Transcription is a crucial step in the life cycle of the human immunodeficiency virus type 1 (HIV 1) and is primarily involved in the maintenance of viral latency. Both viral and cellular transcription factors, including transcriptional activators, suppressor proteins and epigenetic factors, are involved in HIV transcription from the proviral DNA integrated within the host cell genome. Among them, the virus-encoded transcriptional activator Tat is the master regulator of HIV transcription. Interestingly, unlike other known transcriptional activators, Tat primarily activates transcriptional elongation and initiation by interacting with the cellular positive transcriptional elongation factor b (P-TEFb). In this review, we describe the molecular mechanism underlying how Tat activates viral transcription through interaction with P-TEFb. We propose a novel therapeutic strategy against HIV replication through blocking Tat action.

Since the efficiency in the transcription of the HIV genome contributes to the success of viral replication and infectivity, we investigated the downregulating effects of the spirobisindole alkaloids globospiramine (1), deoxyvobtusine (2), and vobtusine lactone (3) from the endemic Philippine medicinal plant, Voacanga globosa, during HIV gene transcription. Alkaloids 1–3 were explored for their inhibitory activity on TNF-α-induced viral replication in two latently HIV-infected cell lines, OM10.1 and J-Lat. The induction of HIV replication from OM10.1 and J-Lat cells elicited by TNF-α was blocked by globospiramine (1) within noncytotoxic concentrations. Furthermore, globospiramine (1) was found to target the NF-ĸB activation cascade in a dose-dependent manner when the transcriptional step at which inhibitory activity is exerted was examined in TNF-α-induced 293 human cells using transient reporter (luciferase) gene expression systems (HIV LTR-luc, ĸB-luc, and mutant ĸB-luc). Interrogation through molecular docking against the NF-ĸB p50/p65 heterodimer and target sites of the subunits comprising the IKK complex revealed high binding affinities of globospiramine (1) against the S281 pocket of the p65 subunit (BE = −9.2 kcal/mol) and the IKKα activation loop (BE = −9.1 kcal/mol). These findings suggest globospiramine (1) as a molecular inspiration to discover new alkaloid-based anti-HIV derivatives.

To evaluate the therapeutic efficacy of a novel inhibitor for IκB kinase alpha (IKKα), noraristeromycin (NAM), for murine experimental model of rheumatoid arthritis, collagen- induced arthritis (CIA). NAM has been chemically synthesized as reported earlier. CIA was induced in DBA/1JNCrlj mice by intradermal inoculation of bovine type II collagen (col II) together with Freund Complete Adjuvant. Following the Day 21 booster injection of col II with Freund Incomplete Adjuvant, the animals were monitored for the development of arthritis and clinically evaluated. NAM was administered orally at different doses prior to induction (prophylactic protocol) or after the emergence of definitive arthritis (therapeutic protocol). Here we demonstrate the experimental evidence that oral administration of NAM could completely prevent the occurrence of experimental arthritis in CIA mouse model at 0.3 mg/kg with ED50 value of approximately 0.1 mg/kg twice daily. Moreover, twice daily oral therapeutic dosage of 1 mg/kg of NAM significantly inhibited the paw swelling and disease progression even after the occurrence of experimental CIA. In addition, NAM exhibited an excellent pharmacokinetics in mice and oral administration of NAM could suppress the production of TNFα elicited by lipopolysaccharide (LPS) in a dose-dependent manner. These results indicated that IKKα inhibition is an effective novel therapy for the treatment of chronic inflammatory processes such as those associated with RA and other related conditions.

Emergence of drug resistance demands new therapeutic strategies against the human immunodeficiency virus (HIV). Currently, there is an increasing research focus on targeting gene expression- the crucial step wherein new viruses and new viral strains are amplified. Moreover, natural products are also being considered as potential candidates for new antivirals. We screened the extract obtained from a Philippine medicinal plant, Mentha cordifolia (Mc). In this study, we demonstrated that Mc ammonium sulfate extract has antiretroviral activity against HIV. HIV-1 latently infected cells (OM10.1) were pre-treated with Mc extract and activated with TNFα. In treated cells, viral replication was inhibited in both cell culture supernatant and whole cell lysates. The level of viral production, as measured by the viral p24 protein concentration, was very much inhibited under noncytotoxic concentrations to the similar level without addition of TNFα. Luciferase assays, however, showed that Mc does not inhibit the HIV-1 LTR driven gene expression. IκBα degradation and p65 nuclear translocation was also not affected as visualized through Western blot and immunofluorescence. These observations demonstrated that Mc possessed an antiviral component against HIV-1 and warrant further work to explore its target of action at a later step of gene expression. Our study introduces a potential source of a lead compound that targets steps in the HIV life cycle.

HIV-1 transcription is specifically augmented by a transcriptional activator complex composed of Tat, an HIV-1-encoded activator, and the host transcription elongation factor P-TEFb, which is composed of cyclin-dependent kinase 9 (CDK9) and cyclin T1. Several observations suggest that P-TEFb is an attractive anti-HIV-1 drug target. However, the long-term cytotoxicity of CDK9 inhibitors hinders their widespread use in HIV-1 therapy. Thus, novel and safe inhibitors are sorely needed. By performing molecular dynamics simulations of the 3D structure of Tat/P-TEFb, we previously identified a unique cavity structure of CDK9, the CDK9 hidden cavity, that is specifically induced by Tat binding. Here, we attempted to identify compounds that fit this cavity and inhibit CDK9 activity by in silico screening. We identified compounds that could inhibit CDK9 activity. One of such compound, 127, showed the strongest inhibitory activity against CDK9. Interestingly, it also inhibited CDK6 to a similar extent. We inspected the amino acid sequence and structural properties of the CDK9 hidden cavity to determine whether it is conserved in other CDKs, such as CDK6. The Ile61, comprising the center of the CDK9 hidden cavity, appears to be crucial for its kinase activity, thus indicating that the identification of the CDK9 hidden cavity may provide vital information for the development of novel CDK9 inhibitors.

Despite the potential of cyclin-dependent kinase 9 (CDK9) as a novel target for various malignancies and HIV replication in infected cells, no effective inhibitors have been developed. In the preceding study, we deciphered a hidden cavity in CDK9 upon molecular dynamics (MD) simulation of the CDK9/CyclinT1/Tat trimolecular complex. This cavity is located near the CDK9 ATP pocket (continuous cavity I, CCI) and extends to the cyclin T1 (CycT1) contact surface (CCII and CCIII). In this study, we searched for compounds similar to previously identified CDK9 inhibitors using cheminformatics to identify compounds that are better suited to this hidden cavity. We identified compounds that effectively targeted CCII and CCIII of CDK9. We confirmed their inhibitory effects on the CDK9/CycT1 complex in vitro. As these inhibitory compounds target only a portion (CCII and CCIII cavities) of CDK9, we examined their combinatorial effects with the known CDK inhibitor BS-181. As expected, this combination exerted an additive inhibitory effect on CDK9 expression. These findings confirm the presence of a CDK9 hidden cavity that was revealed transiently by MD simulations, thus providing promising evidence for the development of CDK9 inhibitors.