Synthesis and Biological Activities of Topopyrones

Structure–activity studies were employed to investigate the stabilization of DNA–topoisomerases I and II covalent binary complexes by topopyrone analogues. The synthesis of five new topopyrone derivatives and study of their ability to stabilize DNA–topoisomerase I and DNA–topoisomerase II covalent binary complexes are described. The biochemical assays suggest that the orientation of the fused 1,4-pyrone ring and halogen substituents contribute importantly to the overall potency of the topopyrones as topoisomerase poisons

Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site

<div><p>Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the identification of several small molecule leads. One of the most promising is the NBD series, which binds within a conserved gp120 cavity and possesses <i>para</i>-halogen substituted aromatic rings, a central oxalamide linker, and a tetramethylpiperidine moiety. In this study, we characterized structurally the interactions of four NBD analogues containing <i>meta</i>-fluoro substitution on the aromatic ring and various heterocyclic ring replacements of the tetramethylpiperidine group. The addition of a <i>meta</i>-fluorine to the aromatic ring improved surface complementarity and did not alter the position of the analogue relative to gp120. By contrast, heterocyclic ring replacements of the tetramethylpiperidine moiety exhibited diverse positioning and interactions with the vestibule of the gp120 cavity. Overall, the biological profile of NBD-congeners was modulated by ligand interactions with the gp120-cavity vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide a structural framework for continued small molecule-entry inhibitor optimization.</p></div

Diverse interaction modes of NBD-analogue Region III with gp120.

<p>Close-up views of NBD-557 (A, B), AS-II-37 (C, D), AS-I-261 (E, F), MAE-II-167 (G, H), and MAE-II-188 (I, J) in the Phe 43 cavity. Region I and II reside inside the Phe 43 cavity. The Region III of the analogues protrudes outside the cavity in diverse conformations. All atoms on gp120 within 5 Šdistance to the Region III of the analogues are shown with dotted lines; hydrogen bonds in red and two atoms within the van der Waals radius in green dotted lines. (B, D, F, H, and J) NBD analogues in <i>2fo-fc</i> electron density map colored by the <i>B</i>-factor. The color scale ranges from blue to red for <i>B</i>-factors of >40 to <150 Ų.</p

The chemical structures of NBD analogues that target the CD4 binding site of gp120.

<p>The general structure of the NBD congeners is shown, defining Regions I (blue), II (red), and III (green). The diverse Region III scaffolds crystalographically characterized in complex with gp120 are shown below.</p

NBD analogue binding to gp120 enhances 17b-gp120 interaction.

<p>(A–D) 100 nM of gp120 core_min or full-length gp120 in the presence of 0–100 µM of NBD analogues was passed over 17b antibody immobilized on a CM5 chip. The binding of gp120 to 17b increased, in a concentration dependent manner, in response to treatment with the NBD analogues. (E) In contrast, the presence of BMS-806, a small molecule inhibitor that has known not to induce gp120 conformation, did not enhance gp120-17b interaction.</p

Design strategy.

<p>Superposition of MAE-II-167 (blue) and MAE-II-188 (cyan) at the Phe 43 cavity suggests a model compound that forms a hydrogen bond with Asp 368 in Area A. The model makes hydrophobic contacts with the tip of β20/21 in Area B. A successful design strategy for a potent drug should include additions of an amine group that will interact with Asp 368 by a salt bridge, a longer hydrophobic tail that will satisfy hydrophobic interactions in Area B, and a moiety that expands contacts in Area C.</p

Structures of HIV-1 gp120 core in complex with NBD-557.

<p>(A) YU2 gp120 coreV3s (surface representation in grey) in complex with NBD-557 (stick representation in green) and Fab 48d depicted in a ribbon diagram (light chain in light blue and heavy chain in blue). (B) NBD-557 (stick representation in cyan) binds the Phe 43_CD4 cavity on clade A/E_93TH057 gp120 core_e. Area colored red represents N-terminal residues (44–89), which are missing in gp120 core in (A). CD4 footprints on gp120 are colored in yellow in (A) and (B). (C) Superposition of NBD-557- and Fab 48d- bound YU2 gp120, NBD-557-bound clade A/E_93TH057 gp120 core, and the CD4-bound gp120. Two NBD-557 (green and cyan) and the side chain of Phe 43_CD4 (yellow) in the cavity are highlighted.</p

Data collection and refinement statistics.

<p>*Values in parentheses are for highest-resolution shell.</p