Series Of Dipeptides Research Articles

Discovery of SARS-CoV-2 Inhibitors Featuring Novel Histidine α-Nitrile Motif.

As COVID-19 infection caused severe public health concerns recently, the development of novel antivirals has become the need of the hour. Main protease (Mpro ) has been an attractive target for antiviral drugs since it plays a vital role in polyprotein processing and virus maturation. Herein we report the discovery of a novel class of inhibitors against the SARS-CoV-2, bearing histidine α-nitrile motif embedded on a simple dipeptide framework. In-vitro and in-silico studies revealed that the histidine α-nitrile motif envisioned to target the Mpro contributes to the inhibitory activity. Among a series of dipeptides synthesized featuring this novel structural motif, some dipeptides displayed strong viral reduction (EC50 =0.48 μM) with a high selectivity index, SI>454.54. These compounds also exhibit strong binding energies in the range of -28.7 to -34.2 Kcal/mol. The simple dipeptide structural framework, amenable to quick structural variations, coupled with ease of synthesis from readily available commercial starting materials are the major attractive features of this novel class of SARS-CoV-2 inhibitors. The histidine α-nitrile dipeptides raise the hope of discovering potent drug candidates based on this motif to fight the dreaded SARS-CoV-2.

Elucidation of a Thermodynamical Feature Attributed to Substrate Binding to the Prokaryotic H+/Oligopeptide Cotransporter YdgR with Calorimetric Analysis: The Substrate Binding Driven by the Change in Entropy Implies the Release of Bound Water Molecules from the Binding Pocket.

Here, we have elucidated the substrate recognition mechanism by a prokaryotic H+/oligopeptide cotransporter, YdgR, using isothermal titration calorimetry. Under acidic conditions (pH 6.0), the binding of a dipeptide, Val-Ala, to YdgR elicited endothermic enthalpy, which compensated for the increase in entropy due to dipeptide binding. A series of dipeptides were used in the binding titration. The dipeptides represent Val-X and X-Val, where X is Ala, Ser, Val, Tyr, or Phe. Most dipeptides revealed endothermic enthalpy, which was completely compensated by the increase in entropy due to dipeptide binding. The change in enthalpy due to binding correlated well with the change in entropy, whereas the Gibbs free energy involved in the binding of the dipeptide to YdgR remained unchanged irrespective of dipeptide sequences, implying that the binding reaction was driven by entropy, that is, the release of bound water molecules in the binding pocket. It is also important to clarify that, based on the prediction of water molecules in the ligand-binding pocket of YdgR, the release of three bound water molecules in the putative substrate binding pocket occurred through binding to YdgR. In the comparison of Val-X and X-Val dipeptides, the N-terminal region of the binding pocket might contain more bound water molecules than the C-terminal region. In light of these findings, we suggest that bound water molecules might play an important role in substrate recognition and binding by YdgR.

Photochemistry of phthalimidoadamantane dipeptides: effect of amino acid side chain on photocyclization.

A series of dipeptides 1 was synthesized that at the N-site contained 3-(N-phthalimidoadamantane-1-carboxylic acid and at the C-site different aliphatic or aromatic L- or D-amino acids. The photochemical reaction of dipeptides 1 under acetone-sensitized conditions gave simple decarboxylation products 6, and decarboxylation-induced cyclization products 7, as well as some secondary products 8 and 9 formed by elimination of H2O or ring enlargement, respectively. Molecules 9 undergo secondary photoinduced H-abstractions by the phthalimide chromophore, delivering more complex polycycles 11. The photodecarboxylation-induced cyclization to 7 was observed only with phenylalanine (Phe), proline (Pro), leucine (Leu) and isoleucine (Ile). Contrary to dipeptides with Phe, the cyclization takes place with almost complete racemization at the amino acid chiral center, but diastereoselectively giving only one pair of enantiomers. The conducted investigation is important as it provides the breath and the scope of dipeptide cyclizations activated by phthalimides.

Photo-induced energy transfer within donor−acceptor dipeptides: Towards an artificial light-harvesting hydrogel system

Well-defined relative orientations and distances between chromophores are prerequisites for high-efficiency energy transfer, which can generally be realized by regularly assembling short peptide compounds with different absorption wavelengths and luminescence positions. Herein, a series of dipeptides are designed and synthesized, where the dipeptides contain different chromophores with several absorption bands. A co-self-assembled peptide hydrogel is prepared for artificial light-harvesting systems. The photophysical properties and assembly behavior of these dipeptide-chromophore conjugates in solution and hydrogel are systematically studied. As a result of the three-dimensional (3-D) self-assembly feature, effective energy transfer between donor and acceptor in the hydrogel system is achieved. These systems exhibit high antenna effect at a high donor/acceptor ratio (2564:1), which is characterized by an increase in the fluorescence intensity. Further, multiple molecules with different absorption wavelengths can be co-assembled as energy donors in order to achieve a wide spectrum of absorption. The method allows flexible light-harvesting systems to be realized. The ratio of energy donors to acceptors can be adjusted arbitrarily, and constructive motifs can be selected based on the application.

Investigating the complexation propensity of self-assembling dipeptides with the anticancer peptide-drug Bortezomib: a computational study.

The investigation of potential self-assembled peptides as carriers for the delivery of anticancer drug Bortezomib is the topic of the present study. The self-assembly of Bortezomib in water is examined using all-atom molecular dynamics simulations and corresponding experimental results from FESEM experiments. In addition, a series of dipeptides with a similar chemical formula to Bortezomib with hydrogel-forming ability are being investigated for their propensity to bind to the drug molecule. Dipeptides are divided into two classes, the protected FF (Fmoc-FF and Z-FF) and the LF-based (Cyclo-LF and LF) ones. The thermodynamic stability of the complexes formed in an aqueous environment, as well as key morphological features of the nanoassemblies are investigated at the molecular level. Binding enthalpy between Bortezomib and dipeptides follows the increasing order: LF < Cyclo-LF < Fmoc-FF < Z-FF under both van der Waals and electrostatic contributions. Protected FF dipeptides have a higher affinity for the drug molecule, which will favor its entrapment, giving them an edge over the LF based dipeptides. By evaluating the various measures, regarding both the binding between the two components and the eventual ability of controlled drug release, we conclude that the protected FF class is a more suitable candidate for drug release of Bortezomib, whereas among its two members, Fmoc-FF appears to be more promising. The selection of the optimal candidates based on the present computational study will be a stepping stone for future detailed experimental studies involving the encapsulation and controlled release of Bortezomib both in vitro and in vivo.

Amine Activation: "Inverse" Dipeptide Synthesis and Amide Function Formation through Activated Amino Compounds.

A copper(II)/HOBt-catalyzed procedure for the synthesis of dipeptides and "general" amides has been developed using microwave irradiation to considerably hasten the reaction. As an alternative to using traditional carboxylic acid activation, the method relies on the use of N-acyl imidazoles as activated amino partners. By doing so, a nonconventional way to reach dipeptides and amides has been proposed through the challenging and less studied N → C direction synthesis. A series of dipeptides and "general" amides have been successfully synthesized, and the applicability of the method has been illustrated in gram-scale syntheses. The mild reaction conditions proposed are completely adequate for couplings in the presence of sensitive amino acids, affording the products without detectable racemization. Furthermore, experimental observations prompted us to propose a plausible reaction pathway for the couplings.

Synthesis of Novel Phthalazinedione-Based Derivatives with Promising Cytotoxic, Anti-bacterial, and Molecular Docking Studies as VEGFR2 Inhibitors.

The parent ester methyl-3-[2-(4-oxo-3-phenyl-3,4-dihydro-phthalazin-1-yloxy)-acetylamino] has 18 compounds. The starting material for alkanoates, their corresponding hydrazides, hydrazones, and dipeptides were produced by chemoselective O-alkylation of 2-phenyl-2,3-dihydrophthalazine-1,4-dione with ethyl chloroacetate(4-oxo-3-phenyl-3,4-dihydro-phthalazin-1-yloxy) acetic acid methyl ester. The starting ester was hydrazinolyzed, then azide coupled with amino acid ester hydrochloride to produce several parent esters, and then hydrazinolyzed to produce parent hydrazides. These hydrazides were used to make a series of dipeptides by reacting them with amino acid ester hydrochloride under azide coupling conditions, and they were also condensed with a number of aldehydes to make the hydrazones. These derivatives were subjected to cytotoxicity against HCT-116 and MDA-MB-231 cells and anti-bacterial and molecular docking studies. Results indicated that the tested compounds, especially 7c and 8b with the phenyl phthalazinone moieties, had promising cytotoxicity against the HCT-116 cells with IC50 values of 1.36 and 2.34 μM, respectively. Additionally, the promising compounds 7c and 8b exhibited poor cytotoxicity against WISH cells with much higher IC50 values, so they were safe against normal cells. Compound 8c exhibited potent anti-bacterial activity with inhibition zones of 12 and 11 mm against Staphylococcus aureus and Escherichia coli, respectively. The molecular docking results of compounds 7c and 8b revealed a good binding disposition and the ligand–receptor interactions like the co-crystallized ligand of the VEGFR2 protein, which may be the proposed mode of action. Finally, compounds 7c and 8b exhibited good ADME pharmacokinetics with good drug-likeness parameters. Hence, detailed studies for the mechanism of action of such compounds are highly recommended for the development of new potent anti-cancer and anti-bacterial agents.

Chiral separation of dipeptides on Cinchona-based zwitterionic chiral stationary phases under buffer-free reversed-phase conditions.

Chiral zwitterion ion exchangers represent efficient chiral stationary phases for stereoselective resolution of various analytes including chiral acids, bases, and zwitterions. In this contribution, we have focused on utilization of chiral zwitterionic sorbents, denoted as ZWIX (+A) and ZWIX (-A). These are analogical chiral systems to commercially available columns, Chiralpak ZWIX (+) and Chiralpak ZWIX (-), which are usually operated with buffered mobile phases. In this contribution, we have studied the enantiorecognition power of the ZWIX (+A) and ZWIX (-A) columns on a series of dipeptides operated under buffer-free reversed-phase conditions. Retention characteristics of zwitterionic dipeptides are discussed using an electrostatically driven adsorption model, which provides a good fit with both monotonous and U-shaped curves.

Distinct electrostatic frequency tuning rates for amide I and amide I′ vibrations

Amide I spectroscopy probes the backbone C=O stretch vibrations of peptides and proteins. Amide I spectra are often collected in deuterated water (D2O) since this provides a cleaner background in the amide I frequency range; such data are often referred to as amide I' spectra since deuteration induces changes in the mode structure, including a roughly ∼10 cm-1 redshift. For biological samples, however, deuteration is often not possible. As amide I frequency maps are increasingly applied to quantitative protein structural analysis, this raises the interesting challenge of drawing direct connections between amide I and amide I' data. We here analyze amide I and amide I' peak frequencies for a series of dipeptides and related compounds. Changes in protonation state induce large electrostatic shifts in the peak frequencies, allowing us to amass a sizable library of data points for direct amide I/amide I' comparison. While we find an excellent linear correlation between amide I and amide I' peak frequencies, the deuteration-induced shift is smaller for more red-shifted vibrations, indicating different electrostatic tuning rates in the two solvents. H2O/D2O shifts were negligible for proline-containing dipeptides that lack exchangeable amide hydrogens, indicating that the intrinsic properties of the solvent do not strongly influence the H/D shift. These findings indicate that the distinct tuning rates observed for the two vibrations arise from modifications to the intrinsic properties of the amide bond and provide (at least for solvated dipeptides) a simple, linear "map" for translating between amide I and amide I' frequencies.

Synthesis of Dipeptide, Amide, and Ester without Racemization by Oxalyl Chloride and Catalytic Triphenylphosphine Oxide.

An efficient triphenylphosphine oxide-catalyzed amidation and esterification for the rapid synthesis of a series of dipeptides, amides, and esters is described. This reaction is applicable to challenging couplings of hindered carboxylic acids with weakly nucleophilic amines or alcohols, giving the products in good yields (67-90%) without racemization. This system employs the highly reactive intermediate Ph3PCl2 as the activator of the carboxylate in a catalytic manner and drives the reaction to completion in a short reaction time (less than 10 min).

Design, synthesis and biological evaluation of dipeptides as novel non-covalent 20S proteasome inhibitors

Based on the interaction modes of the natural 20S proteasome inhibitors TMC-95A, we have previously discovered a dipeptide 1. To explore the SAR around compound 1, we designed and synthesized a series of dipeptides (8–38) with a fragment-based strategy. Among them, nine compounds showed significant inhibitory activities against the chymotrypsin-like activity of human 20S proteasome with IC50 values at the submicromolar level, which were comparable or even superior to the parent compound 1. Meanwhile, they displayed no significant inhibition against trypsin-like and caspase-like activities of 20S proteasome. The results suggested the feasibility to design dipeptides as novel and potent 20S proteasome inhibitors.

The Antiproliferative and Apoptotic Effect of a Novel Synthesized S-Triazine Dipeptide Series, and Toxicity Screening in Zebrafish Embryos.

Several derivatives containing morpholine/piperidine, anilines, and dipeptides as pending moieties were prepared using s-triazine as a scaffold. These compounds were evaluated for their anticancer activity against two human breast cancer cell lines (MCF-7 and MDA-MB-231), a colon cancer cell line (HCT-116), and a non-tumorigenic cell line (HEK 293). Tamoxifen was used as a reference. Animal toxicity tests were carried out in zebrafish embryos. Most of these compounds showed a higher activity against breast cancer than colon cancer. Compound 3a—which contains morpholine, aniline, and glycylglycinate methyl ester—showed a high level of cytotoxicity against MCF-7 cells with IC50 values of less than 1 µM. This compound showed a much lower level of toxicity against the non-tumorigenic HEK-293 cell line, and in the in vivo studies using zebrafish embryos. Furthermore, it induced cell cycle arrest at the G2/M phase, and apoptosis in MCF-7 cells. On the basis of our results, 3a emerges as a potential candidate for further development as a therapeutic drug to treat hormone receptor-positive breast cancer.

α-Amino Acids and Peptides as Bifunctional Reagents: Carbocarboxylation of Activated Alkenes via Recycling CO2

Carboxylic acids, including amino acids (AAs), have been widely used as reagents for decarboxylative couplings. In contrast to previous decarboxylative couplings that release CO2 as a waste byproduct, herein we report a novel strategy with simultaneous utilization of both the alkyl and carboxyl components from carboxylic acids. Under this unique strategy, carboxylic acids act as bifunctional reagents in the redox-neutral carbocarboxylation of alkenes. Diverse, inexpensive, and readily available α-AAs take part in such difunctionalizations of activated alkenes via visible-light photoredox catalysis, affording a variety of valuable but otherwise difficult to access γ-aminobutyric acid derivatives (GABAs). Additionally, a series of dipeptides and tripeptides also participate in this photocatalytic carbocarboxylation. Although several challenges exist in this system due to the low concentration and quantitative amount of CO2, as well as unproductive side reactions such as hydrodecarboxylation of the carboxylic acids and hydroalkylation of the alkenes, excellent regioselectivity and moderate to high chemoselectivity are achieved. This process features low catalyst loading, mild reaction conditions, high step and atom economy, and good functional group tolerance, and it is readily scalable. The resulting products are subject to efficient derivations, and the overall process is amenable to applications in the late-stage modification of complex compounds. Mechanistic studies indicate that a carbanion is generated catalytically and it acts as the key intermediate to react with CO2, which is also generated catalytically in situ and thus remains in low concentration. The overall transformation represents an efficient and sustainable system for organic synthesis, pharmaceutics, and biochemistry.

Synergistic Tricolor Emission-Based White Light from Supramolecular Organic-Inorganic Hybrid Gel.

The development of engineered hybrid systems by encapsulating nanoparticles in gel scaffolds and their synergistic effects are highly crucial for the fabrication of advanced functional materials. Herein, a series of dipeptides containing an aromatic amino acid at the N-terminal and an aliphatic amino acid at the C-terminal were synthesized and studied. Among them, only the dipeptide l-Phe-l-Val can form both hydro- and organogelator, depending on the N- and C-terminal protecting groups. The organogel shows bright blue emission under 366 nm UV irradiation; however, the hydrogel does not show such blue emission. Such kind of emission may be due to the self-assembly and high degree of aggregation in the gel state of the phenyl ring. The blue-emitting organogel efficiently encapsulates green emission source CdSe quantum dots and red emission source LD 700 perchlorate dye. The resulting organic-inorganic hybrid gel exhibits white light emission due to the synergistic effect under 366 nm UV irradiation.

Deamidation Reactions of Asparagine- and Glutamine-Containing Dipeptides Investigated by Ion Spectroscopy

Deamidation is a major fragmentation channel upon activation by collision induced dissociation (CID) for protonated peptides containing glutamine (Gln) and asparagine (Asn) residues. Here, we investigate these NH3-loss reactions for four Asn- and Gln-containing protonated peptides in terms of the resulting product ion structures using infrared ion spectroscopy with the free electron laser FELIX. The influence of the side chain length (Asn versus Gln) and of the amino acid sequence on the deamidation reaction has been examined. Molecular structures for the product ions are determined by comparison of experimental IR spectra with spectra predicted by density functional theory (DFT). The reaction mechanisms identified for the four dipeptides AlaAsn, AsnAla, AlaGln, and GlnAla are not the same. For all four dipeptides, primary deamidation takes place from the amide side chain (and not from the N-terminus) and, in most cases, resembles the mechanisms previously identified for the protonated amino acids asparagine and glutamine. Secondary fragmentation reactions of the deamidation products have also been characterized and provide further insight in – and confirmation of – the identified mechanisms. Overall, this study provides a comprehensive molecular structure map of the deamidation chemistry of this series of dipeptides. Graphical ᅟ Electronic supplementary materialThe online version of this article (doi:10.1007/s13361-016-1462-5) contains supplementary material, which is available to authorized users.

Development of Dipeptidic hGPR54 Agonists.

A series of dipeptides were designed as potential agonists of the human KiSS1-derived peptide receptor (hGPR54). While the sequence Arg-Trp-NH2 was the most efficient in terms of affinity, we established a convergent synthetic strategy to optimize the N terminus. Using two successive Sonogashira cross-coupling reactions on a solid-supported peptide, we were able to introduce various alkynes at the N terminus to afford compounds with sub-micromolar affinities for hGPR54. However, functional assays indicated the benzoylated dipeptide Bz-Arg-Trp-NH2 as the most promising compound in terms of agonistic properties. Interestingly, this compound appeared much more stable than the endogenous neuropeptide kisspeptin, both in serum and in liver microsomes of rats. This compound was also found to be able to induce a significant in vivo increase in testosterone levels in male rats.

Porous peptide frameworks generated by stacking non-self-complementary β-sheets

"One of major approaches in the design of cavity space in the solids utilizes non-self-complementary molecules[1]. The irregular shape of the molecules and/or specific directionality of potential H-bonds prevent close packing of the molecules and yields various architectures hosting a second component, from inclusion compounds and co-crystals to complex non-crystalline patterns in biology. The strategy of non-self-complementary molecules has been extended in our studies to 2D supramolecular polymers based on short peptides[2]. The formation of the peptide layer with a desired overall geometry is controlled by strong, charge-assisted H-bonds (arrows in the Figure) in a β-sheet-like network as well as the segregation of hydrophobic amino acid residues into the interlayer space. The H-bonds add stability to the whole architecture while the hydrophobic groups keep the stacking layers at a distance that generates a cavity space available to a second component (encircled ""G"" in the Figure). A wide range of inclusions and co-crystals have been prepared in our group based on a series of dipeptides and higher peptide oligomers. For example, the incorporation of various organic solvents and bioactive molecules have been demonstrated for leucyl-alanine and similar dipeptides: alcohols, amides, phenols, pyridines, polyols, vitamins, scents and flavors. The crystal structure studies reveal a surprisingly persistent structural motif that can be used for engineering of crystalline materials with a specific property. We believe this type of peptide matrix may be utilized in the solid state organic synthesis [3] as reactive molecules of the second component can be oriented in a predictable way with respect to each other. "

Kinetically Controlled Peptide Synthesis Mediated by Papain Using the Carbamoylmethyl Ester as an Acyl Donor

A series of dipeptides were synthesized generally in good yields with carbamoylmethyl (Cam) esters as acyl donors in the presence of a cysteine protease, papain, immobilized on Celite. Several segment condensations were also achieved generally in high yields without danger of racemization and formation of the secondary-hydrolysis product. Moreover, partial sequences of some bioactive peptides were prepared through segment condensations, and aimed-at peptides were obtained generally in high yields without the racemization of C-terminal residues of the carboxyl components. Thus, the superiority of the Cam ester in the kinetically controlled peptide synthesis was once again ascertained in couplings mediated by the cysteine protease as in those catalyzed by the serine proteases reported earlier.

Alteration of Water Structure by Peptide Clusters Revealed by Neutron Scattering in the Small-Angle Region (below 1 Å−1)

Solution scattering of neutrons and x-rays can provide direct information on local interactions of importance for biomolecular folding and structure. Here, neutron scattering experiments are combined with molecular-dynamics simulation to interpret the scattering signal of a series of dipeptides with varying degrees of hydrophobicity (GlyAla, GlyPro, and AlaPro) in concentrated aqueous solution (1:20 solute/water ratio) in which the peptides form large segregates (up to 50–60 amino acids). Two main results are found: 1), the shift to lower Q of the so-called water-ring peak (Q≈ 2 Å−1) arises mainly from an overlap of water-peptide and peptide-peptide correlations in the region of 1.3 <Q< 2 Å−1, rather than from a shift of the water signal induced by the presence of the clusters; and 2), in the low-Q region (Q≈ 0.6 Å−1) a positive peak is observed originating from both the solute-solute correlations and changes in the water structure induced by the formation of the clusters. In particular, the water molecules are found to be more connected than in the bulk with hydrogen-bonding directions tangential to the exposed hydrophobic surfaces, and this effect increases with increasing peptide hydrophobicity. This work demonstrates that important information on the (hydrophobic) hydration of biomolecules can be obtained in the very-small-angle region.

Silicon-Containing Dipeptidic Aspartame and Neotame Analogues

A series of seven silicon-containing dipeptides ((S,R)-5, (S,S)-5, (S,R)-6, (S,R)-7, (S,S)-7, (S,R)-8, and (S,S)-8) was prepared in multistep syntheses, starting from the enantiopure silicon-containing α-methylated α-amino acids (R)- or (S)-α-[(trimethylsilyl)methyl]alanine ((R)-4 or (S)-4). For the preparation of (R)-4 and (S)-4, a robust synthesis on a multigram scale was developed, using an enzyme-catalyzed stereoselective ester hydrolysis as the key step. Coupling of (R)-4 and (S)-4 with different S-configured aspartate residues yielded a series of dipeptides that can be best described as silicon analogues of the artificial sweeteners aspartame and neotame. The identity of these dipeptides was established by elemental analyses and NMR spectroscopic studies (1H, 13C, 15N, 29Si). Some of the title compounds and some of their precursors were structurally characterized by single-crystal X-ray diffraction. The silicon-containing dipeptides were shown to display attractive ADME properties, including good solubility and plasma protein binding capabilities, no CYP inhibition, and no metabolic stability liabilities. Thus, the silicon-containing α-amino acids (R)-4 and (S)-4 proved to be promising building blocks for the design of biologically active peptides. Attempts to characterize the title compounds for their T1R2/R3 activating properties by testing their ability to induce GLP-1 secretion from the intestinal endocrine cell line STC-1 failed for unknown reasons. Sensory evaluation of the silicon-containing dipeptides demonstrated the aspartame analogue (S,R)-5 and the neotame analogue (S,R)-8 to be very potent artificial sweeteners, whereas the corresponding diastereomers tasted bitter. The silicon compounds (S,R)-5 and (S,R)-8 are approximately 50 and 600 times, respectively, as sweet as sucrose on a weight basis.