Configuration Of Amino Acids Research Articles

Anti-MRSA actinomycins D1-D4 from the marine sponge-associated Streptomyces sp. LHW52447

Actinomycins D1−D4 (1–4), four new D-type actinomycin analogues, were isolated from the fermentation broth of a strain of marine sponge-associated Streptomyces sp. LHW52447, together with actinomycin D (5). The structures of 1−4 were determined by a combination analysis of HRMS and NMR spectroscopic methods, and their absolute configurations of amino acids were determined by Marfey's analysis. Actinomycins D1 (1) and D2 (2) are the first two naturally occurring actinomycins with incorporation an oxazole unit into the central phenoxazinone chromophore. Both 1 and 2 showed more potent antibacterial activities against three strains of pathogenic methicillin-resistant Staphylococcus aureus (MRSA) with MIC values of 0.125–0.25 μg/mL than those of 3−5 with MIC values of 0.5–1.0 μg/mL, which suggested that the anti-MRSA activity might be enhanced by the incorporation of an additional oxazole unit. In addition, the cytotoxicity evaluation against WI-38 human diploid lung fibroblasts revealed that the incorporation of oxazole unit could decrease the cytotoxicity of actinomycins on human normal cells.

Investigating the Clough, Lutz, and Jirgensons Rule for the pH Dependence of Optical Rotation of Amino Acids

Students in an upper-level physical chemistry course used a polarimeter to measure the molar optical rotation of different optically active amino acids to confirm the Clough, Lutz, and Jirgensons (CLJ) rule. This rule states that an amino acid is in the l-configuration if the molar optical rotation becomes more positive upon the addition of acid or the acid is of the d-configuration if the optical rotation becomes more negative in an acidified solution. Students demonstrated this rule for known configurations of amino acids and then applied this rule to determine the configuration of an amino acid with an unknown configuration.

Structures and Activities of Tiahuramides A-C, Cyclic Depsipeptides from a Tahitian Collection of the Marine Cyanobacterium Lyngbya majuscula.

The structures of three new cyclic depsipeptides, tiahuramides A (1), B (2), and C (3), from a French Polynesian collection of the marine cyanobacterium Lyngbya majuscula are described. The planar structures of these compounds were established by a combination of mass spectrometry and 1D and 2D NMR experiments. Absolute configurations of natural and nonproteinogenic amino acids were determined through a combination of acid hydrolysis, derivitization with Marfey's reagent, and HPLC. The absolute configuration of hydroxy acids was confirmed by Mosher's method. The antibacterial activities of tiahuramides against three marine bacteria were evaluated. Compound 3 was the most active compound of the series, with an MIC of 6.7 μM on one of the three tested bacteria. The three peptides inhibit the first cell division of sea urchin fertilized eggs with IC50 values in the range from 3.9 to 11 μM. Tiahuramide B (2), the most potent compound, causes cellular alteration characteristics of apoptotic cells, blebbing, DNA condensation, and fragmentation, already at the first egg cleavage. The cytotoxic activity of compounds 1-3 was tested in SH-SY5Y human neuroblastoma cells. Compounds 2 and 3 showed an IC50 of 14 and 6.0 μM, respectively, whereas compound 1 displayed no toxicity in this cell line at 100 μM. To determine the type of cell death induced by tiahuramide C (3), SH-SY5Y cells were costained with annexin V-FITC and propidium iodide and analyzed by flow cytometry. The double staining indicated that the cytotoxicity of compound 3 in this cell line is produced by necrosis.

Anticancer Gold(III) Peptidomimetics: From Synthesis to in vitro and ex vivo Biological Evaluations

Five new AuIII -peptidodithiocarbamato complexes of the type [AuIII Br2 (dtc-AA1 -AA2 -OR] (in which AA1 =N-methylglycine (Sar), l/d-Pro; AA2 =l/d-Ala, α-aminoisobutyric acid (Aib); R=OtBu, triethylene glycol methyl ether), differing with regard to the amino acid sequence and/or the chiral amino acid configuration, were designed to enhance tumor selectivity and bioavailability. The gold(III)-based moiety was functionalized to exploit the targeting properties of the peptidomimetic ligand toward two peptide transporters (namely PEPT1 and PEPT2), which are upregulated in several tumor cells. The compounds were synthesized and fully characterized, mainly by means of elemental analysis, one- and two-dimensional NMR spectroscopy, FT-IR, and UV/Vis spectrophotometry. The crystal structures of three compounds were also solved by X-ray diffraction. In vitro cytotoxicity studies using a panel of human tumor cell lines (A549 [non-small-cell lung carcinoma], MCF-7 [breast cancer], A2780 [ovarian carcinoma], H1975 [non-small-cell lung carcinoma], H460 [large-cell lung carcinoma], and A431 [human epidermoid carcinoma]) showed the dtc-Pro-Aib-OtBu derivative to be very effective, with GI50 values much lower than those of cisplatin. This complex was thus selected for evaluating stability under physiological conditions and possible interactions with serum albumin, as well in PARP-1 enzyme inhibition assays and preliminary ex vivo toxicity experiments on healthy rat tissues.

Cystargamide B, a cyclic lipodepsipeptide with protease inhibitory activity from Streptomyces sp.

We identified a new cyclic lipodepsipeptide, cystargamide B (1), from the mycelial extract of a Kaempferia galanga rhizome-derived actinomycete strain, Streptomyces sp. PB013. The planar structure was elucidated based on high resolution fast-atom bombardment mass spectrometry (HRFABMS) spectroscopy and one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopic data. The absolute configurations of the constituent amino acids were determined using advanced Marfey's method. Cystargamide B (1) includes rare structural units: a 5-hydroxytryptophan residue and a 2,3-epoxy fatty acid side chain. Notably, cystargamide B (1) inhibited the protease activity of the NS2B/NS3 complex from dengue virus.

Trichodermides A-E: New Peptaibols Isolated from the Australian Termite Nest-Derived Fungus Trichoderma virens CMB-TN16.

Chemical analysis of a fermentation of the Australian termite nest-derived fungus Trichoderma virens CMB-TN16 yielded five new acyclic nonapeptides, trichodermides A-E (1-5). Amino acid residues, configurations, and sequences were determined by a combination of spectroscopic (NMR and MS-MS) and chemical (C3 Marfey's) methods. The trichodermides adhere to the sequence homology pattern common to Trichoderma 11 amino acid residue peptaibols; however, unlike other peptaibols the trichodermides do not exhibit antibacterial or antifungal activity and exhibit low to no cytotoxicity against mammalian cells. This variability in biological activity highlights the importance of knowing both planar structures and absolute configurations when interpreting structure-activity relationships.

Influence of solvent polarity on the separation of leucine enantiomers by β-cyclodextrin: a molecular mechanics and dynamics simulation

The interaction between leucine and β-cyclodextrin with different solvents was studied by molecular mechanics and dynamics simulations. In order to analyse the influence of the solvent polarity on the inclusion complex formation and separation process of leucine enantiomers by β-cyclodextrin, the organic modifiers were characterised by the same value of dielectric constant in the electrostatic contribution to the interaction energy, and a different molecular configuration of amino acids (neutral or zwitterion). The complexes formed in polar solvents were more stable than those in non-polar solvents with the same dielectric constant, because the electrostatic contribution is negative for the former and positive for the latter. The optimized structures obtained for leucine enantiomers and β-cyclodextrin in vacuo are non-inclusion complexes. The solvent polarity contributes to increasing the probability of the presence in an inner position for the guest, whereas the results for non-polar configurations were smaller and distributed in larger areas. The regions where the enantiomers spend more time in the simulation correspond to locations with greater chiral discrimination. d-Leu was the first eluted enantiomer in every case, except for a polar solvent with ε=26.

Cyclic Hexapeptide Dimers, Antatollamides A and B, from the Ascidian Didemnum molle. A Tryptophan-Derived Auxiliary for l- and d-Amino Acid Assignments.

Two dimerized cyclic hexapeptides, antatollamides A (1) and B (2), were isolated from the colonial ascidian Didemnum molle collected in Pohnpei. The amino acid compositions and sequences were determined by interpretation of MS and 1D and 2D NMR data. Raney Ni reduction of antatollamide A cleaved the dimer to the corresponding monomeric cyclic hexapeptide with replacement of Cys by Ala. The amino acid configuration of 1 was established, after total hydrolysis, by derivatization with a new chiral reagent, (5-fluoro-2,4-dinitrophenyl)-Nα-l-tryptophanamide (FDTA), prepared from l-Trp, followed by LCMS analysis; all amino acids were found to be l-configured except for d-Ala.

Adsorption patterns of aromatic amino acids on monolayer MoS2 and Au-modified MoS2 surfaces: A first-principles study

As a pioneering non-graphene material, two dimensional, single-layered molybdenum disulfide (MoS2) has achieved outstanding performance in biosensor research in recent years. However, either reliable exploitation of bio-applications or keeping eyes on biological safety requires clear understanding of the linkage between the MoS2 surface and the biological elementary blocks, such as amino acids. In this manuscript, first-principles density functional theory (DFT) was employed to investigate the adsorption behaviors of aromatic amino acids, phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp), on monolayer pristine MoS2 and Au-modified MoS2 surfaces. Optimal adsorption configurations of amino acids on different surfaces were predicted by adsorption energy calculation. The calculations indicate that three amino acids can be physically adsorbed on pristine MoS2 surface by parallel interaction between the aromatic ring and surface S atoms, which is consistent with previous work. On the Au-modified surface, amino acids demonstrate a coexistence of chemisorption and physisorption through covalent linkage to Au atom and no-covalent interaction to the sheet respectively. And the adsorption energies are almost twice as large as that of on a pure MoS2 surface. Yet there is a same adsorption ability order Trp>Tyr>Phe on both surfaces. By comparing changes in molecular geometry before and after adsorption, it is found that the structure influences of amino acids induced from both surfaces adsorption are limited. The DOS and PDOS analysis show that amino acids adsorption can modify the electronic properties of substrates through π-p interaction and other electronic interactions. Especially, amino acids with Au linker can transform p-type semiconductor of MoS2 into a n-type one. Our calculations clarify the sensitivity of intrinsic MoS2 and Au-modified MoS2 surfaces to Phe, Tyr and Trp in a waterless environment and demonstrate their fleshed-out interaction patterns. The results provide a first-hand theoretical reference for their potential bio-nanotechnical applications of both MoS2 and Au-modified MoS2 materials.

Control of Helical Chirality of Ferrocene-Dipeptide Conjugates by the Secondary Structure of Dipeptide Chains.

Controlling helical chirality and creating protein secondary structures in cyclic/acyclic ferrocene-dipeptide bioorganometallic conjugates were achieved by adjusting the conformational flexibility of the dipeptide chains. In systems reported to date, the helical chirality of a conjugate was determined by the absolute configuration of the adjacent amino acid reside. In contrast, it was possible to induce both M- and P-helical chirality, even when the configuration of the adjacent amino acid was the same. It is particularly interesting to note that M-helical chirality was produced in a cyclic ferrocene-dipeptide conjugate composed of the l-Ala-d-Pro-cystamine-d-Pro-l-Ala dipeptide sequence (1), in which a type II β-turn-like secondary structure was established.

Amino Acid Interaction (INTAA) web server.

Large biomolecules—proteins and nucleic acids—are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein–DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein–DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid–deoxyribonucleotide pairs found at the protein–DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations.

Talarolide A, a Cyclic Heptapeptide Hydroxamate from an Australian Marine Tunicate-Associated Fungus, Talaromyces sp. (CMB-TU011).

A miniaturized 24-well plate microbioreactor approach was used to explore secondary metabolite media dependence in an Australian marine tunicate-associated fungus, Talaromyces sp. (CMB TU011). Detailed chemical investigations of an antifungal M1-saline cultivation yielded talarolide A (1), only the second reported natural cyclic peptide hydroxamate, and the first from a fungus. The antifungal properties of the M1-saline extract were attributed to the known diterpene glycoside sordarin (2). Structure elucidation of 1 and 2 was achieved by detailed spectroscopic analysis, with amino acid configurations in 1 assigned by the C3 and C18 Marfey's methods, and l-Ala and d-Ala regiochemistry by the recently reported 2D C3 Marfey's method.

Biomimetic Chirality Sensing with Pyridoxal-5'-phosphate.

Pyridoxal-5'-phosphate (PLP) is introduced to a biomimetic indicator displacement assay for simultaneous determination of the absolute configuration, enantiomeric composition and concentration of unprotected amino acids, amino alcohols and amines. The chiroptical assay is based on fast imine metathesis with a PLP aryl imine probe to capture the target compound for circular dichroism and fluorescence sensing analysis. The substrate binding yields characteristic Cotton effects that provide information about the target compound ee and the synchronous release of the indicator results in a nonenantioselective off-on fluorescence response that is independent of the enantiomeric sample composition and readily correlated to the total analyte concentration.

Enantioselective Fluorescent Imaging of Free Amino Acids in Living Cells.

1,1'-Spirobiindane-7,7'-diol (SPINOL)-based chiral aldehydes (R)- and (S)-3, in combination with Zn2+ , are highly enantioselective fluorescent sensors for structurally diverse chiral amino acids. Application of this enantiomeric sensor pair in HeLa cells containing a free amino acid shows that the chirality-matched sensor-amino acid interaction leads to strong blue emission and chirality mismatch gives only weak fluorescence. This allows a quick determination of the chiral configuration of the free amino acid in the cells. It represents the first enantioselective fluorescent imaging of free amino acids in living cells.

Prevalence of TEM, SHV, and CTX-M Beta-Lactamase genes in the urinary isolates of a tertiary care hospital.

Introduction:Extended-spectrum beta-lactamases (ESBLs) are the major cause of resistance to beta-lactam antibiotics such as penicillins, cephalosporins, and monobactams. They are derived from the narrow-spectrum beta-lactamases (TEM-1, TEM-2, or SHV-1) by mutations that alter the amino acid configuration around the enzyme active site.Aim:To determine the prevalence of ESBL (blaTEM, blaCTX-M, and blaSHV) genes among the members of Enterobacteriaceae.Methodology:The present prospective study was carried out from January 2015 to June 2015 in the Department of Microbiology and Molecular Medicine of a Teaching Tertiary Care Hospital. A total of 526 urine samples were studied. Seventy-eight isolates were subjected to polymerase chain reaction for detection of ESBL genes.Results:In our study, ESBL genes were detected among 18 (45%) phenotypically confirmed ESBL producers and 20 (52.5%) phenotypically confirmed non-ESBL producers. The gene that predominated was blaTEM (48.7%), followed by blaCTX-M (7.6%) and blaSHV (5.1%).Conclusion:Definitive identification of ESBL genes is only possible by molecular detection methods. Phenotypic tests need to be evaluated periodically as their performance may change with the introduction of new enzymes.

Solid-Phase Synthesis of Cyclic Depsipeptides Containing a Tyrosine Phenyl Ester Bond.

The first solid-phase strategy for the synthesis of cyclic depsipeptides containing a phenyl ester linkage in their structure is described. The key steps of the synthesis were the formation of the phenyl ester bond and the on-resin head-to-side-chain cyclization. The amino acid configuration significantly influenced the formation and the stability of the cyclic depsipeptides. The presence of a l-Tyr(1) and a d-Tyr(7) led to the most stable sequences.

Chilenopeptins A and B, Peptaibols from the Chilean Sepedonium aff. chalcipori KSH 883.

The Chilean Sepedonium aff. chalcipori strain KSH 883, isolated from the endemic Boletus loyo Philippi, was studied in a polythetic approach based on chemical, molecular, and biological data. A taxonomic study of the strain using molecular data of the ITS, EF1-α, and RPB2 barcoding genes confirmed the position of the isolated strain within the S.chalcipori clade, but also suggested the separation of this clade into three different species. Two new linear 15-residue peptaibols, named chilenopeptins A (1) and B (2), together with the known peptaibols tylopeptins A (3) and B (4) were isolated from the semisolid culture of strain KSH 883. The structures of 1 and 2 were elucidated on the basis of HRESIMS(n) experiments in conjunction with comprehensive 1D and 2D NMR analysis. Thus, the sequence of chilenopeptin A (1) was identified as Ac-Aib(1)-Ser(2)-Trp(3)-Aib(4)-Pro(5)-Leu(6)-Aib(7)-Aib(8)-Gln(9)-Aib(10)-Aib(11)-Gln(12)-Aib(13)-Leu(14)-Pheol(15), while chilenopeptin B (2) differs from 1 by the replacement of Trp(3) by Phe(3). Additionally, the total synthesis of 1 and 2 was accomplished by a solid-phase approach, confirming the absolute configuration of all chiral amino acids as l. Both the chilenopeptins (1 and 2) and tylopeptins (3 and 4) were evaluated for their potential to inhibit the growth of phytopathogenic organisms.

Synthesis, biological evaluation and structural analysis of novel peripherally active morphiceptin analogs

Morphiceptin (Tyr-Pro-Phe-Pro-NH2), a tetrapeptide amide, is a selective ligand of the μ-opioid receptor (MOR). This study reports the synthesis and biological evaluation of a series of novel morphiceptin analogs modified in positions 2 or/and 4 by introduction of 4,4-difluoroproline (F2Pro) in l or d configuration. Depending on the fluorinated amino acid configuration and its position in the sequence, new analogs behaved as selective full MOR agonists showing high, moderate, or relatively low potency. The most potent analog, Tyr-F2Pro-Phe-d-F2Pro-NH2, was also able to activate the κ-opioid receptor (KOR), although with low potency. Docking studies and the comparison of results with the high resolution crystallographic structure of a MOR-agonist complex revealed possible structure–activity relationships of this compound family.

Iminolactones as tools for inversion of the absolute configuration of α-amino acids and as inhibitors of cancer cell proliferation

A library of iminolactones was prepared by esterification of several 2-hydroxyketones with a number of N-protected d- and l-α-amino acids. Some of the hydroxyketones were of terpenoid origin while others were obtained via synthesis. After N-deprotection of the intermediate esters, the free amines spontaneously underwent condensation with the ketone to form iminolactones. Esters of (1S,2S,5S)-2-hydroxypinan-3-one with both d- and l-α-amino acids were partially epimerized at the α-carbon atom to give a diastereomeric ester mixture. Only iminolactones of l-amino acids were formed after cyclization of (1S,2S,5S)-2-hydroxypinan-3-one, and correspondingly only d-amino acid iminolactones were formed after reaction with (1R,2R,5R)-2-hydroxypinan-3-one. The protocol thus enables inversion of the absolute configuration of amino acids. Some members of the prepared library of iminolactones displayed significant anti-proliferative effects toward three cancer cell lines (EL4, MCF7, PC3) with insignificant effect on non-malign cell lines (McCoy, MCF10A, NIH3T3). Thus, iminolactones appear to be potential lead structures for preparation of drugs selectively affecting proliferation of malign cell lines.

Synthetic strategy for bicyclic tetrapeptides HDAC inhibitors using ring closing metathesis

Cyclic peptides show diverse biological activities and are considered as good therapeutic agents due to structural rigidity, receptor selectivity and biochemical stability. We have developed bicyclic tetrapeptide HDAC inhibitors based on different cyclic tetrapeptide scaffolds. For the synthesis of these bicyclic tetrapeptides, two cyclization steps, namely, peptide cyclization and fusion of aliphatic side chains by ring closing metathesis (RCM) were involved. In the course of these syntheses, we have established two facts: a lower limit of aliphatic loop length and better synthetic route for bicyclic tetrapeptide synthesis. It was found that nine methylene loop length is the lower limit for aliphatic loop and the synthetic route selection depended on the configuration of amino acids in the cyclic tetrapeptide scaffold. RCM followed by peptide cyclization was the proper route for LDLD configuration and the reverse route was suitable for LLLD configuration. Nine methylene units is the lower limit for aliphatic loop length and the synthetic route selection depends on the configuration of amino acids in the cyclic tetrapeptide scaffold. RCM followed by peptide cyclization is the proper route for LDLD configuration and reverse route for LLLD configuration.