Staurosporine tethered peptide ligands that target cAMP-dependent protein kinase (PKA): optimization and selectivity profiling.
We have recently developed a fragment based selection strategy for targeting kinases, where a small molecule warhead can be non-covalently tethered to a phage-displayed library of peptides. This approach was applied to the conversion of the promiscuous kinase inhibitor, staurosporine, into a potent bivalent ligand for cAMP-dependent protein kinase (PKA). Herein we report a systematic evaluation of this new bivalent ligand (BL); (a) Lineweaver-Burke analysis revealed that the BL, unlike substrate-based bivalent kinase inhibitors, displayed non-competitive inhibition with respect to the peptide substrate, suggesting an allosteric mechanism of action; (b) linker optimization of the BL, afforded one of the most potent, sub-nanomolar, inhibitors of PKA reported to date; (c) the BL was found to be modular, where attachment of active site targeted small molecule warheads in lieu of staurosporine could achieve similar gains in affinity; and (d) profiling studies of both the staurosporine derivative and the BL (amide isostere) against a panel of 90 kinases revealed almost unique enhancement in selectivity against PKA (>5-fold) compared to the starting staurosporine derivative. These combined results provide new insights for BL discovery, which has the potential to provide guidance toward the development of kinase selective reagents while uncovering new allosteric sites on kinases for therapeutic targeting.
Shomin
Carolyn D
CD
Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, United States.
Meyer
Scott C
SC
Ghosh
Indraneel
I
D000495:Allosteric Site; D020134:Catalytic Domain; D017868:Cyclic AMP-Dependent Protein Kinases / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008024:Ligands; D019151:Peptide Library; D047428:Protein Kinase Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D019311:Staurosporine / Q000737:chemistry* / Q000494:pharmacology
D008024:Ligands; D019151:Peptide Library; D047428:Protein Kinase Inhibitors; D017868:Cyclic AMP-Dependent Protein Kinases; D019311:Staurosporine
Curr Pharm Des. 2005;11(14):1845-63
15892678
Bioorg Chem. 2005 Aug;33(4):285-97
16023488
J Med Chem. 2000 Dec 14;43(25):4787-92
11123987
Blood. 2005 Aug 1;106(3):996-1002
15831699
Org Lett. 2005 Apr 28;7(9):1695-8
15844883
Mini Rev Med Chem. 2004 Mar;4(3):301-11
15032676
Nat Biotechnol. 2008 Jan;26(1):127-32
18183025
Nat Struct Biol. 1997 Oct;4(10):796-801
9334743
Biochem J. 1997 May 1;323 ( Pt 3):577-91
9169588
Biochemistry. 1999 Jun 15;38(24):7653-8
10387004
J Am Chem Soc. 2009 May 20;131(19):6686-8
19391594
J Biol Chem. 2005 Apr 8;280(14):13728-34
15657054
Science. 1995 Mar 24;267(5205):1782-8
7892601
J Biol Chem. 1999 Oct 1;274(40):28301-7
10497187
Mol Cell. 2000 Oct;6(4):909-19
11090628
Nat Struct Biol. 2001 Jan;8(1):37-41
11135668
Nat Biotechnol. 2005 Mar;23(3):329-36
15711537
Science. 2002 Dec 6;298(5600):1912-34
12471243
Biochemistry. 1996 Mar 19;35(11):3619-24
8639514
Curr Opin Investig Drugs. 2008 Jun;9(6):605-13
18516760
Biochem J. 2003 Apr 1;371(Pt 1):199-204
12534346
Bioorg Med Chem Lett. 1999 May 17;9(10):1447-52
10360754
Proc Natl Acad Sci U S A. 1981 Jul;78(7):4046-50
16593049
Structure. 1997 Dec 15;5(12):1627-37
9438863
Nat Chem Biol. 2006 Jul;2(7):358-64
16783341
Chem Biol. 2005 Jun;12(6):621-37
15975507
Science. 1998 Jul 24;281(5376):533-8
9677190
J Biol Chem. 2002 Nov 29;277(48):46609-15
12244092
Physiol Rev. 2001 Apr;81(2):807-69
11274345
Med Res Rev. 2002 Jul;22(4):373-84
12111750
ACS Chem Biol. 2007 May 22;2(5):329-36
17465519
J Biol Chem. 2008 Oct 3;283(40):27048-56
18621738
Sci Signal. 2008 Jun 03;1(22):re4
18523239
Biochem J. 2003 Oct 15;375(Pt 2):255-62
12892559
Nat Rev Drug Discov. 2006 Dec;5(12):993-6
17139284
Biochem J. 2000 Oct 1;351(Pt 1):95-105
10998351
Trends Biochem Sci. 2000 Dec;25(12):596-601
11116185
J Pept Res. 2001 Mar;57(3):250-6
11298927
Biochim Biophys Acta. 2004 Mar 11;1697(1-2):243-57
15023365
Pharmacol Ther. 2002 Feb-Mar;93(2-3):145-57
12191607
Chem Biol Drug Des. 2006 Jul;68(1):3-10
16923020
J Am Chem Soc. 2007 Nov 14;129(45):13812-3
17944472
Bioorg Med Chem Lett. 2004 Jun 7;14(11):2951-4
15125966
J Med Chem. 2000 Apr 6;43(7):1413-7
10753478
J Mol Biol. 1999 Jan 15;285(2):713-25
9878439
Chembiochem. 2008 Mar 3;9(4):507-9
18224646