Skip to main content
SpringerLink
Log in

A duplex structure of SARM1 octamers stabilized by a new inhibitor

  • Original Article
  • Published:
Cellular and Molecular Life Sciences Aims and scope Submit manuscript

A Correction to this article was published on 23 February 2023

This article has been updated

Abstract

In recent years, there has been growing interest in SARM1 as a potential breakthrough drug target for treating various pathologies of axon degeneration. SARM1-mediated axon degeneration relies on its TIR domain NADase activity, but recent structural data suggest that the non-catalytic ARM domain could also serve as a pharmacological site as it has an allosteric inhibitory function. Here, we screened for synthetic small molecules that inhibit SARM1, and tested a selected set of these compounds in a DRG axon degeneration assay. Using cryo-EM, we found that one of the newly discovered inhibitors, a calmidazolium designated TK106, not only stabilizes the previously reported inhibited conformation of the octamer, but also a meta-stable structure: a duplex of octamers (16 protomers), which we have now determined to 4.0 Å resolution. In the duplex, each ARM domain protomer is engaged in lateral interactions with neighboring protomers, and is further stabilized by contralateral contacts with the opposing octamer ring. Mutagenesis of the duplex contact sites leads to a moderate increase in SARM1 activation in cultured cells. Based on our data we propose that the duplex assembly constitutes an additional auto-inhibition mechanism that tightly prevents pre-mature activation and axon degeneration.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Availability of data and material

All data and material will become available upon publication.

Change history

References

  1. Osterloh JM, Yang J, Rooney TM, Fox AN, Adalbert R, Powell EH, Sheehan AE, Avery MA, Hackett R, Logan MA, MacDonald JM, Ziegenfuss JS, Milde S, Hou YJ, Nathan C, Ding A, Brown RH Jr, Conforti L, Coleman M, Tessier-Lavigne M, Zuchner S, Freeman MR (2012) dSarm/Sarm1 is required for activation of an injury-induced axon death pathway. Science 337:481–484. https://doi.org/10.1126/science.1223899

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Gerdts J, Summers DW, Sasaki Y, DiAntonio A, Milbrandt J (2013) Sarm1-mediated axon degeneration requires both SAM and TIR interactions. J Neurosci 33:13569–13580. https://doi.org/10.1523/JNEUROSCI.1197-13.2013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Geisler S, Doan RA, Strickland A, Huang X, Milbrandt J, DiAntonio A (2016) Prevention of vincristine-induced peripheral neuropathy by genetic deletion of SARM1 in mice. Brain 139:3092–3108. https://doi.org/10.1093/brain/aww251

    Article  PubMed  PubMed Central  Google Scholar 

  4. Cetinkaya-Fisgin A, Luan X, Reed N, Jeong YE, Oh BC, Hoke A (2020) Cisplatin induced neurotoxicity is mediated by Sarm1 and calpain activation. Sci Rep 10:21889. https://doi.org/10.1038/s41598-020-78896-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Ozaki E, Gibbons L, Neto NG, Kenna P, Carty M, Humphries M, Humphries P, Campbell M, Monaghan M, Bowie A, Doyle SL (2020) SARM1 deficiency promotes rod and cone photoreceptor cell survival in a model of retinal degeneration. Life Sci Alliance. https://doi.org/10.26508/lsa.201900618

    Article  PubMed  PubMed Central  Google Scholar 

  6. Ko KW, Milbrandt J, DiAntonio A (2020) SARM1 acts downstream of neuroinflammatory and necroptotic signaling to induce axon degeneration. J Cell Biol. https://doi.org/10.1083/jcb.201912047

    Article  PubMed  PubMed Central  Google Scholar 

  7. Uccellini MB, Bardina SV, Sanchez-Aparicio MT, White KM, Hou YJ, Lim JK, Garcia-Sastre A (2020) Passenger mutations confound phenotypes of SARM1-deficient mice. Cell Rep 31:107498. https://doi.org/10.1016/j.celrep.2020.03.062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Kim Y, Zhou P, Qian L, Chuang JZ, Lee J, Li C, Iadecola C, Nathan C, Ding A (2007) MyD88-5 links mitochondria, microtubules, and JNK3 in neurons and regulates neuronal survival. J Exp Med 204:2063–2074. https://doi.org/10.1084/jem.20070868

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Sasaki Y, Kakita H, Kubota S, Sene A, Lee TJ, Ban N, Dong Z, Lin JB, Boye SL, DiAntonio A, Boye SE, Apte RS, Milbrandt J (2020) SARM1 depletion rescues NMNAT1-dependent photoreceptor cell death and retinal degeneration. Elife. https://doi.org/10.7554/eLife.62027

    Article  PubMed  PubMed Central  Google Scholar 

  10. Turkiew E, Falconer D, Reed N, Hoke A (2017) Deletion of Sarm1 gene is neuroprotective in two models of peripheral neuropathy. J Peripher Nerv Syst 22:162–171. https://doi.org/10.1111/jns.12219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Hughes RO, Bosanac T, Mao X, Engber TM, DiAntonio A, Milbrandt J, Devraj R, Krauss R (2021) Small molecule SARM1 inhibitors recapitulate the SARM1(-/-) phenotype and allow recovery of a metastable pool of axons fated to degenerate. Cell Rep 34:108588. https://doi.org/10.1016/j.celrep.2020.108588

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Loring HS, Parelkar SS, Mondal S, Thompson PR (2020) Identification of the first noncompetitive SARM1 inhibitors. Bioorg Med Chem 28:115644. https://doi.org/10.1016/j.bmc.2020.115644

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Bosanac T, Hughes RO, Engber T, Devraj R, Brearley A, Danker K, Young K, Kopatz J, Hermann M, Berthemy A, Boyce S, Bentley J, Krauss R (2021) Pharmacological SARM1 inhibition protects axon structure and function in paclitaxel-induced peripheral neuropathy. Brain. https://doi.org/10.1093/brain/awab184

    Article  PubMed  PubMed Central  Google Scholar 

  14. Li WH, Huang K, Cai Y, Wang QW, Zhu WJ, Hou YN, Wang S, Cao S, Zhao ZY, Xie XJ, Du Y, Lee CS, Lee HC, Zhang H, Zhao YJ (2021) Permeant fluorescent probes visualize the activation of SARM1 and uncover an anti-neurodegenerative drug candidate. Elife. https://doi.org/10.7554/eLife.67381

    Article  PubMed  PubMed Central  Google Scholar 

  15. Shi Y, Kerry PS, Nanson JD, Bosanac T, Sasaki Y, Krauss R, Saikot FK, Adams SE, Mosaiab T, Masic V, Mao X, Rose F, Vasquez E, Furrer M, Cunnea K, Brearley A, Gu W, Luo Z, Brillault L, Landsberg MJ, Di Antonio A, Kobe B, Milbrandt J, Hughes RO, Ve T (2022) Structural basis of SARM1 activation, substrate recognition, and inhibition by small molecules. Mol Cell. https://doi.org/10.1016/j.molcel.2022.03.007

    Article  PubMed  Google Scholar 

  16. Bratkowski M, Burdett TC, Danao J, Wang X, Mathur P, Gu W, Beckstead JA, Talreja S, Yang YS, Danko G, Park JH, Walton M, Brown SP, Tegley CM, Joseph PRB, Reynolds CH, Sambashivan S (2022) Uncompetitive, adduct-forming SARM1 inhibitors are neuroprotective in preclinical models of nerve injury and disease. Neuron. https://doi.org/10.1016/j.neuron.2022.08.017

    Article  PubMed  Google Scholar 

  17. Essuman K, Summers DW, Sasaki Y, Mao X, DiAntonio A, Milbrandt J (2017) The SARM1 toll/interleukin-1 receptor domain possesses intrinsic NAD(+) cleavage activity that promotes pathological axonal degeneration. Neuron 93(1334–1343):e5. https://doi.org/10.1016/j.neuron.2017.02.022

    Article  CAS  Google Scholar 

  18. Tong L (2021) How to diSARM the executioner of axon degeneration. Nat Struct Mol Biol 28:10–12. https://doi.org/10.1038/s41594-020-00545-7

    Article  CAS  PubMed  Google Scholar 

  19. Summers DW, Gibson DA, DiAntonio A, Milbrandt J (2016) SARM1-specific motifs in the TIR domain enable NAD+ loss and regulate injury-induced SARM1 activation. Proc Natl Acad Sci U S A 113:E6271–E6280. https://doi.org/10.1073/pnas.1601506113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Chuang CF, Bargmann CI (2005) A Toll-interleukin 1 repeat protein at the synapse specifies asymmetric odorant receptor expression via ASK1 MAPKKK signaling. Genes Dev 19:270–281. https://doi.org/10.1101/gad.1276505

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Gerdts J, Brace EJ, Sasaki Y, DiAntonio A, Milbrandt J (2015) SARM1 activation triggers axon degeneration locally via NAD(+) destruction. Science 348:453–457. https://doi.org/10.1126/science.1258366

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Horsefield S, Burdett H, Zhang X, Manik MK, Shi Y, Chen J, Qi T, Gilley J, Lai JS, Rank MX, Casey LW, Gu W, Ericsson DJ, Foley G, Hughes RO, Bosanac T, von Itzstein M, Rathjen JP, Nanson JD, Boden M, Dry IB, Williams SJ, Staskawicz BJ, Coleman MP, Ve T, Dodds PN, Kobe B (2019) NAD(+) cleavage activity by animal and plant TIR domains in cell death pathways. Science 365:793–799. https://doi.org/10.1126/science.aax1911

    Article  CAS  PubMed  Google Scholar 

  23. Sporny M, Guez-Haddad J, Lebendiker M, Ulisse V, Volf A, Mim C, Isupov MN, Opatowsky Y (2019) Structural evidence for an octameric ring arrangement of SARM1. J Mol Biol 431:3591–3605. https://doi.org/10.1016/j.jmb.2019.06.030

    Article  CAS  PubMed  Google Scholar 

  24. Sporny M, Guez-Haddad J, Khazma T, Yaron A, Dessau M, Shkolnisky Y, Mim C, Isupov MN, Zalk R, Hons M, Opatowsky Y (2020) Structural basis for SARM1 inhibition and activation under energetic stress. Elife. https://doi.org/10.7554/eLife.62021

    Article  PubMed  PubMed Central  Google Scholar 

  25. Figley MD, Gu W, Nanson JD, Shi Y, Sasaki Y, Cunnea K, Malde AK, Jia X, Luo Z, Saikot FK, Mosaiab T, Masic V, Holt S, Hartley-Tassell L, McGuinness HY, Manik MK, Bosanac T, Landsberg MJ, Kerry PS, Mobli M, Hughes RO, Milbrandt J, Kobe B, DiAntonio A, Ve T (2021) SARM1 is a metabolic sensor activated by an increased NMN/NAD(+) ratio to trigger axon degeneration. Neuron 109(1118–1136):e11. https://doi.org/10.1016/j.neuron.2021.02.009

    Article  CAS  Google Scholar 

  26. Jiang Y, Liu T, Lee CH, Chang Q, Yang J, Zhang Z (2020) The NAD(+)-mediated self-inhibition mechanism of pro-neurodegenerative Sarm1. Nature. https://doi.org/10.1038/s41586-020-2862-z

    Article  PubMed  PubMed Central  Google Scholar 

  27. Bratkowski M, Xie T, Thayer DA, Lad S, Mathur P, Yang YS, Danko G, Burdett TC, Danao J, Cantor A, Kozak JA, Brown SP, Bai X, Sambashivan S (2020) Structural and mechanistic regulation of the pro-degenerative NAD hydrolase SARM1. Cell Rep 32:107999. https://doi.org/10.1016/j.celrep.2020.107999

    Article  CAS  PubMed  Google Scholar 

  28. Shen C, Vohra M, Zhang P, Mao X, Figley MD, Zhu J, Sasaki Y, Wu H, DiAntonio A, Milbrandt J (2021) Multiple domain interfaces mediate SARM1 autoinhibition. Proc Natl Acad Sci U S A. https://doi.org/10.1073/pnas.2023151118

    Article  PubMed  PubMed Central  Google Scholar 

  29. Bloom AJ, Mao X, Strickland A, Sasaki Y, Milbrandt J, DiAntonio A (2022) Constitutively active SARM1 variants that induce neuropathy are enriched in ALS patients. Mol Neurodegener 17:1. https://doi.org/10.1186/s13024-021-00511-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Gilley J, Jackson O, Pipis M, Estiar MA, Al-Chalabi A, Danzi MC, van Eijk KR, Goutman SA, Harms MB, Houlden H, Iacoangeli A, Kaye J, Lima L, Queen Square G, Ravits J, Rouleau GA, Schule R, Xu J, Zuchner S, Cooper-Knock J, Gan-Or Z, Reilly MM, Coleman MP (2021) Enrichment of SARM1 alleles encoding variants with constitutively hyperactive NADase in patients with ALS and other motor nerve disorders. Elife. https://doi.org/10.7554/eLife.70905

    Article  PubMed  PubMed Central  Google Scholar 

  31. Sasaki Y, Zhu J, Shi Y, Gu W, Kobe B, Ve T, DiAntonio A, Milbrandt J (2021) Nicotinic acid mononucleotide is an allosteric SARM1 inhibitor promoting axonal protection. Exp Neurol 345:113842. https://doi.org/10.1016/j.expneurol.2021.113842

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Zhao ZY, Xie XJ, Li WH, Liu J, Chen Z, Zhang B, Li T, Li SL, Lu JG, Zhang L, Zhang LH, Xu Z, Lee HC, Zhao YJ (2019) A Cell-Permeant Mimetic of NMN Activates SARM1 to Produce Cyclic ADP-Ribose and Induce Non-apoptotic Cell Death. iScience 15:452–466. https://doi.org/10.1016/j.isci.2019.05.001

  33. Liu HW, Smith CB, Schmidt MS, Cambronne XA, Cohen MS, Migaud ME, Brenner C, Goodman RH (2018) Pharmacological bypass of NAD(+) salvage pathway protects neurons from chemotherapy-induced degeneration. Proc Natl Acad Sci U S A 115:10654–10659. https://doi.org/10.1073/pnas.1809392115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Loreto A, Angeletti C, Gu W, Osborne A, Nieuwenhuis B, Gilley J, Merlini E, Arthur-Farraj P, Amici A, Luo Z, Hartley-Tassell L, Ve T, Desrochers LM, Wang Q, Kobe B, Orsomando G, Coleman MP (2021) Neurotoxin-mediated potent activation of the axon degeneration regulator SARM1. Elife. https://doi.org/10.7554/eLife.72823

    Article  PubMed  PubMed Central  Google Scholar 

  35. Wu T, Zhu J, Strickland A, Ko KW, Sasaki Y, Dingwall CB, Yamada Y, Figley MD, Mao X, Neiner A, Bloom AJ, DiAntonio A, Milbrandt J (2021) Neurotoxins subvert the allosteric activation mechanism of SARM1 to induce neuronal loss. Cell Rep 37:109872. https://doi.org/10.1016/j.celrep.2021.109872

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Angeletti C, Amici A, Gilley J, Loreto A, Trapanotto AG, Antoniou C, Merlini E, Coleman MP and Orsomando G (2022) SARM1 is a multi-functional NAD(P)ase with prominent base exchange activity, all regulated bymultiple physiologically relevant NAD metabolites. iScience 25:103812. https://doi.org/10.1016/j.isci.2022.103812

  37. Daina A, Michielin O, Zoete V (2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7:42717. https://doi.org/10.1038/srep42717

    Article  PubMed  PubMed Central  Google Scholar 

  38. Shacham-Silverberg V, Sar Shalom H, Goldner R, Golan-Vaishenker Y, Gurwicz N, Gokhman I, Yaron A (2018) Phosphatidylserine is a marker for axonal debris engulfment but its exposure can be decoupled from degeneration. Cell Death Dis 9:1116. https://doi.org/10.1038/s41419-018-1155-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Cambronne XA, Stewart ML, Kim D, Jones-Brunette AM, Morgan RK, Farrens DL, Cohen MS, Goodman RH (2016) Biosensor reveals multiple sources for mitochondrial NAD(+). Science 352:1474–1477. https://doi.org/10.1126/science.aad5168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Houtkooper RH, Canto C, Wanders RJ, Auwerx J (2010) The secret life of NAD+: an old metabolite controlling new metabolic signaling pathways. Endocr Rev 31:194–223. https://doi.org/10.1210/er.2009-0026

    Article  CAS  PubMed  Google Scholar 

  41. Hara N, Osago H, Hiyoshi M, Kobayashi-Miura M, Tsuchiya M (2019) Quantitative analysis of the effects of nicotinamide phosphoribosyltransferase induction on the rates of NAD+ synthesis and breakdown in mammalian cells using stable isotope-labeling combined with mass spectrometry. PLoS ONE 14:e0214000. https://doi.org/10.1371/journal.pone.0214000

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Liu L, Su X, Quinn WJ 3rd, Hui S, Krukenberg K, Frederick DW, Redpath P, Zhan L, Chellappa K, White E, Migaud M, Mitchison TJ, Baur JA, Rabinowitz JD (2018) Quantitative analysis of NAD synthesis-breakdown fluxes. Cell Metab. https://doi.org/10.1016/j.cmet.2018.03.018

    Article  PubMed  PubMed Central  Google Scholar 

  43. Sasaki Y, Engber TM, Hughes RO, Figley MD, Wu T, Bosanac T, Devraj R, Milbrandt J, Krauss R, DiAntonio A (2020) cADPR is a gene dosage-sensitive biomarker of SARM1 activity in healthy, compromised, and degenerating axons. Exp Neurol 329:113252. https://doi.org/10.1016/j.expneurol.2020.113252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Ma S, Lapin D, Liu L, Sun Y, Song W, Zhang X, Logemann E, Yu D, Wang J, Jirschitzka J, Han Z, Schulze-Lefert P, Parker JE, Chai J (2020) Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme. Science. https://doi.org/10.1126/science.abe3069

    Article  PubMed  PubMed Central  Google Scholar 

  45. Martin R, Qi T, Zhang H, Liu F, King M, Toth C, Nogales E, Staskawicz BJ (2020) Structure of the activated ROQ1 resistosome directly recognizing the pathogen effector XopQ. Science. https://doi.org/10.1126/science.abd9993

    Article  PubMed  PubMed Central  Google Scholar 

  46. Tal N, Morehouse BR, Millman A, Stokar-Avihail A, Avraham C, Fedorenko T, Yirmiya E, Herbst E, Brandis A, Mehlman T, Oppenheimer-Shaanan Y, Keszei AFA, Shao S, Amitai G, Kranzusch PJ, Sorek R (2021) Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell. https://doi.org/10.1016/j.cell.2021.09.031

    Article  PubMed  PubMed Central  Google Scholar 

  47. Li X, Mooney P, Zheng S, Booth CR, Braunfeld MB, Gubbens S, Agard DA, Cheng Y (2013) Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods 10:584–590. https://doi.org/10.1038/nmeth.2472

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Zhang K (2016) Gctf: Real-time CTF determination and correction. J Struct Biol 193:1–12. https://doi.org/10.1016/j.jsb.2015.11.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Punjani A, Rubinstein JL, Fleet DJ, Brubaker MA (2017) cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods 14:290. https://doi.org/10.1038/Nmeth.4169

    Article  CAS  PubMed  Google Scholar 

  50. Martinez M, Jimenez-Moreno A, Maluenda D, Ramirez-Aportela E, Melero R, Cuervo A, Conesa P, Del Cano L, Fonseca YC, Sanchez-Garcia R, Strelak D, Conesa JJ, Fernandez-Gimenez E, de Isidro F, Sorzano COS, Carazo JM, Marabini R (2020) Integration of Cryo-EM model building Software in scipion. J Chem Inf Model. https://doi.org/10.1021/acs.jcim.9b01032

    Article  PubMed  PubMed Central  Google Scholar 

  51. Tegunov D, Cramer P (2019) Real-time cryo-electron microscopy data preprocessing with Warp. Nat Methods 16:1146–1152. https://doi.org/10.1038/s41592-019-0580-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4 suite and current developments. Acta Cryst D 67:235–242. https://doi.org/10.1107/S0907444910045749

    Article  CAS  Google Scholar 

  53. Krissinel E (2012) Enhanced fold recognition using efficient short fragment clustering. J Mol Biochem 1:76–85

    PubMed  PubMed Central  Google Scholar 

  54. Vagin A, Teplyakov A (2010) Molecular replacement with MOLREP. Acta Cryst D 66:22–25. https://doi.org/10.1107/S0907444909042589

    Article  CAS  Google Scholar 

  55. Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Cryst D 66:486–501. https://doi.org/10.1107/S0907444910007493

    Article  CAS  Google Scholar 

  56. Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Cryst D 67:355–367. https://doi.org/10.1107/S0907444911001314

    Article  CAS  Google Scholar 

  57. Lebedev AA, Young P, Isupov MN, Moroz OV, Vagin AA, Murshudov GN (2012) JLigand: a graphical tool for the CCP4 template-restraint library. Acta Crystallogr D Biol Crystallogr 68:431–440. https://doi.org/10.1107/S090744491200251X

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Guez-Haddad J, Sporny M, Sasson Y, Gevorkyan-Airapetov L, Lahav-Mankovski N, Margulies D, Radzimanowski J, Opatowsky Y (2015) The neuronal migration factor srGAP2 achieves specificity in ligand binding through a two-component molecular mechanism. Structure 23:1989–2000. https://doi.org/10.1016/j.str.2015.08.009

    Article  CAS  PubMed  Google Scholar 

  59. Yom-Tov G, Barak R, Matalon O, Barda-Saad M, Guez-Haddad J, Opatowsky Y (2017) Robo Ig4 is a dimerization domain. J Mol Biol 429:3606–3616. https://doi.org/10.1016/j.jmb.2017.10.002

    Article  CAS  PubMed  Google Scholar 

  60. Demarest TG, Truong GTD, Lovett J, Mohanty JG, Mattison JA, Mattson MP, Ferrucci L, Bohr VA, Moaddel R (2019) Assessment of NAD(+)metabolism in human cell cultures, erythrocytes, cerebrospinal fluid and primate skeletal muscle. Anal Biochem 572:1–8. https://doi.org/10.1016/j.ab.2019.02.019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Maor-Nof M, Homma N, Raanan C, Nof A, Hirokawa N, Yaron A (2013) Axonal pruning is actively regulated by the microtubule-destabilizing protein kinesin superfamily protein 2A. Cell Rep 3:971–977. https://doi.org/10.1016/j.celrep.2013.03.005

    Article  CAS  PubMed  Google Scholar 

  62. Langer G, Cohen SX, Lamzin VS, Perrakis A (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3:1171–1179. https://doi.org/10.1038/nprot.2008.91

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Kandiah E, Giraud T, de Maria AA, Dobias F, Effantin G, Flot D, Hons M, Schoehn G, Susini J, Svensson O, Leonard GA, Mueller-Dieckmann C (2019) CM01: a facility for cryo-electron microscopy at the European Synchrotron. Acta Crystallogr D Struct Biol 75:528–535. https://doi.org/10.1107/S2059798319006880

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Liebschner D, Afonine PV, Baker ML, Bunkoczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD (2019) Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol 75:861–877. https://doi.org/10.1107/S2059798319011471

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr D Struct Biol 74:531–544. https://doi.org/10.1107/S2059798318006551

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We acknowledge the European Synchrotron Radiation Facility for provision of beam time on CM01 and thank the staff of beamline CM01 of ESRF and members of the Opatowsky lab for technical assistance. We thank Gershon Kunin for IT management. The Israel National Center for Personalized Medicine is supported by a research grant from the Nancy and Stephen Grand. This work was supported by funds from ISF grants no. 1425/15 and 909/19, BSF grant no. 2019150, and ICRF grant 2022-2023 to Y.O. Y.O. is a Katzir Professorial Chair of Biophysics, and A.Y. is an incumbent of the Jack and Simon Djanogly Professorial Chair in Biochemistry.

Funding

This work was supported by funds from ISF grants no. 1425/15 and 909/19 and BSF grant no. 2019150 to Y.O.

Author information

Authors and Affiliations

  1. The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel

    Tami Khazma, Julia Guez-Haddad, Atira Grossman, Radhika Sain & Yarden Opatowsky

  2. Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel

    Yarden Golan-Vaishenker, Ran Zalk  & Avraham Yaron

  3. Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel

    Michal Weitman

  4. The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel

    Alexander Plotnikov

  5. Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel

    Ran Zalk

  6. European Molecular Biology Laboratory, Grenoble, France

    Michael Hons

Author notes

  1. Tami Khazma and Yarden Golan-Vaishenker Co-first authors.

    • Yarden Opatowsky Lead contact.

      • Yarden Opatowsky
    Authors
    1. Tami Khazma
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Yarden Golan-Vaishenker
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Julia Guez-Haddad
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Atira Grossman
      View author publications

      You can also search for this author in PubMed Google Scholar

    5. Radhika Sain
      View author publications

      You can also search for this author in PubMed Google Scholar

    6. Michal Weitman
      View author publications

      You can also search for this author in PubMed Google Scholar

    7. Alexander Plotnikov
      View author publications

      You can also search for this author in PubMed Google Scholar

    8. Ran Zalk
      View author publications

      You can also search for this author in PubMed Google Scholar

    9. Avraham Yaron
      View author publications

      You can also search for this author in PubMed Google Scholar

    10. Michael Hons
      View author publications

      You can also search for this author in PubMed Google Scholar

    11. Yarden Opatowsky
      View author publications

      You can also search for this author in PubMed Google Scholar

    Contributions

    YO: Conceptualization, Resources, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Writing—original draft, Project administration, Writing—review and editing. Lead contact and corresponding author. TK: Data curation, Formal analysis, Investigation, Methodology. First author: YG-V: Formal analysis, Investigation, Methodology. Co-first author: JG-H: Data curation, Formal analysis, Supervision, Investigation, Methodology, Project administration, Writing—review and editing. AY: Contribution Conceptualization, Supervision, Methodology, Writing—review and editing. Co-corresponding author with YO. Atira Grossman: Data curation, Methodology, Investigation, Formal analysis, RS: Methodology. MW: Data curation, Methodology, AP: Data curation, Methodology, RZ: Contribution Data curation, Formal analysis, Methodology. MH: Data curation, Formal analysis, Validation, Methodology, Writing—review and editing. Co-corresponding author with YO.

    Corresponding authors

    Correspondence to Michael Hons or Yarden Opatowsky.

    Ethics declarations

    Competing interests

    We declare that we have no competing interests.

    Consent for publication

    We, all the authors give our consent for publication.

    Additional information

    Publisher's Note

    Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

    Supplementary Information

    Below is the link to the electronic supplementary material.

    18_2022_4641_MOESM1_ESM.docx

    Supplementary file1 (DOCX 498 KB) Figure 1 supplement 1. Structure-based sequence alignment of the SARM1 of human, mouse, zebrafish, and the C. elegans ortholog TIR-1. Color-coded highlights and Uniprot protein accession numbers are listed below.

    18_2022_4641_MOESM2_ESM.docx

    Supplementary file2 (DOCX 54 KB) Figure 3 supplement 1. A) Chemical structure of 2 additional hSARM1 inhibitory compounds. B) Determination of IC50 values, as in figure 3.

    18_2022_4641_MOESM3_ESM.docx

    Supplementary file3 (DOCX 130 KB) Figure 5 supplement 1. A) Representative cryo-EM micrograph of TK106 supplemented hSARM1. B) 2D class averages of the entire dataset. C) Flowchart of the cryo-EM processing steps of the entire dataset.

    18_2022_4641_MOESM4_ESM.docx

    Supplementary file4 (DOCX 196 KB) Figure 5 supplement 2. Resolution, angular distribution, and B-factor estimations of the cryo-EM maps of TK106 supplemented hSARM1 duplex and monoplex.

    18_2022_4641_MOESM5_ESM.docx

    Supplementary file5 (DOCX 174 KB) Figure 5 supplement 3. Comparison of available cryo-EM map densities of hSARM1, set to similar contour level at the ARM domain’s concave surface [24-27]. Dashed red oval marks the site of interest, highlighting the difference in map density between apo structures (empty site) and NAD+ or TK106 supplemented structures (occupied sites).

    18_2022_4641_MOESM6_ESM.docx

    Supplementary file6 (DOCX 177 KB) Figure 6 supplement 1. Extended representation of Fig. 6A. Protective and toxic effects of hSARM1 inhibitors over axon degeneration in mouse DRG explants.

    Rights and permissions

    Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Khazma, T., Golan-Vaishenker, Y., Guez-Haddad, J. et al. A duplex structure of SARM1 octamers stabilized by a new inhibitor. Cell. Mol. Life Sci. 80, 16 (2023). https://doi.org/10.1007/s00018-022-04641-3

    Download citation

    • Received:

    • Revised:

    • Accepted:

    • Published:

    • DOI: https://doi.org/10.1007/s00018-022-04641-3

    Keywords

    Search

    Navigation