Organic and Biomimetic Chemistry

Contact details


Prof. Dr. Annemieke Madder

Tel: +(32)9 264 44 72

Organic and Biomimetic Chemistry
Department of Organic and Macromolecular Chemistry
Ghent University
Krijgslaan 281, S4, 1st floor
B-9000 GENT


GPS coordinates: N 51.025739, E 3.713915

Organic and Biomimetic Chemistry

Research Interests

Serine Protease Mimics: oligopeptide approach

The development of artificial catalysts that parallel enzymatic efficiency in terms of rate and turnover constitutes a lasting challenge in organic chemistry. In the context of natural processes, the hydrolysis of inactivated amide bonds as present in peptides and proteins by proteases represents one of the most illustrative cases.
Among the known classes of proteases, the serine proteases have been the subject of intense investigation. The action of the classic serine proteases such as chymotrypsin is known to rely on the cooperative involvement of the catalytic triad serine, histidine and aspartate.

Both proteins and nucleic acids have properties that offer unique advantages in performing catalytic transformations. Proteins possess a wide variety of functional groups that are appropriate for a broad range of chemical tasks, enabling protein enzymes to achieve extraordinary catalytic rate enhancements. The realization of synthetic catalysts or molecular devices using properly assembled alpha-amino acid sequences to take advantage of the self-organization of polypeptides in helices or beta-sheet structures is quite appealing for the easy availability of the constituent building blocks.

We must bear in mind that stable secondary structures such as helices only become important for quite long sequences of polypeptides. Therefore in our design we make use of multipodal scaffold molecules such as 1 and 2 to include different peptide chains and to impose a certain conformation upon these chains and their catalytic groups.

Serine Protease Mimics: oligonucleotide approach

Nucleic acids on the other hand are uniquely suited for sequence-specific recognition of nucleic acids through Watson-Crick base pairing in oligonucleotides, even in very short sequences. This capability allows nucleic acid enzymes to carry out chemical transformations on nucleic acid substrates with high sequence specificity. A major drawback in using oligonucleotides in the design of synthetic catalysts is that they cannot provide functional groups with such diversity and properties as proteins in order to act as bases or Lewis acids. However, with the event of antisense research, a lot of functional group modified nucleoside building blocks have become known and available to synthetic organic chemists. Thus, it is tempting to equip oligonucleotides with the functional tools of peptide chains by building block modification. This should result in a powerful combination of both predefined structural organization (cf. duplex formation) and presence of catalytic entities. Depending on the specific site of incorporation of the functionalities in the nucleoside building blocks, different spatial positions within the duplex grooves can be reached.

Novel techniques for cross-linking of biomacromolecules

The high specificity of nucleic acid - nucleic acid recognition has prompted significant interest in the design of modified oligonucleotides (ONs) that bind irreversibly to their complementary sequence via a covalent cross-link. Such ONs have been shown to interfere with natural nucleic acids and their fragments. This enables selective control of gene expression, leading to the development of potential therapeutics for cancer and a number of other diseases and even allows envisioning chemical alteration of genetic information.

The strategy of interstrand cross-linking is based on the use of ONs incorporating a reactive functionality which, upon hybridization, forms (a) covalent link(s) with the nucleic acid.

A contribution in this area has been recently published by our group. Oligonucleotides containing a furan modified internal nucleoside have been synthesized. Upon selective in situ oxidation of the furan moiety to a reactive enal species with N- Bromosuccinimide (NBS) in the presence of a complementary DNA strand, interstrand cross-link cross-link formation was obtained. Initial experiments show this cross-linking to be fast and very efficient.

The furan moiety is also an interesting group for the postsynthetic modification of ONs. Once a convertible nucleoside unit is introduced into the ON, the ON can be modified with a variety of functional groups. In this case, the easily available and very reactive a,b -unsaturated aldehyde can be used in reactions with a number of nucleophiles. The possibility of converting the unreactive furan into a reactive enal moiety in aqueous conditions adds to the potential of the proposed method for the labeling of oligonucleotides with other hydrophilic entities such as peptides or carbohydrates. Finally, the oxidised furan moiety can also be used for DNA - protein cross-linking.

Construction of conformationally restricted multipodal peptide architectures

Proteins are implicated in almost all biological processes and represent some of the most potent and selective agents known. Yet the use of proteins as drugs is still significantly compromised by poor bioavailability characterised by poor penetration of membranes and low cellular uptake, instability of three dimensional protein structures, which unfold under a variety of conditions, antigenicity, and unfavourable pharmacokinetics due to instability of peptide bonds to degradation by peptidases.

It occurred to us that both templates 1 and 2 ( vide supra) are ideally suited for the construction of complex peptide architectures with defined structural preorganisation. Steroid derivative 1 will impose a rigid parallel orientation on the peptide chains. It is further known that many steroids are drugs with excellent oral bioavailability. Template 2 will result in a more flexible orientation that can be conformationally restrained by binding of a ligand in the cavity created by the three aromatic units. This molecule is easily accessible via a short synthetic sequence starting from simple and cheap starting materials.

We therefore concentrate on the use of these scaffolds in the following areas:

  • Design and synthesis of new DNA-binding peptides:

Inclusion of the natural DNA binding sequences of the Leucine zipper proteins into 1 in order to construct dipodal DNA-binding ligands.

  • Design and synthesis of a new type of peptide vaccins:

The same strategy is applied to the assembly of peptide constructs which incorporate different regions of known conformational epitopes.

The research of this project is based on the Hemagglutinin Noose Epitope (HNE), a sequential B-cell epitope (BCE) located on the measles virus Hemagglutinin protein. The dipodal steroid-based scaffold 1 is used as an attachment point for the HNE to give the latter the necessary preorganisation for it to adopt an analogous conformation to the one it has in the H-protein. In this way, we are aiming at the design of a novel measles vaccine.

Figure: Top view (A) and lateral view (B) of four modelled representative conformations of HNE peptide (M. Putz, C. Muller et al., Eur. J. Biochem. 2003, 1515.

  • Design and synthesis of oestrogen receptor mimics for EDC solid phase extraction:

In recent years the potential role of environmental pollutants with suspected endocrine activity (so-called endocrine disrupting chemicals or EDCs) in a variety of reproductive system-related abnormalities in humans and animals, has strongly been emphasized by the media. Fast and easy methods with low detection limits for the quantitative analysis of EDCs are urgently requested because more exposure data for risk assessment are necessary and synergistic effects of different EDCs are not ruled out. Of the various steps in a sample preparation procedure, the extraction/purification/separation step, which is present in almost all the known analytical procedures described in literature, is the most critical.

Based on the known structure of the receptor and the available data for the numerous receptor-ligand complexes, we aim at the synthesis of model compounds for the ER receptors based on the use of scaffold molecule 2 that allows for the generation of small to medium sized multipodal peptidomimetics with preferred conformation.


Current position:

Professor of Organic Chemistry
Faculty of Sciences
Ghent University


  • July 1992

Master in Chemistry, State University of Gent , Belgium, Faculty of Sciences.
Undergraduate Thesis : "Synthesis of bridgehead compounds through hexatriene-cyclohexadiene electrocyclizations"
Promotor: Prof. Dr. A. Lera;
University of Santiago de Compostela; Spain

  • February 1997

Doctor in Sciences, chemistry, State University of Gent, Belgium, Faculty of Sciences.
Ph.D Thesis : "Stepwise development of non-enzymatic hydrolases"
Promotor: Prof. Dr. P. J. De Clercq; Ghent University; Belgium


  • 1992-1993


  • 1993-1997

Research Assistant of the belgian National Fund for Scientific Research at the Ghent University

  • 1997

Postdoctoral stay in the laboratory of Prof. Dr. C. Gennari, Dipartimento di Chimica Organica e Industriale Milano, Universita' di Milano, Italy
"Synthesis of ligands for a library of b-turn mimetics"

  • 1998-2002

Postdoctoral Research Assistant of the belgian National Fund for Scientific Research

  • 2000-2001

Postdoctoral stay in the laboratory of Prof. Dr. R. Strömberg

Division of Organic and Bioorganic Chemistry, Karolinska Institute, Stockholm, Zweden
Since 1/10/2002 Professor of Organic Chemistry, Faculty of Sciences
Ghent University


1996 VJC-prize : first prize awarded by the Royal Young Chemists Society (KVCV)
1996 DSM-prize in Chemistry and Technology : second prize awarded by DSM
1996 Varian Award for Analytical Chemistry : first prize awarded by Varian