Predicting relative efficiency of amide bond formation using multivariate linear regression

Amides are ubiquitous in biologically active natural products and commercial drugs. The most common strategy for introducing this functional group is the coupling of a carboxylic acid with an amine, which requires the use of a coupling reagent to facilitate elimination of water. However, the optimal reaction conditions often appear rather arbitrary to the specific reaction. Herein, we report the development of statistical models correlating measured rates to physical organic descriptors to enable the prediction of reaction rates for untested carboxylic acid/amine pairs. The key to the success of this endeavor was the development of an end-to-end data science–based workflow to select a set of coupling partners that are appropriately distributed in chemical space to facilitate statistical model development. By using a parameterization, dimensionality reduction, and clustering protocol, a training set was identified. Reaction rates for a range of carboxylic acid and primary alkyl amine couplings utilizing carbonyldiimidazole (CDI) as the coupling reagent were measured. The collected rates span five orders of magnitude, confirming that the designed training set encompasses a wide range of chemical space necessary for effective model development. Regressing these rates with high-level density functional theory (DFT) descriptors allowed for identification of a statistical model wherein the molecular features of the carboxylic acid are primarily responsible for the observed rates. Finally, out-of-sample amide couplings are used to determine the limitations and effectiveness of the model.

Functionalization of Rhodamine Platforms with 3-Hydroxy-4-pyridinone Chelating Units and Its Fluorescence Behavior towards Fe(III)

Functionalization of xanthene fluorophores with specific receptor units is an important topic of research aiming for the development of new analytical tools for biological sciences, clinical diagnosis, food and environmental monitoring. Herein, we report a new dihydrorosamine containing two active amino groups, which was functionalized with 3-benzyloxy-1-(3′-carboxypropyl)-2-methyl-4-pyridinone through an amide coupling strategy. Benzylated mono- and di-functionalized dihydrorosamine derivatives (H in position 9 of the xanthene) were obtained, but with modest reaction yields, requiring long and laborious purification procedures. Looking for a more efficient approach, rhodamine 110 was selected to react with the carboxypropyl pyridinone, enabling the isolation of the corresponding mono- and di-functionalized derivatives in amounts that depend on the excess of pyridinone added to the reaction. The structure of all compounds was established by ¹H and ¹³C NMR, MS (ESI) and their absorption and emission properties were evaluated in dichloromethane. The fluorescence behavior of the debenzylated mono-rhodamine 110 derivative in the presence of Fe(III) was studied, making it an interesting fluorogenic dye for future optical sensing applications.

Identification of Novel and Potent Indole-Based Benzenesulfonamides as Selective Human Carbonic Anhydrase II Inhibitors: Design, Synthesis, In Vitro, and In Silico Studies

In recent decades, human carbonic anhydrase inhibitors (hCAIs) have emerged as an important therapeutic class with various applications including antiglaucoma, anticonvulsants, and anticancer agents. Herein, a novel series of indole-based benzenesulfonamides were designed, synthesized, and biologically evaluated as potential hCAIs. A regioisomerism of the sulfonamide moiety was carried out to afford a total of fifteen indole-based benzenesulfonamides possessing different amide linkers that enable the ligands to be flexible and develop potential H-bond interaction(s) with the target protein. The activity of the synthesized compounds was evaluated against four hCA isoforms (I, II, IX and, XII). Compounds 2b, 2c, 2d, 2f, 2h and 2o exhibited potent and selective profiles over the hCA II isoform with K_i values of 7.3, 9.0, 7.1, 16.0, 8.6 and 7.5 nM, respectively. Among all, compound 2a demonstrated the most potent inhibition against the hCA II isoform with an inhibitory constant (K_i) of 5.9 nM, with 13-, 34-, and 9-fold selectivity for hCA II over I, IX and XII isoforms, respectively. Structure–activity relationship data attained for various substitutions were rationalized. Furthermore, a molecular docking study gave insights into both inhibitory activity and selectivity of the target compounds. Accordingly, this report presents a successful scaffold hoping approach that reveals compound 2a as a highly potent and selective indole-based hCA II inhibitor worthy of further investigation.

Biofunctionalization of Water-Soluble poly(Phenylene Ethynylene)s

We report the use of amide coupling chemistry to covalently link five different biofunctional groups onto an anionic water-soluble poly(phenylene ethynylene) (PPE) polymer. Two of the biofunctionalized PPEs are used in prototype applications, including pH sensing and flow cytometry labeling. The PPE is functionalized with carboxylate (R-CO2-) and sulfonate (R-SO3-) ionic groups. By using an activated ester, the amine-functionalized groups are covalently linked to the PPE polymer via amide linkages. The reaction chemistry is optimized using biotin-ethylene diamine, making it possible to control the loading of the biotin functionality on the PPE chains. Using the optimized approach, a family of five PPEs were prepared that contain biotin, rhodamine, cholesterol, mannose, or folic acid moieties appended to the polymer backbones. The rhodamine- and biotin-modified PPEs were further applied for pH response and flow cytometry applications. The reported approach can be utilized for other classes of water-soluble conjugated polymers, allowing facile development of a variety of new functionalized water-soluble conjugated polymers for a range of applications including sensing, bioimaging, and flow cytometry analysis.

Using Surface Amide Couplings to Assemble Photocathodes for Solar Fuel Production Applications

A facile surface amide-coupling method was examined to attach dye and catalyst molecules to silatrane-decorated NiO electrodes. Using this method, electrodes with a push-pull dye were assembled and characterized by photoelectrochemistry and transient absorption spectroscopy. The dye-sensitized electrodes exhibited hole injection into NiO and good photoelectrochemical stability in water, highlighting the stability of the silatrane anchoring group and the amide linkage. The amide-coupling protocol was further applied to electrodes that contain a molecular proton reduction catalyst for use in photocathode architectures. Evidence for catalyst reduction was observed during photoelectrochemical measurements and via femtosecond-transient absorption spectroscopy demonstrating the possibility for application in photocathodes.

Synthesis and antimicrobial evaluation of piperic acid amides and their lower homologues

Seven piperic acid amides along with their lower homologs (12) were synthesized using HATU-DIPEA coupling reagent. All the synthesized derivatives were evaluated for their antibacterial activities against Staphylococcus aureus, Pseudomonas aeruginosa, and vancomycin-resistant P. aeruginosa. They were found to be more active on P. aeruginosa than on S. aureus. However, they did not exhibit potent activity on Vancomycin resistant P. aeruginosa. Among the tested compounds, methylenedioxycinnamic acid amide of anthranilic acid (MDCA-AA, 2a) was found to be most active against S. aureus with MIC of 3.125 μg/ml. The PAS and INH amides of piperic acid were screened against Mycobacterium tuberculosis H37R_a strain. They were found to be most active among all the tested compounds but were found to be less active than the standard drug, isoniazid.

Oxidative Amide Coupling from Functionally Diverse Alcohols and Amines Using Aerobic Copper/Nitroxyl Catalysis

The aerobic Cu/ABNO catalyzed oxidative coupling of alcohols and amines is highlighted in the synthesis of amide bonds in diverse drug-like molecules (ABNO=9-azabicyclo[3.3.1]nonane N-oxyl). The robust method leverages the privileged reactivity of alcohols bearing electronegative hetero- atoms (O, F, N, Cl) in the β-position. The reaction tolerates over 20 unique functional groups and is demonstrated on a 15 mmol scale under air. Steric constraints of the catalyst allow for chemoselective amidation of primary amines in the presence of secondary amines. All catalyst components are commercially available, and the reaction proceeds under mild conditions with retention of stereocenters in both reaction partners, while producing only water as a by-product.

Oxidative Reactivity and Cytotoxic Properties of a Platinum(II) Complex Prepared by Outer-Sphere Amide Bond Coupling

Benzyl amine was coupled to the dangling carboxylic acid groups of the platinum(II) complex [Pt(edda)Cl₂], where edda = ethylenediamine-N,N'-diacetic acid, to give the diamidetethered complex [Pt(L)Cl₂] (1), where L = ethylenediamine-N,N'-bis(N-benzylacetamide). Complex 1 was oxidized with both PhICl₂ and Br₂. Oxidation with PhICl₂ cleanly afforded the tetrachloride complex, [Pt(L)Cl₄] (2), whereas oxidation with Br₂ gave rise to several mixed halide complexes of the general formula, [Pt(L)Cl_xBr_4-x], where x = 1, 2, or 3. Complexes 1 and 2 were fully characterized by ¹H, ¹³C, and ¹⁹⁵Pt NMR spectroscopy, as well as by ESI-MS. These compounds exist as a mixture of diastereomers that arise from the chirality of the two coordinated nitrogen atoms. Crystal structures of 1, 2, and [Pt(L)Cl_xBr_y] (3) are reported. Although refined as the tetrabromide complex [Pt(L)Br₄], the crystal structure of 3 is a mixture of species with site-occupancy disorder of chloride and bromide ligands. DFT calculations indicate that the two sets of diastereomers of 1 and 2 are effectively thermoneutral, a conclusion that is also supported by the observation of both members of each pair by NMR spectroscopy. The cytotoxicity of 1 and 2 was measured by the MTT assay in HeLa cells and compared to that of cisplatin. Both exhibit IC₅₀ values close to 50 μM and are therefore substantially less toxic than cisplatin, for which the IC₅₀ is 1 μM.

Spheroid organization kinetics of H35 rat hepatoma model cell system on elastin-like polypeptide-polyethyleneimine copolymer substrates

Though two-dimensional systems have yielded some success in deriving morphological and functional markers of hepatocyte culture, they largely fail to capture the three-dimensional organization, long-term viability, and functionality of the hepatic tissue. We have engineered a system for inducing self-assembly of model H35 rat hepatoma spheroids using a copolymer comprised of biocompatible elastin-like polypeptide (ELP) chemically conjugated to positively charged polyethyleneimine (PEI). We have achieved a conjugation ratio of 30 mol %, though our studies analyzing spheroid organization kinetics indicate conjugate ratios of 5 mol % and greater to be optimal for cell culture based on least variability in spheroid sizes and minimum incidence of overgrown aggregates. Furthermore, our ELP-PEI system indicated the potential for influencing ultimate spheroid dimensions, with spheroid size inversely related to polyelectrolyte conjugation. Overall, this study provides a good starting point to investigate functional correlations between spheroid size and functional markers and their future use as an in vitro diagnostic or tissue engineering tool.