Archive for the ‘Hot articles’ Category

The development of novel diagnostic tools in the treatment of infectious diseases

Antibiotic resistance has become a major clinical issue in recent decades and is one of the greatest health problems of our time. Tuberculosis (TB) has been present for thousands of years and according to WHO is globally, one of the leading causes of death from a curable infectious disease. The advent of the antibiotic era represented a major breakthrough for those suffering from TB however the spread of multi-drug resistant strains, which have propagated due to incorrect drug use, prescription errors or low patient compliance has become a major threat to disease control. In order to mitigate this, new drugs and diagnostic tools are desperately needed.

A collaborative study between Peter Woodruff of the University of Southern Maine and Benjamin Swarts of Central Michigan University has looked at in vivo nuclear imaging as a non-invasive means of diagnosing TB as well as disease monitoring and treatment response in real time. This means that vital information regarding disease progression that is complimentary to other forms of diagnosis can be quickly attained.

Current imaging methods rely on radiotracers to provide information on host inflammatory response to the infection however there can be some inaccuracy due to a lack of specificity in cellular uptake. An attractive alternative are radiolabeled analogues of antimycobacterial compounds which specifically label the desired bacteria and can provide in vivo imaging.

In the past, the disaccharide trehalose and its analogues have been applied to study metabolic mechanisms of mycobacteria and provide a means to design specifc probes for the mycobacteria induced infections. In this current publication, the researchers successfully developed a robust and concise synthetic route to access a number of fluorinated trehalose (FDTre) analogues using a rapid chemoenzymatic process followed by a simple purification by ion exchange chromatography. This drastic improvement compared to previously reported synthetic routes, which require lengthy reaction times and often result in low recovery, makes this new route highly desirable as well as compatible with timescale required for radiolabel synthesis. In addition, the authors demonstrated the ability of their FDTre analogues to be successfully recognized and taken up through trehalose transporter pathways in M. smegmatis and pathogenic mycobacteria, allowing for FDTre accumulation within cells.

Further investigations are still required to overcome remaining hurdles such as the cost associated with synthesis, assessment of uptake efficiencies at concentrations closer to in vivo radiotracer concentrations as well as evaluation of the speficity of the FDTre radioprobes. Regardless, the methodology established in this study provides an exceptional platform for the development of a new class of nuclear imaging probes to help treat multi-drug resistant TB and other mycobacterial infections.



To find out more see:

Deoxyfluoro-D-trehalose (FDTre) analogues as potential PET probes for imaging mycobacterial infection
Sarah R. Rundell, Zachary L. Wagar, Lisa M. Meints, Claire D. Olson, Mara K. O’Neill, Brent F. Piligian, Anne W. Poston, Robin J. Hood, Peter J. Woodruff and Benjamin M. Swarts
DOI: 10.1039/C6OB01734G


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)

Application of the paranemic crossover motif in 2D self-assembly

Nature uses a cooperative interplay of noncovalent interactions to control complex self-assembly of organized nanostructures with extreme precision. Taking this as inspiration, the field of structural DNA nanotechnology has been working toward the development of programmable, self-assembling nanomaterials and motion control at the nanoscale level by exploiting the remarkable molecular recognition properties of DNA. A number of basic structural motifs using branched DNA have been designed and are key elements for the construction of supramolecular arrays, molecular scaffolds and mechanical and logical nanodevices.

The paranemic crossover (PX) motif, as described in a recent OBC publication, has been of particular interest due to its unique ability to behave as both a self-assembling building block or tile and cohesive linker. Its application, until now, has been limited to 1D arrays as the level of flexibility within PX tiles needed to be controlled in order to access well-defined 2D and 3D DNA structures.

PX DNA arises from the fusion of two parallel double helices through strand cross-overs wherever the two strands come in contact. The component double strands are not linked and can hypothetically pair with each other indefinitely in a manner similar to the pairing of a buldged double helix. Advantageously, the PX structural motif reduces the need for sticky end cohesion, traditionally used in DNA-based self-assembly, which leads to an overall increase in nanostructure stability as sticky ends are susceptible to enzymatic degradation. In addition, complex DNA nanostructures made solely from PX motifs reduce topological problems during self-assembly thus minimizing error.

Researchers from the National Centre for NanoScience and Technology in Beijing, Anhui Normal University in China and Purdue University in the United States have collaboratively studied various structural parameters in order to optimize PX DNA’s ability to participate in the assembly of highly desirable 2D nanostructures. By varying the number of base pairs that make up the major (wide, W) and minor (narrow, N) grooves of the bulged double helix, several versions of PX tiles were prepared. Optimal parameters were observed when T65 (according to the formula TWN), which assembled into an extended, flat and regular 2D array (see image). Any deviation from this number of base pairs resulted in the tile becomes stressed and twisted leading to random aggregates.

This discovery has made possible the application of the highly desirable PX motif in 2D nanoconstruction which will no doubt lead to the synthesis of more stable and structurally and functionally intricate DNA self-assembling nanostructures.

To find out more see:

The study of the paranemic crossover (PX) motif in the context of self-assembly of DNA 2D crystals
Weili Shen, Qing Liu, Baoquan Ding, Zhiyong Shen, Changqing Zhu and Chendge Mao
DOI: 10.1039/c6ob01146b


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.
Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)

Engineering artificial metalloenzymes for applications in photoredox catalysis

Synthetic methodologies to control the selectivity and specificity of catalytic reactions remain the subject of intense research due to the importance of chiral compounds in pharmaceuticals, agrochemicals and functional materials. Homogenous catalysis takes advantage of weak interactions between the substrate, catalyst and groups distal to the active site to impart selectivity. Such features are ubiquitous in enzymes which display exceptionally high levels of stereochemical control and activity. In order to exploit the advanced capabilities of such enzymes for selective catalytic transformations, researchers have linked transition metal catalysts with different biological scaffolds–proteins, peptides, DNA–to create artificial metalloenzymes.

Since their inception in the late 1970’s, artificial metalloenzymes have emerged as a vibrant area of research with numerous examples of a variety of catalytic transformations reported alongside creative methods for incorporating the transition metal complex into the biomolecular scaffold. Key to their design is the ‘second coordination sphere’ provided by the biological scaffold where supramolecular interactions within the active site contribute to the rate and enantioselectivity of the system.

Prof. Thomas Ward and Prof. Oliver Wenger of the University of Basel have recently reported a novel biotin-streptavidin system equipped with an anchored photosensitizer capable of undergoing electron transfers between the biotinylated electron donor and ruthenium(II)-labeled streptavidin.

In the past, studies of the luminescent properties of biotinylated d6 metal complexes, common in photoredox catalysis, have been carried out for the purposes of cell imaging and ruthenium and rhenium complexes have been employed in the elucidation of electron tunneling pathways of various proteins. The application of phototriggered electron transfers to ruthenium photosensitizers, up until this point, had not yet been realized and this recent discovery demonstrates a significant advancement within this field.

This new biotin-streptavidin artificial metalloenzyme contains a ruthenium catalyst and photosensitizers embedded within the biotin binding pocket of streptavidin through covalent interactions with non-native cysteine residues. Their performance in various electron transfer studies demonstrates their potential to behave as advanced photoredox catalysts and given the diversity of reactions amenable to photoredox processes, these novel artificial metalloenzymes will provide unique opportunities within selective catalysis.

To find out more see:

Light-driven electron injection from a biotinylated triarylamine donor to [Ru(diimine)3]2+-labeled streptavidin
Sascha G. Keller, Andrea Pannwitz, Fabian Schwizer, Juliane Klehr, Oliver S. Wenger and Thomas R. Ward
DOI: 10.1039/C6OB01273F


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)

Past and present methodologies for the synthesis and functionalization of heterocycles and their impact on drug discovery

Heterocycles play a central role in modern drug design and this is reflected in the fact that they are present within the majority of marketed drugs. Their prevalence in medicine is not unexpected as heterocycles are the core elements of natural bioactive molecules and medicinal chemistry is centred around simulating the biological effects elicited by these privileged scaffolds.

Advances in organic synthesis are critical to the drug discovery process. The breadth of available synthetic methodologies related to heterocycle functionalization represents an almost endless source of innovation for the medicinal chemist. What is interesting however is the bias within the pharmaceutical industry toward relatively few reaction types. But why are certain methodologies favoured and what has been the long term impact?

Numerous reviews and analyses have been published wherein the types of chemical reactions used by the pharmaceutical industry over the past 30-50 years have been assessed and it has been established that of the current, most frequently used synthetic reactions—for example, amide bond formation, Suzuki-Miyaura cross-coupling, SNAr—none were discovered within the past 20 years.1 Increase in available commercial reagents, robustness and chemoselectivity has only amplified medicinal chemists’ preference for these reaction types.

The integration of new, ground-breaking methodologies in heterocycle synthesis such as ring-closing metathesis, C–H activation, multi-component reactions, photoredox catalysis etc. has been slow and this reliance on a select few reaction types has resulted in an overpopulation of a small amount of chemical space. Granted, underlying reasons for selected routes in a medicinal chemistry program are complex and the constant pressure to produce, maintain timelines, follow regulations and remain competitive is valid. However, this approach has not necessarily translated into an increase in FDA approved drugs. It’s fair to question whether or not such a practise is fully exploiting the vast toolbox of synthetic methodology available to medicinal chemists which could lead to new, diverse chemical space and new opportunities to tackle issues presently facing the pharmaceutical industry.

In a recently published OBC review as part of the themed collection on Contemporary Synthesis in Drug Discovery, scientists from Pfizer outline recent developments from both industry and academia in heterocycle synthesis and functionalization within the context of drug discovery. The purpose of this and other reviews is to help raise awareness and even popularize novel synthetic methodologies within the pharmaceutical industry. This is likely to be of greater impact in drug discover if more industrial-academic partnerships were to collaborate in the development of novel synthetic approaches toward medicinally relevant heterocycles. Regardless, advancements in synthetic chemistry are intertwined with the development of interesting molecular designs and transformative medicines.

1. Alexandria P. Taylor, Ralph P. Robinson, Yvette M. Fobian, David C. Blakemore, Lyn H. Jones and Olugbeminiyi Fadeyi, Org. Biomol. Chem.2016, 14, 6611–6637


To find out more see:

Contemporary Synthetic Chemistry in Drug Discovery OBC Themed Collection

Modern advances in heterocyclic chemistry in drug discovery
Alexandria P. Taylor, Ralph P. Robinson, Yvette M. Fobian, David C. Blakemore, Lyn H. Jones and Olugbeminiyi Fadeyi
DOI: 10.1039/C6OB00936K


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)

Fluorescent nucleosides provide flexibility in fine-tuning photophysical properties

The ubiquity of radioisotope-based bioprobes is being challenged by their nonradioactive counterparts. In recent years, they have gained significant popularity in life sciences due to major advances in available detection methods and enhanced analytical performance. Many would argue that radioactive labels offer superior results in experiments that require high sensitivity and resolution but their safe handling, stability and the proper disposal of radioactive materials limit speed and convenience of use.

The newest generation of fluorescent and chemifluorescent probes promise greater flexibility and versatility for a range of applications and the development of fully automated instrumentations and powerful imaging systems provide high throughput solutions to meet the increasing demands of the modern lab.

Unique photophysical properties can be incorporated into small biomolecules to generate fluorescent bioprobes. Fluorescently labeled nucleosides have distinct advantages over other synthetic molecules due to inherent fluorescence and minimal steric disruptions, and they can be tuned e.g. to form unusual base-pair preferences. They form noncovalent, highly specific duplexes with a complementary nucleic acid strand and are used to detect a defined DNA or RNA target sequence.

In a recent publication from the group of Yoshio Saito of Nihon University, the development of a novel nucleoside-based bioprobe containing a 3-deaza-2’-deoxyadenosine skeleton was reported. It behaves as an indicator for adenosine-cytosine base pair formation in oligodeoxynucleotide (ODN) duplexes by monitoring base-pair induced protonation. The probe displays distinct changes in its absorption and fluorescence activity as a result of its protonation state. In this way, the group is able to clearly discriminate cytosine from other bases on complementary strands based on absorption and fluorescence spectra.

The development of new biomarkers is providing insight to various genetic disorders, disease susceptibility, cancer predisposition and medication response. When fluorescent bioprobe imaging is coupled with genetic analytical techniques, such as single nucleoside polymorphism (SNP)-typing, the two synergize and provide a much more complete view than either one alone.

To find out more see:

Design and synthesis of a novel fluorescent benzo[g]imidazo[4,5-c]quinoline nucleoside for monitoring base-pair-induced protonation with cytosine: distinguishing cytosine via changes in the intensity and wavelength of fluorescence
Shogo Siraiwa, Azusa Suzuki, Ryuzi Katoh and Yoshio Saito
DOI:10.1039/C6OB00494F


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)

Improving total synthesis of modified histone proteins to elucidate epigenetic mechanisms

In their search to solve complex biological problems by bridging gaps between protein synthesis and biological application, Prof. Jennifer Ottesen and her group at Ohio State University have been successfully developing what they term a ‘chemical toolbox’ for histone protein synthesis.

Within the field of epigenetics, heritable changes in gene expression outside of the DNA sequence are tightly regulated by post-translational modifications (PTMs) of DNA and histone proteins–the proteins that package DNA. Known PTMs of histone proteins include methylation, acetlyation, phosphorylation, sulfonylation and ubiquitination and fall under a hypothesized “histone code” which suggests that combinations of these markers alter DNA accessibility through chromatin restructuring and ultimately regulate gene expression.

In building synthetic histone proteins with distinct combinations of chemical modifications, the role of a specific sequence of PTMs in gene expression and the molecular mechanisms by which they function can be elucidated and targeted. This is of particular interest as epigenetics has become a hot topic in recent years due to an ever-growing understanding of these markers and their potential to act as selective entry points for disease intervention.

Ottesen’s recent publication in Organic and Biomolecular Chemistry outlines a new hybrid phase ligation approach for the synthesis of modified histone proteins which overcomes some long standing issues inherent in histone total synthesis. This method combines both solid and solution-phase ligation chemistry to improve process efficiency and overall yield. The group even demonstrates its ability to produce previously challenging CpA-K12ac histone protein which could not be synthesized with standard approaches.

Key to their success is the application of a dual-linker strategy which led to an efficient, sequence-independent resin attachment that liberates the desired native carboxy terminus of the protein which had been previously difficult to accomplish. Below is a scheme describing the solid-phase native chemical ligation of one of their desired targets, histone H4. A single coupling cycle includes deprotection followed by ligation and cleavage from the resin may be accomplished at either the Rink linker (black), or at the HMBA linker (red) to generate the native terminus.

Studies such as Prof. Ottesen’s are crucial as mechanisms by which certain genes are regulated must first be determined before developing targeted therapeutic approaches. Histone deacetylase (HDAC) inhibitors for example, interfere with histone deacetylase and have shown activity against various cancers, neurological diseases and immune disorders. The utility of this class of compound depends on their ability to target and modulate a subset of genes without causing global biological changes. Presently, additional work is required to define the human epigenome, its role in disease development and the processes that regulate it. Progress in the synthesis of highly desirable modified histone proteins brings us ever closer.

To find out more see:

Hybrid phase ligation for efficient synthesis of histone proteins
Ruixuan R. Yu, Santosh K. Mahto, Kurt Justus, Mallory M. Alexander, Cecil J. Howard, and Jennifer J. Ottesen
DOI: 10.1039/C5OB02195B


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)

Computational chemistry: Solving real-world chemical problems

Computational chemistry is a powerful tool for understanding real-world chemical problems. The gap between experiment and computational models is growing ever smaller. Calculated results for isolated molecules are becoming more relevant and reliable calculations for larger and larger molecular systems are becoming more accessible.

A computational study of enantioselective spiroacetalization catalyzed by phosphoric acids carried out by researchers at the Universidad de Salamanca and Oxford University effectively demonstrates the ability of advanced computational methods to elucidate key and often subtle factors that lead to different reaction outcomes.

The study uses a hybrid quantum mechanics (QM)/molecular mechanics (MM) method which makes computational simulations of large systems feasible by combining an accurate quantum mechanical description of the ‘interesting’ part of the system (i.e. the catalyst active site) with the computational efficiency of molecular mechanics applied to the surroundings. This way, one can assess the importance of environmental effects while avoiding a high computational cost. This is accomplished by partitioning the system’s total energy into inner (or active) and outer parts. The interactions within the inner part are then treated with the computationally higher quantum mechanics level and the outer parts are described using less expensive, lower level molecular mechanics methods.

The origin of greater enantioselectivity for the imidodiphosphoric acid (Figure, cat-II) over the binol phorophoric acid (Figure, cat-I) was determined through exhaustive analysis of transition state conformers using the QM/MM method. Ultimately,  it was determined that the source of chiral discrimination in catalyst II comes from a unique, bifunctional hydrogen bonding interaction between the catalyst and substrate. This confining interaction ends up limiting the accessible area to the imidodiphosphoric oxygen, resulting in an enantioselective outcome.

The significance of this work lies in the utility of theoretical models in explaining important empirical results. The ability to dissect a mechanism and identify the influential factors that determine a selective reaction outcome could not have been so easily accomplished without the use of computational analysis and will no doubt aid in the design of future organocatalysts for small, non-sterically demanding molecules.

To find out more see:

QM/MM study on the enantioselectivity of spiroacetalization catalysed by an imidodiphosphoric acid catalyst: how confinment works
Luis Simón and Robert S. Paton
DOI: 10.1039/C6OB00045B


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)

Continuous Flow Processes as an Enabling Technology in Synthesis

Recent advancements in reaction control and method development strategies have significantly impacted the way in which synthetic chemistry is performed. Arguably, one of the most widely amenable and enabling technologies is continuous flow chemistry, which can offer advantages over batch in terms of cost, reaction efficiency and safety. Its implementation is changing the way in which we think about and conduct chemistry and in some areas has expanded our synthetic capabilities.

As a result, numerous syntheses of commercially and pharmaceutically relevant compounds are being redesigned around flow processes in order to improve efficiency and reproducibility. In addition, the flow reactor configuration can be readily customized to meet specific reaction demands.

These changes are most evident within the pharmaceutical industry where increasing pressure to continually identify and optimize lead compounds has renewed interest in the development of sustainable and cost effective processes for both research and production purposes.1

A direct example of this comes from Prof. Ian Baxendale’s laboratory at Durham University.2 Heterocyclic motifs are prevalent in pharmaceuticals and have constituted one of the largest areas of research in organic chemistry. Through a convenient telescope continuous flow process, ethyl isocyanoacetate—a highly sensitive and reactive compound frequently used as a key building block in heterocycle synthesis—was generated in situ and used to synthesize diverse heterocyclic structures in a convergent manner.

General reaction scheme for the muti-step flow synthesis of 1,2,4-triazole and pyrrole[1,2-c]pyrimidine-based heterocycles.

Continuous flow limits issues related to hazardous exothermic processes, reaction scale-up and handling of highly reactive or toxic intermediates, overcoming numerous safety concerns inherent in batch chemistry. Furthermore, flow chemistries have also been combined with additional features such as microwave irradiation, solid-supported reagents or catalysts, photochemistry, inductive heating and electrochemistry, which greatly increase its application in synthetic organic chemistry.3,4

Significant developments within the last decade indicate that the full potential of flow chemistry has yet to be realized. As with any new up-and-coming technology, there exist limitations that more and more researchers are willing to tackle. This is evident in the prevalence of flow systems now being utilized not only within academic laboratories but also in industrial institutions.

Interesting and innovative examples of synthetic reactions translated to flow systems have recently been published in Organic and Biomolecular Chemistry and can also be found in the joint OBC/ChemComm collection ‘Recent Advances in Flow Synthesis and Continuous Processing’. Select examples are discussed below.


Establishing a multistep continuous flow process is a logical step forward in the development of flow technology. However, genuine applications remain limited due to inherent challenges such as solvent incompatibility, intermediate work-up and dilution effects. Prof. Floris Rutjes and his coworkers at Radboud University have provided a solution to this problem.5 They effectively integrated a two-step chemoenzymatic flow synthesis of incompatible reaction steps through the use of an inline liquid-liquid separation module.

Two step synthesis of cyanohydrins and schematic representation of the flow set up with integrated liquid-liquid phase separation module.

Homogenous metal catalysis has seen limited use in industrial processes due to difficult separation from product material and troublesome recovery of precious metals. To remedy this, an immobilised iridium hydrogen transfer catalyst was developed by Prof. Ian Baxendale and coworkers for use in flow based systems by incorporation of a ligand to a porous polymeric monolithic flow reactor, which limits metal leaching and catalyst deactivation.6

A monolith reactor testing configuration using immobilized iridium hydrogen transfer catalyst.

Finally, Prof. Bradely Pentelute and his group at the Massachusetts Institute of Technology very recently reported an efficient continuous-flow system for the challenging synthesis of peptides containing perfluoroaromatic molecules in place of labile disulfide bonds.7 Application of a rapid flow-based solid-phase peptide synthesis allowed the researchers to circumvent previously encountered problems associated with this chemistry and has resulted in an overall improvement in quality and isolated yield of the peptides.

Flow system for the synthesis of H2 relaxin fragment analogues using modified solid-phase peptide synthesis

To find out more see:

1 Flash chemistry: flow chemistry that cannot be done in batch. J. Yoshida, Y. Takahashi, A. Nagaki, Chem. Commun., 2013, 49, 9896. DOI: 10.1039/C3CC44709J

2 Flow synthesis of ethyl isocyanoacetate enabling the telescoped synthesis of 1,2,4-triazoles and pyrrolo-[1,2-c]pyrimidines. M. Baumann. A. M. Rodriguez Garcia, I. R. Baxendale, Org. Biomol. Chem., 2015, 13, 4231. DOI: 10.1039/C5OB00245A

3 Liquid phase oxidation chemistry in continuous-flow microreactors. H. P. L. Gemoets, Y. Su, M. Shang, V. Hessel, R. Luque, T. Noël, Chem. Soc. Rev.201645, 83. DOI: 10.1039/C5CS00447K

4 Flow chemistry syntheses of natural products. J. C. Pastre, D. L. Browne, S. V. Ley, Chem. Soc. Rev.201342, 8849. DOI: 10.1039/C3CS60246J

5 Chemoenzymatic flow cascade for the synthesis of protected mandelonitrile derivatives. M.M. Delville, K. Koch, J.C.M. van Hest, F.P.J.T. Ruties, Org. Biomol. Chem., 2015, 13, 1634. DOI: 10.1039/C4OB02128B

6 A monolith immobilised iridium Cp* catalyst for hydrogen transfer reactions under flow conditions. M. V. Rojo, L. Guetzoyan, I. R. Baxendale, Org. Biomol. Chem., 2015, 13, 1768. DOI: 10.1039/C4OB02376E

7 A perfluoroaromatic abiotic analog of H2 relaxin enabled by rapid flow-based peptide synthesis. T. Luhmann, S. K. Mong, M. D. Smino, L. Meinel, B. L. Pentelute, Org. Biomol. Chem., 2016, 14, 3345. DOI: 10.1039/C6OB00208K


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)

Developing a fragment-based design-friendly methodology

Target-based approaches to drug discovery have dominated pharmaceutical research since the early 1990s because they allow for increased screening capacity and rational drug design. Advances in combinatorial chemistry, high-throughput screening and gene expression profiling have been effective in the development of novel treatments for validated targets; however, a link between the downward trend in the number of new chemical entities reaching commercialization and the predominance of target-based drug discovery methods in the pharmaceutical industry has been suggested.

To address these issues, new technologies are constantly being developed and fragment-based drug design (FBDD) has emerged as a way to improve the quality and (most importantly) the efficiency of the drug discovery process. FBDD identifies the binding of low molecular weight ligands using techniques such as X-ray crystallography or NMR spectroscopy, and the binding information is then used to assemble potent lead compounds with drug-like properties.

In a recent publication, researchers at Astex Pharmaceuticals have noted that the success of FBDD often relies on the development of new synthetic methodologies for ligand elaboration. Despite the simplicity of fragment-like compounds, challenges lie in their design and synthesis as well as in developing the methodology to combine and grow fragments into high affinity leads. It is therefore important to identify compounds with attractive ‘fragment properties’ which are used as part of a selection process for adding new fragments into the Astex screening library. These include incorporation of diverse polar groups, multiple synthetically accessible positions for fragment growth in three dimensions and synthetic tractability among others.

Dihydroisoquinolone and some of its derivatives were identified in this study as ideal fragment-like compounds for the development of a FBDD-friendly synthetic methodology.

Schematic representation of synthetic elaboration of fragment 1. Growth positions are shown as blue arrows and the incorporation of aromatic heteroatoms and polar binding groups are indicated.

As proof of concept, the previously reported synthesis of dihydroisoquinolone-based compounds using Rh(III)-catalyzed C-H bond activation1 was modified to incorporate additional potential binding groups as well as synthetic handles for efficient fragment-to-lead elaboration.

Their results illustrate an excellent example of how the application of FBDD-friendly synthetic methodology can be used to expand upon published methodologies to increase their utility in developing useful templates for fragment-based drug discovery. Although inventive ideas, such as this work, are making small contributions in pharmaceutical research, there is a need for more organic chemists to engage in these synthetic challenges if drug discovery techniques are to be fruitful in the long-run.

1 N. Guimond et al. J. Am. Chem. Soc., 2011, 133(16), 6449–6457


To find out more see:

Design and synthesis of dihydroisoquinolones for fragment-based drug discovery (FBDD)
Nick Palmer, Torren M. Peakman, David Norton and David C. Rees
DOI: 10.1039/C5OB02461G


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)

Revitalizing palladium-catalyzed α-arylation of enolates to generate diverse isoquinoline-based compounds

Research efforts carried out by Professor Timothy Donohoe of Oxford University have been focussed on connecting new methodologies in organic synthesis and catalysis with impactful applications to the fields of medicinal chemistry and natural product synthesis.

One of the group’s most recent endeavors includes the development of a generalized strategy to access highly functionalized and diverse isoquinoline cores without the use of expensive and highly-specialized starting materials.

The isoquinoline motif and its derivatives are ubiquitous in a number of natural products, pharmaceutical agents, and chiral catalyst ligands. However, classical syntheses are often centered on electrophilic aromatic substitution of electron-rich systems, resulting in limited chemical diversity in accessible products. New routes are still highly desirable and a resurgence in synthetic efforts has resulted in a number of notable contributions using modern synthetic methodology.

In 2012, Prof. Donohoe and coworkers reported a sequential palladium-catalyzed α-arylation of enolates and cyclization to access isoquinolines based on chemistry originally and independently reported by Buckwald, Hartwig and Miura in 1997. Though a powerful reaction, it remained underutilized in the assembly of complex aromatic compounds. Using clever reaction engineering, Donohoe and coworkers envisioned synthesizing a psuedo-1,5-dicarbonyl accessible through α-arylation of enolizable ketones with aryl halides possessing a protected aldehyde or ketone in the ortho-position. In addition, trapping with reactive electrophiles resulted in functionalization at the C4 position. This methodology can be carried out in one pot, tolerates a wide range of substituents and most notably, provides a route to synthetically challenging electron-deficient isoquinoline scaffolds.

Palladium-catalyzed enolate arylation as a key C–C bond-forming reaction for the synthesis of isoquinolines

Their current study presents significant extensions of this earlier work and further demonstrates the innovation possible through transition metal catalysis in enabling the construction of complex architectures in interesting ways. The three- and four-component coupling procedures involve multiple bond formations in one pot from largely commercially available starting materials. Reaction versatility is demonstrated through the use of ketone, ester or nitrile enolates as well as electron-rich, electron-deficient or even sterically hindered aryl halides and in situ functionalization of intermediates to directly access a number of highly functionalized isoquinoline based compounds.

In addition to rejuvenating interesting and underexplored chemistry, Prof. Donohoe and coworkers have appreciably impacted the areas of natural product synthesis and medicinal chemistry through their innovative and streamlined synthesis of isoquinoline-based compounds and it will be interesting to see where their future endeavours will lead.


To find out more see:

Palladium-catalyzed enolate arylation as a key C–C bond-forming reaction for the synthesis of isoquinolines
Ben S. Pilgrim, Alice E. Gatland, Carlos H. A. Esteves, Charlie T. McTernan, Geraint R. Jones, Matthew R. Tatton, Panayiotis A. Procopiou and Timothy J. Donohoe
DOI: 10.1039/C5OB02320C


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

Digg This
Reddit This
Stumble Now!
Share on Facebook
Bookmark this on Delicious
Share on LinkedIn
Bookmark this on Technorati
Post on Twitter
Google Buzz (aka. Google Reader)