Recent development in peptide coupling reagents

Synthesis of the Antimicrobial Peptide Murepavadin Using Novel Coupling Agents

The problem of antimicrobial resistance is becoming a daunting challenge for human society and healthcare systems around the world. Hence, there is a constant need to develop new antibiotics to fight resistant bacteria, among other important social and economic measures. In this regard, murepavadin is a cyclic antibacterial peptide in development. The synthesis of murepavadin was undertaken in order to optimize the preparative protocol and scale-up, in particular, the use of new activation reagents. In our hands, classical approaches using carbodiimide/hydroxybenzotriazole rendered low yields. The use of novel carbodiimide and reagents based on OxymaPure® and Oxy-B is discussed together with the proper use of chromatographic conditions for the adequate characterization of peptide crudes. Higher yields and purities were obtained. Finally, the antimicrobial activity of different synthetic batches was tested in three Pseudomonas aeruginosa strains, including highly resistant ones. All murepavadin batches yielded the same highly active MIC values and proved that the chiral integrity of the molecule was preserved throughout the whole synthetic procedure.

May 1,3,5-Triazine derivatives be the future of leather tanning? A critical review

Leather is produced by a multi-step process among which the tanning phase is the most relevant, transforming animal skin collagen into a stable, non-putrescible material used to produce a variety of different goods, for the footwear, automotive, garments, and sports industry. Most of the leather produced today is tanned with chromium (III) salts or alternatively with aldehydes or synthetic tannins, generating high environmental concern. Over the years, high exhaustion tanning systems have been developed to reduce the environmental impact of chromium salts, which nevertheless do not avoid the use of metals. Chrome-free alternatives such as aldehydes and phenol based synthetic tannins, are suffering from Reach restrictions due to their toxicity. Thus, the need for environmentally benign and economically sustainable tanning agents is increasingly urgent. In this review, the synthesis, use and tanning mechanism of a new class of tanning agents, 1,3,5-triazines derivatives, have been reported together with organoleptic, physical mechanical characteristics of tanned leather produced. Additionally environmental performance and economic data available for 1,3,5-triazines have been compared with those of a standard basic chromium sulphate tanning process, evidencing the high potentiality for sustainable, metal, aldehyde, and phenol free leather manufacturing.

Reactive deep eutectic solvents for EDC-mediated amide synthesis

The sustainability of amide bond formation is an ever-present topic in the pharmaceutical industry, as it represents the common motif in many clinically approved drugs. Despite many procedures for accomplishing eco-friendly amide synthesis having been developed, this transformation still remains a contemporary challenge. Herein, we report a greener approach for amide synthesis by using Reactive Deep Eutectic Solvents (RDESs) acting as both the reaction medium and reactants. The procedure not only avoids the use of hazardous solvents but also provides operationally simple product recovery with high purity and efficiency, without chromatographic purification. This approach was efficiently applied to the synthesis of a key intermediate in the production of an active pharmaceutical ingredient like atenolol. The green metrics of the gram-scale procedure were compared to the conventional industrial strategy showing an advancement in the greening of amide synthesis.

Natural carboxyterminal truncation of human CXCL10 attenuates glycosaminoglycan binding, CXCR3A signaling and lymphocyte chemotaxis, while retaining angiostatic activity

BACKGROUND

Interferon-γ-inducible protein of 10 kDa (IP-10/CXCL10) is a dual-function CXC chemokine that coordinates chemotaxis of activated T cells and natural killer (NK) cells via interaction with its G protein-coupled receptor (GPCR), CXC chemokine receptor 3 (CXCR3). As a consequence of natural posttranslational modifications, human CXCL10 exhibits a high degree of structural and functional heterogeneity. However, the biological effect of natural posttranslational processing of CXCL10 at the carboxy (C)-terminus has remained partially elusive. We studied CXCL10(1-73), lacking the four endmost C-terminal amino acids, which was previously identified in supernatant of cultured human fibroblasts and keratinocytes.

METHODS

Relative levels of CXCL10(1-73) and intact CXCL10(1-77) were determined in synovial fluids of patients with rheumatoid arthritis (RA) through tandem mass spectrometry. The production of CXCL10(1-73) was optimized through Fmoc-based solid phase peptide synthesis (SPPS) and a strategy to efficiently generate human CXCL10 proteoforms was introduced. CXCL10(1-73) was compared to intact CXCL10(1-77) using surface plasmon resonance for glycosaminoglycan (GAG) binding affinity, assays for cell migration, second messenger signaling downstream of CXCR3, and flow cytometry of CHO cells and primary human T lymphocytes and endothelial cells. Leukocyte recruitment in vivo upon intraperitoneal injection of CXCL10(1-73) was also evaluated.

RESULTS

Natural CXCL10(1-73) was more abundantly present compared to intact CXCL10(1-77) in synovial fluids of patients with RA. CXCL10(1-73) had diminished affinity for GAG including heparin, heparan sulfate and chondroitin sulfate A. Moreover, CXCL10(1-73) exhibited an attenuated capacity to induce CXCR3A-mediated signaling, as evidenced in calcium mobilization assays and through quantification of phosphorylated extracellular signal-regulated kinase-1/2 (ERK1/2) and protein kinase B/Akt. Furthermore, CXCL10(1-73) incited significantly less primary human T lymphocyte chemotaxis in vitro and peritoneal ingress of CXCR3+ T lymphocytes in mice. In contrast, loss of the four endmost C-terminal residues did not affect the inhibitory properties of CXCL10 on migration, proliferation, wound closure, phosphorylation of ERK1/2, and sprouting of human microvascular endothelial cells.

CONCLUSION

Our study shows that the C-terminal residues Lys74-Pro77 of CXCL10 are important for GAG binding, signaling through CXCR3A, T lymphocyte chemotaxis, but dispensable for angiostasis.

Synthesis, properties, and applications of a polyampholyte hydroxypropyl chitosan derivative with the phenylboronic acid functional group

Phenylboronic acid (PBA) groups are effective in building glucose-responsive drug delivery systems. Chitosan (CS) offers distinct advantages in the construction of PBA-based biomaterials, such as biodegradability and biocompatibility. However, challenges still persist due to the limited solubility of CS. This study proposes an efficient approach to introduce PBA groups into CS chains within 1 h via the O-(7-azabenzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HATU)-mediated amidation between 3-carboxyphenylboronic acid (CPBA) and O-hydroxypropyl chitosan (HPCS). The results showed that a wide range of substitution degrees, from 0.15 to 0.78, could be finely controlled by the amount of CPBA added. Furthermore, the obtained novel carboxyphenylboronic acid-grafted hydroxypropyl chitosan (PBA-HPCS) derivative showed enhanced crystallinity and thermostability compared to HPCS, and it demonstrated solubility in an alkaline solution. Based on the reversible bonding between the boronic acid group and cis-1,2/1,3-diols, PBA-HPCS was successfully used as an efficient crosslinker for the preparation of hydrogels incorporating sorbitol and polyhydroxy polymers, such as guar gum and polyvinyl alcohol. These hydrogels exhibited rapid gelation, rapid self-healing, injectability, and responsiveness to glucose and pH. These findings suggest that PBA-HPCS holds promise for advancing the development of PBA-based biomaterials.

A clickable melphalan for monitoring DNA interstrand crosslink accumulation and detecting ICL repair defects in Fanconi anemia patient cells

Fanconi anemia (FA) is a genetic disorder associated with developmental defects, bone marrow failure and cancer. The FA pathway is crucial for the repair of DNA interstrand crosslinks (ICLs). In this study, we have developed and characterized a new tool to investigate ICL repair: a clickable version of the crosslinking agent melphalan which we name click-melphalan. Our results demonstrate that click-melphalan is as effective as its unmodified counterpart in generating ICLs and associated toxicity. The lesions induced by click-melphalan can be detected in cells by post-labelling with a fluorescent reporter and quantified using flow cytometry. Since click-melphalan induces both ICLs and monoadducts, we generated click-mono-melphalan, which only induces monoadducts, in order to distinguish between the two types of DNA repair. By using both molecules, we show that FANCD2 knock-out cells are deficient in removing click-melphalan-induced lesions. We also found that these cells display a delay in repairing click-mono-melphalan-induced monoadducts. Our data further revealed that the presence of unrepaired ICLs inhibits monoadduct repair. Finally, our study demonstrates that these clickable molecules can differentiate intrinsic DNA repair deficiencies in primary FA patient cells from those in primary xeroderma pigmentosum patient cells. As such, these molecules may have potential for developing diagnostic tests.

Expeditious Access to the B3NO2 Heterocycle Enabling Modular Derivatization

DATB (1,3-dioxa-5-aza-2,4,6-triborinane) is a unique six-membered heterocycle exhibiting proficient catalytic activity in direct dehydrative amidation. Reported herein is an improved synthetic protocol for DATB derivatives featuring a concise two-step chromatography-free process. Suzuki-Miyaura coupling assembled 2,6-dibromoaniline derivatives and 1,2-phenylenediboronic acid to afford dimeric B-spiroborate salts. Acidic untying of the spiroborates gave rise to the DATB ring system with various substituents.

Synthesis and Characterization of Phenylalanine Amides Active against Mycobacterium abscessus and Other Mycobacteria

Nα-2-thiophenoyl-d-phenylalanine-2-morpholinoanilide [MMV688845, Pathogen Box; Medicines for Malaria Venture; IUPAC: (2R)-N-(1-((2-morpholinophenyl)amino)-1-oxo-3-phenylpropan-2-yl)thiophene-2-carboxamide)] is a hit compound, which shows activity against Mycobacterium abscessus (MIC90 6.25-12.5 μM) and other mycobacteria. This work describes derivatization of MMV688845 by introducing a thiomorpholine moiety and the preparation of the corresponding sulfones and sulfoxides. The molecular structures of three analogs are confirmed by X-ray crystallography. Conservation of the essential R configuration during synthesis is proven by chiral HPLC for an exemplary compound. All analogs were characterized in a MIC assay against M. abscessus, Mycobacterium intracellulare, Mycobacterium smegmatis, and Mycobacterium tuberculosis. The sulfone derivatives exhibit lower MIC90 values (M. abscessus: 0.78 μM), and the sulfoxides show higher aqueous solubility than the hit compound. The most potent derivatives possess bactericidal activity (99% inactivation of M. abscessus at 12.5 μM), while they are not cytotoxic against mammalian cell lines.

Predicting the Success of Fmoc-Based Peptide Synthesis

Synthetic peptides are commonly used in biomedical science for many applications in basic and translational research. While peptide synthesis is generally easy and reliable, the chemical nature of some amino acids as well as the many steps and chemical compounds involved can render the synthesis of some peptide sequences difficult. Identification of these problematic sequences and mitigation of issues they may present can be important for the reliable use of peptide reagents in several contexts. Here, we assembled a large dataset of peptides that were synthesized using standard Fmoc chemistry and whose identity was validated using mass spectrometry. We analyzed the mass spectra to identify errors in peptide syntheses and sought to develop a computational tool to predict the likelihood that any given peptide sequence would be synthesized accurately. Our model, named Peptide Synthesis Score (PepSySco), is able to predict the likelihood that a peptide will be successfully synthesized based on its amino acid sequence.

Discovering inhibitor molecules for pathological crystallization of CaOx kidney stones from natural extracts of medical herbs

ETHNOPHARMACOLOGICAL RELEVANCE

Kidney stones is one of the common diseases of the urinary system. The primary cause of kidney stone formation is the thermodynamic supersaturation of lithogenic solutes in urine, which desaturates by nucleation, crystal growth and aggregation of minerals and salts, mainly Calcium oxalate (CaOx). One of the potential therapies is to develop drug molecules to inhibit or prevent CaOx crystallization in urine. Traditional Chinese medicines (TCMs) provided an efficient approach for the treatment of kidney stones with a specialized-designed recipe of medicinal herbs. But the action details of these herbs were poorly understood due to their complex components, and whether the effective constituents of herbs have an inhibitory effect on the process of stone formation has not been evaluated.

AIM OF THE STUDY

This study aims to develop and identify inhibitor substitutes from a library of kidney stone prescriptions in traditional Chinese medicines to prevent pathological kidney stone formation.

MATERIALS AND METHODS

As many as twenty Chinese medicines were extracted and separated into five different polar extracts, the inhibition performance of which on CaOx crystallization was explored by recording and comparing crystallization kinetics. The potential inhibitor molecules in the inhibitory extracts were confirmed by HPLC and their retardation efficacy was evaluated by quantifying nucleation and growth kinetics using colorimetry. Then the inhibitor-COM crystal interactions and specificity were examined by morphology evolution and surface structure analysis. In vitro inhibition performance of inhibitors on crystal growth and attachment of CaOx crystals to human renal epithelial cells were further evaluated by recording the nucleation and adhesive crystal numbers.

RESULTS AND CONCLUSION

Water- and n-butanol- soluble extracts from 20 kinds of herbs show almost 100% inhibition percentage, and the n-butanol extracts was found better than commercial drug citrate. Twenty-one molecule substitutes were identified from these extracts, and among them polyphenols display the best inhibition efficacy to retard CaOx crystallization. The high-throughput colorimetric assay and morphology examinations reveals thirteen out of 21 molecules show inhibition potential and disrupt growth of CaOx monohydrate crystals by interacting with exposed Ca²⁺ and C₂O₄^2- on the (100) and (010) surfaces. Moreover, these inhibitors also display pronounced performance in protecting renal epithelial cells by inhibiting nucleation and adhesion of CaOx crystals to cells, thus reducing stone formation. The structure-performance correlation among 19 screened molecules that inhibitors having pKa<3.5, logD (pH = 6) <0, H-number>0.1 mmol are the best in suppressing CaOx crystallization. Our findings provide a novel solution to design and manufacture inhibitor drugs from Chinese medicines for preventing pathological kidney stones formation.

Versatile synthesis of pathogen specific bacterial cell wall building blocks

Full details on the design, strategies and tactics for development of a novel synthetic sequence to farnesyl lipid I and II analogs is reported. The modular route was based on a three coupling strategy involving an efficient solid phase synthesis of the elaborate peptide fragment, which proceeded with excellent yield and stereoselectivity and was efficiently applied for the convergent synthesis of 3-lipid I and II. Furthermore, the generality of this route was demonstrated by synthesis of 3-lipid I congeners that are characteristic for S. aureus and E. faecalis. All 3-lipid I and II building blocks were obtained in high purity revealing high spectroscopic resolution.

A modular three coupling strategy involving a versatile solid phase peptide synthesis enables access to pathogen specific lipid analogs in high yield, revealing high spectroscopic resolution of these key bacterial cell wall building blocks.

Chemical Synthesis of a Potent Antimicrobial Peptide Murepavadin Using a Tandem Native Chemical Ligation/Desulfurization Reaction

Classical approaches for the backbone cyclization of polypeptides require conditions that may compromise the chirality of the C-terminal residue during the activation step of the cyclization reaction. Here, we describe an efficient epimerization-free approach for the Fmoc-based synthesis of murepavadin using intramolecular native chemical ligation in combination with a concomitant desulfurization reaction. Using this approach, bioactive murepavadin was produced in a good yield in two steps. The synthetic peptide antibiotic showed potent activity against different clinical isolates of P. aeruginosa. This approach can be easily adapted for the production of murepavadin analogues and other backbone-cyclized peptides.

Synthesis and Antimicrobial Evaluation of Bis-morpholine Triazine Quaternary Ammonium Salts

Efficient, environmentally and economically sustainable, and nontoxic antibacterial products are of global relevance in the fight against microorganism contamination. In this work, an easy and straightforward method for the synthesis of bis-morpholino triazine quaternary ammonium salts (bis-mTQAS) is reported, starting from 2,4,6-trichloro-1,3,5-triazine or 2,4-dichloro-6-methoxy-1,3,5-triazine and various N-alkylmorpholines. Bis-mTQAS were tested as antimicrobials against Gram-negative and Gram-positive bacterial strains. The best-performing bis-mTQAS were found to achieve total disinfection against Staphylococcus aureus ATCC 25923 and Escherichia coli ATCC 25922 at 50 and 400 μg/mL, respectively. Distinctively, bis-mTQAS with the highest antimicrobial efficiency had lowest cytotoxicity.

Design, Synthesis, and Utility of Defined Molecular Scaffolds

A growing theme in chemistry is the joining of multiple organic molecular building blocks to create functional molecules. Diverse derivatizable structures—here termed “scaffolds” comprised of “hubs”—provide the foundation for systematic covalent organization of a rich variety of building blocks. This review encompasses 30 tri- or tetra-armed molecular hubs (e.g., triazine, lysine, arenes, dyes) that are used directly or in combination to give linear, cyclic, or branched scaffolds. Each scaffold is categorized by graph theory into one of 31 trees to express the molecular connectivity and overall architecture. Rational chemistry with exacting numbers of derivatizable sites is emphasized. The incorporation of water-solubilization motifs, robust or self-immolative linkers, enzymatically cleavable groups and functional appendages affords immense (and often late-stage) diversification of the scaffolds. Altogether, 107 target molecules are reviewed along with 19 syntheses to illustrate the distinctive chemistries for creating and derivatizing scaffolds. The review covers the history of the field up through 2020, briefly touching on statistically derivatized carriers employed in immunology as counterpoints to the rationally assembled and derivatized scaffolds here, although most citations are from the past two decades. The scaffolds are used widely in fields ranging from pure chemistry to artificial photosynthesis and biomedical sciences.

Eco-Friendly Synthesis of Peptides Using Fmoc-Amino Acid Chlorides as Coupling Agent Under Biphasic Condition

BACKGROUND

Agro-waste derived solvent media act as a greener process for the peptide bond formation using N^α-Fmoc-amino acid chloride and amino acid ester salt with in situ neutralization and coupling under biphasic condition. The Fmoc-amino acid chlorides are prepared by the reported procedure of freshly distilled SOCl₂ with dry CH₂Cl₂. The protocol found many added advantages such as neutralization of amino acid ester salt and not required additional base for the neutralization, and directly coupling take place with Fmoc-amino acid chloride gave final product dipeptide ester in good to excellent yields. The protocol occurs with complete stereo chemical integrity of the configuration of substrates. Here, we revisited Schotten-Baumann condition, instead of using inorganic base.

OBJECTIVE

To develop green protocol for the synthesis of peptide bond using Fmoc-amino acid chloride with amino acid esters salt.

METHODS

The final product isolated is analyzed in several spectroscopic and analytical techniques such as FT-IR, ¹H-, ¹³C-NMR, Mass spectrometry and RP-HPLC to check stereo integrity and purity of the product.

CONCLUSION

The present method developed greener using natural agro-waste (lemon fruit shell ash) derived solvent medium for the reaction and not required chemical entity.

Design of Affinity Chromatography Peptide Ligands Through Combinatorial Peptide Library Screening

In this chapter, a protocol to design affinity chromatography matrices with short peptide ligands immobilized for protein purification is described. The first step consists of the synthesis of a combinatorial peptide library on the hydroxymethylbenzoyl (HMBA)-ChemMatrix resin by the divide-couple-recombine (DCR) method using the Fmoc chemistry. Next, the library is screened with the protein of interest labeled with a fluorescent dye or biotin. Subsequently, peptides contained on positive beads are identified by tandem matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS/MS), and those sequences showing greater consensus are synthesized in larger quantities and immobilized on chromatographic supports. Finally, target protein adsorption on peptide affinity matrices is evaluated through equilibrium adsorption isotherms and breakthrough curves.

A Broad-Spectrum Catalytic Amidation of Sulfonyl Fluorides and Fluorosulfates*

A broad-spectrum, catalytic method has been developed for the synthesis of sulfonamides and sulfamates. With the activation by the combination of a catalytic amount of 1-hydroxybenzotriazole (HOBt) and silicon additives, amidations of sulfonyl fluorides and fluorosulfates proceeded smoothly and excellent yields were generally obtained (87-99 %). Noticeably, this protocol is particularly efficient for sterically hindered substrates. Catalyst loading is generally low and only 0.02 mol % of catalyst is required for the multidecagram-scale synthesis of an amantadine derivative. In addition, the potential of this method in medicinal chemistry has been demonstrated by the synthesis of the marketed drug Fedratinib via a key intermediate sulfonyl fluoride 13. Since a large number of amines are commercially available, this route provides a facile entry to access Fedratinib analogues for biological screening.

Synthesis of amides and esters containing furan rings under microwave-assisted conditions

In this work, we present a novel method for the synthesis of ester and amide derivatives containing furan rings (furfural derivatives) under mild synthetic conditions supported by microwave radiation. N-(Furan-2-ylmethyl)furan-2-carboxamide and furan-2-ylmethyl furan-2-carboxylate were produced using 2-furoic acid, furfurylamine, and furfuryl alcohol. The reactions were carried out in a microwave reactor in the presence of effective coupling reagents: DMT/NMM/TsO− or EDC. The reaction time, the solvent, and the amounts of the substrates were optimized. After crystallization or flash chromatography, the final compounds were isolated with good or very good yields. Our method allows for the synthesis of N-blocked amides using N-blocked amino acids (Boc, Cbz, Fmoc) and amine. As well as compounds with a monoamide and ester moiety, products with diamides and diester bonds (N,N-bis(furan-2-ylmethyl)furan-2,5-dicarboxamide, bis(furan-2-ylmethyl) furan-2,5-dicarboxylate, and furan-3,4-diylbis(methylene) bis(furan-2-carboxylate)) were synthesized with moderate yields in the presence of DMT/NMM/TsO– or EDC, using 2,5-furandicarboxylic acid and 3,4-bis(hydroxymethyl)furan as substrates.

Automated Solid-Phase Peptide Synthesis

The development of solid-phase peptide synthesis by Bruce Merrifield paved the way for a synthesis carried out by machines. Automated peptide synthesis is a fast and convenient way of synthesizing many peptides simultaneously. This chapter tries to give a general guidance for the development of synthesis protocols for the peptide synthesizer. It also provides some suggestions for the modification of the synthesized peptides. Additionally, many examples of possible challenges during and after the synthesis are given in order to support the reader in finding the best synthesis strategy. Numerous references are given to many of the described matters.

tert-Butyloxycarbonyl-protected amino acid ionic liquids and their application to dipeptide synthesis

Care should be taken when using amino acid ionic liquids (AAILs) for organic synthesis because of their multiple reactive groups. To expand the applicability of AAILs, we prepared a series of room-temperature ionic liquids derived from commercially available tert-butyloxycarbonyl-protected amino acids (Boc-AAILs). The resulting protected AAILs were used as the starting materials in dipeptide synthesis with commonly used coupling reagents. The distinctive coupling reagent N,N′-diethylene-N′′-2-chloroethyl thiophosphoramide was found to enhance amide formation in the Boc-AAILs without addition of base, giving the dipeptides in satisfactory yields in 15 min.

Chemically protected amino acid ionic liquids are synthesized for the first time and employed as triple reactant/solvent/additives in a novel solid-phase peptide synthesis method.

Hydrogen-Bond-Guided Reaction of Cyclohexadienone-aldehydes with Amines: Synthesis of an Aminal Group Containing a Fused Tetracyclic Framework

A modular approach has been developed for an efficient synthesis of an aminal group containing a new tetracyclic framework. The strategy has been devised based on selective hydrogen-bond-guided aza-Michael addition of heteroaromatic amines to cyclohexadienone-aldehydes. The reaction is highly atom economic and practical and involves stereoselective construction of four new C-N bonds and four rings. The synthetic utility of the tetracyclic product was explored. The role of a H-bond was explained with the help of experimental and density functional theory (DFT) computation studies.

Efficient modification of PAMAM G1 dendrimer surface with β-cyclodextrin units by CuAAC: impact on the water solubility and cytotoxicity

The toxicity of the poly(amidoamine) dendrimers (PAMAM) caused by the peripheral amino groups has been a limitation for their use as drug carriers in clinical applications. In this work, we completely modified the periphery of PAMAM dendrimer generation 1 (PAMAM G1) with β-cyclodextrin (β-CD) units through the Cu(i)-catalyzed azide–alkyne cycloaddition (CuAAC) to obtain the PAMAM G1-β-CD dendrimer with high yield. The PAMAM G1-β-CD was characterized by ¹H- and ¹³C-NMR and mass spectrometry studies. Moreover, the PAMAM G1-β-CD dendrimer showed remarkably higher water solubility than native β-CD. Finally, we studied the toxicity of PAMAM G1-β-CD dendrimer in four different cell lines, human breast cancer cells (MCF-7 and MDA-MB-231), human cervical adenocarcinoma cancer cells (HeLa) and pig kidney epithelial cells (LLC-PK1). The PAMAM G1-β-CD dendrimer did not present any cytotoxicity in cell lines tested which shows the potentiality of this new class of dendrimers.

The toxicity of the poly(amidoamine) dendrimers (PAMAM) caused by the peripheral amino groups has been a limitation for their use as drug carriers in clinical applications.

Microwave-assisted One-pot Synthesis of Amide Bond using WEB

Background:

Amide bond plays a key role in medicinal chemistry, and the analysis of bioactive molecular database revealed that the carboxamide group appears in more than 25% of the existing database drugs. Typically amide bonds are formed from the union of carboxylic acid and amine; however, the product formation does not occur spontaneously. Several synthetic methods have been reported for amide bond formation in literature. Present work demonstrated simple and eco-friendly amide bond formation using carboxylic acid and primary amines through in situ generation of O-acylurea. The reaction was found to be more efficient, faster reaction rate; simple work-up gave pure compound isolation in moderate to excellent yield using microwave irradiation as compared to conventional heating.

Methods:

Developed one-pot synthesis of amide compounds using agro-waste derived greener catalyst under microwave irradiation.

Results:

Twenty amide bond containing organic compounds are synthesized from carboxylic acid with primary amine catalyzed by agro-waste derived medium under microwave irradiation. First, the reaction involved carboxylic acid activation using EDC.HCl, which is the required base for the neutralization and coupling. The method employed natural agro-waste derived from banana peel ash (WEB) for the coupling gave target amide product without the use of an external organic or inorganic base.

Conclusion:

In the present work, we demonstrated that agro-waste extract is an alternative greener catalytic medium for the condensation of organic carboxylic acid and primary amine under microwave irradiation. The method found several advantages compared to reported methods like solventfree, non-toxic, cheaper catalyst, and simple reaction condition. The final isolated product achieved chromatographically pure by simple recrystallization and did not require further purification.

Cyclic Tetrapeptides from Nature and Design: A Review of Synthetic Methodologies, Structure, and Function

Small cyclic peptides possess a wide range of biological properties and unique structures that make them attractive to scientists working in a range of areas from medicinal to materials chemistry. However, cyclic tetrapeptides (CTPs), which are important members of this family, are notoriously difficult to synthesize. Various synthetic methodologies have been developed that enable access to natural product CTPs and their rationally designed synthetic analogues having novel molecular structures. These methodologies include the use of reversible protecting groups such as pseudoprolines that restrict conformational freedom, ring contraction strategies, on-resin cyclization approaches, and optimization of coupling reagents and reaction conditions such as temperature and dilution factors. Several fundamental studies have documented the impacts of amino acid configurations, N-alkylation, and steric bulk on both synthetic success and ensuing conformations. Carefully executed retrosynthetic ring dissection and the unique structural features of the linear precursor sequences that result from the ring dissection are crucial for the success of the cyclization step. Other factors that influence the outcome of the cyclization step include reaction temperature, solvent, reagents used as well as dilution levels. The purpose of this review is to highlight the current state of affairs on naturally occurring and rationally designed cyclic tetrapeptides, including strategies investigated for their syntheses in the literature, the conformations adopted by these molecules, and specific examples of their function. Using selected examples from the literature, an in-depth discussion of the synthetic techniques and reaction parameters applied for the successful syntheses of 12-, 13-, and 14-membered natural product CTPs and their novel analogues are presented, with particular focus on the cyclization step. Selected examples of the three-dimensional structures of cyclic tetrapeptides studied by NMR, and X-ray crystallography are also included.

Design, Synthesis, Antibacterial Potential, and Structural Characterization of N-Acylated Derivatives of the Human Autophagy 16 Polypeptide

A synthetic antimicrobial peptide library based on the human autophagy 16 polypeptide has been developed. Designed acetylated peptides bearing lipids of different chain lengths resulted in peptides with enhanced potency compared to the parent Atg16. A 21-residue fragment of Atg16 conjugated to 4-methylhexanoic acid (K30) emerged as the most potent antibacterial, with negligible hemolysis. Several studies, including microscopy, dye leakage, and ITC, were conducted to gain insight into the antibacterial mechanism of action of the peptide. Visual inspection using both SEM and TEM revealed the membranolytic effect of the peptide on bacterial cells. The selectivity of the peptide against bacterial cell membranes was also proven using dye leakage assays. ITC analysis revealed the exothermic nature of the binding interaction of the peptide to D8PG micelles. The three-dimensional solution NMR structure of K30 in complex with dioctanoylphosphatidylglycerol (D8PG) micelles revealed that the peptide adopts a helix-loop-helix structure in the presence of anionic membrane lipids mimicking bacterial membranes. Intermolecular NOEs between the peptide and lipid deciphered the location of the peptide in the bound state, which was subsequently supported by the paramagnetic relaxation enhancement (PRE) NMR experiment. Collectively, these results describe the structure-function relationship of the peptide in the bacterial membrane.

Functional Selectivity Revealed by N-Methylation Scanning of Human Urotensin II and Related Peptides

In accordance with their common but also divergent physiological actions, human urotensin II (1) and urotensin II-related peptide (2) could stabilize specific urotensin II receptor (UTR) conformations, thereby activating different signaling pathways, a feature referred to as biased agonism or functional selectivity. Sequential N-methylation of the amides in the conserved core sequence of 1, 2, and fragment U-II_4-11 (3) shed light on structural requirements involved in their functional selectivity. Thus, 18 N-methylated UTR ligands were synthesized and their biological profiles evaluated using in vitro competition binding assays, ex vivo rat aortic ring bioassays and BRET-based biosensor experiments. Biological activity diverged from that of the parent structures contingent on the location of amide methylation, indicating relevant hydrogen-bond interactions for the function of the endogenous peptides. Conformational analysis of selected N-methyl analogs indicated the importance of specific amide residues of 2 for the distinct pharmacology relative to 1 and 3.

Discovery, absolute assignments, and total synthesis of asperversiamides A-C and their potent activity against Mycobacterium marinum

Integrating molecular networking and ¹H NMR techniques successfully enabled the discovery of three new cycloheptapeptides, asperversiamides A-C (1-3). Their complete structures were further confirmed by total synthesis. All three compounds exhibited potent inhibitory activity against Mycobacterium marinum.

Amidation of methyl ester side chain bearing poly(2-oxazoline)s with tyramine: a quest for a selective and quantitative approach

Three new amidation approaches are evaluated to incorporate tyramine on methyl ester functional poly(2-oxazolines).

Pd-Catalyzed Suzuki-Miyaura Cross-Coupling of Pentafluorophenyl Esters

Although the palladium-catalyzed Suzuki-Miyaura cross-coupling of aryl esters has received significant attention, there is a lack of methods that utilize cheap and readily accessible Pd-phosphane catalysts, and can be routinely carried out with high cross-coupling selectivity. Herein, we report the first general method for the cross-coupling of pentafluorophenyl esters (pentafluorophenyl = pfp) by selective C–O acyl cleavage. The reaction proceeds efficiently using Pd(0)/phosphane catalyst systems. The unique characteristics of pentafluorophenyl esters are reflected in the fully selective cross-coupling vs. phenolic esters. Of broad synthetic interest, this report establishes pentafluorophenyl esters as new, highly reactive, bench-stable, economical, ester-based, electrophilic acylative reagents via acyl-metal intermediates. Mechanistic studies strongly support a unified reactivity scale of acyl electrophiles by C(O)–X (X = N, O) activation. The reactivity of pfp esters can be correlated with barriers to isomerization around the C(acyl)–O bond.

Identification of unexpected unlabeled N,N-dimethylamide formation in the synthesis of deuterated fragment of ribociclib by a HATU-mediated coupling reaction

Starting from N,N-dimethylamine and D₂ O, deuterated fragment of ribociclib was synthesized for use as a mass spectroscopy internal standard. Furthermore, systematic studies on D₀ (unlabeled material) formation during the amidation reaction were performed, leading to the identification of a coupling reagent, HATU (O-(7-azabenzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate), as main cause. Finally, an alternative route was designed using EDCI/HOBT as coupling reagents to produce the desired deuterated compound without D₀ residue.

Chemical activation of biochar for energy and environmental applications: a comprehensive review

Biochar (BC) generated from thermal and hydrothermal cracking of biomass is a carbon-rich product with the microporous structure. The graphene-like structure of BC contains different chemical functional groups (e.g. phenolic, carboxylic, carbonylic, etc.), making it a very attractive tool for wastewater treatment, CO2 capture, toxic gas adsorption, soil amendment, supercapacitors, catalytic applications, etc. However, the carbonaceous and mineral structure of BC has a potential to accept more favorable functional groups and discard undesirable groups through different chemical processes. The current review aims at providing a comprehensive overview on different chemical modification mechanisms and exploring their effects on BC physicochemical properties, functionalities, and applications. To reach these objectives, the processes of oxidation (using either acidic or alkaline oxidizing agents), amination, sulfonation, metal oxide impregnation, and magnetization are investigated and compared. The nature of precursor materials, modification preparatory/conditions, and post-modification processes as the key factors which influence the final product properties are considered in detail; however, the focus is dedicated to the most common methods and those with technological importance.

An Inexpensive and Scalable Synthesis of Shld

A synthesis of the important FKBP ligand Shld is reported. The synthesis avoids stoichiometric use of expensive and chiral reagents, maintains enantioselectivity and provides a high overall yield (39%). The main features in the method are enantioselective alkylation for preparation of the phenyl acetic acid moiety (building block A), catalytic enantioselective reduction for obtaining the chiral diaryl-1-propanol (building block C), and direct acylation of S-pipecolic tartrate rather than use of expensive Fmoc-pipecolic acid. The assembly of the building blocks A-C is reversed in comparison to previous synthesis, which also eliminates the need for protective groups.

Recyclable hypervalent-iodine-mediated solid-phase peptide synthesis and cyclic peptide synthesis

The system of the hypervalent iodine(III) reagent FPID and (4-MeOC6H4)3P was successfully applied to solid-phase peptide synthesis and cyclic peptide synthesis. Four peptides with biological activities were synthesized through SPPS and the bioactive cyclic heptapeptide pseudostellarin D was obtained via solution-phase peptide synthesis. It is worth noting that FPID can be readily regenerated after the peptide coupling reaction.

Automatic procedures for the synthesis of difficult peptides using oxyma as activating reagent: A comparative study on the use of bases and on different deprotection and agitation conditions

Solid-Phase Peptide Synthesis (SPPS) is a rapid and efficient methodology for the chemical synthesis of peptides and small proteins. However, the assembly of peptide sequences classified as "difficult" poses severe synthetic problems in SPPS for the occurrence of extensive aggregation of growing peptide chains which often leads to synthesis failure. In this framework, we have investigated the impact of different synthetic procedures on the yield and final purity of three well-known "difficult peptides" prepared using oxyma as additive for the coupling steps. In particular, we have comparatively investigated the use of piperidine and morpholine/DBU as deprotection reagents, the addition of DIPEA, collidine and N-methylmorpholine as bases to the coupling reagent. Moreover, the effect of different agitation modalities during the acylation reactions has been investigated. Data obtained represent a step forward in optimizing strategies for the synthesis of "difficult peptides".