The evolution of a novel class of pyrazinone direct thrombin inhibitors (DTIs) is described. In an effort to improve the solubility and thereby the drug-like properties of pyrazinones that possess non-basic P, residues, a novel amino P-1-P-2 linker has been designed from X-ray thrombin-inhibitor complexes. Biochemical evaluation demonstrated that nanomolar binding affinity was attained, and X-ray co-crystal structures reveal an unprecedented binding mode that involves an interaction of the new amino linker with Glu192 of the active site of thrombin. A family of soluble pyrazinones has thereby emerged.