Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.
The search for novel leads is a critical step in the drug discovery process. Computational approaches to identify new lead molecules have focused on discovering complete ligands by evaluating the binding affinity of a large number of candidates, a task of considerable complexity. A new computational method is introduced in this work based on the premise that the primary molecular recognition event in the protein binding site may be accomplished by small core fragments that serve as molecular anchors, providing a structurally stable platform that can be subsequently tailored into complete ligands. To fulfill its role, we show that an effective molecular anchor must meet both the thermodynamic requirement of relative energetic stability of a single binding mode and its consistent kinetic accessibility, which may be measured by the structural consensus of multiple docking simulations. From a large number of candidates, this technique is able to identify known core fragments responsible for primary recognition by the FK506 binding protein (FKBP-12), along with a diverse repertoire of novel molecular cores. By contrast, absolute energetic criteria for selecting molecular anchors are found to be promiscuous. A relationship between a minimum frustration principle of binding energy landscapes and receptor-specific molecular anchors in their role as "recognition nuclei" is established, thereby unraveling a mechanism of lead discovery and providing a practical route to receptor-biased computational combinatorial chemistry.
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Agouron Pharmaceuticals Inc., San Diego, CA 92121, USA.
Verkhivker
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D001665:Binding Sites; D002352:Carrier Proteins / Q000037:antagonists & inhibitors*; D004268:DNA-Binding Proteins / Q000037:antagonists & inhibitors*; D016208:Databases, Factual; D015195:Drug Design; D006360:Heat-Shock Proteins / Q000037:antagonists & inhibitors*; D008024:Ligands; D008432:Mathematical Computing; D008954:Models, Biological; D008958:Models, Molecular; D008962:Models, Theoretical; D011485:Protein Binding; D022021:Tacrolimus Binding Proteins; D013816:Thermodynamics
D002352:Carrier Proteins; D004268:DNA-Binding Proteins; D006360:Heat-Shock Proteins; D008024:Ligands; D022021:Tacrolimus Binding Proteins