Structural studies of biomolecules related to cancer and HIV-AIDS

Division Of Basic Sciences - Nci

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Abstract

APOBEC3G (A3G) and APOBEC3H (A3H) are single-stranded DNA cytosine deaminase that can restrict HIV-1 infection by mutating HIV-1 genome. HIV-1 developed a counter defense mechanism by which virion infectivity factor (Vif) leads the degradation of A3G/A3H through ubiquitin-proteasome pathway. Our ultimate goal is to generate small compounds which inhibit the degradation of A3G/A3H. Previously, we had determined NMR and crystal structures of domains of A3 proteins, including the VIf-binding domain and the catalytic domain. In addition, we had determined co-crystal structures of the A3's catalytic domain-ssDNA complex. During 2021-2022, we have developed a technique to selectively stable-isotope label Vif in complex with A3G, and assigned NMR signals of Vif to identify amino acid residues in the interfaces with A3G (published in JMR, 2022). We have made progress in determining the structure of the A3H-Vif E3 ubiquitin ligase complex by using cryoEM, which will provide epitopes to be targeted by small compounds which inhibit formation of the complex. Dysregulation of APOBEC3A (A3A) and APOBEC3B (A3B) proteins contributes a major endogenous source of DNA mutations traced in approximately 75% of cancer types and 50% of all cancers analyzed. A3A/A3B proteins can cause DNA mutations either alone or as the response to cancer therapies which can drive evolution of cancers, and A3A/A3B related mutations maybe associated with poor prognosis and therapeutic resistance in cancers. We are developing ssDNA based A3A/A3B inhibitors as ssDNA is the natural substrate for their catalytic reaction. A transition state analogue, 2'-deoxy-zebularine, was incorporated into the target ssDNA sequence of A3A/A3B, and yielded promising affinity and inhibitory effect. We are currently testing modification of nucleotides in order to resist degradation in cells.