Drug Design and Analytical Chemistry

The know-how of the Drug Design and Analytical Chemistry Unit covers the field of medicinal chemistry and analytics necessary for identifying potential drug candidates from the area of »small molecules« as well as their development towards a clinical candidate.

By applying partially new computational chemistry approaches the potential target molecules are generated in silico and evaluated with regard to their efficacy at the target protein before being synthesized. For this purpose conventional ligand- and structure-based methods as well as quantum mechanical and semi-empirical methods are employed. The unit also provides all relevant prerequisites to conduct drug development in pre-clinical and clinical studies, including a regulatory context. MALDI-TOF-MS and LC-MS systems allow monitoring relevant parameters. The unit offers know-how and experience for developing assays that are established in cooperation with the other units of this department providing the portfolio to survey the treatment success of new therapies, e.g. by applyingication new biomarkers.

TRIGGER: King of hearts, joints and lungs; periodontal pathogens as etiologic factor in RA, CVD and COPD and their impact on treatment strategy

Extensive clinical and epidemiological data clearly shows that chronic periodontal disease (PD), the most prevalent infectious inflammatory disease of mankind, is strongly linked to systemic inflammatory diseases such as cardiovascular diseases (CVD), rheumatoid arthritis (RA), and chronic obstructive pulmonary disease (COPD). Taking into account that up to 30% of the adult population worldwide suffers from severe periodontitis, the impact of this disease on human health is immense and has been recognized by World Health Organization. Nevertheless, in many EU countries PD is a neglected disease, both by the population in general and health-care personnel. Often this negligence comes to the point that, like a hair-loss, the tooth-loss due to periodontitis is still considered as a normal inevitable event associated with aging. To combat this misconception and conceive novel approaches to prevent and/or treat CVD, RA, and COPD we will explore highly innovative ideas that these non-communicable diseases are at least aggravated, if not initiated, by periodontal infection. Results emanating from our project will: i) elucidate a relationship between the presence of specific periodontal pathogens and severity of systemic diseases; ii) show that extensive periodontal treatment improves clinical parameters of investigated systemic diseases; iii) reveal the impact of eradication of specific periodontal pathogen on the level of inflammatory markers; iv) develop novel, periodontal-pathogen selective bactericidal compounds based on specific enzymes that are essential for these pathogens vitality. This will reduce mortality and ameliorate the quality of life of CVD, RA, and COPD patients.

Development of inhibitors for alternative beta-secretases as a new therapeutic approach for Alzheimer’s disease

© Photo Fraunhofer IZI

The number of patients suffering from Alzheimer’s disease will increase dramatically, especially in the industrial nations. The major reason is the increasing lifespan, since age is the main risk factor for this disease. Thus, about 33 % of the whole population above 80 years is diagnosed with Alzheimer’s dementia.

In recent years pharma research was faced with a lot of failures in the development of novel drugs against Alzheimer’s disease that were based on the inhibition of an enzyme – beta secretase BACE-1 – being responsible for the release of a particular neurotoxic peptide (amyloid Abeta) as the main factor for the onset of the disease. The compounds exhibited a good efficacy in vitro, a good bioavailability and were well tolerated by the organism.

However, they failed in clinical trials due to a lack of efficacy in patients with spontaneous Alzheimer´s disease. Only in the case of a small sub population of 5 % of all patients that suffered from a genetically encoded variant of Alzheimer’s disease, the compounds showed promising effects in vivo.

This leads to the assumption of the existence of additional enzymes that might be able to release the neurotoxic amyloid peptide. Within this project we are investigating one of these alternative beta secretases. The aim is the computer aided and structure-based design and development of inhibitors of the isoenzymes Meprin alpha and beta. It was already possible to develop very specific acting compounds, exhibiting better activity than the known non-specific Meprin inhibitors. The IP is filed and we are now able to investigate the pathophysiological roles of Meprin alpha and beta more detailed.

The goal in this project will be the development of new therapeutic options for Alzheimer’s disease in close collaboration with the other units of the department.

Broadening the chemical space of metal binding groups

© Photo Fraunhofer IZI

A lot of potential target enzymes with high medical interest contain a metal ion in their active site which is essential for the catalysis of the corresponding reaction. These metal ions are usually interesting pharmacophoric points for the development of new inhibitors because a binding to them leads very often to potent compounds. Unfortunately only a small amount of different potential metal binding groups are known, limiting the development of new drugs, because of their unselective binding not only to the target but also to other enzymes. One example for the discontinuation of the development of promising new drugs are matrix-metallo-protease inhibitors, where it was not possible to develop selective compounds among the enzyme class.

By the usage of a combination of semi-empirical, quantum chemical, ligand- and structure based approaches we are now able to overcome this limitations and to broaden the available chemical space for metallo enzyme inhibitors. In one example it was possible to extend the amount of the known 4 metal binding groups for a metal dependent acyltransferase by a number of 6, fully new and undescribed. This allows the development of a whole new world of active molecules.

MALDI-TOF mass spectrometry-based assays for the quantification of biomarkers

© Photo Fraunhofer IZI

MALDI-TOF mass spectrometry is routinely used for the investigation of biomolecules of higher molecular weights, e.g. proteins. Examples are the sequencing of proteins and the investigation of different species of one protein or peptide. However, all of these tools are of a qualitative kind, because for a quantification of the proteins other mass spectrometry based tools are used. But these methods need more time for analysis and so the throughput is limited.

Nevertheless, for certain biomarkers the use of MALDI-TOF for quantification is a useful solution, because they need for the full ionization, and thereby quantification, more energy, than other methods are able to provide. As an example a MALDI-TOF based assay for the quantification of a relatively large protein of 4,8 kDa, used as a bio-marker was established. For this a sample preparation routine had to be developed that is easy to handle. For the determination of such critical parameter like LOD and LOQ an internal standard was synthesized (deuterated) and it was successfully used for the determination of a concentration range of 20 ng/µL to 100 ng/µL in human plasma that exactly represents the range, described for this biomarker in healthy persons and patients.

  • Kleinschmidt M, Schoenfeld R, Göttlich C, Bittner D, Metzner JE, Leplow B, Demuth HU. Characterizing Aging, Mild Cognitive Impairment, and Dementia with Blood-Based Biomarkers and Neuropsychology. J Alzheimers Dis. 2015;50(1):111-26. DOI dx.doi.org/10.3233/JAD-143189
  • Ramsbeck, D.; Buchholz, M.; Koch, B.; Böhme, L.; Hoffmann, T.; Demuth, H.-U.; Heiser, U. Structure-activity relationships of benzimidazole-based glutaminyl cyclase inhibitors featuring a heteroaryl scaffold. J Med Chem (2013), 56, 6613–6625. DOI dx.doi.org/10.1021/jm4001709
  • Frost JL, Liu B, Kleinschmidt M, Schilling S, Demuth HU, Lemere CA. Passive immunization against pyroglutamate-3 amyloid-β reduces plaque burden in Alzheimer-like transgenic mice: a pilot study. Neurodegener Dis. (2012);10, 265-70, DOI dx.doi.org/10.1159/000335913
  • Koch, B.; Buchholz, M.; Wermann, M.; Heiser, U.; Schilling, S.; Demuth, H.-U. Probing secondary glutaminyl cyclase (QC) inhibitor interactions applying an in silico-modeling/site-directed mutagenesis approach: implications for drug development. Chemical biology & drug design (2012), 80, 937–946. DOI dx.doi.org/10.1111/cbdd.12046
  • Sun N, Hartmann R, Lecher J, Stoldt M, Funke SA, Gremer L, Ludwig HH, Demuth HU, Kleinschmidt M, Willbold D. Structural analysis of the pyroglutamate-modified isoform of the Alzheimer's disease-related amyloid-β using NMR spectroscopy. J Pept Sci. (2012), 18, 691-5. DOI dx.doi.org/10.1002/psc.2456
  • Buchholz, M.; Hamann, A.; Aust, S.; Brandt, W.; Böhme, L.; Hoffmann, T.; Schilling, S.; Demuth, H.-U.; Heiser, U. Inhibitors for Human Glutaminyl Cyclase by Structure Based Design and Bioisosteric Replacement. J Med Chem (2009), 52, 7069–7080. DOI dx.doi.org/10.1021/jm900969p
  • Buchholz, M.; Heiser, U.; Schilling, S.; Niestroj, A. J.; Zunkel, K.; Demuth, H.-U. The first potent inhibitors for human glutaminyl cyclase: synthesis and structure-activity relationship. J Med Chem (2006), 49, 664–677. DOI dx.doi.org/10.1021/jm050756e