" Rational drug design; a Structural Genomics approach"

Transcription

1 " Rational drug design; a Structural Genomics approach" Meeting the need of time; Dr Sanjan K. Das, PhD. Chief Scientific Officer (CSO), BBUK. Institute of Cancer Therapeutics University of Bradford, UK.

2 Road to Designer Therapeutics Translational Research is the underlying basis for Translational Medicine 'the process which leads from evidence based medicine to sustainable solutions for public health problems. Fulfilling the promise of translational research for improving the health and longevity of the world's populations depends on developing broad-based teams of scientists and scholars who are able to focus their efforts to link basic scientific discoveries with the arena of clinical investigation, and translating the results of clinical trials into changes in clinical practice, informed by evidence from the social and political sciences. Knowledge transfer from laboratory bench to patient bedside on the most effective platform. Target Validation Rational Drug Design Therapeutic Delivery Clinical Trials Genetics Biochemistry Biophysics Chemical, Structural & in silico Biology Nano Technology Animal Models Patient Based Personalized medicine

3 What is X-ray Crystallography? X-ray crystallography is a method of determining the arrangement of atoms arranged within a protein crystal from an analysis of the diffraction patterns created when the crystal is struck by a beam of X-rays. The analysis of the positions, intensities and the determination of the phases of each of these diffracted beams enables a three-dimensional picture of the electron density in the crystal to be observed from which the positions of the atoms can be determined. X-ray crystallography has been fundamental in the development of many scientific fields, including biology, where the technique is often referred to as protein crystallography or macromolecular crystallography.

4 Important milestones in Crystallography In 1611 Kepler proposed that the hexagonal symmetry of snowflake crystals was due to regular packing of spherical water particles. Diffraction from Zincblende (ZnS) by Laue, Friedrich and Knipping, 1912 The first Nobel prize in physics in 1901 was awarded to Röntgen in recognition of the discovery (1895) of the remarkable rays subsequently named after him. Röntgen did not like them being called Röntgen rays and referred to them as X-rays, X being the mathematical designation for something unknown. Medical applications for X-rays led to the rapid development of X-ray tubes which facilitated investigations of what X-rays were and what they could do.

5 Crystallography laid the foundation for understanding the relationship between sequence and structure.

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7 What can X-ray crystallography tell us about biological function? 1. Understand the fold of a protein and hence the relationship between its amino acid sequence and its 3D structure i.e. how residues that are distant in the sequence can come together in space to control function. 2. Analysis of many structures has taught us about the conformation of the polypeptide backbone and of the importance of the secondary structure, the α- helix and the β-sheet. 3. Analysis of structures has taught about the basic principles of folding that water soluble proteins have a buried hydrophobic core and a largely hydrophilic surface. 4. Analysis of the pattern of sequence conservation of a protein across species has taught us that residues at functional site are strongly conserved. 5. Soaking or growing crystals in the presence of substrates and inhibitors has allowed us to understand aspects of substrate specificity and enzyme mechanism. 6. Structural biology can sometimes provide important clues that lead to the identification of the function of a protein.

8 Validation of Cancer inhibitors for CLK family. 1(A) Structural insertions defining the LAMMER kinases and the inhibitor debromohymenialdisine are highlighted. (B) Structural superimposition of the nonphosphorylated CLK1 (red) and CLK3 structures (blue). (C) Sequence identity among the members of the human CLK family. (D) Surface residue conservation mapped onto the CLK1 structure. 2(A) Overview showing the location of the β-hairpin insert conserved within the CLK family and a docking peptide of the MAPK p38. (B) Interactions formed by CLK1 β-hairpin residues with the surface of CLK1. Perieoktic Medicine: There is no point in life, its a curve..

9 Docking Grooves, Substrate and Inhibitor Binding Specificity. The superimposition showing binding of a potential docking peptide is impaired due to the presence of helix αh in CLK family members. Inset shows SRPK1-docking peptide alone. (A) Binding of debromohymenialdisine to CLK1. Electron density (2FoFc) for the inhibitor is shown in blue. (B) Chart showing CLK1 and CLK3 kinase activities relative to the reference in the presence of 100 nm of 11 compounds causing the highest Tm shifts. (C) Table of the inhibitor data with corresponding chemical structures. Perieoktic Medicine: There is no point in life, its a curve..

10 Docking Grooves, Substrate and Inhibitor Binding Specificity. The superimposition showing binding of a potential docking peptide is impaired due to the presence of helix αh in CLK family members. Inset shows SRPK1-docking peptide alone. (A) Binding of debromohymenialdisine to CLK1. Electron density (2FoFc) for the inhibitor is shown in blue. (B) Chart showing CLK1 and CLK3 kinase activities relative to the reference in the presence of 100 nm of 11 compounds causing the highest Tm shifts. (C) Table of the inhibitor data with corresponding chemical structures. Perieoktic Medicine: There is no point in life, its a curve..

11 The final frontier; Membrane Proteins: Baculovirus mediated expression and purification of a novel human K + Channel Kcnk1A. SDS-PAGE analysis of Affinity purification Rb + uptake Measurements Extracted in and purified in Fc M sodium chloride,20mm sodium citrate ph 5.6, 5.5% PEG 3350 Perieoktic Medicine: There is no point in life, its a curve.. One subunit is colored blue-to-red from the N to the C terminus, and the other subunit is gray.

12 Structure of a Mitochondrial ABC Transporter ABCB10 in human is highly over expressed in erythroid cells, that are committed to be red blood cells. Responsible for antioxidant balance. Structure have been solved the structure of ABCB10 in complex with the ATP analogue AMP-PCP to 2.85Å resolution.

13 Personalised Medicine-a PCR platform Genomic Application: PCR, the most sensitive technology with wider usages. Formed partnership with Genesig, UK founded by Professor Tom Brown, University of Oxford. First truly mobile molecular laboratory in a bag. Extensive assay library covering, diagnostics, food safety and manufacturing. >6000 users Worldwide including NHS, CDC and US armed forces medical corps. Engage with the Bangladeshi clinicians closely to conceive, develop and deliver relevant services. User friendly robust template Aim to make it accessible nationwide. The genesig q16 DNA testing for everything, everyone, everywhere.

14 What can be done? The proposition is to build a high tech satellite hub to keep pace with Genome Valley, Hyderabad, India. With the optimal leadership in every level this can be achieved within a generation, bring IT & BT together. Leap frog in next generation healthcare by working with NHS Genomics. GCRF & Newton funds from UK can be channeled with right partners on both sides. It has to be commercially viable at personal level and national landscape. Our biggest asset is human resources, create a student loan fund. Finally it is time to mature as a country to fulfill our destiny by following the vision of our father of nation and be respected on global stage on our own merit. Sanjan.das@barisalbiotech.com & s.das4@bradford.ac.uk Acknowledgements: Prof David W. Rice, Prof Shefan Knapp and Dr Declan Doyle.