Amide Substitution Research Articles

Total synthesis of [β-HIle]2-nodupetide: effect of ester to amide substitution on its antimicrobial activity.

The increasing prevalence of deaths due to multidrug-resistant bacteria (MDRB) in infectious disease therapy has become a global health concern. This led to the development of new antimicrobial therapeutic agents that can combat resistance to pathogenic bacteria. The utilization of natural peptide compounds as potential antimicrobial agents is very promising. Nodupetide, a cyclodepsipeptide with very strong antimicrobial activity against Pseudomonas aeruginosa was isolated from the fermentation of Nodulisporium sp. Unfortunately, one of its residues (3S,4S)-3-hydroxy-4-methylhexanoic acid (HMHA) is not commercially available and the synthesis strategies applied have not been successful. Hence, we synthesized its cyclopeptide analogue [β-HIle]2-nodupetide by replacing HMHA with isoleucine homologue. A combination of solid- and solution-phase peptide synthesis was successfully carried out to synthesize [β-HIle]2-nodupetide with an overall yield of 10.4%. The substitution of HMHA with β-homoisoleucine (β-HIle) changed the ester bond into an amide bond in nodupetide's backbone. The analogue was considerably inactive against Pseudomonas aeruginosa. It can be concluded that the ester bond is crucial for the antimicrobial activity of nodupetide.

Starch-Based Polymer Materials as Advanced Adsorbents for Sustainable Water Treatment: Current Status, Challenges, and Future Perspectives.

Over the past three decades, chemical and biological water contamination has become a major concern, particularly in the industrialized world. Heavy metals, aromatic compounds, and dyes are among the harmful substances that contribute to water pollution, which jeopardies the human health. For this reason, it is of the utmost importance to locate methods for the cleanup of wastewater that are not genuinely effective. Owing to its non-toxicity, biodegradability, and biocompatibility, starch is a naturally occurring polysaccharide that scientists are looking into as a possible environmentally friendly material for sustainable water remediation. Starch could exhibit significant adsorption capabilities towards pollutants with the substitution of amide, amino, carboxyl, and other functional groups for hydroxyl groups. Starch derivatives may effectively remove contaminants such as oil, organic solvents, pesticides, heavy metals, dyes, and pharmaceutical pollutants by employing adsorption techniques at a rate greater than 90%. The maximal adsorption capacities of starch-based adsorbents for oil and organic solvents, pesticides, heavy metal ions, dyes, and pharmaceuticals are 13,000, 66, 2000, 25,000, and 782 mg/g, respectively. Although starch-based adsorbents have demonstrated a promising future for environmental wastewater treatment, additional research is required to optimize the technique before the starch-based adsorbent can be used in large-scale in situ wastewater treatment.

Long-Range Kinetic Effects on the Alternating Ring Opening Metathesis of Bicyclo[4.2.0]oct-6-ene-7-carboxamides and Cyclohexene.

We report an investigation of rates of ruthenium-catalyzed alternating ring opening metathesis (AROM) of cyclohexene with two different Ru-cyclohexylidene carbenes derived from bicyclo[4.2.0]oct-6-ene-7-carboxamides (A monomer) that bear different side chains. These monomers are propylbicyclo[4.2.0]oct-6-ene-7-carboxamide and N-(2-(2-ethoxyethoxy)ethanylbicyclo[4.2.0]oct-6-ene-7-carboxamide. The amide substitution of these monomers directly affects both the rate of the bicyclo[4.2.0]oct-6-ene-7-carboxamide ring opening and the rate of reaction of the resulting carbene with cyclohexene (B monomer). The resulting Ru-cyclohexylidenes underwent reversible ring opening metathesis with cyclohexene. However, the thermodynamic equilibrium disfavored cyclohexene ring opening. Utilization of triphenylphosphine forms a more stable PPh3 ligated complex, which suppresses the reverse ring closing reaction and allowed direct measurements of the forward rate constants for formation of various A-B and A-B-A' complexes through carbene-catalyzed ring-opening metathesis and thus gradient polymer structure-determining steps. The relative rate of the propylbicyclo[4.2.0]oct-6-ene-7-carboxamide ring opening is 3-fold faster than that of the N-(2-(2-ethoxyethoxy)ethanylbicyclo[4.2.0]oct-6-ene-7-carboxamide. In addition, the rate of cyclohexene ring-opening catalyzed by the propyl bicyclooctene is 1.4 times faster than when catalyzed by the ethoxyethoxy bicyclooctene. Also, the subsequent rates of bicyclo[4.2.0]oct-6-ene-7-carboxamide ring opening by propyl-based Ru-hexylidene are 1.6-fold faster than ethoxyethoxy-based Ru-hexylidene. Incorporation of the rate constants into reactivity ratios of bicyclo[4.2.0]amide-cyclohexene provides prediction of copolymerization kinetics and gradient copolymer structures.

Total synthesis, structure elucidation and expanded bioactivity of icosalide A: effect of lipophilicity and ester to amide substitution on its bioactivity.

The first total synthesis of icosalide A, an antibacterial depsipeptide that is unique in that it contains two lipophilic beta-hydroxy acids, has been achieved by following Fmoc solid-phase peptide synthesis in combination with solution-phase synthesis. The ambiguity in the absolute stereochemistry of icosalide A has been resolved by synthesizing the reported structures and other relevant diastereomers of icosalides and comparing their NMR data. NMR-based structure elucidation of icosalide A revealed a well-folded structure with cross-strand hydrogen bonds similar to the anti-parallel beta-sheet conformation in peptides and displayed a synergistic juxtaposition of the aliphatic sidechains. 12 analogues of icosalide A were synthesized by varying the constituent lipophilic beta-hydroxy acid residues, and their biological activities against Bacillus thuringiensis and Paenibacillus dendritiformis were explored. Most of these icosalide analogues showed an MIC of 12.5 μg mL-1 against both bacteria. Swarming inhibition by icosalides was least in B. thuringiensis (8.3%) compared to that in P. dendritiformis (33%). Furthermore, this is the first report of icosalides showing assured inhibitory action (MIC between 2 and 10 μg mL-1) against the active stage of Mycobacterium tuberculosis and cancer cell lines such as HeLa and ThP1. This study could help optimize icosalides for anti-TB, antibacterial, and anti-cancer activities.

Discovery of Novel Benzo[4,5]imidazo[1,2-a]pyrazin-1-amine-3-amide-one Derivatives as Anticancer Human A2A Adenosine Receptor Antagonists.

The blockade of A2A adenosine receptor (A2AAR) activates immunostimulatory response through regulating signaling in tumor microenvironment. Thus, A2AAR has been proposed as a promising target for cancer immunotherapy. In this work, we designed a new series of benzo[4,5]imidazo[1,2-a]pyrazin-1-amine derivatives bearing an amide substitution at 3-position to obtain potent antitumor antagonist in vivo. The structure-activity relationship studies were performed by molecular modeling and radioactive assay. The in vitro anticancer activities were evaluated by 3',5'-cyclic adenosine monophosphate (cAMP) functional and T cell activation assay. The most potent compound 12o·2HCl showed much higher affinity toward A2AAR (Ki = 0.08 nM) and exhibited more significant in vitro immunostimulatory anticancer activity than clinical antagonist AZD4635. More importantly, 12o·2HCl significantly inhibited the growth of triple-negative breast cancer by reversing immunosuppressive tumor microenvironment in the xenograft mouse model without severe toxicity at the testing dose. These results make 12o·2HCl a promising immunotherapy anticancer drug candidate.

Development of highly selective fluorescent ferrocenyl-iminopyridine chemosensor for biologically relevant Fe3.

Design, synthesis, characterization, and ion detection studies of two ferrocene-appended Schiff bases namely N-(2-[ferrocenylamino]ethyl)-5-nitropyridin-2-amine (1) and ferrocenylamino-1H-imidazole-4-carboxamide (2) been reported. Both the chemosensors have been thoroughly characterized using Fourier transfer infrared, 1 H and 13 C nuclear magnetic resonance, high resolution mass spectrometry, and ultraviolet/visible (UV/visible) and fluorescence spectral techniques. Probes 1 and 2 were designed with the aim of appending the ferrocenyl group with pyridine ring having an amine substitution (for 1) and imidazole ring with an amide substitution (for 2). Interaction of these probes with a series of cations and anions was examined through UV/vis and fluorescence spectral techniques. Probe 2 exhibited an insignificant response towards anions and loss of selectivity for cations, whereas 1 displayed highly selective detection towards biologically important Fe3+ in 2:1 (probe:cation) stoichiometry. Notably, none of the cations and anions could interfere the selectivity of Fe3+ ensured by 1 in aqueous medium. The limit of detection for Fe3+ detection using 1 was determined to be 0.2 ppm. The results strongly suggest that 1 could find promising future application as a chemosensor for Fe3+ in biological systems for quantification and qualitative analysis.

Novel inhibitors of eukaryotic elongation factor 2 kinase: In silico, synthesis and in vitro studies

Eukaryotic elongation factor 2 kinase (eEF2K) is an unusual alpha kinase whose expression is highly upregulated in various cancers and contributes to tumor growth, metastasis, and progression. More importantly, eEF2K expression is associated with poor clinical outcome and shorter patient survival in breast, lung and ovarian cancers. Therefore, eEF2K is an emerging molecular target for development of novel targeted therapeutics and precision medicine in solid cancers. Currently, there are not any available potent and specific eEF2K inhibitors for clinical translation. In this study, we designed and synthesized a series of novel compounds with coumarin scaffold with various substitutions and investigated their effects in inhibiting eEF2K activity using in silico approaches and in vitro studies in breast cancer cells. We utilized an amide substitution at position 3 on the coumarin ring with their pharmacologically active groups containing pyrrolidine, piperidine, morpholine and piperazine groups with (CH2)2 bridged for aliphatic amides. Due to their ability to form covalent binding to the target enzyme, we also investigated the effects of boron containing groups on functionalized coumarin ring (3 compounds) and designed novel aliphatic and aromatic derivatives of coumarin scaffolds (10 compounds) and phenyl ring with boron groups (4 compounds). The Glide/SP module of the Maestro molecular modeling package was used to perform in silico analysis and molecular docking studies. According to our combined results, structure activity relationship (SAR) was performed in detail. Among the newly designed, synthesized, and tested compounds, our in vitro findings revealed that several compounds displayed a highly effective eEF2K inhibition at submicromolar concentrations in in vitro breast cancer cells. In conclusion, we identified novel compounds that can be used as eEF2K inhibitors and that they should be further evaluated by in vivo preclinical tumor models studies for antitumor efficacy and clinical translation.

Impact of Backbone Amide Substitution at the Meta- and Para-Positions on the Gas Barrier Properties of Polyimide.

This study designed and synthesised a meta-amide-substituted dianiline monomer (m-DABA) as a stereoisomer of DABA, a previously investigated para-amide-substituted dianiline monomer. This new monomer was polymerised with pyromellitic dianhydride (PMDA) to prepare a polyimide film (m-DABPI) in a process similar to that employed in a previous study. The relationship between the substitution positions on the monomer and the gas barrier properties of the polyimide film was investigated via molecular simulation, wide-angle X-ray diffraction (WXRD), and positron annihilation lifetime spectroscopy (PALS) to gain deeper insights into the gas barrier mechanism. The results showed that compared with the para-substituted DABPI, the m-DABPI exhibited better gas barrier properties, with a water vapour transmission rate (WVTR) and an oxygen transmission rate (OTR) as low as 2.8 g·m−2·d−1 and 3.3 cm3·m−2·d−1, respectively. This was because the meta-linked polyimide molecular chains were more tightly packed, leading to a smaller free volume and lower molecular chain mobility. These properties are not conducive to the permeation of small molecules into the film; thus, the gas barrier properties were improved. The findings have significant implications for the structural design of high-barrier materials and could promote the development of flexible display technology.

1,5-Disubstituted 1,2,3-Triazoles as Amide Bond Isosteres Yield Novel Tumor-Targeting Minigastrin Analogs.

1,5-Disubstituted 1,2,3-triazoles (1,5-Tz) are considered bioisosteres of cis-amide bonds. However, their use for enhancing the pharmacological properties of peptides or proteins is not yet well established. Aiming to illustrate their utility, we chose the peptide conjugate [Nle15]MG11 (DOTA-dGlu-Ala-Tyr-Gly-Trp-Nle-Asp-Phe-NH2) as a model compound since it is known that the cholecystokinin-2 receptor (CCK2R) is able to accommodate turn conformations. Analogs of [Nle15]MG11 incorporating 1,5-Tz in the backbone were synthesized and radiolabeled with lutetium-177, and their pharmacological properties (cell internalization, receptor binding affinity and specificity, plasma stability, and biodistribution) were evaluated and compared with [Nle15]MG11 as well as their previously reported analogs bearing 1,4-disubstituted 1,2,3-triazoles. Our investigations led to the discovery of novel triazole-modified analogs of [Nle15]MG11 with nanomolar CCK2R-binding affinity and 2-fold increased tumor uptake. This study illustrates that substitution of amides by 1,5-disubstituted 1,2,3-triazoles is an effective strategy to enhance the pharmacological properties of biologically active peptides.

Structure-antitumor activity relationships of tripodal imidazolium-amino acid based salts. Effect of the nature of the amino acid, amide substitution and anion.

The antitumor activity of imidazolium salts is highly dependent upon their lipophilicity that can be tuned by the introduction of different hydrophobic substituents on the nitrogen atoms of the imidazolium ring of the molecule. Taking this into consideration, we have synthesized and characterized a series of tripodal imidazolium salts derived from L-valine and L-phenylalanine containing different hydrophobic groups and tested them against four cancer cell lines at physiological and acidic pH. At acidic pH (6.2) the anticancer activity of some of the tripodal compounds changes dramatically, and this parameter is crucial to control their cytotoxicity and selectivity. Moreover, several of these compounds displayed selectivity against the control healthy cell line higher than four. The transmembrane anion transport studies revealed moderate transport abilities suggesting that the observed biological activity is likely not the result of just their transport activity. The observed trends in biological activity at acidic pH agree well with the results for the CF leakage assay. These results strongly suggest that this class of compounds can serve as potential chemotherapeutic agents.

Synthesis and conformation of backbone N-aminated peptides.

The chemical modification of peptides is a promising approach for the design of protein-protein interaction inhibitors and peptide-based drug candidates. Among several peptidomimetic strategies, substitution of the amide backbone maintains side-chain functionality that may be important for engagement of biological targets. Backbone amide substitution has been largely limited to N-alkylation, which can promote cis amide geometry and disrupt important H-bonding interactions. In contrast, N-amination of peptides induces distinct backbone geometries and maintains H-bond donor capacity. In this chapter we discuss the conformational characteristics of designed N-amino peptides and present a detailed protocol for their synthesis on solid support. The described methods allow for backbone N-amino scanning of biologically active parent sequences.

Imidazole and Imidazolium Antibacterial Drugs Derived from Amino Acids.

The antibacterial activity of imidazole and imidazolium salts is highly dependent upon their lipophilicity, which can be tuned through the introduction of different hydrophobic substituents on the nitrogen atoms of the imidazole or imidazolium ring of the molecule. Taking this into consideration, we have synthesized and characterized a series of imidazole and imidazolium salts derived from L-valine and L-phenylalanine containing different hydrophobic groups and tested their antibacterial activity against two model bacterial strains, Gram-negative E. coli and Gram-positive B. subtilis. Importantly, the results demonstrate that the minimum bactericidal concentration (MBC) of these derivatives can be tuned to fall close to the cytotoxicity values in eukaryotic cell lines. The MBC value of one of these compounds toward B. subtilis was found to be lower than the IC50 cytotoxicity value for the control cell line, HEK-293. Furthermore, the aggregation behavior of these compounds has been studied in pure water, in cell culture media, and in mixtures thereof, in order to determine if the compounds formed self-assembled aggregates at their bioactive concentrations with the aim of determining whether the monomeric species were in fact responsible for the observed antibacterial activity. Overall, these results indicate that imidazole and imidazolium compounds derived from L-valine and L-phenylalanine—with different alkyl lengths in the amide substitution—can serve as potent antibacterial agents with low cytotoxicity to human cell lines.

Design, synthesis and evaluation of novel nonquaternary and 3 non-oxime reactivators for acetylcholinesterase inhibited by organophosphates.

A new series of novel nonquaternary conjugates and non-oxime reactivators for reactivation of both nerve agents and pesticides inhibited hAChE were described in this paper. Conjugates with piperazine linked to the substituted salicylaldoxime emerged as efficient reactivators for VX inhibited hAChE. The in vitro reactivation experiment showed that some of them were equal or more efficient reactivators for pesticides inhibited hAChE than obidoxime. It was also found that some non-oxime derivatives of Mannich phenols displayed obvious reactivation potency for VX, sarin and pesticides inhibited hAChE even in very low concentration. It has been proved that introduction of peripheral site ligands with widespread aromatic system and amide substitutions could increase binding affinity for inhibited hAChE in most cases, which contribute to the reactivation efficiency.

Novel curcumin derivatives as P-glycoprotein inhibitors: Molecular modeling, synthesis and sensitization of multidrug resistant cells to doxorubicin

The MDR1/P-glycoprotein (Pgp)/ABCB1 multidrug transporter is being investigated as a druggable target for antitumor therapy for decades. The natural product curcumin is known to provide an efficient scaffold for compounds capable of blocking Pgp mediated efflux and sensitization of multidrug resistant (MDR) cells to the Pgp transported drug doxorubicin (Dox). We performed molecular dynamics simulations and docking of curcumin derivatives into the Pgp model. Based on these calculations, a series of pyrazolocurcumin derivatives with predicted metabolic stability and/or improved binding affinity were proposed for synthesis and evaluation of MDR reversal potency against Dox selected K562/4 subline, a derivative of K562 human chronic myelogenous leukemia cell line. Compounds 16 and 19 which are both dimethylcurcumin pyrazole derivatives bearing an N-p-phenylcarboxylic amide substitution, were the most potent Pgp blockers as determined by intracellular Dox accumulation. Furthermore, at non-toxic submicromolar concentrations 16 and 19 dramatically sensitized K562/4 cells to Dox. Together with good water solubility of 16 and 19, these results indicate that the new pyrazolo derivatives of curcumin are a promising scaffold for development of clinically applicable Pgp antagonists.

Enantioselective HPLC Analysis to Assist the Chemical Exploration of Chiral Imidazolines.

In the present work, we illustrate the ability of high-performance liquid chromatography (HPLC) analysis to assist the synthesis of chiral imidazolines within our medicinal chemistry programs. In particular, a Chiralpak® IB® column containing cellulose tris(3,5-dimethylphenylcarbamate) immobilized onto a 5 μm silica gel was used for the enantioselective HPLC analysis of chiral imidazolines synthesized in the frame of hit-to-lead explorations and designed for exploring the effect of diverse amide substitutions. Very profitably, reversed-phase (RP) conditions succeeded in resolving the enantiomers in nine out of the 10 investigated enantiomeric pairs, with α values always higher than 1.10 and RS values up to 2.31. All compounds were analysed with 50% (v) water while varying the content of the two organic modifiers acetonitrile and methanol. All the employed eluent systems were buffered with 40 mM ammonium acetate while the apparent pH was fixed at 7.5. Based on the experimental results, the prominent role of π-π stacking interactions between the substituted electron-rich phenyl groups outside of the polymeric selector and the complementary aromatic region in defining analyte retention and stereodiscrimination was identified. The importance of compound polarity in explaining the retention behaviour with the employed RP system was readily evident when a quantitative structure-property relationship study was performed on the retention factor values (k) of the 10 compounds, as computed with a 30% (v) methanol containing mobile phase. Indeed, good Pearson correlation coefficients of retention factors (r - log k1st = −0.93; r - log k2nd = −0.94) were obtained with a water solubility descriptor (Ali-logS). Interestingly, a n-hexane/chloroform/ethanol (88:10:2, v/v/v)-based non-standard mobile phase allowed the almost base-line enantioseparation (α = 1.06; RS = 1.26) of the unique compound undiscriminated under RP conditions.

Relay Catalysis To Synthesize β-Substituted Enones: Organocatalytic Substitution of Vinylogous Esters and Amides with Organoboronates

Organocatalysis was shown to facilitate conjugate additions to vinylogous esters and amides for the first time. Subsequent elimination of a β-alcohol or amine provided π-conjugated β-substituted enones. Remarkably, nucleophile addition to the electron-rich vinylogous substrates is more rapid than classical enones, forming monosubstituted products. A doubly organocatalytic (organic diol and methyl aniline) conjugate addition synthesized the products directly from alkynyl ketones. Both of these catalytic transformations are orthogonal to transition metal catalysis, allowing for good yields, easily accessible or commercially available reagents, high selectivity, reagent recovery and recyclability, facile scalability, and exceptional functional group tolerance.

Anion Mobility and Cation Diffusion in Alkali Metal Borohydrides

This study presents a wide spectrum of experimental investigations of alkali borohydrides МВН4 (М = Li, Na, K, Rb, Cs) and complex hydrides with substituted anions Li(BH4)1– yIy, LiLa(BH4)3Cl, and Na2(BH4)(NH2) obtained by the nuclear magnetic resonance method, quasielastic neutron scattering spectroscopy, and X-ray diffraction analysis. Activation energies for reorientational motion of anions in alkali borohydrides have been systematized, and possible configurations and types of jumps of ВН4 groups have been discussed. It has been shown that the activation energy of reorientations of ВН4 groups change nonmonotonously with the growth of the cation radius. Substitution of halides and amides for anions in complex hydrides leads to an enhancement in the frequency of anion reorientations at low temperatures, a change in the translational diffusion of cations at the expense of a change in the crystalline structure, the appearance of vacancies in the lattice, and influence of the paddle-wheel effect. Interrelation between the type of anion reorientations, cation diffusion, and the crystal lattice has been demonstrated.

Iron‐Catalyzed C(sp2)−C(sp3) Cross‐Coupling of Chlorobenzamides with Alkyl Grignard Reagents: Development of Catalyst System, Synthetic Scope, and Application

AbstractDirect preparation of alkylated amide‐derivatives by cross‐coupling chemistry using sustainable protocols is challenging due to sensitivity of the amide functional group to reaction conditions. Herein, we report the synthesis of alkyl‐substituted amides by iron‐catalyzed C(sp2)−C(sp3) cross‐coupling of Grignard reagents with aryl chlorides. The products of these reactions are broadly used in the synthesis of pharmaceuticals, agrochemicals and other biologically‐active molecules. Furthermore, amides are used as versatile intermediates that can participate in the synthesis of valuable ketones and amines, providing access to motifs of broad synthetic interest. The reaction is characterized by its good substrate scope, tolerating a range of amide substitution, including sterically‐bulky, sensitive and readily modifiable amides. The reaction is compatible with challenging organometallics possessing β‐hydrogens, and proceeds under very mild, operationally‐simple conditions. Optimization of the catalyst system demonstrated the beneficial effect of O‐coordinating ligands on the cross‐coupling. The reaction was found to be fully chemoselective for the mono‐substitution at the less sterically‐hindered position. Mechanistic studies establish the order of reactivity and provide insight into the role of amide to control mono‐selectivity of the alkylation. The protocol provides the possibility for convenient access to alkyl‐amide structural building blocks using sustainable cross‐coupling conditions with high efficiency.magnified image

A Carboxylate to Amide Substitution That Switches Protein Folds.

Metamorphic proteins are biomolecules prone to adopting alternative conformations. Because of this feature, they represent ideal systems to investigate the general rules allowing primary structure to dictate protein topology. A comparative molecular dynamics study was performed on the denatured states of two proteins, sharing nearly identical amino-acid sequences (88 %) but different topologies, namely an all-α-helical bundle protein named GA 88 and an α+β-protein named GB 88. The analysis allowed successful design of and experimental validation of a site-directed mutant that promotes, at least in part, the switch in folding from GB 88 to GA 88. The mutated position, in which a glutamic acid was replaced by a glutamine, does not make any intramolecular interactions in the native state of GA 88, such that its stabilization can be explained by considering the effects on the denatured state. The results represent a direct demonstration of the role of the denatured state in sculpting native structure.

A Carboxylate to Amide Substitution That Switches Protein Folds

AbstractMetamorphic proteins are biomolecules prone to adopting alternative conformations. Because of this feature, they represent ideal systems to investigate the general rules allowing primary structure to dictate protein topology. A comparative molecular dynamics study was performed on the denatured states of two proteins, sharing nearly identical amino‐acid sequences (88 %) but different topologies, namely an all‐α‐helical bundle protein named GA88 and an α+β‐protein named GB88. The analysis allowed successful design of and experimental validation of a site‐directed mutant that promotes, at least in part, the switch in folding from GB88 to GA88. The mutated position, in which a glutamic acid was replaced by a glutamine, does not make any intramolecular interactions in the native state of GA88, such that its stabilization can be explained by considering the effects on the denatured state. The results represent a direct demonstration of the role of the denatured state in sculpting native structure.