on the consolidation of RNA research as the driving force toward therapeutical innovation holds the promise that our approach will contribute to redrawing the vision of RNA.
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Affiliation(s)
- Lei Zhang
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
| | - Xiulan Xie
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, University of Belgrade, Belgrade, 11000, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, University of Belgrade, Belgrade, 11000, Serbia
| | - Dmitri Kosenkov
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey 07764, United States
| | - Frank Abendroth
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
| | - Olalla Vázquez
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, D-35043, Germany
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13
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Malbert B, Labaurie V, Dorme C, Paget E. Group I Intron as a Potential Target for Antifungal Compounds: Development of a Trans-Splicing High-Throughput Screening Strategy. Molecules 2023; 28:molecules28114460. [PMID: 37298936 DOI: 10.3390/molecules28114460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The search for safe and efficient new antifungal compounds for agriculture has led to more efforts in finding new modes of action. This involves the discovery of new molecular targets, including coding and non-coding RNA. Rarely found in plants and animals but present in fungi, group I introns are of interest as their complex tertiary structure may allow selective targeting using small molecules. In this work, we demonstrate that group I introns present in phytopathogenic fungi have a self-splicing activity in vitro that can be adapted in a high-throughput screening to find new antifungal compounds. Ten candidate introns from different filamentous fungi were tested and one group ID intron found in F. oxysporum showed high self-splicing efficiency in vitro. We designed the Fusarium intron to act as a trans-acting ribozyme and used a fluorescence-based reporter system to monitor its real time splicing activity. Together, these results are opening the way to study the druggability of such introns in crop pathogen and potentially discover small molecules selectively targeting group I introns in future high-throughput screenings.
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Affiliation(s)
- Bastien Malbert
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
| | - Virginie Labaurie
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
| | - Cécile Dorme
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
| | - Eric Paget
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
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14
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Nadal M, Anton R, Dorca‐Arévalo J, Estébanez‐Perpiñá E, Tizzano EF, Fuentes‐Prior P. Structure and function analysis of Sam68 and hnRNP A1 synergy in the exclusion of exon 7 from SMN2 transcripts. Protein Sci 2023; 32:e4553. [PMID: 36560896 PMCID: PMC10031812 DOI: 10.1002/pro.4553] [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: 08/03/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by the absence of a functional copy of the Survival of Motor Neuron 1 gene (SMN1). The nearly identical paralog, SMN2, cannot compensate for the loss of SMN1 because exon 7 is aberrantly skipped from most SMN2 transcripts, a process mediated by synergistic activities of Src-associated during mitosis, 68 kDa (Sam68/KHDRBS1) and heterogeneous nuclear ribonucleoprotein (hnRNP) A1. This results in the production of a truncated, nonfunctional protein that is rapidly degraded. Here, we present several crystal structures of Sam68 RNA-binding domain (RBD). Sam68-RBD forms stable symmetric homodimers by antiparallel association of helices α3 from two monomers. However, the details of domain organization and the dimerization interface differ significantly from previously characterized homologs. We demonstrate that Sam68 and hnRNP A1 can simultaneously bind proximal motifs within the central region of SMN2 (ex7). Furthermore, we show that the RNA-binding pockets of the two proteins are close to each other in their heterodimeric complex and identify contact residues using crosslinking-mass spectrometry. We present a model of the ternary Sam68·SMN2 (ex7)·hnRNP A1 complex that reconciles all available information on SMN1/2 splicing. Our findings have important implications for the etiology of SMA and open new avenues for the design of novel therapeutics to treat splicing diseases.
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Affiliation(s)
- Marta Nadal
- Molecular Bases of DiseaseBiomedical Research Institute Sant Pau (IIB Sant Pau)BarcelonaSpain
| | - Rosa Anton
- Molecular Bases of DiseaseBiomedical Research Institute Sant Pau (IIB Sant Pau)BarcelonaSpain
| | - Jonatan Dorca‐Arévalo
- Molecular Bases of DiseaseBiomedical Research Institute Sant Pau (IIB Sant Pau)BarcelonaSpain
- Present address:
Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, Campus of BellvitgeHospitalet de Llobregat, University of BarcelonaBarcelonaSpain
| | - Eva Estébanez‐Perpiñá
- Structural Biology of Nuclear Receptors, Department of Biochemistry and Molecular Biomedicine, Faculty of BiologyInstitute of Biomedicine (IBUB) of the University of Barcelona (UB)BarcelonaSpain
| | - Eduardo F. Tizzano
- Medicine Genetics GroupVall d'Hebron Research Institute (VHIR)BarcelonaSpain
- Department of Clinical and Molecular GeneticsHospital Vall d'HebronBarcelonaSpain
| | - Pablo Fuentes‐Prior
- Molecular Bases of DiseaseBiomedical Research Institute Sant Pau (IIB Sant Pau)BarcelonaSpain
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15
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Meanwell NA. The pyridazine heterocycle in molecular recognition and drug discovery. Med Chem Res 2023; 32:1-69. [PMID: 37362319 PMCID: PMC10015555 DOI: 10.1007/s00044-023-03035-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/06/2023] [Indexed: 03/17/2023]
Abstract
The pyridazine ring is endowed with unique physicochemical properties, characterized by weak basicity, a high dipole moment that subtends π-π stacking interactions and robust, dual hydrogen-bonding capacity that can be of importance in drug-target interactions. These properties contribute to unique applications in molecular recognition while the inherent polarity, low cytochrome P450 inhibitory effects and potential to reduce interaction of a molecule with the cardiac hERG potassium channel add additional value in drug discovery and development. The recent approvals of the gonadotropin-releasing hormone receptor antagonist relugolix (24) and the allosteric tyrosine kinase 2 inhibitor deucravacitinib (25) represent the first examples of FDA-approved drugs that incorporate a pyridazine ring. In this review, the properties of the pyridazine ring are summarized in comparison to the other azines and its potential in drug discovery is illustrated through vignettes that explore applications that take advantage of the inherent physicochemical properties as an approach to solving challenges associated with candidate optimization. Graphical Abstract
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16
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Dimitrova YN, Gutierrez JA, Huard K. It's ok to be outnumbered - sub-stoichiometric modulation of homomeric protein complexes. RSC Med Chem 2023; 14:22-46. [PMID: 36760737 PMCID: PMC9890894 DOI: 10.1039/d2md00212d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
An arsenal of molecular tools with increasingly diversified mechanisms of action is being developed by the scientific community to enable biological interrogation and pharmaceutical modulation of targets and pathways of ever increasing complexity. While most small molecules interact with the target of interest in a 1 : 1 relationship, a noteworthy number of recent examples were reported to bind in a sub-stoichiometric manner to a homomeric protein complex. This approach requires molecular understanding of the physiologically relevant protein assemblies and in-depth characterization of the compound's mechanism of action. The recent literature examples summarized here were selected to illustrate methods used to identify and characterize molecules with such mechanisms. The concept of one small molecule targeting a homomeric protein assembly is not new but the subject deserves renewed inspection in light of emerging technologies and increasingly diverse target biology, to ensure relevant in vitro systems are used and valuable compounds with potentially novel sub-stoichiometric mechanisms of action aren't overlooked.
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Affiliation(s)
| | | | - Kim Huard
- Genentech 1 DNA Way South San Francisco CA 94080 USA
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17
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Bofanova NS, Eliseeva AR, Onchina VS. [Modern principles of therapy for patients with spinal muscular atrophy]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:34-40. [PMID: 36946394 DOI: 10.17116/jnevro202312303134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Spinal muscular atrophy (SMA) is a common cause of childhood mortality among hereditary diseases of the central nervous system, which are caused by the processes of degeneration and death of motor neurons of the anterior horns of the spinal cord. An urgent issue of modern neurology is pathogenetic therapy for this group of patients, the purpose of which is to increase the level of motoneuron survival protein. We performed a search on current methods of treating SMA in Web of Science, Scopus, PubMed, Embase by the keywords: spinal muscular atrophy, neuromuscular diseases, pathogenetic therapy. Significant progress has been made in the treatment of SMA over the past 7 years. A major advance is the introduction of disease-modifying therapies using SMN2 splicing modulation or gene replacement therapy. At the moment, there are 3 FDA-approved drugs for pathogenetic therapy: Nusinersen, Risdiplam, Zolgensma. The article compares the drugs, evaluates their safety and effectiveness according to the available literature. Modern drugs for the pathogenetic therapy of SMA are highly effective and reduce the mortality rate. The results of clinical trials predict the emergence of new modern drugs. This suggests a favorable prognosis for the treatment of patients with SMA.
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18
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Palacios DS. Drug Hunting at the Nexus of Medicinal Chemistry and Chemical Biology and the Discovery of Novel Therapeutic Modalities. J Med Chem 2022; 65:13594-13613. [PMID: 36206538 DOI: 10.1021/acs.jmedchem.2c01491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small molecules designed to modulate protein function have been remarkably successful in advancing human health. As the frontiers of medicine and understanding of disease pathogenesis continue to expand, small molecule scientists must also pursue the development of novel therapeutic modalities beyond functional protein modulation to address diseases of unmet medical need. In this vein, this Perspective will highlight two emerging modalities, selective mRNA splice modulation and targeted protein degradation, as mechanisms that affect protein abundance, rather than protein function, to broaden the scope of low-molecular-weight treatable diseases. Key to the elucidation and development of these mechanisms was the interplay and contemporaneous efforts in medicinal chemistry and chemical biology. Continued research at the intersection of these two fields will be critical for the identification of novel targets and mechanisms toward the development of the next generation of small molecule therapeutics.
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Affiliation(s)
- Daniel S Palacios
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
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19
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Abstract
Positional analogue scanning (PAS) is an accepted strategy for multiparameter lead optimization (MPO) in drug discovery. Small structural changes as introduced by PAS can lead to 10-fold changes in binding potency in ∼10-20% of cases, a significant parameter shift irrespective of other MPO objectives. Sometimes performing a complete PAS is challenging due to resource and time constraints, building block availability, or difficulty in synthesis. Calculating relative binding free energies (RBFEs) for all positions can contribute to prioritizing the most promising analogues for synthesis. We tested a well-established RBFE calculation method, Amber GPU-TI, for 20 positional analogue scans in 14 test systems (cyclin-dependent kinase 8 (CDK8), hepatitis C virus nonstructural protein 5B (HCV NS5B), tankyrase, RAC-α serine/threonine-protein kinase (Akt), phosphodiesterase 1B (PDE1B), orexin/hypocretin receptor type 1 (OX1R), orexin/hypocretin receptor type 2 (OX2R), histone acetyltransferase K (lysine) acetyltransferase 6A (KAT6A), peroxisome proliferator-activated receptor γ (PPARγ), extracellular signal-regulated kinases (ERK1/2), coactivator-associated arginine methyltransferase 1 (PRMT4), αvβ6, bromodomain 1 (BD1), human immunodeficiency virus-1 (HIV-1) entry) involving nitrogen, methyl, halogen, methoxy, and hydroxyl scans with at least four analogues per set. Among the 66 analogue positions explored, we found that in 18 cases Amber GPU-TI calculations predicted a more than 10-fold change in potency. In all of these cases, the experimentally observed direction of potency changes agreed with the predictions. In 16 cases, more than 10-fold changes in experimental potency were observed. Again, in all of these cases, Amber GPU-TI predicted the direction of the potency changes correctly. In none of these cases would a decision made for or against synthesis based on a 10-fold change in potency have resulted in missing an important analogue. Therefore, in silico RBFE calculations using Amber GPU-TI can meaningfully contribute to the prioritization of positional analogues before synthesis.
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Affiliation(s)
- Yuan Hu
- Alkermes, Inc., 852 Winter Street, Waltham, Massachusetts 02451-1420, United States
| | - Ingo Muegge
- Alkermes, Inc., 852 Winter Street, Waltham, Massachusetts 02451-1420, United States
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20
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Targeted-Deletion of a Tiny Sequence via Prime Editing to Restore SMN Expression. Int J Mol Sci 2022; 23:ijms23147941. [PMID: 35887289 PMCID: PMC9317564 DOI: 10.3390/ijms23147941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/13/2022] [Accepted: 07/17/2022] [Indexed: 01/27/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a devastating autosomal recessive motor neuron disease associated with mutations in the survival motor neuron 1 (SMN1) gene, the leading genetic cause of infant mortality. A nearly identical copy gene (SMN2) is retained in almost all patients with SMA. However, SMN2 fails to prevent disease development because of its alternative splicing, leading to a lack of exon 7 in the majority of SMN2 transcripts and yielding an unstable truncated protein. Several splicing regulatory elements, including intronic splicing silencer-N1 (ISS-N1) of SMN2 have been described. In this study, targeted-deletion of ISS-N1 was achieved using prime editing (PE) in SMA patient-specific induced pluripotent stem cells (SMA-iPSCs) with a high efficiency of 7/24. FL-SMN expression was restored in the targeted-deletion iPS clones and their derived motor neurons (iMNs). Notably, the apoptosis of the iMNs, caused by the loss of SMN protein that leads to the hyperactivity of endoplasmic reticulum (ER) stress, was alleviated in targeted-deletion iPSCs derived-iMNs. Thus, this is the first study to demonstrate that the targeted-deletion of ISS-N1 via PE for restoring FL-SMN expression holds therapeutic promise for SMA.
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21
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Phenotypic drug discovery: recent successes, lessons learned and new directions. Nat Rev Drug Discov 2022; 21:899-914. [DOI: 10.1038/s41573-022-00472-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2022] [Indexed: 12/29/2022]
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22
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Brakemeier S, Stolte B, Kleinschnitz C, Hagenacker T. Treatment of Adult Spinal Muscular Atrophy: Overview and Recent Developments. Curr Pharm Des 2022; 28:892-898. [PMID: 35352647 DOI: 10.2174/1381612828666220329115433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 02/03/2022] [Indexed: 11/22/2022]
Abstract
Spinal muscular atrophy (SMA) is a rare genetic neuromuscular disease leading to progressive and in many cases severe muscle weakness and atrophy in the natural disease course. An increasing number of gene-based treatment options have become available in recent years. Growing knowledge about the underlying genetic mechanisms makes the disease well amenable to this. Over the past few years, many data on new treatments, their mechanisms of action and therapeutic outcomes have been published, reflecting the current dynamics in this field. With the approval of the antisense oligonucleotide nusinersen, the vector-based therapy with onasemnogene abeparvovec and the small molecule splicing modifier risdiplam, three gene therapeutic drugs are available for the treatment of SMA showing improvement in motor function. But in the pivotal studies several relevant parameters have not been addressed. There is a data gap for the treatment outcome of adult individuals with SMA as well as for several other relevant outcome parameters like bulbary or ventilatory function. With increasing treatment options, additional individual therapies have become necessary. Studies on combination therapies or switch of therapy, e.g. the sequential administration of onasemnogen abeparvovec and nusinersen, are necessary. An overview of current developments in the field of therapeutic options for adult SMA is presented. Important characteristics of each therapeutic option will be discussed so that the reader can comprehend underlying pathophysiological mechanisms as well as advantages and disadvantages of each therapy. The focus is on gene-based treatment options, but options beyond this are also addressed.
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Affiliation(s)
- Svenja Brakemeier
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Benjamin Stolte
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Christoph Kleinschnitz
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Tim Hagenacker
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
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23
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Reprogramming RNA processing: an emerging therapeutic landscape. Trends Pharmacol Sci 2022; 43:437-454. [PMID: 35331569 DOI: 10.1016/j.tips.2022.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
The production of a mature mRNA requires coordination of multiple processing steps, which ultimately control its content, localization, and stability. These steps include some of the largest macromolecular machines in the cell, which were, until recently, considered undruggable due to their biological complexity. Building from an expanded understanding of the underlying mechanisms that drive these processes, a new wave of therapeutics is seeking to target RNA processing. With a focus on impacting gene regulation at the RNA level, such modalities offer potential for sequence-specific resolution in drug design. Here, we review our current understanding of RNA-processing events and their role in gene regulation, with a focus on the therapeutic opportunities that have emerged within this landscape.
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24
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Tang Z, Hegde S, Zhao J, Zhu S, Johnson KA, Lorson CL, Wang J. CRISPR-mediated Enzyme Fragment Complementation Assay for Quantification of the Stability of Splice Isoforms. Chembiochem 2022; 23:e202200012. [PMID: 35235240 DOI: 10.1002/cbic.202200012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/22/2022] [Indexed: 11/06/2022]
Abstract
Small-molecule splicing modulators exemplified by an FDA-approved drug, risdiplam, are a new pharmacological modality for regulating the expression and stability of splice isoforms. We report a CRISPR-mediated enzyme fragment complementation (EFC) assay to quantify the splice isoform stability. The EFC assay harnessed a 42 amino acid split of a β-galactosidase (designate α-tag), which could be fused at the termini of the target genes using CRISPR/cas9. The α-tagged splice isoform would be quantified by measuring the enzymatic activity upon complementation with the rest of β-galactosidase. This EFC assay retained all the sequences of introns and exons of the target gene in the native genomic environment that recapitulates the cell biology of the diseases of interest. For a proof-of-concept, we developed a CRISPR-mediated EFC assay targeting the exon 7 of the survival of motor neuron 2 (SMN2) gene. The EFC assay compatible with 384-well plates robustly quantified the splicing modulation activity of small molecules. In this study, we also discovered that a coumarin derivative, compound 4, potently modulate SMN2 splicing at as low as 1.1 nM.
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Affiliation(s)
- Zhichao Tang
- University of Kansas School of Pharmacy, Medicinal Chemistry, UNITED STATES
| | - Shalakha Hegde
- University of Kansas School of Pharmacy, Medicinal Chemistry, UNITED STATES
| | - Junxing Zhao
- University of Kansas School of Pharmacy, Medicinal Chemistry, UNITED STATES
| | - Shoutian Zhu
- PhenoTarget BioSciences, Inc., Biology, UNITED STATES
| | | | | | - Jingxin Wang
- University of Kansas, Medicinal Chemistry, 2034 Becker Dr, 1050, 66047, Lawrence, UNITED STATES
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25
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Chappie TA, Abdelmessih M, Ambroise CW, Boehm M, Cai M, Green M, Guilmette E, Steppan CM, Stevens LM, Wei L, Xi S, Hasson SA. Discovery of Small-Molecule CD33 Pre-mRNA Splicing Modulators. ACS Med Chem Lett 2022; 13:55-62. [PMID: 35059124 PMCID: PMC8762744 DOI: 10.1021/acsmedchemlett.1c00396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/29/2021] [Indexed: 01/16/2023] Open
Abstract
CD33/Siglec 3 is a myeloid lineage cell surface receptor that is known to regulate microglia activity. Multiple genome-wide association studies (GWAS) have identified genetic variants in the CD33 gene that convey protection from late-onset Alzheimer's disease. Furthermore, mechanistic studies into GWAS-linked variants suggest that disease protection is attributed to the alternative splicing of exon 2 of the CD33 pre-mRNA. Using a phenomimetic screen, a series of compounds were found to enhance the exclusion of CD33 exon 2, acting as a chemomimetic of the GWAS-linked gene variants. Additional studies confirmed that meyloid lineage cells treated with several of these compounds have a reduced full-length V-domain containing CD33 protein, while targeted RNA-seq concordantly demonstrated that compound 1 increases exon 2 skipping in cellular mRNA pools. These studies demonstrate how pharmacological interventions can be used to manipulate disease-relevant pre-mRNA splicing and provide a starting point for future efforts to identify small molecules that alter neuroimmune function that is rooted in the human biology of neurodegenerative disease.
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Affiliation(s)
- Thomas A. Chappie
- Internal
Medicine Medicinal Chemistry, Pfizer, Inc., Cambridge, Massachusetts 02139, United States,
| | - Mario Abdelmessih
- Primary
Pharmacology Group, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Claude W. Ambroise
- Internal
Medicine Research Unit, Pfizer, Inc., Cambridge, Massachusetts 02139, United States
| | - Markus Boehm
- Internal
Medicine Medicinal Chemistry, Pfizer, Inc., Cambridge, Massachusetts 02139, United States
| | - Mi Cai
- Internal
Medicine Research Unit, Pfizer, Inc., Cambridge, Massachusetts 02139, United States
| | - Michael Green
- Internal
Medicine Medicinal Chemistry, Pfizer, Inc., Cambridge, Massachusetts 02139, United States
| | - Edward Guilmette
- Internal
Medicine Research Unit, Pfizer, Inc., Cambridge, Massachusetts 02139, United States
| | - Claire M. Steppan
- Primary
Pharmacology Group, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Lucy M. Stevens
- Primary
Pharmacology Group, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Liuqing Wei
- Internal
Medicine Medicinal Chemistry, Pfizer, Inc., Cambridge, Massachusetts 02139, United States
| | - Simon Xi
- Internal
Medicine Research Unit, Pfizer, Inc., Cambridge, Massachusetts 02139, United States
| | - Samuel A. Hasson
- Internal
Medicine Research Unit, Pfizer, Inc., Cambridge, Massachusetts 02139, United States
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26
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Abstract
In Eukarya, immature mRNA transcripts (pre-mRNA) often contain coding sequences, or exons, interleaved by non-coding sequences, or introns. Introns are removed upon splicing, and further regulation of the retained exons leads to alternatively spliced mRNA. The splicing reaction requires the stepwise assembly of the spliceosome, a macromolecular machine composed of small nuclear ribonucleoproteins (snRNPs). This review focuses on the early stage of spliceosome assembly, when U1 snRNP defines each intron 5’-splice site (5ʹss) in the pre-mRNA. We first introduce the splicing reaction and the impact of alternative splicing on gene expression regulation. Thereafter, we extensively discuss splicing descriptors that influence the 5ʹss selection by U1 snRNP, such as sequence determinants, and interactions mediated by U1-specific proteins or U1 small nuclear RNA (U1 snRNA). We also include examples of diseases that affect the 5ʹss selection by U1 snRNP, and discuss recent therapeutic advances that manipulate U1 snRNP 5ʹss selectivity with antisense oligonucleotides and small-molecule splicing switches.
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Affiliation(s)
- Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Cameron D Mackereth
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
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27
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Spinal muscular atrophy: Where are we now? Current challenges and high hopes. POSTEP HIG MED DOSW 2022. [DOI: 10.2478/ahem-2022-0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disorder characterized by muscle weakness. It causes movement issues and severe physical disability. SMA is classified into four types based on the level of function achieved, age of onset, and maximum function achieved. The deletion or point mutation in the Survival of Motor Neuron 1 (SMN1) gene causes SMA. As a result, no full-length protein is produced. A nearly identical paralog, SMN2, provides enough stable protein to prevent death but not enough to compensate for SMN1's loss. The difference between SMN1 and SMN2 is due to different exon 7 alternative splicing patterns. SMA molecular therapies currently focus on restoring functional SMN protein by splicing modification of SMN2 exon 7 or elevated SMN protein levels. Nusinersen, an antisense oligonucleotide targeting the ISS-N1 sequence in SMN2 intron 7, was the first drug approved by the Food and Drug Administration. Risdiplam, a novel therapeutic that acts as an SMN2 exon 7 splicing modifier, was recently approved. All of these drugs result in the inclusion of SMN2 exon 7, and thus the production of functional SMN protein. Onasemnogene abeparvovec is a gene therapy that uses a recombinant adeno-associated virus that encodes the SMN protein. There are also experimental therapies available, such as reldesemtiv and apitegromab (SRK-015), which focus on improving muscle function or increasing muscle tissue growth, respectively. Although approved therapies have been shown to be effective, not all SMA patients can benefit from them due to age or weight, but primarily due to their high cost. This demonstrates the significance of continuous treatment improvement in today's medical challenges.
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28
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Abstract
Targeting of pre-mRNA splicing has yielded a rich variety of strategies for altering gene expression as a treatment for disease. The search for therapeutics that can modulate splicing has been dominated by antisense oligonucleotides (ASOs) and small molecule compounds, with each platform achieving remarkably effective results in the clinic. The success of RNA-targeting drugs has led to the exploration of new strategies to expand the repertoire of this type of therapeutic. Here, we discuss some of the more common causes of faulty gene expression and provide examples of approaches that have been developed to target and correct these defects for therapeutic value.
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Affiliation(s)
- Jessica L Centa
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Michelle L Hastings
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA.
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29
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Theil D, Valdez R, Darribat K, Doelemeyer A, Sivasankaran R, Hartmann A. Orally administered branaplam does not impact neurogenesis in juvenile mice, rats, and dogs. Biol Open 2021; 10:272197. [PMID: 34528068 PMCID: PMC8565466 DOI: 10.1242/bio.058551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 09/08/2021] [Indexed: 12/05/2022] Open
Abstract
Branaplam is a therapeutic agent currently in clinical development for the treatment of infants with type 1 spinal muscular atrophy (SMA). Since preclinical studies showed that branaplam had cell-cycle arrest effects, we sought to determine whether branaplam may affect postnatal cerebellar development and brain neurogenesis. Here, we describe a novel approach for developmental neurotoxicity testing (DNT) of a central nervous system (CNS) active drug. The effects of orally administered branaplam were evaluated in the SMA neonatal mouse model (SMNΔ7), and in juvenile Wistar Hannover rats and Beagle dogs. Histopathological examination and complementary immunohistochemical studies focused on areas of neurogenesis in the cerebellum (mice, rats, and dogs), and the subventricular zone of the striatum and dentate gyrus (rats and dogs) using antibodies directed against Ki67, phosphorylated histone H3, cleaved caspase-3, and glial fibrillary acidic protein. Additionally, image-analysis based quantification of calbindin-D28k and Ki67 was performed in rats and dogs. The patterns of cell proliferation and apoptosis, and neural migration and innervation in the cerebellum and other brain regions of active adult neurogenesis did not differ between branaplam- and control-treated animals. Quantitative image analysis did not reveal any changes in calbindin-D28k and Ki67 expression in rats and dogs. The data show that orally administered branaplam has no impact on neurogenesis in juvenile animals. Application of selected immunohistochemical stainings in combination with quantitative image analysis on a few critical areas of postnatal CNS development offer a reliable approach to assess DNT of CNS-active drug candidates in juvenile animal toxicity studies. Summary: Branaplam exhibits effects on the cell cycle but does not impair neuronal proliferation in juvenile or young adult animals, as demonstrated by immunohistochemistry and automated digital imaging.
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Affiliation(s)
- Diethilde Theil
- Translation medicine/preclinical safety, Novartis Institutes for Biomedical Research, Basel 4058, Switzerland
| | - Reginald Valdez
- Neuroscience/rare diseases, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Katy Darribat
- Translation medicine/preclinical safety, Novartis Institutes for Biomedical Research, Basel 4058, Switzerland
| | - Arno Doelemeyer
- Translation medicine/preclinical safety, Novartis Institutes for Biomedical Research, Basel 4058, Switzerland
| | - Rajeev Sivasankaran
- Neuroscience/rare diseases, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Andreas Hartmann
- Translation medicine/preclinical safety, Novartis Institutes for Biomedical Research, Basel 4058, Switzerland
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30
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Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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31
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Abstract
Autosomal-recessive spinal muscular atrophy (SMA) is characterized by the loss of specific motor neurons of the spinal cord and skeletal muscle atrophy. SMA is caused by mutations or deletions of the survival motor neuron 1 (SMN1) gene, and disease severity correlates with the expression levels of the nearly identical copy gene, SMN2. Both genes ubiquitously express SMN protein, but SMN2 generates only low levels of protein that do not fully compensate for the loss-of-function of SMN1. SMN protein forms a multiprotein complex essential for the cellular assembly of ribonucleoprotein particles involved in diverse aspects of RNA metabolism. Other studies using animal models revealed a spatio-temporal requirement of SMN that is high during the development of the neuromuscular system and later, in the general maintenance of cellular and tissues homeostasis. These observations define a period for maximum therapeutic efficiency of SMN restoration, and suggest that cells outside the central nervous system may also participate in the pathogenesis of SMA. Finally, recent innovative therapies have been shown to mitigate SMN deficiency and have been approved to treat SMA patients. We briefly review major findings from the past twenty-five years of SMA research. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
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Affiliation(s)
- S Lefebvre
- T3S INSERM UMR 1124, Toxicité Environnementale, Cibles Thérapeutiques, Signalisation Cellulaire et Biomarqueurs, UFR des Sciences Fondamentales et Biomédicales, Campus Saint-Germain-des-prés, Université de Paris, Paris, France.
| | - C Sarret
- Centre de compétence maladies rares des pathologies neuromusculaires, service de génétique médicale, Hôpital Estaing, CHU Clermont-Ferrand, France.
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32
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Navarrete-Opazo A, Garrison S, Waite M. Molecular Biomarkers for Spinal Muscular Atrophy: A Systematic Review. Neurol Clin Pract 2021; 11:e524-e536. [PMID: 34484951 DOI: 10.1212/cpj.0000000000000872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/05/2020] [Indexed: 11/15/2022]
Abstract
Background There is an unmet need for reliable biomarkers to predict disease severity, prognosis, and treatment effect in patients with spinal muscular atrophy (SMA). The purpose of this review is to evaluate the clinical utility of blood-based biomarkers in patients with SMA. Methods A systematic review of MEDLINE, DARE, PEDro, PsycINFO, Cochrane Database, LILACS, OTSeeker, SpeechBITE, CINAHL, Scopus, Science Direct, clinicaltrial.gov, OpenGrey, and Google Scholar was performed with the last search data of June 30, 2019. Results Survival motor neuron (SMN)-related biomarkers showed an important interpatient and cell variability with a wide overlap between SMA phenotypes and healthy controls. Several plasma protein analytes correlated with motor scores; however, validation studies are needed to rule out false positives. DNA methylation analysis distinguished between patients with mild/moderate SMA and healthy controls. Plasma phosphorylated neurofilament heavy chain (pNF-H) levels increased with disease severity and declined considerably after nusinersen treatment. Conclusion There is no sufficient evidence to support the clinical utility of SMN-related biomarkers to predict disease severity in SMA. pNF-H appears to be a promising biomarker of disease activity and treatment effect in SMA. Further studies should include longitudinal assessments of patients with SMA across functional groups and comparisons with age-matched healthy controls to evaluate the stability of putative biomarkers over time and in response to SMA therapeutics. PROSPERO registration: CRD42019139050.
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Affiliation(s)
| | - Sheldon Garrison
- Aurora Research Institute, Advocate Aurora Health, Milwaukee, WI
| | - Mindy Waite
- Aurora Research Institute, Advocate Aurora Health, Milwaukee, WI
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33
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Alternative Splicing Role in New Therapies of Spinal Muscular Atrophy. Genes (Basel) 2021; 12:genes12091346. [PMID: 34573328 PMCID: PMC8468182 DOI: 10.3390/genes12091346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
It has been estimated that 80% of the pre-mRNA undergoes alternative splicing, which exponentially increases the flow of biological information in cellular processes and can be an attractive therapeutic target. It is a crucial mechanism to increase genetic diversity. Disturbed alternative splicing is observed in many disorders, including neuromuscular diseases and carcinomas. Spinal Muscular Atrophy (SMA) is an autosomal recessive neurodegenerative disease. Homozygous deletion in 5q13 (the region coding for the motor neuron survival gene (SMN1)) is responsible for 95% of SMA cases. The nearly identical SMN2 gene does not compensate for SMN loss caused by SMN1 gene mutation due to different splicing of exon 7. A pathologically low level of survival motor neuron protein (SMN) causes degeneration of the anterior horn cells in the spinal cord with associated destruction of α-motor cells and manifested by muscle weakness and loss. Understanding the regulation of the SMN2 pre-mRNA splicing process has allowed for innovative treatment and the introduction of new medicines for SMA. After describing the concept of splicing modulation, this review will cover the progress achieved in this field, by highlighting the breakthrough accomplished recently for the treatment of SMA using the mechanism of alternative splicing.
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34
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Ottesen EW, Luo D, Singh NN, Singh RN. High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome. Int J Mol Sci 2021; 22:ijms22168378. [PMID: 34445083 PMCID: PMC8395096 DOI: 10.3390/ijms22168378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/14/2021] [Accepted: 07/31/2021] [Indexed: 12/17/2022] Open
Abstract
Intronic splicing silencer N1 (ISS-N1) located within Survival Motor Neuron 2 (SMN2) intron 7 is the target of a therapeutic antisense oligonucleotide (ASO), nusinersen (Spinraza), which is currently being used for the treatment of spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. The discovery of ISS-N1 as a promising therapeutic target was enabled in part by Anti-N1, a 20-mer ASO that restored SMN2 exon 7 inclusion by annealing to ISS-N1. Here, we analyzed the transcriptome of SMA patient cells treated with 100 nM of Anti-N1 for 30 h. Such concentrations are routinely used to demonstrate the efficacy of an ASO. While 100 nM of Anti-N1 substantially stimulated SMN2 exon 7 inclusion, it also caused massive perturbations in the transcriptome and triggered widespread aberrant splicing, affecting expression of essential genes associated with multiple cellular processes such as transcription, splicing, translation, cell signaling, cell cycle, macromolecular trafficking, cytoskeletal dynamics, and innate immunity. We validated our findings with quantitative and semiquantitative PCR of 39 candidate genes associated with diverse pathways. We also showed a substantial reduction in off-target effects with shorter ISS-N1-targeting ASOs. Our findings are significant for implementing better ASO design and dosing regimens of ASO-based drugs.
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35
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Behera B. Nusinersen, an exon 7 inclusion drug for spinal muscular atrophy: A minireview. World J Meta-Anal 2021; 9:277-285. [DOI: 10.13105/wjma.v9.i3.277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/20/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
Spinal muscular atrophy is an autosomal recessive neuromuscular disease with incidence of 1 in 5000 to 10000 live births and is produced by homozygous deletion of exons 7 and 8 in the SMN1 gene. The SMN1 and SMN2 genes encode the survival motor neuron protein, a crucial protein for the preservation of motor neurons. Use of the newer drug, Nusinersen, from early infancy has shown improvement in clinical outcomes of spinal muscular atrophy patients.
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Affiliation(s)
- Bijaylaxmi Behera
- Department of Neonatology, Chaitanya Hospital, Chandigarh 160044, India
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36
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Saoudi A, Goyenvalle A. [RNA splicing modulation: Therapeutic progress and perspectives]. Med Sci (Paris) 2021; 37:625-631. [PMID: 34180822 DOI: 10.1051/medsci/2021091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Advances in genetic and genomic research continue to increase our knowledge of hereditary diseases, and an increasing number of them are being attributed to aberrant splicing, thus representing ideal targets for RNA modulation therapies. New strategies to skip or re-include exons during the splicing process have emerged and are now widely evaluated in the clinic. Several drugs have recently been approved in particular for the treatment of Duchenne muscular dystrophy and spinal muscular atrophy. Among these molecules, antisense oligonucleotides, or ASOs, have gained increasing interest and have constantly been improved over the years through chemical modifications and design. However, their limited biodistribution following systemic administration still represents a major hurdle and the development of more potent alternative chemistries or new delivery systems has become a very active line of research in the past few years. In parallel, the use of small molecules with excellent biodistribution properties or of viral vectors to convey antisense sequences is also being investigated. In this review, we summarize the recent advances in splicing therapies through two examples of neuromuscular diseases and we discuss their main benefits and current limitations.
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Affiliation(s)
- Amel Saoudi
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, Handicap neuromusculaire - physiopathologie, biothérapie et pharmacologie appliquées, 78000 Versailles, France - Université Paris-Saclay, CNRS, Institut des neurosciences Paris Saclay, 91190 Gif-sur-Yvette, France
| | - Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, Handicap neuromusculaire - physiopathologie, biothérapie et pharmacologie appliquées, 78000 Versailles, France - Laboratoire international associé Biothérapies appliquées aux handicaps neuromusculaires (LIA BAHN), Centre scientifique de Monaco, Monaco
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37
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Garner AL, Djuric SW. RNA: Opening New Doors in Medicinal Chemistry, a Special Issue. ACS Med Chem Lett 2021; 12:851-853. [PMID: 34141054 PMCID: PMC8201500 DOI: 10.1021/acsmedchemlett.1c00279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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38
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Xie J, Frank AT. Mining for Ligandable Cavities in RNA. ACS Med Chem Lett 2021; 12:928-934. [PMID: 34141071 DOI: 10.1021/acsmedchemlett.1c00068] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/18/2021] [Indexed: 12/23/2022] Open
Abstract
Identifying potential ligand binding cavities is a critical step in structure-based screening of biomolecular targets. Cavity mapping methods can detect such binding cavities; however, for ribonucleic acid (RNA) targets, determining which of the detected cavities are "ligandable" remains an unsolved challenge. In this study, we trained a set of machine learning classifiers to distinguish ligandable RNA cavities from decoy cavities. Application of our classifiers to two independent test sets demonstrated that we could recover ligandable cavities from decoys with an AUC > 0.83. Interestingly, when we applied our classifiers to a library of modeled structures of the HIV-1 transactivation response (TAR) element RNA, we found that several of the conformers that harbored cavities with high ligandability scores resembled known holo-TAR structures. On the basis of our results, we envision that our classifiers could find utility as a tool to parse RNA structures and prospectively mine for ligandable binding cavities and, in so doing, facilitate structure-based virtual screening efforts against RNA drug targets.
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Affiliation(s)
- Jingru Xie
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aaron T. Frank
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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39
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A deep learning approach to identify gene targets of a therapeutic for human splicing disorders. Nat Commun 2021; 12:3332. [PMID: 34099697 PMCID: PMC8185002 DOI: 10.1038/s41467-021-23663-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/07/2021] [Indexed: 01/16/2023] Open
Abstract
Pre-mRNA splicing is a key controller of human gene expression. Disturbances in splicing due to mutation lead to dysregulated protein expression and contribute to a substantial fraction of human disease. Several classes of splicing modulator compounds (SMCs) have been recently identified and establish that pre-mRNA splicing represents a target for therapy. We describe herein the identification of BPN-15477, a SMC that restores correct splicing of ELP1 exon 20. Using transcriptome sequencing from treated fibroblast cells and a machine learning approach, we identify BPN-15477 responsive sequence signatures. We then leverage this model to discover 155 human disease genes harboring ClinVar mutations predicted to alter pre-mRNA splicing as targets for BPN-15477. Splicing assays confirm successful correction of splicing defects caused by mutations in CFTR, LIPA, MLH1 and MAPT. Subsequent validations in two disease-relevant cellular models demonstrate that BPN-15477 increases functional protein, confirming the clinical potential of our predictions.
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40
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Abstract
RNAs are involved in an enormous range of cellular processes, including gene regulation, protein synthesis, and cell differentiation, and dysfunctional RNAs are associated with disorders such as cancers, neurodegenerative diseases, and viral infections. Thus, the identification of compounds with the ability to bind RNAs and modulate their functions is an exciting approach for developing next-generation therapies. Numerous RNA-binding agents have been reported over the past decade, but the design of synthetic molecules with selectivity for specific RNA sequences is still in its infancy. In this perspective, we highlight recent advances in targeting RNAs with synthetic molecules, and we discuss the potential value of this approach for the development of innovative therapeutic agents.
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Affiliation(s)
- Farzad Zamani
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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41
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Grand DL, Gosling M, Baettig U, Bahra P, Bala K, Brocklehurst C, Budd E, Butler R, Cheung AK, Choudhury H, Collingwood SP, Cox B, Danahay H, Edwards L, Everatt B, Glaenzel U, Glotin AL, Groot-Kormelink P, Hall E, Hatto J, Howsham C, Hughes G, King A, Koehler J, Kulkarni S, Lightfoot M, Nicholls I, Page C, Pergl-Wilson G, Popa MO, Robinson R, Rowlands D, Sharp T, Spendiff M, Stanley E, Steward O, Taylor RJ, Tranter P, Wagner T, Watson H, Williams G, Wright P, Young A, Sandham DA. Discovery of Icenticaftor (QBW251), a Cystic Fibrosis Transmembrane Conductance Regulator Potentiator with Clinical Efficacy in Cystic Fibrosis and Chronic Obstructive Pulmonary Disease. J Med Chem 2021; 64:7241-7260. [PMID: 34028270 DOI: 10.1021/acs.jmedchem.1c00343] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel are established as the primary causative factor in the devastating lung disease cystic fibrosis (CF). More recently, cigarette smoke exposure has been shown to be associated with dysfunctional airway epithelial ion transport, suggesting a role for CFTR in the pathogenesis of chronic obstructive pulmonary disease (COPD). Here, the identification and characterization of a high throughput screening hit 6 as a potentiator of mutant human F508del and wild-type CFTR channels is reported. The design, synthesis, and biological evaluation of compounds 7-33 to establish structure-activity relationships of the scaffold are described, leading to the identification of clinical development compound icenticaftor (QBW251) 33, which has subsequently progressed to deliver two positive clinical proofs of concept in patients with CF and COPD and is now being further developed as a novel therapeutic approach for COPD patients.
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Affiliation(s)
- Darren Le Grand
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Martin Gosling
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Urs Baettig
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Parmjit Bahra
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Kamlesh Bala
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Cara Brocklehurst
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Emma Budd
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Rebecca Butler
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Atwood K Cheung
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Hedaythul Choudhury
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Stephen P Collingwood
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Brian Cox
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Henry Danahay
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Lee Edwards
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Brian Everatt
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Ulrike Glaenzel
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Anne-Lise Glotin
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Paul Groot-Kormelink
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Edward Hall
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Julia Hatto
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Catherine Howsham
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Glyn Hughes
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Anna King
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Julia Koehler
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Swarupa Kulkarni
- Novartis Institutes for Biomedical Research, East Hanover, New Jersey 07936, United States
| | - Megan Lightfoot
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Ian Nicholls
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Christopher Page
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Giles Pergl-Wilson
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Mariana Oana Popa
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Richard Robinson
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - David Rowlands
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Tom Sharp
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Matthew Spendiff
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Emily Stanley
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Oliver Steward
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Roger J Taylor
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Pamela Tranter
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Trixie Wagner
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Hazel Watson
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Gareth Williams
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Penny Wright
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Alice Young
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - David A Sandham
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
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42
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McCormack NM, Abera MB, Arnold ES, Gibbs RM, Martin SE, Buehler E, Chen YC, Chen L, Fischbeck KH, Burnett BG. A high-throughput genome-wide RNAi screen identifies modifiers of survival motor neuron protein. Cell Rep 2021; 35:109125. [PMID: 33979606 PMCID: PMC8679797 DOI: 10.1016/j.celrep.2021.109125] [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: 10/19/2020] [Revised: 03/17/2021] [Accepted: 04/22/2021] [Indexed: 11/28/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a debilitating neurological disorder marked by degeneration of spinal motor neurons and muscle atrophy. SMA results from mutations in survival motor neuron 1 (SMN1), leading to deficiency of survival motor neuron (SMN) protein. Current therapies increase SMN protein and improve patient survival but have variable improvements in motor function, making it necessary to identify complementary strategies to further improve disease outcomes. Here, we perform a genome-wide RNAi screen using a luciferase-based activity reporter and identify genes involved in regulating SMN gene expression, RNA processing, and protein stability. We show that reduced expression of Transcription Export complex components increases SMN levels through the regulation of nuclear/cytoplasmic RNA transport. We also show that the E3 ligase, Neurl2, works cooperatively with Mib1 to ubiquitinate and promote SMN degradation. Together, our screen uncovers pathways through which SMN expression is regulated, potentially revealing additional strategies to treat SMA. Treatments for spinal muscular atrophy aim to increase survival motor neuron (SMN) protein. Using a genome-wide RNAi screen, McCormack et al. identify modifiers of SMN expression, including genes that are involved in transcription regulation, RNA processing, and protein stability.
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Affiliation(s)
- Nikki M McCormack
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
| | - Mahlet B Abera
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA
| | - Eveline S Arnold
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Rebecca M Gibbs
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Scott E Martin
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Eugen Buehler
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Yu-Chi Chen
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Lu Chen
- Functional Genomics Lab, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850, USA
| | - Kenneth H Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Barrington G Burnett
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD 20814, USA.
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Thavarajah W, Hertz LM, Bushhouse DZ, Archuleta CM, Lucks JB. RNA Engineering for Public Health: Innovations in RNA-Based Diagnostics and Therapeutics. Annu Rev Chem Biomol Eng 2021; 12:263-286. [PMID: 33900805 PMCID: PMC9714562 DOI: 10.1146/annurev-chembioeng-101420-014055] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA is essential for cellular function: From sensing intra- and extracellular signals to controlling gene expression, RNA mediates a diverse and expansive list of molecular processes. A long-standing goal of synthetic biology has been to develop RNA engineering principles that can be used to harness and reprogram these RNA-mediated processes to engineer biological systems to solve pressing global challenges. Recent advances in the field of RNA engineering are bringing this to fruition, enabling the creation of RNA-based tools to combat some of the most urgent public health crises. Specifically, new diagnostics using engineered RNAs are able to detect both pathogens and chemicals while generating an easily detectable fluorescent signal as an indicator. New classes of vaccines and therapeutics are also using engineered RNAs to target a wide range of genetic and pathogenic diseases. Here, we discuss the recent breakthroughs in RNA engineering enabling these innovations and examine how advances in RNA design promise to accelerate the impact of engineered RNA systems.
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Affiliation(s)
- Walter Thavarajah
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Laura M Hertz
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
| | - David Z Bushhouse
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
| | - Chloé M Archuleta
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA.,Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, Illinois 60208, USA
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RNA-Targeting Splicing Modifiers: Drug Development and Screening Assays. Molecules 2021; 26:molecules26082263. [PMID: 33919699 PMCID: PMC8070285 DOI: 10.3390/molecules26082263] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
RNA splicing is an essential step in producing mature messenger RNA (mRNA) and other RNA species. Harnessing RNA splicing modifiers as a new pharmacological modality is promising for the treatment of diseases caused by aberrant splicing. This drug modality can be used for infectious diseases by disrupting the splicing of essential pathogenic genes. Several antisense oligonucleotide splicing modifiers were approved by the U.S. Food and Drug Administration (FDA) for the treatment of spinal muscular atrophy (SMA) and Duchenne muscular dystrophy (DMD). Recently, a small-molecule splicing modifier, risdiplam, was also approved for the treatment of SMA, highlighting small molecules as important warheads in the arsenal for regulating RNA splicing. The cellular targets of these approved drugs are all mRNA precursors (pre-mRNAs) in human cells. The development of novel RNA-targeting splicing modifiers can not only expand the scope of drug targets to include many previously considered “undruggable” genes but also enrich the chemical-genetic toolbox for basic biomedical research. In this review, we summarized known splicing modifiers, screening methods for novel splicing modifiers, and the chemical space occupied by the small-molecule splicing modifiers.
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Axford J, Sung MJ, Manchester J, Chin D, Jain M, Shin Y, Dix I, Hamann LG, Cheung AK, Sivasankaran R, Briner K, Dales NA, Hurley B. Use of Intramolecular 1,5-Sulfur-Oxygen and 1,5-Sulfur-Halogen Interactions in the Design of N-Methyl-5-aryl- N-(2,2,6,6-tetramethylpiperidin-4-yl)-1,3,4-thiadiazol-2-amine SMN2 Splicing Modulators. J Med Chem 2021; 64:4744-4761. [PMID: 33822618 DOI: 10.1021/acs.jmedchem.0c02173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Spinal muscular atrophy (SMA) is a debilitating neuromuscular disease caused by low levels of functional survival motor neuron protein (SMN) resulting from a deletion or loss of function mutation of the survival motor neuron 1 (SMN1) gene. Branaplam (1) elevates levels of full-length SMN protein in vivo by modulating the splicing of the related gene SMN2 to enhance the exon-7 inclusion and increase levels of the SMN. The intramolecular hydrogen bond present in the 2-hydroxyphenyl pyridazine core of 1 enforces a planar conformation of the biaryl system and is critical for the compound activity. Scaffold morphing revealed that the pyridazine could be replaced by a 1,3,4-thiadiazole, which provided additional opportunities for a conformational constraint of the biaryl through intramolecular 1,5-sulfur-oxygen (S···O) or 1,5-sulfur-halogen (S···X) noncovalent interactions. Compound 26, which incorporates a 2-fluorophenyl thiadiazole motif, demonstrated a greater than 50% increase in production of full-length SMN protein in a mouse model of SMA.
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Affiliation(s)
- Jake Axford
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Moo Je Sung
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - John Manchester
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Donovan Chin
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Monish Jain
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Youngah Shin
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ina Dix
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Lawrence G Hamann
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Atwood K Cheung
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Rajeev Sivasankaran
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Karin Briner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Natalie A Dales
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Brian Hurley
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Nicolau S, Waldrop MA, Connolly AM, Mendell JR. Spinal Muscular Atrophy. Semin Pediatr Neurol 2021; 37:100878. [PMID: 33892848 DOI: 10.1016/j.spen.2021.100878] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023]
Abstract
Spinal muscular atrophy is one of the most common neuromuscular disorders of childhood and has high morbidity and mortality. Three different disease-modifying treatments were introduced in the last 4 years: nusinersen, onasemnogene abeparvovec, and risdiplam. These agents have demonstrated safety and efficacy, but their long-term benefits require further study. Newborn screening programs are enabling earlier diagnosis and treatment and better outcomes, but respiratory care and other supportive measures retain a key role in the management of spinal muscular atrophy. Ongoing efforts seek to optimize gene therapy vectors, explore new therapeutic targets beyond motor neurons, and evaluate the role of combination therapy.
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Affiliation(s)
- Stefan Nicolau
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH.
| | - Megan A Waldrop
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology, Ohio State University, Columbus, OH
| | - Anne M Connolly
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology, Ohio State University, Columbus, OH
| | - Jerry R Mendell
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology, Ohio State University, Columbus, OH
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47
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A high-throughput screening to identify small molecules that suppress huntingtin promoter activity or activate huntingtin-antisense promoter activity. Sci Rep 2021; 11:6157. [PMID: 33731741 PMCID: PMC7969751 DOI: 10.1038/s41598-021-85279-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/09/2021] [Indexed: 12/26/2022] Open
Abstract
Huntington’s disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in exon 1 of huntingtin (HTT). While there are currently no disease-modifying treatments for HD, recent efforts have focused on the development of nucleotide-based therapeutics to lower HTT expression. As an alternative to siRNA or oligonucleotide methods, we hypothesized that suppression of HTT expression might be accomplished by small molecules that either (1) directly decrease HTT expression by suppressing HTT promoter activity or (2) indirectly decrease HTT expression by increasing the promoter activity of HTT-AS, the gene antisense to HTT that appears to inhibit expression of HTT. We developed and employed a high-throughput screen for modifiers of HTT and HTT-AS promoter activity using luminescent reporter HEK293 cells; of the 52,041 compounds tested, we identified 898 replicable hits. We used a rigorous stepwise approach to assess compound toxicity and the capacity of the compounds to specifically lower huntingtin protein in 5 different cell lines, including HEK293 cells, HD lymphoblastoid cells, mouse primary neurons, HD iPSCs differentiated into cortical-like neurons, and HD hESCs. We found no compounds which were able to lower huntingtin without lowering cell viability in all assays, though the potential efficacy of a few compounds at non-toxic doses could not be excluded. Our results suggest that more specific targets may facilitate a small molecule approach to HTT suppression.
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Osmanovic A, Ranxha G, Kumpe M, Wurster CD, Stolte B, Cordts I, Günther R, Freigang M, Müschen LH, Binz C, Hermann A, Deschauer M, Lingor P, Ludolph AC, Hagenacker T, Schreiber-Katz O, Petri S. Treatment satisfaction in 5q-spinal muscular atrophy under nusinersen therapy. Ther Adv Neurol Disord 2021; 14:1756286421998902. [PMID: 33747131 PMCID: PMC7940734 DOI: 10.1177/1756286421998902] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Nusinersen was the first approved disease-modifying therapy for all 5q-spinal muscular atrophy (SMA) patients regardless of age or disease severity. Its efficacy in adults has recently been demonstrated in a large cohort by motor outcome measures, which were only partially suitable to detect changes in very mildly or severely affected patients. Patient-reported outcome measures (PROs) have been suggested as a valuable addition. Here, we aimed to assess treatment satisfaction and investigate whether it may be a useful PRO to monitor SMA patients. Methods: We enrolled 91 mainly adult 5q-SMA patients treated with nusinersen in a national, multicenter, cross-sectional observational study. 21 patients underwent longitudinal follow up. Patients’ satisfaction with treatment in four dimensions (global, effectiveness, convenience, side effects) was assessed by the Treatment Satisfaction Questionnaire for Medication German version 1.4 (TSQM-1.4©) and related to clinical parameters, motor scores, and treatment duration. Results: More than 90% of SMA patients were consistently satisfied over a median treatment duration of 10 months. Highest mean scores were observed in the dimensions ‘side effects,’ ‘global satisfaction,’ and ‘effectiveness’ (93.5 ± 14.8 versus 73.1 ± 21.0 and 64.8 ± 20.6, respectively). Patients’ satisfaction with the convenience of treatment was considerably lower (43.6 ± 20.2). Interestingly, satisfaction with the effectiveness was higher in ambulatory (p = 0.014) compared with non-ambulatory patients and directly correlated to motor outcome measures. Five non-ambulatory patients withdrew from therapy. All of them presented with a deterioration of motor outcome measures and reported dissatisfaction with treatment effectiveness and convenience. Conclusion: Most patients were satisfied with nusinersen treatment effectiveness. Less severely affected patients indicated higher satisfaction. The TSQM-1.4© helped to identify therapy non-responders, who mainly addressed dissatisfaction with effectiveness and convenience. We suggest introducing the TSQM-1.4© as an additional PRO in SMA into clinical practice.
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Affiliation(s)
| | - Gresa Ranxha
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Mareike Kumpe
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | | | - Benjamin Stolte
- Department of Neurology, University Hospital Essen, Essen, Germany
| | - Isabell Cordts
- Department of Neurology, Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - René Günther
- Department of Neurology, Technische Universität Dresden, Dresden, Sachsen, Germany
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
| | - Maren Freigang
- Department of Neurology, Technische Universität Dresden, Dresden, Sachsen, Germany
| | - Lars H. Müschen
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Camilla Binz
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Andreas Hermann
- Translational Neurodegeneration Section ‘Albrecht-Kossel,’ Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
- German Center for Neurodegenerative Diseases (DZNE) Rostock, Rostock, Germany
| | - Marcus Deschauer
- Department of Neurology, Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - Paul Lingor
- Department of Neurology, Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - Albert C. Ludolph
- Department of Neurology, Ulm University, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
| | - Tim Hagenacker
- Department of Neurology, University Hospital Essen, Essen, Germany
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Julio AR, Backus KM. New approaches to target RNA binding proteins. Curr Opin Chem Biol 2021; 62:13-23. [PMID: 33535093 DOI: 10.1016/j.cbpa.2020.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/15/2020] [Accepted: 12/29/2020] [Indexed: 12/13/2022]
Abstract
RNA binding proteins (RBPs) are a large and diverse class of proteins that regulate all aspects of RNA biology. As RBP dysregulation has been implicated in a number of human disorders, including cancers and neurodegenerative disease, small molecule chemical probes that target individual RBPs represent useful tools for deciphering RBP function and guiding the production of new therapeutics. While RBPs are often thought of as tough-to-drug, the discovery of a number of small molecules that target RBPs has spurred considerable recent interest in new strategies for RBP chemical probe discovery. Here we review current and emerging technologies for high throughput RBP-small molecule screening that we expect will help unlock the full therapeutic potential of this exciting protein class.
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Affiliation(s)
- Ashley R Julio
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M Backus
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA; Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA; DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA.
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50
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Ravi B, Chan-Cortés MH, Sumner CJ. Gene-Targeting Therapeutics for Neurological Disease: Lessons Learned from Spinal Muscular Atrophy. Annu Rev Med 2021; 72:1-14. [PMID: 33502897 DOI: 10.1146/annurev-med-070119-115459] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The last few decades have seen an explosion in identification of genes that cause monogenetic neurological diseases, as well as advances in gene-targeting therapeutics. Neurological conditions that were once considered incurable are now increasingly tractable. At the forefront is the motor neuron disease spinal muscular atrophy (SMA), historically the leading inherited cause of infant mortality. In the last 5 years, three SMA treatments have been approved by the US Food and Drug Administration (FDA): intrathecally delivered splice-switching antisense oligonucleotide (nusinersen), systemically delivered AAV9-based gene replacement therapy (onasemnogene abeparvovec), and an orally bioavailable, small-molecule, splice-switching drug (risdiplam). Despite this remarkable progress, clinical outcomes in patients are variable. Therapeutic optimization will require improved understanding of drug pharmacokinetics and target engagement in neurons, potential toxicities, and long-term effects. We review current progress in SMA therapeutics, clinical trials, shortcomings of current treatments, and implications for the treatment of other neurogenetic diseases.
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Affiliation(s)
- Bhavya Ravi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
| | | | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; .,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21202, USA
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