Kernel energy method: Drug–target interaction energies for drug design



The full power of ab initio quantum mechanics applied to obtain the interaction of drugs and their molecular targets can provide detailed energetics useful to understanding of mechanism and drug design. The computational problem is the growth in quantum computational difficulty with the number of atoms in the molecule. As biochemical molecules are often large, the computational difficulty of the full quantum problem is challenging. Two things help alleviate the difficulty, viz., (1) parallel supercomputers, and (2) quantum crystallography and the use of quantum kernels, a method well suited for parallel computation. Calculations are simplified by approximating a full molecule by smaller “kernels” of atoms. Here, it is suggested that problems of medicinal chemistry, such as the rational design of drugs, may be illuminated by the use of the ab initio quantum-mechanical kernel energy method. Example calculations within the MP2/3-21G chemical model are illustrated for three aminoglycoside drugs, which attach to ribosomal A-site RNA nucleotide targets. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010