Towards understanding Ionic interactions with Aromatic Rings


This blog article refers to the very recent work of András Perczel and colleagues in the paper Four Faces of the Interaction between Ions and Aromatic Rings (D. Papp, P. Rovó, I. Jákli, A. G. Császár, A. Perczel J. Comput. Chem. 2017, DOI: 10.1002/jcc.24816). This work is particularly interesting as it uses a mixture of data driven approaches from crystallography and structural biology as well as high level Quantum Mechanical (QM) calculations to answer a question that is raised fairly regularly in molecular design in structurally enabled projects – that of how do we optimise interactions between ionically charged species and aromatic systems.

Biology uses ionic-to-aromatic (IAr) interactions to stabilise macrostructure of proteins and other biological ensembles. Often aromatic residues such as phenylalanine (PHE), tryptophan (TRP) and tyrosine (TYR) interact with charged residues (e.g. negative charged residues (asparagine (ASP) and glutamate (GLU)) or positively charged residues (arginine (ARG) and Lysine (LYS)) to energetically stabilise proteins and peptides. Fundamentally this is the interaction of the charge of the ion and the quadrupole moment of the ring. If we understand this, and the correct vectors and applications of electron density, then we can use it to improve the interactions of aromatic rings in our drug molecules versus charged residues in a target. Take, for instance, a kinase; There are charged catalytic residues in the pocket which are key to activity. Can we use the understanding of these interactions to better get our aromatic rings in our inhibitors to bind to them / disrupt them?

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Fig 1: The interaction preferences of a cation (CP), or an anion (AP) either co-planar (ǁ) or perpendicular () to the ring. The darker green represents the most favoured vectors.

The authors investigated the Protein Databank (PDB) and the Cambridge Structural Database (CSD) to pull information on evidence-based interaction vectors, before engaging in ab initio calculations using Quantum Chemical approaches to attempt to quantify the kinds of energies involved. Below you can see the typical angles and distances of interaction between various ions and aromatic residues from the PDB.

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Fig 2: Occurrences in the PDB vs. the plane angles of interactions between various residues. Plots on the right demonstrate also the distances of these interactions.

This crystallographic information can help demonstrate which vectors and distances are preferred when designing interaction partnerships in your ligands.

The authors also use high level computational methods (FPA, NBO Hartree-Fock) to demonstrate complex electronics situations of electron-rich and deficient-rings in both small molecule and single point ions to give a semi-quantitative value of interactions (in kCalmol-1):

CP (23–37) > AP (14–21) > CPǁ (9–22) > APǁ (6–16)

Notes from the blogger (who’s thoughts are his own)

Aside from the computational chemistry calculations, the authors have demonstrated how a simple search of available databases such as the CSD and PDB can be used to mine meaningful incidental information for drug design. There are implications of using PDB data however in that the mass of crystallography was shot using various conditions, including salt and pH variations between structures. This may weaken the interaction strength between solvent accessible residues across the structures – this wholesale big data approach should be taken with slight caution for this reason.

The information gathered is quite intuitive to the med chemist, but helps to cement in ideas when designing ligands – either how to enable their rings to better make use of charged interactions, or, more subtly, if the rotamers of an aromatic ring is stabilised by one such charge, how best to use the stabilised vectors to go after other things in the pocket.

Their calculations help set up a semi-quantitative design rules, which may help drive interaction priorities, but as for the actual values, well, they may need to be taken with a pinch of something ionic…

Blog written by Ben Wahab

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Who inspires you?


As my close friends, family and colleagues are probably aware, due to the presence of a gigantic (500ml) bottle of Gaviscon (Figure 1), I have been suffering from a condition known as GERD (Gastroesophageal reflux disease).

Figure 1. Ranitidine (H2 receptor blocker) & Gaviscon (500 ml) prescribed for GERD

Admittedly there are far worse diseases to be afflicted with, however, the symptoms include chronic sore & inflamed throat, heartburn and chest pain which can be rather unpleasant. One of the medications I have been prescribed is ranitidine (a H2 receptor blocker, Figure 1), which is thankfully giving me some relief! The development of ranitidine was in response to the first in class H2 receptor blocker, Cimetidine discovered by Sir James Black at Smith, Kline & French. Sir James Black had an impressive career and is credited for the discovery of both Adrenergic β-blockers & H2 receptor blockers. This was obviously an incredible achievement for which he won the Nobel prize in 1988. How did he do it? more specifically, how did he successfully develop H2 blockers?

After discovering Adrenergic β-blockers Black noted the parallels between the pharmacology of both histamine and adrenaline. By making analogues of histamine one would certainly be able to find histamine β receptor antagonists. The physiological role for histamine was ambiguous at the time however Black observed that patients with peptic ulcers showed increased acid production in response to histamine, in fact it was the basis for diagnosis. Like any drug discovery programme, it wasn’t always straightforward. The medicinal chemists got to work on making antagonists based on the structure of histamine, Black thought making ring analogues of histamine would do the trick as this had worked previously for adrenergic β-blockers. After considerable effort by the chemists, testing in a variety of bioassays, no active compounds were found. It has been stated that the chemists were accused of being ‘’unimaginative’’ (as if that would ever be the case!).

After 4 years of chemical synthesis and no antagonism achieved things were not looking good. Black had a change of heart. Perhaps the chemists should have been spending more time investigating the amino acid side chains than substituting ring structures. Scanning back through earlier data, the sixth compound to be synthesized, Nα-gyanylhistamine, a side chain variant, showed a low level of inhibition and was previously missed because it was only a partial agonist (Table 1).  The side chain of Nα-gyanylhistamine was lengthened resulting in 3-[4(5)-imidazolyl]propylguanidine (Table 1) this compound showed an ~6 fold increase in potency but it was still only a partial agonist (Figure 2). Black was eager to find a full antagonist as a partial agonist at a low dose would only stimulate acid production and not block it.

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Figure 2. Enhanced potency of the partial agonist 3-[4(5)-imidazolyl]propylguanidine (91488) in guinea-pig right atrium assay.

One significant challenge for the programme was the fact that the compounds synthesized, namely; guanidines, carboxyamidines, isoureas and isothioureas, are all strong bases so at physiological pH would be protonated and therefore not easily absorbed. When the chemists synthesized a set of non-basic compounds both the agonist and antagonist effects were lost, except for one compound, a thiourea analogue (Table 1, PA2= 3.45), which displayed weak, but full, antagonist action in the in vitro guinea pig right atrium assay. Increasing the side chain produced burimamide (Table 1, PA2= 5.11). As had been seen for the guanindine compound this significantly increased the potency, finally they had a selective H2 histamine receptor antagonist. Burimamide took a year to synthesize.

Burimamide was tested in healthy volunteers and shown to inhibit gastric acid secretion confirming the transferability between the animal models and human disease. Burimamide was still not potent enough to be given orally so further compound optimisation was required to develop an even more potent antagonist. Tautomerism and alteration of electronic effects on the imidazole ring bought the chemists to Metiamide (Table 1). Metiamide increased the rate of ulcer healing in 700 patients, however a few suffered from granulocytopenia toxicity. The chemists came to the rescue again, this time replacing the thiourea moiety with cyanoguanidine, and in the process producing the safe drug Cimetidine (Table 1), the first in class H2 receptor blocker.

These drugs have saved the lives of millions of people with heart disease and peptic ulcers. At the time there were few treatment options for patients with peptic ulcers. The only cure was via surgical intervention. Sir James Black and his team are a definite inspiration, just remember his ‘’three C’s for effective drug discovery: Collaboration, Concentration and Commitment’’.

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Table 1. Lead optimisation of the first H2 blocker (Source: Personal reflections on Sir James Black (1924-2010) and histamine by C. Robin Ganellin)

Blog written by Jess Booth

To hear James Black in person follow this link: https://www.webofstories.com/play/james.black/12;jsessionid=F3B2C475B86A0B279E9FFEA3119B9C22

References:

Personal reflections on Sir James Black (1924-2010) and histamine by C. Robin Ganellin

Dimaprit-[s-[3-(N, N-dimethylamino)propyl] isothiourea] – a highly specific histamine H2-receptor agonist. Part 2. Structure-activity considerations. Agent Actions. Durant, GJ et al. 1977;7:38-43.

Perspectives in Drug Development and Clinical Pharmacology: The Discovery of Histamine H1 and H2 Antagonists by Alan Wayne Jones

Putting Theory into Practice: James Black, Receptor Theory and the Development of the Beta-Blockers at ICI, 1958–1978 by Viviane Quirke

www.webofstories.com

https://www.theguardian.com/science/2010/mar/23/sir-james-black-obituary

 

Sometimes the grass isn’t always greener


High content screening methods or automated microscopy based assays, are a more recent development in drug discovery. This technology is rapidly becoming a mainstream tool in profiling compound activities. One clear harbinger of this uptake in high content screening is the numerous different vendors which have brought their platforms to market enabling this work to proceed.

There are many advantages of using automated microscopy assays, compared to conventional assays. One generally assumed advantage is removal of compounds that cause optical interference due to the type of data obtained by a high content readout and the methods used in the assay (wash steps for example)

This assumption was tested in the following publication:

http://journals.sagepub.com/doi/full/10.1177/2472555217707725

In this article the authors screened 315,000 compounds with a high content assay using the IN cell Analyser 3000 platform, where they were looking for modulators of micro RNA biogenesis pathway using HeLa S3 expressing green fluorescent protein. Active compounds would lead to an increase in expression of the fluorescence signal.

Using a hit threshold of 20% signal increase for the screen, they were able to obtain a hit rate of 0.36% (1130 compounds). The authors were able to retest 836 of these primary screen hits, in both single concentration and concentration response curves with both the original cell line and the parental cell line which did not express the green fluorescent protein. This is where the project hit some trouble.

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Around 22% of hit compounds reconfirmed with the GFP cell line in both the single concentration and concentration response curves, which is not unreasonable. Disappointingly, roughly the same numbers repeated in the cell line which did not contain the GFP expression system. Effectivity all the active compounds were not specific and would suggest that they are all false positives.

These identified false positive compounds were grouped together by structure into four main classes and were listed in the publication by the authors. This could be a useful tool if you want to compare other compounds which you might be working against this list. It should be remembered that (currently) these compounds are only false positives in this assay, with its specific fluorescent wavelengths used. Just because the key compound in your project is a member of one of these classes, it does not mean you need to stop working on them, but it would suggest further investigation would be warranted.

If possible, it would have been interesting to see if the results were repeated with a standard conventional fluorescence assay compared to the automated microscopy method whether the team would have achieved the same results?

So in summary, automated microscopy assay can suffer from optical interference caused by compounds, they are not immune.

However, overall the authors should be commended for releasing this publication; it highlights that all assay formats (including automated microscopy assays) will have a degree of false positive compounds and that you have to use all available methods to ensure your data output is as confident as possible.

Blog written by Gareth Williams

 

Bacterial immunotherapy: Can Salmonella be used to kill cancer?


I was recently at dinner with a family friend, who has survived stomach cancer, but lost his wife to liver cancer two and a half years ago. He is an interesting man, who worked for a large oil company for many years, travelling Saudi Arabia and other areas of the Middle East before retiring about 20 years ago. He has an incredible wealth of knowledge in almost all matters, and there are very few conversations to which he cannot contribute. So, with this in mind and his own past suffering with cancer, it is safe to say that when he starts talking about a novel cancer therapeutic, he probably has done his research and knows a little about the subject matter. I was told that the Telegraph had printed an article on Salmonella and its ability to flag tumours to the immune system. Stories about novel cancer therapeutics often appear in newspapers and social media, and I rarely give them much thought, but this left me somewhat intrigued so I thought it would be interesting to look into it further.

The use of bacterial preparations to stimulate the immune system in cancer patients has been a contested subject for over a hundred years, since William Coley began routinely injecting streptococcal organisms into bone cancer and sarcoma patients. Prior to this, Coley lost one of his first patients due to widespread metastases, despite a forearm amputation in response to a malignant tumour. This deeply moved him and, having trawled through the literature, he found a correlation between concurrent bacterial infection and tumour regression. Results from his bacterial treatment of cancer patients suggested that treatment with “Coley’s toxin” lead to the regression of tumours. However since the advent of chemotherapy and radiotherapy, the use of Coley’s toxin gradually disappeared (McCarthy, E.F., 2006).

Immunology has progressed quite a lot since Coley carried out this work; the mechanisms involved are now better understood and it is for this reason that interest in this area of research has been reignited.

One of the main drawbacks of chemotherapy is its inability to target tumours specifically; this leads to high off-target toxicity in non-cancerous cells and low tumour penetration with the chemotherapeutic. However, the use of bacteria provides unique mechanisms by which site-specific treatment of tumours may be possible.

The natural ability of bacteria to sense their environment through chemoattractants, and then actively follow chemical gradients whilst crossing biological barriers means they are able to penetrate tumour tissue. Metabolically-active, genetically-modified bacteria are also able to perform specific tasks once at the tumour site, such as the production of immunomodulatory molecules (cytokines) or enzymatic conversion of a pro-drug into an active therapeutic (St Jean, A.T., 2008). Bacterial vectors are also inherently immunostimualtory, as Toll-like receptors (TLRs) expressed by innate immune cells recognise bacterial-expressed virulence factors such as peptidoglycan and LPS. This leads to downstream activation of DCs, which travel from the local tumour environment to draining lymph nodes and activate adaptive immune responses through presenting tumour antigens to T-cells (Chorobik, P., 2013).

So, why is Salmonella a favourable candidate for potential bacterial therapy? Salmonella Typhimurium have been shown to have a high affinity for tumour cells and their facultative anaerobic nature means they can happily infiltrate the hypoxic areas of tumours, but they have also been shown to target non-hypoxic regions and metastases. Salmonella spp. are highly motile and can therefore penetrate into therapeutically-resistant regions of tumours, and have been shown to be preferentially attracted to such areas. Salmonella also displays direct tumour-killing activity, as they compete for nutrients and also stimulate primary and secondary immune responses. Toxins produced by the bacteria may have apoptotic effects on tumour cells, and intracellular infection with Salmonella can lead to cell death through autophagy. The combination of all these attributes can lead to reduction in tumour size (Chang, W.W., 2014).

In order to develop new, Salmonella-based vector strains for the administration of therapies, they must be attenuated/altered to stimulate an appropriate immune response. Both S. Typhimurium and S. Typhi are responsive to attenuation, and roughly 50 genes can be inactivated to produce a specific profile of virulence factors, which lends them to being used as appropriate vectors for therapeutics.

The successful use of Salmonella in reducing tumour size in murine models of cancer has been well documented in the literature. Attenuated Salmonella has been shown to work in combination with cisplatin to demonstrate an additive effect on the reduction of tumour size in mice (Lee, C.H., 2005). These results show the impact of untransformed attenuated bacteria as a result of its inherent ability to augment immune responses. Multiple studies using S. Typhimurium, genetically engineered to express pro-inflammatory mediators (e.g. TNF, IL-18) or chemokines (CCL21) also demonstrate similar success in treating tumours in murine models of cancer (Chorobik, P., 2013).

However, the story is not quite so successful when it comes to looking at similar studies in humans. An attenuated strain of S. Typhimurium (VNP20009) has been tested in a phase I study in which metastatic cancer patients were dosed intravenously with the bacteria. None of the 25 patients experienced cancer regression, significant levels of circulating TNF were measured in the peripheral blood and tumour colonisation with Salmonella was only observed in biopsies from three of the 25 patients (Toso et al., 2002). These results are in contrast with all of the animal models and could be a result of limited tumour-specific targeting by the bacteria.

The more recent developments in this field of research, which prompted the news media to publish articles suggesting that Salmonella can cure cancer, uses a much less virulent strain of bacteria, with a much higher lethal dose. This means that larger concentrations of the bacteria can be used without the side effects observed in the original phase I study by Toso et al. The bacteria are also engineered to overexpress and inducibly secrete Vibrio vulinficus flagellin B (flaB), which stimulates innate immune responses through the TLR 5 pathway and in this way acts as an excellent adjuvant for immunotherapy. Three days post infection, levels of intratumoural bacteria were 10000 fold higher than other organs, and it was at this time point that the FlaB payload was delivered through induction with L-arabinose. As a result of this, the off-target toxic effects are massively reduced and targeted therapy is achieved (Zheng, J.H., et al., 2017). So far, this research utilising Salmonella’s innate ability to target tumours, as well as inducibly secrete the therapeutic looks promising in mice, but we will have to wait and see if this is developed for human trials.

In summary, bacteria have been used as immunomodulators for cancer therapy for a long time, but the more recent advances in immunology and molecular biology mean that we are now able to further tailor microbes to create potentially viable therapeutics. The more recent studies look promising in mice, and perhaps the use of genetically engineered bacteria to deliver therapeutics to tumour sites will be used routinely in the future. However, the only recent study in humans shows that the mouse models are not always indicative of how these therapies will fare in man. The unique ability of bacteria to specifically colonise tumour sites and then deliver their payload means they are ideal candidates for tumour-specific therapy, so advances in this area of research will hopefully lead to novel and viable therapies for cancer in the near future.

Blog written by Will Pearce

References

Chang, W.W. and Lee, H.C., (2014), Salmonella as an Innovative Therapeutic Antitumor Agent, nt. J. Mol. Sci. 15(8), 14546-14554

Chorobik, P. et al., (2013); Salmonella and cancer: from pathogens to therapeutics, Acta Biochim Pol.  60 (3):285-97

Lee, C.H.; Wu, C.L.; Tai, Y.S.; Shiau, A.L (2005) Systemic administration of attenuated Salmonella choleraesuis in combination with cisplatin for tumor therapy. Mol. Ther.  11, 707–716

McCarthy, E.F., (2006); The Toxins of William B. Coley and the Treatment of Bone and Soft-Tissue Sarcomas, Iowa Orthop J, 26: 154-158

St Jean, A.T., (2008); Bacterial therapies: completing the cancer treatment toolbox, Curr Opin Biotechnol, 19: 511-517

Toso JF1Gill VJHwu PMarincola FMRestifo NPSchwartzentruber DJSherry RMTopalian SLYang JCStock FFreezer LJMorton KESeipp CHaworth LMavroukakis SWhite DMacDonald SMao JSznol MRosenberg SA (2002), Phase I study of the intravenous administration of attenuated Salmonella typhimurium to patients with metastatic melanoma. J Clin Oncol. 2002 Jan 1;20(1):142-52

Zheung, J.H., Nguyen, V.H, Jian., S.N., Park, S.H., Tan, W., Hong, S.H., Shin, M.G., Chung, I.J., Hong, Y., Bom, H.S., Choy, H.E., Lee, S.E., Rhee, J.H., Min, J.J., (2017), Two-step enhanced cancer immunotherapy with engineered Salmonella typhimurium secreting heterologous flagellin, Science Translational Medicine  Vol. 9, Issue 376,

 

 

 

 

 

 

 

Vaccines: a great human conquest


It was 1796 when Edward Jenner opened a new page in human history by laying the foundations of modern immunisation and successfully developing a vaccine against smallpox. This disfiguring infectious disease with high mortality (>30%, higher in children), left survivors marked for life with terrible scars. The development of the first vaccine was followed by several others (tetanus, whooping cough, tuberculosis, polio, to cite a few), leading to a remarkable decrease of reported cases of common diseases in children and so saving the lives of millions. In 1956, the WHO started a global vaccination campaign to eradicate smallpox from the world; it took 24 years (until 1980) to succeed. Vaccines are now considered one of the greatest medical achievements in modern civilization.

Marco

Fig. 1: Comparison of 20th Century Annual Morbidity and 2010 Morbidity for Vaccine-Preventable Diseases in the United States: 20th century (JAMA 2007, 298(18): 2155-2163) – 2010 (CDC. MMWR January 7, 2011; 59(52);1704-1716)

Despite these tremendous results, there has also been quite a lot of controversy around vaccinations, mainly regarding efficacy and safety. These days, driven by widespread use of the internet and the advent of social media, several anti-vaccination campaigns have been launched and are becoming more and more popular. Surfing the web, it is possible to find all sort of contradicting and confusing information about vaccines and how harmful they can be. Once news has spread, it is very difficult to retract and requires quite a lot of work to establish what is real and what is not. Everyone has the right to gather information and have their own opinion with regards to vaccination, but as the real efficacy and safety of vaccines can be questioned, the opposite should also be taken into consideration and should be evaluated very cautiously (see “Six common misconceptions about immunization”).

One of the most controversial of these campaigns was the publication of a research paper in 1998 in which a link was reported between measles-mumps-rubella (MMR) vaccine and the development of autism in children. Following the publication of the paper, multiple large epidemiological studies were undertaken establishing that there was no link between MMR-vaccine and autism. The original paper was subsequently retracted by the publishing journal. Despite all the evidence, people continue to doubt the safety and efficacy of vaccines, opting out from vaccinating their children. The drop in the number of vaccinations has caused outbreaks of diseases that were previously very well contained, as to be effective at least 95% of the population needs to be vaccinated. One of the most recent is the spread of measles across Europe (> 500 cases reported in January 2017) and US (61 cases in the first quarter of 2017), where it was eliminated in 2000. In a world facing a post-antibiotic era and the increasing instances of cancer amongst several other diseases, there is no space to worry about life-threatening diseases that have been already defeated.

Blog written by Marco Derudas 

 

 

 

 

UK Dementia Research gains momentum


In March of 2012, then Prime Minister David Cameron announced the Prime Minister’s Dementia Challenge (see here), which included the pledge to “More than doubling overall funding for dementia research to over £66m by 2015.” The following year, and in recognition of the looming “tsunami of dementia” as a consequence of an aging global population the world’s first G8 dementia summit was held in London on the 11th December. This meeting involved researchers, drug companies and government ministers and set the ambitious target of identifying a cure, or a disease-modifying therapy, for dementia by 2025 (see here). The Prime Minister maintained momentum with the Prime Minister’s Challenge on Dementia 2020 (see here) “in order for England to be:

  • the best country in the world for dementia care and support and for people with dementia, their carers and families to live
  • the best place in the world to undertake research into dementia and other neurodegenerative diseases”
  • These lofty words and aspirations are actually being matched by actions, such as the establishing of the Dementia Platform UK (DPUK; see here) and the UK Dementia Research Institute (UK DRI; see here) as well as the National Institute for Health Research (NIHR) Dementia Translational Research Collaboration (TRC) which comprises four NIHR Dementia Biomedical Research Units as well as six NIHR Biomedical Research Centres with dementia-related research themes (see here).

JA 1For example, the DPUK (see Figure 1), which is led by Professor John Gallacher at the University of Oxford, aims to study different patients cohorts in order to characterise people with different types and stages of dementias. These population studies have the power to provide insights into the role of health and lifestyle on dementias by using the latest imaging and other technologies.

The DPUK is a public-private partnership established in 2014, with the MRC providing £12m funding over an initial period of five years with an additional £4m being contributed by six industry partners (Araclon Biotech, MedImmune, GlaxoSmithKline, Ixico, Janssen Pharmaceuticals and SomaLogic). In addition, an additional £37m has been contributed to fund networks of clinical research infrastructure focussed around Imaging, Informatics and Stem Cell Networks. An example of a major project that is using the DPUK is the NIHR-MRC Deep and Frequent Phenotyping study, a £6.9m project which aims to identify a combination of biomarkers that change in prodromal Alzheimer’s disease for use in proof of concept phase clinical trials.

The UK DRI is a network of research institutes (see Figure 2)

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established on the basis of £250m in funding from a combination of the Medical Research Council, the Alzheimer’s Society and Alzheimer’s Research UK (see here). The Head of the UK DRI, Prof. Bart de Strooper, and the hub of this research network, UCL, were announced in December 2016 (see here) with additional centres in Cardiff University, University of Edinburgh, University of Cambridge, Imperial College London and King’s College London being announced last month (see here). The initial round of UK DRI £55 million will fund 27 foundation programmes (details of which are available via links on the website). With the foundation programmes in place, the plan will be to attract additional scientists and rising stars from all over the world in order to integrate expertise across different areas of biomedical and translational research. Importantly, in addition to the existing focus on disease mechanisms as the basis for developing novel therapeutics, the DRI will add research into caring to its portfolio in 2018.

In an era when political words are seldom matched by significant actions, David Cameron’s commitment to dementia research has proved to be transformative and will continue in his recently-announced role as President of Alzheimer’s Research UK (see here). It is encouraging that Theresa May appears to be raising the profile of mental health (see here and here) yet only time will tell if her actions can come close to matching those of her predecessor.

Blog written by John Atack

 

Careers away from the laboratory bench


 

Over recent years there have been several articles and reports featuring graphics to highlight the careers taken by PhDs. You know the ones, with only the tiniest arrow leading to a professorial position (like the one below). Disheartening though this can be, what has always struck me the most is that the arrow with the greatest proportion of jobs is usually composed of the rather unhelpful “Careers outside science”. As I am currently considering my options I thought it would be useful to try and answer the question on my lips: “Just what are all these jobs and where can I find them?”

IB 1

Image adapted from “The Scientific Century: securing our future prosperity” produced by the Royal Society in 2010.

As luck would have it, I spotted an email for a careers event held at the Society of Chemical Industry (SCI) in London that offered a broad selection of presenters, which I hoped would shed some light on my query so I booked my (free) place and headed into London. The talks were highly illuminating, with each speaker detailing the steps of their career paths so far in addition to giving insights on what their jobs entail and how to go about getting into their field. For my part, I was most interested in the speakers whose careers had steered away from the laboratory though, if you are interested in following the academic route, I would highly recommend having a chat with Prof. Joe Sweeney, who delivered one of the best talks I have ever seen about what is (and isn’t) important about being an academic in the current research climate. I took the opportunity to network with a few of the presenters and have tried to highlight below what I learned about some of these “alternative” career pathways.

I first spoke to Dr. Samantha Alsbury, Head of Professional Development at The Organisation of Professionals in Regulatory Affairs (TOPRA). Interestingly, Samantha moved into her position at TOPRA after serving as a lecturer at the University of Greenwich. By gaining a teaching qualification and experience in co-ordinating academic programmes, she was in a strong position when the opportunity to join TOPRA came up. In addition to outreach, she is also responsible for the creation of training and development programmes for all career levels in the regulatory affairs (RA) profession. When speaking about careers in RA, Samantha neatly summarised it as “science, in a suit”. Along with the need to delve into the literature to get accurate data on drug efficacy and safety, most RA projects also include a significant amount of interaction with people; willingness to travel and strong communications skills are required to liaise between the various regulatory agencies, stakeholders, and even marketing departments involved in the drug development life cycle. Understandably, new entrants to the field often work on “lower” risk aspects, such as requests for amendments to clinical trial authorisations, or answers to questions posed by regulatory authorities. Once you have demonstrated competency at this level, exposure to higher risk projects such as Investigational New Drug filings where often millions of dollars are on the line. Later on, specialisation in areas such as compliance, operations, publishing, or even consulting, offer interesting career development pathways.

The same could be said for a career in publishing. Samantha Foskett, a Publisher at John Wiley & Sons, went over a couple of different career pathways available to scientists with an interest in gaining commercial experience but who also want to remain in direct contact with science and scientists. Samantha recommended looking for roles as an Assistant editor to start learning the ropes and building up contacts, then progressing to either, the more commercial-minded Journal Editors, or the more scholarly Associate Editors (more involved with peer review and manuscript decisions). She also made a point to mention the opportunities for growth currently in the industry because of the take up of new media and publishing technologies.

At the next networking opportunity, I spoke with Dr. Darren Smyth, a partner at IP firm EIP who offered an illuminating view on the kind of work involved in his career as a patent attorney. Darren emphasised the importance of detail and accuracy, as well as the flexibility to engage with a wide range of stakeholders in his day-to-day activities. A patent attorney will find themselves dealing with investors, large and small businesses, other patent examiners, and even liaising with solicitors and barristers if a dispute goes to trial. As with regulatory affairs, communication and strong research skills are very important, but the rewards are certainly worth the effort. Darren advised that, although the field is notoriously difficult to get into, these days there are numerous boutique firms in addition to the larger pharmaceutical companies where someone from a life sciences background could apply for a training position. Even then, it is a long road to becoming fully accredited, 4 to 6 years in most cases, and a large amount of private study would be expected in addition to working office hours. The exams are tough, with higher failure rates than you might be used to, and mostly essay based, however most firms are often supportive of good candidates and would try to help them overcome these difficulties.

Finally, I managed to have a chat with Dr. Nathalie Huther, a Business Development Manager for Arcinova, a contract research and development organisation based in Northumberland. Nathalie’s role is to serve as an intermediary between clients and company headquarters, using her technical knowledge to propose solutions to clients’ problems while also identifying areas of expertise or new technologies that could be used to enhance the services her company provides. In addition to technical experience, a willingness to travel, a talent for scouting new opportunities, and negotiating skills are key aspects of this role. In Nathalie’s case, these were acquired in her various roles as a laboratory scientist, then in marketing and sales force training in industry. Nathalie pointed out that a variety of job experience helps accelerate progression on this career pathway but, as it is a sales role, being able to deal with the pressure to make sales, as well as the pain of lost sales, is another key component to consider.

As you may have guessed, I left the SCI with a lot to think about! Please bear in mind that there are several career pathways I did not get to dive into on this occasion, including: Technical or Application Specialists, Clinical or Medical Science Liaisons, Clinical Trials Associates, and Data Analysts. I would say the take home message is to keep an open mind when thinking of alternatives careers choices. You might be surprised by what you find.

I would like to end with just a few pointers on how to approach a job search.

  • First and foremost is probably to update your online profile, be it on LinkedIn or ResearchGate. You never know who might be looking for someone just like you! Make sure to include the link on your CV, which should also be formatted appropriately for the type of job you are looking for.
  • Do a thorough analysis of your skills and try to categorise them in terms that recruiters in your field of interest will use, such as “Communication”, and “Project Management”. The Careers and Employability Centre at Sussex offers a range of tools that can help with this, including a Skills Checklist, and you can also arrange one-to-ones with advisors. Another resource recommended to me by a friend is the “Individual Development Plan” hosted at Science Careers. This is a free resource tailored for Life Scientists that are really unsure (yep, that’s me!) of what they would like to do, offering a prediction of what careers might suit their particular set of skills and interests.
  • Reach out to people in fields you are interested in via LinkedIn (remember that from the first point?) or ResearchGate and ask for “informational interviews”. These serve numerous purposes, principally, to provide you with information about what a job entails, and what skills you might want to brush up on before applying. These also allow you to start building up a network that can help you to land a job, offer career support when you get one, and perhaps even offer you bigger opportunities further down the line.
  • Keep your eyes peeled for opportunities in your network and don’t be afraid to apply, even if you don’t think you have enough experience. Recruiters have a habit of hanging onto CVs that catch their eye and can come back to you with alternatives that may not be openly advertised.

Blog written by Iain Barrett

References:

“The Scientific Century: securing our future prosperity” ISBN: 978-0-85403-818-3 © The Royal Society, 2010

(https://royalsociety.org/~/media/Royal_Society_Content/policy/publications/2010/4294970126.pdf)

 

TRPV6 In Prostate Cancer: What is the significance?


The transient receptor potential proteins (TRPs) are a family of ion channels involved in different cellular functions. TRP channels are ubiquitously distributed throughout the mammalian system. And based on their sequence homology they have been divided into six families: TRPC, TRPV, TRPM, TRPN, TRPA, and TRPP. TRP subunits assemble as homo- or hetero-tetramers to form cation selective channels which are activated by a wide range of stimuli including intra- and extracellular messengers, chemical, mechanical and osmotic stress, temperature, growth factors and by the depletion of intracellular calcium stores.

TRPV6 channel cDNA was cloned in 1999 from rat duodenum by expression cloning using Xenopus oocytes (Peng et al. 1999). Like other TRP family members it is necessary for a wide variety of physiological functions. TRPV6 expression is mainly confined to epithelial tissue of different organs such as digestive tract, kidney, testis, ovaries and skin. TRPV6 has a high calcium selectivity and is involved in the regulation of calcium homeostasis in the body. Published data have demonstrated its upregulation in cancer and correlation with the advanced stages in prostate cancer (stage pT2a and pT2b). However its role in the initiation or progression of most cancers is not yet understood. The in vitro oncogenicity of TRPV6 in prostate cancer has been proposed to operate via calcium signalling control of processes such as proliferation and resistance to apoptosis (Prevarskaya et. al., 2007)

Many publications over the years have demonstrated a correlation between TRV6 expression in prostate tissue and prostate cancer. Lehen (2007) have shown that Ca2+ entry via TRPV6 controlled proliferation directly and promoted apoptotic resistance in prostate cancer cells and concluded that the upregulation of TRPV6 may represent a mechanism for maintaining a higher proliferation rate. In view of the strong correlation between TRPV6 expression levels with the Gleason score >7 tumor grading, the channel represents a promising new therapeutic target prostate cancer treatment.

Conversely, other studies have shown that in healthy and benign human prostate tissue the expression levels of TRPV6 mRNA are very low if not undetectable. In 2012 Raphael et al used in situ hybridization methods to demonstrate that TRPV6 mRNA transcripts were undetectable in high-grade prostatic neoplasia and incidental adenocarcinoma but were increased in prostate adenocarcinoma (1B). Additionally, work by Wissenbach et al., (2004) on biopsies of prostate cancer tissue has shown that TRPV6 mRNA expression increases with the degree of aggressiveness of the cancer (1A), as assessed by the Gleason score and the degree of metastasic spread. Both studies suggest that expression levels of TRPV6 could be an excellent marker to predict the clinical outcome of prostate cancer.

Figure 1: Expression of TRPV6 in prostate cancer.

1A                                         1B

 

Figure 1 A. Northern blot analysis using cDNA probes of human TRPV6, TRPM4 and TRPM8 cDNA. (Ref). Both TRPm4 and TRPV6 transcripts are detectable in prostate cancer but not in benign prostate tissue (Biochemical and biophysical Research communication 322 (2004) 1359-1363).

Figure 1B. Immuno-histochemical staining of human prostate tissue using Anti-TRPV6 antibody. Very low expression of TRPV6 is observed in normal and benign hyperplasia (BHP) as opposed to significant expression in prostate adenocarcinoma (ADC 7). Adapted from Raphael, M. et al. (2014) Proc. Natl. Acad. Sci. U.S.A. 111, E3870.

In summary, the specific expression pattern in prostate cancer coupled with its physiological function as a calcium selective channel suggests that TRPV6 may be a promising drug discovery target for the possible treatment of prostate cancer.

 Blog written by H I Choudhury (Shamim)

References:

  • Maylis Raphael¨ et. al. (2012); Role of the TRPV6 channel in cancer. J Physiol 590.6 pp 1369–1376 1369
  • V Lehen’Kyi et al., (2007) TRPV6 channel controls prostate cancer cell proliferation via Ca2+/NFAT-dependent pathways Oncogene 26, 7380–7385
  • Wissenbach et al., (2004) TRPV6 and prostate cancer: growth beyond the prostate correlates with increase TRPv6 Ca+ channel expression. Biochemical and biophysical Research communication 322, 1359-1363
  • Thomas Fixemer et al., (2003) Expression of the Ca2þ-selective cation channel TRPV6 in human prostate cancer: a novel prognostic marker for tumor progression. Oncogene (2003) 22, 7858–7861
  • Natalia Prevarskaya et. al., (2007) TRP channels in cancer Biophysica Acta 1772, 937–946

 

 

Spoilt by choice – Which CYP-specific probe to use?


The use of in vitro metabolic surrogates (e.g. microsomes, recombinant CYP450s, cyro-preserved hepatocytes) is now widespread in drug discovery and evermore refined methods improving the utility of these model are in constant development. However, as any IVIV extrapolation is always subject to the reduced complexity of those model systems it is vital to understand their limitations (e.g. reduced expression of CYP3A4, PXR and CAR in CACO-2s; rapid loss of metabolic competence, canalicular and basolateral efflux transport in freshly isolated hepatocytes.) to avoid misinterpretation of data

In order to predict possible Drug-Drug Interactions (DDIs) it is necessary to understand the relative contribution of individual CYPs to the overall phase I metabolism of an NCE and to this end Relative Activity Factor (RAF), developed twenty years ago (1), has been used alongside inhibition approaches to elucidate the CYP reaction phenotype. Individual recombinant CYPs (rCYP), expressed in and isolated on bacterial membranes, can be used to measure the clearance (CLrCYP) of a CYP-selective probe.  The probe is then assayed in microsomes to obtain CLHLM and a correlation made of the relative levels of clearance in each system (RAF) for that particular CYP.  Once established the RAFs for each CYP can be used to assess the relative contribution of the individual CYPs to the metabolism of a NCE in microsomes.

Highly diverse RAFs are generated between various institutions due to the variability of microsome batches, rCYP expression levels and assay conditions but as long as these variables are maintained within any given laboratory the RAFs should generate internally consistent data. However, whilst it has been known for some time that the promiscuity of CYPs may be facilitated by multiple binding regions in the active site (2), until recently no one has directly assessed the effect of probe choice on whether the scaling from rP450 to HLMs is consistent between various P450-selective probe reactions and those of the test NCE by that P450 isoform.

To demonstrate this issue Sui et al (3) generated RAFs for 2C9 and 3A4 from three CYP-selective probes each.

CYP CYP-selective substrate
2C9 Diclofenac

Tolbutamide

Warfarin

3A4 Midazolam

Nifedipine

Testosterone

Using the RAF generated by one probe the predicted microsome clearance (CLHLM (p)) was calculated for the other two probes then compared with the directly measured CLHLM for those probes.  This was performed in a crossover manner for each of the probes.

The CLrCYP and CLHLM were derived using standard Michaelis-Menton kinetics

snip 1

The RAF was then generated as a ratio between CLHLM and CLrCYP.snip 2

In each crossover the CLHLM (p) was then simply calculated as the measured clearance of the test probe with rCYP multiplied by the RAF.

snip 3

These predicted CLHLM(p) values were then subsequently compared with the actual measured CLHLM to give a value for the Intersystem Clearance Ratio (ICR)

snip 4

Fig 1. Crossover analysis of ICRs based on the RAFs derived from A = Diclofenac, B = tolbutamide and C = Warfarin for 2C9 and D = Midazolam, E = Nifedipine and F = Testosterone for 3A4

marcus

Whilst it is clear to see the effects of probe choice on ICR this then has a knock on effect when determining the relative CYP contribution to the metabolism of a test NCE. Fig 2. Shows the comparison of % relative contributions for CYP metabolism of substrates with RAFs generated from various combinations of 2C9 and 3A4 probes (RAFs generated 1A2, 2C19, and 2D6 from single probe throughout)

Fig 2. Variations in relative CYP contribution (fm, fraction of total metabolism attributed to specific CYPs) calculations subject to probe choice

marcus second

With Physiologically based pharmacokinetic (PBPK) modelling and simulation playing an increasingly large role in drug development the accuracy of the input data is therefore crucial to the predictive accuracy of a model. Here, the generation of fm is demonstrably affected by probe choice and if the RAFs for a given probe/CYP pair are not appropriate for the test NCE, deviations in fm from the true value may significantly impact, for instance, generation of risk assessments for drugs as potential DDI victims.

This study would suggest that for test NCEs, fm should be generated using various combinations of a limited number of CYP-specific probes which represent the full range of specific substrate binding sites for a given CYP.  Presently our understanding of CYP binding site multiplicity is limited although studies indicate that we may soon have probe/inhibitor pairs for discreet pharmacophores (4, 5) facilitating increased accuracy of fm prediction.

Blog written by Marcus Hanley

References

  1. Clarke S. E. (1998) In vitro assessment of human cytochrome P450. xenobiotica, 1998, vol. 28, no. 12, 1167-1202
  2. Korzekwa, K R (1998) Evaluation of atypical cytochrome P450 kinetics with two-substrate models: evidence that multiple substrates can simultaneously bind to cytochrome P450 active sites. Biochemistry, 24 March 1998, Vol.37(12), pp.4137-47
  3. Siu Y.A (2017) Impact of Probe Substrate Selection on Cytochrome P450 ReactionPhenotyping Using the Relative Activity Factor. Drug Metab Dispos 45:183–189
  4. Kumar V. (2006) CYP2C9 Inhibition: Impact of Probe Selection and Pharmacogenetics on in Vitro Inhibition Profiles. Drug Metab Dispos Vol. 34 (12):1966-1975
  5. Foti R.S. (2008) CYP2C19 Inhibition: The Impact of Substrate Probe Selection on in Vitro Inhibition Profiles. Drug Metab Dispos Vol. 36 (3): 523-528

Organs-on-a-chip: The future of drug discovery?


Organs- on-a-chip were initially established at the Wyss Institute for Biologically Inspired Engineering located at Harvard University. The polymer chips containing microtubules are designed to recapitulate the structural, functional and mechanical attributes of human organs and they are only the size of a USB stick (Wyss Institute (2017)).

The chips are not just incredibly cool but also provide an innovative platform for drug discovery, which was recognised by the National Centre for the Replacement, Refinement and Reduction of animals in research (NC3Rs) back in 2012 (3Rs (2012)). The fact that the organs-on-a-chip mimic multiple aspects of the human body means that they could one day be used as an alternative approach to in vivo testing – a controversial but currently essential aspect of drug development.

The lung-on-a-chip, just one of the many organs developed, reconstructs the alveolar-capillary interface of the lung (Huh, D.et al (2010)). A central porous membrane is coated in extracellular matrix proteins that are present in the human lung. One side of the membrane is lined with alveolar epithelial cells isolated from a human lung and human pulmonary microvascular endothelial cells cover the other. The principal compartment allows for air to flow over the epithelial cells and for a blood-like solution containing nutrients to run beneath the endothelial cells. A vacuum on either side of the membrane causes the cells to stretch, in term conveying the movement experienced in the lung when we breathe.

 

olivia 1

Figure 1: Lung-on-a-chip diagram From Keane, J. (2013)

This model has proven to replicate a lung infection, where white blood cells migrate from the blood-like solution through onto the epithelial side and are observed engulfing bacteria present in the air space using time-lapse fluorescence microscopy (Huh, D.et al (2010)). Small airways-on-a-chip with its goblet and ciliated epithelial cells can be used to model diseases like chronic obstructive pulmonary disease (COPD) and asthma. Addition of interleukin 13 (IL-13) to the epithelium further replicates an asthmatic phenotype inducing goblet cell hyperplasia and cytokine hypersecretion. A paper in Nature has reported to be able to reverse this response with an inhibitor of the JAK-STAT pathway involved in the signalling of IL-13, showing the application of these models in the screening of new treatments (Benam, K. Villenave, R. et al. (2016)).

The next focus is the humans-on-a-chip, which utilize an automated device to connect multiple organs-on-a-chip via a shared vascular network (figure 2). This platform would enable scientist to investigate the pharmacokinetics and pharmacodynamics of a drug in a relevant system (Abaci, H.E. Shuler, M.L. (2015)). Whereby drugs could be administered via the lung-on-a-chip, absorbed by the gut-on-a-chip, metabolised by the liver-on-a-chip and excreted by the kidney-on-a-chip while accessing the efficacy and any toxicity throughout.

Olivia 2

Figure 2: Human-on-a-chip schematic From Mok, J. (2015)

An interesting application of this technology is in the scope of personalized drugs. A chip can be developed with an individual’s cell to determine personal response to a drug, providing a tailor made drug with optimal efficacy (Hamilton, G. (2016)). This notion can also be implemented to clinical trials, where potential new drugs could be tested on cells from a certain genetic populations or on cells from children for paediatric medicines. This technology still has a way to go but one day it may transform the drug discovery process.

Blog written by Olivia Simmonds

References

Abaci, H.E. Shuler, M.L. (2015). Human-on-a-chip design strategies and principles for physiologically based pharmocokinetics/pharmacodynamics modeling. Integr Biol (Camb). 7 (4), 383-391.

Benam, K. Villenave, R. et al. (2016) Small airway-on-a-chip enables analysis of human lung inflammation and drug responses in vitro Nature Methods. 13 (2), 151-157

Hamilton, G. (2016). Body parts on a chip. Available:  https://www.ted.com/talks/geraldine_hamilton_body_parts_on_a_chip. Last accessed 20th April 2017.

Huh, D.et al (2010) Reconstituting Organ-Level Lung Functions on a Chip Science. 328, 1662-1668

Keane, J. (2013) The End of Drug Testing on Animals, Lung-on-a-Chip Device. Available: http://www.industrytap.com/lung-on-a-chip-device-to-end-drug-testing-on-animals/2160. Last accessed 21st April 2017

Mok, J. (2015) Organs-on-Chips Emulates Human Organs for Better Biomedical Testing. Available: https://thenewstack.io/organs-on-chips-emulates-human-organs-for-better-biomedical-testing/. Last accessed 21st April 2017

Wyss Institute (2017)Human organs on a chip. Avalible: https://wyss.harvard.edu/technology/human-organs-on-chips/. Last accessed 21st April 2017.

3Rs (2012). 3Rs Prize winners. Available: https://www.nc3rs.org.uk/3rsprizewinners. Last accessed 21st April 2017.