ISDA

Entry Detail

PDB ID:

6WNK

Keywords:

HYDROLASE/HYDROLASE INHIBITOR

Title:

Macrocyclic peptides TDI5575 that selectively inhibit the Mycobacterium tuberculosis proteasome

Biological Source:

Source Organism:

Mycobacterium tuberculosis

Host Organism:

Escherichia coli BL21(DE3)

PDB Version:

Deposition Date:

2020-04-22

Release Date:

2021-04-28

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.28 Å

R-Value Free:

0.23

R-Value Work:

0.19

R-Value Observed:

0.20

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Proteasome subunit alpha
Chain IDs:A, B, C, D, E, F, G, O, P, Q, R, S, T, U
Chain Length:240
Number of Molecules:14
Biological Source:Mycobacterium tuberculosis

UniProt ID:P9WHU1 Pfam ID:PF00227

Protein Blast

Polymer Type:polypeptide(L)
Description:Proteasome subunit beta
Chain IDs:H, I, J, K, L, M, N, V, W, X, Y, Z, AA (auth: a), BA (auth: b)
Chain Length:240
Number of Molecules:14
Biological Source:Mycobacterium tuberculosis

UniProt ID:P9WHT9 Pfam ID:PF00227

Ligand Molecules

CIT

DMF

U5Y

Peptide-like Molecules

PRD_002377

Primary Citation

Macrocyclic Peptides that Selectively Inhibit the Mycobacterium tuberculosis Proteasome.

Zhang, H, Hsu, H.C, Kahne, S.C, Hara, R, Zhan, W, Jiang, X, Burns-Huang, K, Ouellette, T, Imaeda, T, Okamoto, R, Kawasaki, M, Michino, M, Wong, T.T, Toita, A, Yukawa, T, Moraca, F, Vendome, J, Saha, P, Sato, K, Aso, K, Ginn, J, Meinke, P.T, Foley, M, Nathan, C.F, Darwin, K.H, Li, H, Lin, G.Show

J.Med.Chem. 64 6262 6272 (2021)

PMID: 33949190 DOI: 10.1021/acs.jmedchem.1c00296

Abstact

Treatment of tuberculosis (TB) currently takes at least 6 months. Latent Mycobacterium tuberculosis (Mtb) is phenotypically tolerant to most anti-TB drugs. A key hypothesis is that drugs that kill nonreplicating (NR) Mtb may shorten treatment when used in combination with conventional drugs. The Mtb proteasome (Mtb20S) could be such a target because its pharmacological inhibition kills NR Mtb and its genetic deletion renders Mtb unable to persist in mice. Here, we report a series of macrocyclic peptides that potently and selectively target the Mtb20S over human proteasomes, including macrocycle 6. The cocrystal structure of macrocycle 6 with Mtb20S revealed structural bases for the species selectivity. Inhibition of 20S within Mtb by 6 dose dependently led to the accumulation of Pup-tagged GFP that is degradable but resistant to depupylation and death of nonreplicating Mtb under nitrosative stress. These results suggest that compounds of this class have the potential to develop as anti-TB therapeutics.

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Primary Citation of related structures