Mechanistic Basis for Red Light Switching of Azonium Ions.

Azonium ions formed by the protonation of tetra-ortho-methoxy-substituted aminoazobenzenes photoisomerize with red light under physiological conditions. This property makes them attractive as molecular tools for the photocontrol of physiological processes, for example, in photopharmacology. However, a mechanistic understanding of the photoisomerization process and subsequent thermal relaxation is necessary for the rational application of these compounds as well as for guiding the design of derivatives with improved properties. Using a combination of sub-ps/ns transient absorption measurements and quantum chemical calculations, we show that the absorption of a photon by the protonated E-H+ form of the photoswitch causes rapid (ps) isomerization to the protonated Z-H+ form, which can also absorb red light. Proton transfer to solvent then occurs on a microsecond time scale, leading to an equilibrium between Z and Z-H+ species, the position of which depends on the solution pH. Whereas thermal isomerization of the neutral Z form to the neutral E form is slow (∼0.001 s-1), thermal isomerization of Z-H+ to E-H+ is rapid (∼100 s-1), so the solution pH also governs the rate at which E/E-H+ concentrations are restored after a light pulse. This analysis provides the first complete mechanistic picture that explains the observed intricate photoswitching behavior of azonium ions at a range of pH values. It further suggests features of azonium ions that could be targeted for improvement to enhance the applicability of these compounds for the photocontrol of biomolecules.

Interplay between Dual-State and Aggregation-Induced Emission with ESIPT Scaffolds Containing Triphenylamine Substituents: Experimental and Theoretical Studies.

We detail the synthesis of a series of fluorophores containing triphenylamine derivatives along with their photophysical, electrochemical, and electronic structure properties. These compounds include molecular structures derived from imino-phenol (anil) and hydroxybenzoxazole scaffolds originating from similar salicylaldehyde derivatives and display excited-state intramolecular proton transfer. We show that depending on the nature of the π-conjugated scaffold, different photophysical processes are observed: aggregation-induced emission or dual-state emission, with a modulation of the fluorescence color and redox properties. The photophysical properties are further rationalized with the help of ab initio calculations.

Identification of sulfonamide compounds active on the insect nervous system: Molecular modeling, synthesis and biological evaluation.

Insect nicotinic acetylcholine receptors (nAChRs) are a recognized target for insecticide design. In this work, we have identified, from a structure-based approach using molecular modeling tools, ligands with potential selective activity for pests versus pollinators. A high-throughput virtual screening with the Openeye software was performed using a library from the ZINC database, thiacloprid being used as the target structure. The top sixteen molecules were then docked in α6 cockroach and honeybee homomeric nAChRs to check from a theoretical point of view relevant descriptors in favor of pest selectivity. Among the selected molecules, one original sulfonamide compound has afterward been synthesized, together with various analogs. Two compounds of this family have been shown to behave as activators of the cockroach cholinergic synaptic transmission.

Synthesis and biological evaluation of DIDS analogues as efficient inhibitors of RAD51 involved in homologous recombination.

RAD51 is a pivotal protein of the homologous recombination DNA repair pathway, and is overexpressed in some cancer cells, disrupting then the efficiency of cancer-treatments. The development of RAD51 inhibitors appears as a promising solution to restore these cancer cells sensitization to radio- or chemotherapy. From a small molecule identified as a modulator of RAD51, the 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS), two series of analogues with small or bulky substituents on the aromatic parts of the stilbene moiety were prepared for a structure-activity relationship study. Three compounds, the cyano analogue (12), and benzamide (23) or phenylcarbamate (29) analogues of DIDS were characterized as novel potent RAD51 inhibitors with HR inhibition in the micromolar range.

Exploring structural dynamics and optical properties of UnaG fluorescent protein upon N57 mutations.

UnaG is a new class of fluorescence protein in which an endogenous ligand, namely bilirubin (BLR), plays the role of chromophore. Upon photoexcitation, holoUnaG emits green light. A single mutation at residue 57 induces a decrease in the fluorescence quantum yield. To our knowledge, no atomic simulation at the atomic level has been carried out to date to explain this fluorescence decay in N57A and N57Q mutants. Herein molecular dynamics simulations were carried out on wild-type (WT) UnaG and both mutants to investigate the structural impact of the mutation on its global structure, on BLR and the absorption spectra. Our study reveals significant global changes upon mutation at the protein entrance (L3, H2, and, H3) governing a BLR modification. BLR in WT UnaG is rather rigid while when embedded into N57A or N57Q, dihedral angles between endo and exo vinyl moieties and between A and B rings at the entrance of UnaG are strongly modified along with the number of inter-/intramolecular interactions. The water molecules play an important role in the modification of the shape of the binding cavity. For the first time, we show that the structural modifications upon ligand mutations are tightly related to the key structural changes in the protein such as Loop3 (L3), ß sheet 2 (B2), and ß sheet 3 (B3) dynamics. The present work suggests that the quenching of the fluorescence properties of UnaG mutants is mainly a non-radiative process closely related to the BLR flexibility induced by global structural changes.

Excited-State Intramolecular Proton Transfer Dyes with Dual-State Emission Properties: Concept, Examples and Applications.

Dual-state emissive (DSE) fluorophores are organic dyes displaying fluorescence emission both in dilute and concentrated solution and in the solid-state, as amorphous, single crystal, polycrystalline samples or thin films. This comes in contrast to the vast majority of organic fluorescent dyes which typically show intense fluorescence in solution but are quenched in concentrated media and in the solid-state owing to π-stacking interactions; a well-known phenomenon called aggregation-caused quenching (ACQ). On the contrary, molecular rotors with a significant number of free rotations have been engineered to show quenched emission in solution but strong fluorescence in the aggregated-state thanks to restriction of the intramolecular motions. This is the concept of aggregation-induced emission (AIE). DSE fluorophores have been far less explored despite the fact that they are at the crossroad of ACQ and AIE phenomena and allow targeting applications both in solution (bio-conjugation, sensing, imaging) and solid-state (organic electronics, data encryption, lasing, luminescent displays). Excited-State Intramolecular Proton Transfer (ESIPT) fluorescence is particularly suitable to engineer DSE dyes. Indeed, ESIPT fluorescence, which relies on a phototautomerism between normal and tautomeric species, is characterized by a strong emission in the solid-state along with a large Stokes' shift, an enhanced photostability and a strong sensitivity to the close environment, a feature prone to be used in bio-sensing. A drawback that needs to be overcome is their weak emission intensity in solution, owing to detrimental molecular motions in the excited-state. Several strategies have been proposed in that regard. In the past few years, a growing number of examples of DSE-ESIPT dyes have indeed emerged in the literature, enriching the database of such attractive dyes. This review aims at a brief but concise overview on the exploitation of ESIPT luminescence for the optimization of DSE dyes properties. In that perspective, a synergistic approach between organic synthesis, fluorescence spectroscopy and ab initio calculations has proven to be an efficient tool for the construction and optimization of DSE-ESIPT fluorophores.

IL-15Rα membrane anchorage in either cis or trans is required for stabilization of IL-15 and optimal signaling.

Interleukin (IL)-15 plays an important role in the communication between immune cells. It delivers its signal through different modes involving three receptor chains: IL-15Rα, IL-2Rß and IL-2Rγc. The combination of the different chains result in the formation of IL-15Rα/IL-2Rß/γc trimeric or IL-2Rß/γc dimeric receptors. In this study, we have investigated the role of the IL-15Rα chain in stabilizing the cytokine in the IL-2Rß/γc dimeric receptor. By analyzing the key amino acid residues of IL-15 facing IL-2Rß, we provide evidence of differential interfaces in the presence or in the absence of membrane-anchored IL-15Rα. Moreover, we found that the anchorage of IL-15Rα to the cell surface regardless its mode of presentation - i.e. cis or trans - is crucial for complete signaling. These observations show how the cells can finely modulate the intensity of cytokine signaling through the quality and the level of expression of the receptor chains.

Dual Solution-/Solid-State Emissive Excited-State Intramolecular Proton Transfer (ESIPT) Dyes: A Combined Experimental and Theoretical Approach.

Excited-state intramolecular proton transfer (ESIPT) dyes typically show strong solid-state emission, but faint fluorescence intensity is observed in the solution state owing to detrimental molecular motions. This article investigates the influence of direct (hetero)arylation on the optical properties of 2-(2'-hydroxyphenyl)benzoxazole ESIPT emitters. The synthesis of two series of ESIPT emitters bearing substituted neutral or charged aryl, thiophene, or pyridine rings is reported herein along with full photophysical studies in solution and solid states, demonstrating the dual solution-/solid-state emission behavior. Depending on the nature of substitution, several excited-state dynamics are observed: quantitative or partially frustrated ESIPT process or deprotonation of the excited species. Protonation studies revealed that pyridine substitution triggered a strong increase of quantum yield in the solution state for the protonated species owing to favorable quinoidal stabilization. These attractive features led to the development of a second series of dyes with alkyl or aryl pyridinium moieties showing strong tunable solution/solid fluorescence intensity. For each series, ab initio calculations helped rationalize and ascertain their behavior in the excited state and the nature of the emission observed by the experimental results.

Structure-based identification of inhibitors disrupting the CD2-CD58 interactions.

The immune system has very intricate mechanisms of fighting against the invading infections which are accomplished by a sequential event of molecular interactions in the body. One of the crucial phenomena in this process is the recognition of T-cells by the antigen-presenting cells (APCs), which is initiated by the rapid interaction between both cell surface receptors, i.e., CD2 located on T-cells and CD58 located on APCs. Under various pathological conditions, which involve undesired immune response, inhibiting the CD2-CD58 interactions becomes a therapeutically relevant opportunity. Herein we present an extensive work to identify novel inhibiting agents of the CD2-CD58 interactions. Classical molecular dynamics (MD) simulations of the CD2-CD58 complex highlighted a series of crucial CD58 residues responsible for the interactions with CD2. Based on such results, a pharmacophore map, complementary to the CD2-binding site of CD58, was created and employed for virtual screening of ~ 300,000 available compounds. On the ~ 6000 compounds filtered from pharmacophore mapping, ADME screening leads to ~ 350 molecules. Molecular docking was then performed on these molecules, and fifteen compounds emerged with significant binding energy (< - 50 kcal/mol) for CD58. Finally, short MD simulations were performed in triplicate on each complex (i) to provide a microscopic view of the ligand binding and (ii) to rule out possibly weak binders of CD58 from the identified hits. At last, we suggest eight compounds for in vitro testing that were identified as promising hits to bind CD58 with a high binding affinity.

How To Make Nitroaromatic Compounds Glow: Next-Generation Large X-Shaped, Centrosymmetric Diketopyrrolopyrroles.

Red-emissive π-expanded diketopyrrolopyrroles (DPPs) with fluorescence reaching λ=750 nm can be easily synthesized by a three-step strategy involving the preparation of diketopyrrolopyrrole followed by N-arylation and subsequent intramolecular palladium-catalyzed direct arylation. Comprehensive spectroscopic assays combined with first-principles calculations corroborated that both N-arylated and fused DPPs reach a locally excited (S1 ) state after excitation, followed by internal conversion to states with solvent and structural relaxation, before eventually undergoing intersystem crossing. Only the structurally relaxed state is fluorescent, with lifetimes in the range of several nanoseconds and tens of picoseconds in nonpolar and polar solvents, respectively. The lifetimes correlate with the fluorescence quantum yields, which range from 6 % to 88 % in nonpolar solvents and from 0.4 % and 3.2 % in polar solvents. A very inefficient (T1 ) population is responsible for fluorescence quantum yields as high as 88 % for the fully fused DPP in polar solvents.

Binding of Sulfoxaflor to Aplysia californica-AChBP: Computational Insights from Multiscale Approaches.

Structural features and binding properties of sulfoxaflor (SFX) with Ac-AChBP, the surrogate of the insect nAChR ligand binding domain (LBD), are reported herein using various complementary molecular modeling approaches (QM, molecular docking, molecular dynamics, and QM/QM'). The different SFX stereoisomers show distinct behaviors in terms of binding and interactions with Ac-AChBP. Molecular docking and Molecular Dynamics (MD) simulations highlight the specific intermolecular contacts involved in the binding of the different SFX isomers and the relative contribution of the SFX functional groups. QM/QM' calculations provide further insights and a significant refinement of the geometric and energetic contributions of the various residues leading to a preference for the SS and RR stereoisomers. Notable differences in terms of binding interactions are pointed out for the four stereoisomers. The results point out the induced fit of the Ac-AChBP binding site according to the SFX stereoisomer. In this process, the water molecules-mediated contacts play a key role, their energetic contribution being among the most important for the various stereoisomers. In all cases, the interaction with Trp147 is the major binding component, through CH···π and π···π interactions. This study provides a rationale for the binding of SFX to insect nAChR, in particular with respect to the new class of sulfoximine-based insect nAChR competitive modulators, and points out the requirements of various levels of theory for an accurate description of ligand-receptor interactions.

Investigation of Phospholipase Cγ1 Interaction with SLP76 Using Molecular Modeling Methods for Identifying Novel Inhibitors.

The enzyme phospholipase C gamma 1 (PLCγ1) has been identified as a potential drug target of interest for various pathological conditions such as immune disorders, systemic lupus erythematosus, and cancers. Targeting its SH3 domain has been recognized as an efficient pharmacological approach for drug discovery against PLCγ1. Therefore, for the first time, a combination of various biophysical methods has been employed to shed light on the atomistic interactions between PLCγ1 and its known binding partners. Indeed, molecular modeling of PLCγ1 with SLP76 peptide and with previously reported inhibitors (ritonavir, anethole, daunorubicin, diflunisal, and rosiglitazone) facilitated the identification of the common critical residues (Gln805, Arg806, Asp808, Glu809, Asp825, Gly827, and Trp828) as well as the quantification of their interaction through binding energies calculations. These features are in agreement with previous experimental data. Such an in depth biophysical analysis of each complex provides an opportunity to identify new inhibitors through pharmacophore mapping, molecular docking and MD simulations. From such a systematic procedure, a total of seven compounds emerged as promising inhibitors, all characterized by a strong binding with PLCγ1 and a comparable or higher binding affinity to ritonavir (∆Gbind < -25 kcal/mol), one of the most potent inhibitor reported till now.

Mechanistic and Structural Insights on the IL-15 System through Molecular Dynamics Simulations.

Interleukin 15 (IL-15), a four-helix bundle cytokine, is involved in a plethora of different cellular functions and, particularly, plays a key role in the development and activation of immune responses. IL-15 forms receptor complexes by binding with IL-2Rß- and common γ(γc)-signaling subunits, which are shared with other members of the cytokines family (IL-2 for IL-2Rß- and all other γc- cytokines for γc). The specificity of IL-15 is brought by the non-signaling α-subunit, IL-15Rα. Here we present the results of molecular dynamics simulations carried out on four relevant forms of IL-15: its monomer, IL-15 interacting individually with IL-15Rα (IL-15/IL-15Rα), with IL-2Rß/γc subunits (IL-15/IL-2Rß/γc) or with its three receptors simultaneously (IL-15/IL-15Rα/IL-2Rß/γc). Through the analyses of the various trajectories, new insights on the structural features of the interfaces are highlighted, according to the considered form. The comparison of the results with the experimental data, available from X-ray crystallography, allows, in particular, the rationalization of the importance of IL-15 key residues (e.g. Asp8, Lys10, Glu64). Furthermore, the pivotal role of water molecules in the stabilization of the various protein-protein interfaces and their H-bonds networks are underlined for each of the considered complexes.

Influence of the Nature of the Amino Group in Highly Fluorescent Difluoroborates Exhibiting Intramolecular Charge Transfer.

A series of difluoroborates were synthesized from CH acids. All compounds were substituted with dialkylamino groups (NR2). The lone electron pair of the nitrogen atom of this donor moiety is variably delocalized toward the difluoroborate core that acts as the electron acceptor. This was rationalized in light of the various geometries of the amino group. The degree of charge transfer was quantified on the basis of the results of time-dependent density functional theory calculations.

Investigating cyclic peptides inhibiting CD2-CD58 interactions through molecular dynamics and molecular docking methods.

The CD2-CD58 protein-protein interaction is known to favor the recognition of antigen presenting cells by T cells. The structural, energetics, and dynamical properties of three known cyclic CD58 ligands, named P6, P7, and RTD-c, are studied through molecular dynamics (MD) simulations and molecular docking calculations. The ligands are built so as to mimic the C and F ß-strands of protein CD2, connected via turn inducers. The MD analyses focus on the location of the ligands with respect to the experimental binding site and on the direct and water-mediated hydrogen bonds (H bonds) they form with CD58. Ligand P6, with a sequence close to the experimental ß-strands of CD2, presents characteristics that explain its higher experimental affinity, e.g., the lower mobility and flexibility at the CD58 surface, and the larger number and occurrence frequency of ligand-CD58 H bonds. For the two other ligands, the structural modifications lead to changes in the binding pattern with CD58 and its dynamics. In parallel, a large set of molecular docking calculations, carried out with various search spaces and docking algorithms, are compared to provide a consensus view of the preferred ligand binding modes. The analysis of the ligand side chain locations yields results that are consistent with the CD2-CD58 crystal structure and suggests various binding modes of the experimentally identified hot spot of the ligands, i.e., Tyr86. P6 is shown to form a number of contacts that are also present in the experimental CD2-CD58 structure.

Computational simulations determining disulfonic stilbene derivative bioavailability within human serum albumin.

Disulfonic stilbene (DS) derivatives are a member of the large family of compounds widely employed in medicine and biology as modulators for membrane transporters or inhibitors of a protein involved in DNA repair. They constitute interesting compounds that have not yet been investigated within the bioavailability framework. No crystallographic structures exist involving such compounds embedded in the most common drug carrier, human serum albumin (HSA). The present work studies, for the first time, the physico-chemical features driving the inclusion of three DS derivatives (amino, nitro and acetamido, named DADS, DNDS and DATDS, respectively) within the four common HSA binding sites using combined molecular docking and molecular dynamics simulations. A careful analysis of each ligand within each of the studied binding sites is carried out, highlighting specific interactions and key residues playing a role in stabilizing the ligand within each pocket. The comparison between DADS, DNDS and DATDS reveals that depending on the binding site, the conclusions are rather different. For instance, the IB binding site shows a specificity to DADS compounds while IIIA is the most favorable site for DNDS and DATDS.

Tailoring Photoisomerization Pathways in Donor-Acceptor Stenhouse Adducts: The Role of the Hydroxy Group.

Donor-acceptor Stenhouse adducts (DASAs) are a rapidly emerging class of visible light-activatable negative photochromes. They are closely related to (mero)cyanine dyes with the sole difference being a hydroxy group in the polyene chain. The presence or absence of the hydroxy group has far-reaching consequences for the photochemistry of the compound: cyanine dyes are widely used as fluorescent probes, whereas DASAs hold great promise for visible light-triggered photoswitching. Here we analyze the photophysical properties of a DASA lacking the hydroxy group. Ultrafast time-resolved pump-probe spectroscopy in both the visible and IR region show the occurrence of E-Z photoisomerization on a 20 ps time scale, similar to the photochemical behavior of DASAs, but on a slower time scale. In contrast to the parent DASA compounds, where the initial photoisomerization is constrained to a single position (next to the hydroxy group), 1H NMR in situ-irradiation studies at 213 K reveal that for nonhydroxy DASAs E-Z photoisomerization can take place at two different bonds, yielding two distinct isomers. These observations are supported by TD-DFT calculations, showing that in the excited state the hydroxy group (pre)selects the neighboring C2-C3 bond for isomerization. The TD-DFT analysis also explains the larger solvatochromic shift observed for the parent DASAs as compared to the nonhydroxy analogue, in terms of the dipole moment changes evoked upon excitation. Furthermore, computations provide helpful insights into the photoswitching energetics, indicating that without the hydroxy group the 4π-electrocyclization step is energetically forbidden. Our results establish the central role of the hydroxy group for DASA photoswitching and suggest that its introduction allows for tailoring photoisomerization pathways, presumably both through (steric) fixation via a hydrogen bond with the adjacent carbonyl group of the acceptor moiety, as well as through electronic effects on the polyene backbone. These insights are essential for the rational design of novel, improved DASA photoswitches and for a better understanding of the properties of both DASAs and cyanine dyes.

Solvent Effects on the Actinic Step of Donor-Acceptor Stenhouse Adduct Photoswitching.

Donor-acceptor Stenhouse adducts (DASAs) are negative photochromes that switch with visible light and are highly promising for applications ranging from smart materials to biological systems. However, the strong solvent dependence of the photoswitching kinetics limits their application. The nature of the photoswitching mechanism in different solvents is key for addressing the solvatochromism of DASAs, but as yet has remained elusive. Here, we employ spectroscopic analyses and TD-DFT calculations to reveal changing solvatochromic shifts and energies of the species involved in DASA photoswitching. Time-resolved visible pump-probe spectroscopy suggests that the primary photochemical step remains the same, irrespective of the polarity and protic nature of the solvent. Disentangling the different factors determining the solvent-dependence of DASA photoswitching, presented here, is crucial for the rational development of applications in a wide range of different media.

Shedding Light on the Photoisomerization Pathway of Donor-Acceptor Stenhouse Adducts.

Donor-acceptor Stenhouse adducts (DASAs) are negative photochromes that hold great promise for a variety of applications. Key to optimizing their switching properties is a detailed understanding of the photoswitching mechanism, which, as yet, is absent. Here we characterize the actinic step of DASA-photoswitching and its key intermediate, which was studied using a combination of ultrafast visible and IR pump-probe spectroscopies and TD-DFT calculations. Comparison of the time-resolved IR spectra with DFT computations allowed to unambiguously identify the structure of the intermediate, confirming that light absorption induces a sequential reaction path in which a Z-E photoisomerization of C2-C3 is followed by a rotation around C3-C4 and a subsequent thermal cyclization step. First and second-generation DASAs share a common photoisomerization mechanism in chlorinated solvents with notable differences in kinetics and lifetimes of the excited states. The photogenerated intermediate of the second-generation DASA was photo-accumulated at low temperature and probed with time-resolved spectroscopy, demonstrating the photoreversibility of the isomerization process. Taken together, these results provide a detailed picture of the DASA isomerization pathway on a molecular level.

Exploring the Solvatochromism of Betaine†30 with Ab Initio Tools: From Accurate Gas-Phase Calculations to Implicit and Explicit Solvation Models.

Betaine 30 is known for the extraordinary solvatochromism of its visible absorption band that goes from λ=882 nm in tetrachloromethane to λ=453 nm in water (Δλ=-429 nm). This large blueshift partly originates from a dramatic decrease of the dipole moment upon excitation. Despite several decades of research, experimental works still disagree on the exact value of the excess dipole moment, the orientation of the dipole moment of the excited-state, the role and amplitude of the change of the polarisability upon excitation as well as on the gas-phase excitation energy. In this work, we present an in-depth theoretical investigation. First, we carefully tested several levels of theory on the model system and next calculated the electric properties of betaine 30 at the CC2 level. Our best estimates are Δµ=-7 D for the excess dipole moment, that is, a significant decrease but no change of direction, a Δα value of -120 a.u. and a gas-phase vertical excitation energy of 1.127 eV. The implicit solvation models are able to reproduce the experimental trends, with large correlation coefficients for non-hydrogen-bond-donating solvents, the smallest root-mean-square deviation error being reached with the vertical excitation model (VEM). The explicit effective fragment potential method combined with time-dependent density functional theory (TD-DFT) in a QM/MM framework provides accurate estimates for hydrogen-bond-donating solvents, whereas the addition of a dispersion correction is needed to restore the correct solvatochromic direction in tetrachloromethane.