Analysis of model 6 and creation of the dimeric model 7 HIV-1 CRF02_AG IN structure.

<p>(A) Domain organization of HIV-1 and PFV IN domains showing regions of structural and sequence overlap as well as structural gaps. (B) Structural alignment of modeled chain A (yellow) aligned with templates 3OY9 (cyan) and 1EX4 (dark green); (C) Comparative Verify3D analysis of the two templates with model 6; (D) Modeled Chain B (yellow) is aligned to PFV chain B (light green) and non-overlapping segments have been removed; (E) Dimeric CRF02_AG IN structure (pink and green cartoon) overlays well with the dimeric PFV structure (shown as sticks) with a global RMSD <1.5Å. With the exception of carbon atoms, all coloration of the PFV stick structure is based on the Corey-Pauling-Koltun (CPK) coloration scheme [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128310#pone.0128310.ref018" target="_blank">18</a>]; white for hydrogen, blue for nitrogen, and red for oxygen.</p

Biochemical Characterisation of HDS1 on purified HIV-1 IN enzyme.

<p>(A) Inhibition of the strand transfer reaction. (B) Inhibition of the 3' processing reaction. (C) Inhibition of the DNA binding activity of HIV integrase. (D) Test for the ability of HDS1 to bind to DNA.</p

FZ41 and HDS1 may directly inhibit DNA binding to integrase.

<p>The HDS1 docked structure (shown as a spherical structure with black carbon atoms) (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128310#pone.0128310.g004" target="_blank">Fig 4F</a>) was overlaid onto the FZ41 structure (shown as a spherical structure with yellow carbon atoms) in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128310#pone.0128310.g002" target="_blank">Fig 2D</a> together with DNA (stick structure with white carbon atoms) coordinates from the PFV 3OY9 structure. The active site is indicated by a yellow rectangle. The two monomers of the dimer are represented by different shades of magenta. All other coloration is based on the CPK standard [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128310#pone.0128310.ref018" target="_blank">18</a>].</p

Screening of compounds for interaction with dimeric CRF02_AG IN in the absence of DNA ligands.

<p>Interactions of ZINC00337691 (A), ZINC01703953 (B), and ZINC04689544 (C) with residues at the dimer interface. (D) The binding interface of HDS1 spans the dimer (red oval) and DNA binding (blue oval) interfaces. (E) Binding of HDS1 at the dimer interface and (F) DNA interface. In all panels above, the docked compound is represented by yellow main-chain sticks, while the global structure is represented by lines or cartoons and interacting residues are shown as cyan stick structures. Standard CPK coloration is used for stick and line structures. Putative interacting atoms are indicated by a black dashed line.</p

Location of docking grid box and docking of FZ41 to the IN dimer.

<p>(A) Grid box size and coordinates overlapped with the DNA binding domain as well as the dimerization interface. (B) Pockets within the dimeric model at the DNA interface (blue arrow) and at the dimer interface (red arrow). (C) FZ41 (yellow stick structure within grey mesh) binds within the DNA binding domain. Domains spanning regions corresponding to NTD, CCD, CTD for monomer A and CCD* for monomer B are indicated. (D) Interactions of FZ41 with IN residues. Docking simulations were performed utilizing AutoDock Vina [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128310#pone.0128310.ref052" target="_blank">52</a>] on a PyRx platform [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128310#pone.0128310.ref051" target="_blank">51</a>]. All image processing was done using PyMOL [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128310#pone.0128310.ref059" target="_blank">59</a>]. Solvent accessible pockets with a radius larger than 5Å are shown and colored grey. In the figure, the two monomers of the dimer are represented by different shades of magenta. CPK standard coloration is used for stick structural representations. Putative interacting atoms are indicated by a black dashed line.</p

Inhibition of HIV-1 in MT-4 cell cultures by HDS1.

<p>(A) Dose-dependent inhibition of HIV-1 replication in cell cultures by HDS1. HIV-1 reverse transcriptase activity in cell culture fluids was measured using a tritiated thymidine triphosphate based assay as previously described [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128310#pone.0128310.ref053" target="_blank">53</a>]. (B) Effect of AZT (1 μM), RAL(0.5 μM) and HDS1 (20 μM) on production of late HIV-1 reverse transcripts as measured by qPCR.</p

Flueggether A and Virosinine A, Anti-HIV Alkaloids from <i>Flueggea virosa</i>

Two new alkaloids, flueggether A (<b>1</b>) and virosinine A (<b>2</b>), were isolated from a Chinese medicinal plant, <i>Flueggea virosa</i>. Their structures were assigned via spectroscopic methods with the absolute configurations of <b>1</b> and <b>2</b> being established by X-ray diffraction analysis and calculated electronic circular dichroism data, respectively. Compound <b>1</b> represents the first example with an ether bridge of <i>Securinega</i> alkaloid oligomers, and <b>2</b> bears a new heterocyclic backbone. Both alkaloids showed mild in vitro anti-HIV activity

Time trends in the monitored viral load.

<p>Trends in the proportion of samples with suppressed [<1.7 log₁₀ copies/ml (<50 copies/ml)] and unsuppressed plasma HIV viral loads, from 2001 to 2011. [<i>P</i> for trend <0.001 for all categories; OR corresponding to the change in frequency per year for: HIV RNA<50 copies/ml (OR = 1.17), HIV RNA 50–<500 copies/ml (OR = 0.93), HIV RNA 500–<5,000 copies/ml (OR = 0.87), HIV RNA 5,000–<50,000 copies/ml (OR = 0.90) and HIV RNA>500,000 copies/ml (OR = 0.92)].</p

Time trends in frequency of antiretroviral resistance mutations among treatment-naïve patients.

<p>Frequency of antiretroviral resistance mutations at selected codons associated with decreased susceptibility to NRTIs, NNRTIs and PIs.</p

Treatment-experienced patients with drug resistance: frequency (%) of drug resistance over time, by drug class and their dual or triple combinations.

<p>n: number of resistance tests (first test/patient per year) presenting with mutations associated to resistance; N: Total number of patients with resistance test in that period; CI: confidence interval; Significant effects (P≤0.05) are bolded. NS: not significant.</p><p>Treatment-experienced patients with drug resistance: frequency (%) of drug resistance over time, by drug class and their dual or triple combinations.</p