Presentation on theme: "INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY (ICGEB), NEW DELHI, INDIA Structural and Computational Biology Group."— Presentation transcript:
1 INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY (ICGEB), NEW DELHI, INDIA Structural and Computational Biology Group
2 Structural Biology Medicine and Biology at Atomic Scale Organ Tissue Cell Molecule AtomsTitle only.You have just heard from Chris Wright and Randy Blakely about the their studies to understand how organs, tissues and cells work. Now I am going to take you deeper into the puzzle and zoom in on biology at the level of molecules and atoms. Along the way I will show you how the fundamental principles of math, physics, chemistry and computer science can be used to study complex biology. This information generates unique insights for understanding how to distinguish health and disease and is especially powerful for the development of new drug therapies.So let’s zoom in.FIRST ITEMWe all know that organs such as the brain or a kidney are collections of various brain and kidney tissues, which are themselves made up of brain and kidney cells. In continuing to zoom in with greater and greater and magnification on an organ, we eventually will see the millions of molecules that make up a cell. So how do all of these molecules work together to make up a functioning cell?SECOND ITEMWell, it turns out that communication is the key. If the molecules can all communicate properly, then the cell works just fine. But if something goes wrong in the communication, even with just one type of molecule, then the whole cell can be knocked out of kilter and set the stage for disease. Following this logic, it therefore makes sense to try and figure out how molecules communicate. Following the progression from organ to tissue to cell to moleculeTHIRD ITEMWe need to zoom in on the molecules to study how they are made up. In fact, the key to understanding how molecules communicate is to determine the arrangements of their atoms. What is so fantastic about achieving this ultra high resolution view of biology is that it then becomes possible to understand how what distinguishes health and disease at its most basic level. This in turn means that we have a kind of magic bullet to target drugs to the specific molecules that are causing a disease, without inadvertantly hitting other molecules and causing side-effects.LAST ITEMIt is this approach of studying the atomic structure of molecules important in biology that is termed Structural Biology, and last year I came here from the Scripps Research Institute in La Jolla, CA to create a new research program to bring this powerful technology to Vanderbilt and work with the outstanding researchers who make this such a successful institution.Now, I would like to show you just one brief example of how Structural Biology works, in this case, how an extremely potent anticancer agent is targeted to a precise location on a molecule of DNA.
3 High Resolution Structural Biology Atomic structure - communication
4 Evolution: Machine and Control Anti-tumor ActivityDuocarmycin SAAtomic interactionsTo get a glimpse of the Structural Biology approach, I will now show you an example from the cancer research in our laboratory.2nd SLIDE- TITLEI will describe how taking a snapshot of the atomic structure of two molecules at the moment when they are communicating can be used to understand how an extremely potent anticancer agent is targeted to a precise location on a molecule of DNA. First itemIn this picture the green and pink sticks represent the atomic structure of one small portion of a DNA sequence from a gene. If you look carefully, you can see the well-known features of the intertwined DNA double helix in these atoms.2nd and 3rd itemThe blue sticks that are placed within the cloud represent the atoms of the anticancer drug duocarmycin SA. The simple stick representation is used to help visualize the molecules but in fact, the cloud is a much more realistic representation of the atoms.4th itemThis picture show how well the drug and the DNA fit together, like a key in a lock. This gives a graphic representation of one of the key elements of designing a drug: the need to make the shape of the drug complementary the target. Many of the other key elements needed for drug design require an even deeper level of inspection of the structure of the molecule.Next items- show small box and build the new larger box including the picture insideWe will zoom in closer to the atoms for a better view. At this level of magnification we can examine the details of the interactions between each atom in the drug and DNA target.Next item- label “atomic interactions”In this picture, the critical information is where the surface of the clouds come close to the sticks. It is here at this level of ultra magnification where we can really fine tune the details of the drug to generate the specificity that is needed to ensure there are no side effects to a drug.Lights up to talkStructural Biology is providing a whole new strategy for the design of drugs with higher specificity and fewer side effects than has been achievable with traditional approaches where hundreds or even thousands of random drug candidates must be scanned.There is tremendous excitement in univeristies and the pharmaceutical industry because this structure-based drug design strategy will save huge amounts of time and money in the effort to develop new therapeutics for the clinic.I look forward with anticipation to the opening of the new building when we will be placed in close juxtaposition with many of the most exciting laboratories on campus. I hope I have given you a sense of our excitement over the vast possibities of using the structural biology approach for advancing medicine and biology.
5 Biological linguistics RPANERBERRRI dinked around w/colors, but there’s a plain white version at the very end if you prefer.Also, see next slide for an animated versionMoleculeStructural GenomicsPathwayStructural ProteomicsActivitySystems Biology
35 Gametocytogenesis in P. falciparum SH3PFG27AUGCCUUANovel foldUnique 3D structureRNA bindingSH3 bindingPxxP motifsSignaling intermediate
36 Review of binding sites of interest on Pfg27 Two RNA-binding sites per dimerFour SH3-binding sites per dimerA dimer interfaceFrom literature 3 sites have been identified by the group who have solved the crystal structure of pfg27. these sites are the RNA and SH3 binding sites. The dimer interface where the 2 monomers interact is also considered of potential interest, as the prevention of dimerisation of pfg27 could inhibit the activity of pfg27. from a visual inspection of the surface, the deepest cavity is also considered as a binding site.Pfg27 monomerRNA-binding site Deep cavitySH3-binding site Dimer interface
37 Visual analysis of top 200 dockings Docking pattern on Pfg27Visual analysis of top 200 dockingsFlexX GOLDDeep cavityRNA-binding siteDimer interfaceSH3-binding siteOther sites(values in percent)
38 Docking at RNA-binding site surfacedeeperRNA-binding siteligandfragment
39 Dockings at RNA-binding site surfacedeeperligandfragment
40 Ligand profiles at RNA-binding site 2D structural similarity: ~35% for top 20Notable base fragment(present in 6 ligands)Functional group: SO3 (present in 11 ligands)H-bonding interactions: Ser72,Arg75, Tyr76, Lys79hydrophobic interactions/close contacts: Leu52, Phe87, Leu52, Asn82Molecular weight:Drug likeness: 20% (WDI)
41 Development of Databases for Screenings NCI 1990 diverseOpen collection 240,000Pubchem250,000Chembridge50,000 diverseMaybridge60,000 diverseSpecs10,000 diverseAll libraries converted into relational database formatPubchem - 46,000 diverse library generatedFiltered based on lipinski’s rule of 5Redundancy checks performedFinal database: 149,865 compounds with < 90% structural similarity
43 Structural and functional dissection of the two nucleosome assembly proteinsfrom Plasmodium falciparumAmit SharmaICGEB, New Delhi
44 Nucleosome assembly in P. falciparum ImportanceNucleosome assembly in P. falciparum
45 Nucleosome assembly in P. falciparum WorkplanNucleosome assembly in P. falciparumNCPfNAPSPfNAPL1. Expressed in all stages of the parasite2. Localized both to the cytoplasm and the nucleus3. Differential localization in asexual/sexual stages4. Differential phosphorylation of the two NAPz5. Similar histone binding specificities