Transplant-insert-constrain-relax-assemble (TICRA): protein-ligand complex structure modeling and application to kinases.
We introduce TICRA (transplant-insert-constrain-relax-assemble), a method for modeling the structure of unknown protein-ligand complexes using the X-ray crystal structures of homologous proteins and ligands with known activity. We present results from modeling the structures of protein kinase-inhibitor complexes using p38 and Lck as examples. These examples show that the TICRA method may be used prospectively to create and refine models for protein kinase-inhibitor complexes with an overall backbone rmsd of less than 0.75 Å for the kinase domain, when compared to published X-ray crystal structures. Further refinement of the models of the kinase domains of p38 and Lck in complex with their cognate ligands from the published crystal structures was able to improve the rmsd's of the model complexes to below 0.5 Å. Our results show that TICRA is a useful approach to the problem of structure-based drug design in cases where little structural information is available for the target proteins and the binding mode of active compounds is unknown.
Ansaris, Four Valley Square, 512 Township Line Rd, Blue Bell, Pennsylvania 19422, United States. smeshkat@Locuspharma.com
Siavash
S
Meshkat
Anthony E
AE
Klon
Jinming
J
Zou
Jeffrey S
JS
Wiseman
Zenon
Z
Konteatis
D000255:Adenosine Triphosphate / Q000737:chemistry; D000494:Allosteric Regulation; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D008024:Ligands; D019860:Lymphocyte Specific Protein Tyrosine Kinase p56(lck) / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D047428:Protein Kinase Inhibitors / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D011494:Protein Kinases / Q000737:chemistry* / Q000378:metabolism*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D048051:p38 Mitogen-Activated Protein Kinases / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism
D008024:Ligands; D047428:Protein Kinase Inhibitors; D011506:Proteins; D000255:Adenosine Triphosphate; D011494:Protein Kinases; D019860:Lymphocyte Specific Protein Tyrosine Kinase p56(lck); D048051:p38 Mitogen-Activated Protein Kinases