Customised peptides via nickel/photoredox-catalysed bioconjugation

Proteins have an expansive utility in the structure, function, replication and regulation of all cells, and developing tools to study each role is to the benefit of our continued health and wellbeing. One tool is protein bioconjugation, the covalent pairing of a molecule with a protein. Molecule-protein combinations are endless, provided there are efficient methods available to couple molecules with amino acids. Among bioconjugation methods, cysteine functionalisation is a popular choice because the primary thiol is highly nucleophilic thus aiding chemoselectivity. Furthermore, cysteine is rare, reducing the likelihood of many competing, reactive residues.

Transition metal catalysed transformations are uncommon in bioconjugations, despite prominence in other areas of synthetic chemistry. This is because only the most robust methods can overcome the challenges of this chemistry: the solubility of substrates in solvents other than aqueous media, the presence of other amino acids bearing reactive functional groups, and the requirement for low temperatures, low concentrations and mild pH to preserve protein structure.

Catalytic cycle for the nickel/phororedox catalysed synthesis of cysteine bioconjugates

Catalytic cycle for the nickel/phororedox catalysed synthesis of cysteine bioconjugates

A group of researchers from the University of Pennsylvania headed by Professor Gary Molander have developed a bioconjugation method in which aryl halides are cross-coupled with cysteine residues in peptides. Two complexes catalyse the reaction in two connected cycles: the photoredox cycle by a ruthenium-bipyridine complex, and the catalytic cycle by a nickel-bipyridine complex.

The reaction is efficient at room temperature and does not require prior functional group protection. The reaction can also be performed under dilute conditions (10 mM) and on gram scale (3.5 mmol). The scope table includes more than 35 reactions coupling a broad range of aryl halides with small peptides (4 and 9 amino acids) and biologically relevant molecules such as coenzyme A and sulphur-containing pharmaceuticals.

Protecting-group free functionalisation of small peptides under dilute conditions using nickel and ruthenium photoredox catalysis for cysteine functionalization

Protecting group free functionalisation of small peptides under dilute conditions

Included in the reaction scope are a number of substrates which highlight how this work can adapt to established techniques for studying proteins. Coupling of a coumarin generates a fluorescent molecule, which could be used to study the cellular localisation of a protein. Reaction with an aryl-bound biotin derivative demonstrates that affinity tags can be coupled, and utilising aryl-containing pharmaceutical agents is relevant to the synthesis of antibody-drug conjugates.

With this research the authors have contributed a robust catalytic system, which convincingly shows the value of combining a transition metal and photoredox catalyst to functionalise cysteine residues in biomolecules. A necessary next step for this chemistry, and no small task, is to further optimise the reaction conditions for whole proteins.

Read the research article:

Scalable thioarylation of unprotected peptides and biomolecules under Ni/photoredox catalysis

Chem. Sci., 2018, DOI: 10.1039/C7SC04292B

Brandon A. Vara, Xingpin Li, Simon Berritt, Christopher R. Walters, E. James Petersson, Gary A. Molander.


About the Author: 

Zoë Hearne is a PhD candidate in chemistry at McGill University in Montréal, Canada, under the supervision of Professor Chao-Jun Li. She hails from Canberra, Australia, where she completed her undergraduate degree. Her current research focuses on transition metal catalysis to effect novel transformations, and out of the lab she is an enthusiastic chemistry tutor and science communicator.

 

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Chemical Science is moving to weekly issues!

A gold open-access journal that’s free to read & free to publish in

We have exciting news here at Chemical Science! From 2018, the journal will be moving from publishing monthly issues to weekly issues. This is one of the biggest changes to the journal since it was launched in 2010.

Why are we doing this? By publishing weekly issues, we’ll be able to make our articles more accessible to keep up with the large number of articles we currently publish. With the journal being free to access, it would be a shame for the community to miss the latest exceptional findings due to less frequent, larger issues.

What are the benefits for the chemical sciences community? For our readers, it will be easier to find the latest relevant articles, with weekly table-of-contents alerts and a shorter contents list for each issue. For our authors, articles will be assigned page numbers more quickly and will be indexed in databases such as PubMed Central® sooner.

You can learn more about this change in our Editorial by Executive Editor, May Copsey, published in the first ever Chemical Science weekly issue!

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Meet Vincent Artero: Chemical Science Associate Editor

We are delighted to welcome Professor Vincent Artero as Chemical Science Associate Editor, handling submissions in the area of energy.

Vincent Artero graduated from the Ecole Normale Supérieure (Ulm) and the University Pierre et Marie Curie (Paris 6). He received his Ph.D. in 2000 under the supervision of Professor A. Proust and Professor P. Gouzerh. His doctoral work dealt with organometallic derivatives of polyoxometalates. After a postdoctoral stay at the University of Aachen (Aix la Chapelle) with Professor U. Kölle, he joined in 2001 the group of Professor M. Fontecave in Grenoble where he obtained a position in the Life Science Division of the CEA.

Since 2016, he leads the SolHyCat group as Research Director in the Laboratory of Chemistry and Biology of Metals (a research unit cooperated by CEA, CNRS and Univ. Grenoble Alpes) in Grenoble. Vincent Artero received the “Grand Prix Mergier-Bourdeix de l’Académie des Sciences” in 2011. In 2012, he was granted with a Consolidator Grant from the European Research Council (ERC). He currently acts as Chair of the Scientific Advisory Board of the ARCANE Excellence Laboratory Network (LABEX) for bio-driven chemistry in Grenoble and co-chair of the French Research Network (GDR) on solar fuels.

His current research interests are in the structural and functional modelisation of hydrogenases, the design of artificial organometallic proteins and the photo- and electro-production of hydrogen. Vincent is keen to receive submissions in his area of expertise.  Below is a list of recent Chemical Science articles published within the energy-related field – all free to read. We hope you enjoy them!

Porous dendritic copper: an electrocatalyst for highly selective CO2 reduction to formate in water/ionic liquid electrolyte
Tran Ngoc Huan, Philippe Simon, Gwenaëlle Rousse, Isabelle Génois, Vincent Artero and Marc Fontecave
Chem. Sci., 2017,8, 742-747
DOI: 10.1039/C6SC03194C

Ligand effect on the catalytic activity of porphyrin-protected gold clusters in the electrochemical hydrogen evolution reaction
Daichi Eguchi, Masanori Sakamoto and Toshiharu Teranishi
Chem. Sci., 2018, Advance Article
DOI: 10.1039/c7sc03997b

A matrix of heterobimetallic complexes for interrogation of hydrogen evolution reaction electrocatalysts
Pokhraj Ghosh, Shengda Ding, Rachel B. Chupik, Manuel Quiroz, Chung-Hung Hsieh, Nattami Bhuvanesh, Michael B. Hall
and Marcetta Y. Darensbourg
Chem. Sci., 2017,8, 8291-8300
DOI: 10.1039/c7sc03378h

Site-isolated manganese carbonyl on bipyridine-functionalities of periodic mesoporous organosilicas: efficient CO2 photoreduction and detection of key reaction intermediates
Xia Wang, Indre Thiel, Alexey Fedorov, Christophe Copéret, Victor Mougel and Marc Fontecave
Chem. Sci., 2017,8, 8204-8213
DOI: 10.1039/C7SC03512H

You can submit your high quality research in the area of energy to Vincent Artero’s Editorial Office.

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Old and new spectroscopic techniques team up to decipher intricate alkaloids

Cutting-edge strategies set to increase our access to chemical space after researchers use them to verify unprecedented structures

Scientists have identified the structures of two marine natural products that were previously considered too complicated to characterise.1 A combination of well-known spectroscopic tools and new experiments probing orientation-dependant bonding allowed the team to unpick the structures.

Source: © Royal Society of Chemistry
Structures of caulamidines A (left) and B (right)

Natural products are a rich source of pharmacologically-active compounds. The problem is: they are often difficult to purify and identify.

Gary Martin, of Merck Research Laboratories in the US, and Kirk Gustafson, from the US National Cancer Institute, have been studying and characterising natural products for years. ‘There has been a continuing flow of incorrectly reported complex natural product structures into the published literature … at present, there are more than 1200 structure revision papers. Stopping investigators from reporting incorrect structures in the first place will free up their time to pursue and identify new molecular entities,’ they say.

Read the full story by Hannah Kerr on Chemistry World.

1 D J Milanowski et al, Chem. Sci., 2017, DOI: 10.1039/c7sc01996c (This paper is open access.)

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What’s left isn’t always right in total synthesis

Using detective skills that would make Hercule Poirot proud, researchers in the US have solved a longstanding mystery around the absolute configuration of natural product (+)-frondosin B.1

Source: Royal Society of Chemistry Summary of the enantioselective frondosin B syntheses reported to date

(+)-Frondosin B is part of a family of marine sesquiterpenes found in underwater sponges that exhibit anti-inflammatory properties and have potential applications in anticancer and HIV therapy. Starting with Samuel Danishefsky’s route in 2001,2 there have been 5 total syntheses of (+)-frondosin B. However, due to a discrepancy in the optical rotation of the final product during Dirk Trauner’s 2002 synthesis,3 which was observed to have S rather than the expected R configuration, there has been a fierce debate in the synthetic community about the true stereochemistry at C8 in the natural product. After more than decade of attempts by synthetic organic chemists to explain this, particularly focused on different inversion processes, no definitive answer had arisen.

Read the full story by Jason Woolford on Chemistry World.

1 L A Joyce et al, Chem. Sci., 2017, DOI: 10.1039/c7sc04249c (This paper is open access.)

2 M Inoue et al, J. Am. Chem. Soc., 2001, 123, 1878 (DOI: 10.1021/ja0021060)

 

 

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Benchmark for molecular machine learning

A team at Stanford University in the US has developed a benchmark for machine learning in chemistry. By providing a consistent way to test different techniques across a range of chemical data, it aims to accelerate the growth of this new type of scientific problem-solving.

Source: Royal Society of Chemistry
MoleculeNet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurisation and learning algorithms (released as part of the DeepChem open source library)

Machine learning methods train a computer to efficiently get from raw data to already-known answers. Once the expected results are consistently reproduced, the software is ready to perform the same task with entirely new data. To fairly compare different learning approaches, research groups around the globe need to train and test their methods using a shared set of problems. Reference databases already exist for images and text; MoleculeNet, an extension of the DeepChem project, provides such a benchmark for chemistry.

Read the full story by Alexander Whiteside on Chemistry World.

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Protonation enhances water splitting

Researchers in China and Singapore have designed a new platinum electrocatalyst for the hydrogen evolution reaction that outperforms existing catalysts and also performs better than theoretical calculations suggest it should.

Source: Royal Society of Chemistry
Transmission electron microscopy image of the new electrocatalyst showing its branched structure

Hydrogen can serve as a clean fuel, and electrochemical water splitting through the hydrogen evolution reaction is one way to generate this valuable resource. Many current electrocatalysts for the hydrogen evolution reaction are based on platinum, which, although expensive, can be very efficient. Researchers are always looking to improve the efficiency of platinum electrocatalysts to make the hydrogen evolution reaction a suitable replacement for fossil fuels.

Read the full story by Suzanne Howson on Chemistry World.

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Peptide vehicle drives CRISPR delivery of Cas9 into cells

Scientists in Spain have put forward what they describe as the first non-covalent strategy for delivering the CRISPR Cas9 ribonucleoprotein into cells.1

Cas9 is a large RNA-guided DNA endonuclease enzyme that is responsible for accurately recognising and cutting the desired sequence of DNA in a cell’s genome during the gene editing process known as CRISPR. At the moment, CRISPR scientists typically transfect cells with a plasmid containing instructions to make Cas9: however, this isn’t ideal as it might result in permanent DNA recombination and persistent expression, which could have adverse effects. Researchers are therefore exploring methods that deliver Cas9 into cells.

Read the full story by Adrian Robinson on Chemistry World.

Peptide/Cas9 nanostructures for ribonucleoprotein cell membrane transport and gene edition

1 I Lostalé-Seijo et al, Chem. Sci., 2017, DOI: 10.1039/c7sc03918b (This paper is open access.)

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Zirconium MOF buckles under dynamite pressure

Scientists in the US have found that a metal–organic framework (MOF) known for its robustness takes in the same amount of energy as a TNT blast releases when it breaks.

Shock-absorber MOF

Source: Royal Society of Chemistry After compression, the effective number of Zr–carboxylate oxygen bonds (shown in yellow) for each Zr(IV) ion decreased from 4 to ≈2

MOF materials are porous framework solids whose typical applications include gas storage, separation and catalysis. Scientists have studied the zirconium-based MOF, UiO-66, in more detail than most. It’s easily synthesised, has a well-known structure and is strong. Unlike some other MOFs, it doesn’t react with water, and on removing its residual solvent, the framework remains intact with true, empty voids.

Read the full story by Emma Stephen on Chemistry World.

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Quick test on pinprick of blood could help stop Ebola in its tracks

Scientists have developed a quick, cheap, safe and field-deployable method to detect the Ebola virus in unprocessed whole blood.

artist's impression of an ebola virus in the body

Source: Shutterstock The World Health Organization declared an end to the most recent Ebola epidemic in January 2016

The recent Ebola epidemic in West Africa was responsible for 11,310 deaths. Containing this deadly virus relies on rapid, reliable diagnoses, but Ebola is difficult to diagnose because it shares its initial symptoms with other diseases such as malaria and yellow fever. It usually takes weeks before patients develop the bleeding associated with Ebola haemorrhagic fever; by this time, they may have passed the infection on to others.

The standard method of detection is reverse transcription polymerase chain reaction (RT-qPCR), where chemical probes flag nucleic acids in the virus genome. This is reliable but involves deploying whole mobile laboratories and trained personnel. It is also expensive and results can take hours or even days, while the virus continues to spread. Another drawback is that it requires a blood draw, which is risky for both medical personnel and haemorrhagic patients.

Read the full story by Will Bergius on Chemistry World.

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