Unprocessed Viral DNA Could Be the Primary Target of the HIV-1 Integrase Inhibitor Raltegravir

Integration of HIV DNA into host chromosome requires a 3′-processing (3′-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA. Here, we assessed whether free viral DNA could be a primary target for RAL, assuming that the DNA molecule is a receptor for a huge number of pharmacological agents. Optical spectroscopy, molecular dynamics and free energy calculations, showed that RAL is a tight binder of both processed and unprocessed LTR (long terminal repeat) ends. Complex formation involved mainly van der Waals forces and was enthalpy driven. Dissociation constants (Kds) revealed that RAL affinity for unbound LTRs was stronger than for bound LTRs. Moreover, Kd value for binding of RAL to LTRs and IC50 value (half concentration for inhibition) were in same range, suggesting that RAL binding to DNA and ST inhibition are correlated events. Accommodation of RAL into terminal base-pairs of unprocessed LTR is facilitated by an extensive end fraying that lowers the RAL binding energy barrier. The RAL binding entails a weak damping of fraying and correlatively of 3′-P inhibition. Noteworthy, present calculated RAL structures bound to free viral DNA resemble those found in RAL-intasome crystals, especially concerning the contacts between the fluorobenzyl group and the conserved 5′C4pA33′ step. We propose that RAL inhibits IN, in binding first unprocessed DNA. Similarly to anticancer drug poisons acting on topoisomerases, its interaction with DNA does not alter the cut, but blocks the subsequent joining reaction. We also speculate that INSTIs having viral DNA rather IN as main target could induce less resistance

The HIV-1 Integrase α4-Helix Involved in LTR-DNA Recognition Is also a Highly Antigenic Peptide Element

Monoclonal antibodies (MAbas) constitute remarkable tools to analyze the relationship between the structure and the function of a protein. By immunizing a mouse with a 29mer peptide (K159) formed by residues 147 to 175 of the HIV-1 integrase (IN), we obtained a monoclonal antibody (MAba4) recognizing an epitope lying in the N-terminal portion of K159 (residues 147–166 of IN). The boundaries of the epitope were determined in ELISA assays using peptide truncation and amino acid substitutions. The epitope in K159 or as a free peptide (pep-a4) was mostly a random coil in solution, while in the CCD (catalytic core domain) crystal, the homologous segment displayed an amphipathic helix structure (α4-helix) at the protein surface. Despite this conformational difference, a strong antigenic crossreactivity was observed between pep-a4 and the protein segment, as well as K156, a stabilized analogue of pep-a4 constrained into helix by seven helicogenic mutations, most of them involving hydrophobic residues. We concluded that the epitope is freely accessible to the antibody inside the protein and that its recognition by the antibody is not influenced by the conformation of its backbone and the chemistry of amino acids submitted to helicogenic mutations. In contrast, the AA →Glu mutations of the hydrophilic residues Gln148, Lys156 and Lys159, known for their interactions with LTRs (long terminal repeats) and inhibitors (

Photoluminescence quenching of chemically functionalized porous silicon by a ruthenium cluster

NRC publication: Ye

New routes to \u3b71- and (\u3b73\u2194\u3b75)-indenylpalladium complexes: synthesis, characterization, and reactivities

The dimer {(\u3b73-Ind)Pd(\u3bc-Cl)}2 (6) reacts with t-BuNC to give the dimeric species {(\u3b71-Ind)(t-BuNC)Pd(\u3bc-Cl)}2 (10), whereas reaction with PR3 gives the complexes (\u3b7-Ind)Pd(PR3)Cl (R = Ph (4), Cy (7), Me (8), OMe (9)). Complexes 4 and (1-Me-Ind)Pd(PPh3)Cl (5) can also be prepared by reacting (PhCN)2PdCl2 with LiInd and PPh3. The structural characterization of complexes 4 127, 9, and 10 by 1H and 13C NMR spectroscopy and single-crystal X-ray diffraction studies has allowed an analysis of the indenyl ligand's mode of coordination, both in the solid-state and in solution. Compounds 4, 6, and 7 react with PhSiH3 in the absence of cocatalysts, whereas reaction with ethylene requires the presence of excess MAO to give polyethylene.NRC publication: Ye

Estimating local bonding/antibonding character of canonical molecular orbitals from their energy derivatives. The case of coordinating lone pair orbitals

International audienceAccording to Koopmans theorem, the derivative of the energy of a canonical MO with respect to nuclear coordinates quantifies its bonding/antibonding character. This quantity allows predictions of bond length variation upon ionisation in a panel of 19 diatomic species. In polyatomic molecules, the derivative of a MO energy with respect to a given bond length reveals the nature and the degree of the bonding/antibonding contribution of this MO with respect to this bond. Accordingly, the HOMO “lone pairs” of CO and CN and the HOMO-2 of CH3CN are found to be antibonding with respect to the C-X bond (X = N, O), whereas the HOMO of N2 is found to be bonding. With the same approach, the variation of the bonding character in the MOs of CO and CH3CN upon interaction with an electron acceptor (modelled through the approach of a proton) or by applying an electric field was studied

New Palladium(II) 12(\u3b73/5- or \u3b71-Indenyl) and Dipalladium(I) 12(\u3bc,\u3b73-Indenyl) Complexes

Reaction of the dimeric species [(3-Ind)Pd(-Cl)]2 (1) (Ind = indenyl) with NEt3 gives the complex (3-5-Ind)Pd(NEt3)Cl (3), whereas the analogous reactions with BnNH2 (Bn = PhCH2) or pyridine (py) afford the complexes trans-L2Pd(1-Ind)Cl (L = BnNH2 (4), py (5)). Similarly, the one-pot reaction of 1 with a mixture of BnNH2 and the phosphine ligands PR3 gives the mixed-ligand, amino and phosphine species (PR3)(BnNH2)Pd(1-Ind)Cl (R = Cy (6a), Ph (6b)); the latter complexes can also be prepared by addition of BnNH2 to (3-5-Ind)Pd(PR3)Cl (R = Cy (2a), Ph (2b)). Complexes 6 undergo a gradual decomposition in solution to generate the dinuclear PdI compounds (,3-Ind)(-Cl)Pd2(PR3)2 (R = Cy (7a), Ph (7b)) and the PdII compounds (BnNH2)(PR3)PdCl2 (R = Cy (8a), Ph (8b)), along with 1,1'-biindene. The formation of 7 is proposed to proceed by a comproportionation reaction between in situ-generated PdII and Pd0 intermediates. Interestingly, the reverse of this reaction, disproportionation, also occurs spontaneously to give 2. All new compounds have been characterized by NMR spectroscopy and, in the case of 3, 4, 5, 6a, 7a, 7b, and 8a, by X-ray crystallography.NRC publication: Ye