Exact Sciences Master Guide2005/2006



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Part-time studying


In principle this master's programme is full-time.
    1. Dual training


Under specific conditions, a tailored master's programme can be composed, in which in-service training is included.
    1. Research tracks


Research training: minimum 42 cp

 

Master coordinator

dr. J.N.M. Commandeur, room P2.56, phone: +31 (0) 20 59 87595

 

Students graduating with the O-variant often continue as PhD-student in order to obtain positions such as scientific researcher, group leader etc. at universities, research institutes, government and industry.



 

In the Master in Pharmaceutical Sciences students can specialize in one out of five disciplines:

 

Section Medicinal Chemistry (prof. dr. R. Leurs)


  • Drug Design and Synthesis

  • Drug Discovery & Target Finding (Molecular Pharmacology)

Section Molecular Toxicology (prof.N.Vermeulen)

  • Computational Medicinal Chemistry & Toxicology

  • Drug Disposition and Safety (Molecular Toxicology)

Section Analytical Chemistry and Applied Spectroscopy (prof. H. Irth)

 

Students are urged to contact the master coordinator of Pharmaceutical Sciences as soon as possible with their choice of research group.  Research training (Major) will be wound up with a Master thesis and an oral presentation.  Research training (Minor) ends with a written report.


      1. Drug Design & Synthesis


Contact: dr. I. de Esch, room G3.43a, phone: +31 (0) 20 59 87841, prof. dr. R. Leurs.

To gain experience in formulating a scientific question in the field of Drug Design and Synthesis, setting up and carrying out experiments to answer that question, interpreting data obtained and reporting both orally and in writing.

The student will participate in one of the research projects within the Departmental research programme "Structure-activity relationships of biological active compounds.  Research focuses on the histaminergic receptors, with emphasis on the recently cloned H3 (multiple isoforms) and H4 (new potential target inflammation) subtype receptors. A recently initiated new line focuses on human and viral-encoded chemokine receptors. Furthermore, new ligands for ligand-gated ion channels are being synthesized, using structure-based design approaches.

Research topics involve the (computational) design of ligands and the synthesis of these entities. The computational approaches include pharmacophore generation and structure analysis of the protein targets. In silico screening using extensive in house compound databases can identify molecules that verify or falsify the developed models. The modelling efforts result in the design of novel ligands, that are subsequently synthesized. Techniques used are those common in modern drug synthesis, including state of the art chemistry equipment that enables parallel approaches. Intermediates and final products are characterized by analytical tools (chromatography, NMR, MS, etc.). Research is performed in collaboration with the molecular pharmacology and other computational groups.


      1. Drug Discovery & Target Finding (Molecular Pharmacology)


Contact: dr. M.J. Smit,  O2.26, phone: +31 (0) 20 59 875 79, dr. R.A. Bakker, prof. dr. R. Leurs.

To gain experience in formulating a scientific question, setting up and carrying out molecular pharmacological experiments, to answer that question, interpreting data obtained, designing further experiments and reporting both orally and in writing.

The student will participate in one of the research projects within the research programme "Structure-function relationships of biological active compounds: G protein coupled receptors and their ligands".  The membrane-bound G protein coupled receptors play a key role in cellular (patho) physiology and are currently one of the most favoured drug targets. Research focuses on the histaminergic receptors, with emphasise on the recently cloned H3 (multiple isoforms) and H4 (new potential target inflammation) receptors and recently initiated new line on human and viral-encoded chemokine receptors. Interest is directed at the ligand-receptor interaction and signaling pathways activated by these receptors. Research  topics comprise intriguing pharmacological concepts such as constitutive activity and dimerization of receptors and their role in the process of drug discovery.

Besides classical pharmacological, molecular biological approaches, cell culture techniques and modern techniques (reportergene, fluorescent techniques) are applied to obtain more insight in the receptors. Research is performed in close collaboration with the synthetical and computational groups in order to ensure a multidisciplinary approach.


      1. Computational Medicinal Chemistry & Toxicology


Contact: dr. B.C. Oostenbrink  (room P2.62; phone: +31 (0) 20 59 87606),  prof. dr. N.P.E. Vermeulen.

Aim: To obtain knowledge and experience in the field of computational medicinal chemistry and bioinformatics, getting acquainted with various computational approaches to study protein-ligand interactions, and reporting both orally and in writing.

Contents: The student will participate in one of the research projects within the group of Computational Medicinal Chemistry and Toxicology (CMCT). In this group various aspects of the specific binding of small molecules to biomacromolecules, such as the binding of agonists and antagonists to receptors and substrates and inhibitors to enzymes, are studied by computational techniques. The aim of these studies is to predict and/or rationalize the affinity and biological activity of chemicals on the basis of their chemical and physical properties and characterization of protein-ligand interactions. Some of the techniques that are used and further developed are conformational analysis, ab initio calculations, generation of pharmacophore models, docking, virtual screening, and calculations of binding free energies of ligands and substrates. Protein models are used whenever available or developed using homology modeling. Proteins which are studied include biotransformation enzymes (cytochrome P450s), and receptors (histamine receptors, chemokine receptors and estrogen receptors). Molecular dynamics simulations will be performed to test the stability and dynamics of these protein models and protein-ligand complexes.

The results of these projects will be used to rationalize experimental binding and activity data and to a priory predict these properties for novel compounds. Specific amino acid mutations for experimental validation and modifications of protein activity will be suggested. Comparison to and prediction of experiments are done in close collaboration with the experimental groups.


      1. Drug Disposition & Safety Assessment (Molecular Toxicology)


Contact: dr. J.N.M. Commandeur, room P2.56, phone: +31 (0) 20 59 87595, prof. dr. N.P.E. Vermeulen.

Training in and gaining experience in defining a scientific research question, designing and carrying out molecular toxicological experiments to answer that question, validating and interpreting of the experimental data, evaluating and discussing the results and the perspectives, and reporting both orally and in writing.

The research performed in the division of Molecular Toxicology, is focused on the role of biotransformation enzymes in the bioactivation and detoxification of xenobiotics, and the characterization of the structure and properties of the metabolites formed. In the research training, students can participate in one of the research projects carried out at this division. Subjects of the research projects include: expression of wild-type and mutant cytochrome P450s (P450s) and characterization of their structural and catalytic properties; investigation of dynamics of P450s using various (laser)spectroscopical methods (RAMAN, FRET, NMR); development and use of wild-type and mutant P450s as bioreactors to produce bioactive compounds; development of automated high-resolution bioaffinity screening and detection systems using cytochrome P450s and estrogen receptors as detector proteins; development and evaluation of selenium-containing compounds as chemoprotective compounds; role of biotransformation in estrogenic properties of xenobiotica. Research is performed in close cooperation with the computational group.

      1. Biomolecular & Drug Analysis


Contact: prof. dr. H. Irth, dr. H. Lingeman, room M3.30, phone: +31 (0) 20 59 87539.

To obtain knowledge and experience in the field of biomolecular and drug analysis, getting acquainted with various analytical approaches to study protein-ligand interactions, drug-matrix interactions, development of quantitative bio-analytical and pharmaceutical methods and reporting both orally and in writing.



The main goal is to improve the selectivity and sensitivity / analytical detectability of total analytical systems. With large series of samples such as frequently encountered in real-life screening (e.g. biological samples) or monitoring studies, speed of analysis is another aspect of current interest. The emphasis, therefore, is on the development of on-line and, preferably, fully automated systems. This implies that much attention is devoted to the design and optimization of multidimensional methods. In this context important developments are in coupled-column systems, in combination with on-line bio-specific reaction and mass-spectrometric detection.  The emphasis will be on systems that can be used for drug-protein interactions, determination of metabolic products, enzymes, proteins, nucleotides, receptors, etc.
    1. Programme Pharmaceutical Sciences

      1. Master's programme


An overview of the available courses is given below. A description of the various courses can be found in the chapter Course Descriptions.
      1. Compulsory courses





Course code

Course name

Cr.

Period

435675

Principles of Pharmaceutical Sciences / Pharmacochemistry

6

1

435597

Bio-Analytical Aspects of Drug Discovery I

6

1 and 3

435674

Molecular Pharmacology and Toxicology of Drugs

6

2

435673

Computational Design and Synthesis of Drugs

6

2



      1. Basic courses





Course code

Course name

Cr.

Period

435689

Synthetic Approaches in Medicinal Chemistry I

3

4

435686

Pharmacodynamics of Drug Action

3

4

435682

Drug Toxicity: Basic Concepts and Experimental Approaches

3

4

435671

Computational Medicinal Chemistry and Toxicology I

3

4

      1. Advanced courses





Course code

Course name

Cr.

Period

435685

Synthetic Approaches in Medicinal Chemistry II

6

4, 5 and 6

435672

Computational Medicinal Chemistry and Toxicology II

6

4, 5 and 6

435680

Receptor Structure and Function

6

4, 5 and 6

435598

Bio-Analytical Aspects of Drug Discovery II

6

4, 5 and 6

435681

Advanced Course on Drug Disposition & Safety Assessment (Molecular Toxicology)

6

4, 5 and 6



      1. Optional courses (Major/Minor)





  • Biochemical mechanisms of toxicology

  • Capita Pharmacochemistry

  • Drug Registration and Safety Assessment

  • In vitro Pharmacology and High-Throughput Screening

  • In vitro Toxicology and High-Throughput Screening

  • (Pharmaco / Toxico) Genomics and -proteomics

  • Combinatorial Chemistry

  • Protein Modeling & Bioinformatics

  • Courses LACDR (Leiden - Amsterdam Centre of Drug Research)

  • Courses MNS

  • Courses Chemistry
    1. Society oriented variant (M-variant)

      1. General


Due to the growing complexity of technological and medical issues and the interaction with society, organisations working in this sector have a growing and urgent need for academic professionals in the natural and life sciences, who have knowledge of policy management and entrepreneurship. The M-variant offers students with a bachelor degree in the natural and life sciences the chance to combine a specialization in this field with a specialization in research, communication or education.
      1. Programme


The programme of the M-variant is equal to the first year of the master programme Management Policy- Analysis and entrepreneurship (MPA) (for a detailed description of the programme see the description of the master programme MPA). The programme of the M-variant consists of 60 cp (15 cp compulsory courses; 15 cp optional courses and 30 cp internship)  The course language is English, unless all students participating in the course speak Dutch, the course language will be Dutch. The program coordinator is: dr. M.B.M. Zweekhorst. Address: Faculty of Earth and Life Sciences, department Biology and Society, De Boelelaan 1087, Room A0.62, phone: +31 (0) 20 59 87033, e-mail marjolein.zweekhorst@falw.vu.nl


M-variant compulsory courses




Course code

Course name

Cr.

Period

470572

Communication, Organization and Management

6

03.10.05-28.10.05

470571

Analysis of Governmental Policy

6

05.09.05 ¿ 30.09.05

470573

Business Management in Health and Life Sciences

3

31.10.05 ¿ 11.11.05




M-variant optional courses

Recommended courses



Course code

Course name

Cr.

Period

991000

Interpersoonlijke communicatie

3

28-11-2005/09-12-2005

470576

Policy Research Project

6

09.01.2006 ¿ 03.02.2006

470562

Interactive Communication

3

12.12.05-23.12.05

470574

Clinical Development and Clinical Trials

3

14.11.05 - 25.11.05

470578

Interactive Health Technology Assessment

3

14.11.05 - 25.11.05

470575

Entrepreneurship in Health and Life sciences

6

28.11.05-23.12.05

470564

Caput Criteria for Corporate Social Responsibility

3

31.10.05 - 11.11.05

470581

Caput Success Factors in Sustainable Innovations

3

In consultation





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