HIV integrase is a rational target for treating HIV infection and preventing AIDS. It took approximately 12 years to develop clinically usable inhibitors of integrase, and Phase I clinical trials of integrase inhibitors have just begun. This review focuses on the molecular basis and rationale for developing integrase inhibitors. The main classes of lead compounds are also described, as well as the concept of interfacial inhibitors of protein-nucleic-acid interactions that might apply to the clinically used strand-transfer inhibitors.

Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students’ interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training.

To examine the role of the mitochondrial polymerase (Pol ␥) in clinically observed toxicity of nucleoside analogs used to treat AIDS, we examined the kinetics of incorporation catalyzed by Pol ␥ for each Food and Drug Administration-approved analog plus 1-(2-deoxy-2-fluoro-␤-D-arabinofuranosyl)-5-iodouracil (FIAU), ␤-L-(؊)-2,3-dideoxy-3-thiacytidine (؊)3TC, and (R)-9-(2-phosphonylmethoxypropyl)adenine (PMPA). We used recombinant exonuclease-deficient (E200A), reconstituted human Pol ␥ holoenzyme in single turnover kinetic studies to measure K d (K m ) and k pol (k cat ) to estimate the specificity constant (k cat /K m ) for each nucleoside analog triphosphate. The specificity constants vary more than 500,000-fold for the series ddC > ddA (ddI) > 2,3-didehydro-2,3-dideoxythymidine (d4T) > > (؉)3TC > > (؊)3TC > PMPA > azidothymidine (AZT) > > Carbovir (CBV). Abacavir (prodrug of CBV) and PMPA are two new drugs that are expected to be least toxic. Notably, the higher toxicities of d4T, ddC, and ddA arose from their 13-36-fold tighter binding relative to the normal dNTP even though their rates of incorporation were comparable with PMPA and AZT. We also examined the rate of exonuclease removal of each analog after incorporation. The rates varied from 0.06 to 0.0004 s ؊1 for the series FIAU > (؉)3TC ϳ (؊)3TC > CBV > AZT > PMPA ϳ d4T > > ddA (ddI) > > ddC. Removal of ddC was too slow to measure (<0.00002 s ؊1 ). The high toxicity of dideoxy compounds, ddC and ddI (metabolized to ddA), may be a combination of high rates of incorporation and ineffective exonuclease removal. Conversely, the more effective excision of (؊)3TC, CBV, and AZT may contribute to lower toxicity. FIAU is readily extended by the next correct base pair (0.13 s ؊1 ) faster than it is removed (0.06 s ؊1 ) and, therefore, is stably incorporated and highly mutagenic. We define a toxicity index for chain terminators to account for relative rates of incorporation versus removal. These results provide a method to rapidly screen new analogs for potential toxicity.Current treatment of HIV 1 includes a mixture that generally consists of a combination of nucleoside and nonnucleoside analogs directed against HIV RT, plus an inhibitor of HIV protease. Treatment with this mixture allows patients to coexist with a low level of virus for years, but treatments are limited by the development of resistance of HIV to the drugs on the one hand and toxicity of nucleoside analogs on the other. Toxicity of nucleoside analogs is particularly troublesome for the long term management of the viral infection. Nucleoside analogs function as chain terminators to suppress viral replication by HIV-1 RT, and because HIV RT lacks a proofreading exonuclease, the specificity of nucleoside analogs toward HIV RT results from selective discrimination during incorporation and/or from removal by the proofreading exonuclease of the host DNA polymerase.Six nucleoside analogs have received Food and Drug Administration approval for treatment of HIV, and these analogs are illustrated with others...

Temperate phages are common and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses infecting mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity, and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages reveals at least five distinct prophage-expressed viral defense systems that interfere with infection of lytic and temperate phages that are either closely-related (homotypic defense) or unrelated (heterotypic defense). Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defense systems include a single-subunit restriction system, a heterotypic exclusion system, and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival, and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, that acts as a highly effective counter-defense system. Prophage-mediated viral defense offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defense promotes phage co-evolution.