Structural Studies of Specific Intermolecular Interactions and Self-Aggregation of Biomolecules and Their Application to Drug Design

Abstract

Information on the structural basis of intermolecular recognition or self-aggregation of biomolecules at the atomic level is important to understand biological functions and to develop devices for treating disorders caused by abnormal functions. Thus structural analysis of specific intermolecular or intramolecular interactions of biomolecules has been performed using various physicochemical approaches. Herein, the following three subjects are reviewed: (1) structural analyses of mRNA cap structure recognition by eukaryotic initiation factor 4E and its functional regulation by endogenous 4E-binding protein; (2) structural studies of self-aggregation mechanism of microtubule-binding domain in tau protein and aggregation inhibitor; and (3) molecular design of cathepsin B-specific inhibitor.Key words recognition; aggregation; inhibition; initiation factor 4E; tau protein; cathepsin B Chem. Pharm. Bull. 57(12) 1309-1334 (2009) Review© 2009 Pharmaceutical Society of Japan e-mail: ishida@gly.oups.ac.jp 1310 Vol. 57,No. 12 because the selective recognition of a specific nucleotide or nucleic acid sequence by an amino acid residue or its sequence in an enzyme is an essential biological event in the life cycle.Quantum chemical analysis clarified that the N-quaternization of nucleic acid bases (adenine, guanine, and cytosine) lowers the lowest unoccupied molecular orbital (LUMO) energy level to close to the level of the highest occupied molecular orbital (HOMO) energy of the Trp indole ring, reinforcing the HOMO-LUMO interaction; an example of a guanine base is shown in Fig. 2a. Because this implies that Trp can selectively recognize the N-alkylated nucleic bases through prominent p-p-stacking interactions, much experimental evidence was accumulated by the structural analyses of related model complexes to clarify the function of the Trp residue in the interaction with nucleotide bases. [8][9][10][11][12][13][14][15][16][17][18][19] The X-ray crystal structure of the Trp-Glu-N7-methyl guanosine 5Ј-monophosphate (m 7 GMP) complex 20,21) and the solution NMR structure of the Trp-Leu-Glu-m 7 GpppA complex 22,23) are shown in Fig. 2b. The results suggest the importance of cooperative stacking and hydrogen bond pairing interactions of Trp and Glu residues for the selective recognition of the mRNA cap structure, 24) in which the cap structure of mRNA is characterized by N7-methyl guanosine linked with the 5Ј-terminal portion of mRNA via a 5Ј,5Ј-triphosphate (Fig. 1). Further structural and spectroscopic refinements showed that the sequence -Trp-(Gly) m -Asp/Glu-(Gly) n -Trp-(mϭ0-2, nϭ0-2) is most preferred for the N7-methyl guanine base (m 7 G). [25][26][27] These model interaction studies enabled us to confirm whether this specific recognition mode of the m 7 G base by the cooperation of Trp and acidic amino acid residues is actually applied to the recognition of the mRNA cap structure by eIF4E. Gene Construction, Expression, and Purification and Cap-Binding Ability of Recombinant Human eIF4EHuman eIF4E (ca. 25 kDa) consis...