PDBsum entry 6g7f

Hydrolase

PDB id: 6g7f

Contents

Protein chains

250 a.a.

244 a.a.

240 a.a.

235 a.a.

231 a.a.

243 a.a.

241 a.a.

226 a.a.

204 a.a.

195 a.a.

212 a.a.

222 a.a.

229 a.a.

196 a.a.

Ligands

EPW ×6

Metals

_CL ×2

_MG ×8

Waters ×454

PDB id:

6g7f

Name:

Hydrolase

Title:

Yeast 20s proteasome in complex with cystargolide b

Structure:

Proteasome subunit alpha type-2. Chain: a, o. Synonym: macropain subunit y7,multicatalytic endopeptidase complex subunit y7,proteasome component y7,proteinase ysce subunit 7. Proteasome subunit alpha type-3. Chain: b, p. Synonym: macropain subunit y13,multicatalytic endopeptidase complex subunit y13,proteasome component y13,proteinase ysce subunit 13. Proteasome subunit alpha type-4.

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: pre2, doa3, prg1, ypr103w, p8283.10. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Strain: atcc 204508 / s288c

Resolution:

2.70Å R-factor: 0.189 R-free: 0.214

Authors:

M.Groll,R.Tello-Aburto

Key ref:

D.Niroula et al. (2018). Design, synthesis, and evaluation of cystargolide-based β-lactones as potent proteasome inhibitors. Eur J Med Chem, 157, 962-977. PubMed id: 30165344 DOI: 10.1016/j.ejmech.2018.08.052

Date:

05-Apr-18 Release date: 12-Sep-18

Protein chains

P23639  (PSA2_YEAST) -  Proteasome subunit alpha type-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 250 a.a.

Struc: 250 a.a.

Protein chains

P23638  (PSA3_YEAST) -  Proteasome subunit alpha type-3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 258 a.a.

Struc: 244 a.a.

Protein chains

P40303  (PSA4_YEAST) -  Proteasome subunit alpha type-4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 254 a.a.

Struc: 240 a.a.

Protein chains

P32379  (PSA5_YEAST) -  Proteasome subunit alpha type-5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 260 a.a.

Struc: 235 a.a.

Protein chains

P40302  (PSA6_YEAST) -  Proteasome subunit alpha type-6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 234 a.a.

Struc: 231 a.a.

Protein chains

P21242  (PSA7_YEAST) -  Probable proteasome subunit alpha type-7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 288 a.a.

Struc: 243 a.a.

Protein chains

P21243  (PSA1_YEAST) -  Proteasome subunit alpha type-1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 252 a.a.

Struc: 241 a.a.

Protein chains

P25043  (PSB2_YEAST) -  Proteasome subunit beta type-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 261 a.a.

Struc: 226 a.a.

Protein chains

P25451  (PSB3_YEAST) -  Proteasome subunit beta type-3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 205 a.a.

Struc: 204 a.a.

Protein chains

P22141  (PSB4_YEAST) -  Proteasome subunit beta type-4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 198 a.a.

Struc: 195 a.a.

Protein chains

P30656  (PSB5_YEAST) -  Proteasome subunit beta type-5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 287 a.a.

Struc: 212 a.a.

Protein chains

P23724  (PSB6_YEAST) -  Proteasome subunit beta type-6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 241 a.a.

Struc: 222 a.a.

Protein chains

P30657  (PSB7_YEAST) -  Proteasome subunit beta type-7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 266 a.a.

Struc: 229 a.a.

Protein chains

P38624  (PSB1_YEAST) -  Proteasome subunit beta type-1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 215 a.a.

Struc: 196 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b: E.C.3.4.25.1 - proteasome endopeptidase complex.
• Reaction: Cleavage at peptide bonds with very broad specificity.

DOI no: 10.1016/j.ejmech.2018.08.052

Eur J Med Chem 157:962-977 (2018)

PubMed id: 30165344

Design, synthesis, and evaluation of cystargolide-based β-lactones as potent proteasome inhibitors.

D.Niroula, L.P.Hallada, C.Le Chapelain, S.K.Ganegamage, D.Dotson, S.Rogelj, M.Groll, R.Tello-Aburto.

ABSTRACT

The peptidic β-lactone proteasome inhibitors (PIs) cystargolides A and B were used to conduct structure-activity relationship (SAR) studies in order to assess their anticancer potential. A total of 24 different analogs were designed, synthesized and evaluated for proteasome inhibition, for cytotoxicity towards several cancer cell lines, and for their ability to enter intact cells. X-ray crystallographic analysis and subunit selectivity was used to determine the specific subunit binding associated with the structural modification of the β-lactone (P₁), peptidic core, (P_x and P_y), and end-cap (P_z) of our scaffold. The cystargolide derivative 5k, structurally unique at both P_y and P₁, exhibited the most promising inhibitory activity for the β5 subunit of human proteasomes (IC₅₀ = 3.1 nM) and significant cytotoxicity towards MCF-7 (IC₅₀ = 416 nM), MDA-MB-231 (IC₅₀ = 74 nM) and RPMI 8226 (IC₅₀ = 41 nM) cancer cell lines. Cellular infiltration assays revealed that minor structural modifications have significant effects on the ability of our PIs to inhibit intracellular proteasomes, and we identified 5k as a promising candidate for continued therapeutic studies. Our novel drug lead 5k is a more potent proteasome inhibitor than carfilzomib with mid-to-low nanomolar IC₅₀ measurements and it is cytotoxic against multiple cancer cell lines at levels approaching those of carfilzomib.