Library Of Amides Research Articles

Enabling Modular Click Chemistry Library through Sequential Ligations of Carboxylic Acids and Amines.

High-throughput synthesis and screening of chemical libraries play pivotal roles in drug discovery. Click chemistry has emerged as a powerful strategy for constructing highly modular chemical libraries. However, the development of new click reactions and unlocking new clickable building blocks remain exceedingly challenging. Herein, we describe a double-click strategy that enables the sequential ligations of widely available carboxylic acids and amines with fluorosulfuryl isocyanate (FSO2NCO) via a modular amidation/SuFEx (sulfur-fluoride exchange) process. This method provides facile access to chemical libraries of N-fluorosulfonyl amides (RCONHSO2F) and N-acylsulfamides (RCONHSO2NR'R'') in near-quantitative yields under simple and practical conditions. The robustness and efficiency of this double click strategy is showcased by the facile construction of chemical libraries in 96-well microtiter plates from a large number of carboxylic acids and amines. Preliminary biological activity screening reveals that some compounds exhibit high antimicrobial activities against Gram-positive bacterium S. aureus and drug-resistant MRSA (MIC up to 6.25 μg ⋅ mL-1). These results provide compelling evidence for the potential application of modular click chemistry library as an enabling technology in high-throughput medicinal chemistry.

Development of New Drugs to Treat Tuberculosis Based on the Dinitrobenzamide Scaffold.

Tuberculosis (TB) continues to be a major global health challenge and a leading cause of death from infectious diseases. Inspired by the results from a previous work by our group on antimycobacterial N-alkylnitrobenzamides, which are structurally related to the nitrobenzamide family of decaprenylphosphoryl-β-d-ribose oxidase (DprE1) inhibitors, the present study explored a broad array of substituted benzamides. We particularly focused on previously unexplored 3,5-dinitrobenzamide derivatives. Starting with 3,5-dinitrobenzoic acid, we synthesized a diverse library of amides, incorporating both linear and cyclic amine moieties and also assessed the impact of terminal aromatic groups connected through ether, ester, or amide bonds on the bioactivity of the compounds. The synthesis primarily utilized nucleophilic addition/elimination, SN2, and Mitsunobu reactions. The activity was impacted mainly by two structural features, the addition of an aromatic moiety as a terminal group and the type of linker. The most interesting compounds (c2, d1, and d2, MIC = 0.031 μg/mL) exhibited activities against Mycobacterium Tuberculosis (Mtb) H37Rv comparable to isoniazid. Complementary computational studies helped elucidate potential interactions with DprE1, enhancing our understanding of the molecular basis of their action. Our findings suggest that the most active compounds provide a promising foundation for the continued development of new antimycobacterial agents.

Expanding the Chemical Space of Transforming Growth Factor-β (TGFβ) Receptor Type II Degraders with 3,4-Disubstituted Indole Derivatives.

The TGFβ type II receptor (TβRII) is a central player in all TGFβ signaling downstream events, has been linked to cancer progression, and thus, has emerged as an auspicious anti-TGFβ strategy. Especially its targeted degradation presents an excellent goal for effective TGFβ pathway inhibition. Here, cellular structure-activity relationship (SAR) data from the TβRII degrader chemotype 1 was successfully transformed into predictive ligand-based pharmacophore models that allowed scaffold hopping. Two distinct 3,4-disubstituted indoles were identified from virtual screening: tetrahydro-4-oxo-indole 2 and indole-3-acetate 3. Design, synthesis, and screening of focused amide libraries confirmed 2r and 3n as potent TGFβ inhibitors. They were validated to fully recapitulate the ability of 1 to selectively degrade TβRII, without affecting TβRI. Consequently, 2r and 3n efficiently blocked endothelial-to-mesenchymal transition and cell migration in different cancer cell lines while not perturbing the microtubule network. Hence, 2 and 3 present novel TβRII degrader chemotypes that will (1) aid target deconvolution efforts and (2) accelerate proof-of-concept studies for small-molecule-driven TβRII degradation in vivo.

Cyclobutanone Inhibitors of Diaminopimelate Desuccinylase (DapE) as Potential New Antibiotics.

Based on our previous success in using cyclobutanone derivatives as enzyme inhibitors, we have designed and prepared a 37-member library of α-aminocyclobutanone amides and sulfonamides, screened for inhibition of the bacterial enzyme diaminopimelate desuccinylase (DapE), which is a promising antibiotic target, and identified several inhibitors with micromolar inhibitory potency. Molecular docking suggests binding of the deprotonated hydrate of the strained cyclobutanone, and thermal shift analysis with the most potent inhibitor (3y, IC50 = 23.1 µM) enabled determination of a Ki value of 10.2 +/- 0.26 µM and observed two separate Tm values for H. influenzae DapE (HiDapE).

Broad Spectrum Enantioselective Amide Bond Synthetase from Streptoalloteichus hindustanus.

The synthesis of amide bonds is one of the most frequently performed reactions in pharmaceutical synthesis, but the requirement for stoichiometric quantities of coupling agents and activated substrates in established methods has prompted interest in biocatalytic alternatives. Amide Bond Synthetases (ABSs) actively catalyze both the ATP-dependent adenylation of carboxylic acid substrates and their subsequent amidation using an amine nucleophile, both within the active site of the enzyme, enabling the use of only a small excess of the amine partner. We have assessed the ability of an ABS from Streptoalloteichus hindustanus (ShABS) to couple a range of carboxylic acid substrates and amines to form amine products. ShABS displayed superior activity to a previously studied ABS, McbA, and a remarkable complementary substrate specificity that included the enantioselective formation of a library of amides from racemic acid and amine coupling partners. The X-ray crystallographic structure of ShABS has permitted mutational mapping of the carboxylic acid and amine binding sites, revealing key roles for L207 and F246 in determining the enantioselectivity of the enzyme with respect to chiral acid and amine substrates. ShABS was applied to the synthesis of pharmaceutical amides, including ilepcimide, lazabemide, trimethobenzamide, and cinepazide, the last with 99% conversion and 95% isolated yield. These findings provide a blueprint for enabling a contemporary pharmaceutical synthesis of one of the most significant classes of small molecule drugs using biocatalysis.

Synthesis, docking study and antimicrobial activity evaluation of pyridyl amides of thieno[2,3-d]pyrimidine-4-carboxylic acid

The aim. The combination in one molecule of pharmacophore fragments of thieno[2,3-d]pyrimidine-4-carboxylic acids with the fragments of 2- or 4-aminopyrimidine by peptide coupling promoted acylation in order to develop the new drug-like molecules with antimicrobial activity. Materials and methods. The molecular docking studies were performed with the AutoDock Vina та AutoDockTools 1.5.6 programs; TrmD Pseudomonas aeruginosa PDB ID – 5ZHN was used as the protein target. Synthetic methods of peptide coupling were used. 1H and 13C NMR spectra were recorded with a Varian-400 spectrometer at 400 MHz and Bruker Avance DRX 500 device at 500 MHz and 125 MHz in DMSO-d6 as a solvent, using TMS as the internal standard. LC-MS analysis of the compounds was carried out with Agilent 1100 HPLC з with atmospheric pressure chemical ionization (APCI). The studied derivates were tested in vitro for their antibacterial and anti-fungal activities using agar diffusion and serial dilutions resazurin-based microdilution assays (RBMA). Results and discussion. By the combination of the pharmacophore fragments of thieno[2,3-d]pyrimidine-4-carboxylic acids with the fragments of 2- of 4-aminopyrimidine, the combinatorial library of amides was constructed. For this library of compounds, the potential of antimicrobial activity was revealed using docking studies to the TrmD enzyme isolated from P. aeruginosa. The peptide coupling promoted by 1,1'-carbonyldiimidazole was found to be effective for the synthesis of pyridyl amides of thieno[2,3-d]pyrimidine-4-carboxylic acids, and it allowed to combine these pharmacophores in one molecule. The results of antimicrobial activity study revealed the broad spectrum of antimicrobial activity for N-(pyridin-4-yl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidine-4-carboxamide (2g), while 5,6-dimethyl-N-(6-methylpyridin-2-yl)thieno[2,3-d]pyrimidine-4-carboxamide (2c) showed the best MIC value against the reference strain of Pseudomonas aeruginosa ATCC 10145. N-(6-Methylpyridin-2-yl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidine-4-carboxamide (2h) was also found to be active against Pseudomonas aeruginosa. Conclusions. An effective method for the synthesis of pyridyl amides of thieno[2,3-d]pyrimidine-4-carboxylic acid has been developed. The amides molecular docking method showed their ability to inhibit TrmD enzyme isolated from P. aeruginosa; the further in vitro studies of the compounds showed the rationality of the further studies of the derivatives with 2-amino-6-methylpyridine in amide substituent because this fragment favoured the selectivity against Pseudomonas aeruginosa

Synthesis of Nitrone-derived Pyrrolidine Scaffolds and Their Combinatorial Libraries to Develop Selective α-l-Rhamnosidase Inhibitors.

A general and flexible approach toward the development of α-l-rhamnosidase (α-l-Rha-ase) inhibitors is described. Five enantiopure poly-substituted pyrrolidine-based scaffolds bearing the C1-aminomethyl moiety were designed and synthesized from five-membered cyclic nitrones. Each structurally diversified amide library of these scaffolds was rapidly generated via combinatorial parallel synthesis and applied for in-situ inhibition study against α-l-Rha-ase, allowing us to efficiently identify new inhibition hits. Surprisingly, all promising inhibitors are derived from the same scaffold 3. Among them, the most potent and selective inhibitor is pyrrolidine 19 with Ki =0.24 μM, approximately 24-fold more potent than the reference compound DAA (Ki =5.7 μM). It is the first study to comprehensively prepare pyrrolidine-based scaffolds and libraries for inhibition study against α-l-Rha-ase.

Platanic acid derived amides are more cytotoxic than their corresponding oximes

Albeit platanic acid has been known since 1956, its potential to act as a valuable starting material for the synthesis of cytotoxic agents has been neglected for many years. Hereby we describe the synthesis of a small library of amides and oximes derived from 3-O-acetyl-platanic acid, and the results of their screening as cytotoxic agents for several human tumor cell lines. As a result, while the cytotoxicity of the oximes was diminished as compared to the parent amides, the homopiperazinyl amide 5 held the highest cytoxicity (EC50 = 0.9 μM for A375 human melanoma cells). Extra FACS and cell cycle measurements showed compound 5 to act onto A375 cells rather by apoptosis than by necrosis.Clinical trial registrationNo clinical trials are associated with this studyGraphical abstract

Design, synthesis and screening of a drug discovery library based on an Eremophila-derived serrulatane scaffold

Chemical studies of the aerial parts of the Australian desert plant Eremophila microtheca afforded the targeted and known diterpenoid scaffolds, 3,7,8-trihydroxyserrulat-14-en-19-oic acid and 3-acetoxy-7,8-dihydroxyserrulat-14-en-19-oic acid. The most abundant serrulatane scaffold was converted to the poly-methyl derivatives, 3-hydroxy-7,8-dimethoxyserrulat-14-en-19-oic acid methyl ester and 3,7,8-trimethoxyserrulat-14-en-19-oic acid methyl ester using simple and rapid methylation conditions consisting of DMSO, NaOH and MeI at room temperature. Subsequently a 12-membered amide library was synthesised by reacting the methylated scaffolds with a diverse series of commercial primary amines. The chemical structures of the 12 undescribed semi-synthetic analogues were fully characterised following 1D/2D NMR, MS, UV, ECD and [α]D data analyses. All compounds were evaluated for their anthelmintic, anti-microbial and anti-viral activities. While none of the compounds significantly inhibited motility or development of the exsheathed third-stage larvae (xL3s) of a pathogenic ruminant parasite, Haemonchus contortus, the tri-methylated analogue induced a skinny phenotype in fourth-stage larvae (L4s) after seven days of treatment (IC50 = 14 μM). Anti-bacterial and anti-fungal activities were not observed at concentrations up to 20 μM. Activity against HIV latency reversal was tested in inducible, chronically-infected cells, with the tri-methylated analogue being the most active (EC50 = 38 μM).

Synthesis, In Silico Designing, Microbiological Evaluation and Structure Activity Relationship of Novel Amide Derivatives of 1-(2,4-Dinitrophenyl)-2-(3-Methylbenzo[b]Thiophen-6-yl)-1H-Benzo[d]Imidazole-5-Carboxylic Acid

Background Due to the growing crisis of antibiotic resistance, ample of different antibiotics accessible is declining and there are only a few of new antibiotics in the drug discovery pipeline. Therefore, there is an imperative need for the progress of new antimicrobial drugs. Method In the present study, synthesized amide derivatives of 1-(2,4-dinitrophenyl)-2-(3-methylbenzo[b]thiophen-6-yl)-1H-benzo[d]imidazole-5-carboxylic acid by centralize the tyrosyl-tRNA synthetase and aminoacyl-tRNA synthetase (AaRS)enzymes and inhibition study by docking leads to antimicrobial activity. Molecular docking studies were conceded out on a designed amide library, and the best 23 focused amide compounds of 1-(2,4-dinitrophenyl)-2-(3-methylbenzo[b]thiophen-6-yl)-1H-benzo[d]imidazole-5-carboxylic acid were privileged for synthesis based on the dock score evaluated by Schrodinger’s maestro package and AutoDock Vina 4.2 docking software against crystal structure of enzymes (PDB ID: 1wny.PDBQT and1jil.PDBQT) and investigated for in vitro antimicrobial activity. Results Among the library, the best compound A-4, A-5 and A-23 showing excellent dock score by AutoDock Vina/Schrodinger’s maestro against 1wny.PDBQT:1jil.PDBQT is −9.2:–10.6/–5.402: –5.653, −9.2: –10.6/–5.526/–5.734, −9.2: –10.6/–5.183: −5.679 as compared to standard drug dock score −10.2: –10.6/–5.847: –5.895 Derivatives A-4, A-5 and A-23 also flourished good MIC against six representative microorganisms as compared to standard by tube dilution method. Conclusions In vitro outcome naked that new synthesized compounds having excellent antimicrobial activity can be accustomed for in vivo studies for future.

A Series of Ferulic Acid Amides Reveals Unexpected Peroxiredoxin 1 Inhibitory Activity with in vivo Antidiabetic and Hypolipidemic Effects.

Insulin resistance is a major pathophysiological feature in the development of type 2 diabetes (T2DM). Ferulic acid is known for attenuating the insulin resistance and reducing the blood glucose in T2DM rats. In this work, we designed and synthesized a library of new ferulic acid amides (FAA), which could be considered as ring opening derivatives of the antidiabetic PPARγ agonists Thiazolidinediones (TZDs). However, since these compounds displayed weak PPAR transactivation capacity, we employed a proteomics approach to unravel their molecular target(s) and identified the peroxiredoxin 1 (PRDX1) as a direct binding target of FAAs. Interestingly, PRDX1, a protein with antioxidant and chaperone activity, has been implied in the development of T2DM by inducing hepatic insulin resistance. SPR, mass spectrometry-based studies, docking experiments and in vitro inhibition assay confirmed that compounds VIe and VIf bound PRDX1 and induced a dose-dependent inhibition. Furthermore, VIe and VIf significantly improved hyperglycemia and hyperlipidemia in streptozotocin-nicotinamide (STZ-NA)-induced diabetic rats as confirmed by histopathological examinations. These results provide guidance for developing the current FAAs as new potential antidiabetic agents.

The influence of high pressure on static combinatorial libraries of chiral BINOL-based macrocyclic amides

In this work we presented two-, three-, and four-substrate static combinatorial libraries (SCLs) obtained via macrocyclization of BINOL-based dimethyl ester and five α,ω-diaminoethers of varying lengths. We investigated the distribution of macrocyclic products and measured the conversion of ester, comparing the results under atmospheric pressure to those obtained under high pressure conditions. Overall, we found that pressurization had a great impact on the proportions between macrocyclic products, promoting diamides with smaller macrocyclic cavities, i.e. those formed with shorter diaminoethers. Furthermore, static combinatorial chemistry (SCC) approach allow us to receive various potential macrocyclic receptors in single experiment.

Antiproliferative activities of tricyclic amides derived from β-caryophyllene via the Ritter reaction against MDA-MB-231 breast cancer cells.

A library of novel tricyclic amides has been synthesised via the Ritter reaction from β-caryophyllene 1 and its monoepoxy derivative 4. The compounds were assessed for antiproliferative activities against the aggressive MDA-MB-231 breast cancer cell line. Of the synthesised compounds, eight were active. 3c and 6b were the most potent and inhibited proliferation with IC50 of 9.7 and 8.2 μM, respectively. Mechanistic studies revealed differences in their antiproliferative actions. 6b inhibited cell cycle progression and induced predominantly apoptotic cell death. In contrast, 3c did not affect cell cycle kinetics and favoured necrotic over apoptotic pathways. Screening against mammalian cells (VERO cells) indicates that 3c and 6b were more active towards MDA-MB-231 cells than noncancerous cells. Facile synthesis and biological results suggest that these caryophyllene derived amides are viable lead compounds for further development.

An improved, scalable synthesis of Notum inhibitor LP-922056 using 1-chloro-1,2-benziodoxol-3-one as a superior electrophilic chlorinating agent.

Background: The carboxylesterase Notum has been shown to act as a key negative regulator of the Wnt signalling pathway by mediating the depalmitoleoylation of Wnt proteins. LP-922056 (1) is an orally active inhibitor of Notum. We are investigating the role of Notum in modulating Wnt signalling in the central nervous system and wished to establish if 1 would serve as a peripherally restricted control. An accessible and improved synthetic route would allow 1 to become more readily available as a chemical tool to explore the fundamental biology of Notum and build target validation to underpin new drug discovery programs.Results: An improved, scalable synthesis of 1 is reported. Key modifications include: (1) the introduction of the C7-cyclopropyl group was most effectively achieved with a Suzuki–Miyaura cross-coupling reaction with MIDA-boronate 11 (5 → 6), and (2) C6 chlorination was performed with 1-chloro-1,2-benziodoxol-3-one (12) (6 → 7) as a mild and selective electrophilic chlorination agent. This 7-step route from 16 has been reliably performed on large scale to produce multigram quantities of 1 in good efficiency and high purity. Pharmacokinetic studies in mouse showed CNS penetration of 1 is very low with a brain/plasma concentration ratio of just 0.01. A small library of amides 17 were prepared from acid 1 to explore if 1 could be modified to deliver a CNS penetrant tool by capping off the acid as an amide. Although significant Notum inhibition activity could be achieved, none of these amides demonstrated the required combination of metabolic stability along with cell permeability without evidence of P-gp mediated efflux.Conclusion: Mouse pharmacokinetic studies demonstrate that 1 is unsuitable for use in models of disease where brain penetration is an essential requirement of the compound but would be an ideal peripherally restricted control. These data will contribute to the understanding of drug levels of 1 to overlay with appropriate in vivo efficacy endpoints, i.e., the PK-PD relationship. The identification of a suitable analogue of 1 (or 17) which combines Notum inhibition with CNS penetration would be a valuable chemical probe for investigating the role of Notum in disease models.

Identification of Gibberellic Acid Derivatives That Deregulate Cholesterol Metabolism in Prostate Cancer Cells.

The naturally occurring pentacyclic diterpenoid gibberellic acid (1) was used in the generation of a drug-like amide library using parallel-solution-phase synthesis. Prior to the synthesis, a virtual library was generated and prioritized based on drug-like physicochemical parameters such as log P, hydrogen bond donor/acceptor counts, and molecular weight. The structures of the synthesized analogues (2-13) were elucidated following analysis of the NMR, MS, UV, and IR data. Compound 12 afforded crystalline material, and its structure was confirmed by X-ray crystallographic analysis. All compounds were evaluated in vitro for cytotoxicity and deregulation of lipid metabolism in LNCaP prostate cancer cells. While no cytotoxic activity was identified at the concentrations tested, synthesized analogues 3, 5, 7, 10, and 11 substantially reduced cellular uptake of free cholesterol in prostate cancer cells, suggesting a novel role of gibberellic acid derivatives in deregulating cholesterol metabolism.

RETRACTED ARTICLE: Design, synthesis of novel oxazolidino-amides/sulfonamides conjugates and their impact on antibacterial activity

In view of generating new compounds for future drug development, we have synthesized oxazolidinones library of aryl amides and aryl sulfonamide derivatives. These compounds were screened in vitro against panel of susceptible and resistant Gram-positive (Staphylococcus aureus and Bacillus subtilis), Gram-negative bacteria (Pseudomonas aeruginosa), fungi (Candida albicans) strains, and Mycobacterium tuberculosis (Mtb). Among them, 10d and 11a compounds have been evaluated against 12 fungal strains and have displayed significant antimycotic activities approximately 37 folds more potent than fluconazole.

Synthesis and preliminary assessment of the anticancer and Wnt/\u03b2-catenin inhibitory activity of small amide libraries of fenamates and profens

As part of an ongoing program to study the anticancer activity of non-steroidal anti-inflammatory drugs (NSAIDs) through generating diversity libraries of multiple NSAID scaffolds, we synthesized a series of NSAID amide derivatives and screened these sets against three cancer cell lines (prostate, colon and breast) and Wnt/β-catenin signaling. The evaluated amide analog libraries show significant anticancer activity/cell proliferation inhibition, and specific members of the sets show inhibition of Wnt/β-catenin signaling.

The design, synthesis, and anti-inflammatory evaluation of a drug-like library based on the natural product valerenic acid

The plant natural product, valerenic acid (1) was chosen as a desirable scaffold for the generation of a novel screening library due to its drug-like physicochemical parameters (such as LogP, hydrogen bond donor/acceptor counts, and molecular weight). An 11-membered amide library (2–12) was subsequently generated using parallel solution-phase synthesis and Ghosez’s reagent. The chemical structures of all semi-synthetic analogues (2–12) were elucidated following analysis of the NMR, MS, UV and IR data. The structures of compounds 8 and 11 were also confirmed by X-ray crystallographic analysis. All library members were evaluated for their ability to inhibit the release of IL-8 and TNF-α. Six analogues showed moderate activity in the IL-8 assay with IC50 values of 2.8–8.3μM, while none of the tested compounds showed any significant effect on inhibiting TNF-α release.

Synthesis and Anticonvulsant Properties of New 3,3-Diphenyl-2,5-dioxo-pyrrolidin-1-yl-acetamides and 3,3-Diphenyl-propionamides.

The focused library of new amides derived from 3,3-diphenyl-2,5-dioxo-pyrrolidin-1-yl-acetic acid (2a-t) and 3,3-diphenyl-propionic acid (3a-t) as potential anticonvulsant agents was synthesized. The final products were obtained in the amidation reaction of the given carboxylic acid (2, 3) with appropriate secondary amines in the presence of carbonyldiimidazole (CDI) as a coupling reagent. The initial anticonvulsant screening was performed in mice intraperitoneally (i.p.) using the "classical" maximal electroshock (MES) and subcutaneous pentylenetetrazole (scPTZ) seizure models, whereas the acute neurological toxicity was determined applying the rotarod test. Additionally, several compounds were studied also in the 6-Hz seizures recognized as the animal model of human pharmacoresistant epilepsy. In this series, compound 3q displayed a broad spectrum of activity across the preclinical seizure models (ED50 MES = 31.64 mg/kg; ED50 scPTZ = 75.41 mg/kg, ED50 6-Hz (32 mA) = 38.15 mg/kg). Consequently, compound 3q revealed a wider spectrum of protection, higher activity or/and a better safety profile than the commonly used antiepileptic drugs such as phenytoin, ethosuximide, valproic acid, or/and levetiracetam. Notably, the in vitro studies showed that the most possible mechanism of action of 3q may be connected to the interaction with neuronal voltage-sensitive sodium channels (site 2). Other substances were active predominantly in the chemically induced seizures. The results of the current studies indicate that the presence of the pyrrolidine-2,5-dione ring is important but not indispensable for anticonvulsant activity.

Study on the propylphosphonic anhydride (T3P®) mediated Ugi-type three-component reaction. Efficient synthesis of an α-amino amide library

In the present work, a mild and simple synthesis of α-amino amides has been developed via the one-pot three-component ABC type Ugi reaction of a wide variety of aromatic aldehydes and primary aromatic amines, and two different aliphatic isocyanides. The reactions took place rapidly at room temperature in the presence of 1-propanephosphonic acid cyclic anhydride (T3P®), rendering possible the highly efficient preparation of an α-amino amide library in medium to excellent yields. This study represents the first case in which T3P® has been used in the Ugi reaction.