Monday, 27 October 2014

First UTC Scientific Conference Commentary

You will all now be putting your feet up as half term begins, but I thought I would give you a little help in preparing your abstracts and summaries of your favourite seminar from the Malaria Meeting held at the University of Liverpool, last Wednesday in the Muspratt Lecture Theatre (appropriately chosen after one of the founding fathers of Chemistry at the University). 

Just to remind you all (and those who missed it) the running order was as follows:

1.35pm Professor David Hornby, Liverpool Life Sciences UTC
Opening Remarks

1.40pm Dr Alexandre Lawrenson, The Kingsway Academy
Virtual Screening to Identify Novel Antimalarial Chemotypes

2.00pm Emeritus Professor Michael Clarkson, University of Liverpool
Local Mosquitos – My Hobby

2.25pm Professor Paul O’Neill, University of Liverpool
Antimalarial Drug Discovery and Development in Academia

2.45pm Break

2.55pm Rachel Winrow, Liverpool Life Sciences UTC
My experience of Malaria

3.00pm Professor Richard Pleass, Liverpool School of Tropical Medicine
HexaGard: a biomimetic replacement for IVIg therapy

3.20pm The Memusi Foundation Team, Liverpool Life Sciences UTC

3.30pm Dr Mark Paine, Liverpool School of Tropical Medicine
Malaria: Of Men and Mosquitos

3.50pm Gap Medics

4.10pm Alison McGovern, MP
An Economic and Political Perspective on Malaria in Africa

4.30pm Professor Neil Hall, University of Liverpool
Genetics of the Malaria Parasite

4.50pm Professor David Hornby, Liverpool Life Sciences UTC
Closing Remarks

First of all,as an audience (Y12s and 13s) you were exemplary: engaged and, despite the intensity of the session, and the level of many of the talks, you were all an audience to die for. At least that's what all of the visiting speakers asked me to pass on. So incredibly well done! I found your questions to be searching and challenging and your confidence was at a level I rarely see amongst graduates!

So let me give my own synopsis of the talks. I am going to concentrate on the visitors' talks and say something separately about the UTC student talks in a separate Blog. The theme was Malaria, as you all know, but the content varied from Alison McGovern's consideration of our social responsibility as a developed nation in supporting the reduction in deaths from Malaria. Alison's style was more interactive than all of the other speakers and I would ask you to consider looking into the Millennium Goals that she discussed. You can find more information here. Your engagement was excellent, but mostly I hope she stimulated your interest in the important economic, societal and ethical issues she raised. As responsible citizens, when you are able to vote for the first time, you should really follow Alison's advice and inform yourself about the challenges and responsibilities that she discussed in such a lively and passionate manner.

The first seminar of the day was delivered with great clarity by Alex Lawrenson, formerly a PhD student in Paul O'Neill's chemistry lab at the University of Liverpool who has moved through industry before re-surfacing at the Kingsway Academy. Alex explained the frustrations for all pharmaceutical companies in tackling the 15 year barrier to "getting drugs on the market". Clearly, we don't want drugs to be made available before they are thoroughly tested, but 15 years is a long time. Just look at the debate surrounding Ebola treatment at the moment. The suggestion that Alex discussed, with examples drawn from his own research, was to utilise algorithms that search chemical and structural features of "compound libraries" in order to reduce the time taken to identify promising therapeutic molecules. This "in silico" approach utilises software that matches ideas from the medicinal chemist (which include not only the potential steric fit of a compound to its target [often a protein, and in Alex's case a cytochrome], but also its potential toxicity, stability, solubility etc.) in order to limit (or filter) the number of compounds to be screened. It is clear that these approaches are beginning to make a difference and I am looking forward to chatting to Alex further when he visits us at the UTC.

Paul O'Neill followed Alex later in the day, giving us a tour de force of Malaria drug discovery. The most interesting aspect from my perspective was the way in which Paul's group have taken Natural Products, in this case quinine and artemisinin (left), two historic treatments for Malaria, and addressed the challenge of not only improving upon them in an empirical manner (Science speak for systematic trial and error!), but also by using the insight gained from the target for these compounds: our old friend Haemoglobin, the Molecule of the Month in May. Since we have been using conjugated dyes to simplify our chromatography experiments over the last month, you will be familiar with me describing how molecules that are made up of "aromatic" rings are able to absorb visible light as a consequence of the reorganisation of electrons. Well, Paul suggested that the porphyrin ring (the key element of Haem, often written heme) can make highly favourable interactions with the compounds he has been designing and synthesising, inspired by the aforementioned natural products. In fact I went to PubMed to find the affinity constants and was surprised to find work dating back to the early 1980s on quinine interactions with porphyrin (eg Moreau et al (1985)). I'd love to read your thoughts on Paul's talk, since I know some of you found Alex and Paul's talks the most interesting. You should think about the fact, as Paul discussed, that female mosquitoes feed on blood and the accumulation of Haem that results is the drug target. This makes for an interesting story in itself, regarding Malaria and drug resistance mechanisms.

The Wirral's own Lake District
Before I cover the two talks from the Liverpool School of Tropical Medicine (LSTM), I just wanted to mention the seminar that proved to be popular with everyone (in fact, out of 50 students I asked, he was first choice as favourite by 48!). Michael Clarkson's talk proved a delight. He discussed his retirement "hobby" (Michael is Emeritus Professor in Veterinary Science at Liverpool: the title emeritus is conferred upon retired professorial staff who have given distinguished service at their institution, and often remain active in their field): monitoring mosquitoes on the Wirral. I thoroughly enjoyed Michael's delivery and the elegant way he developed his scientific thinking, while keeping us amused at the same time. It was an important addition as well, since he raised the important issue of diversity among insects: not all mosquitoes carry malaria and their life cycle preferences differ in many subtle ways, illustrating the challenges of managing insect borne diseases. This aspect could be something you might want to think about if you choose Michael's talk for your essay. I was also interested in why so many students found Michael so engaging. It wasn't difficult: his relaxed style and his natural enthusiasm combined with his perfect judgement in his use of language to develop his story, all made his presentation, the people's favourite by far.

The two talks from the LSTM illustrated the quite different approaches that form part of the School's strategy for supporting the eradication of Malaria. Richard Pleass described how his lab are manipulating the scaffolds of antibodies in order to understand the fundamental processes in immunity that lead to antigen elimination. As you will recall from my Molecule of the Month in January 2013, the structure of antibodies is broadly a Y shape. Richard described how his team are hijacking and remodelling, the stem of the antibody (called the Fc region) in order to steer the interaction with different classes of receptors. Richard is working with the Biotech sector in order to improve existing treatments for auto-mimmune disease, and these approaches are hopefully set to inform our approach to vaccine design. Mark Paine's group by contrast, bring together the enzymes used by humans to deal with toxic compounds that enter our blood stream, which in insects form part of a suite of defensive mechanisms for combating insecticides. As Mark explained, at the Biochemical level, we know how to kill mosquitoes, but we also know that unregulated (or excessive) exposure of insects to insecticides leads ultimately to "resistance" through mechanisms identical to similar bad practise in the management of antibiotics. Mark was clear that elimination of mosquitoes was his solution, and he explained how the use of bed nets (partly supply, education and politics!) and spraying regimes could be improved by the introduction of simple quality control and quality assurance assays. The importance of pragmatism in combating Malaria was evident in the way Mark combined Science, Education and the logistics and realities of life in those countries where Malaria prevails. It might be interesting for someone to compare and contrast Mark's presentation with Alison's above. 

Finally, Neil Hall presented a riveting account of the road to the Plasmodium genome. Neil moved from the Wellcome Trust Sanger Institute several years ago and heads up the Centre for Genomic Research at the University of Liverpool. As you might expect, such projects involve many people (although Neil's name is easy to spot in the two landmark papers in Nature in 2002!) and the clear advances in technology that have taken place (and continue to do so) are making genome sequencing faster day by day. Neil explained not only the methodology, but the impetus (from a historical context) for addressing Malaria through genomics, specifically discussing the regions of the Plasmodium chromosomes that make the organism such a surface "chameleon". In addition, he explained how a comprehensive knowledge of the entire genome, could address questions that were inconceivable before genomics. The integration of metabolic pathways and the analysis of the evolutionary mechanisms that have led to the peculiar organelles found in Plasmodium whose origins may lie more towards chloroplasts. These ideas would not have been possible without genomics. It is also timely to consider genomics, a Science that is part experimental and increasingly computational. When you return after half term, we shall begin our Bioinformatics project and using search tools provided by the National Center for Biotechnology Information (NCBI) in the USA, we shall be looking at some of the aspects Neil discussed in his excellent closing seminar.

Finally, a reminder: I am after a Scientific Abstract and a separate 1 page description of your chosen seminar for Monday the 3rd November, in the meantime have a good break (in between revision!). 

Tuesday, 21 October 2014

UTC Transmits preview

It's just over a year since the Life Sciences UTC in Liverpool welcomed its first intake of students. Along the way there have been some noteworthy events and achievements, as well as challenges of course. However, tomorrow a group of leading researchers, educators and policy makers, will come together at the University of Liverpool to deliver a programme of talks, that would not look at all out of place at an International Scientific conference. The significance of the event should not be underestimated. It is the culmination of a year of overwhelmingly positive support from our partners in helping us "raise the game" of school level education. Y12 students will be given the opportunity to bring together their curriculum knowledge along with their innovation lab experiences and the broad range of enrichment experiences that are at the heart of the UTC. This new term has seen a thematic focus on Malaria and the challenges facing the world of infectious diseases. It could not have been more timely!

The scientific part of the programme will be delivered by senior academics whose research interests span genomics, through the application of molecular immunology and insecticide resistance mechanisms, to state of the art medicinal chemistry. In addition there will be presentations on the wider implications of Malaria from a societal and educational perspective. I look forward to introducing the speakers, engaging with the students and I shall report back on the highlights by the end of the week! For details see this week's UTC Home Page.

Friday, 17 October 2014

Having spoken this week to students about the Science, the Scientists and the Significance of Nobel Prizes from the first to the last, the work of Pauling and Sanger came to the fore. I thought I would therefore provide a link from one of the earliest Nobel prizes (here I am referring to Emil Fischer's ground-breaking work on peptides, even though his award was for his work on sugars and purines! [NP 1902]) through Linus Pauling's work on the chemical bond, including the peptide bond [NP 1954, ], Fred Sanger's first Nobel Prize [NP 1958] for his work on the structure of proteins, and finally to the NP 2009 awarded to Yonath, Steitz and Ramakrishnan for determining the structure of the macromolecular machine that is responsible for peptide bond synthesis in all living organisms: the Ribosome. These prizes provide a great opportunity to consider, Biology, Chemistry and Physics from an experimental and theoretical standpoint. They also illustrate the enduring influence of work of Nobel Laureates. I shudder to think of the intellect of Emil Fischer (top left),who carried out his work in such "low-tech" circumstances, unencumbered by over 100 years of massive research outputs in Science!

One of the early concepts that students of Biochemistry have to learn is that the amino acids that make up proteins are only of the L form: the D form is found in Nature, but the L form has emerged after many years of evolution as the "enantiomer" found in proteins. You can read the basics on amino acids at this wikipedia site. Understanding the chemical linkage between amino acids occupied the mind of Fischer over ten years at the turn of the last century. Having obtained several amino acids in an optically pure form, he synthesised several dipeptides and laid the foundation for our understanding of the peptide bond. There is a nice little Blog post on the peptide bond here, by "Sandwalk" at the University of Toronto. The figure above (RHS) illustrates the bonds in a polypeptide chain and in particular the contrast between the rotational freedom at bonds adjacent to the peptide bond. It was largely through work by Linus Pauling (and Robert Corey) that the rigidity and partial double bond character of the peptide bond was understood. There is a nice historical sketch to be found at Edison, where he discusses the resonance stabilisation that underpins the nature of the peptide bond. In essence, the distribution of electrons of the peptide bond, is so energetically favourable that it essentially fixes the polypeptide chain and constrains the secondary structure of a protein. This, along with the rule that hydrogen bonds between amino and carbonyl pairs prevail, provided Pauling and colleagues with the impetus to predict the formation of alpha helices and beta sheets in protein structures. Pauling was proved right some years later by X ray crystallography from the Cambridge Nobel laureates,  Max Perutz and John Kendrew.

It is worth taking a moment to reflect on the intellect of Pauling, notwithstanding his contributions to enzyme catalysis and other aspects of chemical bonding. The coalescence of his knowledge of chemical bonds, both covalent and hydrogen, together with an ability to identify patterns and deliver a robust visual expression through molecular modelling, is in my view quite formidable! If you are interested in Pauling, you might look here and an interesting intellectual exercise is to read the original papers from Pauling and Watson and Crick, side by side, on the interpretation of experimental data that led to the proposals for the structure of DNA. We take the structure of DNA for granted, but working with so little data, these two interpretations demonstrate how challenging it is when you are tackling a problem of immense importance.

To summarise, the work of Fischer (and of course others) in establishing the chemical linkage between amino acids followed three decades later by Pauling's insights regarding the conformational characteristics of the peptide bond, provided Biochemists and X ray crystallographers with a framework for elucidating the three dimensional properties of Proteins (the image on the RHS is John Kendrew's original model of Myoglobin: the "sausages" are Pauling's alpha helices). Let us not forget here the importance of Fred Sanger's contribution in proving by his elegant chemistry, the uniqueness of the primary structure of proteins! Now  let us look at two further aspects of the life of the peptide bond: its formation via the ribosome and its hydrolysis through the action of proteases. I shall confine myself to the Serine Proteases in this Blog. 

The active site of Trypsin
The energy locked up in the peptide bond is approximately 3kcal/mol, although there are known to be differences arising say when one amino acid is added to another compared with consecutive additions. Moreover there will be local variations in the susceptibility of some peptide bonds to hydrolysis caused by factors such as local structure and side chain chemistry. [When thinking about biosynthesis, the hydrolysis of ATP and GTP generates significantly more energy, but not all is channelled into bond formation, some is used to drive the movement of the ribosome along the mRNA (among other essential reaction steps)]. The Serine proteases include the enzymes Trypsin, Chymotrypsin and Elastase: "The Holy Trinity" of undergraduate enzymology, when I was a student at least! These enzymes contain a catalytic triad (Histidine, Aspartate and Serine), in a constellation that promotes the hydrolysis of the peptide bond. The structural properties of the R group of the amino acid side chain such as Lysine or Arginine (in the case of Trypsin) provide the "specificity" determinant for directing the hydrolysis reaction. Some of the most interesting early experiments using site directed mutagenesis were carried out on the serine proteases and this helped us to develop a more robust understanding of some of the general features of enzyme catalysis (you can read a recent review of the early work and more recent experiments here). The combination of these three amino acids in creating an O- (or oxyanion) to facilitate hydrolysis coupled with the "attachment" to a distinctive chemical group (such as the long positively charged side chains of Lysine or Arginine), is an important theme in our understanding of hydrolytic enzymes that act on biopolymers. [Can you think of an analogy in the field of nucleic acids?] In vivo, proteases can serve many roles: from nutritional, like Trypsin, to regulatory (in the cell cycle) to recycling of amino acids via the proteosome. 

Finally, making peptide bonds. So far this has been a proteo-centric Blog. But just think for a minute about the origins of Life (at the molecular level). Proteins are pretty complex molecules and enzymes have taken years of evolutionary time to settle into their catalytically efficient sequences and shapes. The determination of the structure of the Ribosome, together with earlier work by geneticists and biochemists, revealed that the catalytic centre of peptide bond synthesis is made of RNA, not protein! The task of producing crystals of the quality required to determine the high resolution structure of the Ribosome had been a labour of love for many groups, for many years. However finally in around 2000, the first high resolution structures appeared (see here). The award of the NP to Steitz, Yonath and Ramakrishnan was just recognition (in my view) for the tenacity of their research teams over many years in providing us with a working template for understanding the molecular stages of protein synthesis and the mode of action of a number of antibiotics. The condensation of an amino acid with the growing polypeptide chain on the Ribosome is where nucleic acid and protein chemistry converge. The flow of information from the digitally encoded genes through to the functionality of proteins is at the heart of all Life on Earth. Anyone with an interest in Life Sciences must take time to understand the chemistry underpinning, what Francis Crick called the "central dogma" of Molecular Biology. [Before I finish, it would be remiss of me not to mention the reverse flow of information that was discovered in viruses through their recruitment of Reverse Transcriptases, but that's for another time!]

Sunday, 5 October 2014

An explosive Molecule of the Month: Dynamite the source of Alfred Nobel's wealth

The coming week is one of the most eagerly anticipated weeks in Science. It is the week in which the Nobel Prizes are announced and last year, we had an impromptu celebration during the week, by showing the live stream of announcements from Stockholm, where the prizes are announced . It made me think about the molecule to choose for October and I immediately thought of the organic molecule that formed the basis of Alfred Nobel's lucrative and famous invention: dynamite. The molecular structure shows that nitroglycerin (or Trinitroglycerin, NG for short)  is a rather simple compound which can be made by adding concentrated nitric acid to glycerol (see the wiki page for more information). Its formal name is 1,2,3 trinitroxypropane (A level chemists, make sure you can work this out!). Without Alfred Nobel's wealth, largely resulting from his invention of dynamite, used in construction work as well as for military purposes, there would be no Nobel Prize ceremony.

I wont spend a great deal of time on the background to the Prizes (you can read about them at the web site of the Nobel Foundation), but the prizes that are of interest to us this week are:

Monday:The Physiology or Medicine Prize
Tuesday: The Physics Prize
Wednesday: The Chemistry Prize

The countdown page can be found at this link and we will log in on Monday morning in the Innovation labs. The fuse is already burning slowly! 

Returning to the molecule, the original formulation of dynamite comprised NG, sodium carbonate and a "filler" called diatomaceous earth (a clay formed from silicates derived from fossilised diatoms). But why is NG so unstable? Why does it release so much energy when it is activated by physical shock or disruption, typically delivered via a fuse and termed detonation (from the French for "of thunder")? The release of energy in this highly exothermic process is a result of the favourable formation of gas molecules (N2/CO2/O2 and water vapour as the compound is detonated): compared with the instability of the weak bonds in NG, the hydrocarbon core is also a fuel. Looking at the charged nitrates makes me think of the three phosphates in ATP (the body's natural fuel) and the thermodynamic gain from hydrolysis of three charged moieties in a confined molecular volume. On a final note, NG is also used to treat heart conditions such as angina, the molecule releases nitric oxide following a reaction catalysed by aldehyde dehydrogenase. This duality of nitroglycerin's place in Science, was reinforced when Alfred Nobel, the inventor was prescribed NG for heart disease close to his death!

Wednesday, 1 October 2014

Does your right hand know what your left hand is doing? Some thoughts on the importance of Physics for Life Sciences.

A commentary published this week in the Journal Nature, entitled 

Force of nature gave life its asymmetry

'Left-handed' electrons destroy certain organic molecules faster than their mirror versions.
made me think about the discussions relating to the possible role of epigenetic factors in the development of unique fingerprint patterns. It also prompted the thought that whilst we appreciate the aesthetic of symmetry (facial beauty is generally correlated with beauty), our existence as living organisms,  depends upon asymmetry at both the molecular and cellular levels. Thus, many biosynthetic precursors and metabolites, including glucose and most biological amino acids, are ‘chiral’. This means that one of the two mirror-image forms are preferred in vivo (think of your left and right hands, as I have discussed before, Jimi Hendrix and Paul McCartney both played guitar left handed: notice the controls on Hendrix's guitar are upside down, since he is playing a right handed Fender Stratocaster). In the same way, precursors (or building blocks) lead to a preferred "handedness" in for example,the DNA double helix or protein structural elements like the alpha helix. 
The origins of bilateral symmetry in living organisms is easy to see in the   image of a butterfly, with the dotted line indicating the symmetry axis (RHS). In the case of human embryogenesis, the initial division of the fertilised egg generates two identical cells, positioned as mirror images. From here on in, the line of symmetry is drawn and, through simple physical principles relating to molecular diffusion, coupled with differential gene expression (and a sprinkling of epigenetic factors), the body plan of many organisms is laid down. (You may want to look also at radial symmetry in Nature). Handedness is of fundamental importance in Biology, from sexual evolution through to drug interactions with protein targets. This is why it is so important to understand its origins, as well as appreciating its significance. 
So what has been discovered? It has been known for some time that molecules can sometimes adopt left or right handed forms, which both possess the same chemical formulae. We refer to this as chirality. It has been demonstrated by the authors of this work that the rate of decay of left and right forms are not identical and therefore an intrinsic level of preference may be possible in the selection of right over left in the early stages of the evolution of life forms. As descried in Nature (with some minor alterations):
Two physicists, Gay and Dreiling, at the University of Nebraska–Lincoln, fired low-energy, spin-polarized electrons at a gas of the organic compound and bromocamphor, used in some parts of the world as a sedative. In the resulting reaction, some electrons were captured by the molecules, in a manner similar to the capture of electromagnetic (think of my explanation of colour in solutions of dyes) radiation, which then were raised to an excited state. The molecules then degrade, producing bromide ions and other reactive compounds. By measuring the flow of ions produced, the researchers could see how often the reaction occurred for each handedness of electron.
The researchers found that left-handed bromocamphor was just slightly more likely to react with right-handed electrons than with left-handed ones. The converse was true when they used right-handed bromocamphor molecules. At the lowest energies, the direction of the preference flipped, causing an opposite asymmetry. In all cases the asymmetry was tiny, but consistent, like tossing a biased coin. “The scale of the asymmetry is small, but as in all matters evolutionary, significant: out of 20,000 coins tossed again and again, on average, 10,003 of them land on heads while 9,997 land on tails,” says Dreiling.Their research was published in Physical Review Letters on the 12th September 2014. 
You may wish to look at my previous post on thalidomide as an example of how (racemic)mixtures of different forms of a molecule can have a profound effect on human development. But for today, I want you to appreciate how experiments in physical chemistry can impact on Life Scientists (illustrated as a Venn diagram, left). Without a robust understanding of the molecular (and quantum) principles that underpin Life, we will surely make mistakes in designing drugs, developing new materials and generally translating our knowledge of Science into everyday use. 
This “duty” of all Scientists to “keep on top of the literature” is what the public expects and should, in my view be what the public demand. Those who are funded by taxes, to carry out scientific research, must be the best and must be prepared to keep abreast of all important developments in the wider sphere of Science. On the other hand, this is a daunting problem, since the number of research papers published every week is unmanageable. We are fortunate therefore, that the premier journals in Science (including Nature and Science), together with shrewd observers and commentators, pick out such breakthroughs on our behalf. As we approach Nobel Prize week, the handful of scientists who will be honoured, in my (limited) experience, will not only be experts in their own fields, but will also be able to demonstrate a much broader perspective on Science than most others.