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

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

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

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

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

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

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


To find out more see:

Contemporary Synthetic Chemistry in Drug Discovery OBC Themed Collection

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


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

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Prize winners at the Southampton Supramolecular Chemistry Conference

Congratulations to all the prize winners at the Southampton Supramolecular Chemistry Conference 2016.

We were pleased to present prizes to these winners:

Valentina Santolini (Imperial College London) - ChemSocRev Talk Prize

Daniel Cornwell (York University) – Organic & Biomolecular Chemistry Talk Prize

Chris Taylor (Sheffield University) - ChemComm Poster Prize

The conference took place at University of Southampton on 24th June 2016.
It was focused on early career researchers working within Supramolecular Chemistry.  The conference was a great opportunity for PhDs and postdocs to present their research and network with their peers and leaders within this field.
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‘Microbial protein targets: towards understanding and intervention’ meeting

Hosted by The British Society of Parasitology in collaboration with the Royal Society of Chemistry

Microbial protein targets: towards understanding and intervention

14–16 September 2016, Durham, UK

This symposium will bring together leading expertise in protein structure determination, biochemical characterization and chemical biology to explore the most recent advances in the understanding of protein function and inhibition in microbial pathogens – both bacteria and parasites.

An exciting line-up of speakers will present their recent work in the area. Some of the confirmed speakers are:

  • Chris Abell University of Cambridge, UK
  • Gerald Spaeth Institut Pasteur, Paris, France
  • Ed Tate Imperial College London, UK
  • Maria Marco-Martin GSK Tres Contos, Spain

Take advantage of this opportunity to showcase your work alongside leaders in the field and submit an abstract for an oral or poster presentation today. Through generous sponsorship from the RSC Chemical Biology Interface Division and the BSP there are bursaries available for early career researchers to support their participation at this meeting.

The oral abstract deadline has just been extended until 15 July 2016, and poster abstracts are welcome until 5 August 2016. For more information and to register please visit the conference webpage.

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New Editorial and Advisory Board Members

A warm welcome to Géraldine Masson, Govindasamy Mugesh, Gonçalo Bernardes and Ratmir Derda

We are very pleased to welcome two new members to our Organic & Biomolecular Chemistry Editorial Board and two new members to our Advisory Board – Dr Géraldine Masson (Institut de Chimie des Substances Naturelles, France) and Professor Govindasamy Mugesh (Indian Institute of Science, Bangalore, India), and Dr Gonçalo Bernardes (University of Cambridge, UK) and Dr Ratmir Derda (University of Alberta, Canada).

Géraldine Masson received her PhD in 2003 from the Joseph Fourier University, (France), under the supervision of Dr. Sandrine Py and Prof. Yannick Vallée. In the years 2003–2005 she was a Marie Curie postdoctoral research fellow with Prof. Jan van Maarseveen and Prof. Henk Hiemstra at the University of Amsterdam (Holland). In 2005, she joined the Institut de Chimie des Substances Naturelles (CNRS, France) as Chargé de Recherche and was promoted to Director of Research 2nd class in 2014. Her group’s research activities are directed toward the development of new organocatalytic enantioselective reactions and novel synthetic methodologies, and photoredox catalysis and their application in the synthesis of diverse natural and unnatural molecules displaying biologically activities.


Mugesh received his B.Sc. (1990) and M.Sc. (1993) degrees from the University of Madras and Bharathidasan University, respectively. He obtained his Ph.D. (1998) at the Indian Institute of Technology, Bombay. He was an Alexander von Humboldt Fellow at the Technical University, Braunschweig, Germany and a Skaggs postdoctoral fellow at the Scripps Research Institute, La Jolla, USA. Mugesh is an author of more than 120 publications in international peer reviewed journals. He received several awards and recognitions, which include: J. C. Bose National Fellowship, Government of India (2016); Asian Rising Star Commemorative Plaque, Asian Chemical Congress (2013), Fellow, Royal Society of Chemistry (FRSC, 2013), Shanti Swarup Bhatnagar Prize (2012), Fellow, The National Academy of Sciences, India (2012), AstraZeneca Excellence in Chemistry Award (2012); Fellow, Indian Academy of Sciences (2012); Swarnajayanti Fellowship, Government of India (2006-07).

His research interests include:

  • chemistry of thyroid hormone metabolism,
  • development of novel therapeutics for endothelial dysfunction and neurodegenerative diseases, and
  • nanomaterials for biological applications.

Gonçalo Bernardes graduated in Chemistry from the University of Lisbon in 2004 and soon moved to the University of Oxford where he completed his D.Phil. in 2008 under the supervision of Prof. Ben Davis. He was then awarded a Marie-Curie Fellowship to perform postdoctoral studies with Prof. Peter H. Seeberger. After a short period in Portugal working as a Group Leader at Alfama Lda., Gonçalo moved to the ETH Zürich to join the lab of Prof. Dario Neri. Gonçalo started his independent research career in 2013 at the Department of Chemistry, University of Cambridge after being awarded a prestigious Royal Society University Research Fellowship. Simultaneously, he founded a pioneering research unit in Chemical Pharmacology at the Instituto de Medicina Molecular in Lisbon. Despite his early age, he has published >50 papers and 5 patents. He has picked many accolades during his research career such as the European Young Chemist Award – Silver Medal in 2014, and more recentlythe Chem Soc Rev Emerging Investigator Lectureship 2016 and the RSC Harrison–Meldola Memorial Prize. For his efforts in translational research, Gonçalo was distinguished by the Portuguese Ministry of Health (MH) of Portugal for relevant services to Public Health and Medicine.

He now spends his time between his labs in Cambridge and Lisbon, directing a research program at the interface of chemistry and biology with a focus on the development of novel chemoselective reactions for the modification of biomolecules, and their use to understand and influence human disease.

Ratmir Derda received his undergraduate degree in Physics from Moscow Institute of Physics and Technology in 2001 and Ph.D. in Chemistry from the University of Wisconsin-Madison in 2008, under the supervision of Laura L. Kiessling. From 2008 to 2011, he was a postdoctoral researcher at Harvard University working under the supervision of George M. Whitesides and Donald E. Ingber. He joined University of Alberta in 2011 as an Assistant Professor in Chemistry and the Principal Investigator at the Alberta Glycomics Centre.

The Derda Lab centers on the development and mechanistic investigation of chemical transformations of genetically-encoded substrates. We employ genetically-encoded chemical libraries to attack unsolved problems in molecular recognition to aid the discovery of new therapeutics, biomaterials and molecular diagnostics.


Find some of their most recent RSC publications below or find out more about the other members of our Editorial and Advisory Boards here.


Insights into the catalytic mechanism of synthetic glutathione peroxidase mimetics
Debasish Bhowmick and Govindasamy Mugesh
Org. Biomol. Chem. , 2015, 13, 10262-10272, DOI: 10.1039/C5OB01665G, Review Article

Introduction of a catalytic triad increases the glutathione peroxidase-like activity of diaryl diselenides
Debasish Bhowmick and Govindasamy Mugesh
Org. Biomol. Chem., 2015, 13, 9072-9082, DOI: 10.1039/C5OB01294E, Paper

Iminoboronates are Efficient Intermediates for Selective, Rapid and Reversible N-Terminal Cysteine Functionalisation
Hélio Faustino, Maria José Silva, Luis F. Veiros, Gonçalo J. L. Bernardes and Pedro M. P. Gois
Chem. Sci., 2016, Accepted Manuscript, DOI: 10.1039/C6SC01520D, Edge Article

Natural product modulators of transient receptor potential (TRP) channels as potential anti-cancer agents
Tiago Rodrigues, Florian Sieglitz and Gonçalo J. L. Bernardes
Chem. Soc. Rev., 2016, Advance Article, DOI: 10.1039/C5CS00916B, Tutorial Review

Phage-displayed macrocyclic glycopeptide libraries
Simon Ng and Ratmir Derda
Org. Biomol. Chem., 2016, 14, 5539-5545, DOI: 10.1039/C5OB02646F, Communication

Heat-enhanced peptide synthesis on Teflon-patterned paper
Frédérique Deiss, Yang Yang, Wadim L. Matochko and Ratmir Derda
Org. Biomol. Chem., 2016, 14, 5148-5156, DOI: 10.1039/C6OB00898D, Paper

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Fluorescent nucleosides provide flexibility in fine-tuning photophysical properties

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

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

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

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

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

To find out more see:

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


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

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Improving total synthesis of modified histone proteins to elucidate epigenetic mechanisms

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

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

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

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

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

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

To find out more see:

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


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

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Computational chemistry: Solving real-world chemical problems

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

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

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

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

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

To find out more see:

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


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

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What are your colleagues reading in Organic & Biomolecular Chemistry?

The articles below are some of the most read Organic & Biomolecular Chemistry articles in January, February and March 2016.

Development of a stable phosphoarginine analog for producing phosphoarginine antibodies
Han Ouyang, Chuan Fu, Songsen Fu, Zhe Ji, Ying Sun, Peiran Deng and Yufen Zhao
DOI: 10.1039/C5OB02603B, Communication

Bifunctional primary amine-thioureas in asymmetric organocatalysis
Olga V. Serdyuk, Christina M. Heckel and Svetlana B. Tsogoeva
DOI: 10.1039/C3OB41403E, Perspective

Transition-metal catalyzed valorization of lignin: the key to a sustainable carbon-neutral future
Markus D. Kärkäs, Bryan S. Matsuura, Timothy M. Monos, Gabriel Magallanes and Corey R. J. Stephenson
DOI: 10.1039/C5OB02212F, Review Article

Design and synthesis of analogues of natural products
Martin E. Maier
DOI: 10.1039/C5OB00169B, Review Article

Organic synthetic transformations using organic dyes as photoredox catalysts
Shunichi Fukuzumi and Kei Ohkubo
DOI: 10.1039/C4OB00843J, Review Article

Biomineralization-inspired synthesis of functional organic/inorganic hybrid materials: organic molecular control of self-organization of hybrids
Atsushi Arakaki, Katsuhiko Shimizu, Mayumi Oda, Takeshi Sakamoto, Tatsuya Nishimura and Takashi Kato
DOI: 10.1039/C4OB01796J, Review Article

Synthesis of substituted pyrenes by indirect methods
Juan M. Casas-Solvas, Joshua D. Howgego and Anthony P. Davis
DOI: 10.1039/C3OB41993B, Review Article

Recent synthetic additions to the visible light photoredox catalysis toolbox
Ricardo A. Angnes, Zhou Li, Carlos Roque D. Correia and Gerald B. Hammond
DOI: 10.1039/C5OB01349F, Review Article

A protocol for amide bond formation with electron deficient amines and sterically hindered substrates
Maria E. Due-Hansen, Sunil K. Pandey, Elisabeth Christiansen, Rikke Andersen, Steffen V. F. Hansen and Trond Ulven
DOI: 10.1039/C5OB02129D, Communication

Metal catalyzed defunctionalization reactions
Atanu Modak and Debabrata Maiti
DOI: 10.1039/C5OB01949D, Review Article

Read more »

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Balticum Organicum Syntheticum (BOS) conference 2016

Balticum Organicum Syntheticum (BOS) conference 2016

3rd – 6th July 2016, Riga, Latvia

Organic & Biomolecular Chemistry and Natural Product Reports are pleased to support the 2016 BOS conference.  The conference aims to provide a forum for organic synthetic chemists to speak of their work and discuss important scientific problems and to promote discussion between academic and industrial scientists about the possibilities of mutual cooperation.

This international conference has a balanced program of academic and industrial speakers presenting fundamental and practical aspects of organic synthesis.  This year the speakers include:

  • Emily Balskus (Harvard University, USA) Chemical Discovery in the Microbial World
  • Inga Cikotiené (Vilnius University, Lithuania) From Curiosity to Development of New Synthetic Methods
  • Nuno Maulide (University of Vienna, Austria) Catalytic Rearrangements: Inspiration for Methods and Total Synthesis
  • Per-Ola Norrby (AstraZeneca, Sweden) Predictive Chemistry: Virtual Screening in Asymmetric Catalysis
  • Virgil Percec (University of Pennsylvania, USA) A Materials Genome Approach to Mimics of Biological Membranes and their Programmable Glycan Ligands
  • Stefan Schunk (Grünenthal GmbH, Germany) Cebranopadol, A Novel Analgesic – It’s Discovery from the MedChem Perspective
  • Ryan Shenvi (The Scripps Research Institute) Chemical Synthesis of Secondary Metabolites
  • John Sutherland (MRC Laboratory of Molecular Biology, Cambridge UK) Origins of Life Systems Chemistry
  • Māris Turks (Riga Technical University, Latvia) Sulfer Dioxide: Useful Reagent and Solvent in Organic Chemistry

For more information and to register please visit the website.

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XXVIII International Carbohydrate Symposium 2016

XXVIII International Carbohydrate Symposium 2016

17th – 21st July 2016, New Orleans, Louisiana USA

Organic & Biomolecular Chemistry are pleased to support the 28th International Carbohydrate Symposium.  The conference will feature an excellent range of speakers including:

  • Carolyn Bertozzi (Stanford University and Howard Hughes Medical Institute) – Glycocalyx engineering toward probing cancer glycome evolution
  • Vincent Bulone (University of Adelaide) – A journey into the world of Eukaryotic cell walls: structure and biosynthesis of essential polysaccharides
  • Bruce Hamaker (Purdue University) – Carbohydrate quality and how the concept may relate to healthier foods
  • Koichi Kato (Nagoya City University) – Structural views of glycen-dependent determination of glycoprotein fates in cells
  • Muthiah Manoharan (Alnylam Pharmaceuticals) – Carbohydrate Conjuated RNAi Therapeutics
  • James C Paulson (The Scripps Research Institute) – Sialic acids determinants of self
  • Soledad Penades (Centro de Investigacion Cooperativa en Biomateriales, CIC biomaGUNE) – Glycans and Glyconanotechnology
  • Stephen G Withers (University of British Columbia) – Accessing new and improved CAZymes through metagenomics and directed evolution

For more information and to book your place please visit the website.

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