Structure and Dynamics of Macrophage Infectivity Potentiator Proteins from Pathogenic Bacteria and Protozoans Bound to Fluorinated Pipecolic Acid Inhibitors.

Pérez Carrillo VH, Whittaker JJ, Wiedemann C, Harder JM, Lohr T, Jamithireddy AK, Dajka M, Goretzki B, Joseph B, Guskov A, Harmer NJ, Holzgrabe U, Hellmich UA, J Med Chem (2025) Europe PMC

SASDWF4 – Outer membrane protein MIP from Legionella pneumophila (LpMIP) in complex with inhibitor NJS224

Outer membrane protein MIP
(2S)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐4‐methyl‐N‐[(pyridin‐3‐ yl)methyl]pentanamide
MWI(0) 42 kDa
MWexpected 46 kDa
VPorod 61 nm3
log I(s) 2.32×10-1 2.32×10-2 2.32×10-3 2.32×10-4
Outer membrane protein MIP (2S)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐4‐methyl‐N‐[(pyridin‐3‐ yl)methyl]pentanamide small angle scattering data  s, nm-1
ln I(s)
Outer membrane protein MIP (2S)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐4‐methyl‐N‐[(pyridin‐3‐ yl)methyl]pentanamide Guinier plot ln 2.33×10-1 Rg: 2.9 nm 0 (2.9 nm)-2 s2
(sRg)2I(s)/I(0)
Outer membrane protein MIP (2S)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐4‐methyl‐N‐[(pyridin‐3‐ yl)methyl]pentanamide Kratky plot 1.104 0 √3 sRg
p(r)
Outer membrane protein MIP (2S)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐4‐methyl‐N‐[(pyridin‐3‐ yl)methyl]pentanamide pair distance distribution function Rg: 3.0 nm 0 Dmax: 9.7 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Outer membrane protein MIP (2S)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐4‐methyl‐N‐[(pyridin‐3‐ yl)methyl]pentanamide SREFLEX model
log I(s)
 s, nm-1
Outer membrane protein MIP (2S)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐4‐methyl‐N‐[(pyridin‐3‐ yl)methyl]pentanamide SREFLEX model
log I(s)
 s, nm-1
Outer membrane protein MIP (2S)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐4‐methyl‐N‐[(pyridin‐3‐ yl)methyl]pentanamide SREFLEX model
log I(s)
 s, nm-1
Outer membrane protein MIP (2S)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐4‐methyl‐N‐[(pyridin‐3‐ yl)methyl]pentanamide SREFLEX model
log I(s)
 s, nm-1
Outer membrane protein MIP (2S)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐4‐methyl‐N‐[(pyridin‐3‐ yl)methyl]pentanamide SREFLEX model
Synchrotron SAXS data from solutions of outer membrane protein MIP in complex with inhibitor NJS224 in 20 mM Tris, 150 mM NaCl, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 7.00 mg/ml was measured at 20°C. 24 successive 0.095 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

NJS224: https://pubchem.ncbi.nlm.nih.gov/compound/169192439

Outer membrane protein MIP (LpMIP)
Mol. type   Protein
Organism   Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
Olig. state   Dimer
Mon. MW   22.8 kDa
 
UniProt   Q5ZXE0 (21-233)
Sequence   FASTA
 
(2S)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐4‐methyl‐N‐[(pyridin‐3‐ yl)methyl]pentanamide (NJS224)
Mol. type   Other
Olig. state   Monomer
Mon. MW   0.5 kDa
Chemical formula