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Mohsen M, Midy MK, Balaji A, Breaker RR. Engineered Branaplam Aptamers Exploit Structural Elements from Natural Riboswitches. ACS Chem Biol 2024; 19:1447-1452. [PMID: 38954594 PMCID: PMC11267568 DOI: 10.1021/acschembio.4c00358] [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: 05/23/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024]
Abstract
Drug candidates that fail in clinical trials for efficacy reasons might still have favorable safety and bioavailability characteristics that could be exploited. A failed drug candidate could be repurposed if a receptor, such as an aptamer, were created that binds the compound with high specificity. Branaplam is a small molecule that was previously in development to treat spinal muscular atrophy and Huntington's disease. Here, we report the development of a small (48-nucleotide) RNA aptamer for branaplam with a dissociation constant of ∼150 nM. Starting with a combinatorial RNA pool integrating the secondary and tertiary structural scaffold of a Guanine-I riboswitch aptamer interspersed with regions of random sequence, in vitro selection yielded aptamer candidates for branaplam. Reselection and rational design were employed to improve binding of a representative branaplam aptamer candidate. A resulting variant retains the pseudoknot and two of the paired elements (P2 and P3) from the scaffold but lacks the enclosing paired element (P1) that is essential for the function of the natural Guanine-I riboswitch aptamer. A second combinatorial RNA pool based on the scaffold for TPP (thiamin pyrophosphate) riboswitches also yielded a candidate offering additional opportunities for branaplam aptamer development.
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Affiliation(s)
- Michael
G. Mohsen
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
- Howard
Hughes Medical Institute, Yale University, New Haven, Connecticut 06511, United States
| | - Matthew K. Midy
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Aparaajita Balaji
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - Ronald R. Breaker
- Department
of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
- Howard
Hughes Medical Institute, Yale University, New Haven, Connecticut 06511, United States
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2
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Nowak I, Paździor M, Sarna R, Madej M. Molecular Mechanisms in the Design of Novel Targeted Therapies for Neurodegenerative Diseases. Curr Issues Mol Biol 2024; 46:5436-5453. [PMID: 38920997 PMCID: PMC11202845 DOI: 10.3390/cimb46060325] [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: 03/28/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
Neurodegenerative diseases are a diverse group of diseases characterized by a progressive loss of neurological function due to damage to nerve cells in the central nervous system. In recent years, there has been a worldwide increase in the expanding associated with increasing human life expectancy. Molecular mechanisms control many of the essential life processes of cells, such as replication, transcription, translation, protein synthesis and gene regulation. These are complex interactions that form the basis for understanding numerous processes in the organism and developing new diagnostic and therapeutic approaches. In the context of neurodegenerative diseases, molecular basis refers to changes at the molecular level that cause damage to or degeneration of nerve cells. These may include protein aggregates leading to pathological structures in brain cells, impaired protein transport in nerve cells, mitochondrial dysfunction, inflammatory processes or genetic mutations that impair nerve cell function. New medical therapies are based on these mechanisms and include gene therapies, reduction in inflammation and oxidative stress, and the use of miRNAs and regenerative medicine. The aim of this study was to bring together the current state of knowledge regarding selected neurodegenerative diseases, presenting the underlying molecular mechanisms involved, which could be potential targets for new forms of treatment.
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Affiliation(s)
- Ilona Nowak
- Silesia LabMed, Centre for Research and Implementation, Medical University of Silesia in Katowice, 18 Medykow Str., 40-752 Katowice, Poland; (M.P.); (R.S.); (M.M.)
| | - Marlena Paździor
- Silesia LabMed, Centre for Research and Implementation, Medical University of Silesia in Katowice, 18 Medykow Str., 40-752 Katowice, Poland; (M.P.); (R.S.); (M.M.)
| | - Robert Sarna
- Silesia LabMed, Centre for Research and Implementation, Medical University of Silesia in Katowice, 18 Medykow Str., 40-752 Katowice, Poland; (M.P.); (R.S.); (M.M.)
| | - Marcel Madej
- Silesia LabMed, Centre for Research and Implementation, Medical University of Silesia in Katowice, 18 Medykow Str., 40-752 Katowice, Poland; (M.P.); (R.S.); (M.M.)
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland
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3
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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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4
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Yang X, Zhang B, Wang S, Lu Y, Chen K, Luo C, Sun A, Zhang H. OTTM: an automated classification tool for translational drug discovery from omics data. Brief Bioinform 2023; 24:bbad301. [PMID: 37594310 PMCID: PMC10516341 DOI: 10.1093/bib/bbad301] [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: 05/29/2023] [Revised: 07/22/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
Omics data from clinical samples are the predominant source of target discovery and drug development. Typically, hundreds or thousands of differentially expressed genes or proteins can be identified from omics data. This scale of possibilities is overwhelming for target discovery and validation using biochemical or cellular experiments. Most of these proteins and genes have no corresponding drugs or even active compounds. Moreover, a proportion of them may have been previously reported as being relevant to the disease of interest. To facilitate translational drug discovery from omics data, we have developed a new classification tool named Omics and Text driven Translational Medicine (OTTM). This tool can markedly narrow the range of proteins or genes that merit further validation via drug availability assessment and literature mining. For the 4489 candidate proteins identified in our previous proteomics study, OTTM recommended 40 FDA-approved or clinical trial drugs. Of these, 15 are available commercially and were tested on hepatocellular carcinoma Hep-G2 cells. Two drugs-tafenoquine succinate (an FDA-approved antimalarial drug targeting CYC1) and branaplam (a Phase 3 clinical drug targeting SMN1 for the treatment of spinal muscular atrophy)-showed potent inhibitory activity against Hep-G2 cell viability, suggesting that CYC1 and SMN1 may be potential therapeutic target proteins for hepatocellular carcinoma. In summary, OTTM is an efficient classification tool that can accelerate the discovery of effective drugs and targets using thousands of candidate proteins identified from omics data. The online and local versions of OTTM are available at http://otter-simm.com/ottm.html.
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Affiliation(s)
- Xiaobo Yang
- ShanghaiTech University
- School of Life Science and Technology, ShanghaiTech University, 393 Huaxiazhong Road, Shanghai 200031, China
| | - Bei Zhang
- Shanghai Institute of Materia Medica
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Siqi Wang
- Beijing Proteome Research Center
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, and National Center for Protein Sciences (Beijing)
| | - Ye Lu
- Nanjing University of Chinese Medicine
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; Chemical Biology Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kaixian Chen
- academician medicinal scientist of the Chinese Academy of Sciences
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, 393 Huaxiazhong Road, Shanghai 200031, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Cheng Luo
- Shanghai Institute of Materia Medica
- Chemical Biology Research Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Aihua Sun
- Beijing Proteome Research Center
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics; Research Unit of Proteomics-driven Cancer Precision Medicine, Chinese Academy of Medical Sciences
| | - Hao Zhang
- Shanghai Institute of Materia Medica
- Chemical Biology Research Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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5
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Krach F, Stemick J, Boerstler T, Weiss A, Lingos I, Reischl S, Meixner H, Ploetz S, Farrell M, Hehr U, Kohl Z, Winner B, Winkler J. An alternative splicing modulator decreases mutant HTT and improves the molecular fingerprint in Huntington's disease patient neurons. Nat Commun 2022; 13:6797. [PMID: 36357392 PMCID: PMC9649613 DOI: 10.1038/s41467-022-34419-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/21/2022] [Indexed: 11/12/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by poly-Q expansion in the Huntingtin (HTT) protein. Here, we delineate elevated mutant HTT (mHTT) levels in patient-derived cells including fibroblasts and iPSC derived cortical neurons using mesoscale discovery (MSD) HTT assays. HD patients' fibroblasts and cortical neurons recapitulate aberrant alternative splicing as a molecular fingerprint of HD. Branaplam is a splicing modulator currently tested in a phase II study in HD (NCT05111249). The drug lowers total HTT (tHTT) and mHTT levels in fibroblasts, iPSC, cortical progenitors, and neurons in a dose dependent manner at an IC50 consistently below 10 nM without inducing cellular toxicity. Branaplam promotes inclusion of non-annotated novel exons. Among these Branaplam-induced exons, there is a 115 bp frameshift-inducing exon in the HTT transcript. This exon is observed upon Branaplam treatment in Ctrl and HD patients leading to a profound reduction of HTT RNA and protein levels. Importantly, Branaplam ameliorates aberrant alternative splicing in HD patients' fibroblasts and cortical neurons. These findings highlight the applicability of splicing modulators in the treatment of CAG repeat disorders and decipher their molecular effects associated with the pharmacokinetic and -dynamic properties in patient-derived cellular models.
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Affiliation(s)
- Florian Krach
- grid.5330.50000 0001 2107 3311Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Judith Stemick
- grid.5330.50000 0001 2107 3311Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Tom Boerstler
- grid.5330.50000 0001 2107 3311Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | | | - Ioannis Lingos
- grid.428240.80000 0004 0553 4650Evotec SE, Hamburg, Germany
| | - Stephanie Reischl
- grid.5330.50000 0001 2107 3311Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Holger Meixner
- grid.5330.50000 0001 2107 3311Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sonja Ploetz
- grid.5330.50000 0001 2107 3311Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Michaela Farrell
- grid.5330.50000 0001 2107 3311Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ute Hehr
- Zentrum für Humangenetik Regensburg, Regensburg, Germany
| | - Zacharias Kohl
- grid.7727.50000 0001 2190 5763Department of Neurology, University of Regensburg, Regensburg, Germany
| | - Beate Winner
- grid.5330.50000 0001 2107 3311Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany ,grid.5330.50000 0001 2107 3311Center for Rare Diseases Erlangen (ZSEER), University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Juergen Winkler
- grid.5330.50000 0001 2107 3311Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany ,grid.5330.50000 0001 2107 3311Center for Rare Diseases Erlangen (ZSEER), University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
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6
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Bower N, Achanzar WE, Boulifard V, Brinck PR, Kittel B, Vahle JL. The Dog as a Second Species for Toxicology Testing Provides Value to Drug Development. Int J Toxicol 2022; 41:431-441. [DOI: 10.1177/10915818221125670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The objective of the pharmaceutical industry is to develop new drugs that are safe for human use. In many cases, the accepted approach codified in guidance from regulatory authorities to assess the nonclinical safety profile of potential pharmaceuticals is to perform toxicity testing in two species. However, the use of a second species to establish the safety of new pharmaceuticals has been the subject of much scrutiny in recent years and the industry has been repeatedly challenged to reduce, refine, or replace some or all of the animals used to establish the safety of these pharmaceutical candidates. Specifically, the value of the dog in this testing paradigm has been questioned. Publications reviewing available data for marketed drugs suggest that for many drugs, the dog does not identify unique toxicities critical to human safety. The weakness of this approach, however, is that many of the cases where the dog (or any other species) has the greatest impact on drug development are cases for which development decisions based on safety concerns are not shared publicly. The European Federation of Pharmaceutical Industries and Associations (EFPIA) Preclinical Development Expert Group (PDEG) decided to share case studies collected from its membership and the literature to illustrate the value of the dog in drug development decision-making and clinical monitoring practices to protect the safety of trial subjects.
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Affiliation(s)
- Nancy Bower
- Global Nonclinical Regulatory Affairs, Eisai Inc, Woodcliff Lake, NJ, USA
| | | | | | | | - Birgit Kittel
- Preclinical Safety, Novartis Pharma, Basel, Switzerland
| | - John L. Vahle
- Lilly Corporate Center, Lilly Research Laboratories, Indianapolis, IN, USA
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