Organic & Biomolecular Chemistry Blog

From left to right: Indranil Chatterjee, Sourav Roy and Gautam Kumar

Mr. Gautam Kumar obtained his M. Tech (Chemical Science and Technology) degree from DIAT(DU)-DRDO-Pune in 2018. He joined the IC research group under the guidance of Prof. Dr. Indranil Chatterjee in July 2018 at Indian Institute of Technology, Ropar, India as a Ph.D. student. He is working on the methodology developments for organic synthesis.

Mr. Sourav Roy completed his Masters at Bidhannagar Govt. College, Bidhannagar, West Bengal State University in 2017. He joined the IC research group under the guidance of Prof. Dr. Indranil Chatterjee in July 2018 at Indian Institute of Technology, Ropar, India as a Ph.D. student. He is working on the methodology developments in organic synthesis.

Dr. Indranil Chatterjee was born in Kolkata, India in 1983. He obtained his B.Sc. from Calcutta University, India in 2006, before joining IIT Kharagpur for his M.Sc. study. In 2008 he moved to Germany for his Ph.D. study at Westfälische Wilhelms-University Muenster under the guidance of Prof. Dr. Armido Studer. After finishing his Ph.D. study in November 2011, he became a Postdoctoral fellow in the group of Prof. Paolo Melchiorre in ICIQ, Tarragona, Spain. From 2014 to 2016, he was a Post-Doc with Prof. Martin Oestreich at the Technische Universität Berlin. He is currently an Assistant Professor at the Indian Institute of Technology Ropar, India.

What inspired you to write this Review article?

The wondrous reactivity of BCF prompted us to work in this field. The versatile capability of BCF is not only restricted to FLP catalysis but extends as a potential Lewis acid to develop verities of transition-metal-free transformation. Therefore, we thought compiling all recent reports in a single frame would be beneficial to the synthetic chemistry community and to new readers looking to develop innovative synthetic methodologies and do more exploration in this blooming area of catalysis.

What primary research are you carrying out in the area?

We started our journey in the field of BCF catalysis in 2018. We were able to successfully develop“Boron Lewis Acid-Catalyzed Regioselective Hydrothiolation of Conjugated Dienes with Thiols” (ACS Catal. 2019, 9, 12, 11627–11633). This unique and high regioselectivity prompted us to explore various regioselective C−heteroatom bond forming reactions using BCF catalysis as an ongoing project.

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

This review collectively highlights the recent development and displays a strong prospective towards a new direction for further discovery and sustainable synthesis in this area. We hope this reactivity can be a potential alternative for transition-metal-based catalysts to discover numerous synthetic protocols in the near future with industrial applications. We expect that BCF chemistry will be explored in various C−H bond functionalization strategies and utilized as a co-catalyst in numerous asymmetric transformations.

Read the full article: Tris(pentafluorophenyl)borane Catalyzed C−C and C−heteroatom Bond Formation

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

See all the full articles on our publishing platform

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 Professor Lei Liu 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.

Lei’s Selection: 

Development of functionalized peptides for efficient inhibition of myostatin by selective photooxygenation

Hideyuki Okamoto,  Atsuhiko Taniguchi,  Shoya Usami,  Masahiro Katsuyama,  Sho Konno,  Akihiro Taguchi,  Kentaro Takayama and Yoshio Hayashi

Lei’s comment: “Myostatin, a major negative regulator protein of skeletal muscle growth, has been shown to play a key role in homeostasis of skeletal muscle. To develop new approaches for myostatin-targeting therapy, a series of photooxygenation-functionalized molecules were developed through the conjugation of myostatin-binding peptide and on/off-switchable photooxygenation catalyst. One of these molecules can very efficiently inactivate myostatin through irreversible and catalytic photooxygenation. This study demonstrates a novel strategy for myostatin inhibition.”

Find out more in our interview with the authors

Cobalt-catalyzed carbonylation of the C–H bond

Lukass Lukasevics and Liene Grigorjeva

Lei’s comment: “The use of cobalt catalysts for C-H activation and functionalization reactions has received increasing attentions in recent years due to two reasons: first, cobalt is a cheap metal; second, cobalt catalysis may provide novel reactivity and selectivity. In the review article the authors surveyed the utility of high-valent cobalt catalysis in C–H carbonylation reactions, showing their applications to many pharmaceutically interesting molecules including benzamides, sulphonamides, benzylamines, aryl anilines, phenols and amino alcohols. The success of cobalt catalysis suggests the need to expand studies in the field, particularly carbonylation of the C(sp3 )–H bond.”

Find out more in our interview with the authors

DNAzymes for amine and peptide lysine acylation

Tianjiong Yao,  Jack J. Przybyla,  Peter Yeh,  Austin M. Woodard,  Hannah J. Nilsson,  Benjamin M. Brandsen and Scott K. Silverman

Lei’s comment: “Site-selective Lys modification of peptides and proteins at various sequence sites is very important to many biotechnology-related fields. The authors report a very interesting work showing that DNAzymes can be used to catalyze amine acylation, including acylation of a Lys residue in a short DNA-anchored peptide. This study not only expands the scope of DNAzyme catalysis, but also suggests the future possible applicability of DNAzymes for sequence-selective Lys modification of pharmaceutically interesting peptides and proteins.”

Find out more in our interview with the authors

Integrating abiotic chemical catalysis and enzymatic catalysis in living cells

Christopher Adamson and Motomu Kanai

Lei’s comment: “Recent experiments have indicated that abiotic catalyst modalities can achieve co-operativity with the enzymatic machinery of living cells. Studies in the direction open doors to two very exciting opportunities: First, “catalysis medicine” where synthetic catalysis is used as a bona fide pharmaceutical modality; second, ‘semi-synthetic life’ that combines the desirable features of living organisms with the unique reactivity of abiotic catalysts. This important review article provides very interesting insights into what need to be done in the coming years, a truly exciting area that would combine the powers of modern chemistry and biology.”

Find out more in our interview with the authors

Meet the Editor:

ORCID: http://orcid.org/0000-0001-6290-8602

Professor Lei Liu graduated from University of Science and Technology of China in 1999. He obtained his PhD from Columbia University (2004), and conducted post-doctoral research work at Scripps Research Institute until 2007 when he Liu joined Tsinghua University. Lei Liu works as a Professor in the Chemistry department. His research group is interested in chemical protein synthesis.

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 Kate Jolliffe has highlighted some of her favourite recent works. Take a look at what she thought of the articles below, and find out more about the research and the researchers behind the papers in our interviews with the authors.

Kate’s Selection: 

Rational Design of Small Molecule Fluorescent Probes for Biological Applications

Joomyung V. Jun, David M. Chenoweth and E. James Petersson

Kate’s comment: “New fluorophores are highly sought after for the development of tools for biological applications. This review provides a nice overview of the functional fluorescent probes and the factors effecting their photophysical properties. Importantly it provides general guidelines for the rational design of new fluorophores with tailored photophysical properties for applications in chemical biology.”

Find out more in our interview with the authors

One-pot synthesis of porphyrin-based [5]rotaxanes

Pablo Martinez-Bulit, Benjamin H. Wilson and Stephen J. Loeb

Kate’s comment: “The synthesis of mechanically interlocked molecules with high degrees of complexity frequently requires multiple synthetic steps, which limits the ability to explore their functionality. Here, Loeb and co-workers report a clever synthesis of porphyrin containing [5]rotaxanes , in a one-pot reaction, opening the door to the synthesis of a wide range of mechanically locked architectures that can be fine-tuned for specific applications.”

Find out more in our interview with the authors

Absolute handedness control of oligoamide double helices by chiral oxazolylaniline induction

Ling Yang, Chunmiao Ma, Brice Kauffmann, Dongyao Lia and Quan Gan

Kate’s comment: “The incorporation of a chiral group at the terminus of an aromatic oligoamide strand has been shown to provide complete chiral control in the self-assembly of synthetic antiparallel double helices from quinoline containing foldamers, opening opportunities for the future exploitation of these materials as chiral sensors or catalysts.”

Find out more in our interview with the authors

Facile synthesis of sulfotyrosine-containing α-conotoxins

Changpeng Li and Chunmao He

Kate’s comment: “Tyrosine sulfation is an important post-translational modification that is believed to modulate biological function but is underexplored because of difficulties with both the isolation and synthesis of sulphated peptides. Here, He and Li demonstrate the facile synthesis of sulfated conotoxins by combining the sulfate ester deprotection and folding steps into a one pot procedure. Importantly they show that, in the case of conotoxins, the sulfate ester is not as acid labile as expected.”

Find out more in our interview with the authors

Meet the Editor:

Katrina (Kate) Jolliffe received her BSc (Hons) in 1993 and PhD in 1997 from the University of New South Wales. She then held positions at Twente University, The Netherlands; the University of Nottingham, UK and the Australian National University before taking up an Australian Research Council QEII fellowship at The University of Sydney in 2002. In 2007 she became a Senior lecturer at the same institution and was promoted to Associate Professor in 2008 and to full Professor in 2009. She currently holds the position of Payne-Scott Professor at The University of Sydney. She is a Fellow of the Australian Academy of Science and has been awarded the Beckwith (2004), Biota (2006), Birch (2017) and H. G. Smith (2018) medals of the Royal Australian Chemical Institute. Her research interests are in the areas of supramolecular, peptide and organic chemistry, with a focus on the design and synthesis of functional molecules, such as molecular sensors capable of detecting anions in biological environments or cyclic peptides for application in biology and medicine.

Introducing the researchers:

Ling Yang was born in 1991 in Qian Jiang, Hu Bei, China. In 2012 she received her bachelor’s degree in Chemical Engineering and Technology from Hubei University. After that, she obtained her Ph.D. degree in January 2018 under the supervision of Prof. Hua Jiang at the Institute of Chemistry, Chinese Academy of Sciences, working toward the synthesis and the characterization of aryl-triazole foldamer receptors to anion recognition. In 2018/2019, she worked as a postdoctoral fellow at Huazhong University of Science and Technology under the guidance of Prof. Quan Gan.

Chunmiao Ma was born in Hubei, China. She received her bachelor’s degree in chemistry from China University of Geosciences, Wuhan in 2016. She is now working toward a Ph.D. under the supervision of Prof. Quan Gan at Huazhong University of Science & Technology, working on design, synthesis and characterization of artificial foldamers based on aromatic oligoamides.

Dr. Brice Kauffmann is Crystallographer and head of IECB’s Biophysical and Structural Chemistry core facility. After a PhD in protein crystallography (2003, University of Nancy I), Brice Kauffmann spent three years at the European Molecular Biology Laboratory (EMBL) in Hamburg (Germany) working on the development of a new synchrotron beamline (X12, DESY). He joined the European Institute of Chemistry and Biology in January 2006 as a CNRS Scientist.

Dongyao Li was born in Xiangyang, Hubei, China. In 2015 he received his BS degree in chemistry at Hubei Normal University. He obtained his MS degree from Huazhong University of Science and Technology in 2017 under the supervision of Prof. Gan. and is currently working toward a Ph.D. in the same group, focusing on design, synthesis and applications of artificial foldamers based on aromatic oligoamides.

Quan Gan was born in 1982 in Wuhan, China. He received bachelor’s degree and master’s degree in Organic Chemistry from Central China Normal University in 2005 and 2008. After that, he took part in a joint doctoral programme under the supervision of Prof. Hua Jiang at the Institute of Chemistry, Chinese Academy of Sciences and Dr. Ivan Huc at the European Institute of Chemistry and Biology, Bordeaux, working toward the synthesis and the characterization of aromatic foldamers to mimic the structures and functions of biomacromolecules, and received his Ph.D. degree in early 2013. In 2013/2014, he worked as a Marie Curie Postdoctoral Research Fellow at the University of Cambridge under the guidance of Prof. Jonathan Nitschke. He has been a Professor working on supramolecular chemistry at the Huazhong University of Science and Technology, China, since December 2014.

What inspired your research in this area?

The fantastic structures and functions of biomacromolecules always inspire our research.

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

The hybridization of single helices of aromatic foldamers with full handedness control can give rise to the complete chiral control of double helices.

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

To explore the functions such as chiral sensors or catalysts is the aim that we focus on with foldamers. Here, the complete chiral control of aromatic helices offering a stable chiral environment within the cavity would provide chances to develop these functions, and which is currently being made in our laborotary.

Read the full article: Absolute handedness control of oligoamide double helices by chiral oxazolylaniline induction

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

See all the full articles on our publishing platform

Introducing Dr Pablo Martinez Bulit, first author on “One-pot synthesis of porphyrin-based [5]rotaxanes”

Pablo was born in Mexico City, where he received his B.Sc. in Chemistry from Universidad Nacional Autónoma de México, (UNAM). He obtained his Ph.D. from the University of Windsor, Canada, in 2019, under the supervision of Prof. Stephen Loeb where his research was focused on crystalline materials incorporating rotaxanes and porphyrins. He is currently working as a Postdoctoral Research Associate at the University of Glasgow.

Dr. Pablo Martinez Bulit

What inspired your research in this area? 
The long-term focus of this research was to prepare metal-organic frameworks (MOFs) incorporating both a rotaxane linker and a porphyrin linker. We had some initial success and characterised the solvent dependent dynamics of a rotaxane wheel in the solid-state for a porphyrin-based MOF (https://pubs.acs.org/doi/abs/10.1021/acs.cgd.9b00669). However, it remained a challenge to synthesize complex linkers that combined multiple rotaxanes on a porphyrin backbone. This project was a nice challenge as it combined the different research areas of the Loeb Research Group: organic synthesis, supramolecular chemistry to make mechanically interlocked molecules, and crystallography.

What do you personally feel is the most interesting outcome of your study? 
The fact that you can make and isolate these molecules this easily still amazes me. As the paper shows, this method is tolerant to a variety of functional groups so the potential to tailor the porphyrin-rotaxane hybrids for different applications is readily achievable.

What directions are you planning to take with your research in future?
Upscale the syntheses to make gram quantities and explore their possible incorporation into MOFs. Ideally these types of dynamic rotaxane linkers can be used as mechanically interlocked  switches in the solid-state.

Read the full article: One-pot synthesis of porphyrin-based [5]rotaxanes

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

See all the full articles on our publishing platform

Left to right: E. James Petersson, Joomyung (Vicky) Jun, and David M. Chenoweth

Let’s meet the researchers!

Joomyung (Vicky) Jun was born in South Korea and received her B.Sc. degree in chemical biology at U. C. Berkeley in 2012, performing undergraduate research with Kenneth Raymond. She then worked with Ronald Zuckermann at the Molecular Foundry in Lawrence Berkeley National Laboratory until 2014. Her research (Ph.D. 2019) at University of Pennsylvania focused on the development of novel and underexplored fluorogenic small molecules. She was co-advised by Professors Chenoweth and Petersson. She is currently a postdoctoral scholar with Ronald T. Raines in the Department of Chemistry at Massachusetts Institute of Technology.

David M. Chenoweth was born in Indiana, USA and received his B.S. degree from Indiana University-Purdue University Indianapolis (IUPUI) in 1999. He worked at Dow AgroSciences and Eli Lilly before joining Peter Dervan’s group at the California Institute of Technology to pursue a Ph.D. After graduation in 2009, he was an NIH Postdoctoral Fellow with Timothy Swager at Massachusetts Institute of Technology. David was appointed Assistant Professor in the Department of Chemistry at the University of Pennsylvania in 2011 and was promoted to Associate Professor with tenure in 2017.  He is also a member of the Biochemistry and Molecular Biophysics Graduate Group in the Perelman School of Medicine and the Bioengineering Graduate Group in the School of Engineering and Applied Science.

E. James Petersson was born in Connecticut, USA and completed his undergraduate education at Dartmouth College and his graduate study under Dennis Dougherty at the California Institute of Technology. After receiving his Ph.D. in 2005, he was an NIH Postdoctoral Fellow at Yale University with Alanna Schepartz. He joined the Department of Chemistry at the University of Pennsylvania in 2008 and the Department of Biochemistry and Molecular Biophysics in the Perelman School of Medicine in 2018. His research has been recognized by several awards, including the Searle Scholar, an NSF CAREER award, and a Sloan Fellowship.

What inspires your interest in fluorescent probes?

It is said that “seeing is believing,” and fluorescent probes allow one to directly visualize molecules in complex biological processes, often with high specificity. Small molecule fluorophores enable highly sophisticated microscopy techniques for “seeing” into the body or into cells, techniques that are essential for basic biological research as well as for the diagnosis of diseases, which I find fascinating.

What primary research are you carrying out in the area?

Although numerous fluorescent probes are known, the vast majority of these probes consist of a diminutive set of classical “core” dyes such as coumarin, fluorescein, or BODIPY. Dr. Jun’s thesis research focused on developing underexplored or novel fluorescent cores based on modular scaffolds that exhibited advantages over classic and contemporary dyes.  Prof. Petersson and Prof. Chenoweth have collaborated for many years on various optically active probes, including genetic encoding of fluorescent unnatural amino acids from the Petersson laboratory and photo-convertible small molecules from the Chenoweth laboratory, as well as synergistic projects using tools from the Chenoweth laboratory in protein labeling.

How do you hope this review will help and inspire future research in the area?

One of the challenges in this field is the gap between new probe development and its practical application in a biological system, which are much more complicated than the in vitro system. Says Jun: “I hope this review can be helpful for both chemists and biologists to understand the underlying concept of fluorophore design and to reach a point where chemists can tailor the probe based on the specific biological system of interest.”

Read the full article: Rational Design of Small Molecule Fluorescent Probes for Biological Applications

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

See all the full articles on our publishing platform