Final Amide Research Articles

Use of ionic liquids in amidation reactions for proteolysis targeting chimera synthesis.

Selective degradation of disease-causing proteins using proteolysis targeting chimeras (PROTACs) has gained great attention, thanks to its several advantages over traditional therapeutic modalities. Despite the advances made so far, the structural chemical complexity of PROTACs poses challenges in their synthetic approaches. PROTACs are typically prepared through a convergent approach, first synthesizing two fragments separately (target protein and E3 ligase ligands) and then coupling them to produce a fully assembled PROTAC. The amidation reaction represents the most common coupling exploited in PROTACs synthesis. Unfortunately, the overall isolated yields of such synthetic procedures are usually low due to one or more purification steps to obtain the final PROTAC with acceptable purity. In this work, we focused our attention on the optimization of the final amidation step for the synthesis of an anti-SARS-CoV-2 PROTAC by investigating different amidation coupling reagents and a range of alternative solvents, including ionic liquids (ILs). Among the ILs screened, [OMIM][ClO4] emerged as a successful replacement for the commonly used DMF within the HATU-mediated amidation reaction, thus allowing the synthesis of the target PROTAC under mild and sustainable conditions in very high isolated yields. With the optimised conditions in hand, we explored the scalability of the synthetic approach and the substrate scope of the reaction by employing different E3 ligase ligand (VHL and CRBN)-based intermediates containing linkers of different lengths and compositions or by using different target protein ligands. Interestingly, in all cases, we obtained high isolated yields and complete conversion in short reaction times.

The reaction of acetonitrile with hydrogen peroxide in alkaline medium: a DFT mechanistic study of green production of amides.

We have investigated using DFT methods the reaction mechanism of the Radzisewski reaction to obtain an amide via the reaction of ACN and H2O2 under alkaline conditions. The direct reaction between ACN and H2O2 showed a quite high activation energy (about 45 kcal mol-1) rendering this path unreliable. Instead, a fast reaction between ACN and HOO- forming the deprotonated species (PAIA-) of the peroxyacetimidic acid (PAIA) was observed. From this, PAIA- was guessed to form PAIA through a fast reaction of hydrolysis. Moreover, a second way of formation of PAIA, through an OH- catalyzed path, made the rate determining step (RDS) in very good agreement with experimental data, hence neglecting the contribution of the kinetically favored hydrolysis of PAIA-. This discrepancy was reconciled by considering that the final amide was obtained through a regioselective path forming the PAIA and the further reaction involving the decomposition of PAIA and PAIA-. Indeed, the PAIA obtained from the hydrolysis reaction showed a configuration which did not match the configurational behavior required. Conversely, the PAIA formed from the RDS path matched the required configuration needed to obtain the amide. Our findings also disentangled the experimenal debate on the assignment of the RDS.

Enantioselective Organophotocatalytic Telescoped Synthesis of a Chiral Privileged Active Pharmaceutical Ingredient.

The continuous flow, enantioselective, organophotoredox catalytic asymmetric alkylation of aldehydes was studied, by using a homemade, custom‐designed photoreactor for reactions under cryogenic conditions. Going from microfluidic conditions up to a 10 mL mesofluidic reactor, an increase of productivity by almost 18000 % compared to the batch reaction was demonstrated. Finally, for the first time, a stereoselective photoredox organocatalytic continuous flow reaction in a fully telescoped process for an active pharmaceutical ingredient (API)synthesis was successfully achieved. The final process consists of four units of operation: visible light‐driven asymmetric catalytic benzylation under continuous flow, inline continuous work‐up, neutralisation and a final oxidative amidation step afforded the pharmaceutically active molecule in 95 % e.e.

Anticancer Evaluation of Novel Quinazolinone Acetamides: Synthesis and Characterization.

According to the global cancer report 2019, the burden of cancer will exceed more than 18 million, becoming one of the major causes of global mortality rate. There is a pressing need to establish novel drug candidates for cancer treatment, though many anticancer agents are available in the market owing to their adverse effects. In recent years, quinazoline and its derivatives have been considered as a novel class of cancer chemotherapeutic agents that show promising activity against different tumors. To evaluate the anti-cancer potential of the novel class of quinazoline tethered acetamide derivatives against six different cancer cell lines. A novel series of various substituted quinazolinone acetamides were synthesized through a feasible scheme. The synthetic scheme involves the conversion of benzoxazinone (from anthranilic acid and benzoyl chloride) intermediate to 3-amino quinazoline-4-one which further converted to the final amide by tethering with the propionyl chloride employing Schotten-Baumann Reaction conditions. All the synthesized derivatives characterized by IR, 1HNMR and MASS spectral methods and anti-cancer activity were evaluated by employing MTT assay for six cancer cell lines and one normal human cell line. All the synthesized compounds were screened for anti-cancer activity against six cancer cell lines, including A 549 (lung), DU 145 (prostate), HT 29 (colon), MCF-7 (breast), SiHA (cervical), B16F10 (mouse skin melanoma) and one normal human fibroblast cell lines. All the compounds displayed a decent cytotoxicity profile when compared with the standard drug doxorubicin. Among the synthesized compounds (5a to 5n) tested, two compounds, 5f and 5g have demonstrated excellent cytotoxicity against SiHA and MCF-7 cancer cell lines. Comparatively most of the compounds displayed decent cytotoxicity potential relative to the standard drug doxorubicin. Further investigations are needed to establish the detailed mechanism of action of the developed novel quinazolinone acetamides.

An Efficient Second-Generation Manufacturing Process for the pan-RAF Inhibitor Belvarafenib

Herein, the development of a streamlined manufacturing process for the pan-RAF inhibitor belvarafenib (GDC-5573) is reported. The process to belvarafenib features a number of efficient key reactions, including a robust and scalable Pd-catalyzed carbonylation reaction to generate thienopyrimidine 2 and a highly chemoselective Pt/V/C-catalyzed nitro group reduction to access the penultimate intermediate 3. The final amide coupling was accomplished by a mild and safe protocol employing N,N,N′,N′-tetramethylchloroformamidinium hexafluorophosphate as the coupling reagent, which afforded belvarafenib on a multikilogram production scale after recrystallization.

Design, synthesis and nematicidal activitives of trifluorobutene amide derivatives against Meloidogyne incognita

Plant parasitic nematodes have always been a pressing problem in the field of plant protection. Well-established chemical nematicides, especially organophosphorus and carbamates are the most used products for nematode control worldwide. Due to long-term overuse, they have developed serious resistance and new innovative solutions are urgently required. In this study, thirty-one novel trifluorobutene amide derivatives were designed and synthesized, and their nematicidal activities were determined. Three different synthetic methods have been developed for the final amidation reaction enabling the successfully syntheses of the target compounds independently from the nucleophilicities of the substrate amino group. Most target compounds showed good nematicidal activity in our in vitro test. Among all the compounds, compounds A8 and A23 exhibited excellent nematicidal activity against Meloidogyne incognita, their LC50 values are 2.02 mg L−1 and 0.76 mg L−1, respectively. In particular, compound A23 has found to be almost as active as the commercial nematicide fluensulfone. Furthermore, most compounds gave full control (100% inhibition) of M. incognita at 40 mg L−1 in the in vivo tests in sandy soil, the best compounds were further investigated for in vivo activity in matrix soil. Among the compound tested, compound A8 showed excellent in vivo nematicidal activity. At a concentration of 5 mg L−1 still 56% inhibition was observed. The results of our study indicate that compound A8 possesses excellent in vitro and in vivo nematicidal activity, and can be considered as promising lead molecule for further modification.

Mechanistic studies of Cp*Ir(III)/Cp*Rh(III)-catalyzed branch-selective allylic C-H amidation: why is Cp*Ir(III) superior to Cp*Rh(III)?

Density functional theory calculations have revealed the mechanism and origins of the reactivity and regioselectivity of the Cp*Ir(iii)/Cp*Rh(iii)-catalyzed allylic C-H amidation of alkenes and dioxazolones. Generally, the catalytic cycle consists of alkene coordination, C(sp3)-H activation, dioxazolone oxidative addition, reductive elimination and proto-demetallation to give the final amidation product. The C-H activation is found to be the rate-determining step, and it controls the reactivity of the reaction. For the Cp*Ir(iii)-catalyzed system, the C-H activation undergoes an Ir(iii)-assisted proton transfer process with a low energy barrier, elucidating its high reactivity. In contrast, the C-H activation step is more like a direct deprotonation in the Cp*Rh(iii)-catalyzed system, which is responsible for its higher barrier and lower reactivity. The branched-selectivity arises from the electronic effect of the alkyl group on the charge distribution over the allylic moiety. Herein, iridium(v) polarizes the allylic group greater than that of the rhodium(v) system, which accounts for its good regioselectivity. The mechanistic insights will be useful for the further development of transition metal-catalyzed selective C-H amination reactions.

Radiolabeling of amide functionalized multi-walled carbon nanotubes for bioaccumulation study in fish bone using whole-body autoradiography

Commercial and medicinal applications of functionalized carbon nanotubes (f-CNTs) such as amidated f-CNTs are expanding rapidly with a potential risk exposure to living organisms. The effects of amidated f-CNTs on aquatic species have received a limited attention. In this work, an easy wet method to prepare [14C]-label amide multi-walled carbon nanotubes (MWNTs) is reported. Labeled carbon nanotubes were prepared by successive reactions of carboxylation, chloroacylation, and final amidation using [14C]-labeled ethanolamine. The f-CNTs were characterized using elemental analysis, electron dispersive X-ray, transmission electron microscopy, thermogravimetric analysis, and Raman and FTIR spectroscopy. An uptake experiment was carried out with juvenile Arctic char (Salvelinus alpinus) using water dispersed amidated [14C]-f-CNTs to assess their biodistribution in fish tissues using whole body autoradiography. The radioactivity pattern observed in fish head suggests that f-CNTs were accumulated in head bone canals, possibly involving an interaction with mineral or organic phases of bones such as calcium and collagen. This f-CNTs distribution illustrates how important is to consider the surface charges of functionalized carbon nanotubes in ecotoxicological studies.

Synthesis of PI3K inhibitor GDC-0077 via a stereocontrolled N-arylation of α-amino acids

An efficient synthesis of PI3K inhibitor GDC-0077, featuring two consecutive Cu-catalyzed CN coupling reactions, is reported. The described synthetic route involves a chemoselective Ullmann-type coupling of a chiral difluoromethyl-substituted oxazolidinone, a Cu-catalyzed N-arylation of l-alanine with high stereochemical integrity, and a high-yielding final amide bond formation step to produce GDC-0077 in >99.5 area % HPLC purity.

Relaxation-compensated APT and rNOE CEST-MRI of human brain tumors at 3 T.

Relaxation-compensated CEST-MRI (i.e., the inverse metrics magnetization transfer ratio and apparent exchange-dependent relaxation) has already been shown to provide valuable information for brain tumor diagnosis at ultrahigh magnetic field strengths. This study aims at translating the established acquisition protocol at 7 T to a clinically relevant magnetic field strength of 3 T. Protein model solutions were analyzed at multiple magnetic field strengths to assess the spectral widths of the amide proton transfer and relayed nuclear Overhauser effect (rNOE) signals at 3 T. This prior knowledge of the spectral range of CEST signals enabled a reliable and stable Lorentzian-fitting also at 3 T where distinct peaks are no longer resolved in the Z-spectrum. In comparison to the established acquisition protocol at 7 T, also the image readout was extended to three dimensions. The observed spectral range of CEST signals at 3 T was approximately ±15 ppm. Final relaxation-compensated amide proton transfer and relayed nuclear Overhauser effect contrasts were in line with previous results at 7 T. Examination of a patient with glioblastoma demonstrated the applicability of this acquisition protocol in a clinical setting. The presented acquisition protocol allows relaxation-compensated CEST-MRI at 3 T with a 3D coverage of the human brain. Translation to a clinically relevant magnetic field strength of 3 T opens the door to trials with a large number of participants, thus enabling a comprehensive assessment of the clinical relevance of relaxation compensation in CEST-MRI.

Synthesis of Mepivacaine and Its Analogues by a Continuous‐Flow Tandem Hydrogenation/Reductive Amination Strategy

Herein we report a convenient, fast, and high‐yielding method for the generation of the racemic amide anaesthetics mepivacaine, ropivacaine, and bupivacaine. Coupling of α‐picolinic acid and 2,6‐xylidine under sealed‐vessel microwave conditions generates the intermediate amide after a reaction time of only 5 min at 150 °C. Subsequent reaction in a continuous‐flow high‐pressure hydrogenator (H‐Cube ProTM) in the presence of the respective aldehyde directly converts the intermediate to the final amide anaesthetics in a continuous, integrated, multi‐step ring‐hydrogenation/reductive amination protocol. Merits and limitations of the protocol are discussed.

An improved and practical route for the synthesis of enzalutamide and potential impurities study

An improved and practical synthesis of enzalutamide was accomplished in five steps. Starting from 4-bromo-2-fluoro-benzonic acid, a methyl esterification, Ullmann ligation, methyl esterification, ring closing reaction and final methyl amidation provided the target in 35% total yield with 99.8% purity. Five identified impurities were also synthesized. This efficient and economical procedure avoids the use of highly toxic reagents and multiple recrystallization operations, which is suitable for further industrialization.

The Development of an Effective Synthetic Route of Belinostat

A practical synthetic route of belinostat is reported. Belinostat was obtained via a five-step process starting from benzaldehyde and including addition reaction with sodium bisulfite, sulfochlorination with chlorosulfonic acid, sulfonamidation with aniline, Knoevenagel condensation, and the final amidation with hydroxylamine. Key to the strategy is the preparation of 3-formylbenzenesulfonyl chloride using an economical and practical protocol. The main advantages of the route include inexpensive starting materials and acceptable overall yield. The scale-up experiment was carried out to provide 169 g of belinostat with 99.6% purity in 33% total yield.

The Amidation Step of Diphthamide Biosynthesis in Yeast Requires DPH6, a Gene Identified through Mining the DPH1-DPH5 Interaction Network

Diphthamide is a highly modified histidine residue in eukaryal translation elongation factor 2 (eEF2) that is the target for irreversible ADP ribosylation by diphtheria toxin (DT). In Saccharomyces cerevisiae, the initial steps of diphthamide biosynthesis are well characterized and require the DPH1-DPH5 genes. However, the last pathway step—amidation of the intermediate diphthine to diphthamide—is ill-defined. Here we mine the genetic interaction landscapes of DPH1-DPH5 to identify a candidate gene for the elusive amidase (YLR143w/DPH6) and confirm involvement of a second gene (YBR246w/DPH7) in the amidation step. Like dph1-dph5, dph6 and dph7 mutants maintain eEF2 forms that evade inhibition by DT and sordarin, a diphthamide-dependent antifungal. Moreover, mass spectrometry shows that dph6 and dph7 mutants specifically accumulate diphthine-modified eEF2, demonstrating failure to complete the final amidation step. Consistent with an expected requirement for ATP in diphthine amidation, Dph6 contains an essential adenine nucleotide hydrolase domain and binds to eEF2. Dph6 is therefore a candidate for the elusive amidase, while Dph7 apparently couples diphthine synthase (Dph5) to diphthine amidation. The latter conclusion is based on our observation that dph7 mutants show drastically upregulated interaction between Dph5 and eEF2, indicating that their association is kept in check by Dph7. Physiologically, completion of diphthamide synthesis is required for optimal translational accuracy and cell growth, as indicated by shared traits among the dph mutants including increased ribosomal −1 frameshifting and altered responses to translation inhibitors. Through identification of Dph6 and Dph7 as components required for the amidation step of the diphthamide pathway, our work paves the way for a detailed mechanistic understanding of diphthamide formation.

A Novel Convergent Synthesis of the Antiglaucoma PGF2α Analogue Bimatoprost

The 17-phenyl PGF(2α) analogue bimatoprost (10a) is the most efficacious ocular hypotensive agent currently available for the treatment of glaucoma or ocular hypertension. A novel convergent synthesis of 13,14-en-15-ol prostamideF(2α) analogues was developed employing Julia-Lythgoe olefination of the structurally advanced phenylsulfone (+)-(5Z)-15 with an enantiomerically pure aldehyde ω-chain synthon (-)-(S)-16a. Subsequent hydrolysis of protecting groups and final amidation of the diol 26a yielded bimatoprost (10a). The main advantage of the current strategy is the preparation of high-purity bimatoprost (10a). The novel convergent strategy allows the synthesis of a whole series of 13,14-en-15-ol prostamideF(2α) analogues with the desired C-15 asymmetric center configuration from a common and structurally advanced prostaglandin intermediate (+)-(5Z)-15. The preparation and identification of two synthetic impurities, 15-epi isomer (10b) of bimatoprost and a new prostaglandin related amide (+)-(5Z)-18, are also described.

Sequential covalent bonding activation and general base catalysis: insight into N-heterocyclic carbene catalyzed formylation of N–H bonds using carbon dioxide and silane

The detailed catalytic mechanisms of N-heterocyclic carbenes (NHCs) in the formylation of N–H bonds using carbon dioxide and silane were investigated using density functional theory (DFT) calculations. Among all the examined reaction pathways, we found that the most favorable pathway involves collaboration between the covalent bonding activation and general base catalysis. The overall reaction can be divided into four stages, including silane activation through a covalent bonding mechanism, CO2 insertion into the Si–H bond of silane to yield a key intermediate formoxysilane (FOS), the NHC-catalyzed coupling of amine and FOS through a general base mechanism, and C–O bond breaking through general base catalysis to obtain the final amide product. The carbamic acid anion (Me2NCOO−) is an inevitable intermediate from the side reactions, and its formation is almost barrier free. NHC can act as a base to abstract a proton from the nucleophiles (such as amines or alcohol), and facilitate C–N bond or C–O bond formation or cleavage, and such a general base mechanism is remarkably favorable over the covalent binding mechanism for C–N bond (or C–O) bond formation (or cleavage). The calculated thermodynamic properties are in good agreement with the available experimental findings.

Variation of the Net Charge, Lipophilicity, and Side Chain Flexibility in Dmt1-DALDA: Effect on Opioid Activity and Biodistribution

The influence of the side chain charges of the second and fourth amino acid residues in the peptidic μ opioid lead agonist Dmt-d-Arg-Phe-Lys-NH(2) ([Dmt(1)]-DALDA) was examined. Additionally, to increase the overall lipophilicity of [Dmt(1)]-DALDA and to investigate the Phe(3) side chain flexibility, the final amide bond was N-methylated and Phe(3) was replaced by a constrained aminobenzazepine analogue. The in vitro receptor binding and activity of the peptides, as well as their in vivo transport (brain in- and efflux and tissue biodistribution) and antinociceptive properties after peripheral administration (ip and sc) in mice were determined. The structural modifications result in significant shifts of receptor binding, activity, and transport properties. Strikingly, while [Dmt(1)]-DALDA and its N-methyl analogue, Dmt-d-Arg-Phe-NMeLys-NH(2), showed a long-lasting antinociceptive effect (>7 h), the peptides with d-Cit(2) generate potent antinociception more rapidly (maximal effect at 1h postinjection) but also lose their analgesic activity faster when compared to [Dmt(1)]-DALDA and [Dmt(1),NMeLys(4)]-DALDA.

Development of an Enantioselective Hydrogenation Based Synthesis of a Glucokinase Activator

This article describes the development and optimization of chemical reactions and subsequent multikilogram preparation of the glucokinase activator (R)-1 to fund clinical evaluation as a potential therapeutic for type II diabetes. The major process developments presented here are a Wittig olefination isomerization based synthesis of an E-acrylic acid, an optimized enantioselective hydrogenation of the E-acrylic acid, and a challenging final amide coupling.

Insights into Dehydrogenative Coupling of Alcohols and Amines Catalyzed by a (PNN)–Ru(II) Hydride Complex: Unusual Metal–Ligand Cooperation

Density functional theory calculations were performed to elucidate the mechanism of dehydrogenative coupling of primary alcohols and amines mediated by a PNN-Ru(II) hydride complex (PNN = (2-(di-tert-butylphosphinomethyl)-6-(diethylaminomethyl)pyridine)). A plausible reaction pathway was proposed which contains three stages: (1) The alcohol dehydrogenation reaction to generate the aldehyde and H(2); (2) The aldehyde-amine condensation reaction to form the hemiaminal intermediate; (3) The dehydrogenation process of the hemiaminal intermediate to yield the final amide product with the liberation of H(2). The first and third stages occur via a similar pathway: (a) Proton transfer from the substrate to the PNN ligand; (b) Intramolecular rearrangement of the deprotonated substrate to form an anagostic complex; (c) Hydride transfer from the deprotonated substrate to the Ru center to yield the trans-dihydride intermediate and the aldehyde (or amide); (d) Benzylic proton migration from the PNN ligand to the metal center forming a dihydrogen complex and subsequent H(2) liberation to regenerate the catalyst. In all these steps, the metal-ligand cooperation plays an essential role. In proton transfer steps (a) and (d), the metal-ligand cooperation is achieved through the aromatization/dearomatization processes of the PNN ligand. While in steps (b) and (c), their collaboration are demonstrated by the formation of an anagostic interaction between Ru and the C-H bond and two ionic hydrogen bonds supported by the PNN ligand.

The Total Synthesis of (±)‐Fumimycin

The antibiotic agent fumimycin has been synthesized for the first time. This natural product was found to inhibit the bacterial peptide deformylase and may represent a lead structure to a class of novel antibacterials. Our synthetic strategy towards fumimycin involved the following steps: Dakin oxidation of an aldehyde functionality, conversion of an oxime through radical fragmentation to form an N-diphenylphosphoryl group, construction of an α-trisubstituted amine by 1,2-addition to a ketimine, a Claisen rearrangement with subsequent transition-metal-catalyzed olefin isomerization to install a propenyl chain and final amidation.