Synthesis of One Double Bond-Inserted Retinal Analogs and Their Binding Experiments with Opsins: Preparation of Novel Red-Shifted Channelrhodopsin Variants.

In optogenetics, red-shifted channelrhodopsins (ChRs) are eagerly sought. We prepared six kinds of new chromophores with one double bond inserted into the polyene side chain of retinal (A1) or 3,4-didehydroretinal (A2), and examined their binding efficiency with opsins (ReaChR and ChrimsonR). All analogs bound with opsins to afford new ChRs. Among them, A2-10ex (an extra double bond is inserted at the C10-C11 position of A2) showed the greatest red-shift in the absorption spectrum of ChrimsonR, with a maximum absorbance at 654 nm (67 nm red-shifted from that of A1-ChrimsonR). Moreover, a long-wavelength spectral boundary of A2-10ex-ChrimsonR was extended to 756 nm, which reached into the far-red region (710-850 nm).

FTIR Spectroscopy and DFT Calculations to Probe the Kinetics of ß-Carotene Thermal Degradation.

The thermal degradation of ß-carotene in air was investigated. The sample was heated at different temperatures (90, 100, 115, and 130 °C) for periods of up to 8 h to perform a complete kinetic study, the product analysis having been carried out via infrared spectroscopy in attenuated total reflectance mode coupled to density functional theory (DFT) calculations. The kinetics of this thermal degradation process was found to follow a first-order scheme, with rate coefficients varying from k90 °C = (2.0 ± 0.3) × 10-3 to k130 °C = (11.0 ± 0.7) × 10-3 min-1, the experimental activation energy having been calculated as (52 ± 1) kJ mol-1. This Ea value is close to the DFT energies corresponding to a C15-15' or a C13-14 cis-trans isomerization, followed by the formation of a carotene-oxygen diradical, which was characterized for the first time. Comparison between the experimental and calculated infrared data confirmed the C15-15'- cis rupture as the predominant reaction pathway and retinal as the major degradation product.

Synthesis of isotopically labeled all-trans retinals for DNP-enhanced solid-state NMR studies of retinylidene proteins.

Three all-trans retinals containing multiple 13 C labels have been synthesized to enable dynamic nuclear polarization enhanced solid-state magic angle spinning NMR studies of novel microbial retinylidene membrane proteins including proteorhodpsin and channelrhodopsin. The synthetic approaches allowed specific introduction of 13 C labels in ring substituents and at different positions in the polyene chain to probe structural features such as ring orientation and interaction of the chromophore with the protein in the ground state and in photointermediates. [10-18-13 C9 ]-All-trans-retinal (1b), [12,15-13 C2 ]-all-trans-retinal (1c), and [14,15-13 C2 ]-all-trans-retinal (1d) were synthesized in in 12, 8, and 7 linear steps from ethyl 2-oxocyclohexanecarboxylate (5) or ß-ionone (4), respectively.

Synthesis and use of stable isotope enriched retinals in the field of vitamin A.

The role of vitamin A and its metabolites in the life processes starting with the historical background and its up to date information is discussed in the introduction. Also the role of 11Z-retinal in vision and retinoic acid in the biological processes is elucidated. The essential role of isotopically enriched systems in the progress of vision research, nutrition research etc. is discussed. In part B industrial commercial syntheses of vitamin A by the two leading companies Hoffmann-La Roche (now DSM) and BASF are discussed. The knowledge obtained via these pioneering syntheses has been essential for the further synthetic efforts in vitamin A field by other scientific groups. The rest of the paper is devoted to the synthetic efforts of the Leiden group that gives an access to the preparation of site directed high level isotope enrichment in retinals. First the synthesis of the retinals with deuterium incorporation in the conjugated side chain is reviewed. Then, 13C-labeled retinals are discussed. This is followed by the discussion of a convergent synthetic scheme that allows a rational access to prepare any isotopomer of retinals. The schemes that provide access to prepare any possible isotope enriched chemically modified systems are discussed. Finally, nor-retinals and bridged retinals that give access to a whole (as yet incomplete) library of possible isotopomers are reviewed.

[Synthesis of spyropyran derivatives of retinal and study of their interaction with bacterioopsin from Halobacterium salinarum].

The synthesis of retinal analogue series that contain a spyropyran moiety instead of a trimethylcyclohexene ring was proposed. The process of the retinal analogue interaction with bacterioopsin from apomembranes of Halobacterium salinarum and the spectral properties of the newly formed pigments were studied. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2008, vol. 34, no. 2; see also http://www.maik.ru.

Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore.

By engineering a microbial rhodopsin, Archaerhodopsin-3 (Arch), to bind a synthetic chromophore, merocyanine retinal, in place of the natural chromophore all-trans-retinal (ATR), we generated a protein with exceptionally bright and unprecedentedly red-shifted near-infrared (NIR) fluorescence. We show that chromophore substitution generates a fluorescent Arch complex with a 200-nm bathochromic excitation shift relative to ATR-bound wild-type Arch and an emission maximum at 772 nm. Directed evolution of this complex produced variants with pH-sensitive NIR fluorescence and molecular brightness 8.5-fold greater than the brightest ATR-bound Arch variant. The resulting proteins are well suited to bacterial imaging; expression and stability have not been optimized for mammalian cell imaging. By targeting both the protein and its chromophore, we overcome inherent challenges associated with engineering bright NIR fluorescence into Archaerhodopsin. This work demonstrates an efficient strategy for engineering non-natural, tailored properties into microbial opsins, properties relevant for imaging and interrogating biological systems.

Retinal-conjugated pH-sensitive micelles induce tumor senescence for boosting breast cancer chemotherapy.

Evoking tumor cellular senescence, an irreversible status of cell growth quiescence, has been recently proposed as a potential strategy to improve the efficacy of cancer treatment. In the current study, all-trans retinal, the precursor of all-trans retinoic acid, was conjugated to dextran via hydrazone bond to generate amphiphilic dextran-retinal (DR) conjugates, which self-assembled into pH-sensitive DR micelles. Our results showed that DR micelles moderately inhibited MCF-7 breast cancer cell growth through inducing p21-associated cellular senescence, which relied on retinoic acid receptors (RARs) and was accompanied by significant G0/G1 cell cycle arrest. Moreover, DR micelles were capable of encapsulating doxorubicin (DOX) to generate DOX-loaded DD micelles, facilitating the uptake and release of DOX in cancer cells. Compared with free DOX, DD micelles more effectively suppressed tumor growth and prolonged survival time of mouse xenograft model through inducing tumor apoptosis and cellular senescence. However, blocking cellular senescence diminished DD-caused apoptosis in MCF-7 cells by 40-50%. Therefore, pH-sensitive DR micelles not only served as a potent platform for DOX delivery, but also enhanced the anti-tumor effect of DOX by inducing tumor cellular senescence. These data reveal a great potential of evoking tumor senescence with retinal-conjugated micelles for boosting breast cancer chemotherapy.

Potential prophylactic antitumor activity of retinylidene 1,3-diketones.

Treatment of all-trans-retinal with a series of 1,3-diketones using Knoevenagel conditions gave the expected condensation products. These retinylidene 1,3-diketones were characterized and their biological activities in the hamster tracheal organ culture test measured. It was found that the cyclohexane- 1,3-dione derivatives are highly active in this in vitro assay, while other 1,3-diketones are less active. Retinylidenedimedone has been chosen for further evaluation.

Azidotetrafluorophenyl retinal analogue: synthesis and bacteriorhodopsin pigment formation.

The retinal derivative, all-trans-9-(4-azido-2,3,5,6-tetrafluorophenyl)-3,7- dimethyl-2,4,6,8-nonatetraenal, was synthesized by two routes as a potential photoactivatable cross-linking agent for studies in bacteriorhodopsin (BR) of the chromophore interaction with its apoprotein. The retinal analogue formed a stable, moderately functional BR pigment confirming that the ring cavity of the retinal binding site has a significant tolerance for derivatization on that portion of the molecule. Attempts to cross-link the azido chromophore to the protein by photoactivation were unsuccessful. The electron delocalization effect of the conjugated polyene side chain of the retinal appears to interfere with the formation or reactivity of the nitrene intermediate to the extent that photoactivated cross-linking is not achieved. These results demonstrate a limitation to the use of fluorinated aryl azides as photoaffinity reagents.

Constraints of opsin structure on the ligand-binding site: studies with ring-fused retinals.

Ring-fused retinal analogs were designed to examine the hula-twist mode of the photoisomerization of the 9-cis retinylidene chromophore. Two 9-cis retinal analogs, the C11-C13 five-membered ring-fused and the C12-C14 five-membered ring-fused retinal derivatives, formed the pigments with opsin. The C11-C13 ring-fused analog was isomerized to a relaxed all-trans chromophore (lambda(max) > 400 nm) at even -269 degrees C and the Schiff base was kept protonated at 0 degrees C. The C12-C14 ring-fused analog was converted photochemically to a bathorhodopsin-like chromophore (lambda(max) = 583 nm) at -196 degrees C, which was further converted to the deprotonated Schiff base at 0 degrees C. The model-building study suggested that the analogs do not form pigments in the retinal-binding site of rhodopsin but form pigments with opsin structures, which have larger binding space generated by the movement of transmembrane helices. The molecular dynamics simulation of the isomerization of the analog chromophores provided a twisted C11-C12 double bond for the C12-C14 ring-fused analog and all relaxed double bonds with a highly twisted C10-C11 bond for the C11-C13 ring-fused analog. The structural model of the C11-C13 ring-fused analog chromophore showed a characteristic flip of the cyclohexenyl moiety toward transmembrane segments 3 and 4. The structural models suggested that hula twist is a primary process for the photoisomerization of the analog chromophores.

Studies on pyrylretinal analogues of bacteriorhodopsin.

The retinal analogues 3-methyl-5-(1-pyryl)-2E,4E-pentadienal (1) and 3,7-dimethyl-9-(1-pyryl)-2E,4E,6E,8E-nonatetr aenal (2), which contain the tetra aromatic pyryl system, have been synthesized and characterized in order to examine the effect of the extended ring system on the binding capabilities and the function of bacteriorhodopsin (bR). The two bR mutants, E194Q and E204Q, known to have distinct proton-pumping patterns, were also examined so that the effect of the bulky ring system on the proton-pumping mechanism could be studied. Both retinals formed pigments with all three bacterioopsins, and these pigments were found to have absorption maxima in the range 498-516 nm. All the analogue pigments showed activity as proton pumps. The pigment formed from wild-type apoprotein bR with 1 (with the shortened polyene side chain) showed an M intermediate at 400 nm and exhibited fast proton release followed by proton uptake. Extending the polyene side chain to the length identical with retinal, analogue 2 with wild-type apoprotein gave a pigment that shows M and O intermediates at 435 nm and 650 nm, respectively. This pigment shows both fast and slow proton release at pH 7, suggesting that the pKa of the proton release group (in the M-state) is higher in this pigment compared to native bR. Hydrogen azide ions were found to accelerate the rise and decay of the O intermediate at neutral pH in pyryl 2 pigment. The pigments formed between 2 and E194Q and E204Q showed proton-pumping behavior similar to pigments formed with the native retinal, suggesting that the size of the chromophore ring does not alter the protein conformation at these sites.

Synthesis of isotopically labelled retinal. Structural and functional studies at the atomic level of the chromophore in visual pigments.

OBJECTIVE: To describe the strategy followed in studying the structure and function of the chromophore in visual pigments at the atomic level. METHODS: A three-step strategy was followed. First, 11-cis retinal with high enrichment (99% 13C or 99% 2H) at pre-determined positions or combinations of positions was synthesized. Second, the rhodopsins with isotope label in the chromophore were prepared combining opsin with the isotopically labelled 11-cis retinal. Third, these systems were studied with isotope-sensitive physical techniques. CONCLUSIONS: Isotope labelling together with isotope-sensitive spectroscopy is a highly promising method for obtaining information at the atomic level of biologically active systems. Strategies based on specific stable isotope labelling are likely to be applicable to many research areas.

Spectral sensitivity, structure and activation of eukaryotic rhodopsins: activation spectroscopy of rhodopsin analogs in Chlamydomonas.

Retinal normally binds opsin forming the chromophore of the visual pigment, rhodopsin. In this investigation synthetic analogs were bound by the opsin of living cells of the alga Chlamydomonas reinhardtii; the effect was assayed by phototaxis to give an activation spectrum for each rhodopsin analog. The results show the influence of different chromophores and the protein on the absorption of light. The maxima of the phototaxis action spectra shifted systematically with the number of double bonds conjugated with the imine (C = N+H) bond of the chromophore. Chromophores lacking a beta-ionone ring, methyl groups and all C = C double bonds photoactivated the rhodopsin of Chlamydomonas with normal efficiency. On the basis of a simple model involving one-electron transitions between occupied and virtual molecular orbitals, we estimate the charge distribution along the chromophore in the binding site. With this restraint we define a unique structural model for eukaryotic rhodopsins and explain the spectral clustering of pigments, the spectral differences between red and green rhodopsins and the molecular basis of color blindness. Our results are consistent with the triggering of the activation of rhodopsin by the light-mediated change in electric dipole moment rather than the steric cis-trans isomerization of the chromophore.

[Synthesis and properties of C13-substituted retinals]. / Sintez i svoistva C13-zameshchennykh retinalei.

Several analogues of all-trans-retinal were synthesised, containing, instead of CH3-group at C13, the following substituents: H, C[2H]3, C2H5, iso-C3H7, C4H9, C6H5 or alpha-C10H8. The compounds synthesised on coupling with bacterioopsin gave artificial chromoproteins, which retained the ability to participate in the cycle of photochemical transformations and H+-transport.

[A convenient synthesis of retinal derivatives with a modified trimethylcyclohexene ring]. / Udobnyi sposob polucheniia proizvodnykh retinalia, modifitsirovannykh po trimetiltsiklogeksenovomy kol'tsu.

A method of simultaneous one-stage synthesis of three retinal derivatives (5,6-dioxo-5,6-seco-, 5,6-dihydro-5,6-epoxy-, and 4-oxoretinal) was proposed, with the yield of the first derivative being approximately 50%. These compounds are useful tools for studying the antitumor activity of retinoids, the reconstituted bacteriorhodopsin analogues with changed parameters of photocycle, and the reactivity of retinal derivatives in the processes of oxidation by molecular oxygen. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2002, vol. 28, no. 6; see also http://www.maik.ru.

Increased bioavailability of rifampicin from stimuli-responsive smart nano carrier.

Stimuli responsive polymeric nanocarrier (RCOP-2) functionalized with frontline antituberculosis drug (Rifampicin) is demonstrated for sustained release. Bioavailability of Rifampicin is taken care of by conjugating this drug through a acylhydrazine linker to the polymeric backbone. The poly(ethylene glycol) structural motif is introduced in the copolymer architecture for water solubility. Releasing retinal along with Rifampicin is hypothesized to reduce the risk of side effects due to Rifampicin. The self-assembly of RCOP-2, due to the amphiphilicity present in the copolymer, is explored in detail. The pH responsiveness of RCOP-2 is demonstrated in mild acidic environment as well as in cell lines. The 4T cell line, due to its acidic nature, shows time-dependent cellular internalization. On the basis of the results, our unique design is expected to provide an increased bioavalaibility of Rifampicin with reduced side effects. From the flow cytometry results on A549 cell lines, it is clear that the newly designed copolymer RCOP-2 can internalize efficiently and serve as an effective Rifampicin delivery system.

Probing a polar cluster in the retinal binding pocket of bacteriorhodopsin by a chemical design approach.

Bacteriorhodopsin has a polar cluster of amino acids surrounding the retinal molecule, which is responsible for light harvesting to fuel proton pumping. From our previous studies, we have shown that threonine 90 is the pivotal amino acid in this polar cluster, both functionally and structurally. In an attempt to perform a phenotype rescue, we have chemically designed a retinal analogue molecule to compensate the drastic effects of the T90A mutation in bacteriorhodopsin. This analogue substitutes the methyl group at position C(13) of the retinal hydrocarbon chain by and ethyl group (20-methyl retinal). We have analyzed the effect of reconstituting the wild-type and the T90A mutant apoproteins with all-trans-retinal and its 20-methyl derivative (hereafter, 13-ethyl retinal). Biophysical characterization indicates that recovering the steric interaction between the residue 90 and retinal, eases the accommodation of the chromophore, however it is not enough for a complete phenotype rescue. The characterization of these chemically engineered chromoproteins provides further insight into the role of the hydrogen bond network and the steric interactions involving the retinal binding pocket in bacteriorhodopsin and other microbial sensory rhodopsins.