Targeting Uracil-DNA Glycosylases for Therapeutic Outcomes Using Insights from Virus Evolution

Abstract

Ung-type uracil-DNA glycosylases are frontline defenders of DNA sequence fidelity in bacteria, plants, and animals; Ungs also directly assist both innate and humoral immunity. Critically important in viral pathogenesis, whether acting for or against viral DNA persistence, Ungs also have therapeutic relevance to cancer, microbial, and parasitic diseases. Ung catalytic specificity is uniquely conserved, yet selective antiviral drugging of the Ung catalytic pocket is tractable. However, more promising precision therapy approaches present themselves via insights from viral strategies, including sequestration or adaptation of Ung for non-canonical roles. A universal Ung inhibition mechanism, converged upon by unrelated viruses, could also inform design of compounds to inhibit specific distinct Ungs. Extrapolating current developments, the character of such novel chemical entities is proposed. Executive Summary • Introduction Ungs are essential enzymes at the forefront of pathogenic states, both defending cells and being co-opted by pathogens. • Ung structure and mechanism Ung is an exquisitely specific catalytic domain, but pre-catalytic variations promise specificity between targeting the host enzyme and pathogenic variants. • Origins and significance of uracil-substituted DNA in pathogenesis Viruses have evolved to silence, or co-opt Ung to facilitate pathogenic states. Understanding these origins allows search for novel Ung-interacting proteins. Knowledge of Ung-interacting protein interfaces can facilitate drug discovery. • Motivations and contexts for therapeutic interventions targeting Ung Understanding the significance of Ung in diverse pathogenic states permits suitable intervention to be designed and implemented. • Convergence on a universal Ung-inhibitory mechanism by unrelated virus proteins Natural protein-protein interactions that irreversibly inhibit Ung activity, by convergence on a common mechanism have independently evolved at least 3 times from different protein architectures. The naturally evolved inhibitor proteins do not target uracil specificity of Ung. • Synthetic selective Ung inhibition and future trends Drug design centred upon uracil-analogues has shown specificity is achievable. Compounds featuring uracil and hydrophobic tails are not ideal drug candidate molecules. Compounds targeting Ung protein-protein interactions have shown selective potency against poxviruses. • Conclusions Eschewing uracil-specificity to emulate features of natural protein-protein interactions, promises novelty in selective drug discovery to target Ungs in pathogenic states. Herpesviruses (g-/ EBV, KSHV) Elongated/structured pre-catalytic loop is essential to replication [34,35]. Poxviruses [vaccinia] Divergent features/ variant pre-catalytic loop, resistant to phage-mediated inhibition; potent PPI inhibitors identified [26-28]. Mycobacterium tuberculosis Atypical catalytic structure, weakened phage-mediated inhibition [36,37]. Plasmodium falciparum Divergent sequence; uracil-analogue inhibitors identified [38]. * Pe...

The Essential Co-Option of Uracil-DNA Glycosylases by Herpesviruses Invites Novel Antiviral Design

“…excluding archaea, which instead employ other branches of UDG superfamily enzymes). In fact, the ubiquity of Ung extends to its appearance in the genomes of some viruses: For example, Ung is encoded by poxviruses [40,41], and herpesviruses [41][42][43][44][45][46][47][48][49][50][51][52].…”

“…Cellular utilisation of Ung activity is not limited to its role in DNA repair (Figure 4), thus Ung is observed to play important roles in other key cellular programs, such as innate cellular immunity as a frontline defence against viral pathogens. The importance of this role for Ung is underlined by the fact that diverse virus lineages, whether targeting prokaryotes or eukaryotes, actively silence Ung at the mRNA or/and at the protein level [41,[53][54][55][56][57][58][59][60]. It would appear that viruses, in general, are sensitive to uracil in DNA for varying reasons.…”

“…Although not investigated in as much detail at the present time, structural molecular insights could also provide the potential for similar approaches to selective inhibition. This key motif in Ung, is, therefore, a promising target for the design and development of novel antiviral compounds [41,76], especially given the structural differences relative to the host cell enzyme ( Figure 5). , a protein mimic of DNA that specifically targets Ung.…”

“…Intriguingly this conserved mechanism has evolved convergently from three independent, unrelated protein architectures: Ugi [and its structural homologue SAUGI, a horizontally transferred gene found in SCCmec mobile genetic elements of Staphylococcaceae] from myoviruses, p56 from salasviruses and Vpr from primate lentiviruses. Charge-based alignment and contact from the inhibitor protein elicits concerted Ung loop motion, resulting in an effectively irreversible sterically-blockaded sequestration of Ung via hydrophobic trapping of the apical aliphatic side chain of the Ung loop by the virus inhibitor protein ( Figure 5) [41,[70][71][72]76].…”

“…This may be the reason why abrogation of the loop adaptation in herpersvirus Ungs ablates replication so effectively [50]. It is proposed that the near-surface location of this site, and the general mixed polar nature of the environs and within the loop structure itself, lends itself well to a structure-based drug design campaign ( Figure 5) [41]. In fact protein engineering studies involving the Ung inhibitor protein SaUgi, which targets the Ung DNA binding cleft and minor groove DNA binding loop region show that impressive selectivity between Ung encoded by human, bacterial, α-herpesvirus and γ-herpesvirus can be demonstrated [76].…”