Computer-Aided Identification of Fragments as CDK9 Inhibitors with Anti-HIV-1 Tat-Mediated Transcription Activity

Although remarkable progress has been made in the treatment of HIV infection, the current therapy, beside suffering from the emergence of drug-resistant viral strains, results unable to completely eradicate the virus from infected individuals, thus prompting for innovative ad more effective treatment options.1 Among the many host factors involved in the modulation of the post integration latency, the Positive Transcriptional Elongation Factor b (P-TEFb) was shown by several experimental evidences to be druggable.2 In particular, the inhibition of kinase subunit CDK9 could be a good strategy to obtain indirect antiviral drugs that should be active against mutant viruses eventually escaping current therapies besides controlling the reactivation from viral latency. Using as target the crystallographic structure of P-TEFb in complex with flavopiridol,3 a docking-based virtual screening was performed on vendor and in-house libraries, and on a fragment-based database we built specifically for this task. The selected hits were submitted to biologically testing, confirming for some of them the ability to inhibit the activity of CDK9. The optimization of two fragment-based “real” hits was carried on taking advantage of several in silico and experimental techniques, and led to the identification of non toxic 2-phenylquinazolinone derivatives able to inhibit Tat-mediated transactivation as well as HIV-1 reactivation from latency in latently infected cells. Of note, a derivative showed an anti-HIV potency in the latently infected cell model superior to what could be predicted looking just at its anti-CDK9 activity, thus leading us to speculate about an additional target. Indeed, CDK2, which plays a supportive role within the transcriptional machinery and shares structural features with CDK9, was also inhibited by the derivative at comparable concentrations. An insight into the double activity of the compound has been achieved studying the docking-predicted binding mode into both enzymes followed by its comparison to several published crystallographic structures and to literature data that show the chemical features needed to obtain selectivity. Thus, the identified 2-phenylquinazolinones, which conforming to the rule of 3 can be categorized as fragments,4 represent a good template for the development of anti-HIV agents optimized in both potency and selectivity.