Unconventional Interaction Forces in Protein and Protein-ligand Systems and their Impacts to Drug Design

Qing-Yan      Wang; Jian      Lu; Si-Ming      Liao; Qi-Shi      Du; Ri-Bo      Huang

Abstract

In drug design and enzyme engineering, the information of interactions between receptors and ligands is crucially important. In many cases, the protein structures and drug-target complex structures are determined by a delicate balance of several weak molecular interaction types. Among these interaction forces several unconventional interactions play important roles, however, less familiar for researchers. The cation-π interaction is a unique noncovalent interaction only acting between aromatic amino acids and organic cations (protonated amino acids) and inorganic cations (proton and metallic). This article reports new study results in the interaction strength, the behaviors and the structural characters of cation-π interactions between aromatic amino acids (Phe, Tyr, and Trp) and organic and inorganic cations (Lys⁺, Arg⁺, H⁺, H3O⁺, Li⁺, Na⁺, K⁺, Ca²⁺, and Zn²⁺) in gas phase and in solutions (water, acetonitrile, and cyclohexane). Systematical research revealed that the cation-π interactions are point-to-plane (aromatic group) interactions, distance and orientationdependent, and the interaction energies change in a broad range. In gas phase the cation-π interaction energies between aromatic amino acids (Phe, Tyr, and Trp) and metallic cations (Li⁺, Na⁺, K⁺, Ca²⁺, and Zn²⁺) are in the range -12 to -160 kcal/mol, and the interaction energies of protonated amino acids (Arg⁺ and Lys⁺) are in the range from -9 to -18 kcal/mol. In solutions the cation-π energies decrease with the dielectric constant ε of solvents. However, in aqueous solution the cation-π energies of H₃O⁺ and protonated amino acids are less affected by solvation effects. The applications of unconventional interaction forces in drug design and in protein engineering are introduced.