Crude Reaction Mixture Research Articles

Rapid optimisation of fragments and hits to lead compounds from screening of crude reaction mixtures

Fragment based methods are now widely used to identify starting points in drug discovery and generation of tools for chemical biology. A significant challenge is optimization of these weak binding fragments to hit and lead compounds. We have developed an approach where individual reaction mixtures of analogues of hits can be evaluated without purification of the product. Here, we describe experiments to optimise the processes and then assess such mixtures in the high throughput crystal structure determination facility, XChem. Diffraction data for crystals of the proteins Hsp90 and PDHK2 soaked individually with 83 crude reaction mixtures are analysed manually or with the automated XChem procedures. The results of structural analysis are compared with binding measurements from other biophysical techniques. This approach can transform early hit to lead optimisation and the lessons learnt from this study provide a protocol that can be used by the community.

Cover Feature: Activity‐Directed Synthesis of Inhibitors of the p53/hDM2 Protein–Protein Interaction (Chem. Eur. J. 47/2020)

Activity-directed synthesis was harnessed in the function-driven discovery of inhibitors of a protein–protein interaction. Pairs of substrates, inspired by known ligands, were exploited in 346 microscale reactions. The crude reaction mixtures were screened for biological function, and the products of promising reactions purified and characterised. Four novel and distinct inhibitor series were discovered. The artwork illustrates how motifs found in known ligands were incorporated into substrates, ultimately enabling scaffold-hopping to new inhibitor series. More information can be found in the Communication by A. Nelson et al. on page 10682.

HPLC method for the determination of monomer conversion and composition during the poly(styrene-r-methylmethacrylate) polymerization

Copolymers of styrene (STY) and methylmetacrylate (MMA) are widely employed due to the low price of the starting monomers coupled with their synthetic versatility. A chromatographic method was developed for the simultaneous determination of the conversion degree of the single components of the polymer during the copolymerization reaction and the composition of the produced copolymer. The crude reaction mixture is directly analyzed during the reaction with only a dilution pretreatment. Accordingly, the method allows quick and simple monitoring of the reaction as it proceeds.

Dual C‐C Bond Forming Heck and Sonogashira Couplings Followed by Hydroarylation: Synthesis of Tricyclic Frameworks

AbstractHerein, a concise approach to construct the novel tricyclic ether frameworks, is presented. Microwave‐assisted dual C‐C bond‐forming palladium‐catalyzed intramolecular Heck/intermolecular Sonogashira couplings were implemented, for the synthesis of dihydrobenfurans bearing acetylene moiety, followed by acid‐induced intramolecular hydroarylation reaction of the crude reaction mixture furnished the tricyclic ether systems. Notably, these tricyclic ether frameworks have been achieved, in excellent yields, through a single column chromatography process.

An improved preparation of [18 F]AV-45 by simplified solid-phase extraction purification.

Amyvid (florbetapir f18, [18 F]AV-45, [18 F]5) was the first FDA-approved positron emission tomography imaging agent targeting β-amyloid (Aβ) plaques for assisting the diagnosis of Alzheimer disease. This work aimed to improve the [18 F]AV-45 ([18 F]5) preparation by using solid-phase extraction (SPE) purification. [18 F]AV-45 ([18 F]5) was synthesized by direct nucleophilic radiofluorination of O-tosylated precursor (1 mg) at 120°C in anhydrous dimethyl sulfoxide (DMSO), followed by acid hydrolysis of the N-Boc protecting group. Purification was accomplished by loading the crude reaction mixture to a cartridge (Oasis HLB 3 cc) and eluting with different combinations of solvents. This method removed the chemical impurity while leaving [18 F]AV-45 ([18 F]5) on the cartridge. The final dose was eluted by ethanol. [18 F]AV-45 ([18 F]5) was produced within 51 minutes (radiochemical yield 42.7 ± 5.9%, decay corrected, n = 3), and the radiochemical purity was greater than 95%. Total chemical impurity per batch (24.1 ± 2.7 μg per batch) was below the limit described in the package insert of Amyvid, florbetapir f18 (chemical mass: less than 50 μg/dose). In summary, [18 F]AV-45 ([18 F]5) was produced efficiently and reproducibly using a cartridge-based SPE purification. This method brings the process closer for routine preparation, similar to the commercially used [18 F]FDG.

Direct regioisomer analysis of crude reaction mixtures via molecular rotational resonance (MRR) spectroscopy.

Direct analyses of crude reaction mixtures have been carried out using molecular rotational resonance (MRR) spectroscopy. Two examples are presented, a demonstration application in photocatalytic CH-arylation as well as generation of an intermediate in a natural product synthesis. In both cases, the reaction can proceed at more than one site, leading to a mixture of regioisomers that can be challenging to distinguish. MRR structural parameters were calculated for the low lying conformers for the desired compounds, and then compared to the experimental spectra of the crude mixtures to confirm the presence of these species. Next, quantitation was performed by comparing experimentally measured line intensities with simulations based on computed values for the magnitude and direction of the molecular dipole moment of each species. This identification and quantification was performed without sample purification and without isolated standards of the compounds of interest. The values obtained for MRR quantitation were in good agreement with the chromatographic values. Finally, previously unknown impurities were discovered within the photocatalytic CH-arylation work. This paper demonstrates the utility of MRR as a reaction characterization tool to simplify analytical workflows.

Recent Contributions of Nuclear Magnetic Resonance in Organocatalysis Mechanism Elucidation

Background: Nuclear Magnetic Resonance (NMR) is one of the most employed techniques in structural elucidation of organic compounds. In addition to its use in structural characterization, it has been widely employed in the investigation of reaction mechanisms, especially those involving catalysis. Objective: In this review, we aim to provide recent examples of the interface of NMR and organocatalysis reaction mechanism. Methods: Selected examples of different approaches for mechanism elucidation will be presented, such as isotopic effect, catalyst labelling and online reaction monitoring. A discussion involving the use of solid-state NMR will also be disclosed. Conclusion: NMR consists of a non-destructive technique, extremely useful in the real-time identification of intermediates in crude reaction mixtures. With the advent of two-dimensional experiments and high field NMR spectrometers, the reports of studies involving mechanistic elucidation were greatly enhanced. In this context, nowadays NMR appears as a powerful tool for the comprehension of reaction mechanisms, including the possibility of the proposal of unknown reaction mechanisms within organocatalysis.

Discovery and Comparison of Homogeneous Catalysts in a Standardized HOT‐CAT Screen with Microwave‐Heating and qNMR Analysis: Exploring Catalytic Hydration of Alkynes

AbstractA HOT‐CAT (homogeneous thermal catalysis) screen using microwave‐heating and quantitative NMR (qNMR) analysis has been developed for identification and comparison of catalyst activity in homogeneous metal‐based catalysis. The hydration of terminal alkynes to ketones or aldehydes served as a model reaction in this proof‐of‐concept study. Key aspects of the screen are the use of a high‐temperature setting (e. g., 160 °C) at a fixed, short reaction time (e. g., 15 min) for all samples. Analysis of crude reaction mixtures by a standardized, quantitative 1H NMR protocol gives a comprehensive picture of catalyst chemo‐ and regioselectivity, which permits broad comparisons and the discovery of non‐target reactivity. For catalytic alkyne hydration, data for 105 runs involving 81 catalyst systems with 15 different metals is presented. The activity of all established catalyst systems was reproduced, and new catalyst systems with Markovnikov hydration selectivity were discovered and applied to preparative runs, namely Cu2O−CSA (CSA=camphorsulfonic acid), Co(OAc)2−tetraphenylporphyrin−CSA and [IrCl(COD)]−CSA.

High-Throughput Solid-Phase Building Block Synthesis for DNA-Encoded Libraries.

Herein we provide a generalizable method for the cost-effective synthesis of thousands of building blocks (BBs) employing DNA-incompatible chemistries. The ability to produce large numbers of crude products via solid-phase synthesis has existed for decades; however, our work demonstrates a practical use of such crude reaction mixtures and employs DNA-conjugation to simultaneously encode, purify, and rapidly analyze the desired products. This workflow generated sp3-rich BBs that could be encoded by DNA in a high-throughput manner.

Synthesis of Dihydropyrimidinones (DHPMs) and Hexahydro Xanthene Catalyzed by 1,4-Diazabicyclo [2.2.2] Octane Triflate Under Solvent-Free Condition.

DABCO salts were evaluated as catalysts for the Biginelli reaction between 4- methoxybenzaldehyde, urea and ethyl acetoacetate under solvent-free conditions. 1,4-Diazabicyclo [2.2.2] octane triflate was found to be a simple, inexpensive, highly efficient catalyst for Biginelli reaction for a variety aromatic aldehyde with urea and ethyl acetoacetate at 80°C afforded corresponding 3,4-dihydropyrimidinones in 50-99% yields after 30-120 minutes. 1,3-Cyclohexadione was used in place of ethyl acetoacetate in the absence of urea this methodology is giving hexahydro xanthene derivatives in good to excellent yields after 3-4 hours. DABCO salt 4 (5 mol%), 4-methoxybenzaldehyde (0.73 mmol) and urea (0.73 mmol) were stirred for 10 minutes at 80°C, then ethyl acetoacetate (1.5 equiv.) was added and reaction mixture was stirred at 80°C for specified time. The resulting solution was stirred continuously and progress of the reaction was followed by TLC. The crude reaction mixture was purified by flash column chromatography on silica gel (hexane/ethyl acetate (1:2)) to give pure desired product. Reaction conditions of the Biginelli reaction were optimized using 4-methoxybenzaldehyde (0.73 mmol), urea (0.73 mmol), and ethyl acetoacetate (5 equiv.) as model substrates catalyzed by 1,4-Diazabicyclo [2.2.2] octane triflate (5 mol%) in a different solvents, screening of different catalysts and different temperatures. Neat condition was found to be the best for the Biginelli condensation and corresponding 3,4- dihydropyrimidinones was obtained in good to excellent yields. When the reaction was carried out with benzaldehyde derivatives and cyclohexane-1,3-dione in place of ethyl acetoacetate in the absence of urea, solely corresponding hexahydro xanthene derivatives were obtained in 61-91% yields. In conclusion, we have applied salts of 1,4-Diaza-bicyclo [2.2.2] octane as catalysts in the Biginelli condensation and corresponding 3,4-dihydropyrimidinones were obtained in 50- 99% yields under solvent free conditions. This methodology is having advantages like simple work-up; low loading of catalyst and reaction was performed at moderate temperature under solvent-free conditions.

Fast and efficient copper-mediated 18F-fluorination of arylstannanes, aryl boronic acids, and aryl boronic esters without azeotropic drying

BackgroundCopper-mediated radiofluorination is a straightforward method to produce a variety of [18F]fluoroarenes and [18F]fluoroheteroarenes. To minimize the number of steps in the production of 18F-labelled radiopharmaceuticals, we have developed a short and efficient azeotropic drying-free 18F-labelling method using copper-mediated fluorination. Our goal was to improve the copper-mediated method to achieve wide substrate scope with good radiochemical yields with short synthesis time.ResultsSolid phase extraction with Cu (OTf)2 in dimethylacetamide is a suitable activation method for [18F]fluoride. Elution efficiency with Cu (OTf)2 is up to 79% and radiochemical yield (RCY) of a variety of model molecules in the crude reaction mixture has reached over 90%. Clinically relevant molecules, norepinephrine transporter tracer [18F]NS12137 and monoamine transporter tracer [18F]CFT were produced with 16.5% RCY in 98 min and 5.3% RCY in 64 min, respectively.ConclusionsCu (OTf)2 is a suitable elution agent for releasing [18F]fluoride from an anion exchange cartridge. The method is fast and efficient and the Cu-complex is customizable after the release of [18F]fluoride. Alterations in the [18F]fluoride elution techniques did not have a negative effect on the subsequent labelling reactions. We anticipate this improved [18F]fluoride elution technique to supplant the traditional azeotropic drying of [18F]fluoride in the long run and to concurrently enable the variations of the copper-complex.

Synthesis and structural characterization of nickel(II) complexes of 20-membered macrocyclic rings bearing chelating bis(N-heterocyclic carbene) ligands

20-Membered macrocyclic rings (Lbenz and Limid) containing two amine moieties and two N-heterocyclic carbene (NHC) moieties coordinate in a κ2 coordination mode to Ni(II) through the NHC moieties. Complexes 3a and 3b were synthesized by generating free carbenes in situ from bis-benzimidazolium bromide salts and subsequent addition of one equivalent of [Ni(DME)X2] (X = Cl, Br) at 25 °C. Free carbenes of 20-membered macrocyclic ligands Lbenz and Limid can be generated in situ in THF-d8 and characterized by 1H and 13C NMR spectroscopy. 3b can also be synthesized by treatment of silver(I)-bis(NHC) complex 2a with one equivalent of [NiBr2(DME)] in refluxing methylene chloride for 20 h affording yields of up to70%. Complexes 3a and 3b were characterized by X-ray diffraction. [NiI2(Lbenz)] 5c was prepared by halogen exchange of 3a or 3b with NaI at 25 °C. Ni complexes of Limid can be prepared and characterized in situ but cannot be isolated cleanly from the reaction mixtures. The cis and trans isomers of [NiCl2(Limid)] (4a and 4b) and the bromide derivative 4c were characterized by X-ray crystallography by judicious selection of individual, high-quality crystals obtained from crude reaction mixtures.

Separation of Unprecedented Degradants of Domperidone by Ultra-Performance Convergence Chromatography and Their Structure Elucidation.

Domperidone, a gastroprokinetic agent, is a common drug to treat emesis. It was subjected to acid, base-mediated hydrolysis, peroxide-mediated oxidation, photolysis and thermal degradation according to ICH guidelines to observe stability of the selected drug under the stress conditions. Although the drug is resistant to base hydrolysis, photolysis and thermal stressors, two degradants (DP-ISO1 and DP-ISO2) were formed in acid mediated hydrolysis. Oxidation with hydrogen peroxide also resulted in one product (DP-OX). All three degradants were isolated from the crude reaction mixture by preparative high-performance liquid chromatography and supercritical fluid chromatography. Structures of isolated compounds were unambiguously characterized as 5-chloro-1-(1-(3-(6-chloro-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)propyl)piperidin-4-yl)-1,3-dihydro-2H-benzo[d]imidazol-2-one (DP-ISO1), 5-chloro-1-(3-(4-(5-chloro-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)piperidin-1-yl)propyl)-1,3-dihydro-2H-benzo[d]imidazol-2-one (DP-ISO2), 4-(5-chloro-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)-1-(3-(2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)propyl)piperidine 1-oxide (DP-OX) by analysis of mass spectrometry, 1D and 2D nuclear magnetic resonance spectra. To the best of our knowledge, DP-ISO1 and DP-ISO2 are new and DP-OX was previously reported as domperidone impurity.

A Synthetic Route Toward Tetrazoles: The Thermolysis of Geminal Diazides.

A new synthetic route toward the tetrazole core is described, which is based on a general fragmentation pattern that was found in a range of compounds featuring geminal diazido units. Through a simple two‐step procedure, the synthesis of structurally diverse target compounds containing a tetrazole, such as tetrazoloquinoxalinones, benzoylaryltetrazoles, tetrazolotriazinones, and tetrazoloazepinones, was easily accomplished, starting from broadly accessible substrates (i.e., oxindoles, diarylethanones, pyrazolones, and phenanthrols). The initial oxidative diazidation reaction with iodine and sodium azide under mild conditions is followed by the thermal fragmentation under microwave irradiation, leading to the tetrazole products. Noteworthy, an experimental solution is presented in which the potentially hazardous diazide intermediates are not isolated and the concentration of crude reaction mixtures containing diazides is not required to achieve the tetrazoles in good yields.

Subminute micro-isolation of pharmaceuticals with ultra-high pressure liquid chromatography

The drive for faster separations while maintaining quality and yield remains an important consideration for enhanced productivity as well as cost reduction for drug discovery laboratories in the pharmaceutical industry. High-throughput experimentation (HTE) and high-throughput screening (HTS) techniques can benefit from rapid and efficient isolation of product at high purity and recovery from microgram-scale crude reaction mixtures. In this study we describe the isolation of small molecule and biomolecule crude mixtures at the microgram-scale (100–2500 μg) in single or library format with methods as fast as 1.0 min and system pressures averaging 10,000 psi with an ultra-high pressure liquid chromatography (UHPLC) setup. UHPLC technology provides several advantages for rapid (<1.0 min) separations with small-particle (1.8–3.5 μm) size 4.6 × 50 mm C18 columns such as minimal extra column and delay volume, fast detector response time, and higher linear velocities for improved speed and resolution. We typically see a 5–10 fold improvement in purification time and overall sample processing time with low fraction volumes and same-day drying when compared with traditional semi-preparative techniques. There is a significant 50-fold reduction in solvent usage per run, resulting in a much lower cost of solvent and waste handling. Fluidic pathways have been optimized for collection into tared high-density 96 or 384 well 2D barcoded storage tubes in a microtiter plate (MTP) layout. Coupling the system to robotics has enabled us to implement a fully integrated automation platform with additional capabilities for small-scale purification at high speed and reduced cost of materials. The resulting arrays of small-quantity, high-purity compounds enable synthetic route scouting for HTE and HTS for biological target validation.

Streamlined Asymmetric Reaction Development: A Case Study with Isatins.

Asymmetric reaction development within a day or two has been a dream of synthetic chemists for several decades. We now show that such a task is feasible with a highly efficient streamlined screening strategy using the asymmetric allylation of isatins with a chiral boron complex as a case study. Our high-throughput screening (HTS) method is based on fast optical UV/CD analysis of minute amounts of crude reaction mixtures (≈3 mg scale) and it obviates product isolation and the general need for reference compounds which greatly reduces preliminary work and analysis time. The setup, reaction screening, analysis and data processing for 54 asymmetric allylations of nine different isatins in six different solvents was handled by a single operator in less than 20 work hours. One could easily extend this HTS strategy to hundreds of reactions in roughly the same time frame and further reduce the labor with commercially available automated high-throughput experimentation equipment. The effectiveness of this asymmetric reaction development strategy is confirmed with the upscale synthesis of two representative 3-allyl-3-hydroxyisatins in 98-99 % yield and with 91-94 % ee under optimized conditions.

7-(Biphenyl-4-yl)-6-hydroxyindan-1-one

The title compound, C21H16O2, was isolated from the reaction of 1-(2-methoxyethoxy)-1-vinylcyclopropane, 4-ethynylbiphenyl, and CO in a [5 + 1 + 2 + 1] cycloaddition reaction catalysed by [Rh(CO)2Cl]2. The crystals precipitated directly from the crude reaction mixture. A hydrogen-bonding framework between the hydroxy and carbonyl groups of a symmetry-related neighbour connects the molecules into chains running parallel to the crystallographic c axis. A minor non-merohedral twin component was included in the refinement.

Frustrated Lewis pairs: A real alternative to deuteride/tritide reductions.

Deuterium- and tritium-labeled compounds play a principal role in tracing of biologically active molecules in complicated biochemical systems. The state-of-the-art techniques using noble metal catalysts or strong reducing agents often suffers from low functional group tolerances, poor selectivity, tricky or multistep synthesis of reagents, and low specific activity of the labeled product. Herein, we demonstrate a mild and nonmetallic technique of deuteration and tritiation of polarized double bonds, such as carbonyl compounds, yielding labeled alcohols of high specific activities. This one-pot synthesis uses carrier-free hydrogen gas in situ activated by a freshly prepared frustrated Lewis pair, generating reducing reagents. This labeling strategy shows better selectivity and functional group tolerances compared with current reductive methods. Reported is an example of the selective reduction of the aldehyde moiety of 3-acetylbenzaldehyde. What makes this technology groundbreaking is its mildness, selectivity, and generation of limited amount of radioactive waste as almost no byproducts were generated after use of (B(C6 F5 )33 H)(3 HTMP) reducing reagent. Radiochemical purity of desired 3 H-labeled product in a crude reaction mixture was determined of over 94%. This work provides, to the community of radiochemists, a practical protocol for frustrated Lewis pairs (FLP)-assisted deuterium/tritium labeling technology.

Simple one pot synthesis of ketone from carboxylic acid using DCC as an activator

Simple one pot procedure for the conversion of carboxylic acid to ketone is described. Various carboxylic acids were converted to the corresponding ketones in excellent manner in presence of N,N′-dicyclohexylcarbodiimide (DCC) and organometallic reagents. Aromatic, heteroaromatic and aliphatic acids were converted to the corresponding ketones smoothly under the optimum conditions using organolithium reagents. In this process, desired products have been isolated from the crude reaction mixtures in moderate yields during the purification process.

TsNBr2 Mediated Synthesis of 2‐Acylbenzothiazoles and Quinoxalines from Aryl Methyl Ketones under Metal Free Condition

AbstractAn efficient one pot strategy has been developed for the synthesis of 2‐acylbenzothiazoles and quinoxalines from aryl methyl ketones. A variety of heterocycles of these two categories could be prepared in a two‐step sequence in excellent yields. The reaction was performed starting from aromatic ketones via an aryl gloxal intermediate which, on further condensation with 2‐aminobenzenethiol or o‐phenylenediamine, produces the corresponding heterocyclic skeleton. Aromatic ketones are initially treated with TsNBr2 in DMSO at 65 °C for 3 h and the crude reaction mixture was treated with 2‐aminobenzenethiol (at 80 °C) or o‐phenylenediamine (at RT) to generate the final compound.