Synthesis and properties of diuridine phosphate analogues containing thio and amino modifications

JB Thomson, BK Patel, V Jiménez… - The Journal of …, 1996 - ACS Publications
JB Thomson, BK Patel, V Jiménez, K Eckart, F Eckstein
The Journal of Organic Chemistry, 1996ACS Publications
Several analogues of diuridine phosphate (UpU) were synthesized in order to investigate
why replacing the 2 '-hydroxyl with a 2 '-amino group prevents hydrolysis. These analogues
were designed to investigate what influence the 2 '-substituent and 5 '-leaving group have
upon the rate of hydrolysis. All the analogues were considerably more labile than UpU
toward acid− base-catalyzed hydrolysis. In the pH region from 6 to 9, the rate of hydrolysis of
uridylyl (3 '− 5 ') 5 '-thio-5 '-deoxyuridine (UpsU) hydrolysis rose, in a log linear fashion, from …
Several analogues of diuridine phosphate (UpU) were synthesized in order to investigate why replacing the 2‘-hydroxyl with a 2‘-amino group prevents hydrolysis. These analogues were designed to investigate what influence the 2‘-substituent and 5‘-leaving group have upon the rate of hydrolysis. All the analogues were considerably more labile than UpU toward acid−base-catalyzed hydrolysis. In the pH region from 6 to 9, the rate of hydrolysis of uridylyl (3‘−5‘) 5‘-thio-5‘-deoxyuridine (UpsU) hydrolysis rose, in a log linear fashion, from a value of 5 × 10-6 s-1 at pH 6 to 3200 × 10-6 s-1 at pH 9, indicating that attack on the phosphorus by the 2‘-oxo anion is rate-limiting in the hydrolysis mechanism. In contrast, the rate of uridylyl (3‘−5‘) 5‘-amino-5‘-deoxyuridine (UpnU) hydrolysis fell from a value of 1802 × 10-6 s-1 at pH 5 to 140 × 10-6 s-1 at pH 7.5, where it remained constant up to pH 11.5, thus indicating an acid-catalyzed reaction. The analogue 2‘-amino-2‘-deoxyuridylyl (3‘−5‘) 5‘-thio-5‘-deoxyuridine (amUpsU) was readily hydrolyzed above pH 7, in contrast to the hydrolytic stability of amUpT, with rates between 85 × 10-6 s-1 and 138 × 10-6 s-1. The hydrolysis of 2‘-amino-2‘-deoxyuridylyl (3‘−5‘) 5‘-amino-5‘-deoxythymidine (amUpnT) rose from 17 × 10-6 s-1 at pH 11.5 to 11 685 × 10-6 s-1 at pH 7.0, indicating an acid-catalyzed reaction, where protonation of the 5‘-amine is rate limiting. The cleavage rates of UpsU, UpnU, and amUpsU were accelerated in the presence of Mg2+, Zn2+, and Cd2+ ions, but a correlation with interaction between metal ion and leaving group could only be demonstrated for amUpsU. UpsU and UpnU are also substrates for RNase A with UpsU having similar Michaelis−Menten parameters to UpU. In contrast, UpnU is more rapidly degraded with an approximate 35-fold increase in catalytic efficiency, which is reflected purely in an increase in the value of kcat.
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