Design and Synthesis of Artificial Nucleobases for Sequence-Selective DNA Recognition within the Major Groove

We present the design and synthesis of artificial specific nucleobases, each one recognizing a single base pair within the major groove of duplex DNA. Computational calculations indicate that PNAs modified with these nucleobases enable the formation of highly stable triple helices with no sequence restrictions through multiple hydrogen bonding and π⋅⋅⋅π stacking interactions, without significantly widening the DNA double helix. New synthetic routes were developed to the structures of these fused heterocycles which have rarely been described in the literature. NMR titration experiments indicate specific hydrogen bonding at the Hoogsteen sites. The new building blocks allow the construction of four PNA monomers for each canonic base pair and their covalent connection to PNA oligomers. These can be designed complementary to any given DNA sequence. With high efficiency and relative simplicity of operation, the described methodologies and strategies hence form the basis for a new supramolecular ligand system targeting double-stranded DNA without strand invasion.

Mechanistic Understanding of KOtBu-Mediated Direct Amidation of Esters with Anilines: An Experimental Study and Computational Approach

A sustainable and cost-effective protocol has been reported for the synthesis of amide bonds from unactivated esters and non-nucleophilic amines promoted by potassium tert -butoxide under aerobic conditions. The reaction proceeds under relatively mild conditions, encompassing wide substrate scope. A combined experimental and quantum chemical study has been performed to shed light on the mechanism, which implied that a radical pathway is operating for the present protocol.

A cyanide-catalyzed imino-Stetter reaction enables the concise total syntheses of rucaparib

Two routes toward the synthesis of rucaparib, an FDA-approved drug used for the treatment of ovarian and prostate cancers, have been developed from commercially available starting materials utilizing the cyanide-catalyzed imino-Stetter reaction as the key step for the construction of the indole motif bearing all the desired substituents in their correct positions. In the first-generation synthesis, meta-fluorobenzoate, the starting material currently used in the process chemistry route of rucaparib, was converted into 4,6-disubstituted 2-aminocinnamic acid derivatives (ester or amide). The cyanide-catalyzed imino-Stetter reaction of aldimines derived from the resulting 2-aminocinnamic acid derivatives and a commercially available aldehyde afforded the desired indole-3-acetic acid derivatives. The final azepinone formation completed the total synthesis of rucaparib in 27% overall yield. To resolve the issues raised in the first-generation synthesis, we further developed a second-generation synthesis of rucaparib. The Heck reaction of a commercially available ortho-iodoaniline derivative with acrylonitrile provided 4,6-disubstituted 2-aminocinnamonitrile, which was subjected to the imino-Stetter reaction with the same aldehyde to provide the desired indole-3-acetonitrile product. Subsequent construction of the azepinone scaffold completed the total synthesis of rucaparib in 59% overall yield over three separation operations. The synthetic strategy reported herein can provide a highly practical route to access rucaparib from commercially available starting materials (5.2% overall yield in the current process chemistry route vs. 59% overall yield in the second-generation synthesis).

Amide Bonds Meet Flow Chemistry: A Journey into Methodologies and Sustainable Evolution

Formation of amide bonds is of immanent importance in organic and synthetic medicinal chemistry. Its presence in "traditional" small-molecule active pharmaceutical ingredients, in linear or cyclic oligo- and polypeptidic actives, including pseudopeptides, has led to the development of dedicated synthetic approaches for the formation of amide bonds starting from, if necessary, suitably protected amino acids. While the use of solid supported reagents is common in traditional peptide synthesis, similar approaches targeting amide bond formation in continuous-flow mode took off more significantly, after a first publication in 2006, only a couple of years ago. Most efforts rely upon the transition of traditional approaches in flow mode, or the combination of solid-phase peptide synthesis principles with flow chemistry, and advantages are mainly seen in improving space-time yields. This Review summarizes and compares the various approaches in terms of basic amide formation, peptide synthesis, and pseudopeptide generation, describing the technological approaches and the advantages that were generated by the specific flow approaches. A final discussion highlights potential future needs and perspectives in terms of greener and more sustainable syntheses.

Direct Amidation of Esters by Ball Milling*

The direct mechanochemical amidation of esters by ball milling is described. The operationally simple procedure requires an ester, an amine, and substoichiometric KOtBu and was used to prepare a large and diverse library of 78 amide structures with modest to excellent efficiency. Heteroaromatic and heterocyclic components are specifically shown to be amenable to this mechanochemical protocol. This direct synthesis platform has been applied to the synthesis of active pharmaceutical ingredients (APIs) and agrochemicals as well as the gram-scale synthesis of an active pharmaceutical, all in the absence of a reaction solvent.

Total Synthesis of Hinckdentine A

The total synthesis of (±)-hinckdentine A is described herein. A cyanide-catalyzed imino-Stetter reaction of the aldimine derived from ethyl 2-amino-3,5-dibromocinnamate and 5-bromo-2-nitrobenzaldehyde followed by oxidative rearrangement afforded a 2,2-disubstituted 3-indolinone derivative containing the carbon skeleton and all of the functional groups present in the natural product correctly positioned, including three bromine atoms. Subsequent D-ring formation and seven-membered C-ring construction completed the total synthesis of hinckdentine A.

Monoacylation of Symmetrical Diamines in Charge Microdroplets

Monoacylation of symmetrical diamine is achieved when the primary α,ω-diamines (carbon numbers n = 3, 5 and 12) are diluted in ethyl acetate, and the resultant mixture is electrosprayed across a 10 mm distance in ambient air toward a mass spectrometer. The N-acylated product is formed in charged microdroplets without acidifying and activating agents and in the absence of heat. This result provided an insight into the orientation of the amines in the droplets, suggesting that the ester is activated to react with the amine at the droplet surface due to the high abundance of protons at the air-droplet interface.

An Overview of Drug Substance Manufacturing Processes

To develop a comprehensive understanding of pharmaceutical drug substance manufacturing (DSM) processes, we conducted a data mining study to examine 50 new drug applications (NDAs) approved in 2010-2016. We analyzed the prevalence of several frequently deployed in-process control (IPC) techniques and postreaction workup procedures, as well as the operational conditions specified for reactions and workups. Our findings show that crystallization and high-performance liquid chromatography (HPLC) were the most commonly used workup steps and in-process controls, respectively, in drug substance manufacturing. On average, each NDA implemented 12.6 in-process controls and 11.3 workups. Operation time for reactions and workup procedures varied from a few minutes to multiple days, though 61% of these were between 1 and 10 h.

Flow chemistry as a tool to access novel chemical space for drug discovery

This perspective scrutinizes flow chemistry as a useful tool for medicinal chemists to expand the current chemical capabilities in drug discovery. This technology has demonstrated his value not only for the traditional reactions used in Pharma for the last 20 years, but also for bringing back to the lab underused chemistries to access novel chemical space. The combination with other technologies, such as photochemistry and electrochemistry, is opening new avenues for reactivity that will smoothen the access to complex molecules. The introduction of all these technologies in automated platforms will improve the productivity of medicinal chemistry labs reducing the cycle times to get novel and differentiated bioactive molecules, accelerating discovery cycle times.

Divergent synthesis of 1,3,5-tri and 1,3-disubstituted pyrazoles under transition metal-free conditions

Pyrazole cores are common structural motifs existing in various agrochemicals and pharmaceuticals. Herein, a transition metal-free, three-component reaction of arylaldehydes, ethyl acrylate and N-tosylhydrazones is described, which leads to the formation of 1,3,5-trisubstituted and 1,3-disubstituted pyrazoles divergently under slightly different conditions.

Reaction screening and optimization of continuous-flow atropine synthesis by preparative electrospray mass spectrometry

Preparative electrospray (ES) exploits the acceleration of reactions in charged microdroplets to perform a small scale chemical synthesis. In combination with on-line mass spectrometric (MS) analysis, it constitutes a rapid screening tool to select reagents to generate specific products. A successful reaction in preparative ES triggers a refined microfluidic reaction screening procedure which includes the optimization for stoichiometry, temperature and residence time. We apply this combined approach for refining a flow synthesis of atropine. A successful preparative ES pathway for the synthesis of the phenylacetyl ester intermediate, using tropine/HCl/phenylacetyl chloride, was optimized for solvent in both the preparative ES and microfluidics flow systems and a base screening was conducted by both methods to increase atropine yield, increase percentage conversion and reduce byproducts. In preparative ES, the first step yielded 55% conversion (judged using MS) to intermediate and the second step yielded 47% conversion to atropine. When combined in two discrete steps in continuous-flow microfluidics, a 44% conversion of the starting material and a 30% actual yield of atropine were achieved. When the reactions were continuously telescoped in a new form of preparative reactive extractive electrospray (EES), atropine was synthesized with a 24% conversion. The corresponding continuous-flow microfluidics experiment gave a 55% conversion with an average of 34% yield in 8 min residence time. This is the first in depth study to utilize telescoped preparative ES and the first use of dual ESI emitters for multistep synthesis.

Structure-Affinity Relationships and Structure-Kinetic Relationships of 1,2-Diarylimidazol-4-carboxamide Derivatives as Human Cannabinoid 1 Receptor Antagonists

We report on the synthesis and biological evaluation of a series of 1,2-diarylimidazol-4-carboxamide derivatives developed as CB₁ receptor antagonists. These were evaluated in a radioligand displacement binding assay, a [³⁵S]GTPγS binding assay, and in a competition association assay that enables the relatively fast kinetic screening of multiple compounds. The compounds show high affinities and a diverse range of kinetic profiles at the CB₁ receptor and their structure–kinetic relationships (SKRs) were established. Using the recently resolved hCB₁ receptor crystal structures, we also performed a modeling study that sheds light on the crucial interactions for both the affinity and dissociation kinetics of this family of ligands. We provide evidence that, next to affinity, additional knowledge of binding kinetics is useful for selecting new hCB₁ receptor antagonists in the early phases of drug discovery.

Direct amidation of esters with nitroarenes

Esters are one of the most common functional groups in natural and synthetic products, and the one-step conversion of the ester group into other functional groups is an attractive strategy in organic synthesis. Direct amidation of esters is particularly appealing due to the omnipresence of the amide moiety in biomolecules, fine chemicals, and drug candidates. However, efficient methods for direct amidation of unactivated esters are still lacking. Here we report nickel-catalysed reductive coupling of unactivated esters with nitroarenes to furnish in one step a wide range of amides bearing functional groups relevant to the development of drugs and agrochemicals. The method has been used to expedite the syntheses of bio-active molecules and natural products, as well as their post-synthetic modifications. Preliminary mechanistic study indicates a reaction pathway distinct from conventional amidation methods using anilines as nitrogen sources. The work provides a novel and efficient method for amide synthesis.

Direct conversion of esters to amides, while attractive, is often limited to activated esters or highly nucleophilic amines. Here the authors report a nickel-catalysed reductive coupling between unactivated esters and nitroarenes, giving a direct route to aromatic amides.

A flow reactor setup for photochemistry of biphasic gas/liquid reactions

A home-built microreactor system for light-mediated biphasic gas/liquid reactions was assembled from simple commercial components. This paper describes in full detail the nature and function of the required building elements, the assembly of parts, and the tuning and interdependencies of the most important reactor and reaction parameters. Unlike many commercial thin-film and microchannel reactors, the described set-up operates residence times of up to 30 min which cover the typical rates of many organic reactions. The tubular microreactor was successfully applied to the photooxygenation of hydrocarbons (Schenck ene reaction). Major emphasis was laid on the realization of a constant and highly reproducible gas/liquid slug flow and the effective illumination by an appropriate light source. The optimized set of conditions enabled the shortening of reaction times by more than 99% with equal chemoselectivities. The modular home-made flow reactor can serve as a prototype model for the continuous operation of various other reactions at light/liquid/gas interfaces in student, research, and industrial laboratories.

Taming hazardous chemistry by continuous flow technology

Over the last two decades, flow technologies have become increasingly popular in the field of organic chemistry, offering solutions for engineering and/or chemical problems. Flow reactors enhance the mass and heat transfer, resulting in rapid reaction mixing, and enable a precise control over the reaction parameters, increasing the overall process selectivity, efficiency and safety. These features allow chemists to tackle unexploited challenges in their work, with the ultimate objective making chemistry more accessible for laboratory and industrial applications, avoiding the need to store and handle toxic, reactive and explosive reagents. This review covers some of the latest and most relevant developments in the field of continuous flow chemistry with the focus on hazardous reactions.

Direct amide synthesis over core–shell TiO2@NiFe2O4 catalysts in a continuous flow radiofrequency-heated reactor

A core–shell TiO₂@NiFe₂O₄ catalyst showed high activity and stability in direct amide synthesis with easy regeneration from coke by a treatment with a 30 wt% hydrogen peroxide solution.

The synthesis of active pharmaceutical ingredients (APIs) using continuous flow chemistry

The implementation of continuous flow processing as a key enabling technology has transformed the way we conduct chemistry and has expanded our synthetic capabilities. As a result many new preparative routes have been designed towards commercially relevant drug compounds achieving more efficient and reproducible manufacture. This review article aims to illustrate the holistic systems approach and diverse applications of flow chemistry to the preparation of pharmaceutically active molecules, demonstrating the value of this strategy towards every aspect ranging from synthesis, in-line analysis and purification to final formulation and tableting. Although this review will primarily concentrate on large scale continuous processing, additional selected syntheses using micro or meso-scaled flow reactors will be exemplified for key transformations and process control. It is hoped that the reader will gain an appreciation of the innovative technology and transformational nature that flow chemistry can leverage to an overall process.

Continuous-flow technology—a tool for the safe manufacturing of active pharmaceutical ingredients

In the past few years, continuous-flow reactors with channel dimensions in the micro- or millimeter region have found widespread application in organic synthesis. The characteristic properties of these reactors are their exceptionally fast heat and mass transfer. In microstructured devices of this type, virtually instantaneous mixing can be achieved for all but the fastest reactions. Similarly, the accumulation of heat, formation of hot spots, and dangers of thermal runaways can be prevented. As a result of the small reactor volumes, the overall safety of the process is significantly improved, even when harsh reaction conditions are used. Thus, microreactor technology offers a unique way to perform ultrafast, exothermic reactions, and allows the execution of reactions which proceed via highly unstable or even explosive intermediates. This Review discusses recent literature examples of continuous-flow organic synthesis where hazardous reactions or extreme process windows have been employed, with a focus on applications of relevance to the preparation of pharmaceuticals.

Efficient amide bond formation through a rapid and strong activation of carboxylic acids in a microflow reactor

The development of highly efficient amide bond forming methods which are devoid of side reactions, including epimerization, is important, and such a method is described herein and is based on the concept of rapid and strong activation of carboxylic acids. Various carboxylic acids are rapidly (0.5 s) converted into highly active species, derived from the inexpensive and less-toxic solid triphosgene, and then rapidly (4.3 s) reacted with various amines to afford the desired peptides in high yields (74%-quant.) without significant epimerization (≤3%). Our process can be carried out at ambient temperature, and only CO2 and HCl salts of diisopropylethyl amine are generated. In the long history of peptide synthesis, a significant number of active coupling reagents have been abandoned because the highly active electrophilic species generated are usually susceptible to side reactions such as epimerization. The concept presented herein should renew interest in the use of these reagents.

Practical preparation of challenging amides from non-nucleophilic amines and esters under flow conditions

Preparation of amides from low nucleophilic heterocyclic amines is achieved in 2 minutes under mild conditions.

Inhibition of PCAF histone acetyltransferase, cytotoxicity and cell permeability of 2-acylamino-1-(3- or 4-carboxy-phenyl)benzamides

Small molecule HAT inhibitors are useful tools to unravel the role of histone acetyltransferases (HATs) in the cell and they also have relevance in oncology. We synthesized a series of 2-acylamino-1-(3- or 4-carboxyphenyl)benzamides 8–19 bearing C6, C8, C10, C12, C14, and C16 acyl chains at the 2-amino position of 2-aminobenzoic acid. Enzyme inhibition of these compounds was investigated using in vitro PCAF HAT assays. The inhibitory activities of compounds 8–10, 16, and 19 were similar to that of anacardic acid, and 17 was found to be more active than anacardic acid at 100 μM. Compounds 11–15 showed the low inhibitory activity on PCAF HAT. The cytotoxicity of the synthesized compounds was evaluated by SRB (sulforhodamine B) assay against seven human cancer cell lines: HT-29 (colon), HCT-116 (colon), MDA-231 (breast), A549 (lung), Hep3B (hepatoma), HeLa (cervical) and Caki (kidney) and one normal cell line (HSF). Compound 17 was more active than anacardic acid against human colon cancer (HCT 116, IC₅₀: 29.17 μM), human lung cancer (A549, IC₅₀: 32.09 μM) cell lines. 18 was more active than anacardic acid against human colon cancer (HT-29, IC₅₀: 35.49 μM and HCT 116, IC₅₀: 27.56 μM), human lung cancer (A549, IC₅₀: 30.69 μM), and human cervical cancer (HeLa, IC₅₀: 34.41 μM) cell lines. The apparent permeability coefficient (P_app, cm/s) values of two compounds (16 and 17) were evaluated as 68.21 and 71.48 × 10⁻⁶ cm/s by Caco-2 cell permeability assay.

Micro Reactors, Flow Reactors and Continuous Flow Synthesis

Dr Paul Watts is a reader in organic chemistry at The University of Hull and since graduating from the University of Bristol, where he completed a PhD in bio-organic natural product synthesis, he has led the Micro Reactor Group at Hull. In this role, he has published 90 papers, and he regularly contributes to the field by way of invited book chapters, review articles, and keynote lecturers on the subject of micro reaction technology in organic synthesis.

Dr Charlotte Wiles is the Chief Technology Officer at Chemtrix BV, and has been actively researching within the area of micro reaction technology for 10 years, starting with a PhD entitled Micro reactors in organic chemistry, which she obtained from The University of Hull in 2003. In the past decade, she has authored many scientific papers and review articles, recently co-authoring a book on the subject of micro reaction technology in organic synthesis. More recently, she has tailored her experience to the development and evaluation of commercially available continuous flow reactors, systems and peripheral equipment.

This review article explains the advantages of micro reactors and flow reactors as tools for conducting organic synthesis and describes how the technology may be used in research and development as well as production. A selection of examples is taken from the literature to illustrate how micro reactors enables chemists to perform their reactions more efficiently than when using batch processes.

Application of metal-based reagents and catalysts in microstructured flow devices

Over the years, organic synthesis has witnessed several improvements through the development of new chemical transformations or more efficient reagents for known processes. Likewise, technological advances, aiming at speeding up reactions and facilitating their work-up, have established themselves in academic as well as in industrial laboratories. In this Minireview, we highlight very recent developments in flow chemistry, focusing on organometallic reagents and catalysts. First, we describe reactions with homogeneous catalysts immobilized on different support materials using the concept of packed bed reactors. In the last chapter, we will discuss applications that utilize organometallic reagents.

Solid-supported gallium triflate: an efficient catalyst for the three-component ketonic Strecker reaction

In light of the growing interest in the use of rare earth metal triflates as water-tolerant Lewis acid catalysts, we embarked upon the development of a solid-supported gallium triflate (PS-Ga(OTf)(2) ) derivative as a means of increasing the cleanliness and cost effectiveness of using these increasingly expensive catalytic materials in synthetic processes. Having previously highlighted the advantages associated with coupling solid-supported catalysis and the emerging area of micro-reaction technology, we screened PS-Ga(OTf)(2) for activity towards the ketonic Strecker reaction, in which the target α-aminonitriles were obtained in higher yield and purity compared to reactions reported in literature, in which the analogous homogeneous catalyst was used.

Synthesis of a drug-like focused library of trisubstituted pyrrolidines using integrated flow chemistry and batch methods

A combination of flow and batch chemistries has been successfully applied to the assembly of a series of trisubstituted drug-like pyrrolidines. This study demonstrates the efficient preparation of a focused library of these pharmaceutically important structures using microreactor technologies, as well as classical parallel synthesis techniques, and thus exemplifies the impact of integrating innovative enabling tools within the drug discovery process.

Unusual behavior in the reactivity of 5-substituted-1H-tetrazoles in a resistively heated microreactor

The decomposition of 5-benzhydryl-1H-tetrazole in an N-methyl-2-pyrrolidone/acetic acid/water mixture was investigated under a variety of high-temperature reaction conditions. Employing a sealed Pyrex glass vial and batch microwave conditions at 240 °C, the tetrazole is comparatively stable and complete decomposition to diphenylmethane requires more than 8 h. Similar kinetic data were obtained in conductively heated flow devices with either stainless steel or Hastelloy coils in the same temperature region. In contrast, in a flow instrument that utilizes direct electric resistance heating of the reactor coil, tetrazole decomposition was dramatically accelerated with rate constants increased by two orders of magnitude. When 5-benzhydryl-1H-tetrazole was exposed to 220 °C in this type of flow reactor, decomposition to diphenylmethane was complete within 10 min. The mechanism and kinetic parameters of tetrazole decomposition under a variety of reaction conditions were investigated. A number of possible explanations for these highly unusual rate accelerations are presented. In addition, general aspects of reactor degradation, corrosion and contamination effects of importance to continuous flow chemistry are discussed.