Thursday, 22 January 2015

Natural Products: a source and an inspiration for new drugs

The theme of last term at the UTC was malaria, with lab work for Y12s centred on the development of skills and the recording and evaluating of data. This week you will be presenting your results in the form of posters and scientific reports. All of this has been the first step on your journey to become young scientific explorers. Our theme for the second term is virology, in particular the threat posed by HIV and Ebola in creating international health crises, and how Science can intervene, both for diagnosis and for therapy. Of course, we aren't able to work directly with such hazardous viruses, but we can explore the methods and strategies used to isolate new drugs and, after the first half term, the methods of molecular biology as applied to the investigation of viral genomes using a bacterial virus: bacteriophage lambda (or just lambda for short). I wont discuss lambda in this post, but I shall return to this wonderful molecular machine towards the end of this half term. Here I want to explain how we shall "model" the process of drug discovery and screening using Natural Products. This allows us to appreciate one of the most important experimental approaches taken by the Pharmaceutical sector in both identifying new drugs, but also in helping inform the synthesis of new drugs using the methods of organic chemistry. (You may recall the seminars during our first UTC Transmits Symposium, in which synthetic chemists discussed the ways in which Natural Products with known therapeutic effects, improved the efficiency of their synthetic strategies).

What do I mean by Natural Products? Very simply, we know that all living organisms utilise a common set of biochemical strategies to extract energy from food (and light, sometimes) and to recycle the building blocks of carbohydrates, fats and proteins into our own macromolecules. However, whilst we share core chemistries, it has been known for many years that plants in particular, sometimes produce molecules that have therapeutic value. For example, you will all be familiar with aspirin, a well known analgaesic (or pain killer): the bark of willow trees contains the compound salicin, which we now regularly take in the form of acetylsalicylic acid (aspirin, top LHS). Similarly, the mould Penicillium chrysogenes, produces a molecule which we all know as penicillin, the key component of Fleming's first discovery of an antibiotic. Molecules like penicillin and salicin are sometimes referred to as secondary metabolites: they are clearly part of the fabric of these organisms, but they are not found in man. We can say that they are not part of the human metabolome. However, even in the absence of a knowledge of the mode of action of compounds like penicillin and aspirin, they have been a major success in alleviating disease and pain respectively.

The project this half term for Y12 students draws on the historic value of plant extracts as sources of therapeutic molecules as a way of introducing the steps in a typical drug discovery programme:

Choose a rich source of "molecules" (you can choose one or more plants)

Make extracts, i.e. mixtures of molecules in a reproducible way using aqueous or organic solvents

Establish a reliable method for exploring the anti-bacterial properties of your impure extracts (we shall use top agar plating with E.coli K12 as the organism to test).

Plan your strategy, the use of controls and how you evaluate your data in a quantitative manner.

Purify: how might you isolate any active component and assay/measure its capacity to kill bacteria.

Finally, how does your extract compare with known antibacterials?

As I chatted to some of you this week, I was impressed by your ideas, but don't forget, you should plan ahead and don't dive in too quickly with the extraction phase. See the link to the flow diagram and planning Blog from last year.

Coming soon........... the molecule for February will be the HIV particle (LHS). Although this is formally a group of molecules, the importance of structural biology in understanding and battling viral infection can be appreciated by such impressive work. I shall compare HIV with some other viruses including influenza and the bacteriophage that we will study next half term in the innovation labs.

Friday, 2 January 2015

January, 2015 Molecule of the month: Cytochrome P450(s)

It's a new year and I thought I would bring out the molecule I had intended to write about in November, I thought I would focus on another topic that links to the theme of malaria (at the UTC) , but which is of wider importance in understanding the way animals, in particular, deal with chemical challenges. The cytochrome P450 family of proteins (often abbreviated to CYPs; an example is shown on the LHS), is an important target for insecticides (take a look at the links at Nicole Joussen's web site in Germany) in dealing with the spread of malaria via mosquitoes, but it is also an important class of enzymes in the process of drug validation (I like the way Emily Scott has organised her research into CYPs and drug discovery here [and then follow her research links]). The first thing to say is that it isn't a single enzyme. The CYPs are a group of enzymes which facilitate the "metabolism" of foreign compounds (xenobiotics). From an evolutionary perspective, they provide a selective advantage in mitigating the impact of potentially toxic molecules. From an enzymological point of view, they are of interest since they handle a wide range of substrates, making the relationship between the chemistry of catalysis and the specificity of substrate recognition an intriguing challenge. Let's look at the general structure function relationships in the CYP superfamily and then consider their importance both fundamentally and translationally with respect to toxicology: drugs and insecticides.

The CYPs are modular molecules (top figure, LHS) comprising two domains: the substrate binding domain and the redox domain: the structure of the first mammalian CYP was published in 2000. The reaction catalysed by these enzymes can be generalised in the schematic figure shown Left. The structures of the substrates can be substantially different (see below, RHS for a comparison of two substrates handled by a single P450). The CYPs represent a class of enzymes where there is a common redox centre that is used to diffuse the dangerous aspects of the toxic molecule. Enzymes exist with specificities that are unique, but there are also situations where evolution has led to the retention of a useful engine (the redox centre) which is then attached through historic (genetic) events including gene fusions and recombination, to generate a range of primary structures that recognise different small molecules. 

This structure-function concept is a theme found a number of times in Biology. For example all Immunoglobulins (antibodies: see my January 2013 Blog on these molecules) have a common stem (called the Fc region) which binds to cell receptors, associated with many different antigen combining elements, enabling us to eliminate many thousands of potentially harmful molecules. In the case of CYPs, a catalytic engine is harnessed to a range of small molecule scavenging units, which then prepare the offensive molecules for downstream elimination (in humans) in the liver. 

The interest in CYPs lies not only in their role in toxicological investigations of new drugs, but also in the application of insecticides in the battle against malaria. The role played by CYPs (as well as other enzymes including glutathione-S-transferases and haem metabolising enzymes) has formed a major part of the research programme at the Liverpool School of Tropical Medicine. You can read more about this here by following the links from Professor Hilary Ranson, Head of the Department of Vector Biology at the School. Understanding the relationship between mutation and the genetics of insecticide resistance, in particular in respect of the CYPs, is one of the major areas of research in the field of Tropical Medicine. So the molecule for January, 2015 represents a major challenge for fundamental Biochemistry, but also occupies a pivotal position in the delivery of new drugs to the market and in the management of malaria.