Monitoring Conformation and Protonation States of Glutathione by Raman Optical Activity and Molecular Dynamics.

Glutathione (GSH) is a common antioxidant and its biological activity depends on the conformation and protonation state. We used molecular dynamics, Raman and Raman optical activity (ROA) spectroscopies to investigate GSH structural changes in a broad pH range. Factor analysis of the spectra provided protonation constants (2.05, 3.45, 8.62, 9.41) in good agreement with previously published values. Following the analysis, spectra of differently protonated forms were obtained by extrapolation. The complete deprotonation of the thiol group above pH 11 was clearly visible in the spectra; however, many spectral features did not change much with pH. Experimental spectra at various pH values were decomposed into the simulated ones, which allowed us to study the conformer populations and quality of molecular dynamics (MD). According to this combined ROA/MD analysis conformation of the GSH backbone is affected by the pH changes only in a limited way. The combination of ROA with the computations thus has the potential to improve the MD force field and obtain more accurate populations of the conformer species. The methodology can be used for any molecule, but for a more detailed insight better computational techniques are needed in the future.

'A careful disorderliness' in biomolecular structure revealed by Raman optical activity.

Following its first observation 50 years ago Raman optical activity (ROA), which refers to a circular polarization dependence of Raman scattering from chiral molecules, has evolved into a powerful chiroptical spectroscopy for studying a large range of biomolecules in aqueous solution. Among other things ROA provides information about motif and fold as well as secondary structure of proteins; structure of carbohydrates and nucleic acids; polypeptide and carbohydrate structure of intact glycoproteins; and protein and nucleic acid structure of intact viruses. Quantum chemical simulations of observed Raman optical activity spectra can provide complete three-dimensional structures of biomolecules, together with information about conformational dynamics. This article reviews how ROA has provided new insight into the structure of unfolded/disordered states and sequences, ranging from the complete disorder of the random coil to the more controlled type of disorder exemplified by poly L-proline II helix in proteins, high mannose glycan chains in glycoproteins and constrained dynamic states of nucleic acids. Possible roles for this 'careful disorderliness' in biomolecular function, misfunction and disease are discussed, especially amyloid fibril formation.

Chiral Seeded Growth of Gold Nanorods Into Fourfold Twisted Nanoparticles with Plasmonic Optical Activity.

A robust and reproducible methodology to prepare stable inorganic nanoparticles with chiral morphology may hold the key to the practical utilization of these materials. An optimized chiral growth method to prepare fourfold twisted gold nanorods is described herein, where the amino acid cysteine is used as a dissymmetry inducer. Four tilted ridges are found to develop on the surface of single-crystal nanorods upon repeated reduction of HAuCl4 , in the presence of cysteine as the chiral inducer and ascorbic acid as a reducing agent. From detailed electron microscopy analysis of the crystallographic structures, it is proposed that the dissymmetry results from the development of chiral facets in the form of protrusions (tilted ridges) on the initial nanorods, eventually leading to a twisted shape. The role of cysteine is attributed to assisting enantioselective facet evolution, which is supported by density functional theory simulations of the surface energies, modified upon adsorption of the chiral molecule. The development of R-type and S-type chiral structures (small facets, terraces, or kinks) would thus be non-equal, removing the mirror symmetry of the Au NR and in turn resulting in a markedly chiral morphology with high plasmonic optical activity.

Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity.

The histidine residue has an exceptional affinity for metals, but solution structure of its complexes are difficult to study. For zinc and nickel complexes, Raman and Raman optical activity (ROA) spectroscopy methods to investigate the link between spectral shapes and the geometry were used. The spectra were recorded and interpreted on the basis of ionic equilibria, molecular dynamics, ab initio molecular dynamics, and density functional theory. For zwitterionic histidine the dominant tautomer was determined by the decomposition of experimental spectra into calculated subspectra. An octahedral structure was found to prevail for the ZnHis2 complex in solution, in contrast to a tetrahedral arrangement in the crystal phase. The solution geometry of NiHis2 is more similar to the octahedral structure found by X-ray. The Raman and ROA structural determinations of metal complexes are dependent on extensive computations, but reveal unique information about the studied systems.

Raman Optical Activity of N-Acetyl-L-Cysteine in Water and in Methanol: The "Clusters-in-a-Liquid" Model and ab Initio Molecular Dynamics Simulations.

Raman and Raman Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral molecule, were measured in water and in methanol to evaluate the solvent effects. Two different solvation approaches, that is, the DFT based "clusters-in-a-liquid" solvent model and the ab initio molecular dynamics (AIMD) simulations, were applied to simulate the Raman and ROA spectra. Systematic conformational searches were carried out using a recently developed conformational searching tool, CREST, with the inclusion of polarizable continuum model of water and of methanol. The CREST candidates of NALC and the NALC-solvent complexes were re-optimized and their Raman and ROA simulations were done at the B3LYP-D3BJ/def2-TZVP and the B3LYP-aug-cc-pVDZ//cc-pVTZ levels. Also, AIMD simulations, which includes some anharmonic effects and all intermolecular interactions in solution, were performed. By empirically weighting the computed Raman and ROA spectra of each conformer, good agreements with the experimental data were achieved with both approaches, while AIMD offered some improvements in the carbonyl and in the low wavenumber regions over the static DFT approach. The pros and cons of these two different approaches for accounting the solvent effects on Raman and ROA of this flexible chiral system will also be discussed.

Nanoengineered Bifidobacterium bifidum with Optical Activity for Photothermal Cancer Immunotheranostics.

There is substantial interest regarding the understanding and designing of nanoengineered bacteria to combat various fatal diseases. Here, we report the nanoengineering of Bifidobacterium bifidum using Cremophor EL to encapsulate organic dye molecules by simple incubation and washing processes while maintaining the bacterial morphology and viability. The prepared functional bacteria exhibit characteristics such as optical absorbance, unique fluorescence, powerful photothermal conversion, low toxicity, excellent tumor targeting, and anticancer efficacy. They also displayed significant in vivo fluorescent expression in implanted colorectal cancerous tumors. Moreover, the powerful photothermal conversion of the functional bacteria could be spatiotemporally evoked by biologically penetrable near-infrared laser for effective tumor regression in mice, with the help of immunological responses. Our study demonstrates that a nanoengineering approach can provide the strong physicochemical traits and attenuation of living bacterial cells for cancer immunotheranostics.

Probing the solvation of the α-helix with extended amide III bands in Raman optical activity.

Experimental and theoretical Raman optical activity (ROA) study of α-helical peptides and proteins has suggested that the relative intensity of two extended amide III ROA bands at ∼1340 cm-1 (I band) and ∼1300 cm-1 (II band) can be used to monitor the permittivity of the surrounding medium of the α-helix. So far, the ROA intensity ratio, II/III, has been interpreted from two different viewpoints. The first one is in terms of a direct effect of permittivity around the α-helix. The second one is based on a structural equilibrium of two types of α-helical structures, "hydrated" and "unhydrated" ones. In the present study, temperature- and solvent-dependences of II/III are measured for highly-α-helical peptides and compared to the theoretical spectra while varying the permittivity or the type of α-helical structure. A fragment method with partial optimization in the normal modes is adopted in density functional theory calculations. The main features of the experimental spectra and a trend of the observed II/III are well reproduced by the simulations, which leads us to a conclusion that the II/III is dominantly governed by a direct influence of the permittivity of the environment and just accessorily by the equilibrium of the two types of α-helices. The simulations also opposed the conventional assignments of the I and II bands to "hydrated" and "unhydrated" α-helical structures, respectively. In the case of α-helical proteins, solvent exposure of the α-helix may be monitored by the ROA ratio.

Identification of limonoids from Walsura yunnanensis and evaluation of their cytotoxicity against cancer cell lines.

Three new limonoids, walsurauias A-C (1-3), along with four known ones, were isolated from the leaves and twigs of Walsura yunnanensis C. Y. Wu. Their structures were determined on the basis of comprehensive spectroscopic data analysis. The new limonoids were screened for their cytotoxic activity (IC50 0.81-5.73 µM) against four human cancer cell lines, including A549, HepG2, HCT116 p21KO and CNE-2. And α,ß-unsaturated ketone moieties in rings A and B are essential for their cytotoxic activity. Selected compounds were further investigated. Compounds 1-3 effectively induced G2/M cell cycle arrest and apoptosis in a dose-dependent manner in cancer cells. In addition, compounds 1-3 inhibited the colony formation and compounds 2 and 3 suppressed the migration of cancer cells.

21,24-Cyclolanostanes revisited: Structural revision and biological evaluation.

Chemical fractionation of the EtOH extract of a medicinal macro fungus, Inonotus obliquus, afforded an array of lanostane-type triterpenoids (1-11) including two new ones (1 and 8). The structures of these compounds were determined on the basis of spectroscopic analyses, single crystal X-ray crystallography of 3-6 and biosynthetic considerations. With the confirmatory structural information provided by X-ray diffraction analysis in hand, several previously reported 21,24-cyclolanostanes, such as inonotsutriols A-C and (20R,21S,24S)-21,24-cyclopenta-3ß,21,25-trihydroxylanosta-8-ene, were structurally corrected. In addition, the NMR data of other types of 21,24-cyclo triterpenoids were also re-examined and structural revisions were thus suggested. Compounds 2, 6 and 8 showed significant cytostatic effects against a panel of tumor cell lines with IC50 values ranging from 7.80 to 18.5 µM. Further assays established that compound 2 exerted promising in vitro anti-breast cancer potential by inhibiting the proliferation and migration of 4T1 cells.

New iridal-type triterpenoid analogues with 6/5/6-fused carbon skeleton from the rhizomes of Belamcanda chinensis.

Five new iridal-type triterpenoid derivatives with 6/5/6 tricyclic ring skeleton (1-5) were obtained from the rhizomes of Belamcanda chinensis. Their structures were determined on the basis of detailed spectroscopic data and ECD calculation. Compounds 1-5 possessed the same 6/5/6-fused carbon skeleton as Belamchinenin A, which further enriched this kind of iridals. In vitro bioassay, compounds 2 and 3 exhibited 51.95 and 54.52% inhibitory activities, respectively, against Fe2+/cysteine-induced liver microsomal lipid peroxidation at a concentration of 10 µM. A putative biogenetic pathway for compounds 1-5 was proposed.

Intense chiral signal from α-helical poly-L-alanine observed in low-frequency Raman optical activity.

Raman optical activity (ROA) spectral features reliably indicate the structure of peptides and proteins, but the signal is often weak. However, we observed significantly enhanced low-frequency bands for α-helical poly-L-alanine (PLA) in solution. The biggest ROA signal at ∼100 cm-1 is about 10 times stronger than higher-frequency bands described previously, which facilitates the detection. The low-frequency bands of PLA were compared to those of α-helical proteins. For PLA, density functional simulations well reproduced the experimental spectra and revealed that about 12 alanine residues within two turns of the α-helix generate the strong ROA band. Averaging based on molecular dynamics (MD) provided an even more realistic spectrum compared to the static model. The low-frequency bands could be largely related to a collective motion of the α-helical backbone, partially modulated by the solvent. Helical and intermolecular vibrational coordinates have been introduced and the helical unwinding modes were assigned to the strongest ROA signal at 101-128 cm-1. Further analysis indicated that the helically arranged amide and methyl groups are important for the strong chiral signal of PLA, while the local chiral centers CαH contribute in a minor way only. The strong low-frequency ROA can thus provide precious information about the motions of the peptide backbone and facilitate future protein studies.

Ultrasound processing of rutin in food-grade solvents: Derivative compounds, antioxidant activities and optical rotation.

The effect of ultrasound was studied on the flavonoid rutin to understand its hydrolysis to aglycones, antioxidant capacity and optical rotation. The total phenolic content increased >56% at 3.6-36 kJ/cm3, indicating production of phenolic compounds. In the water media, at 27 kJ/cm3 and 47 °C, the total flavonoid content increased from control 0.26 ± 0.01 to 0.45 ± 0.02 mg catechin equivalent/mg rutin hydrate. Quercetin yield in citric acid media increased with change in energy density from 0.34 ± 0.09% at 0.1 kJ/cm3 (68 °C) to 2.23 ± 0.04% at 7.0 kJ/cm3 (86 °C). A plummeting effect was only observed in water media after 27 kJ/cm3 by FRAP (47 °C) and DPPH (86 °C) antioxidant activities, indicating that the presence of solutes (citric acid and NaCl) after 27 kJ/cm3 reduced degradation of flavonoids. Furthermore, ultrasonication increased levorotatory rutin enantiomers, that can be used to further modify physico-chemical properties of other food components.

Fluorescence and Optical Activity of Chiral CdTe Quantum Dots in Their Interaction with Amino Acids.

Ligand-induced chirality in semiconducting nanocrystals has been the subject of extensive study in the past few years and shows potential applications in optics and biology. Yet, the origin of the chiroptical effect in semiconductor nanoparticles is still not fully understood. Here, we examine the effect of the interaction with amino acids on both the fluorescence and the optical activity of chiral semiconductor quantum dots (QDs). A significant fluorescence enhancement is observed for l/d-Cys-CdTe QDs upon interaction with all the tested amino acids, indicating suppression of nonradiative pathways as well as the passivation of surface trap sites brought via the interaction of the amino group with the CdTe QDs' surface. Heterochiral amino acids are shown to weaken the circular dichroism (CD) signal, which may be attributed to a different binding configuration of cysteine molecules on the QDs' surface. Furthermore, a red shift of both CD and fluorescence signals in l/d-Cys-CdTe QDs is only observed upon adding cysteine, while other tested amino acids do not exhibit such an effect. We speculate that the thiol group induces orbital hybridization of the highest occupied molecular orbital (HOMOs) of cysteine and the valence band of CdTe QDs, leading to the decrease of the energy band gap and a concomitant red shift of CD and fluorescence spectra. This is further verified by density functional theory calculations. Both the experimental and theoretical findings indicate that the addition of ligands that do not "directly" interact with the valence band (VB) of the QD (noncysteine moieties) changes the QD photophysical properties, as it probably modifies the way cysteine is bound to the surface. Hence, we conclude that it is not only the chemistry of the amino acid ligand that affects both CD and PL but also the exact geometry of binding that modifies these properties. Understanding the relationship between the QD's surface and chiral amino acid thus provides an additional perspective on the fundamental origin of induced chiroptical effects in semiconductor nanoparticles, potentially enabling us to optimize the design of chiral semiconductor QDs for chiroptic applications.

N-Pyrazinoyl Substituted Amino Acids as Potential Antimycobacterial Agents-The Synthesis and Biological Evaluation of Enantiomers.

Tuberculosis is an infectious disease caused by Mycobacterium tuberculosis (Mtb), each year causing millions of deaths. In this article, we present the synthesis and biological evaluations of new potential antimycobacterial compounds containing a fragment of the first-line antitubercular drug pyrazinamide (PZA), coupled with methyl or ethyl esters of selected amino acids. The antimicrobial activity was evaluated on a variety of (myco)bacterial strains, including Mtb H37Ra, M. smegmatis, M. aurum, Staphylococcus aureus, Pseudomonas aeruginosa, and fungal strains, including Candida albicans and Aspergillus flavus. Emphasis was placed on the comparison of enantiomer activities. None of the synthesized compounds showed any significant activity against fungal strains, and their antibacterial activities were also low, the best minimum inhibitory concentration (MIC) value was 31.25 µM. However, several compounds presented high activity against Mtb. Overall, higher activity was seen in derivatives containing ʟ-amino acids. Similarly, the activity seems tied to the more lipophilic compounds. The most active derivative contained phenylglycine moiety (PC-ᴅ/ʟ-Pgl-Me, MIC < 1.95 µg/mL). All active compounds possessed low cytotoxicity and good selectivity towards Mtb. To the best of our knowledge, this is the first study comparing the activities of the ᴅ- and ʟ-amino acid derivatives of pyrazinamide as potential antimycobacterial compounds.

Four New C9 Metabolites from the Sponge-Associated Fungus Gliomastix sp. ZSDS1-F7-2.

Four new structurally related metabolites, one γ-lactone named gliomasolide F (1), one δ-lactone named gliomasolide G (2), and two medium-chain fatty acids named gliomacids A⁻B (3⁻4), each containing nine carbons in total, were identified from the sponge-associated fungus Gliomastix sp. ZSDS1-F7-2. The planar chemical structures of these novel C9 metabolites were elucidated by nuclear magnetic resonance (NMR) spectroscopic methods, in connection with the analysis of high-resolution mass spectrometry (HRMS) and infrared (IR) data. The absolute configuration of 1, was determined by comparisons of experimental circular dichroism (CD) and optical rotation (OR) value with corresponding ones computed by quantum chemistry. The relative configuration of 2 was determined by the Nuclear Overhauser effect spectroscopy (NOESY) spectrum, while its absolute configuration was tentatively determined in view of the biogenetic and biosynthetic relationships between 1 and 2. Compounds 3⁻4, originally as an inseparable mixture, were successfully isolated after chemical modifications. The stereo-chemistries of compounds 3⁻4 were assumed by comparison of 13C NMR with those of the similar moiety reported in literature, in addition to the biogenetic and biosynthetic relationships with 1. The plausible biosynthetic relationships among these four C9 metabolites were supposed. Biologically, compounds 1⁻4 showed no cytotoxic effect against HeLa cell line at concentrations up to 25 μg/mL, while 1 exhibited moderate antifouling activity against the settlement of Balanus amphitrite larvae with IC50 being 12.8 μg/mL and LC50 > 25 μg/mL. The co-occurrence of macrolides gliomasolides A—E and four C9 metabolites in the same fermentation culture made us assume that these C9 metabolites might be biosynthetic building blocks toward the construction of more complex macrolides such as gliomasolides A—E or other unidentified polyketides.

Amino-acid- and peptide-directed synthesis of chiral plasmonic gold nanoparticles.

Understanding chirality, or handedness, in molecules is important because of the enantioselectivity that is observed in many biochemical reactions 1 , and because of the recent development of chiral metamaterials with exceptional light-manipulating capabilities, such as polarization control2-4, a negative refractive index 5 and chiral sensing 6 . Chiral nanostructures have been produced using nanofabrication techniques such as lithography 7 and molecular self-assembly8-11, but large-scale and simple fabrication methods for three-dimensional chiral structures remain a challenge. In this regard, chirality transfer represents a simpler and more efficient method for controlling chiral morphology12-18. Although a few studies18,19 have described the transfer of molecular chirality into micrometre-sized helical ceramic crystals, this technique has yet to be implemented for metal nanoparticles with sizes of hundreds of nanometres. Here we develop a strategy for synthesizing chiral gold nanoparticles that involves using amino acids and peptides to control the optical activity, handedness and chiral plasmonic resonance of the nanoparticles. The key requirement for achieving such chiral structures is the formation of high-Miller-index surfaces ({hkl}, h ≠ k ≠ l ≠ 0) that are intrinsically chiral, owing to the presence of 'kink' sites20-22 in the nanoparticles during growth. The presence of chiral components at the inorganic surface of the nanoparticles and in the amino acids and peptides results in enantioselective interactions at the interface between these elements; these interactions lead to asymmetric evolution of the nanoparticles and the formation of helicoid morphologies that consist of highly twisted chiral elements. The gold nanoparticles that we grow display strong chiral plasmonic optical activity (a dis-symmetry factor of 0.2), even when dispersed randomly in solution; this observation is supported by theoretical calculations and direct visualizations of macroscopic colour transformations. We anticipate that our strategy will aid in the rational design and fabrication of three-dimensional chiral nanostructures for use in plasmonic metamaterial applications.

Isolation and Absolute Configurations of Diversiform C17, C21 and C25 Terpenoids from the Marine Sponge Cacospongia sp.

Chemical investigation of MeOH extract of a South China Sea sponge Cacospongia sp. yielded 15 terpenoids belonging to three different skeleton-types, including the unusual C17 γ-lactone norditerpenoids (1⁻3), the rare C21 pyridine meroterpenoid (7), and the notable C25 manoalide-type sesterterpenoids (4⁻6, 8⁻10). Compounds 1⁻5 were initially obtained as enantiomers, and were further separated to be optically pure compounds (1a, 1b, 2a, 2b, 3a-r, 3b-r, 4a, 4b, 5a and 5b) by chiral HPLC, with a LiAlH4 reduction aid for 3. Compounds 3a/3b (a pair of inseparable enantiomers), 4a, 5a, 6, and 7 were identified as new compounds, while 1a/1b and 2a/2b were obtained from a natural source and were determined for their absolute configurations for the first time. This is also the first time to encounter enantiomers of the well-known manoalide-type sesterterpenoids from nature. The structures with absolute configurations of the new compounds were unambiguously determined by comprehensive methods including HR-ESI-MS and NMR data analysis, optical rotation comparison, experimental and calculated electronic circular dichroism (ECD), and Mo2(OAc)4 induced circular dichroism (ICD) methods. The cytotoxicity of the isolates against selected human tumor cell lines was evaluated, however, the tested compounds showed no activity against selected cell lines.

Raman optical activity of tetra-alanine in the poly(l-proline) II type peptide conformation.

The poly(l-proline) II (PPII) helix is considered to be a major conformation in disordered polypeptides and unfolded proteins in aqueous solution. The PPII conformation can be identified by using Raman optical activity (ROA), which measures the different intensities of right- and left-circularly polarized Raman scattered light from chiral molecules and provides information on stereochemistry associated with vibrational motions. In the present study, we used tetra-alanine (Ala4) as a model system, since its central amide bond adopts the PPII conformation. The predominance of the PPII conformation was supported by 11 ns molecular dynamics (MD) simulations at 300 K. The MD snapshots were used for subsequent quantum mechanical/molecular mechanical (QM/MM) calculations to compute the Raman and ROA spectra. The present MD + QM/MM analysis leads to a good agreement between the observed and simulated spectra, allowing us to assign most of the spectral features including the ROA band near 1320 cm-1, which has been used as a marker for the PPII conformation. This positive ROA band has three components. The lower frequency component near 1310 cm-1 arises from an internal peptide bond, whereas the higher frequency components around 1320-1335 cm-1 appear due to N- and C-terminal peptide groups. The MD + QM/MM calculations also reproduced the electronic circular dichroism spectra of Ala4. The present results provide a satisfactory framework for future investigations of unfolded/disordered proteins as well as peptides in solutions by chiral spectroscopic methods.

Multi-functionality Redefined with Colloidal Carotene Carbon Nanoparticles for Synchronized Chemical Imaging, Enriched Cellular Uptake and Therapy.

Typically, multiplexing high nanoparticle uptake, imaging, and therapy requires careful integration of three different functions of a multiscale molecular-particle assembly. Here, we present a simpler approach to multiplexing by utilizing one component of the system for multiple functions. Specifically, we successfully synthesized and characterized colloidal carotene carbon nanoparticle (C(3)-NP), in which a single functional molecule served a threefold purpose. First, the presence of carotene moieties promoted the passage of the particle through the cell membrane and into the cells. Second, the ligand acted as a potent detrimental moiety for cancer cells and, finally, the ligands produced optical contrast for robust microscopic detection in complex cellular environments. In comparative tests, C(3)-NP were found to provide effective intracellular delivery that enables both robust detection at cellular and tissue level and presents significant therapeutic potential without altering the mechanism of intracellular action of ß-carotene. Surface coating of C(3) with phospholipid was used to generate C(3)-Lipocoat nanoparticles with further improved function and biocompatibility, paving the path to eventual in vivo studies.

A new flavane acid from the fruits of Illicium verum.

A new compound, illiciumflavane acid (1), along with 13 known compounds (2-14), were isolated from the fruits of Illicium verum Hook. F. Their structures were elucidated through various spectroscopic methods, including 1D NMR ((1)H NMR, (13)C NMR), 2D NMR (HMQC, HMBC and NOESY) and HRMS. The stereochemistry at the chiral centres was determined using CD spectrum as well as analyses of coupling constants and optical rotation data. Cytotoxicity evaluation of four compounds showed that illiciumflavane acid and (E)-1,2-bis(4-methoxyphenyl)ethene exhibited potential against A549 activities with IC50 values of 4.63 µM and 9.17 µM, respectively.