Atomic Displaying and Medication Disclosure

Presentation Transcript

Sub-atomic Modeling and Drug Discovery Judith Klein-Seetharaman Assistant Professor Department of Pharmacology University of Pittsburgh School of Medicine and School of Computer Science Carnegie Mellon University USA

Background View of living beings as sub-atomic hardware: Molecular hardware = biochemical procedures, that frame and reuse particles in a planned and adjusted form expected methods of operation = sound state unusual methods of operation = ailment state Diagnosis: recognize the sub-atomic premise of sickness Therapy: manage biochemical hardware back to solid state

Information Sources New innovation creates enormous measures of information (regularly put away in freely open databases): Genomics and Proteomics Protein and DNA arrangements/Whole genome successions Protein structure information Protein pathways and systems Protein collaboration information Expression information

Genomics - Proteomics Mapping Sequence to Protein Structure and Dynamics Primary Sequence MNGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVFGG FTTTLYTSLH GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLVGWSRYIP EGMQCSCGID YYTPHEETNN ESFVIYMFVV HFIIPLIVIF FCYGQLVFTV KEAAAQQQES ATTQKAEKEV TRMVIIMVIA FLICWLPYAG VAFYIFTHQG SDFGPIFMTI PAFFAKTSAV YNPVIYIMMN KQFRNCMVTT LCCGKNPLGD DEASTTVSKT ETSQVAPA Folding 3D Structure

Genomics - Proteomics Mapping Sequence to Protein Structure, Dynamics and Function Primary Sequence MNGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVFGG FTTTLYTSLH GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLVGWSRYIP EGMQCSCGID YYTPHEETNN ESFVIYMFVV HFIIPLIVIF FCYGQLVFTV KEAAAQQQES ATTQKAEKEV TRMVIIMVIA FLICWLPYAG VAFYIFTHQG SDFGPIFMTI PAFFAKTSAV YNPVIYIMMN KQFRNCMVTT LCCGKNPLGD DEASTTVSKT ETSQVAPA Folding 3D Structure

Disease Challenge 1: Disease Causing Mutations Primary Sequence MNGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVFGG FTTTLYTSLH GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLVGWSRYIP EGMQCSCGID YYTPHEETNN ESFVIYMFVV HFIIPLIVIF FCYGQLVFTV KEAAAQQQES ATTQKAEKEV TRMVIIMVIA FLICWLPYAG VAFYIFTHQG SDFGPIFMTI PAFFAKTSAV YNPVIYIMMN KQFRNCMVTT LCCGKNPLGD DEASTTVSKT ETSQVAPA Folding 3D Structure Complex capacity inside system of proteins

Challenge 1: Non-malady bringing on transformations Primary Sequence MNGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVFGG FTTTLYTSLH GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLVGWSRYIP EGMQCSCGID YYTPHEETNN ESFVIYMFVV HFIIPLIVIF FCYGQLVFTV KEAAAQQQES ATTQKAEKEV TRMVIIMVIA FLICWLPYAG VAFYIFTHQG SDFGPIFMTI PAFFAKTSAV YNPVIYIMMN KQFRNCMVTT LCCGKNPLGD DEASTTVSKT ETSQVAPA Folding 3D Structure Complex capacity inside system of proteins Normal

Challenge 1 How would we be able to recognize useful from non-practical protein groupings? Required: grouping to structure and capacity mapping

Challenge 2: Which protein is a medication target?

? Challenge 3: How to plan a medication without a structure? Medicate Target:

Challenge 4: Drug activity, viability and reactions? Medicate Target:

Challenges How would we be able to recognize practical from non-utilitarian protein arrangements? Which protein is a medication target? How to outline a medication without a structure? Understanding medication activity, adequacy and reactions Fundamental Scientific Challenge: Mapping the relationship between genome arrangement and protein structures, elements and capacities in complex cell situations

Meaning for medication disclosure If one could foresee the structure of proteins from succession, one could find new medications at a quick pace If one could anticipate the relationship amongst isozyme and tissue expression, one could outline drugs particular to specific tissues If one could foresee the communications of proteins in various protein systems, one could decipher complex information, for example, creature models If one could…

Mapping connections: 7 progressive layers Layer 5. Foreseeing practical structures (DNA - RNA - proteins - lipids - sugars) Homology displaying stomach muscle initio formats halfway data general design restricting pocket protein spine Layer 6. Atomic collaborations (Protein-ligand, - protein, - DNA, - RNA, - lipid, - starch) Layer 7. Quality expression, metabolic and administrative systems Layer 1. Sequencing support (physical mapping, section get together result: crude genome arrangement) Layer 2. DNA succession examination Gene discovering non-coding groupings administrative arrangements discovering orthologous and paralogous successions Evolution Layer 3. Protein arrangement examination homology location arrangement utilitarian comment cell limitation Layer 4. From straight grouping to three-dimensional shapes conformational space models for protein (mis)folding segregating structures conformational vagueness

Specific Challenges for Bioinformatics in Drug Discovery Data should be sorted out, mined and imagined to permit logical disclosure Linking assortment of databases Linking the distinctive layers Interpretation of information Drug revelation

Outline Drug Discovery Approach utilize the data in the databases and deduce data that is not gave specifically by genomics and proteomics information: more elevated amount data => sort out all accessible data - to get definite photo of a sub-atomic process (or sickness) - to recognize new protein targets - to create drugs in light of substance similitude of known medications judicious (structure-based) sedate plan intelligently on PC screen sub-atomic docking (programmed, orderly PC based forecast of structure and restricting liking of complex) high-throughput screening and combinatorial science

Molecular displaying in medication revelation I. Two contextual analyses for arrangement to structure mapping: Small changes in protein grouping cause sensational distinction in medication authoritative: COX inhibitors Large changes in protein succession still keep up comparable structure: G protein coupled receptors Protein Structure Prediction III. Ligand Docking to Protein Structures

Molecular displaying in medication disclosure I. Two contextual analyses for grouping to structure mapping: Small changes in protein succession cause emotional contrast in medication official: COX inhibitors Large changes in protein arrangement still keep up comparative structure: G protein coupled receptors Protein Structure Prediction III. Ligand Docking to Protein Structures

Case ponder COX A Wonder Drug: What is the most regularly taken medication today? It is a compelling painkiller. It diminishes fever and aggravation when the body gets exuberant in its barriers against disease and harm. It moderates blood coagulating, decreasing the possibility of stroke and heart assault in vulnerable people. It might be a compelling expansion to the battle against growth. Headache medicine has been utilized professionally for a century, and customarily since old times. A comparable compound found in willow bark, salicylic corrosive, has a long history of utilization in natural treatment. In any case, just in the most recent couple of decades have we saw how headache medicine functions, and how it may be enhanced http://www.rcsb.org/pdb/particles/pdb17_1.html

Prostaglandins As you may anticipate from a medication with such various activities, ibuprofen hinders a focal procedure in the body: Aspirin obstructs the creation of prostaglandins, key hormones that are utilized to convey nearby messages. Not at all like most hormones, which are delivered in specific organs and after that conveyed all through the body by the blood, prostaglandins are made by cells and afterward act just in the encompassing region before they are separated. Prostaglandins control a number of these area forms, including the choking of muscle cells around veins, accumulation of platelets amid blood coagulating, and narrowing of the uterus amid work. Prostaglandins likewise convey and fortify agony flags and instigate aggravation. These various procedures are altogether controlled by various prostaglandins, yet all made from a typical antecedent particle . http://www.rcsb.org/pdb/particles/pdb17_1.html

Arachidonic Acid and COX

COX = Cyclooxygenase (PDB passage 1prh ) plays out the initial phase in the formation of prostaglandins from a typical unsaturated fat . It adds two oxygen atoms to arachidonic corrosive, starting an arrangement of responses. Headache medicine hinders the official of arachidonic corrosive in the cyclooxygenase dynamic site. The ordinary messages are not conveyed, so we don't feel the torment and don't dispatch an aggravation reaction. http://www.rcsb.org/pdb/atoms/pdb17_1.html What does COX do?

Structural Organization of COX Two distinctive dynamic locales, by and large prostaglandin synthase: 1, the cyclooxygenase dynamic site talked about; 2, is has a completely isolate peroxidase site, which is expected to enact the heme amasses that take part in the cyclooxygenase response. Dimer of indistinguishable subunits (two cyclooxygenase dynamic locales and two peroxidase dynamic destinations in closeness) Each subunit has a little carbon-rich handle, indicating descending mooring the complex the layer of the endoplasmic reticulum, appeared in light blue. The cyclooxygenase dynamic site is covered profound inside the protein, and is reachable by a passage that opens out amidst the handle. This demonstrations like a channel, managing arachidonic corrosive out of the film and into the chemical for preparing. PDB passage 4cox http://www.rcsb.org/pdb/atoms/pdb17_1.html

Why is there a COX-1 and COX-2? COX-1 and COX-2 are made for various purposes. COX-1 is implicit a wide range of cells to make prostaglandin