Effect of methyl substitution in a ligand on the selectivity and binding affinity for a nucleobase: a case study with isoxanthopterin and its derivatives.
Isoxanthopterin (IX) has two edges with hydrogen bond-forming sites suitable for binding to thymine (T) and cytosine (C). The binding affinity of IX for T or C is stronger than for adenine (A) and guanine (G), whereas the base selectivity of IX for T over C (and vice versa) is moderate. In order to improve both the binding affinity and base selectivity for T over C or C over T, a methyl group is introduced respectively at the N-3 or N-8 position of IX. This leads to the known ligands 3-methyl isoxanthopterin (3-MIX) and 8-methyl isoxanthopterin (8-MIX), and the binding affinity for C or T is expected to be tuned and improved by methyl substitution. Indeed, 3-MIX selectively binds to T more strongly than IX with a binding constant of 1.5 x 10(6) M(-1) and it loses its binding affinity for C. In contrast, 8-MIX selectively binds to C over T with a binding constant of 1.0 x 10(6) M(-1) and the binding affinity is greatly improved compared to the parent ligand IX. The thermodynamics of the ligand-nucleotide interaction is analyzed by isothermal calorimetric titrations, and the results show that the interaction follows a 1:1 stoichiometry and is enthalpy-driven. The introduction of methyl groups at both N-3 and N-8 positions results in an increase in enthalpy of the ligand-nucleotide interaction, which leads to the improved binding affinity.
Rajendar
Burki
B
Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
Rajendran
Arivazhagan
A
Sato
Yusuke
Y
Nishizawa
Seiichi
S
Teramae
Norio
N
D001665:Binding Sites; D002151:Calorimetry; D003596:Cytosine / Q000737:chemistry; D008024:Ligands; D008745:Methylation; D011744:Pyrimidinones / Q000737:chemistry*; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry; D014976:Xanthopterin / Q000737:chemistry*
D008024:Ligands; D011744:Pyrimidinones; C008217:isoxanthopterin; D003596:Cytosine; D013941:Thymine; D014976:Xanthopterin