Organic & Biomolecular Chemistry Blog

Electron paramagnetic resonance (EPR) is powerful technique for studying chemical species containing unpaired electrons. It has far reaching applications in a number of fields as it can be used to elucidate structural, electronic and conformational dynamic features in a given system. 

In biological settings, paramagnetic probes have been developed to ‘spin-label’ desired biomolecules using a technique called site-directed spin labelling (SDSL). In combination with other methods, EPR has emerged as an efficient means of studying proteins close to their native physiological states and can be used to glean information regarding the immediate environment of the spin-labeled side-chain as well as measure intra- and intermolecular distances within the protein. A challenge has been in developing rigid spin-labels to improve the accuracy of distance measurements as the most reliable information is attained if the distance between spin-labels is unchanged by conformational flexibility.

In their most recent OBC publication, Prof. Snorri Sigurdsson of the University of Iceland and Prof. Thomas Prisner of Goethe University describe the development of an enhanced isoindoline-nitroxide derivative of uridine (^ImUm), the first example of a conformationally constrained spin label for RNA.

Limited mobility of ^ImUM is a result of the nitroxide N-O bond lying in the same axis as the bond used to link it to the uridine base. As a result, bond rotation does not drastically alter the position of the nitroxide. Additionally, ^ImUm was shown to bind specifically and with high affinity to abasic sites in duplex RNAs. Here, rigidity is further enhanced through intramolecular hydrogen bonding between the nitroxide probe and the orphaned uracil base. ^ImUm is a promising label for EPR studies of RNA, providing highly useful and dynamic structural information unbiased by conformational flexibility.

To find out more see:

A semi-rigid isoindoline-derived nitroxide spin label for RNA
Dnyaneshwar B. Gophane,  Burkhard Endeward,  Thomas F. Prisner  and  Snorri Th. Sigurdsson 
DOI: 10.1039/C7OB02870A

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 building blocks which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

According to statistics published by the World Health Organization (WHO), tuberculosis (TB) is globally one of the leading causes of death from a curable infectious disease. While antibiotics represent a major breakthrough for modern medicine, the spread of multi-drug resistant (MDR) bacterial strains, such as Mycobacterium tuberculosis, have become a major threat to healthcare.

Encouragingly, renewed efforts in antibiotic research have resulted in the identification of new leads, some of which are currently in clinical trials. Even in light of these promising efforts, Dr. Ehmke Pohl of Durham University and collaborators from the Cambridge Crystallographic Data Centre and Institut Pasteur de Lille are emphasizing the need to optimize existing TB treatments as well as develop an efficient means of identifying novel therapeutics.

Structure-based drug discovery is an integral part of most industrial drug discovery programs and as a result, there is an ever-growing number of protein X-ray crystal structures available in databases such as the Protein Data Bank (PDB). Pohl and collaborators outline a robust and versatile strategy for an in silico screening protocol based on compounds in the ZINC database (a free resource of commercially available chemical compounds) and crystal structures in the PDB.

Their current OBC study focuses on the transcriptional regulator EthR which is involved in M. tuberculosis resistance. EthR has been shown to limit the efficacy of ethionamide-based drugs by downregulating the EthA enzyme involved in activation of ethionamide prodrugs. EthR has therefore been validated as a suitable target as its inhibition boosts ethionamide action.

Using tailored chemical and physicochemical descriptors (for example: compound volume) and a detailed knowledge of the EthR binding pocket, approximately 6 million compounds were evaluated for compatibility using KNIME pipeline software. 409 201 diverse compounds were identified for docking studies and surprisingly, only 6 compounds failed to produce feasible binding interactions. After a careful post-docking filter, 284 chemically diverse compounds were obtained and a visual analysis of all binding poses and ligand geometries in combination with computational analysis narrowed the screen down to 85 substrates. These in silico hits were then evaluated for their capability to bind to EthR using thermal protein stability studies which resulted in 20 new potential candidates for lead optimization with reasonable EC₅₀ values.

Given the ever-growing number of high resolution crystal structures in the PDB, in silico screening approaches can be tailored to any well-characterized protein structure and utilized as an efficient tool for identifying new active molecules.

To find out more see:

New active leads for tuberculosis booster drugs by structure-based drug discovery
Natalie J. Tatum, John W. Liebeschuetz,  Jason C. Cole,  Rosangela Frita,  Adrien Herledan, Alain R. Baulard, Nicolas Willand and Ehmke Pohl
DOI:10.1039/C7OB00910K

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 building blocks which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

The reductive amination reaction between amines and carbonyls is a highly useful and versatile means of forming C-N bonds. Given the accessibility of starting materials and its modular nature, reductive aminations have found extensive application not only in organic synthesis but medicinal chemistry and the production of agro- and industrial chemicals.

Developing efficient and economical processes to access valuable materials is a priority in industry. One of the most fundamental ways of doing this is to adhere to the principle of atom economy which moves to minimize waste generated by a chemical reaction at the molecular level. While traditionally, chemists have focused on improving yield or minimizing the number of steps in a reaction sequence, atom economy aims to design reactions in which all atoms involved in a chemical process are present in the desired products.

An international team of researchers have recently published a novel iridium-catalyzed reductive amination using carbon monoxide (CO) as an alternative reductant. This process does not require an external hydrogen source as the hydride is abstracted by the catalyst/carbon monoxide complex from the hemiaminal intermediate, forming an iridium-hydride species. Essentially, the hydride is derived internally (from the amine) as a result of the deoxygenative potential of carbon monoxide. The reaction is also tolerant to a number of functional groups that are incompatible with other commonly employed reducing reagents.

This is a very interesting twist on the reductive amination reaction for which external sources of hydrogen are often required. While it could be called atomic economic from this standpoint, the fact that carbon dioxide is a major by product of the reaction detracts from this claim and could be problematic on an industrial level. Regardless, this work is a significant first step and demonstrates the importance of optimizing the efficiency of well-established protocols in organic synthesis for large scale purposes.

To find out more see:

Reductive amination catalyzed by iridium complexes using carbon monoxide as a reducing agent
Alexey P. Moskovets,  Dmitry L. Usanov,  Oleg I. Afanasyev,  Vasilii A. Fastovskiy,  Alexander P. Molotkov,  Karim M. Muratov,  Gleb L. Denisov,  Semen S. Zlotskii,  Alexander F. Smol’yakov, Dmitry A. Loginov and  Denis Chusov*
DOI:10.1039/C7OB01005B

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 building blocks which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

Complex coacervation refers to a liquid-liquid phase separation that arises from the association of oppositely charged polyelectrolytes in water. It is a widely used laboratory technique and coacervate-based materials have extensive application in the food and cosmetic industries as well as drug delivery and the development of biomedical adhesives.

Under favourable conditions, the coalescence of coacervate droplets leads to a separation of a system into two liquid layers: a polymer-rich coacervate phase in equilibrium with a polymer poor supernatant. Coacervation is entropically driven and occurs through an initial electrostatic attraction between oppositely charged molecules followed by the release of counterions and rearrangement of water molecules. However, our understanding of factors that control self-assembly and stability at the molecular level remains limited.

In the past, many studies have focused on how the chemical nature of a polymer affects coacervation without considering the effect of polymer architecture. In a collaborative study recently published in OBC, Prof. Sarah Perry and Prof. Todd Emerick et al., of the University of Massachusetts Amherst investigate the effect of branching in polypeptide-based comb polymers on the self-assembly and stability of complex coacervates.

In comparison to branched copolymers, the interaction of oppositely charged linear copolymers to form charge-neutral coacervate complexes is understandably straightforward. However, the extent to which a mismatched polymer architecture would alter coalescence is relatively unclear and a question that Perry and Emerick sought to answer.

The self-assembly and stability of complex coacervates resulting from oppositely charged linear polymers, linear and comb polymer and two comb polymers (see Figure) were determined/compared through turbidity measurements, optical microscopy and Monte Carlo simulations. Ultimately, it was observed that the comb structure did not form coacervates as the branched structure prevents cooperative interactions between oppositely charged polymer pairs and releases fewer counterions, leading to a weaker driving force for coacervation.

This study provides insight to the role that polymer architecture plays on complex coacervation and highlights the need to develop a detailed and predictable understanding of molecular level effects of polymer chemistry and architecture in coacervate formation.

To find out more see:

The effect of comb architecture on complex coacervation
Brandon M. Johnston,  Cameron W. Johnston,  Rachel A. Letteri,  Tyler K. Lytle,  Charles E. Sing, Todd Emrick and Sarah L. Perry
DOI:10.1039/C7OB01314K

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 building blocks which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

Catalysis is a fundamental concept in chemistry, allowing chemists to effectively carry out difficult transformations to access valuable materials with precision and control. For the most part, research has focused on the development of new catalysts for optimized performance to achieve high conversion and selectivity. However, special attention is now being paid to engineering catalysts whose activity can be tuned through external stimuli. This concept is ubiquitous in nature and its implementation into artificial systems offers unique opportunities and promising future applications.

A recent OBC publication by Prof. Ben Feringa of the University of Groningen Nijenborgh discusses his group’s success in developing two novel bisthiourea catalysts which display dynamic control over activity and stereoselectivity in the Henry reaction using light and heat as external stimuli.

This catalyst design is based on a molecular motor previously reported by Feringa and inspired by nature where control over function, activity and selectivity can be attained through conformational changes within the catalyst’s active site induced by external stimuli.

In the current publication, upon irradiation of the catalyst in its stable trans state, (R,R)-(P,P)-trans (see Scheme), an unstable cis state is obtained, (R,R)-(M,M)-cis, in which the catalytic groups A and B are brought into proximity to carry out the desired enantioselective transformation. The catalyst can then be converted through heating to a stable cis state, the (R,R)-(M,M)-cis isomer, via a thermal helix inversion. In this conformation, the two active groups A and B remain within reaction proximity, however, as the helicity of the motor core is inverted, a pseudoenantiomeric catalytic environment is produced which results in the formation of the opposite enantiomer.

This is the first example of a tunable bisthiourea catalyst and represents an important advancement in the field of dynamic stimuli responsive catalysis. This new area of research offers great potential for advanced materials and solving long-standing challenges that have thus far been impossible to overcome using conventional methodologies.

To find out more see:
Dynamic control over catalytic function using responsive bisthiourea catalysts
M. Vlatković,  J. Volarić,  B. S. L. Collins, L. Bernardi and  B. L. Feringa*
DOI:10.1039/C7OB01851G

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.

Synthetic oligosaccharides and glycoconjugates are being increasingly used to solve important problems within biological research for vaccine development and drug discovery purposes. However, due to their complicated isolation and characterization from biological fluids, as well as a lack of general and efficient protocols for their preparation, progress within the field has been limited.

A recent OBC publication from Prof. Carmen Galan of the University of Bristol seeks to overcome this longstanding challenge using imidazolium-labeled (ITag) glycosides. Ionic liquid-based labels are emerging as a new class of covalent chemical labels that provide a unique handle for facile identification and purification of substrates from complex reaction mixtures using mass spectroscopy.

It was hypothesised that the ITag-glycan probes could be used to harness the natural biosynthetic machinery present in human breastmilk (i.e. glycosyltransferases) to access biologically important oligosaccharides. This study circumvents lengthy and costly chemical syntheses as well as the need to isolate a specific enzyme which can be challenging to express and applicable only to small-scale production.

In a matter of days, the group was able to access a series of highly desirable oligosaccharides, including LacNAc-ITag, ITag-Lewisx and ITAg-Lewisa through incubation of a labelled glycoside in readily sourced human breast milk. The capability of ITag to aid in the synthesis of oligosaccharides from a complex, multi-enzyme environment is pivotal. This technology could revolutionize the way in which synthetic, enzymatic transformations are carried out and has the potential to expand outside of carbohydrate chemistry.

To find out more see:

Imidazolium-labeled glycosides as probes to harness glycosyltransferase activity in human breast milk
I. Sittel and M. C. Galan
DOI: 10.1039/C7OB00550D

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.

The rare phenomenon of enantioselectivity reversal, using a simple change in reaction temperature control, is presented in the latest HOT article published in OBC.

The ability to mimic nature’s stereochemical control in the production of complex molecules has been a longstanding challenge in chemistry. There are numerous strategies chemists have implemented to generate stereochemically complex structures, however, with the advent of asymmetric catalysis, highly stereoselective reactions can be achieved using chiral reagents and catalysts.

In a recent OBC publication by Prof. Kenso Soai of Tokyo University and researchers from Merck, one of the very few examples in which the enantioselective outcome of a reaction is controlled through temperature was presented. Gaining enantioselective control by changing simple reaction parameters has been an attractive and long sought after advancement within the field of asymmetric catalysis. While there are examples of enantioselective control using solvent, metals and additives, very few examples exist that use temperature alone.

The study outlines the effect of temperature on the asymmetric autocatalysis of pyrimidal alkanol in the addition reaction of diisopropyl zinc to the pyrimidine-5-carbaldehyde. After reaction initiation using a chiral initiator, the product alkanol behaves as an asymmetric catalyst for its own formation and infers its chirality to the product in an autocatalytic cycle. When the reaction was performed at 0 ºC in the presence of (S)-1-phenyl-ethyl alcohol, as expected, (S)-pyrimidal alkanol was afforded in high enantiomeric excess. Interestingly, when the reaction was cooled to -44 ºC, the opposite enantioselectivity was observed though with a slightly lower enantiomeric excess of the desired alkanol.

The exact mechanism through which this reversal happens is still unclear however, it’s speculated that the relationship between temperature and the relative enthalpic vs. entropic contributions to free energy may play a part or the temperature dependent aggregation of zinc alkoxide may also be involved.

It’s important to remember that the temperature effect on reactions involving organozinc reagents is not always straight forward and may not always lead to the best outcome.

Regardless, this study provides interesting insight into temperature controlled enantioselectivity that may lead to a more detailed understanding of such processes and how they can be synthetically exploited.

To find out more see:

Unusual reversal of enantioselectivity in the asymmetric autocatalysis of pyrimidyl alkanol triggered by chiral aromatic alkanols and amines
Arimasa Matusmoto, Satoshi Fujiwara, Yui Hiyoshi,aKerstin Zawatzky, Alexey A. Makarov, Christopher J. Welch and Kenso Soai
DOI: 10.1039/C6OB02415G

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.

Over the past several decades, advances in cell imaging have dramatically transformed biology and medicine. Fluorescence spectroscopy and microscopy are currently the most popular imaging techniques however, there are intrinsic limitations; many substrates are non-fluorescent or weakly fluorescent, fluorescent labels are often perturbative for small molecules and peptides and, perhaps most importantly, labelling or staining with fluorophores are not recommended for in vivo medicinal applications in humans. Hence, the search for highly sensitive optical imaging methods is increasingly desirable in biomedical and material sciences.

Nonlinear optical imaging is an emerging technology that encompasses a range of optical phenomena. In a recent study by Prof. Koen Clays of the University of Leuven and Prof. Harry Anderson of Oxford University, a new group of chromophores based on pyropheophorbide-a methyl ester (PPa-OMe) was developed for the linear and nonlinear optical imaging of membrane potentials as well as biological imaging of structures through two-photon excited fluorescence (TPEF) and second harmonic generation (SGH) microscopy.

In TPEF, a fluorophore is excited by the simultaneous absorption of two photons in the infrared spectral range. In conventional one-photon fluorescence, the same transition to higher energy levels requires photons in the ultraviolet or visible range. The longer incident wavelength in TPEF leads to improved depth penetration in tissues, with reduced potential for photolytic damage. SHG, on the other hand, is a nonlinear process where two photons interact with a nonlinear material and are effectively combined to generate new photons with twice the energy. This process does not involve absorption of photons but relies on virtual energy states and can only occur in materials that exhibit a non-centrosymmetric structure.

Unlike incoherent processes such as fluorescence, coherent nonlinear optical spectroscopies generate different optical signals depending on the underlying processes. They have broad utility as biomedical tools, offering contrasting mechanisms to fluorescence emissions and provide a useful alternative to label-based imaging.

In this OBC publication, the electronic structure of PPa-OMe (1a) was altered to tune it’s linear and nonlinear optical properties. Porphyrins and related porphyrinoid chromophores inherently possess excellent linear and nonlinear optical properties due to their large, conjugated π-system. By incorporating both electron-donating and –accepting groups, a push-pull type system was generated in which greater SHG intensity was observed due to the increased polarization of its π-system. A hydrophilic group, bis-triethyleneglycol (TEG) amide, was attached to make PPa-OMe amphiphilic and was then suspended in lipid-based water in oil monolayer droplets—a simple model system used to probe potentials across cellular membranes. TPEF and SHG images of the bis-TEG amide attached dyes revealed that the TPEF and SHG involve transition dipole moments in different orientations. While TPEF is detectable in all directions around the sample, SHG is detected in the forward direction of the incident light meaning there is an overall cancelling of the SHG signal from anti-parallel dyes. In order to improve these systems, control over orientation within cell membranes is crucial however, chromophores based on these PPa-OMe derivatives are promising prototypes for future cell imaging studies.

To find out more see:

Push-pull pyropheophorbides for nonlinear optical imaging
Anjul Khadria, Yovan de Coene, Przemyslaw Gawel, Cécile Roche, Koen Clays and Harry L. Anderson
DOI: 10.1039/C6OB02319C

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.