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Protonation of an α-Hydroxytropolone HIV RNase H Inhibitor through QM/MM Methods

posted Feb 1, 2020, 1:42 PM by Judy Wei   [ updated Feb 1, 2020, 1:47 PM ]
α-Hydroxytropolones are potential anti-HIV drugs that inhibit the processing of the DNA/RNA hybrid by the RNase H enzyme. It is known that these molecules bind to the Mg2+ metal ion cofactors of the enzyme. However, the specific protonation state of the bound inhibitor is unclear. The molecule we intend to study is the bound structure of β-thujaplicinol to HIV-1 RNase H. In order to figure out the protonation state of the oxygen substituents, we proposed four different states to find out which one is most consistent with the known crystal structure by the method of QM/MM geometry optimization.
Figure 3. the structure comparison of the calculated molecule to the original structure.
Figure 3. the structure comparison of the calculated molecule to the original structure 
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