ISDA

Entry Detail

PDB ID:

7P2M

Keywords:

DNA BINDING PROTEIN

Title:

E.coli GyrB24 with inhibitor LMD43 (EBL2560)

Biological Source:

Source Organism:

Escherichia coli (strain K12)

Host Organism:

Escherichia coli BL21(DE3)

PDB Version:

Deposition Date:

2021-07-06

Release Date:

2022-07-20

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.16 Å

R-Value Free:

0.16

R-Value Work:

0.13

R-Value Observed:

0.13

Space Group:

C 1 2 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA gyrase subunit B
Chain IDs:A
Chain Length:220
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AES6 Pfam ID:PF02518 EC:5.6.2.2

Ligand Molecules

N1N

PO4

Primary Citation

Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa.

Cotman, A.E, Durcik, M, Benedetto Tiz, D, Fulgheri, F, Secci, D, Sterle, M, Mozina, S, Skok, Z, Zidar, N, Zega, A, Ilas, J, Peterlin Masic, L, Tomasic, T, Hughes, D, Huseby, D.L, Cao, S, Garoff, L, Berruga Fernandez, T, Giachou, P, Crone, L, Simoff, I, Svensson, R, Birnir, B, Korol, S.V, Jin, Z, Vicente, F, Ramos, M.C, de la Cruz, M, Glinghammar, B, Lenhammar, L, Henderson, S.R, Mundy, J.E.A, Maxwell, A, Stevenson, C.E.M, Lawson, D.M, Janssen, G.V, Sterk, G.J, Kikelj, D.Show

J.Med.Chem. 66 1380 1425 (2023)

PMID: 36634346 DOI: 10.1021/acs.jmedchem.2c01597

Abstact

We have developed compounds with a promising activity against Acinetobacter baumannii and Pseudomonas aeruginosa, which are both on the WHO priority list of antibiotic-resistant bacteria. Starting from DNA gyrase inhibitor 1, we identified compound 27, featuring a 10-fold improved aqueous solubility, a 10-fold improved inhibition of topoisomerase IV from A. baumannii and P. aeruginosa, a 10-fold decreased inhibition of human topoisomerase IIα, and no cross-resistance to novobiocin. Cocrystal structures of 1 in complex with Escherichia coli GyrB24 and (S)-27 in complex with A. baumannii GyrB23 and P. aeruginosa GyrB24 revealed their binding to the ATP-binding pocket of the GyrB subunit. In further optimization steps, solubility, plasma free fraction, and other ADME properties of 27 were improved by fine-tuning of lipophilicity. In particular, analogs of 27 with retained anti-Gram-negative activity and improved plasma free fraction were identified. The series was found to be nongenotoxic, nonmutagenic, devoid of mitochondrial toxicity, and possessed no ion channel liabilities.

Legend

Protein

Chemical

Disease

Primary Citation of related structures