Interesting Developments

Historic trends in biotech fields

Top cited papers published in 2010 by field

X-ray crystallography - How it works and what it is used for

First we will watch a cartoon.http://richannel.org/a-case-of-crystal-clarity

Then we will look at the first protein molecule to have its structure worked out using x-ray crystallography.http://richannel.org/collections/2013/crystallography#/myoglobin-a-brief-history-of-structural-biology

Now we will see how to grow and examine a protein crystal to get the protein structure. http://richannel.org/understanding-crystallography-part-one

Korea has a synchrotron at Pohang.The Pohang Light Source was designed to provide synchrotron radiation with continuous wavelengths down to 1Å. It's construction was completed in September, 1994. The PLS is a national user facility, owned and operated by the Pohang Accelerator Laboratory (PAL) and POSTECH on behalf of the Korean Government.

Here is an example of how this information might be used. The development of Imatinib Targeted development is imatinib mesylate (Gleevec), a small molecule which inhibits a signaling molecule kinase.

The genetic abnormality causing chronic myelogenous leukemia(CML) has been known for a long time to be a chromosomal translocation creating an abnormal fusion protein, kinase BCR-ABL, which signals wrongly, leading to uncontrolled proliferation of the leukemia cells.

s

The Philadelphia chromosomeThe karyotypic abnormality for chronic myelogenous leukemia is shown in the banded chromosomes 9 and 22. There is a reciprocal translocation of 22q to the lower arm of 9 and 9q (c-abl to a specific breakpoint cluster region [bcr] of chromosome 22)

In 1983, researchers demonstrated that the human c-abl oncogene is located in the region of chromosome 9 that translocates to become part of the Philadelphia chromosome. in 1990, scientists infected bone marrow cells with a retrovirus encoding the fusion gene and demonstrated that, indeed, the presence of an active bcr-abl gene initiates CML or CML-like symptoms

In 1990, the function of the bcr-abl fusion gene: production of an abnormal tyrosine kinase protein that is not properly regulated. Tyrosine kinase is a common signaling molecule that, when activated, triggers cells to divide.

In CML, the mutated tyrosine kinase is active for too long, causing cells to multiply at an abnormally high rate. This results in the overproduction and accumulation of immature white blood cells. A milliliter of blood from a healthy person contains about 4,000 to 10,000 white blood cells, the same volume of blood from a person with CML contains 10 to 25 times that amount.

Scientists learned about kinase structure, and found considerable variation in the ATP-binding pockets of the different kinases. This meant that a drug that specifically blocks the bcr-abl ATP binding site might be possible. Ciba-Geigy (which later became Novartis), were conducting tyrosine kinase inhibitor research. They had already synthesized some kinase-blocking inhibitor compounds, using computer models to predict which molecular structures might fit the ATP-binding site of the fusion protein.

Brian Druker had extensively researched the abnormal enzyme kinase in CML. He thought precisely inhibiting this kinase with a drug would control the disease and have little effect on normal cells. He collaborated with Nicholas Lydon, who developed several candidate inhibitors. Imatinib was found to have the most promise in laboratory experimentsWhen this small molecule is used to treat patients with chronic-phase CML, 90% achieve complete haematological remission.

Like all tyrosine-kinase inhibitors, imatinib works by preventing a tyrosine kinase enzyme, in this case BCR-Abl, from phosphorylating subsequent proteins and initiating the signalling cascade necessary for cancer development, thus preventing the growth of cancer cells and leading to their death by apoptosis. Because the BCR-Abl tyrosine kinase enzyme exists only in cancer cells and not in healthy cells, imatinib works as a form of targeted therapy—only cancer cells are killed through the drug's action.

Crystallographic structure of tyrosine-protein kinase ABL (rainbow colored, N-terminus = blue, C-terminus = red) complexed with imatinib (spheres, carbon = white, oxygen = red, nitrogen = blue).

Flow chart for structure based drug design. By Laozhengzz CC A-SA 3.0 http://en.wikipedia.org/wiki/File:Flow_chart_for_structure_based_drug_design.jpg

Structure-based drug design (or direct drug design) relies on knowledge of the three dimensional structure of the biological target obtained through methods such as x-ray crystallography or NMR spectroscopy. If an experimental structure of a target is not available, it may be possible to create a homology model of the target based on the experimental structure of a related protein.

Using the structure of the biological target, candidate drugs that are predicted to bind with high affinity and selectivity to the target may be designed using interactive graphics and the intuition of a medicinal chemist. Alternatively various automated computational procedures may be used to suggest new drug candidates.

The 3D structures of biomolecular targets are obtained from X-ray crystallography and NMR. In parallel, information about the structural dynamics and electronic properties about ligands are obtained from calculations. This has encouraged the rapid development of the structure-based drug design. Current methods for structure-based drug design can be divided roughly into two categories.

The first category is about “finding” ligands for a given receptor, which is usually referred as database searching. In this case, a large number of potential ligand molecules are screened to find those fitting the binding pocket of the receptor. This method is usually referred as ligand-based drug design. The key advantage of database searching is that it saves synthetic effort to obtain new lead compounds.

Another category of structure-based drug design methods is about “building” ligands, which is usually referred as receptor-based drug design. In this case, ligand molecules are built up within the constraints of the binding pocket by assembling small pieces in a stepwise manner. These pieces can be either individual atoms or molecular fragments. The key advantage of such a method is that novel structures, not contained in any database, can be suggested.