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Structure paper

TitleTargeting ryanodine receptors with allopurinol and xanthine derivatives for the treatment of cardiac and musculoskeletal weakness disorders.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 122, Issue 24, Page e2422082122, Year 2025
Publish dateJun 17, 2025
AuthorsMarco C Miotto / Estefania Luna-Figueroa / Carl Tchagou / Laith Bahlouli / Steven Reiken / Haikel Dridi / Yang Liu / Gunnar Weninger / Andrew R Marks /
PubMed AbstractRyanodine receptors (RyRs) are intracellular Ca channels essential for muscle contraction. Caffeine, a xanthine derivative, has been known for decades to increase muscle contraction and enhance ...Ryanodine receptors (RyRs) are intracellular Ca channels essential for muscle contraction. Caffeine, a xanthine derivative, has been known for decades to increase muscle contraction and enhance activation of RyRs by increasing the sensitivity to Ca. We previously showed that xanthine, the only physiologically relevant xanthine derivative, also binds to and activates RyR2. Most xanthine derivatives and analogs are safe and widely prescribed, with the most popular being the xanthine oxidoreductase inhibitor allopurinol (~15M yearly prescriptions in USA). We propose that xanthine derivatives and analogs that enhance RyRs activity could be used for lead optimization and eventually for the treatment of the diseases that exhibit decreased muscle contraction and reduced RyRs activity, such as RyR1-related diseases, sarcopenia, and heart failure. Here, we show by cryo-EM that xanthine derivatives, analogs, and other related compounds bind to the xanthine/caffeine binding site and activate RyR1, and identify 4-oxopyrimidine as the minimal motif necessary for such interaction.
External linksProc Natl Acad Sci U S A / PubMed:40512792 / PubMed Central
MethodsEM (single particle)
Resolution2.12 - 4.49 Å
Structure data

EMDB-47336: Structure of PKA phosphorylated human RyR2-R2474S in the open state in the presence of Calmodulin - focused map on xanthine
Method: EM (single particle) / Resolution: 2.38 Å

EMDB-47357: Structure of RyR1 in the primed state in the presence of caffeine - focused map (reprocessed from EMPIAR-10997)
Method: EM (single particle) / Resolution: 2.12 Å

EMDB-47385, PDB-9e18:
Structure of RyR1 in the primed state in the presence of pentoxifylline
Method: EM (single particle) / Resolution: 2.68 Å

EMDB-47386, PDB-9e19:
Structure of RyR1 in the open state in the presence of pentoxifylline
Method: EM (single particle) / Resolution: 4.04 Å

EMDB-47387, PDB-9e1a:
Structure of RyR1 in the primed state in the presence of dyphylline
Method: EM (single particle) / Resolution: 3.35 Å

EMDB-47388, PDB-9e1b:
Structure of RyR1 in the open state in the presence of dyphylline
Method: EM (single particle) / Resolution: 4.49 Å

EMDB-47389, PDB-9e1c:
Structure of RyR1 in the primed state in the presence of IBMX
Method: EM (single particle) / Resolution: 2.63 Å

EMDB-47390, PDB-9e1d:
Structure of RyR1 in the primed state in the presence of enprofylline
Method: EM (single particle) / Resolution: 2.76 Å

EMDB-47391, PDB-9e1e:
Structure of RyR1 in the primed state in the presence of uracil
Method: EM (single particle) / Resolution: 2.92 Å

EMDB-47392, PDB-9e1f:
Structure of RyR1 in the primed state in the presence of allopurinol
Method: EM (single particle) / Resolution: 3.03 Å

EMDB-47393, PDB-9e1g:
Structure of RyR1 in the primed state in the presence of oxypurinol
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-47394, PDB-9e1h:
Structure of RyR1 in the primed state in the presence of oxopyricid
Method: EM (single particle) / Resolution: 3.26 Å

EMDB-47395, PDB-9e1i:
Structure of RyR1 in the open state in the presence of oxopyricid
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-47396: Structure of RyR1 in the primed state in the presence of pentoxifylline, focused refinement
Method: EM (single particle) / Resolution: 2.35 Å

EMDB-47397: Structure of RyR1 in the open state in the presence of pentoxifylline, focused refinement
Method: EM (single particle) / Resolution: 3.49 Å

EMDB-47398: Structure of RyR1 in the primed state in the presence of dyphylline, focused refinement
Method: EM (single particle) / Resolution: 3.14 Å

EMDB-47399: Structure of RyR1 in the open state in the presence of dyphylline, focused refinement
Method: EM (single particle) / Resolution: 4.16 Å

EMDB-47400: Structure of RyR1 in the primed state in the presence of IBMX, focused refinement
Method: EM (single particle) / Resolution: 2.34 Å

EMDB-47401: Structure of RyR1 in the primed state in the presence of enprofylline, focused refinement
Method: EM (single particle) / Resolution: 2.42 Å

EMDB-47402: Structure of RyR1 in the primed state in the presence of uracil, focused refinement
Method: EM (single particle) / Resolution: 2.47 Å

EMDB-47403: Structure of RyR1 in the primed state in the presence of allopurinol, focused refinement
Method: EM (single particle) / Resolution: 2.56 Å

EMDB-47404: Structure of RyR1 in the primed state in the presence of oxypurinol, focused refinement
Method: EM (single particle) / Resolution: 2.69 Å

EMDB-47405: Structure of RyR1 in the primed state in the presence of oxopyricid, focused refinement
Method: EM (single particle) / Resolution: 2.64 Å

EMDB-47406: Structure of RyR1 in the open state in the presence of oxopyricid, focused refinement
Method: EM (single particle) / Resolution: 2.65 Å

PDB-9e17:
Structure of RyR1 in the primed state in the presence of caffeine (reprocessed/reanalyzed from EMPIAR-10997, 7TZC, EMD-26205)
Method: ELECTRON MICROSCOPY / Resolution: 2.45 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-ZN:
Unknown entry

ChemComp-CFF:
CAFFEINE / medication*YM

ChemComp-KVR:
4-[(7-methoxy-2,3-dihydro-1,4-benzothiazepin-4(5H)-yl)methyl]benzoic acid

ChemComp-L9R:
(2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / SOPC, phospholipid*YM

ChemComp-HOH:
WATER

ChemComp-PNX:
3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE

PDB-1bd2:
COMPLEX BETWEEN HUMAN T-CELL RECEPTOR B7, VIRAL PEPTIDE (TAX) AND MHC CLASS I MOLECULE HLA-A 0201

ChemComp-IBM:
3-ISOBUTYL-1-METHYLXANTHINE

PDB-1bd3:
STRUCTURE OF THE APO URACIL PHOSPHORIBOSYLTRANSFERASE, 2 MUTANT C128V

ChemComp-URA:
URACIL

PDB-1bd4:
UPRT-URACIL COMPLEX

ChemComp-141:
Oxypurinol

PDB-1bd5:
Unknown entry

Source
  • homo sapiens (human)
  • oryctolagus cuniculus (rabbit)
KeywordsTRANSPORT PROTEIN / calcium channel / sarcoplasmic reticulum

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