BiVO4 Photoanode with NiV2O6 Back Contact Interfacial Layer for Improved Hole-Diffusion Length and Photoelectrochemical Water Oxidation Activity.

The short hole diffusion length (HDL) and high interfacial recombination are among the main drawbacks of semiconductor-based solar energy systems. Surface passivation and introducing an interfacial layer are recognized for enhancing HDL and charge carrier separation. Herein, we introduced a facile recipe to design a pinholes-free BiVO4 photoanode with a NiV2O6 back contact interfacial (BCI) layer, marking a significant advancement in the HDL and photoelectrochemical activity. The fabricated BiVO4 photoanode with NiV2O6 BCI layer exhibits a 2-fold increase in the HDL compared to pristine BiVO4. Despite this improvement, we found that the front surface recombination still hinders the water oxidation process, as revealed by photoelectrochemical (PEC) studies employing Na2SO3 electron donors and by intensity-modulated photocurrent spectroscopy measurements. To address this limitation, the surface of the NiV2O6/BiVO4 photoanode was passivated with a cobalt phosphate electrocatalyst, resulting in a dramatic enhancement in the PEC performance. The optimized photoanode achieved a stable photocurrent density of 4.8 mA cm-2 at 1.23 VRHE, which is 12-fold higher than that of the pristine BiVO4 photoanode. Density Functional Theory (DFT) simulations revealed an abrupt electrostatic potential transition at the NiV2O6/BiVO4 interface with BiVO4 being more negative than NiV2O6. A strong built-in electric field is thus generated at the interface and drifts photogenerated electrons toward the NiV2O6 BCI layer and photogenerated holes toward the BiVO4 top layer. As a result, the back-surface recombination is minimized, and ultimately, the HDL is extended in agreement with the experimental findings.

Ab initio calculations on structure and stability of BN/CC isosterism in azulene.

Herein, we investigated the thermodynamic stability and opto-electronic properties of a newly BN-doped azulene. The gas-phase formation enthalpies of 11 BN-doped azulene were calculated by the atomization energy method using three computational models (CBS-APNO, CBS-QB3, and G3MP2). The results suggest that AZ-1N9B exhibits the highest stability among the studied isomers. On the other hand, AZ-1B9N and AZ-9B10N display nearly equal stability with relative energies of 19.36 and 19.82 kcal/mol at CBS-QB3, respectively. These two isomers are considered the least stable among the investigated compounds. The frontier molecular orbitals (FMO), ionization energies (IE), and electron affinities (EA) of these isomers were discussed. Additionally, the electronic absorption spectra of the BN-doped azulenes were computed using the TD-B3LYP/6-31 + G(d,p) and TD-CAM-B3LYP level of theories, which using a long-range corrected hybrid functional in acetone. The computational results obtained in this research are align closely with the existing literature, thereby reinforcing the credibility and reliability of our findings.

Electrochemical and Computational Insights on the Application of Expired Metformin Drug as a Novel Inhibitor for the Sweet Corrosion of C1018 Steel.

An expired metformin drug (MET) was used as a corrosion inhibitor for C1018 carbon steel in a CO2-saturated 3.5 wt % NaCl + 340 ppm acetic acid solution under static conditions. The inhibitor was evaluated using electrochemical methods complemented with surface analytical measurements and computational modeling. The drug displayed a high inhibition efficiency of ∼90% at 200 ppm. Impedance analyses revealed a rise in the charge transfer resistance at the steel-solution interface upon the addition of the inhibitor. Polarization measurements suggested that MET acted more like a cathodic-type corrosion inhibitor and significantly reduced the corrosion current density. The adsorption of MET on the steel substrate followed the Langmuir isotherm, showing a mixed type of physical and chemical modes of adsorption. The thermodynamic parameters revealed strong and spontaneous adsorption on the steel surface. The surface analysis using SEM supported the inhibitor adsorption on the steel substrate. Based on the DFT simulation, inhibition by MET is mainly achieved by its protonated form, which leads to the formation of a thin film on the steel surface rather than the modification of the work function of the steel surface. The experimental and theoretical estimations of pKa complemented the DFT results, both agreeing that the monoprotonated form of MET is the dominant form in which the inhibitor adsorbs on the steel surface to form a thin film rather than modify the work function of the steel surface.

Highly Efficient Permeation and Separation of Gases with Metal-Organic Frameworks Confined in Polymeric Nanochannels.

This work demonstrates the confinement of porous metal-organic framework (HKUST-1) on the surface and walls of track-etched nanochannel in polyethylene terephthalate (np-PET) membrane using a liquid-phase epitaxy (LPE) technique. The composite membrane (HKUST-1/np-PET) exhibits defect-free MOF growth continuity, strong attachment of MOF to the support, and a high degree of flexibility. The high flexibility and the strong confinement of the MOF in composite membrane results from (i) the flexible np-PET support, (ii) coordination attachment between HKUST-1 and the support, and (iii) the growth of HKUST-1 crystal in nanoconfined geometries. The MOF has a preferred growth orientation with a window size of 3.5 Å, resulting in a clear cut-off of CO2 from natural gas and olefins. The experimental results and DFT calculations show that the restricted diffusion of gases only takes place through the nanoporous MOF confined in the np-PET substrate. This research thereby provides a new perspective to grow other porous MOFs in artificially prepared nanochannels for the realization of continuous, flexible, and defect-free membranes for various applications.

Design and synthesis of two new terbium and europium complex-based luminescent probes for the selective detection of zinc ions.

Zinc plays a key role in many physiological processes and has implications for the environment. Consequently, detection of chelatable zinc ion (Zn2+ ) has attracted widespread interest from the research community. Lanthanide-based luminescent probes offer particular advantages, such as high water solubility, long luminescence lifetimes and a large Stokes' shift, over common organic dye-based fluorescent sensors. Here, we report the synthesis of terbium and europium complex-based probes, Tb-1 and Eu-1, for sensitive and selective detection of Zn2+ in water. These probes featured the incorporation of bis(2-pyridylmethyl)]amine (DPA) receptor for Zn2+ chelation and the 1,4,7-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecane (DO3A) ring to chelate lanthanide (Ln3+ ). Tb-1 and Eu-1 displayed high selectivity for Zn2+ ions over a wide range of competing ions, with limits of detection of 0.50 ± 0.1 µM and 1.5 ± 0.01 µM, respectively. Density functional theory simulations were in good agreement with experimental observations, displaying high Zn2+ selectivity compared with most competing ions. In the competing ions experiments, the luminescence response of Tb-1 and Eu-1 was moderately quenched by some ions such as Cu2+ , this was linked to the comparable binding abilities of these ions for the receptor of the probe.

Revisiting OPLS-AA Force Field for the Simulation of Anionic Surfactants in Concentrated Electrolyte Solutions.

Hereby, we developed a set of nonbonded parameters within all-atom optimized potentials for liquid simulations (OPLS-AA) force field for the simulation of concentrated electrolyte solutions of anionic surfactants. More specifically, the aim of this paper is to assess the performance of five sets of atomic charges calculated using different population analyses (DDEC6, CHelpG, CHelpG-SMD, RESP, and CM5), as well as the original set of charges used in the literature for sodium dodecyl sulfate (SDS) simulation. Recently, Farafonov et al. have revised the SDS OPLS-AA force field; however, we were unable to obtain the experimental rodlike micelles using this parameter set on long time scale. In fact, the initial SDS bilayer micelle adopted a rodlike shape transiently and then broke down into spherical micelles. Updating OPLS-AA force field with DDEC6, CHelpG, and CHelpG-SMD charges resulted in stable rod micelles for a long simulation time (1 µs). The atomic charges of Farafonov (taken from Shelley et al.), RESP, and CM5 could not correctly describe SDS in concentrated electrolyte solutions. Analysis of the interaction of SDS with the counterions and solvent highlights the role of a balance of the intermolecular forces that must be met to describe adequately the anionic surfactant electrolyte solutions. Further, the optimization of the SDS Lennard-Jones parameters enabled the Farafonov set to properly reproduce the experimental rod micelle. In addition, we have examined the performance of different parameters of sodium ions: the first developed based on the Kirkwood-Buff integrals (KBI) and the second developed by Joung et al. The excessive ion pairing caused by KBI parameters screens significantly SDS-water interactions, which stabilize the rod micelle. Further, a tight interaction of the Na+-SDS head group resulted in stabilization of the bilayer micelle as observed in the case of Na+ parameters developed by Joung et al.

Molybdenum Nitride Nanocrystals Anchored on Phosphorus-Incorporated Carbon Fabric as a Negative Electrode for High-Performance Asymmetric Pseudocapacitor.

Pseudocapacitors hold great promise to provide high energy-storing capacity; however, their capacitances are still far below their theoretical values and they deliver much lower power than the traditional electric double-layer capacitors due to poor ionic accessibility. Here, we have engineered MoN nanoparticles as pseudocapacitive material on phosphorus-incorporated carbon fabric with enhanced ionic affinity and thermodynamic stability. This nanocomposite boosts surface redox kinetics, leading to pseudocapacitance of 400 mF/cm2 (2-fold higher than that of molybdenum nitride-based electrodes) with rapid charge-discharge rates. Density functional theory simulations are used to explain the origin of the good performance of MoN@P-CF in proton-based aqueous electrolytes. Finally, an all-pseudocapacitive solid-state asymmetric cell was assembled using MoN@P-CF and RuO2 (RuO2@CF) as negative and positive electrodes, respectively, which delivered good energy density with low relaxation time constant (τ0) of 13 ms (significantly lower than that of carbon-based supercapacitors).

Limits for Recombination in a Low Energy Loss Organic Heterojunction.

Donor-acceptor organic solar cells often show high quantum yields for charge collection, but relatively low open-circuit voltages (VOC) limit power conversion efficiencies to around 12%. We report here the behavior of a system, PIPCP:PC61BM, that exhibits very low electronic disorder (Urbach energy less than 27 meV), very high carrier mobilities in the blend (field-effect mobility for holes >10-2 cm2 V-1 s-1), and a very low driving energy for initial charge separation (50 meV). These characteristics should give excellent performance, and indeed, the VOC is high relative to the donor energy gap. However, we find the overall performance is limited by recombination, with formation of lower-lying triplet excitons on the donor accounting for 90% of the recombination. We find this is a bimolecular process that happens on time scales as short as 100 ps. Thus, although the absence of disorder and the associated high carrier mobility speeds up charge diffusion and extraction at the electrodes, which we measure as early as 1 ns, this also speeds up the recombination channel, giving overall a modest quantum yield of around 60%. We discuss strategies to remove the triplet exciton recombination channel.

A targeted DNA substrate mechanism for the inhibition of HIV-1 integrase by inhibitors with antiretroviral activity.

We recently reported that viral DNA could be the primary target of raltegravir (RAL), an efficient anti-HIV-1 drug, which acts by inhibiting integrase. To elucidate this mechanism, we conducted a comparative analysis of RAL and TB11, a diketoacid abandoned as an anti-HIV-1 drug for its weak efficiency and marked toxicity, and tested the effects of the catalytic cofactor Mg(2+) (5 mm) on drug-binding properties. We used circular dichroism and fluorescence to determine drug affinities for viral DNA long terminal repeats (LTRs) and peptides derived from the integrase active site and DNA retardation assays to assess drug intercalation into DNA base pairs. We found that RAL bound more tightly to LTR ends than did TB11 (a diketo acid bearing an azido group) and that Mg(2+) significantly increased the affinity of both RAL and TB11. We also observed a good relationship between drug binding with processed LTR and strand transfer inhibition. This unusual type of inhibition was caused by Mg(2+)-assisted binding of drugs to DNA substrate, rather than to enzyme. Notably, while RAL bound exclusively to the cleavable/cleaved site, TB11 further intercalated into DNA base pairs and interacted with the integrase-derived peptides. These unwanted binding sites explain the weaker bioavailability and higher toxicity of TB11 compared with the more effective RAL.

The D173G mutation in ADAMTS-13 causes a severe form of congenital thrombotic thrombocytopenic purpura. A clinical, biochemical and in silico study.

Congenital thrombotic thrombocytopenic purpura (TTP) is a rare form of thrombotic microangiopathy, inherited with autosomal recessive mode as a dysfunction or severe deficiency of ADAMTS-13 (A Disintegrin And Metalloprotease with ThromboSpondin 1 repeats Nr. 13), caused by mutations in the ADAMTS-13 gene. About 100 mutations of the ADAMTS-13 gene were identified so far, although only a few characterised by in vitro expression studies. A new Asp to Gly homozygous mutation at position 173 of ADAMTS-13 sequence was identified in a family of Romanian origin, with some members affected by clinical signs of TTP. In two male sons, this mutation caused a severe (< 3%) deficiency of ADAMTS-13 activity and antigen level, associated with periodic thrombocytopenia, haemolytic anaemia and mild mental confusion. Both parents, who are cousins, showed the same mutation in heterozygous form. Expression studies of the mutant ADAMTS-13, performed in HEK293 cells, showed a severe decrease of the enzyme's activity and secretion, although the protease was detected inside the cells. Molecular dynamics found that in the D173G mutant the interface area between the metalloprotease domain and the disintegrin-like domain significantly decreases during the simulations, while the proline-rich 20 residues linker region (LR, 285-304) between them undergoes extensive conformational changes. Inter-domain contacts are also significantly less conserved in the mutant compared to the wild-type. Both a decrease of the inter-domain contacts along with a substantial conformational rearrangement of LR interfere with the proper maturation and folding of the mutant ADAMTS-13, thus impairing its secretion.

Biochemical stability and molecular dynamic characterization of Aspergillus fumigatus cystathionine γ-lyase in response to various reaction effectors.

Cystathionine γ-lyase (CGL) is a key enzyme in the methionine-cysteine cycle in all living organisms forming cysteine, α-ketobutyrate and ammonia via homocysteine and cystathionine intermediates. Although, human and plant CGLs have been extensively studied at the molecular and mechanistic levels, there has been little work on the molecular and catalytic properties of fungal CGL. Herein, we studied in detail for the first time the molecular and catalytic stability of Aspergillus fumigatus CGL, since conformational instability, inactivation and structural antigenicity are the main limitations of the PLP-dependent enzymes on various therapeutic uses. We examined these properties in response to buffer compositions, stabilizing and destabilizing agents using Differential Scanning Fluorometery (DSF), steady state and gel-based fluorescence of the intrinsic hydrophobic core, stability of internal aldimine linkage and catalytic properties. The activity of the recombinant A. fumigatus CGL was 13.8U/mg. The melting temperature (Tm) of CGL in potassium phosphate buffer (pH 7.0-8.0) was 73.3°C, with ∼3°C upshifting in MES and sodium phosphate buffers (pH 7.0). The conformational thermal stability was increased in potassium phosphate, sodium phosphate and MES buffers, in contrast to Tris-HCl, HEPES (pH 7.0) and CAPS (pH 9.0-10.0). The thermal stability and activity of CGL was slightly increased in the presence of trehalose and glycerol that might be due to hydration of the enzyme backbone, unlike the denaturing effect of GdmCl and urea. Modification of surface CGL glutamic and aspartic acids had no significant effect on the enzyme conformational and catalytic stability. Molecular modeling and dynamics simulations unveil the high conformational stability of the overall scaffold of CGL with high flexibility at the non-structural regions. CGL structure has eight buried Trp residues, which are reoriented to the enzyme surface and get exposed to the solvent under perturbation of destabilizers. Furthermore, electrostatic calculations of selected snapshots of CGL 3D structure under different experimental conditions showed a remarkable differences on the polarity of the enzyme surface.

Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE).

IspG is the penultimate enzyme in non-mevalonate biosynthesis of the universal terpene building blocks isopentenyl diphosphate and dimethylallyl diphosphate. Its mechanism of action has been the subject of numerous studies but remained unresolved due to difficulties in identifying distinct reaction intermediates. Using a moderate reducing agent and an epoxide substrate analogue, we were now able to trap and crystallographically characterize various stages in the IspG-catalyzed conversion of 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate into (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate. In addition, the enzyme's structure was determined in complex with several inhibitors. These results, combined with recent electron paramagnetic resonance data, allowed us to deduce a detailed and complete IspG catalytic mechanism, which describes all stages from initial ring opening to formation of (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate via discrete radical and carbanion intermediates. The data presented in this article provide a guide for the design of selective drugs against many prokaryotic and eukaryotic pathogens to which the non-mevalonate pathway is essential for survival and virulence.

Mechanistic insights into the reductive dehydroxylation pathway for the biosynthesis of isoprenoids promoted by the IspH enzyme.

Here, we report an integrated quantum mechanics/molecular mechanics (QM/MM) study of the bio-organometallic reaction pathway of the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) into the so called universal terpenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), promoted by the IspH enzyme. Our results support the viability of the bio-organometallic pathway through rotation of the OH group of HMBPP away from the [Fe4S4] cluster at the core of the catalytic site, to become engaged in a H-bond with Glu126. This rotation is synchronous with π-coordination of the C2[double bond, length as m-dash]C3 double bond of HMBPP to the apical Fe atom of the [Fe4S4] cluster. Dehydroxylation of HMBPP is triggered by a proton transfer from Glu126 to the OH group of HMBPP. The reaction pathway is completed by competitive proton transfer from the terminal phosphate group to the C2 or C4 atom of HMBPP.

Molecular dynamics characterization of five pathogenic Factor X mutants associated with decreased catalytic activity.

Factor X (FX) is one of the major players in the blood coagulation cascade. Upon activation to FXa, it converts prothrombin to thrombin, which in turn converts fibrinogen into fibrin (blood clots). FXa deficiency causes hemostasis defects, such as intracranial bleeding, hemathrosis, and gastrointestinal blood loss. Herein, we have analyzed a pool of pathogenic mutations, located in the FXa catalytic domain and directly associated with defects in enzyme catalytic activity. Using chymotrypsinogen numbering, they correspond to D102N, T135M, V160A, G184S, and G197D. Molecular dynamics simulations were performed for 1.68 µs on the wild-type and mutated forms of FXa. Overall, our analysis shows that four of the five mutants considered, D102N, T135M, V160A, and G184S, have rigidities higher than those of the wild type, in terms of both overall protein motion and, specifically, subpocket S4 flexibility, while S1 is rather insensitive to the mutation. This acquired rigidity can clearly impact the substrate recognition of the mutants.

Tethering metal ions to photocatalyst particulate surfaces by bifunctional molecular linkers for efficient hydrogen evolution.

A simple and versatile method for the preparation of photocatalyst particulates modified with effective cocatalysts is presented; the method involves the sequential soaking of photocatalyst particulates in solutions containing bifunctional organic linkers and metal ions. The modification of the particulate surfaces is a universal and reproducible method because the molecular linkers utilize strong covalent bonds, which in turn result in modified monolayer with a small but controlled quantity of metals. The photocatalysis results indicated that the CdS with likely photochemically reduced Pd and Ni, which were initially immobilized via ethanedithiol (EDT) as a linker, were highly efficient for photocatalytic hydrogen evolution from Na2S-Na2SO3-containing aqueous solutions. The method developed in this study opens a new synthesis route for the preparation of effective photocatalysts with various combinations of bifunctional linkers, metals, and photocatalyst particulate materials.

MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories.

BACKGROUND: Molecular Dynamics (MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. RESULTS: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. CONCLUSIONS: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.

Structural basis for the recognition in an idiotype-anti-idiotype antibody complex related to celiac disease.

Anti-idiotype antibodies have potential therapeutic applications in many fields, including autoimmune diseases. Herein we report the isolation and characterization of AIM2, an anti-idiotype antibody elicited in a mouse model upon expression of the celiac disease-specific autoantibody MB2.8 (directed against the main disease autoantigen type 2 transglutaminase, TG2). To characterize the interaction between the two antibodies, a 3D model of the MB2.8-AIM2 complex has been obtained by molecular docking. Analysis and selection of the different obtained docking solutions was based on the conservation within them of the inter-residue contacts. The selected model is very well representative of the different solutions found and its stability is confirmed by molecular dynamics simulations. Furthermore, the binding mode it adopts is very similar to that observed in most of the experimental structures available for idiotype-anti-idiotype antibody complexes. In the obtained model, AIM2 is directed against the MB2.8 CDR region, especially on its variable light chain. This makes the concurrent formation of the MB2.8-AIM2 complex and of the MB2.8-TG2 complex incompatible, thus explaining the experimentally observed inhibitory effect on the MB2.8 binding to TG2.

Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs.

The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch.

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'C(4)pA(3)3' 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.

In Silico and In Vitro Comparison of HIV-1 Subtypes B and CRF02_AG Integrases Susceptibility to Integrase Strand Transfer Inhibitors.

Most antiretroviral medical treatments were developed and tested principally on HIV-1 B nonrecombinant strain, which represents less than 10% of the worldwide HIV-1-infected population. HIV-1 circulating recombinant form CRF02_AG is prevalent in West Africa and is becoming more frequent in other countries. Previous studies suggested that the HIV-1 polymorphisms might be associated to variable susceptibility to antiretrovirals. This study is pointed to compare the susceptibility to integrase (IN) inhibitors of HIV-1 subtype CRF02_AG IN respectively to HIV-1 B. Structural models of B and CRF02_AG HIV-1 INs as unbound enzymes and in complex with the DNA substrate were built by homology modeling. IN inhibitors-raltegravir (RAL), elvitegravir (ELV) and L731,988-were docked onto the models, and their binding affinity for both HIV-1 B and CRF02_AG INs was compared. CRF02_AG INs were cloned and expressed from plasma of integrase strand transfer inhibitor (INSTI)-naïve infected patients. Our in silico and in vitro studies showed that the sequence variations between the INs of CRF02_AG and B strains did not lead to any notable difference in the structural features of the enzyme and did not impact the susceptibility to the IN inhibitors. The binding modes and affinities of INSTI inhibitors to B and CRF02_AG INs were found to be similar. Although previous studies suggested that several naturally occurring variations of CRF02_AG IN might alter either IN/vDNA interactions or INSTIs binding, our study demonstrate that these variations do affect neither IN activity nor its susceptibility to INSTIs.