ONIOM investigation of nucleotide selectivity in phosphodiesterases 3 and 4

Abstract The cyclic nucleotide phosphodiesterases (PDEs) are drug‐targeted enzymes that down regulate cyclic nucleotide concentrations in the cell by catalyzing the hydrolysis of the O3′‐phosphorous bond, yielding the noncyclic nucleotides. Selectivity for cAMP versus cGMP (cyclic 3′,5′‐adenosine/‐guanosine monophosphate) as the favored substrate is primarily attributed to the orientation of a conserved glutamine residue which binds to the adenine/guanine ring. We use ONIOM hybrid quantum methods to accurately describe substrate binding within the catalytic sites of the cAMP‐specific PDE4 and the cGMP‐inhibited, dual‐specific PDE3 in order to understand subtle aspects of substrate selectivity. We estimate PDE4's net preference for cAMP binding to be about 16 kcal/mol; the cause of cAMP's known preference resides both in its fixed glutamine orientation (Gln 369 in PDE4D) and in the differential free energy of solvation, which disfavors the binding of cGMP relative to cAMP by about 15 kcal/mol. Also, we discuss the contributing role played by Asn 321, held in place by a partner Asp 167, in the deselection of cGMP by PDE4. PDE3's conserved glutamine (Gln 988 in PDE3B) is free to take on either a cGMP‐favorable or cAMP‐favorable orientation. We find that enthalpies of binding favor cGMP for PDE3, but only by the same amount as free energies of solvation disfavor cGMP binding. Comparison of the PDE3‐cAMP and ‐cGMP complexes and energetics reveals cAMP to be more susceptible to the attack of the hydroxide nucleophile in PDE3. We identify a key threonine residue (Thr 952) as responsible for PDE3's kinetic relative disfavor of cGMP hydrolysis by causing Gln 988 to tilt out of cGMP's purine plane. Our results are consistent with the PDE3's kinetic specificity for cAMP hydrolysis and the known competitive inhibition of PDE3 by cGMP. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008