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Volumn 18, Issue 1, 2008, Pages 318-323

Biphenyl amide p38 kinase inhibitors 1: Discovery and binding mode

Author keywords

Binding mode; Biphenyl amide; Biphenyl amides; BPA; BPAs; CSBP; Focused screen; Inhibitors; kinase selectivity; MAP kinase; p38; p38 alpha; p38 kinase; Pharmacophore search; Protein kinase X ray structure; Structure based drug design; Virtual screening

Indexed keywords

4 (4 FLUOROPHENYL) 2 (4 METHYLSULFINYLPHENYL) 5 (4 PYRIDYL)IMIDAZOLE; BIPHENYL DERIVATIVE; MITOGEN ACTIVATED PROTEIN KINASE 12; MITOGEN ACTIVATED PROTEIN KINASE 14; MITOGEN ACTIVATED PROTEIN KINASE P38 INHIBITOR; PROTEIN KINASE LCK;

EID: 37549041341     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmcl.2007.10.076     Document Type: Article
Times cited : (41)

References (26)
  • 14
    • 37549037219 scopus 로고    scopus 로고
    • Human p38α was expressed in Escherichia coli as described in Ref. 11 and purified as follows: purification was at 4 °C unless stated otherwise. Cell paste from the culture expressing hexahis-tagged p38α was lysed by sonication in Hepes, 25 mM, NaCl, 325 mM, imidazole, 25 mM, pH 7.5. The lysate was clarified by centrifugation and filtration before Ni-affinity chromatography and stepwise elution with imidazole up to 100 mM concentration. Pooled fractions were filtered before fivefold dilution into Hepes, 25 mM, DTT, 1 mM, pH 7.5 and loading onto an anion exchange Q Sepharose FF column followed by elution with a NaCl gradient to 1.0 M in the same buffer. At room temperature, the NaCl concentration of eluted fractions was made 2.0 M before application to a Phenyl Sepharose column equilibrated in Hepes, 25 mM, NaCl, 2.0 M, DTT, 1 mM, pH 7.5, and elution in a decreasing gradient of NaCl from 2 to 0 M. The eluate was diluted fivefold into Tris-HCl, 25 mM, DTT, 1 mM, pH 7.5 and loaded onto a Source Q column, equilibrated in the same buffer with 0.1 M NaCl. Elution was performed by washing successively with 0.1 and 0.2 M NaCl in the equilibration buffer and then by gradient to 0.45 M NaCl.
  • 15
    • 37549017854 scopus 로고    scopus 로고
    • 4, 18-22% PEG5000MME, 3-4% Jeffamine ED600, 2 mM β-ME) and took ∼2 weeks to grow. Typically crystals were soaked in well buffer solution containing 25% PEG5000MME with 2-2.5 mM compound for ∼24 h, followed by brief immersion in cryoprotectant (soaking buffer containing 10% glycerol for compound 1, or a different cryoprotectant (100 mM ADA pH6.5, 25% PEG5000MME, 25% glycerol, 5% PEG400) for compounds 3 and 4) prior to data collection.
  • 16
    • 37549060117 scopus 로고    scopus 로고
    • *TREK (Pflugrath, J.W. Acta Cryst. 1999, D55, 1718-1725) or HKL (Otwinowski, Z; Minor, W. Methods Enzymol., 1997, 276 (Macromol. Cryst. part A), 307-326) and structures solved using the native p38 coordinates (PDB entry 1WFC) as the initial model in refinement by REFMAC (Murshudov, G.; Vagin, A.; and Dodson, E. Acta Cryst. 1997, D53, 240-255). The final R-factors achieved for each complex were 19.8% (compound 1), 17.2% (compound 3) and 16.9% (compound 4). Coordinates have been deposited with the PDB as entries 2ZAZ, 2ZB0 and 2ZB1. Activated p38α has proved intractable to crystallisation and no structures have yet been published, but inactive p38α readily gives crystals. These structures are frequently used to rationalise SAR of activated p38α, for example as discussed in Refs. 9 and 11.
  • 20
    • 37549010081 scopus 로고    scopus 로고
    • Pharmacophore modelling and 3D database searching was carried out using Catalyst from Accelrys Software Inc., http://www.accelrys.com.
  • 21
    • 37549036056 scopus 로고    scopus 로고
    • note
    • p38α and JNK3 assays were carried out as described in Ref. 14. Lck activity was measured as described in Ref. 7.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.