Sequence-specific targeting of Caenorhabditis elegans C-Ala to the D-loop of tRNAAla.

Alanyl-tRNA synthetase retains a conserved prototype structure throughout its biology. Nevertheless, its C-terminal domain (C-Ala) is highly diverged and has been shown to play a role in either tRNA or DNA binding. Interestingly, we discovered that Caenorhabditis elegans cytoplasmic C-Ala (Ce-C-Alac) robustly binds both ligands. How Ce-C-Alac targets its cognate tRNA and whether a similar feature is conserved in its mitochondrial counterpart remain elusive. We show that the N- and C-terminal subdomains of Ce-C-Alac are responsible for DNA and tRNA binding, respectively. Ce-C-Alac specifically recognized the conserved invariant base G18 in the D-loop of tRNAAla through a highly conserved lysine residue, K934. Despite bearing little resemblance to other C-Ala domains, C. elegans mitochondrial C-Ala robustly bound both tRNAAla and DNA and maintained targeting specificity for the D-loop of its cognate tRNA. This study uncovers the underlying mechanism of how C. elegans C-Ala specifically targets the D-loop of tRNAAla.

Consequences of incorporating thiaproline and its oxidized derivatives into collagen triple helices.

(2R)-4-thiaproline (Thp) is an analog of proline, replacing Cγ in the pyrrolidine ring with sulfur. Its thiazolidine ring easily interconverts between endo and exo puckers due to a small energy barrier, which leads to destabilize polyproline helices. Collagen, composed of three polyproline II helices, mainly consists of X-Y-Gly triplets, where X is often proline and Y is frequently (2S,4R)-hydroxyproline. In this study, we incorporated Thp into either position-X or position-Y to investigate the consequences of such a replacement on the triple helix. Circular dichroism and differential scanning calorimetry analyses showed that the Thp-containing collagen-mimetic peptides (CMPs) can fold into stable triple helices, in which the substitution at position-Y exhibits a larger destabilization effect. Additionally, we also prepared the derivative peptides by oxidizing Thp in the peptide to N-formyl-cysteine or S,S-dioxide Thp. The results showed that the oxidized derivatives at position-X only slightly affect collagen stability, but those at position-Y induce a large destabilization effect. The consequences of incorporating Thp and its oxidized derivatives into CMPs are position dependent. Computational results suggested that the ease of interconversion between exo and endo puckers for Thp and the twist conformation of S,S-dioxide Thp may cause the destabilization effect at position-Y. We have revealed new insights into the impacts of Thp and its oxidized derivatives on collagen and demonstrated that Thp can be used to design collagen-related biomaterials.

Design and synthesis of fluorinated peptides for analysis of fluorous effects on the interconversion of polyproline helices.

The unique interaction between fluorine atoms has been exploited to alter protein structures and to develop synthetic and analytical applications. To expand such fluorous interaction for novel applications, polyproline peptides represent an excellent molecular nanoscaffold for controlling the presentation of perfluoroalkyl groups on their unique secondary structure. We develop approaches to synthesis fluorinated peptides to systematically investigate how the number, location and types of the fluorous groups on polyproline affect the conformation by monitoring the transition between the two major polyproline structures PPI and PPII. This work provides valuable information on how fluorous interaction affects the peptide structure and also benefits the design of functional fluorous molecules.

Modulating the Stability of Collagen Triple Helices by Terminal Charged Residues.

Cationic or anionic residues are frequently located at the termini of proteins because their charged side chain can form electrostatic interactions with a terminal carboxylate or ammonium group to stabilize the structure under physiological conditions. Here, we used collagen-mimetic peptides (CMPs) to examine how the terminal charge-charge interactions affect the collagen triple helix stability. We designed a series of CMPs with either a Lys or Glu incorporated into the terminus and measured their pH-dependent stability. The results showed that the terminal electrostatic attractions stabilized the triple helix, while the terminal electrostatic repulsions destabilized the trimer. The data also revealed that the repulsions imposed a greater effect than did the attractions on the triple helix. An amino acid with a shorter side chain, such as aspartate and ornithine, was also installed to investigate the length effect on electrostatic interactions, which was found to be insignificant. Meanwhile, simultaneously incorporating cationic and anionic residues into the termini showed slight additive stabilization effects but pronounced additive destabilization consequences. We have demonstrated that the collagen triple helix stability can be modulated by introducing a cationic or anionic residue into the terminus of a peptide, giving useful information for the design of collagen-associated materials.

Leucettamine B analogs and their carborane derivative as potential anti-cancer agents: Design, synthesis, and biological evaluation.

Leucettamine B is a natural product found in marine sponge Leucetta microraphis. Several of analogs of its family, such as aplysinopsine and clathridine, are medicinally active molecules which have applications in many pharmaceuticals and healthcare products; however, thus far, leucettamine B has not been studied. In this report, we describe the synthesis of a new class of analogs of leucettamine B obtained by Knoevenagel condensation using a microwave reactor. The 25 newly synthesized compounds were tested against MDA-MB-468, SW480, and Mahlavu cell lines for anticancer activity. Among them, the carborane-based compound (Z)-5-(benzo[d][1,3]dioxol-5-ylmethylene)-3-(1-closo-carboranyl)-2-thioxo -thiazolidin-4-one (49) and (Z)-5-(benzo[d][1,3]dioxol-5-ylmethylene)-3-(2-(pyrrolidin-1-yl)ethyl)-2-thioxothiazolidin-4-one (31) derivatives were found to have the most potential for use against tumor cells. The carborane derivative 49 had the lowest IC50 value against the SW480 cell line (4.7 µM) and the Mahlavu (6.6 µM) cell line. Furthermore, compound 31 also had a low IC50 value against SW480 (7.5 µM). Our research shows that leucettamine B analogs might have potential for use in cancer chemotherapy.

Conjugating Catalytic Polyproline Fragments with a Self-Assembling Peptide Produces Efficient Artificial Hydrolases.

A polyproline fragment containing a catalytic dyad of His-His or Ser-His was coupled with a self-assembling peptide MAX1 to design new hydrolases (H2H5 and H2S5) for catalyzing ester hydrolysis. Circular dichroism measurements indicated that the peptides change their conformation from random coils to ß-sheets when pH increases from 5 to 10. IR spectra also displayed the vibration modes corresponding to their ß-structures at pH 9.0. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) measurements showed that in solution, the designed peptides self-assemble into network fibrils having a significantly increased catalytic efficiency on ester hydrolysis. On p-nitrophenyl acetate (p-NPA) substrate, the designed peptides exhibit high catalytic efficiency at pH 9.0 (kcat/KM = 12.1 M-1 s-1 for H2H5, 13.3 M-1 s-1 for H2S5), and their efficiency is even better at pH 10.0 (kcat/KM = 24.3 M-1 s-1 for H2H5, 99.4 M-1 s-1 for H2S5). Additionally, H2H5 and H2S5 also display good activity on catalyzing the hydrolysis of p-nitrophenyl-(2-phenyl)-propanoate (p-NPP) and p-nitrophenyl methoxyacetate (p-NPMA). Combining the polyproline-based catalytic scaffold with a self-assembling peptide generates an efficient hydrolase, providing a new design for effective artificial enzymes.

Investigation of the cis-trans structures and isomerization of oligoprolines by using Raman spectroscopy and density functional theory calculations: solute-solvent interactions and effects of terminal positively charged amino acid residues.

Using low-wavenumber Raman spectroscopy in combination with theoretical calculations via solid-state density functional theory (DFT)-D3, we studied the vibrational structures and interaction with solvent of poly-l-proline and the oligoproline P12 series. The P12 series includes P12, the positively charged amino acid residue (arginine and lysine) N-terminus proline oligomers RP11 and KP11, and the C-terminus P11R and P11K. We assigned the spring-type phonon mode to 74-76 cm-1 bands for the PPI and PPII conformers and the carbonyl group ring-opening mode 122 cm-1 in the PPI conformer of poly-l-proline. Amide I and II were assigned based on the results of mode analysis for O, N, and C atom displacements. The broad band feature of the H-bond transverse mode in the Raman spectra indicates that the positively charged proline oligomers PPII form H-bonds with water in the solid phase, whereas P12 is relatively more hydrophobic. In propanol, the PPI conformer of the P12 series forms less H-bond network with the solvent. The PPII conformer exhibits a distinct Raman band at 310 cm-1, whereas the PPI has bands at 365, 660, and 960 cm-1 with reasonable intensity that can be used to quantitatively determine these two conformational forms. The 365 cm-1 mode comprising the motion of a C[double bond, length as m-dash]O group turning to the helix axis was used to monitor the isomerization reaction PPI ↔ PPII. In pure propanol, RP11 and KP11 were found to have mostly PPI present, but P11R and P11K preferred PPII. After adding 20% water, the PPI in P11R and P11K was completely converted to PPII, whereas a small fraction of PPI remained in RP11 and KP11. The substituted positively charged amino acid affected the balance of the PPI/PPII population ratio.

Artificial peptide-controlled protein release of Zn2+-triggered, self-assembled histidine-tagged protein microparticle.

Protein microparticles have received attention as drug delivery systems because of their high protein stability and prolonged release in vivo. However, most current preparation processes introduce chemical crosslinkers, which often lead to protein inactivation and limit drug efficacy in delivery systems. In this study, we employed the well-known hexahistidine (His)-tag recombinant protein technology and a metal-triggerable collagen-mimetic peptide to enhance the binding strength between the protein and metal ion and fine-tuned the protein drug release. His-tagged proteins self-assembled to form microparticles (∼2 µm) upon zinc ion treatment and sustained protein drug release was achieved in physiological saline. The results also indicated that by adjusting the peptide concentration and N- and C-terminal hexahistidine-tags, protein release could be controlled. Moreover, no protein denaturation was observed. We developed a universal strategy for facile protein microparticle fabrication under mild conditions and we demonstrated its potential as a therapeutics formulation with tunable protein release.

Design and Synthesis of Benzimidazole-Chalcone Derivatives as Potential Anticancer Agents.

Numerous reports have shown that conjugated benzimidazole derivatives possess various kinds of biological activities, including anticancer properties. In this report, we designed and synthesized 24 new molecules comprising a benzimidazole ring, arene, and alkyl chain-bearing cyclic moieties. The results showed that the N-substituted benzimidazole derivatives bearing an alkyl chain and a nitrogen-containing 5- or 6-membered ring enhanced the cytotoxic effects on human breast adenocarcinoma (MCF-7) and human ovarian carcinoma (OVCAR-3) cell lines. Among the 24 synthesized compounds, (2E)-1-(1-(3-morpholinopropyl)-1H-benzimidazol-2 -yl)-3-phenyl-2-propen-1-one) (23a) reduced the proliferation of MCF-7 and OVCAR-3 cell lines demonstrating superior outcomes to those of cisplatin.

Synthesis, Isolation, and Characterization of Mono- and Bis-norbornene-Annulated Biarylamines through Pseudo-Catellani Intermediates.

A palladium-catalyzed C-H functionalization of an external ring of N-acyl 2-aminobiaryl with bicyclo[2.2.1]hept-2-ene (norbornene) via multiple C-H bond activations was developed. This study is the first report of the formation of bis-norbornene annulated biarylamines isomers ( syn-3a'/ anti-3a' = 36:64) from multiple C-H bond functionalizations. Additionally, nondirected C-H bond functionalization at the C-4' position with alkenes rendered complete C-H functionalization of five C-H bonds that formed a stable hexasubstituted benzene ring.

Impacts of the Terminal Charged Residues on Polyproline Conformation.

Cis-trans isomerization of proline is involved in various biological processes, such as protein folding, cell signaling, and ion-channel gating. Polyproline is a useful system for better understanding proline isomerization because it exists predominantly as two forms, all-cis polyproline I (PPI) and all-trans polyproline II (PPII) helices. The stability of PPI and PPII can be modulated by various effects, including aromatic-proline interactions, terminal charges, and stereoelectronic effects. Here, we used a series of oligoproline peptides in which positively charged or negatively charged amino acids were incorporated into the termini to investigate their effects on polyproline conformation. Circular dichroism measurements show that a cationic residue at the C-terminus or an anionic residue at the N-terminus increases the stability of a PPII helix; in particular, the C-terminal cationic residues impose an enormous impact on PPII stability. The electrostatic attractions between a cationic sidechain and the C-terminal carboxylate exhibit a greater effect than those between an anionic sidechain and the N-terminal ammonium on the conversion of PPII to PPI, suggesting that the stabilization effect of electrostatic interactions on PPII is directional. In contrast, incorporating a cationic residue seems more favorable than adding an anionic residue into the N-terminus because the cationic residue can stabilize PPI. Moreover, the predicted dipole moments from optimized oligopeptide models reveal that the macrodipole of the peptides with a cationic residue at the C-terminus exhibits the opposite direction to that of other peptides in the PPI conformation, suggesting that such a dipole distortion may cause these peptides to disfavor PPI helices. Together, we have found that the introduction of terminal electrostatic interactions can have a significant effect on PPII stability, providing useful information to the design of polyproline-based scaffolds for biomedical applications.

Strategy and Effects of Polyproline Peptide Stapling by Copper(I)-Catalyzed Alkyne-Azide Cycloaddition Reaction.

Polyproline is a unique type of peptide that has a stable, robust, and well-defined helical structure in an aqueous environment. These features have allowed polyproline to be used as a nanosized scaffold for applications in chemical biology and related fields. To understand its structural properties and to expand the applications, this secondary structure was tested systematically by stapling the peptide at different locations with staples of various lengths. Using the efficient copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC), we successfully prepared stapled polyproline and investigated the impact of this peptide macrocyclization through circular dichroism analysis. Whereas the stapling seems to have no significant effect on polyproline helix II (PPII) conformation in water, the location and the length of the staple affect the transformation of conformation in n-propanol. These results provide valuable information for future research using peptide stapling to manipulate polyproline conformation for various applications.

Zinc(II)-Histidine Induced Collagen Peptide Assemblies: Morphology Modulation and Hydrolytic Catalysis Evaluation.

Collagen-related materials have many potential biomedical applications because of their high biocompatibility and biodegradability. Designed collagen-mimetic peptides (CMPs) could self-assemble into supramolecular structures via a variety of interactions. In particular, metal-ligand interactions can induce microscale sizes of collagen assemblies. Our previous study also successfully applied metal-histidine coordination method to promote the self-assembly of CMPs into micrometers of constructs. In an effort to broaden the metal-induced strategies on assembling designed CMPs and explore the new insights into their assembly process, herein we designed and synthesized a series of short CMPs with one or more histidine residues incorporated into the peptides and used Zn(II) to induce the formation of collagen assembled microstructures. By altering the location and the number of histidine residues, we found that the assembly rate was significantly affected as well as the morphology of the assembled architectures. The CMPs containing terminal histidine residues were found to assemble into less ordered granulated and spherical microstructures while that with only one single histidine in its middle site could form pinwheel or floret-like constructs, showing that we could modulate the morphology of collagen assemblies by changing the location and number of Zn(II)-His coordination sites. Additionally, these CMPs also exhibited catalytic activities on ester hydrolysis in the presence of Zn(II) ions, which suggested that Zn(II)-CMP assemblies could be potentially applied to the development of artificial enzymes.

NADH/NADPH bi-cofactor-utilizing and thermoactive ketol-acid reductoisomerase from Sulfolobus acidocaldarius.

Ketol-acid reductoisomerase (KARI) is a bifunctional enzyme in the second step of branched-chain amino acids biosynthetic pathway. Most KARIs prefer NADPH as a cofactor. However, KARI with a preference for NADH is desirable in industrial applications including anaerobic fermentation for the production of branched-chain amino acids or biofuels. Here, we characterize a thermoacidophilic archaeal Sac-KARI from Sulfolobus acidocaldarius and present its crystal structure at a 1.75-Å resolution. By comparison with other holo-KARI structures, one sulphate ion is observed in each binding site for the 2'-phosphate of NADPH, implicating its NADPH preference. Sac-KARI has very high affinity for NADPH and NADH, with K M values of 0.4 µM for NADPH and 6.0 µM for NADH, suggesting that both are good cofactors at low concentrations although NADPH is favoured over NADH. Furthermore, Sac-KARI can catalyze 2(S)-acetolactate (2S-AL) with either cofactor from 25 to 60 °C, but the enzyme has higher activity by using NADPH. In addition, the catalytic activity of Sac-KARI increases significantly with elevated temperatures and reaches an optimum at 60 °C. Bi-cofactor utilization and the thermoactivity of Sac-KARI make it a potential candidate for use in metabolic engineering or industrial applications under anaerobic or harsh conditions.

Chemopreventive Potential of Ethanolic Extracts of Luobuma Leaves (Apocynum venetum L.) in Androgen Insensitive Prostate Cancer.

Luobuma (Apocynum venetum L. (AVL)) is a popular beverage in Asia and has been reportedly to be associated with the bioactivities such as cardiotonic, diuretic, antioxidative, and antihypertensive. However, its biofunction as chemoprevention activity is seldom addressed. Herein, we aimed to characterize the anti-androgen-insensitive-prostate-cancer (anti-AIPC) bioactive compounds of Luobuma, and to investigate the associated molecular mechanisms. Activity-guided-fractionation (antioxidative activity and cell survivability) of Luobuma ethanolic extracts was performed to isolate and characterize the major bioactive compounds using Ultra Performance Liquid Chromatography (UPLC), Liquid Chromatography-Mass Spectrometry (LC-MS), and Nuclear Magnetic Resonance (NMR). Plant sterols (lupeol, stigamasterol and ß-sitosterol) and polyphenolics (isorhamnetin, kaempferol, and quercetin) were identified. Lupeol, a triterpene found in the fraction (F8) eluted by 10% ethyl acetate/90% hexane and accounted for 19.3% (w/w) of F8, inhibited the proliferation of PC3 cells. Both lupeol and F8 induced G2/M arrest, inhibition of ß-catenin signaling, regulation of apoptotic signal molecules (cytochrome c, Bcl-2, P53, and caspase 3 and 8), and suppression DNA repair enzyme expression (Uracil-DNA glycosylase (UNG)). To our knowledge, our study is the first report that lupeol inhibited the expression of UNG to elicit the cytotoxicity against androgen-insensitive-prostate-cancer cells. Collectively, Luobuma, which contains several antitumor bioactive compounds, holds the potential to be a dietary chemopreventive agent for prostate cancer.

Reductive Deamination by Benzyne for Deoxy Sugar Synthesis Through a Domino Reaction.

Benzyne was developed as a reducing agent in the key step of converting amino sugars and ketoses into deoxy sugars, which occur widely in natural products. Many deoxy sugars exhibit antibiotic and anticancer activities, and furthermore, they play essential biological roles. By treatment with CS2 and then Ac2O, amino sugars and ketoses were converted into the corresponding 1,3-thiazolidine-2-thiones. In the key step, these intermediates were treated with 2-trimethylsilylphenyl triflate (2.0 equiv.) and CsF (3.0 equiv.) in MeCN at 25 °C to produce acyclic enol acetates in 60-63 % yields. Saponification of the enol acetates with NaOMe/MeOH followed by intramolecular cyclization afforded the target 2-deoxy sugars. The key step of the reductive deamination involved a domino 1,2-elimination/[3+2]-cycloaddition/retro [3+2]-ring-opening sequence. The generality of this new method was proven by the use of various substrates, including pentoses, hexoses, monosaccharides, disaccharides, aldoses, and ketoses.

Formation of AAB-Type Collagen Heterotrimers from Designed Cationic and Aromatic Collagen-Mimetic Peptides: Evaluation of the C-Terminal Cation-π Interactions.

Most of natural collagens are heterotrimers composed of two (AAB) or three (ABC) different peptide chains, and thus heterotrimeric constructs are preferable to mimic natural collagens. Exploring the forces to assemble synthetic collagen-mimetic peptides (CMPs) into heterotrimers has been an attractive topic in preparing collagen-related biomaterials. Here we designed and synthesized two cationic CMPs (CR and CK) in which multiple Arg or Lys residues are installed in their C-terminal region, and one aromatic CMP (CF) whose C-terminal end contains multiple Phe residues. Circular dichroism and NMR spectroscopy showed that AAB-type heterotrimers could form in both CR-CF and CK-CF mixtures, suggesting that the C-terminal cation-π interactions between cationic and aromatic residues could serve as a nucleation force and substantially promote the folding of heterotrimers. In particular, only one major heterotrimeric fold was found in each mixture. For CR-CF mixtures, either the heterotrimer with two CR chains and one CF chain or that with one CR chain and two CF chains could form, depending on the molar ratios of CR to CF in solution. By contrast, in CK-CF mixtures only the heterotrimer consisting of two CK chains and one CF chain was found in solution even increasing the ratio of CF, implying that the heterotrimer composed of one CK chain and two CF chains is highly unstable. Additionally, differential scanning calorimetry analysis showed that the folding of these heterotrimers is governed by entropic effects. Together, our results provide a new design to prepare AAB-type collagen heterotrimers and reveal new insights into their folding thermodynamics.

Design of Polyproline-Based Catalysts for Ester Hydrolysis.

A number of simple oligopeptides have been recently developed as minimalistic catalysts for mimicking the activity and selectivity of natural proteases. Although the arrangement of amino acid residues in natural enzymes provides a strategy for designing artificial enzymes, creating catalysts with efficient binding and catalytic activity is still challenging. In this study, we used the polyproline scaffold and designed a series of 13-residue peptides with a catalytic dyad or triad incorporated to serve as artificial enzymes. Their catalytic efficiency on ester hydrolysis was evaluated by ultraviolet-visible spectroscopy using the p-nitrophenyl acetate assay, and their secondary structures were also characterized by circular dichroism spectroscopy. The results indicate that a well-formed polyproline II structure may result in a much higher catalytic efficiency. This is the first report to show that a functional dyad or triad engineered into a polyproline helix framework can enhance the catalytic activity on ester hydrolysis. Our study has also revealed the necessity of maintaining an ordered structure and a well-organized catalytic site for effective biocatalysts.

Effects of glycosylated (2S,4R)-hydroxyproline on the stability and assembly of collagen triple helices.

Functionalized collagen-mimetic peptides (CMPs) have been widely used in the preparation of collagen-related biomaterials. Among the reported results, the induced noncovalent interactions between the implanted functional groups or moieties were frequently the key elements to promote the self-assembly of small CMPs. In this work, we designed and synthesized a series of glycosylated CMPs in which 4-O-[ß-D-galactopyranosyl]-(2S,4R)-4-hydroxyproline (Hyp(Gal)) was incorporated to explore the effects of glycosylation on the stability and assembly of collagen triple helices. Circular dichroism measurements showed that glycosylation of hydroxyproline slightly destabilized the collagen triple helices, but did not reduce their refolding rate. Compared to non-glycosylated CMPs, the incorporation of Hyp(Gal) speeded up the assembly of CMPs, indicating that this modification could assist the self-assembly of CMPs into higher-order structures, such as fibrils. O-Galactosylation of hydroxyproline imposes contrary effects on the triple helix stability and the self-assembly rate of collagen triple helices, exhibiting a piece of important and useful information for designing collagen-related biomaterials. Our finding also suggests that instead of stabilizing the triple helical conformation of CMPs, installing additional forces between CMPs could be a crucial factor to promote the assembly of CMPs into large-scale constructs.

Synthesis and Structure-Activity Relationships of Imidazole-Coumarin Conjugates against Hepatitis C Virus.

A series of new conjugated compounds with a -SCH2- linkage were synthesized by chemical methods from imidazole and coumarin derivatives. The experimental results indicate that of the twenty newly synthesized imidazole-coumarin conjugates, three of them exhibited appealing EC50 values (5.1-8.4 µM) and selective indices >20 against hepatitis C virus. Their potency and selectivity were increased substantially by modification of their structure with two factors: imidazole nucleus with a hydrogen atom at the N(1) position and coumarin nucleus with a substituent, such as Cl, F, Br, Me, and OMe. These guidelines provide valuable information for further development of conjugated compounds as anti-viral agents.