Editor’s Collection: Motomu Kanai

In this month’s Editor’s collection, Motomu Kanai shares some of their favourite recent Organic & Biomolecular Chemistry articles

The Organic & Biomolecular Chemistry Editor’s collection is a showcase of some of the best articles published in the journal, hand selected by our Associate Editors and Editorial Board members.

For this month’s selection, Associate Editor Motomu Kanai has highlighted some of his favourite recent works.

Take a look at what he thought of the articles below, and find out more about the research and the researchers behind the papers in our interviews with the authors.

Motomu’s Selection:

The effect of deoxyfluorination and O-acylation on the cytotoxicity of N-acetyl-D-gluco- and D-galactosamine hemiacetals
Vojtěch Hamala, Lucie Červenková Šťastná, Martin Kurfiřt, Petra Cuřínová, Martin Balouch, Roman Hrstka, Petr Voňka and Jindřich Karban

Motomu’s comments:
Introducing fluorine atoms into biologically active molecules almost always induces interesting effects. Substitution of hydroxy groups in sugars with fluorine atoms is a typical example. Here Hamala et al. systematically synthesized deoxyfluorinated sugar analogues and studied their cytotoxicity to cancer cells. These molecules may be also interesting fluorine NMR probes, as well as tools for studying CH/π interactions between sugars and proteins.

Find out more in our interview with the authors


An air-stable, Zn2+-based catalyst for hydrosilylation of alkenes and alkynes
Kristina Groutchik, Kuldeep Jaiswal and Roman Dobrovetsky

Motomu’s comments:
Hydrosilylation of alkenes and alkynes is an important reaction in both chemical laboratories and industries, the latter of which produce silicon polymers such as rubbers and oils, which are essential for our daily life. Platinum catalysts are commonly used to promote this reaction. However, use of sustainable, earth abundant catalysts is more preferable. In this paper, Groutchik et al. report that an air-stable zinc complex generated from a hemilabile tetradentate ligand promotes efficient hydrosilylation of alkenes and alkynes. The rection proceeds thorough frustrated Lewis pair activation of hydrosilane. This achievement promises novel reactivity of metal complex catalysts based on smart ligand design.

Find out more in our interview with the authors


Deuteration of terminal alkynes realizes simultaneous live cell Raman imaging of similar alkyne-tagged biomolecules
Syusuke Egoshi, Kosuke Dodo, Kenji Ohgane and Mikiko Sodeoka

Motomu’s comments:
Alkynes are a unique tag for biorthogonal reactions as well as Raman imaging. For the latter, alkynes provide characteristic Raman signals in the region where other cellular molecules do not interfere. Thus, use of alkyne tags is beneficial to enhance the signal-to-noise ratio. In this paper, Egoshi et al. found that deuteration at the terminal carbon of alkyne tags markedly shifted the Raman signal by 135 cm-1. This finding enabled two-color in-cell Raman imaging, simultaneously using two similar tags containing either H or D at the alkyne terminus.

Find out more in our interview with the authors


Meet the Editor:
Motomu Kanai, OBC Associate Editor

Motomu Kanai obtained his PhD from Osaka University in 1995. Then, he moved to University of Wisconsin, USA, for postdoctoral studies with Professor Laura L. Kiessling. In 1997 he returned to Japan and joined Professor Masakatsu Shibasaki’s group at The University of Tokyo as an assistant professor. After being a lecturer (2000~2003) and an associate professor (2003~2010), he started his position as a professor at The University of Tokyo (since 2010) and a principal investigator of ERATO Kanai Life Science Project (2011~2017). He has received The Pharmaceutical Society of Japan Award for Young Scientists (2001), Thieme Journals Award (2003), Merck-Banyu Lectureship Award (MBLA: 2005), Asian Core Program Lectureship Award (2008 and 2010), and Thomson-Reuters The 4th Research Front Award (2016).

His research interests entail design and synthesis of functional (especially, biologically active) molecules.

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Editor’s Collection: Meet the authors – Dr Jindřich Karban et al.

In this Editor’s Collection, Motomu Kanai highlighted ‘The effect of deoxyfluorination and O-acylation on the cytotoxicity of N-acetyl-D-gluco- and D-galactosamine hemiacetals’ by Dr Jindřich Karban et al. as one of his personal favourite recent Organic & Biomolecular Chemistry articles. Here, we catch up with the authors to find out a little bit more about their research

Vojtěch Hamala

Roman Hrstka

Petr Voňka

Martin Balouch

Petra Cuřínová

Jindřich Karban

Lucie Červenková Šťastná

Martin Kurfiřt

Introducing the researchers:

Vojtěch Hamala obtained his MSc at the University of Chemistry and Technology in Prague in 2019. He is a PhD student at the Institute of Chemical Process Fundamentals in Prague under the supervision of Dr Jindřich Karban. His main interests focus on the synthesis of cytotoxic carbohydrate analogues and antitumor carbohydrate-organometallic complexes.

Roman Hrstka obtained his PhD degree in cellular and molecular biology at Masaryk University in Brno. Currently he works as a principal investigator at Masaryk Memorial Cancer Institute. His research is focused on cancer cell signalling and metastasis development. In parallel, he also serves in the Czech national node of the BBMRI-ERIC (European research infrastructure for biobanking).

Petr Voňka graduated in biochemistry and physical chemistry at Palacký University in Olomouc in 2017. He is currently studying for his PhD degree in experimental biology under the supervision of Assoc. prof. Roman Hrstka at Palacký University in Olomouc. His research is focused on the interactions of small molecules (steroids or organometallic compounds) with selected proteins.

 Martin Balouch obtained his MSc at the University of Chemistry and Technology in Prague where he continues to study for his PhD degree. He combines pharmaceutical research under prof. Stepanek (UCT Prague) with in silico permeation models under supervision of doc. Karel Berka (UP Olomouc). His research is focused on molecule/biomembrane interactions using both experimental and computational approaches.

Petra Cuřínová obtained her PhD in organic chemistry at the University of Chemistry and Technology in Prague. After the return from the Exeter University (UK) where she dealt with the synthesis and properties of anion-recognizing receptors, she continued her carrier at the Institute of Chemical Process Fundamentals in Prague. She won the O. Wichterle Award for young scientists in 2016. Her main areas of interest comprise preparation, characterisation and application of host-guest systems, chiral recognition and spectroscopic methods.

Jindřich Karban received his PhD in organic chemistry in 1998 under the supervision of Prof Miloslav Černý at Charles University in Prague. After a few years of practise in analytical chemistry and mass spectrometry, he continued his research in carbohydrate chemistry as a senior scientist at the Institute of Chemical Process Fundamentals in Prague. His research interests include the synthesis and properties of fluorinated sugar analogues and antitumor carbohydrate-organometallic conjugates.

Lucie Červenková Šťastná obtained her PhD in organic technology at the University of Chemistry and Technology in Prague where she studied fluorinated cyclopentadienyl complexes. Recently she started working as a researcher at the Institute of Chemical Process Fundamentals in Prague. Her research is focused on structure elucidation by NMR spectroscopy, catalysis and fluorinated sugar analogues.

Martin Kurfiřt obtained his MSc in the field of organic chemistry at the University of Chemistry and Technology in Prague in 2019. He is currently a PhD student at the Institute of Chemical Process Fundamentals in Prague under the supervision of Dr Jindřich Karban. His professional interests comprise the organic synthesis of carbohydrates and study of their interactions with proteins by NMR spectroscopy.


What inspired your research in this area?

Our research in this area was motivated by curiosity. Two separate facts had been known: (1) acylated 2-acetamido-pyranoses become moderately cytotoxic if we selectively deprotect the anomeric hydroxyl group and increase the acyl chain length at the remaining hydroxyls from acetyl to butyryl, (2) fluorination of some monosaccharides renders them cytotoxic. We wished to know what would happen to cytotoxicity if we combine these structural features in one molecule. Therefore, we synthesised fluorinated acylated glucosamine and galactosamine analogues possessing a free anomeric hydroxyl (hemiacetals) and two-to-four carbon acyl chains at the non-anomeric positions, and determined their cytotoxicity.

What do you personally feel is the most interesting/important outcome of your study?

We suggested a hypothesis that the observed cytotoxicity could be the result of the recently discovered nonspecific glycosylation of histidine residues termed S-glyco-modification (J. Am. Chem. Soc. 2020, 142, 9382–9388.) This reaction occurs when acylated amino sugar hemiacetals react with histidine residues by an elimination-addition mechanism in a protein microenvironment rich in lysine. Surprisingly, there was no correlation between the cytotoxicity of our compounds and their ability to react with the thiol group by the suggested mechanism in vitro. This indicates that our compounds probably exert their cytotoxic properties by other, so far unspecified or unknown mechanisms.

What directions are you planning to take with your research in future?

We want to prepare conjugates of some of the most cytotoxic fluorinated hemiacetals with cytotoxic or anti-invasive ruthenium complexes. We expect that conjugation of a ruthenium complex to a cytotoxic sugar may potentiate their antitumor properties. At the moment we work on a suitable synthetic method to link an antitumor ruthenium complex to fluorinated amino sugar hemiacetals.


Read the full article: The effect of deoxyfluorination and O-acylation on the cytotoxicity of N-acetyl-D-gluco- and D-galactosamine hemiacetals

See the other articles showcased in this month’s Editor’s Collection

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Editor’s Collection: Meet the authors – Dr Kosuke Dodo, Dr Mikiko Sodeoka et al.

In this Editor’s Collection, Motomu Kanai highlighted ‘Deuteration of terminal alkynes realizes simultaneous live cell Raman imaging of similar alkyne-tagged biomolecules’ by Dr Kosuke Dodo, Dr Mikiko Sodeoka et al. as one of his personal favourite recent Organic & Biomolecular Chemistry articles. Here, we catch up with the authors to find out a little bit more about their research

Syusuke Egoshi

Kosuke Dodo

Kenji Ohgane

Mikiko Sodeoka

Introducing the researchers:

Syusuke Egoshi received his PhD in 2015 under the supervision of Prof. Minoru Ueda at Tohoku University graduate school of science. He joined the group of Prof. Mikiko Sodeoka at RIKEN as postdoctoral fellows in 2016, and as special postdoctoral researcher in 2018, thereafter he was promoted to a research scientist. His research interests are the development of unique chemical imaging technologies including Raman tags/probes and their application for biological research of elucidating the mode of action of small bioactive molecules.

Kosuke Dodo graduated from the University of Tokyo in 1999 and received his PhD from Tohoku University in 2004. After the postdoctoral training at RIKEN, he was appointed as an assistant professor at the University of Tokyo in 2007. Then, he returned to RIKEN as a research scientist and a group leader in the ERATO Sodeoka Live Cell Chemistry Project from 2008 to 2013, thereafter he was promoted to a senior research scientist in 2014. His research interests span the development of unique chemical probes/technologies including Raman probes and their application for biological research related to cell death signaling.

Kenji Ohgane received his PhD (Pharmaceutical Science) in 2013 under the supervision of Prof. Yuichi Hashimoto at the University of Tokyo (the Laboratory of Bioorganic and Medicinal Chemistry at the Institute for Molecular and Cellular Biosciences). In 2013, he joined the group of Prof. Mikiko Sodeoka at RIKEN and performed chemical biology researches. After 4 years of postdoctoral research, he returned to the University of Tokyo as an Assistant Professor, and then moved to the Tokyo University of Science (Prof. Kouji Kuramochi) in 2020. In 2021, he started his laboratory at the Department of Chemistry, Ochanomizu University (Tokyo). His research group is currently focusing on small molecules that stabilize or destabilize their target proteins (screening, medicinal chemistry, and analysis of the mode of action), and also interested in understanding new bioactivities of sterols and lipids.

Mikiko Sodeoka received her BS, MS, and PhD degrees from Chiba University. After working at the Sagami Chemical Research Center, Hokkaido University, Harvard University, and the University of Tokyo, she became a Group Leader at the Sagami Chemical Research Center in 1996. She moved to the University of Tokyo as an Associate Professor and then to Tohoku University as a Full Professor in 2000. Since 2004, she has been a Chief Scientist at RIKEN. Her current researches cover development of new reactions based on transition metal chemistry and fluorine chemistry and development of new methodologies for chemical biology research.


What inspired your research in this area?

Raman imaging using alkyne tag is useful tool to observe small biomolecules in cells because alkyne exhibits a vibrational frequency in Raman-silent region that is free of interference from intracellular molecules. The development of various alkynes is important to observe a wide variety of biomolecules in cells. Therefore, we are working on the development of novel alkyne tags/ probes.

What do you personally feel is the most interesting/important outcome of your study?

The most interesting findings are the alkyne vibrational frequency shifts by 135 cm-1 upon deuteration, and the D/H exchange of alkynes occurs depending on pH. The large difference in Raman shift of D/H alkynes successfully realized simultaneous two-color imaging of similar small molecules. The pH dependency of D/H exchange of alkynes indicates the potency of D-alkyne to monitor the intracellular dynamics.

What directions are you planning to take with your research in future? 

In the next step, we will develop various types of D-alkyne probes from H-alkyne probes and apply them for multi-color Raman imaging to observe small molecules in cells. In addition, we are planning to develop Raman probes using D/H exchange of D-alkynes, such as the pH sensor.


Read the full article: Deuteration of terminal alkynes realizes simultaneous live cell Raman imaging of similar alkyne-tagged biomolecules

See the other articles showcased in this month’s Editor’s Collection

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Editor’s Collection: Meet the authors – Dr Roman Dobrovetsky et al.

In this Editor’s Collection, Motomu Kanai highlighted ‘An air-stable, Zn2+-based catalyst for hydrosilylation of alkenes and alkynes’ by Dr Roman Dobrovetsky et al. as one of his personal favourite recent Organic & Biomolecular Chemistry articles. Here, we catch up with the authors to find out a little bit more about their research

Roman Dobrovetsky

Kuldeep Jaiswal

Kristina Gruchik

Introducing the researchers:

Roman Dobrovetsky was born in Uzbekistan in 1979. At age of 12, his family moved to Israel. After finishing school in 1998, he joined the army. Soon after the army, he started his BSc in Technion. In 2005, he joined Prof. Apeloig’s group for his PhD studies in the field of silicon chemistry. After finishing his PhD, he moved to Toronto to work with Prof. Stephan, where he did his research in the field of frustrated Lewis pairs and Lewis acid catalysis. In 2015, he moved back to Israel to start his independent career at Tel Aviv University. His research interests are in the main group chemistry and transition-metal free catalysis.

Kuldeep Jaiswal was born in 1988 in Sonipat/India studied chemistry at the Hindu college Sonipat (2005-2008) and at the Kurukshetra University Kurukshetra (2008-2010) and completed his Ph.D. in Inorganic Chemistry under the supervision of Prof. Sanjay Singh (2012-2016) at the Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali (India). His Ph.D is supported by a scholarship of the University Grants Commission (2012-2016). Kuldeep then joined the laboratory of Prof. Chunming Cui (State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, China) as a postdoctoral researcher (2016-18), and later joined Prof. Roman Dobrovetsky group (2018 onwards) at the School of Chemistry at Tel Aviv University.

Kristina Gruchik was born in Magadan, Russian Federation. Received her BSc and MSc from Tel-Aviv University. Currently, she is pursuing her PhD at the same institution under the supervision of Prof. Roman Dobrovetsky, exploring the chemistry of the main group elements.


What inspired your research in this area?

I’d say that what inspires me the most is a scientific curiosity. Questions like can we do chemistry that transition metals do with non-transition metal based complexes are very interesting to me.

What do you personally feel is the most interesting/important outcome of your study?

Actually, for me the most interesting and surprising in this chemistry was the fact that the Zn complex that we made was air- and moisture stable. This of course makes it more convenient for use in catalysis.

What directions are you planning to take with your research in future?

We’re now looking into other ligands at Zn-center and other main group elements and at other catalytic hydroelementation reactions that we can do with these new catalysts.


Read the full article: An air-stable, Zn2+-based catalyst for hydrosilylation of alkenes and alkynes

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Editor’s Collection: Scott Silverman

In this month’s Editor’s collection, Scott Silverman shares some of his favourite recent Organic & Biomolecular Chemistry articles

The Organic & Biomolecular Chemistry Editor’s collection is a showcase of some of the best articles published in the journal, hand selected by our Associate Editors and Editorial Board members.

For this month’s selection, Associate Editor Scott Silverman has highlighted some of his favourite recent works. Take a look at what they thought of the articles below, and find out more about the research and the researchers behind the papers in our interviews with the authors.

Scott’s Selection:

Post-synthetic transamination at position N4 of cytosine in oligonucleotides assembled with routinely used phosphoramidites

Rémy Lartia, Coelio Valléea and Eric Defrancq

Scott’s comments: Lartia et al. offer an elegant way to prepare site-specifically modified DNA oligonucleotides using standard and inexpensive reagents. This interesting approach is analogous to “convertible nucleotides” but takes advantage of the reactivity of the standard benzoyl-deoxycytidine (BzdC) monomer with various nucleophilic amines. The findings should be practically useful for investigators in several contexts, such as when wanting to prepare a series of sequence-related modified oligonucleotides without high cost.

Find out more in our interview with the authors


Hydrated metal ion as a general acid in the catalytic mechanism of the 8–17 DNAzyme

Catalina Cortés-Guajardo, Francisca Rojas-Hernández, Romina Paillao-Bustos and Marjorie Cepeda-Plaza

Scott’s comments: Cepeda-Plaza and coworkers nicely build on prior work by examining the role of a specific nucleobase in the catalytic activity of an RNA-cleaving DNAzyme. They distinguish two proton-transfer steps and find that a hydrated Mg2+ ion acts as a general acid to protonate the leaving group during the reaction. This mechanistic insight is valuable, especially given how little is known overall about DNAzyme mechanisms.

Find out more in our interview with the authors


Approaches for peptide and protein cyclisation

Heather C. Hayes, Louis Y. P. Luk and Yu-Hsuan Tsai

Scott’s comments: Peptide and protein cyclization is important process for both biology and chemistry. In this review, Luk and coworkers summarize various methods for cyclization that use chemical reagents, enzymes, and protein tags. Considering the broad importance of peptide and protein cyclization in many fields, this review should be useful for a variety of investigators as they plan their own experiments.

Find out more in our interview with the authors


Meet the Editor:

Scott Silverman, OBC Associate Editor

Scott K. Silverman was born in 1972 and raised in Los Angeles, California. He received his BS in chemistry from UCLA in 1991, working with Christopher Foote on photooxygenation mechanisms. He obtained his PhD in chemistry from Caltech in 1997, working with Dennis Dougherty to study high-spin organic polyradicals and molecular neurobiology. After postdoctoral research on RNA biochemistry with Thomas Cech at the University of Colorado at Boulder, he joined the University of Illinois in 2000, where he is currently Professor of Chemistry.

Professor Silverman’s research is in the chemistry and biochemistry of nucleic acids, especially investigations of DNA as an enzyme (DNAzyme, deoxyribozyme).

 

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Editor’s Collection: Meet the authors – Dr Marjorie Cepeda-Plaza et al.

In this Editor’s Collection, Scott Silverman highlighted ‘Hydrated metal ion as a general acid in the catalytic mechanism of the 8–17 DNAzyme’ by Dr Marjorie Cepeda-Plaza et al. as one of his personal favourite recent Organic & Biomolecular Chemistry articles. Here, we catch up with the authors to find out a little bit more about their research

 

Marjorie Cepeda-Plaza

Francisca Rojas Hernández

Catalina Cortés Guajardo

Romina Paillao Bustos

Introducing the researchers:

Marjorie Cepeda-Plaza studied Chemistry at Universidad Chile and received her Doctorate in Chemistry from Pontificia Universidad Católica de Chile. After postdoctoral work with Dr. Yi Lu at the University of Illinois at Urbana Champaign, she joined the Chemical Science Department at Universidad Andrés Bello in Chile. Her research is focused on the study of the mechanisms of catalysis of DNAzymes. She is currently part of the Committee for Gender Equality in Research and the Academic Committee of the Center for the Communication of Science at the same University.

Francisca Rojas Hernández obtained her bachelor´s degree in Chemistry from Universidad Andrés Bello (UNAB) in 2020. Her thesis was focused on understanding the role of divalent metal ion in the catalytic mechanism of the 8-17 DNAzyme. She is currently working as a research assistant at the Laboratory of Bioinorganic Chemistry at UNAB. She also a great visual artist.

Catalina Cortés Guajardo obtained her master’s degree in Chemistry from Universidad de Chile in 2020. Her thesis was focused on fluorescent probes for singlet oxygen. She spent two years working as research assistant at the Laboratory of Bioinorganic Chemistry at UNAB. Now she is pursuing her doctorate degree on Chemistry at Universidad de Chile.

Romina Paillao Bustos is a biotechnologist from Universidad Mayor. She recently obtained her master’s degree in management and technological entrepreneurship from Universidad Adolfo Ibáñez. After spending six months doing research at the Laboratory of Bioinorganic Chemistry at UNAB she joined IQVIA working as CRA I.


What inspired your research in this area?

As a chemist, it was wonderful to discover the catalytic capabilities of DNA. What motivates my research is putting together the puzzle that relates DNA functional groups and conformations with their catalytic activity. Also, it is stimulating to be involved in the scientific formation of undergraduate students in Chile and relate them with the fascinating field of DNA catalysis.

What do you personally feel is the most interesting/important outcome of your study?

Our findings point out the stabilization of the 5′-O leaving group by the hydrated metal ion acting as a general acid in the phosphodiester transfer reaction catalyze by the 8-17 DNAzyme. These results are valuable to understand the precise role of divalent metal ion cofactors in the catalytic mechanisms of DNAzymes.

What directions are you planning to take with your research in future? What are you going to be working on next?

We continue working to understand the role of metal ions in the catalytic mechanism of the 8-17 DNAzyme. We are also trying to find out secondary and tertiary catalytic strategies that assist the RNA-cleavage reaction. In addition, we are interested in exploring similarities and differences among RNA-cleaving DNAzymes.


Read the full article: Hydrated metal ion as a general acid in the catalytic mechanism of the 8–17 DNAzyme

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Editor’s Collection: Meet the authors – Dr Remy Lartia & Dr Eric Defrancq et al.

In this Editor’s Collection, Scott Silverman highlighted ‘Post-synthetic transamination at position N4 of cytosine in oligonucleotides assembled with routinely used phosphoramidites’ by Dr Remy Lartia and Dr Eric Defrancq et al. as one of his personal favourite recent Organic & Biomolecular Chemistry articles. Here, we catch up with the authors to find out a little bit more about their research

 

Rémy Lartia

Eric Defrancq

Coélio Vallée

Introducing the researchers:

Rémy Lartia. After an engineer diploma and master degree (Univ. Rennes, France, 1998-2001), his Ph.D. research, under the supervision of Dr. Ulysse Asseline at CBM (Univ. Orléans, France,  2001-2004), focused on synthesis of fluorescent oligonuceotidic bioconjugates. In 2010, he joined the group of Prof. Marie-Paule Teulade-Fichou at the Collège de France (Paris, 2004-2006). During his two years of post-doctoral experience, he worked on synthesis of fluorescent triphenylamine derivatives.
He is currently research engineer on the Nanobio facility hosted by DCM (Univ. Grenoble, France, 2006) and works on peptide and oligonucleotides chemistry.

Eric Defrancq received his PhD (Organic Chemistry) in 1989 under the supervision of Prof. Jean Lhomme at the University Joseph Fourier of Grenoble. After two years of postdoctoral research with Prof. Tabacchi at the Institute of Chemistry at Neuchâtel (Switzerland), he returned to Grenoble in 1992 as an Assistant Professor, where he currently works as a full Professor.
His research interests lie in the field of modified oligonucleotide design for applications such as G-quadruplex and i-motif mimetics, aptamers as well as the design of photoreactive metal complexes for DNA targeting.

Coélio Vallée graduated from his Technician Diploma in General Chemistry in 2018 at the University of Montpellier. He joined the Nanobio facility in 2019 as technician on biomolecules synthesis where he performed the elaboration of peptides and oligonucleotides.


What inspired your research in this area?

Current trends in research mainly focus on more and more sophisticated reagents and/or investigation methods. Oppositely, it was thrilling to find out that very standard reagents can afford complex biomolecules such as orthogonally modified nucleic acids.

What do you personally feel is the most interesting outcome of your study?

For bioconjugates design, fine tuning of some parameters (notably tether length between the oligonucleotide and the reporter group) can afford dramatic change of the properties of the whole molecule. However, these parameters are rarely investigated as it often involves tedious multistep synthesis. Our method could easily overcome this difficulty. In the same context, another important outcome is that our method is relatively cheap in comparison with the others thus allowing the aforementioned investigations.

What directions are you planning to take with your research in future?

One direction is to use this method for the preparation of oligonucleotides bearing the cyclopropylamine reporter for photochemical purpose (it was the original need) because the previously described method required the use of very expensive phosphoramidite derivative.
Also, we are open to any collaboration with colleagues who are interested to obtain oligonucleotide conjugates.


Read the full article: Post-synthetic transamination at position N4 of cytosine in oligonucleotides assembled with routinely used phosphoramidites

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Editor’s Collection: Meet the authors – Dr Louis YP Luk & Dr Yu-Hsuan Tsai et al.

In this Editor’s Collection, Scott Silverman highlighted ‘Approaches for peptide and protein cyclisation’ by Dr Louis YP Luk and Dr Yu-Hsuan Tsai et al. as one of his personal favourite recent Organic & Biomolecular Chemistry articles. Here, we catch up with the authors to find out a little bit more about their research

Researchers: Louis Luk (Cardiff Univeristy, School of Chemistry Lecturer) , Yu-Hsuan Tsai (Shenzhen Bay Laboratory) & Heather Hayes (Cardiff University PhD student)


What inspired you to write this Review article?

We are interested in the biophysical effects of polypeptide cyclisation. Considering the benefits cyclisation can confer (e.g. enhanced stability and activity), we wonder why it is not observed more often in nature. While there is a wealth of cyclisation methods to choose from, the suitability of particular techniques towards specific applications is infrequently discussed. Hence, we wanted to organise our thoughts by summarising the current state-of-the-art in this field.

What primary research are you carrying out in the area?

We have been preparing cyclised biocatalysts with the aim of improving their thermostability and solvent tolerance.

What are your thoughts on the future of this research field?

We believe negative results should also be published. Though it seems less exciting, the scientific community should know that the effect of cyclisation is case-dependent and does not necessarily improve the stability of a protein. By collecting sufficient data (both positive and negative), we may be able to apply AI and deep learning to better predict and design experiments.


Read the full article: Approaches for peptide and protein cyclisation

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Editor’s Collection: Meet the authors – Michael L. Singleton et al.

In the July Editor’s Collection, Judy Wu highlighted ‘Water binding stabilizes stacked conformations of ferrocene containing sheet-like aromatic oligoamides’ by Michael L. Singleton et al. as one of her personal favourite recent Organic & Biomolecular Chemistry articles. Here, we catch up with the authors to find out a little bit more about their research

Authors : (From left to right) Dr. Ya-Zhou Liu, Dr. Xiao Mu, Dr. Chieh-Kai Chan, Dr. Koen Robeyns, Dr. Cheng-Chung Wang, Dr. Michael Singleton

Introducing the researchers:

Dr. Ya-Zhou Liu was born in Linyi, China. He received his MSc degree from Guizhou University in 2015 under the supervision of Prof. Weidong Pan. He then joined the Université Catholique de Louvain for his PhD degree under the supervision of Prof. Istvan E. Marko on the development of indole chalcones for non-apoptotic cancer cell death. In 2017, he joined Prof. Michael L. Singleton’s group to continue his PhD research under the topic of using non-covalent interactions to control fluxional molecules into ordered conformations. After receiving his PhD degree in 2020, he joined the Chengdu Institute of Biology (CIB), Chinese Academy of Sciences as an assistant research fellow with Prof. Xiaofeng Ma, working on the development of enzyme-mimetic catalysts.

Dr. Xiao Mu was born in Zibo, China. She received her MSc degree from Zhejiang Normal University in 2015. In 2016, she arrived in Belgium and started her doctoral studies sponsored by the China Scholarship Council under the supervision of Prof. Michael Singleton on the topic of histidine brace-containing ligand scaffolds for developing biomimetics of lytic polysaccharide monooxygenases. She received her PhD degree in 2020.

Dr. Chieh-Kai Chan received his B.S. from the Department of Medicinal and Applied Chemistry, Kaohsiung Medical University in 2012. He later obtained his M.S. in 2014 and PhD in 2017 in the same department under the supervision of Prof. Meng-Yang Chang . He has been performing his postdoctoral studies with Prof. Cheng-Chung Wang in the Institute of Chemistry at Academia Sinica since 2017, and was awarded the Postdoctoral Scholar Program from Academia Sinica in 2018 and 2020. His current research interests are carbohydrate chemistry, the development of methodologies on small molecules and their applications on drug screening.

Dr. Koen Robeyns was born in Flanders, Belgium. He started undergraduate studies in chemistry at the KULeuven, Kortrijk, and completed his graduate studies at the KULeuven, Leuven, where he was first introduced to crystallography. He began his PhD studies in 2002 on the structural determination of modified DNA sequences, which he defended in 2006. After some years of postdoctoral research, combining both small-molecule and macromolecular crystallography, he moved to the UCLouvain, where he now works as permanent researcher in charge of single crystal studies.

Dr. Cheng-Chung Wang is an Associate Research Fellow at the Institute of Chemistry, Academia Sinica, Taiwan. He received his Ph.D. from TIGP, Academia Sinica under the supervision of Prof. Shang-Cheng Hung in 2008. He joined Prof. Peter H. Seeberger’s laboratory for his postdoctoral research at ETH, Switzerland, in 2008, and then moved to the Max-Planck-Institute of Colloids and Interfaces with Prof. Seeberger in 2009. He started his independent career in 2010, and his group in Academia Sinica is currently focusing on stereoselective glycosylation reactions, the synthesis of complex carbohydrate molecules and facile preparations of small molecules.

Dr. Michael Singleton received his PhD in 2010 from Texas A&M University under the supervision of Prof. Marcetta Darensbourg. He then moved to Bordeaux, France, where he worked as a Marie Curie Postdoctoral Fellow at the European Institute for Chemistry and Biology, working with Prof. Ivan Huc. In 2014, he started his independent career in the Institute of Condensed Matter and Nanoscience at the Université Catholique de Louvain in Belgium. His group’s research focuses on the synthesis and structural control of self-organized/self-assembled molecular architectures for mimicking the reactivity of biological molecules.


What inspired your research in this area?

Large-scale conformational changes in certain proteins can lead to switching of their function or self-assembly properties. Mimicking this process with synthetic oligomers can be used to control self-assembly, permit exchange between larger self-assembled structures, or to change interactions with small molecules.  The current work stems from this idea and our interest in understanding factors that can influence the stability of different folded states.

What do you personally feel is the most interesting/important outcome of your study?

The fluxional character of aromatic oligoamides is not only important as it relates to the stability of their structures, but also to their applications in molecular recognition and catalysis. As numerous members of this type of foldamer have been shown to bind discrete water molecules in the solid state and/or solution, this study highlights the influence this binding can have on the fluxional properties of the oligomer.

What directions are you planning to take with your research in future? What are you going to be working on next?

In the near future, the next steps will be finding conditions or sequences that allow stabilizing or switching to other conformations, for example helices or double helices. Ultimately, it will be interesting to use this conformational exchange to permit one aromatic oligoamide  sequence to perform multiple distinct functions, for instance, incorporating catalytic sites and switching between different catalytic reactions.

 

Read the full article: Water binding stabilizes stacked conformations of ferrocene containing sheet-like aromatic oligoamides

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Editor’s Collection: Meet the authors – Dr Guilhem Chaubet and Dr Alain Wagner et al.

In the July Editor’s Collection, Judy Wu highlighted ‘Plasma induced acceleration and selectivity in strain-promoted azide–alkyne cycloadditions’ by Dr Guilhem Chaubet and Dr Alain Wagner et al. as one of her personal favourite recent Organic & Biomolecular Chemistry articles. Here, we catch up with the authors to find out a little bit more about their research

Dr Alain Wagner and Dr Guilhem Chaubet

Introducing the researchers:

Dr Guilhem Chaubet is the co-director of the Biofunctional Chemistry team in Strasbourg. He joined the CNRS as an independent researcher in 2017 after a PhD at the University of Montpellier II (2010-2013) and a postdoctoral position at the University of Oxford (2014-2017). He investigates chemical conjugation of native proteins, focusing especially on the development of new strategies.

Dr Alain Wagner was born in Saint Avold, France in 1964.  After graduate studies at Strasbourg University under the supervision of Prof.Charles Mioskowski, he took up a postdoctoral fellowship at Affymax Research, Palo Alto, working under the supervision of Prof. Peter Schultz. He entered the CNRS in 1994. In 2001, he co-funded the company Novalix, now one of largest CROs in France. He returned to academic research in 2007 to start the biofunctional chemistry team. In 2014, he co-funded Syndivia, a start-up exploiting new bioconjugations and linker technologies in the field of ADC, and a few months ago, embarked on a new adventure of single cell secretion analysis by co-funding MicroOmiX. His current research focuses on studying chemical reactivity in complex biological systems with applications in drug delivery and droplet microfluidic-based single cell analysis.


What inspired your research in this area?

This work originated almost 10 years ago, when we started investigating in-vivo drug inactivation via strain-promoted azide-alkyne cycloaddition (SPAAC). We had selected an azide analogue of warfarin as our model drug and proved that its anticoagulant activity could be neutralized in mice after injection of a PEG-containing strained alkyne. While this work ended up being published a few years ago, it was during the course of its development that we noticed this odd behaviour of SPAAC being accelerated in human plasma compared to traditional solvent mixtures. Being puzzled by this observation, we decided to dig deeper, which ultimately led to this work published in OBC.

What do you personally feel is the most interesting/important outcome of your study?

I think it is the revision of classical synthetic chemistry rules when reactions are conducted in such a complex medium rather than in a flask, where you can precisely control the environment. Bioorganic chemistry thus challenges the way chemists think about and design their experiments, which fosters innovation and originality.

What directions are you planning to take with your research in future? What are you going to be working on next?

We keep working on new methodologies to access site-specific conjugation of native proteins, which ultimately could lead to protein-selective strategies and applications of these reactions in complex biological media.

 

Read the full article: Plasma induced acceleration and selectivity in strain-promoted azide–alkyne cycloadditions

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