Synthesis of all nineteen appropriately protected chiral alpha-hydroxy acid equivalents of the alpha-amino acids for Boc solid-phase depsi-peptide synthesis

Enniatin A Analogues as Novel Hsp90 Inhibitors that Modulate Triple-Negative Breast Cancer

The 90 kilo-Dalton heat shock protein (Hsp90) is a molecular chaperone that facilitates the maturation of nascent polypeptides into their biologically active conformation. Because many of the >400 known client protein substrates are implicated in the development/progression of cancer, it is hypothesized that Hsp90 inhibition will simultaneously shut down numerous oncogenic pathways. Unfortunately, most of the small molecule Hsp90 inhibitors that have undergone clinical evaluation thus far have failed due to various toxicities. Therefore, the disruption of Hsp90 protein-protein interactions with cochaperones and/or client substrates has been proposed as an alternative way to achieve Hsp90 inhibition without such adverse events. The hexadepsipeptide Enniatin A (EnnA) has recently been reported to be one such inhibitor that also manifests immunogenic activity. Herein, we report preliminary structure-activity relationship (SAR) studies to determine the structural features that confer this unprecedented activity for an Hsp90 inhibitor. Our studies find that EnnA's branching moieties are necessary for its activity, but some structural modifications are tolerated.

RyR2 Binding of an Antiarrhythmic Cyclic Depsipeptide Mapped Using Confocal Fluorescence Lifetime Detection of FRET

Hyperactivity of cardiac sarcoplasmic reticulum (SR) ryanodine receptor (RyR2) Ca2+-release channels contributes to heart failure and arrhythmias. Reducing the RyR2 activity, particularly during cardiac relaxation (diastole), is a desirable therapeutic goal. We previously reported that the unnatural enantiomer (ent) of an insect-RyR activator, verticilide, inhibits porcine and mouse RyR2 at diastolic (nanomolar) Ca2+ and has in vivo efficacy against atrial and ventricular arrhythmia. To determine the ent-verticilide structural mode of action on RyR2 and guide its further development via medicinal chemistry structure-activity relationship studies, here, we used fluorescence lifetime (FLT)-measurements of Förster resonance energy transfer (FRET) in HEK293 cells expressing human RyR2. For these studies, we used an RyR-specific FRET molecular-toolkit and computational methods for trilateration (i.e., using distances to locate a point of interest). Multiexponential analysis of FLT-FRET measurements between four donor-labeled FKBP12.6 variants and acceptor-labeled ent-verticilide yielded distance relationships placing the acceptor probe at two candidate loci within the RyR2 cryo-EM map. One locus is within the Ry12 domain (at the corner periphery of the RyR2 tetrameric complex). The other locus is sandwiched at the interface between helical domain 1 and the SPRY3 domain. These findings document RyR2-target engagement by ent-verticilide, reveal new insight into the mechanism of action of this new class of RyR2-targeting drug candidate, and can serve as input in future computational determinations of the ent-verticilide binding site on RyR2 that will inform structure-activity studies for lead optimization.

Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides

Naturally occurring peptides with high membrane permeability often have ester bonds on their backbones. However, the impact of amide-to-ester substitutions on the membrane permeability of peptides has not been directly evaluated. Here we report the effect of amide-to-ester substitutions on the membrane permeability and conformational ensemble of cyclic peptides related to membrane permeation. Amide-to-ester substitutions are shown to improve the membrane permeability of dipeptides and a model cyclic hexapeptide. NMR-based conformational analysis and enhanced sampling molecular dynamics simulations suggest that the conformational transition of the cyclic hexapeptide upon membrane permeation is differently influenced by an amide-to-ester substitution and an amide N-methylation. The effect of amide-to-ester substitution on membrane permeability of other cyclic hexapeptides, cyclic octapeptides, and a cyclic nonapeptide is also investigated to examine the scope of the substitution. Appropriate utilization of amide-to-ester substitution based on our results will facilitate the development of membrane-permeable peptides.

Synthesis and antiproliferative activities of steroidal lactam conjugates bearing a new nitrogen mustard

Alkylating agents are potent anticancer compounds that exert their anticancer properties through the inhibition of cell replication and transcription leading to cell death. Despite the numerous benefits, these agents also have serious drawbacks such as their high toxicity and low specificity towards cancer cells. As previously reported by our group, conjugation of alkylating agents with azasteroids can reduce their systemic toxicity and enhance their anticancer activity. In this work, novel steroidal alkylating agents bearing POPAM-OH were synthesized and their anticancer efficacy was evaluated in vitro and in vivo. All the novel hybrids demonstrated high antiproliferative effects against 5 different cancer cell lines in the low micromolar range. Treatment of SCID mice bearing SKOV-3 or PC-3 tumor xenografts with the most potent hybrid 19 led to significant reduction of tumor size (tumor inhibition TI = 95% in SKOV3 models and TI = 85.2% in PC3 models). Importantly, the acute toxicity of hybrid 19 (LD₁₀ = 36 μΜ, LD₅₀ = 62 μΜ) in CB17 SCID mice exhibited three-fold decrease compared to the acute toxicity of previously reported hybrids of POPAM-NH₂. This is an important finding since systemic cytotoxicity is a critical limitation of alkylating agents. Collectively, the steroidal conjugates of POPAM-OH displayed significant anticancer efficacy and reduced toxicity in vitro and in vivo rendering them as good candidates for cancer therapy.

Sustainable Synthesis of α-Hydroxycarboxylic Acids by Manganese Catalyzed Acceptorless Dehydrogenative Coupling of Ethylene Glycol and Primary Alcohols

Herein, we report a straightforward synthesis of valuable α-hydroxycarboxylic acid molecules via an acceptorless dehydrogenative coupling of ethylene glycol and primary alcohols. A bench-stable manganese complex catalyzed the reaction, which is scalable, with the product being isolated with high yields and selectivities under mild conditions. The protocol is environmentally benign, producing water and hydrogen gas as the only byproducts. Methanol can also be used as a C1 source for producing the platform molecule lactic acid, with a high turnover of >10⁴ . The methodology was also used to functionalize alcohols derived from natural products and fatty acids. Furthermore, it was applied for synthesizing α-amino acid, α-thiocarboxylic acid, and several drugs and bioactive molecules, including endogenous metabolites, Danshensu, Enalapril, Lisinopril, and Rosmarinic acid. Preliminary mechanistic studies were performed to shed light on the mechanism involved in the reaction.

Deamination of 1-Aminoalkylphosphonic Acids: Reaction Intermediates and Selectivity

Deamination of 1-aminoalkylphosphonic acids in the reaction with HNO₂ (generated "in situ" from NaNO₂) yields a mixture of substitution products (1-hydroxyalkylphosphonic acids), elimination products (vinylphosphonic acid derivatives), rearrangement and substitution products (2-hydroxylkylphosphonic acids) as well as H₃PO₄. The variety of formed reaction products suggests that 1-phosphonoalkylium ions may be intermediates in such deamination reactions.

Ni-Catalyzed Enantioselective Dialkyl Carbinol Synthesis via Decarboxylative Cross-Coupling: Development, Scope, and Applications

The first enantioselective decarboxylative Negishi-type alkylations of α-oxy carboxylic acids are reported via the intermediacy of redox-active esters (RAEs). This transformation enables a radical-based retrosynthesis of seemingly trivial enantiopure dialkyl carbinols. This article includes a discussion of the history of such couplings, the retrosynthetic ramifications of such a coupling, the development of general conditions, and an extensive series of applications that vividly demonstrate how it can simplify synthesis.

L-Cysteine as a reducing/capping/gel-forming agent for the preparation of silver nanoparticle composites with anticancer properties

The present article reports the in situ preparation of silver nanoparticles (AgNPs) homogeneously distributed in the gel matrix formed using only L-cysteine (CYS) as a bio-reducing agent. The physicochemical methods of analysis confirmed the formation of a gel-network from aggregates consisting of spherical/elliptical cystine-stabilized AgNPs (core) and cysteine/Ag⁺ complexes (shell) regardless of the used silver salt - AgNO₃, AgNO₂ or AgOOCCH₃. CYS/AgNO₃ and CYS/AgOOCCH₃ aqueous solution systems needed the addition of electrolytes (Cl^- and SO₄^2-) for the gelation process, but the gel-formation in CYS/AgNO₂ occurred in one stage without any additional components. The AgNP sizes were about 1-5 nm in diameter for CYS/AgNO₃, 5-10 nm for CYS/AgOOCCH₃ and 20-40 nm for CYS/AgNO₂ systems. The zeta-potential values varied from +60 mV for CYS/AgNO₃ to +25 mV for the CYS/AgNO₂ system. The MTT-test showed that the obtained composites suppressed the MCF-7 breast cancer cells and the CYS/AgNO₃ system possessed the highest activity. Flow cytofluorimetry confirmed that the cell death occurred by apoptosis and this effect was the strongest for the CYS/AgNO₃ system. All systems were non-toxic to fibroblast cells. The novel simplest "green chemistry" approach, combining the knowledge of organic, inorganic, physical and supramolecular chemistry could open possibilities for the creation of the newest soft gel materials used in various fields of our life.

Hydrothermal water enabling one-pot transformation of amines to alcohols via supported Pd catalysts

The simple, direct conversion of amines to alcohols is quite rare and remains challenging. Here, with the unique catalytic role of hydrothermal water, two green and one-pot strategies were proposed...

A Guideline for the Synthesis of Amino-Acid-Functionalized Monomers and Their Polymerizations

Amino acids have emerged as a sustainable source for the design of functional polymers. Besides their wide availability, especially their high degree of biocompatibility makes them appealing for a broad range of applications in the biomedical research field. In addition to these favorable characteristics, the versatility of reactive functional groups in amino acids (i.e., carboxylic acids, amines, thiols, and hydroxyl groups) makes them suitable starting materials for various polymerization approaches, which include step- and chain-growth reactions. This review aims to provide an overview of strategies to incorporate amino acids into polymers. To this end, it focuses on the preparation of polymerizable monomers from amino acids, which yield main chain or side chain-functionalized polymers. Furthermore, postpolymerization modification approaches for polymer side chain functionalization are discussed. Amino acids are presented as a versatile platform for the development of polymers with tailored properties.

Copper-Promoted N-Arylation of the Imidazole Side Chain of Protected Histidine by Using Triarylbismuth Reagents

The N-arylation of the side chain of histidine by using triarylbismuthines is reported. The reaction is promoted by copper(II) acetate in dichloromethane at 40 °C under oxygen in the presence of diisopropylethylamine and 1,10-phenanthroline and allows the transfer of aryl groups with substituents at any position of the aromatic ring. The reaction shows excellent functional group tolerance and is applicable to dipeptides where the histidine is located at the N terminus. A histidine-guided backbone N-H arylation was observed in dipeptides where the histidine occupies the C terminus.

Amycolapeptins A and B, Cyclic Nonadepsipeptides Produced by Combined-culture of Amycolatopsis sp. and Tsukamurella pulmonis

Two nonapeptide natural products, amycolapeptins A (1) and B (2) with a 22-membered cyclic depsipeptide skeleton, β-hydroxytyrosine, and a highly modified side chain, which were not produced in a monoculture of the rare actinomycete Amycolatopsis sp. 26-4, were discovered in broth of its combined-culture with Tsukamurella pulmonis TP-B0596. The planar structures were elucidated by spectroscopic analyses (extensive 2D-NMR and MALDI-TOF MS/MS). The absolute configurations of component amino acids were unambiguously determined by the highly sensitive advanced Marfey's method we recently developed. Additionally, the structures of unstable/unusual moieties were corroborated by chemical synthesis and CD analysis.

Targeting the APP-Mint2 Protein-Protein Interaction with a Peptide-Based Inhibitor Reduces Amyloid-β Formation

There is an urgent need for novel therapeutic approaches to treat Alzheimer's disease (AD) with the ability to both alleviate the clinical symptoms and halt the progression of the disease. AD is characterized by the accumulation of amyloid-β (Aβ) peptides which are generated through the sequential proteolytic cleavage of the amyloid precursor protein (APP). Previous studies reported that Mint2, a neuronal adaptor protein binding both APP and the γ-secretase complex, affects APP processing and formation of pathogenic Aβ. However, there have been contradicting results concerning whether Mint2 has a facilitative or suppressive effect on Aβ generation. Herein, we deciphered the APP-Mint2 protein-protein interaction (PPI) via extensive probing of both backbone H-bond and side-chain interactions. We also developed a proteolytically stable, high-affinity peptide targeting the APP-Mint2 interaction. We found that both an APP binding-deficient Mint2 variant and a cell-permeable PPI inhibitor significantly reduced Aβ₄₂ levels in a neuronal in vitro model of AD. Together, these findings demonstrate a facilitative role of Mint2 in Aβ formation, and the combination of genetic and pharmacological approaches suggests that targeting Mint2 is a promising therapeutic strategy to reduce pathogenic Aβ levels.

L-Cysteine/AgNO2 low molecular weight gelators: self-assembly and suppression of MCF-7 breast cancer cells

We report a new supramolecular hydrogel based on simple amino acids and silver salt compounds with low molecular weights. The in situ formation of silver nanoparticles during the self-assembly process endows the hydrogel with high cytotoxicity towards adenocarcinoma breast cells but no toxic effects towards embryonic fibroblasts.

Constituents of Bupleurum praealtum and Bupleurum veronense with Potential Immunomodulatory Activity

In this investigation, chromatographic separations of the diethyl ether extracts of two European annual Bupleurum taxa, B. praealtum and B. veronense, yielded nine new natural products, namely, a series of esters of stereoisomeric tetradeca-5,7,9,11-tetraen-1-ols (1-4 and 8), a tetra-unsaturated γ-tetradecalactone (5), a dibenzylbutyrolactone lignan (7-oxoarcitin, 6), a falcarinol-related 17-membered macrolide (7) possessing a conjugated diyne-system, and an acylphloroglucinol derivative (9). All these new compounds were fully characterized by NMR, IR, UV, MS, and optical rotation measurement, including ¹H NMR full spin spectral simulation, whereas the absolute configurations of 1, 5, and 9 were determined via chemical correlations and NMR analysis of Mosher esters. The in vitro potential immunomodulatory activities of 1, 4, 5, and (+)-arcitin were assessed by determining their effects on the functional properties of isolated rat splenocytes and peritoneal macrophages. The results obtained support the known immunomodulatory ethnomedicinal usage of Bupleurum species.

Characterization and Catalytic-Site-Analysis of an Aldo-Keto Reductase with Excellent Solvent Tolerance

Aldo-keto reductases (AKRs) mediated stereoselective reduction of prochiral carbonyl compounds is an efficient way of preparing single enantiomers of chiral alcohols due to their high chemo-, enantio-, and regio-selectivity. To date, the application of AKRs in the asymmetric synthesis of chiral alcohols has been limited, due to the challenges of cloning and purifying. In this work, the aldo-keto reductase (AKR3-2-9) from Bacillus sp. was obtained, purified and proved to be NADPH-dependent. It exhibits good bioactivity and stability at 37 °C, pH 6.0. AKR3-2-9 is catalytically active on 11 pairs of substrates such as 3-methylcyclohexanone and methyl pyruvate, among which it showed the highest catalytic activity for acetylacetone. In addition, AKR3-2-9 was able to be resistant to five common organic solvents such as methanol and ethanol, it retained high catalytic activity even in a reaction system containing 10% v/v organic solvent for 6 h, which indicates its broad substrate spectrum and exceptional organic solvent tolerance. Furthermore, its three-dimensional structure was constructed and catalytic-site-analysis of the enzyme was conducted. Notably, it was capable of catalyzing the reaction of the key intermediates of duloxetine. The extensive substrate spectrum and predominant organic solvents resistance makes AK3-2-9 a promising enzyme which can be potentially applied in medicine synthesis.

Etherification of phenols by amines via transient diazonium intermediates

In this paper, the synthesis of alkyl aryl ethers from electron poor phenols and amines, using 1,3-propanedinitrite, is described. Due to the mild conditions, functionalized primary, secondary, and tertiary alkyl groups were successfully introduced, denoting a highly tolerant process that allows for unprotected alcohols and acetals. The reaction is thought to proceed through the formation of a diazonium intermediate that undergoes subsequent SN2 or SN1 reactions.

Substituted glycolides from natural sources: preparation, alcoholysis and polymerization

Herein we present a comparative study of substituted glycolides MeGL, iPrGL, iBuGL, BnGL, PhGL and MePhGL, synthesized from natural sources and polymers therefrom.

Diazotization of S-Sulfonyl-cysteines

We report the preparation of enantiomerically enriched β-thio-α-hydroxy and α-chloro carboxylic acid and ester building blocks by diazotization of S-sulfonyl-cysteines. The thiosulfonate protecting group demonstrated resistance to oxidation and attenuation of sulfur’s nucleophilicity by the anomeric effect. The key transformation was optimized by a 2² factorial design of experiment, highlighting the unique reactivity of cysteine derivatives in comparison with aliphatic amino acids.

Probing Backbone Hydrogen Bonds in Proteins by Amide-to-Ester Mutations

All proteins contain characteristic backbones formed of consecutive amide bonds, which can engage in hydrogen bonds. However, the importance of these is not easily addressed by conventional technologies that only allow for side-chain substitutions. By contrast, technologies such as nonsense suppression mutagenesis and protein ligation allow for manipulation of the protein backbone. In particular, replacing the backbone amide groups with ester groups, that is, amide-to-ester mutations, is a powerful tool to examine backbone-mediated hydrogen bonds. In this minireview, we showcase examples of how amide-to-ester mutations can be used to uncover pivotal roles of backbone-mediated hydrogen bonds in protein recognition, folding, function, and structure.

Gene expression and activity of methionine converting enzymes in broiler chickens fed methionine isomers or precursors

Common dietary supplemental methionine (Met) sources include DL-methionine (DL-Met) and the Met precursor DL-2-hydroxy-4-(methylthio) butanoic acid (DL-HMTBA). For bio-utilization, D-Met and DL-HMTBA are converted into L-Met through oxidation and transamination. The objective of this study was to determine the effect of different dietary supplemental Met sources on gene expression and enzyme activity of Met oxidases in male broiler chickens. Liver, muscle, duodenum, jejunum, and ileum were collected at days 10 (d 10), 21 (d 21), and 26 (d 26) post-hatch from male broiler chickens that were fed a basal diet deficient in sulfur amino acids (SAA) (control), or the control diet supplemented with DL-Met, L-Met, or DL-HMTBA to meet SAA requirements. The mRNA abundance of D-Met oxidase, L-HMTBA oxidase, and D-HMTBA oxidase was measured by real-time PCR, and oxidase activities were measured using colorimetric assays (n = 5). Liver expressed more D- and L-HMTBA oxidase mRNA, while breast muscle and liver expressed more D-Met oxidase mRNA than other tissues. In the liver, DL-HMTBA and L-Met supplementation were associated with greater mRNA abundance of L-HMTBA oxidase compared to the control diet-fed group at d 10 but not d 21 or d 26. DL-HMTBA supplementation, however, was not associated with changes in the mRNA abundance of D-HMTBA oxidase. The Met-deficient diet at d 26 was associated with greater hepatic abundance of DAO mRNA, which is responsible for oxidation of amino acids. Oxidase activities were similar among the Met deficient and Met-supplemented groups. In conclusion, dietary Met supplementation influenced the transcriptional regulation and activity of Met oxidases in a tissue and age-specific manner. Met oxidases may thus act as a determining factor in the bioefficacy of different dietary supplemental Met sources.

Stepwise O-Atom Transfer in Heme-Based Tryptophan Dioxygenase: Role of Substrate Ammonium in Epoxide Ring Opening

Heme-based tryptophan dioxygenases are established immunosuppressive metalloproteins with significant biomedical interest. Here, we synthesized two mechanistic probes to specifically test if the α-amino group of the substrate directly participates in a critical step of the O atom transfer during catalysis in human tryptophan 2,3-dioxygenase (TDO). Substitution of the nitrogen atom of the substrate to a carbon (probe 1) or oxygen (probe 2) slowed the catalytic step following the first O atom transfer such that transferring the second O atom becomes less likely to occur, although the dioxygenated products were observed with both probes. A monooxygenated product was also produced from probe 2 in a significant quantity. Analysis of this new product by HPLC coupled UV-vis spectroscopy, high-resolution mass spectrometry, 1H NMR, 13C NMR, HSQC, HMBC, and infrared (IR) spectroscopies concluded that this monooxygenated product is a furoindoline compound derived from an unstable epoxyindole intermediate. These results prove that small molecules can manipulate the stepwise O atom transfer reaction of TDO and provide a showcase for a tunable mechanism by synthetic compounds. The product analysis results corroborate the presence of a substrate-based epoxyindole intermediate during catalysis and provide the first substantial experimental evidence for the involvement of the substrate α-amino group in the epoxide ring-opening step during catalysis. This combined synthetic, biochemical, and biophysical study establishes the catalytic role of the α-amino group of the substrate during the O atom transfer reactions and thus represents a substantial advance to the mechanistic comprehension of the heme-based tryptophan dioxygenases.

Poly(α-hydroxy acid)s and poly(α-hydroxy acid-co-α-amino acid)s derived from amino acid

Polyesters derived from the α-hydroxy acids, lactic acid, and glycolic acid, are the most common biodegradable polymers in clinical use. These polymers have been tailored for a range of applications that require a physical material possessing. The physical and mechanical properties of these polymers fit the specific application and also safely biodegrade. These polymers are hydrophobic and do not possess functional side groups. This does not allow hydrophilic or hydrophobic manipulation, conjugation of active agents along the polymer chain, etc. These manipulations have partly been achieved by block copolymerization with, for example, poly(ethylene glycol), to obtain an amphiphilic copolymer. The objective of this review is to survey PLA functional copolymers in which functional α-hydroxy acids derived from amino acids are introduced along the polymer chain, allowing endless manipulation of PLA. Biodegradable functional polyesters are one of the most versatile biomaterials available to biomedical scientists. Amino acids with their variable side chains are ideal candidates for synthesizing such structural as well as stereochemically diverse polymers. They render control over functionalization, conjugation, crosslinking, stimulus responsiveness, and tunable mechanical/thermal properties. Functionalized amino acid derived polyesters are widely used, mainly due to advancement in ring opening polymerization (primarily O-carboxyanhydride mediated). The reaction proceeds under milder conditions and yields high molecular weight polymers. We reviewed on advances in the synthetic methodologies for poly-α-hydroxy esters derived from amino acids with appropriate recent examples.

Metal-free one-pot α-carboxylation of primary alcohols

An efficient metal-free procedure for the formal α-carboxylation of primary alcohols has been developed. The method involves a one-pot oxidation/Passerini/hydrolysis sequence and provides access to α-hydroxy acids bearing a broad range of functional groups. A minor modification to the reaction conditions extends the range of accessible products to α-hydroxy esters.

Design, synthesis, and biological evaluation of α-hydroxyacyl-AMS inhibitors of amino acid adenylation enzymes

Biosynthesis of bacterial natural-product virulence factors is emerging as a promising antibiotic target. Many such natural products are produced by nonribosomal peptide synthetases (NRPS) from amino acid precursors. To develop selective inhibitors of these pathways, we have previously described aminoacyl-AMS (sulfamoyladenosine) macrocycles that inhibit NRPS amino acid adenylation domains but not mechanistically-related aminoacyl-tRNA synthetases. To improve the cell permeability of these inhibitors, we explore herein replacement of the α-amino group with an α-hydroxy group. In both macrocycles and corresponding linear congeners, this leads to decreased biochemical inhibition of the cysteine adenylation domain of the Yersina pestis siderophore synthetase HMWP2, which we attribute to loss of an electrostatic interaction with a conserved active-site aspartate. However, inhibitory activity can be regained by installing a cognate β-thiol moiety in the linear series. This provides a path forward to develop selective, cell-penetrant inhibitors of the biosynthesis of virulence factors to probe their biological functions and potential as therapeutic targets.

Probing backbone hydrogen bonding in PDZ/ligand interactions by protein amide-to-ester mutations

PDZ domains are scaffolding modules in protein-protein interactions that mediate numerous physiological functions by interacting canonically with the C-terminus or non-canonically with an internal motif of protein ligands. A conserved carboxylate-binding site in the PDZ domain facilitates binding via backbone hydrogen bonds; however, little is known about the role of these hydrogen bonds due to experimental challenges with backbone mutations. Here we address this interaction by generating semisynthetic PDZ domains containing backbone amide-to-ester mutations and evaluating the importance of individual hydrogen bonds for ligand binding. We observe substantial and differential effects upon amide-to-ester mutation in PDZ2 of postsynaptic density protein 95 and other PDZ domains, suggesting that hydrogen bonding at the carboxylate-binding site contributes to both affinity and selectivity. In particular, the hydrogen-bonding pattern is surprisingly different between the non-canonical and canonical interaction. Our data provide a detailed understanding of the role of hydrogen bonds in protein-protein interactions.

Selective inhibition of mutant isocitrate dehydrogenase 1 (IDH1) via disruption of a metal binding network by an allosteric small molecule

Cancer-associated point mutations in isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) confer a neomorphic enzymatic activity: the reduction of α-ketoglutarate to d-2-hydroxyglutaric acid, which is proposed to act as an oncogenic metabolite by inducing hypermethylation of histones and DNA. Although selective inhibitors of mutant IDH1 and IDH2 have been identified and are currently under investigation as potential cancer therapeutics, the mechanistic basis for their selectivity is not yet well understood. A high throughput screen for selective inhibitors of IDH1 bearing the oncogenic mutation R132H identified compound 1, a bis-imidazole phenol that inhibits d-2-hydroxyglutaric acid production in cells. We investigated the mode of inhibition of compound 1 and a previously published IDH1 mutant inhibitor with a different chemical scaffold. Steady-state kinetics and biophysical studies show that both of these compounds selectively inhibit mutant IDH1 by binding to an allosteric site and that inhibition is competitive with respect to Mg(2+). A crystal structure of compound 1 complexed with R132H IDH1 indicates that the inhibitor binds at the dimer interface and makes direct contact with a residue involved in binding of the catalytically essential divalent cation. These results show that targeting a divalent cation binding residue can enable selective inhibition of mutant IDH1 and suggest that differences in magnesium binding between wild-type and mutant enzymes may contribute to the inhibitors' selectivity for the mutant enzyme.

Solid-phase synthesis of tetrahydropyridazinedione-constrained peptides

The design and solid-phase synthesis of tetrahydropyridazine-3,6-dione (Tpd) peptidomimetics derived from backbone-aminated peptides is reported. The described protocol features the synthesis of chiral α-hydrazino acids suitable for chemoselective incorporation into growing peptide chains. Acid-catalyzed cyclization to form the Tpd ring during cleavage affords the target peptidomimetics in good yield and purity. The scope of Tpd incorporation is demonstrated through the synthesis of constrained peptides featuring nucleophilic/electrophilic side chains and sterically encumbered α-substituted hydrazino acid residues.

Biocontrolled formal inversion or retention of L-α-amino acids to enantiopure (R)- or (S)-hydroxyacids

Natural L-α-amino acids and L-norleucine were transformed to the corresponding α-hydroxy acids by formal biocatalytic inversion or retention of absolute configuration. The one-pot transformation was achieved by a concurrent oxidation reduction cascade in aqueous media. A representative panel of enantiopure (R)- and (S)-2-hydroxy acids possessing aliphatic, aromatic and heteroaromatic moieties were isolated in high yield (67-85 %) and enantiopure form (>99 % ee) without requiring chromatographic purification.

New bio-renewable polyester with rich side amino groups from l-lysine via controlled ring-opening polymerization

Lysine, a renewable resource from biomass fermentation, was converted to pure O-carboxyanhydride monomer, then well-defined polyester with amino groups was prepared via controlled ring-opening polymerization.

Highly stereoselective biosynthesis of (R)-α-hydroxy carboxylic acids through rationally re-designed mutation of D-lactate dehydrogenase

An NAD-dependent d-lactate dehydrogenase (d-nLDH) of Lactobacillus bulgaricus ATCC 11842 was rationally re-designed for asymmetric reduction of a homologous series of α-keto carboxylic acids such as phenylpyruvic acid (PPA), α-ketobutyric acid, α-ketovaleric acid, β-hydroxypyruvate. Compared with wild-type d-nLDH, the Y52L mutant d-nLDH showed elevated activities toward unnatural substrates especially with large substitutes at C-3. By the biocatalysis combined with a formate dehydrogenase for in situ generation of NADH, the corresponding (R)-α-hydroxy carboxylic acids could be produced at high yields and highly optical purities. Taking the production of chiral (R)-phenyllactic acid (PLA) from PPA for example, 50 mM PPA was completely reduced to (R)-PLA in 90 min with a high yield of 99.0% and a highly optical purity (>99.9% e.e.) by the coupling system. The results presented in this work suggest a promising alternative for the production of chiral α-hydroxy carboxylic acids.

Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations

One of the most frequent protein-protein interaction modules in mammalian cells is the postsynaptic density 95/discs large/zonula occludens 1 (PDZ) domain, involved in scaffolding and signaling and emerging as an important drug target for several diseases. Like many other protein-protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1)). This decrease in affinity was mainly due to an increase in the dissociation rate constant, but a significant decrease in the association rate constant was found for some amide-to-ester mutations suggesting that native hydrogen bonds have begun to form in the transition state of the binding reaction. This study provides a general framework for studying the role of backbone hydrogen bonds in protein-peptide interactions and for the first time specifically addresses these for PDZ domain-peptide interactions.