19th RSC/SCI Medicinal Chemistry Symposium

I recently attended the 19th RSC/SCI Medicinal Chemistry Symposium held at Churchill College, University of Cambridge (UK) – this was the first medicinal chemistry symposium I have attended since joining the field approximately 3 years ago, and it certainly didn’t disappoint. The symposium was held over 4 days, with the first day dedicated to a medicinal chemistry workshop for early career researchers (those with 5 years or less experience within medicinal chemistry). I found the medicinal chemistry workshop a good learning experience – we started from a series of hits and had to try to progress at least one compound into a preclinical candidate. The team that I was working in came 2nd out of 7, just being pipped to the post for 1st place.

Mark 1

Introduction to Technical Programme

 The technical programme started on the second day, and from the outset the talks were quite diverse with projects from many therapeutic areas being discussed, with several first disclosures being presented. There was a dedicated Neglected Tropical Diseases session that was webcast live through the RSC website, highlighting a range of diseases that require much more attention than they currently receive. Although a lot of great medicinal chemistry was discussed, it was a talk by Gianni Chessari from Aztex Pharmaceuticals that I found particularly fascinating. Gianni described a fragment-based screening approach using PyramidTM for the discovery of inhibitors of apoptosis proteins (IAP). He described structure-based hit optimization utilizing computational and NMR studies – by analysing the confirmation of their hit compounds, they were able to increase binding affinity and subsequently develop a potent non-peptidic IAP antagonist ASTX660 that is currently being tested in a Phase 2 clinical trial.

Overall I found this conference a great learning experience and a good opportunity to meet like-minded individuals from both academia and industry – I particularly enjoyed the opportunity to network at the Gala Dinner in the impressive surroundings of St John’s College!

Mark 2

Gala Dinner at St John’s College

Blog written by Mark Honey






Alzheimer’s Disease – Dopamine first

Alzheimer’s disease (AD) is a progressive neurodegenerative brain disorder that causes a significant disruption of normal brain structure and function. At the cellular level, AD is characterized by a massive neuronal loss that primarily affects the hippocampus and cortex, mainly due to the accumulation of intracellular neurofibrillary tangles and extracellular amyloidal neuritic plaques.


Fig.1 -Schematic representation of AD-related mechanisms (Medicinal Research Reviews · 2013)

The hippocampus is a critical brain structure for memory development and damages in this area are believed to be the primary cause for memory loss in AD patients. However, progressive structural alterations in different brain areas may play a pivotal role in the worsening of memory and cognitive dysfunctions. Consistent with these observations, several alterations in the dopaminergic system have been reported in AD patients, together with reduced levels of dopamine (DA) and its receptors. Moreover, DA is a well-recognized modulator of hippocampal synaptic plasticity and its binding to dopaminergic receptors in the dorsal hippocampus is a major determinant of memory encoding.

A recent study published on Nature Communications (DOI: 10.1038/ncomms14727) highlighted how, in a mouse model of AD, at a stage when no Ab-plaque deposition, hyperphosphorylated tau tangles or any sign of neuronal loss in cortical and hippocampal regions has yet occurred, a specific apoptotic process is taking place in the dopaminergic neuronal population in ventral tegmental area. The loss of dopaminergic neurons is paralleled by a reduced outflow of DA in the hippocampus, thus contributing to the deficits of hippocampus-dependent memory and synaptic plasticity, as well as impairment in reward processing. These symptoms are improved by stimulating the dopaminergic system with the administration of L-DOPA or the reduction of its endogenous degradation.

Although the abovementioned process has been observed in an experimental model of AD, it might provide an interesting explanation to recent evidences in AD patients, indicating that the clinical diagnosis of dementia is associated with early non-cognitive symptoms, such as depression and apathy. Based on that, changings in the mood of AD patients would be not a consequence of this pathology but rather an alarm for an early stage development of AD, confirming the strict correlation between depression and subsequent loss of memory.

This picture is somehow symmetrical to what researchers involved in Parkinson’s disease and although the molecular mechanisms underlying early dopaminergic neuron degeneration in the ventral tegmental area remain to be elucidated, these results suggest DA as an important player to consider in the context of AD.

Blog written by Samuele Maramai

A Word to the Wise about Ketamine

Major depressive disorder (MDD), also known simply as depression, and its impact on functioning and well-being has been compared to that of other chronic medical conditions such as diabetes. The World Health Organization estimates depression as the fourth highest burden of disease in the world1 .

Sri 1

Figure 1: Proposed neurobiological model of depression2

Prolonged stress and depression alter prefrontal glutamate release and reduce glutamate uptake, leading to increased extracellular glutamate and excitotoxicity3. High levels of extracellular glutamate precipitates neuronal atrophy through dendritic retraction4, reduced dendritic arborization5, and reduced synaptic strength. An example of the effect of prolonged stress on dendritic arborization and length in rats is shown on the right (Fig. 1).

Research on antidepressants has achieved little success in developing fundamentally novel antidepressant mechanisms, leaving psychiatrists with relatively few pharmacologic options. Several antidepressants that are currently in use are mainly targeting the monoaminergic system where substantial numbers of patients are failing to achieve a sustained remission6. Moreover, conventional antidepressants are only beneficial when prescribed over a long- term period. It is clear that we are in urgent need to find a rapidly acting antidepressant with robust efficacy in patients who are resistant to traditional antidepressants.

Sri 2Ketamine is a drug used illicitly as a hallucinogen and was first tested in humans in 1964. It was approved 1970 in the USA as a surgical anaesthesia that was used in Vietnam War due to its safety7. Ketamine can be a prototype for the new generation of antidepressants by showing good efficacy in patients who are refractory to the existing treatments. Low dosages of ketamine reduce depression symptoms within 4 hours of intravenous administration in severely treatment-resistant depressed patients8.

Ketamine exhibits promising antidepressant effects even in patients with bipolar disorder and patients with severe symptoms that did not respond to ECT9. A critical obstacle to the broader study and implementation of ketamine treatment for depression is the lack of clarity as to how to sustain its antidepressant effects. Pilot studies suggest that ketamine may be sustained by repeated intermittent administration with persistence of the antidepressant effects for longer periods in some patients10.

Briefly, ketamine works by enhancing synaptic plasticity (mechanism through which neural circuits regulate their excitability and connectivity) through regulating AMPA and NMDA receptors.

Sri 3

Figure 2: Prefrontal synaptic connectivity during normal mood, depression, and after remission (Abbreviations: ⦿, activate; ∅, block; , decrease; AMPA, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid; BDNF, brain-derived neurotrophic factor; GABA, γ-aminobutyric acid; mTORC1, mammalian target of rapamycin complex 1.)

There have been some clinical trials where ketamine shows acute efficacy 11 in treating TRD (treatment resistant depression) , bipolar depression12 and major depressive disorder with suicidal ideation13, but the number of subjects in these trials ranges from 20 to 57 patients. Inverse-Frequency Analysis of eight million reports from the FDA Adverse Effect Reporting System (FAERS) revealed that patients who received ketamine had a significantly lower frequency of reports of depression than patients who took any other combination of drugs for pain14.

It is encouraging that FAERS makes a case for study of ketamine as a psychiatric drug but there are financial and ethical obstacles for a larger scale clinical trial to validate further the safety and efficacy of Ketamine. To date, Ketamine is not only the most extensively studied NMDA antagonist, with 12 published randomized clinical trials, but is the only NMDA antagonist to date consistently demonstrating antidepressant efficacy across multiple trials15

While Ketamine efficacy and safety are under caution, forthcoming ketamine research should continue to examine three major concerns: 1) elucidating ketamine’s mechanism of action; 2) understanding the administration profile necessary to provide a sustained therapeutic benefit; and 3) examining ketamine’s safety profile, particularly with repeated and likely low-dose administration. Knowing Ketamine can be a drug of abuse, it is difficult to argue its future as a potential drug to treat depression.

Blog written by Srini Natarajan

Nitrogen-Centered Radicals: A Forgotten Species?

In the late 1990s I was working on a chemistry project involving cascade reactions of C-centred radicals (CCRs). At that time, N-centered radicals (NCRs) were little used compared to their C-centered relatives and I was wondering if things had changed much since then.

Considering that the first example of the Hofmann-Löffler-Freytag reaction was reported in 18831 it seems that the development of the chemistry of NCRs has been fairly slow. More recently, in 2008, Zard2 described NCRs as a forgotten species with significant synthetic potential in a comprehensive review of intramolecular NCR cyclisation. NCRs have suffered from limitations because traditional methods for their generation have relied on the synthesis of N-X precursors and required harsh conditions for bond homolysis (Scheme 1, path A). New developments in metal catalysis (path B) and visible-light photocatalysis (path C) have resulted in greater use of NCR chemistry (for C-N bond formation) and advances in this field were reviewed by Zhang3 last year.

Micheal 1

 Scheme 13 Strategies in C-N bond formation based on NCR chemistry

Generation of NCRs using visible-light photocatalysis is particularly attractive due to low catalyst loading and mild conditions, with most reactions occurring at room temperature without the need for highly reactive radical initiators. This technology has been widely applied to radical amination chemistry in the last three years. An interesting example of this approach entitled ‘’Visible-Light-Mediated Generation of Nitrogen Centered Radicals: Transition Metal Free Hydroimination and Iminohydroxylation Cyclisation Reactions’’ was published by Leonori.4 One of the transformations described is a 5-exotrig cyclisation of iminyl radicals to give pyrrolines without the use of a transition metal catalyst (Scheme 2). A diverse range of oximes were converted to the corresponding pyrrolines, in good yields, and bicyclic heterocycles were also prepared using this methodology.


Micheal 2 

Scheme 24 Visible-light mediated hydroimination

The mechanism of this reaction involves single electron transfer (SET) reduction of the aryl oxime ether (A) by a visible-light exited photocatalyst (*PC), followed by N-O bond fragmentation to give iminyl radical (D) which can then cyclise onto the pendant alkene (Scheme 3). The role of cyclohexadiene (CHD) is to reduce the intermediate radical (E), followed by a second reduction of the photocatalyst (PC), which is then irradiated (PC®PC*) completing the catalytic cycle. Cyclic voltammetry studies suggested that that the key single electron transfer (SET) reduction, by excited state organic dye eosin Y, would only be efficient when using nitro-substituted aryl oxime ethers (1a-1d) with suitable reduction potentials. The 2,4-dinitro-aryl oxime (1a) was found to be the best substrate.

Micheal 3.png

Scheme 34 Proposed photoredox cycle and electrochemical studies. EY = eosin Y, ppy = 2-phenylpyridine

It was found that a different activation mode could be used to generate the iminyl radical without the presence of a photocatalyst (Scheme 4). When a solution of the aryl oxime ether (2a) and triethylamine in acetonitrile was irradiated with visible-light in the presence of CHD the previously observed hydroimination product (3a) was obtained, and also an unexpected iminoalcohol (4a). When CHD was not in the reaction mixture iminoalcohol (4a) was the main product. The mechanism proposed for this process involves formation of an unusual electron donor-acceptor complex (5) which undergoes SET giving the dipolar species (6). This species can then fragment, and undergo 5-exo-trig cyclisation to give radical (7). If the radical is not reduced by CHD it can be oxidised by attacking the nitro group (8) which after N-O bond homolysis, and hydrogen atom abstraction, gives the iminoalcohol (4a). Evidence for the source of the oxygen was provided by generation of 2-NO-4-NO2C6H3OH (10) from the reaction which was in contrast to 2,4-dinitrophenol that was produced from the original hydroimination.

Micheal 4

Scheme 44 Initial findings and proposed reaction mechanism for the iminohydroxylation

The chemistry of NCRs has been developing in recent years, but they still remain less well used than CCRs. Significant problems, such a functional group compatibility, need to be solved before they can become routinely used for C-N bond construction alongside traditional ionic chemistry. Visible-light photocatalysis seems very likely to play a role in future developments.

Blog written by Michael Annis


1. J. L. Jeffrey and R. Sarpong, Chem. Sci., 2013, 4, 4092

2. S. Z. Zard, Chem. Soc. Rev., 2008, 37, 1603

3. T. Xiong and Q. Zhang, Chem. Soc. Rev., 2016, 45, 3069

4. J. Davies, S. G. Booth, S. Esaffi, R. A. W. Dryfe and D. Leonori, Angew. Chem. Int. Ed. 2015, 54, 14017

Chemical tools on trial: recent misleading information cases

For this week’s blog, I have picked it a still-hot and enjoyable Nature article by Monya Baker.1

How many times have you had screening results which make no sense to you end in frustration and unexplicable conclusions? How many times have you encountered that your chemical tools (hits) are neither as you thought, behaved oddly or even conducted regular quality controls on them and enough analytical tests? Read more to recognise unexpected setbacks.

The author goes through a few examples where researchers have encountered, for example, that chemical probes hitting specific targets suddenly became inactive when alternatives suppliers came onto stage. A futher realisation that one isomer was presented in different proportions if it was mixed with its other enantiomer (mirror-image like compounds sharing the same molecular formula) altering its activity leading to discover that sometimes, researchers do not know what they have in their hands if too much trust is put on commercial sources or the lack of further structural corroborations.2

When screening large compound libraries and identifying hits, the presence of false positives, impurities, degradation, mixed-up and messed-up stocks could also lead to infructouos crusades. Especially when liquid stocks are kept for months or years, at variable temperatures, the effect of poor solubility, side-reaction impurities, solvent effects and cockails of natural product mixtures amongst others. 3

Suggested online resources like: Chemical Probes Portal, Probe Miner and Probes and Drugs Portal 4 have been created to be used as a good first port of call toolbox with advice and information on which chemicals or drugs to use as well as public assessments.

The infamous case of BOSUTINIB, an approved cancer drug which was sold by nearly 20 suppliers with the chemical substituents wrongly located (please see ‘Spot the difference’ cartoon) has created havoc. jose

Both bosutinib and the other mis-identified isomer target cell-signalling proteins but with different potencies putting under trial numerous papers which reported data on the isomer of bosutinib rather on itself.5

Another researcher, Kim Janda caused an uproar when in its group they could not synthesise a molecule described to boost cell production of a powerful natural antitumor protein, TRAIL. The distributors had perpetuated the mistake in the original publication and after even clinical trials and patents were issued, he filled a patent with the proposed new active version of the TIC10 structure. 6

Another case emphasises how activity showed a big drop after small changes in contrast with bigger changes. Scientists realised that the present of Zn in their preparation was responsible for this activity without effect from the organic molecule whatsoever. Copper or Palladium from its use in catalytic reactions have been reported showing false positives.7

Even the present of NMP (N-methyl-2-pyrrolidone) a polar solvent used in some cases for keeping chemical probes in solution has recenlty showed anticancer activity in control tests, with potential implications in misleading the potency of the substances contained on it. 8

A list of common-sense leading practises to suppress these errors are given in the paper:

  • Use and buy chemicals by their CAS number (unique identification to chemical structures)
  • Request a detailed quality control certificate from external suppliers
  • Place enquires about the synthetic method used
  • Perform independent or in-house analysis upon receipt of the starting chemicals and reagents
  • Structural forms, chiral compounds, potential ambiguity in their chemistry substitution, then determine their optical purity and apply chiral chromatography techniques to isolate single forms.
  • If possible, previous in-house synthesis and determination with structural characterization.

Mismatching results, not-well documented suppliers, dubious chemical insertions (not well validated) as well as poor purities and the presence of contaminants (even at low concentrations) are always to blame for cases like those described in the article over the years. Albeit the final responsibility lies on the chemist’s team who need to be reassured by exploring and conducting further unequivocal tests.

The views represented in this blog are the author’s own.

Blog written by Jose Gascon


  1. https://www.nature.com/nature/journal/v548/n7668/pdf/548485a.pdf
  2. Huber, K. V. M. Nature, 508, 222–227 (2014).
  3. Bisson, J. et al. J. Med. Chem. 59, 1671–1690 (2016)
  4. See: Chemical Probes Portal (www.chemicalprobes.org ), Probe Miner (www.probeminer.icr.ac.uk) and Drugs Portal (www.probes-drugs.org )
  5.  https://www.chemistryworld.com/news/pfizers-response-to-compound-fraud-spotlights-quality-issues-/9234.article
  6. https://phys.org/news/2014-05-chemists-cancer-drug-candidate.html ,Oncotarget, 2014, 5(24): 12728–12737 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4350349/
  7. Hermann, J. C. et al. ACS Med. Chem. Lett. 4, 197–200 (2013)
  8.  Shortt, J. et al. Cell Rep. 7, 1009–1019 (2014).









Pronucleotides Assemble! A multifunctional catalyst designed to stereoselectively synthesise prodrugs

Nucleosides have emerged as a key chemical class in successful antiviral and anticancer drugs with nearly half of currently marketed drugs possessing these cores.1 However, the biologically active nucleoside phosphates, which are generated in vivo by phosphorylation, are poor drug candidates due to issues of permeability and stability. One pronucleotide strategy developed to address these challenges has been described by McGuigan. His ProTide platform introduces a 5’-arlyoxy phosphoramidite to the drug candidate which can result in improved cell permeability and rate of phosphorylation compared with non-phosphoramidite containing nucleosides.2,3

However the introduction of the phosphoramadite in the prodrug can have a significant effect on the potency, toxicity and rate of metabolism, effects which can be associated with the stereochemistry at the phosphoramidite phosphorus. Unlike for carbon chemistry, where stereocontrol is a sophisticated branch of asymmetric catalysis, p-chiral chemistry is far less developed. Although methods do exist to steer products towards a preferred p-chiral isomer, such as dynamic kinetic asymmetric transformation (DYKAT) using chiral auxiliaries or desymmetrisation of achiral species,3 these approaches have significant drawbacks with the former suffering from poor selectivities and low catalytic turnovers, whilst the latter is often a complicated multistep synthesis.

In addition to the stereo-isomeric challenges during prodrug assembly there also remains the challenge of chemoselectivity for 5’ versus 3’ phosphoramidation. With these challenges in mind, I wanted to highlight an excellent paper published by a team from the process research and development group of Merck & Co., USA, where they report the first good example of a catalyst being designed to address the issue of stereo- and chemoselectivity in the synthesis of pronucleotide prodrug candidates. In their paper they focused on a hepatitis C virus RNA polymerase inhibitor currently in late stage clinical trials (MK-3682, Figure 1).4

Figure 1Figure 1: General phosphoramidation scheme and the best in-class catalysts developed to effect the coupling. Yield is the total yield of phosphoramidite isolated, chemoselectivity for 5’ vs 3’ is represented by ratio 5’:3’and d.r is the ratio of P(R) to P(S).

Using mechanistic studies, computational modeling and an understanding about the enzymatic mechanism of P-O bond formation in the phosphorylation of nucleosides, the team successfully developed several small molecule organic catalysts that mimic the concomitant series of activation modes used by enzymes to effect the P-O bond formation. Early studies identified carbamates as a privileged class for controlling stereo- and chemoselectivities with catalyst (R)-B being the best of the first generation catalysts developed. Using computational modeling the carbamate was theorized to carryout 3 roles; leaving group activation, general base catalysis and oxyanion stabilization via a pentavalent transition state, giving rise to a 2.3kcal/mol differentiation between the desired R-stereochemistry and the S-stereochemistry at the phosphoramidite phosphorus (Figure 2). Catalyst I, the best of the catalysts reported, evolved from a conscious effort to increase the transition state differentiation by decreasing the entropy of the system via linkage of catalyst (R)-B. As highlighted in Figure 1 the linked catalyst, Catalyst I, was able to achieve excellent yields and high selectivities for both the desired 5’ product (99:1 in favour of the 5’ product) and with a d.r (of 99:1) in favour of the desired P(R) isomer.

Figure 2Figure 2: Transition state model showing multiple catalyst modes of action. Reproduced from reference 4.

This work demonstrates an excellent step forward in the controlled synthesis of pronucleotide prodrugs by continuing to employ rational design beyond the discovery phase SAR, well into the late stage development of the prodrug. Moreover the published work is an elegant example of the power of using an interdisciplinary approach to solve chemical problems via a rational design cycle.


Written By Jason A. Gillespie



  1. P. Jordheim, D. Durantel, F. Zoulim, C. Dumontet, Nat. Rev. Drug Discov. 12, 447–464 (2013).
  2. Cahard, C. McGuigan, J. Balzarini, Mini Rev. Med. Chem. 4, 371–381 (2004).
  3. J. Sofia et al., J. Med. Chem. 53, 7202–7218 (2010).
  4. A. DiRocco et al., Science, 356, 426–430 (2017).

CrispR technology: Designer babies and Swine Donors

Nisha 1


The last decade has seen tremendous progress in ‘gene-editing’ techniques to make them more accurate, fast and replace the potential hit-and-miss methods of genetic engineering over the past few decades. The new technique called CrispR (pronounced Crisper!!) that emerged from pioneering work in bacterial cells in the early 2000s has evolved over the years to find applications in biotechnology, fundamental research and medical science.

The preliminary CrispR toolkit involved a RNA molecule called gRNA (guide-RNA) that is homologous to the area of DNA you wish to modify and a nuclease Cas9. The gRNA, as the name suggests, guides Cas9 to the region of interest to create a double strand break (DSB). The native cellular repair machinery: NHEJ (Non-homologous end joining) or HR (Homologous recombination), then repairs and introduces the necessary changes using a template DNA. Once the basic methodology of this technique was established, CrispR was used widely for gene-editing in almost every living organism from cells to bacteria, insects to plants and animals to now human embryos Doudna & Charpentier 2014; Sander & Joung 2014).

Nisha 2

Two studies published in the recent months show promising results with CrispR-mediated gene editing in embryos. The first study at Oregon Health & Science University (OHSU) and Salk Institute in the US, focuses on using CrispR for genome-correction to avoid transmitting genetic disorders in human embryos (Ma et al. 2017). The authors were keen on targeting genetic disorders that manifest in late-adulthood such as MYCBP3 gene mutation, which leads to hypertrophic cardiomyopathy (HCM). This genetic disease occurs in one in 500 and is a common cause of death in young athletes. The scientists CrispR-ed the mutated allele of MYCBP3 in embryos from IVF donors and replaced it with the wild-type maternal allele instead of a synthetic DNA template. By injecting the Crisp-R-Cas-9 cocktail along with the sperm (from a HCM male patient) into a wild-type oocyte (source of maternal DNA), they achieved increased correction rates and avoided mixed populations in the resulting embryos. Additionally, whole genome sequencing identified very few off-target effects of the gene editing, promising a potential break-through in germ line gene therapy. For ethical reasons these embryos could not be implanted into a uterus to develop a baby.

Yet another promising venture for CrispR was in the organ-transplant arena, where scientists in China have successfully CrispR-ed the retroviral gene in pigs (Niu et al. 2017). The study has attracted huge media attention as it promises xeno-transplants from pigs to humans without the fear of an immune attack. Traditionally such transplants are rejected in humans, as the PERV gene from pigs leads to retroviral infection in humans. The scientists attempted to target 25 copies of the PERV-gene (Porcine Endogenous Retrovirus) all at once using CrispR in adult cells, that would be later fused with ova (female reproductive cell) to grow into embryos and implanted in sows. Although, they met with disappointment in their initial trails due to ‘shredded-genomes’ in the targeted cells, Laika – the PERV inactivated piglet, was born after using a specific cocktail that kept the Crisp-R cells alive despite the aggressive gene-editing. Many other similar studies are underway exploring organ transplants from swine donors, by modifying their genome to ‘humanise’ them for successful transplants (Petersen et al. 2016; Martens et al. 2017) . While controversies continue in the field, if gene editing is required to replace anti-viral drugs in such a transplant, CrispR surely shows immense potential in the clinic.

Owing to the recent discoveries this gene-editing tool is now under the scrutiny of ethical committees and policy makers, as they fear a domino effect and the advent of ‘designer babies’. Nature, earlier this month published a report that marked down this technology due to the unintended mutations it caused in-vivo in a mice experiment (Schaefer et al. 2017). The study asserts the importance whole genome sequencing if these tools were to be applied in ‘real-people’. Although geneticists are not unaware of the potential pitfalls in genome editing, if Crisp-R will survive these hurdles only time will tell.

Blog written by Nisha Peter


Doudna, J.A. & Charpentier, E., 2014. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science (New York, NY), 346(6213), pp.1258096–1258096.

Ma, H. et al., 2017. Correction of a pathogenic gene mutation in human embryos. Nature, 72, p.1117.

Martens, G.R. et al., 2017. Humoral Reactivity of Renal Transplant-Waitlisted Patients to Cells From GGTA1/CMAH/B4GalNT2, and SLA Class I Knockout Pigs. Transplantation, 101(4), pp.e86–e92.

Niu, D. et al., 2017. Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science (New York, NY), p.eaan4187.

Petersen, B. et al., 2016. Efficient production of biallelic GGTA1 knockout pigs by cytoplasmic microinjection of CRISPR/Cas9 into zygotes. Xenotransplantation, 23(5), pp.338–346.

Sander, J.D. & Joung, J.K., 2014. CRISPR-Cas systems for editing, regulating and targeting genomes. Nature Biotechnology, 32(4), pp.347–355.

Schaefer, K.A. et al., 2017. Unexpected mutations after CRISPR-Cas9 editing in vivo. Nature Methods, 14(6), pp.547–548.

Fabulous Fluorine in Medicinal Chemistry

Since the FDA approved the steroid fludrocortisone, the first fluorine-containing drug, in 1955, the number of fluorine-containing drugs appearing on the market has rapidly risen to approximately 25% of drugs.1 These include the blockbuster drugs Prozac, Lipitor and Prevacid, Fig. 1. This may seem like an unusual trend considering fluorine-containing natural products are quite rare, so why is it that fluorine is so abundant in drugs? When you consider the unique chemical properties that fluorine has, the reason for a drug designer’s love of fluorine becomes clearer.

Catherine 1

Fig. 1: Examples of fluorine-containing drugs

Fluorine is a small, highly electronegative and lipophilic atom. The incorporation of fluorine into a molecule is an increasingly popular strategy to improve drug potency. Fluorine substitution can enhance potency and impact target selectivity by affecting pKa, modulating conformation, hydrophobic interactions and lipophilicity. Fluorine is also frequently used to improve drug metabolism. More recently, radiolabelled fluorine drugs have been used in positron emission tomography (PET) for imaging and diagnosis purposes in medicine.2

Catherine 2.JPG

Fig. 2: Effects of fluorine in medicinal chemistry3

Fluorine is much more lipophilic than hydrogen, so incorporating fluorine atoms in a molecule will often make it more fat soluble. This means permeability across membranes is increased resulting in a higher bioavailability. Because of the strong electron withdrawing ability of fluorine, it’s inclusion in a molecule has a very strong effect on the acidity or basicity of proximal functional groups. Altering the pKa can strongly modify the binding affinity and the pharmacokinetic properties of a pharmaceutical agent. Often, fluorine is introduced to lower the basicity of a compound which aids in permeability.4

Fluorine can play an important and unique role in influencing molecular conformation. Sterically, fluorine is similar in size to a hydrogen atom, but the high electronegativity of fluorine results in a highly polarised C-F bond with a strong dipole moment and a low-lying C-F anti-bonding orbital available for hyperconjugative donation.2 This can cause fluorine-containing molecules to adopt a different preferential conformation compared to the non-fluorinated molecule which may result in increased binding affinity to a receptor.

One of the major challenges in drug discovery is that of low metabolic stability of compounds. Lipophilic compounds are susceptible to oxidation by liver enzymes, in particular cytochrome P450. Fluorine substitution at the metabolically labile site or at adjacent sites to the site of metabolic attack is a common strategy to improve metabolic stability. The inductive effect of fluorine should result in decreased susceptibility of adjacent groups to metabolic attack by cytochrome P450. Additionally, fluorine can modulate lipophilicity and restrict conformation, which may afford improved metabolic stability.3

PET imaging using 18F tracers is a rapidly developing area in medicinal chemistry. PET scans show biological processes which can give invaluable metabolic information. PET is used as a diagnostic tool, particularly in oncology, but also as an in vivo pharmacological imaging tool in drug development, especially in the areas of biodistribution and drug occupancy studies.4

One drawback of introducing fluorine substituents into drugs is that fluorination can be rather difficult and many processes create challenges in the manufacturing process. However, numerous new, safe and mild fluorinating reagents have been invented in recent years, many of which are commercially available, making the process much simpler.5,6

Blog written by Catherine Tighe


  1. Wang, J.; Sánchez-Roselló, M.; Aceña, J. L.; del Pozo, C.; Sorochinsky, A. E.; Fustero, S.; Soloshonok, V. A.; Liu, H. Chemical Reviews 2014, 114, 2432.
  2. Zhou, Y.; Wang, J.; Gu, Z.; Wang, S.; Zhu, W.; Aceña, J. L.; Soloshonok, V. A.; Izawa, K.; Liu, H. Chemical Reviews 2016, 116, 422.
  3. Gillis, E. P.; Eastman, K. J.; Hill, M. D.; Donnelly, D. J.; Meanwell, N. A. Journal of Medicinal Chemistry 2015, 58, 8315.
  4. Purser, S.; Moore, P. R.; Swallow, S.; Gouverneur, V. Chemical Society Reviews 2008, 37, 320.
  5. Yerien, D. E.; Bonesi, S.; Postigo, A. Organic & Biomolecular Chemistry 2016, 14, 8398.
  6. Campbell, M. G.; Ritter, T. Organic Process Research & Development 2014, 18, 474.



Letting the public loose in our labs

On Sunday 25th June 2017, University of Sussex hosted its first Community Festival. The local public were invited to explore the Falmer campus and get involved with a number of hands-on activities across the various schools and departments. There were taster activity sessions at the Sussex Sport facilities, nature walks around the campus, live jazz, talks and more. Thousands of people turned up for the day (1).


Sussex Drug Discovery Centre was represented on the programme by a delegation of our group – Trudy Myers (SDDC Co-ordinator), Jess Booth (Assay Development and Screening Biologist), Kay Osborn (Biology Technician), Lucas Kraft (PhD Student) and myself. Those who signed up to our activity were taken on a whistle-stop tour through the drug discovery process.

First of all, Jess gave an overview of what the drug discovery process entails (see Figure 1) and where the SDDC fits into that process.

Fiona 3.png

Figure 1 : the drug discovery process (2)

After this introduction, our guests donned lab coats and safety glasses and were given a tour of the group’s protein purification suite. Kay explained how the term “protein” is used in the context of drug discovery to describe tiny molecular machines in our bodies that carry out a variety of functions, and in some cases, cause disease symptoms. She showed the group some incubating flasks containing E. coli which is often used to produce a large quantity of these disease-causing protein. Then she explained how that protein can be later isolated from the bacteria cells via a technique called FPLC (fast protein liquid chromatography) (3) which separates proteins out by their different sizes.

Fiona 4

Next, the newly-briefed scientists were taken into the main biology lab where they were able to run their own biochemical assay. While some took to the pipettes quicker than others, all had fun pipetting reagents onto plates that had lots of different drug compounds in them to see if they got any hits – wells that turned pink indicated a successful compound that had bound to the protein and inhibiting its function while blue ones were unsuccessful ones.

Fiona 5

During the last part of our activity I showed our participants around the oncology chemistry lab. I pointed out many of the similar pieces of kit that they would find in their kitchen. We discussed how the results from the assay they had just run in the biology lab informs the work that is carried out by chemists and how we vary the procedures (or “recipes”) we use to make new drug compounds.

The feedback for the activity was overall very positive and our enthused guests went away knowing a lot more about the drug discovery process than when they arrived, which was our aim.

Fiona Scott is a first year PhD student at the SDDC.


  1. University welcomes local residents for fun-filled day of discovery. University of Sussex News. [Online] [Cited: 1st August 2017.] http://www.sussex.ac.uk/newsandevents/index?page=5&id=40722.
  2. NMT Pharmaceuticals. [Online] [Cited: 1st August 2017.] http://nmtpharma.com/en/drug-development-stages/.
  3. Dermot Walls, Sinéad T. Loughran. Protein Chromatography Methods and Protocols. New York : Humana press, 2011. pp. 439-447.


Malaria taking control – increasing its chances for reinfection?

This week I attended the ISNTD Bites conference 2017 at the Institute of Child Health, London. I was really impressed with one of the talks given by Ailie Robinson on the work that she had conducted for her PhD at the London School of Hygiene and Tropical Medicine. Ailie has been investigating the influence of Plasmodium infection on the human volatile odour profiles in an endemic setting.

What caught my interest was something that I hadn’t previously considered with vector borne pathogenic diseases; which was how pathogens can affect its host in order to improve the likelihood of its host to be bitten by its vector and thus completing its life cycle.

Ailie presented her work where she had analysed the volatile odour profiles from three groups of participants with varying asymptomatic infections of malaria. The three groups investigated were: low density malaria (Plasmodium falciparum) infection, high density malaria infection or negative infection as a control.

Interestingly the gas-chromatographic-mass-spectrometry (GCMS) analysis of the volatile odour profiles from the people in the three groups showed that the high density infection group had significant increases in 3 organic compounds over the other 2 groups. To further investigate this interesting observation Ailie went on to present her work using gas-chromotography-electroantennography (GC-EAG); which is a technique that can be used to determine if the malaria causing mosquito (Anopheles gambiae) is attracted to a certain chemical; to show that all three of the observed molecules that were significantly increased in the high density infection group were highly attractive to the female mosquito. Inferring that the malaria parasite is by someway (either by expressing these chemicals itself or via a host response to infection) maximising its chances for reinfection.

Another interesting outcome from these experiments is the potential for the simple detection of asymptomatic malaria infection by using a breath test. See Ailie Robinson’s article here – (http://www.scidev.net/global/malaria/news/malaria-breath-test-CSIRO.html). I look forward to seeing her published data soon.

Blog written by Ryan West