Therapeutics

DNL343

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Overview

Name: DNL343
Chemical Name: 2-(4-chlorophenoxy)-N-(3-(5-((1s,3s)-3-(trifluoromethoxy)cyclobutyl)-1,3,4-oxadiazol-2-yl)bicyclo[1.1.1]pentan-1-yl)acetamide
Therapy Type: Small Molecule (timeline)
Target Type: Other (timeline)
Condition(s): Amyotrophic Lateral Sclerosis
U.S. FDA Status: Amyotrophic Lateral Sclerosis (Phase 2/3)
Company: Denali Therapeutics Inc.

Background

DNL343 is a brain-penetrant activator of the eukaryotic initiation factor EIF2b. It inhibits the cell's unfolded protein response in an attempt to restore protein synthesis. Normally, EIF2b, with its EIF2a subunit, functions to initiate mRNA translation. Under conditions of cellular stress, phosphorylation of the EIF2a subunit by the PERK kinase leads to inhibition of EIF2b, and pauses protein synthesis as part of the cell’s integrated stress response (ISR). Loss-of-function mutations in EIF2b that impair protein translation cause a progressive neurodegenerative syndrome affecting the brain and spinal cord, called vanishing white-matter disease (see OMIM).

In some neurodegenerative diseases, maladaptive PERK activation and EIF2b inhibition occur as part of the cellular response to an accumulation of misfolded proteins in the endoplasmic reticulum (for example, Stutzbach et al., 2013). The resulting deficit in protein synthesis contributes to synaptic dysfunction and memory impairment. EIF2b inhibition is also linked to stress granule formation and pathogenic protein aggregation.

Restoring EIF2b activity using PERK inhibitors or genetic approaches has been shown to protect against neurodegeneration in preclinical models of prion disease, frontotemporal dementia, and ALS (reviewed in Smith and Mallucci, 2016).

A publication describes the discovery and optimization of DNL343 for clinical development (Craig et al., 2024). In animal studies, DNL343 had a long half-life and high oral availability, and readily entered the CNS. Preclinical toxicology revealed no safety signs. In mice with a mutated, low-activity form of EIF2b, the compound normalized expression of genes related to the integrated stress response in brain.

While no other preclinical data are published on DNL343, there is a growing literature on the EIF2b activator, ISRIB, that formed the basis for research at Denali and at least one other company, Calico Life Sciences (see Wong et al., 2019). ISRIB counteracts the effects of EIF2a phosphorylation, increasing protein synthesis and preventing stress granule formation; it also improves learning and memory in mice (Sidrauski et al., 2013; Sidrauski et al., 2015; Sidrauski et al., 2015). The ISRIB binding site on EIF2b has been resolved by X-ray crystallography (Zyryanova et al., 2018; Tsai et al., 2018; and review by Marintchev and Ito, 2020).

In preclinical work, ISRIB was neuroprotective in models of head trauma, Down's syndrome, and vanishing white-matter disease (Chou et al., 2017; Zhu et al., 2019; Abbink et al., 2019). It also protected neurons from SOD-1 toxicity in a cellular model of ALS (Bugallo et al., 2020). In prion-infected mice, ISRIB appeared safer than the PERK inhibitor GSK2606414, which showed pancreatic toxicity (Halliday et al., 2015).

In Alzheimer’s models, ISRIB prevented Aβ-induced cell death (Hosoi et al., 2016) but did not improve cognition in either the APPswe or hAPP-J20 models, and daily dosing led to significant mortality in the former (Briggs et al., 2017; Johnson and Kang, 2016). More recent studies did report effects counteracting synaptic and memory loss in AD mouse models and in a rat model of Aβ42 injection (Oliveira et al., 2021; Hu et al., 2022). ISRIB also prevented tau phosphorylation at residues 181 and 217 that occurred in response to synaptic long-term depression (Zhang et al., 2022).

Findings

In February 2020, Denali began a Phase 1 trial testing single and multiple ascending oral doses of DNL343 in 88 healthy adults. The primary outcomes are safety and plasma pharmacokinetics measured up to 20 days. Secondary outcomes include DNL343 uptake into the CSF, renal clearance, and pharmacodynamic measures of integrated stress response protein and mRNA levels in blood by ELISA and quantitative PCR. The study was expected to end in October 2020, but was delayed to August 2021 after enrollment was paused due to COVID-19 (press release). Denali presented results at a conference in October 2021 (press release). DNL343 was claimed to be safe and well-tolerated up to 14 days of dosing, and to have entered the CNS with pharmacokinetics suited to once-daily dosing. The company reported changes in blood biomarkers of the ISR, confirming target engagement.

In December 2020, a second Phase 1 trial began to investigate effects of formulation and food on DNL343's safety and pharmacokinetics in 31 healthy men and women. It was completed in June 2021.

In August 2021, a Phase 1b trial began recruiting 30 people with ALS to compare multiple doses of DNL343 against placebo on measures of safety and pharmacokinetics. The 28-day study is to be followed by an 18-month, open-label extension. The trial will run through December 2023.

On December 5, 2022, Denali announced interim results of the 1b trial (press release). Once-daily oral dosing for 28 days was "generally well tolerated" by 20 participants who had completed the double-blind portion of the study. The ratio of CSF to blood drug concentrations ranged from 1.02-1.23. Treatment inhibited ISR pathway biomarkers ATF4 and CHAC1 in blood. 

Also on December 5, Denali and the Massachusetts General Hospital announced that DNL343 would advance to a Phase 2/3 study in the Healey ALS Platform Trial, an ongoing, multicenter clinical trial evaluating potential new treatments for ALS (press release). The study began in May 2023 to randomize 240 patients to daily drug or placebo for 24 weeks. The primary outcome is disease progression on the ALS-Functional Rating Scale-Revised, and mortality. Secondary outcomes include muscle strength, respiratory function, and serum neurofilament light chain levels. In May 2024, enrollment finished (press release). The trial will run through July 2025.

In early 2024, the company completed a Phase 1 trial assessing the absorption, metabolism, and secretion of [14C]-DNL343 in healthy men.

Calico/AbbVie are also evaluating an EIF2b activator in ALS (see ABBV-CLS-7262).

For details on DNL343 trials, see clinicaltrials.gov.

Last Updated: 14 Jul 2024

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References

Therapeutics Citations

  1. ABBV-CLS-7262

Paper Citations

  1. Stutzbach LD, Xie SX, Naj AC, Albin R, Gilman S, PSP Genetics Study Group, Lee VM, Trojanowski JQ, Devlin B, Schellenberg GD. The unfolded protein response is activated in disease-affected brain regions in progressive supranuclear palsy and Alzheimer's disease. Acta Neuropathol Commun. 2013 Jul 6;1(1):31. PubMed.
  2. Smith HL, Mallucci GR. The unfolded protein response: mechanisms and therapy of neurodegeneration. Brain. 2016 Aug;139(Pt 8):2113-21. Epub 2016 May 11 PubMed.
  3. Craig RA 2nd, De Vicente J, Estrada AA, Feng JA, Lexa KW, Canet MJ, Dowdle WE, Erickson RI, Flores BN, Haddick PC, Kane LA, Lewcock JW, Moerke NJ, Poda SB, Sweeney Z, Takahashi RH, Tong V, Wang J, Yulyaningsih E, Solanoy H, Scearce-Levie K, Sanchez PE, Tang L, Xu M, Zhang R, Osipov M. Discovery of DNL343: A Potent, Selective, and Brain-Penetrant eIF2B Activator Designed for the Treatment of Neurodegenerative Diseases. J Med Chem. 2024 Apr 11;67(7):5758-5782. Epub 2024 Mar 21 PubMed.
  4. Wong YL, LeBon L, Basso AM, Kohlhaas KL, Nikkel AL, Robb HM, Donnelly-Roberts DL, Prakash J, Swensen AM, Rubinstein ND, Krishnan S, McAllister FE, Haste NV, O'Brien JJ, Roy M, Ireland A, Frost JM, Shi L, Riedmaier S, Martin K, Dart MJ, Sidrauski C. eIF2B activator prevents neurological defects caused by a chronic integrated stress response. Elife. 2019 Jan 9;8 PubMed.
  5. Sidrauski C, Acosta-Alvear D, Khoutorsky A, Vedantham P, Hearn BR, Li H, Gamache K, Gallagher CM, Ang KK, Wilson C, Okreglak V, Ashkenazi A, Hann B, Nader K, Arkin MR, Renslo AR, Sonenberg N, Walter P. Pharmacological brake-release of mRNA translation enhances cognitive memory. Elife. 2013;2:e00498. PubMed.
  7. Sidrauski C, McGeachy AM, Ingolia NT, Walter P. The small molecule ISRIB reverses the effects of eIF2α phosphorylation on translation and stress granule assembly. Elife. 2015 Feb 26;4 PubMed.
  8. Zyryanova AF, Weis F, Faille A, Alard AA, Crespillo-Casado A, Sekine Y, Harding HP, Allen F, Parts L, Fromont C, Fischer PM, Warren AJ, Ron D. Binding of ISRIB reveals a regulatory site in the nucleotide exchange factor eIF2B. Science. 2018 Mar 30;359(6383):1533-1536. PubMed.
  9. Tsai JC, Miller-Vedam LE, Anand AA, Jaishankar P, Nguyen HC, Renslo AR, Frost A, Walter P. Structure of the nucleotide exchange factor eIF2B reveals mechanism of memory-enhancing molecule. Science. 2018 Mar 30;359(6383) PubMed.
  10. Marintchev A, Ito T. eIF2B and the Integrated Stress Response: A Structural and Mechanistic View. Biochemistry. 2020 Apr 7;59(13):1299-1308. Epub 2020 Mar 26 PubMed.
  11. Chou A, Krukowski K, Jopson T, Zhu PJ, Costa-Mattioli M, Walter P, Rosi S. Inhibition of the integrated stress response reverses cognitive deficits after traumatic brain injury. Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):E6420-E6426. Epub 2017 Jul 10 PubMed.
  12. Zhu PJ, Khatiwada S, Cui Y, Reineke LC, Dooling SW, Kim JJ, Li W, Walter P, Costa-Mattioli M. Activation of the ISR mediates the behavioral and neurophysiological abnormalities in Down syndrome. Science. 2019 Nov 15;366(6467):843-849. PubMed.
  13. Abbink TE, Wisse LE, Jaku E, Thiecke MJ, Voltolini-González D, Fritsen H, Bobeldijk S, Ter Braak TJ, Polder E, Postma NL, Bugiani M, Struijs EA, Verheijen M, Straat N, van der Sluis S, Thomas AA, Molenaar D, van der Knaap MS. Vanishing white matter: deregulated integrated stress response as therapy target. Ann Clin Transl Neurol. 2019 Aug;6(8):1407-1422. Epub 2019 Jul 18 PubMed.
  14. Bugallo R, Marlin E, Baltanás A, Toledo E, Ferrero R, Vinueza-Gavilanes R, Larrea L, Arrasate M, Aragón T. Fine tuning of the unfolded protein response by ISRIB improves neuronal survival in a model of amyotrophic lateral sclerosis. Cell Death Dis. 2020 May 26;11(5):397. PubMed.
  15. Halliday M, Radford H, Sekine Y, Moreno J, Verity N, le Quesne J, Ortori CA, Barrett DA, Fromont C, Fischer PM, Harding HP, Ron D, Mallucci GR. Partial restoration of protein synthesis rates by the small molecule ISRIB prevents neurodegeneration without pancreatic toxicity. Cell Death Dis. 2015 Mar 5;6:e1672. PubMed.
  16. Hosoi T, Kakimoto M, Tanaka K, Nomura J, Ozawa K. Unique pharmacological property of ISRIB in inhibition of Aβ-induced neuronal cell death. J Pharmacol Sci. 2016 Aug;131(4):292-5. Epub 2016 Aug 12 PubMed.
  17. Briggs DI, Defensor E, Memar Ardestani P, Yi B, Halpain M, Seabrook G, Shamloo M. Role of Endoplasmic Reticulum Stress in Learning and Memory Impairment and Alzheimer's Disease-Like Neuropathology in the PS19 and APPSwe Mouse Models of Tauopathy and Amyloidosis. eNeuro. 2017 Jul-Aug;4(4) Epub 2017 Jul 14 PubMed.
  18. Johnson EC, Kang J. A small molecule targeting protein translation does not rescue spatial learning and memory deficits in the hAPP-J20 mouse model of Alzheimer's disease. PeerJ. 2016;4:e2565. Epub 2016 Oct 19 PubMed.
  19. Oliveira MM, Lourenco MV, Longo F, Kasica NP, Yang W, Ureta G, Ferreira DD, Mendonça PH, Bernales S, Ma T, De Felice FG, Klann E, Ferreira ST. Correction of eIF2-dependent defects in brain protein synthesis, synaptic plasticity, and memory in mouse models of Alzheimer's disease. Sci Signal. 2021 Feb 2;14(668) PubMed.
  20. Hu Z, Yu P, Zhang Y, Yang Y, Zhu M, Qin S, Xu JT, Duan D, Wu Y, Wang D, Rowan MJ, Hu NW. Inhibition of the ISR abrogates mGluR5-dependent long-term depression and spatial memory deficits in a rat model of Alzheimer's disease. Transl Psychiatry. 2022 Mar 8;12(1):96. PubMed.
  21. Zhang Y, Yang Y, Hu Z, Zhu M, Qin S, Yu P, Li B, Xu J, Ondrejcak T, Klyubin I, Rowan MJ, Hu NW. Long-Term Depression-Inducing Low Frequency Stimulation Enhances p-Tau181 and p-Tau217 in an Age-Dependent Manner in Live Rats. J Alzheimers Dis. 2022;89(1):335-350. PubMed.

External Citations

  1. press release
  2. press release
  3. press release
  4. press release
  5. press release
  6. clinicaltrials.gov
  7. OMIM

Further Reading

Papers

  1. Marintchev A, Ito T. eIF2B and the Integrated Stress Response: A Structural and Mechanistic View. Biochemistry. 2020 Apr 7;59(13):1299-1308. Epub 2020 Mar 26 PubMed.
  2. Smith HL, Freeman OJ, Butcher AJ, Holmqvist S, Humoud I, Schätzl T, Hughes DT, Verity NC, Swinden DP, Hayes J, de Weerd L, Rowitch DH, Franklin RJ, Mallucci GR. Astrocyte Unfolded Protein Response Induces a Specific Reactivity State that Causes Non-Cell-Autonomous Neuronal Degeneration. Neuron. 2020 Mar 4;105(5):855-866.e5. Epub 2020 Jan 7 PubMed.
  3. Sekine Y, Zyryanova A, Crespillo-Casado A, Fischer PM, Harding HP, Ron D. Stress responses. Mutations in a translation initiation factor identify the target of a memory-enhancing compound. Science. 2015 May 29;348(6238):1027-30. Epub 2015 Apr 9 PubMed.
  4. Rabouw HH, Langereis MA, Anand AA, Visser LJ, de Groot RJ, Walter P, van Kuppeveld FJ. Small molecule ISRIB suppresses the integrated stress response within a defined window of activation. Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2097-2102. Epub 2019 Jan 23 PubMed.
  5. Kenner LR, Anand AA, Nguyen HC, Myasnikov AG, Klose CJ, McGeever LA, Tsai JC, Miller-Vedam LE, Walter P, Frost A. eIF2B-catalyzed nucleotide exchange and phosphoregulation by the integrated stress response. Science. 2019 May 3;364(6439):491-495. PubMed.
  6. Rabouw HH, Langereis MA, Anand AA, Visser LJ, de Groot RJ, Walter P, van Kuppeveld FJ. Small molecule ISRIB suppresses the integrated stress response within a defined window of activation. Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2097-2102. Epub 2019 Jan 23 PubMed.
  7. Wong YL, LeBon L, Edalji R, Lim HB, Sun C, Sidrauski C. The small molecule ISRIB rescues the stability and activity of Vanishing White Matter Disease eIF2B mutant complexes. Elife. 2018 Feb 28;7 PubMed.
  8. Krukowski K, Nolan A, Frias ES, Grue K, Becker M, Ureta G, Delgado L, Bernales S, Sohal VS, Walter P, Rosi S. Integrated Stress Response Inhibitor Reverses Sex-Dependent Behavioral and Cell-Specific Deficits after Mild Repetitive Head Trauma. J Neurotrauma. 2020 Jun 1;37(11):1370-1380. Epub 2020 Feb 11 PubMed.
  9. Sekine Y, Zyryanova A, Crespillo-Casado A, Fischer PM, Harding HP, Ron D. Stress responses. Mutations in a translation initiation factor identify the target of a memory-enhancing compound. Science. 2015 May 29;348(6238):1027-30. Epub 2015 Apr 9 PubMed.
  10. Hanson FM, Hodgson RE, de Oliveira MI, Allen KE, Campbell SG. Regulation and function of elF2B in neurological and metabolic disorders. Biosci Rep. 2022 Jun 30;42(6) PubMed.
  11. Boone M, Wang L, Lawrence RE, Frost A, Walter P, Schoof M. A point mutation in the nucleotide exchange factor eIF2B constitutively activates the integrated stress response by allosteric modulation. Elife. 2022 Apr 13;11 PubMed.
  12. Schoof M, Wang L, Cogan JZ, Lawrence RE, Boone M, Wuerth JD, Frost A, Walter P. Viral evasion of the integrated stress response through antagonism of eIF2-P binding to eIF2B. Nat Commun. 2021 Dec 7;12(1):7103. PubMed.
  13. Wang X, Proud CG. The role of eIF2 phosphorylation in cell and organismal physiology: new roles for well-known actors. Biochem J. 2022 May 27;479(10):1059-1082. PubMed.