Enabling synthesis in fragment-based drug discovery (FBDD): microscale high-throughput optimisation of the medicinal chemist's toolbox reactions.

Miniaturised high-throughput experimentation (HTE) is widely employed in industrial and academic laboratories for rapid reaction optimisation using material-limited, multifactorial reaction condition screening. In fragment-based drug discovery (FBDD), common toolbox reactions such as the Suzuki-Miyaura and Buchwald-Hartwig cross couplings can be hampered by the fragment's intrinsic heteroatom-rich pharmacophore which is required for ligand-protein binding. At Astex, we are using microscale HTE to speed up reaction optimisation and prevent target down-prioritisation. By identifying catalyst/base/solvent combinations which tolerate unprotected heteroatoms we can rapidly optimise key cross-couplings and expedite route design by avoiding superfluous protecting group manipulations. However, HTE requires extensive upfront training, and this modern automated synthesis technique largely differs to the way organic chemists are traditionally trained. To make HTE accessible to all our synthetic chemists we have developed a semi-automated workflow enabled by pre-made 96-well screening kits, rapid analytical methods and in-house software development, which is empowering chemists at Astex to run HTE screens independently with minimal training.

Accelerated Chemical Reaction Optimization Using Multi-Task Learning.

Functionalization of C-H bonds is a key challenge in medicinal chemistry, particularly for fragment-based drug discovery (FBDD) where such transformations require execution in the presence of polar functionality necessary for protein binding. Recent work has shown the effectiveness of Bayesian optimization (BO) for the self-optimization of chemical reactions; however, in all previous cases these algorithmic procedures have started with no prior information about the reaction of interest. In this work, we explore the use of multitask Bayesian optimization (MTBO) in several in silico case studies by leveraging reaction data collected from historical optimization campaigns to accelerate the optimization of new reactions. This methodology was then translated to real-world, medicinal chemistry applications in the yield optimization of several pharmaceutical intermediates using an autonomous flow-based reactor platform. The use of the MTBO algorithm was shown to be successful in determining optimal conditions of unseen experimental C-H activation reactions with differing substrates, demonstrating an efficient optimization strategy with large potential cost reductions when compared to industry-standard process optimization techniques. Our findings highlight the effectiveness of the methodology as an enabling tool in medicinal chemistry workflows, representing a step-change in the utilization of data and machine learning with the goal of accelerated reaction optimization.

A comparison of culture methods and polymerase chain reaction in detecting Clostridioides difficile from hospital surfaces.

Introduction. Environmental surveillance for Clostridioides difficile is challenging. There are no internationally agreed recommendations on which method should be used when environmental surveillance is undertaken.Aim. To compare the detection of C. difficile by RT-PCR to culture-based methods and to determine which is more sensitive and specific in the clinical environment.Methods. Forty-four near-patient areas of C. difficile-positive patients were sampled using contact plates and moistened flocked swabs.Results. Detection using moistened flocked swabs followed by RT-PCR or culture detected more C. difficile than contact plates. The sensitivity and specificity of a RT-PCR assay for tcdB compared to the culture methods was 76 and 91 %, respectively.Conclusion. Despite the lower sensitivity and specificity, RT-PCR could potentially offer a more rapid and practical alternative.

A Brief Introduction to Chemical Reaction Optimization.

From the start of a synthetic chemist's training, experiments are conducted based on recipes from textbooks and manuscripts that achieve clean reaction outcomes, allowing the scientist to develop practical skills and some chemical intuition. This procedure is often kept long into a researcher's career, as new recipes are developed based on similar reaction protocols, and intuition-guided deviations are conducted through learning from failed experiments. However, when attempting to understand chemical systems of interest, it has been shown that model-based, algorithm-based, and miniaturized high-throughput techniques outperform human chemical intuition and achieve reaction optimization in a much more time- and material-efficient manner; this is covered in detail in this paper. As many synthetic chemists are not exposed to these techniques in undergraduate teaching, this leads to a disproportionate number of scientists that wish to optimize their reactions but are unable to use these methodologies or are simply unaware of their existence. This review highlights the basics, and the cutting-edge, of modern chemical reaction optimization as well as its relation to process scale-up and can thereby serve as a reference for inspired scientists for each of these techniques, detailing several of their respective applications.

C-H functionalisation tolerant to polar groups could transform fragment-based drug discovery (FBDD).

We have analysed 131 fragment-to-lead (F2L) examples targeting a wide variety of protein families published by academic and industrial laboratories between 2015-2019. Our assessment of X-ray structural data identifies the most common polar functional groups involved in fragment-protein binding are: N-H (hydrogen bond donors on aromatic and aliphatic N-H, amides and anilines; totalling 35%), aromatic nitrogen atoms (hydrogen bond acceptors; totalling 23%), and carbonyl oxygen group atoms (hydrogen bond acceptors on amides, ureas and ketones; totalling 22%). Furthermore, the elaboration of each fragment into its corresponding lead is analysed to identify the nominal synthetic growth vectors. In ∼80% of cases, growth originates from an aromatic or aliphatic carbon on the fragment and more than 50% of the total bonds formed are carbon-carbon bonds. This analysis reveals that growth from carbocentric vectors is key and therefore robust C-H functionalisation methods that tolerate the innate polar functionality on fragments could transform fragment-based drug discovery (FBDD). As a further resource to the community, we have provided the full data of our analysis as well as an online overlay page of the X-ray structures of the fragment hit and leads: https://astx.com/interactive/F2L-2021/.

Transition metal-free cross-dehydrogenative arylation of unactivated benzylic C-H bonds.

The cross-dehydrogenative arylation of benzylic C-H bonds with arenes provides straightforward access to synthetically useful 1,1-diarylmethanes, from readily available starting materials. Current approaches suffer from limited substrate scope, requirement for large excesses of alkyl arene and/or non-trivial reaction set up. We report a transition metal-free cross-dehydrogenative arylation of benzylic C-H bonds using alkyl benzene derivatives and electron-rich arenes as coupling partners. The method proceeds through the in situ generation of a reactive benzyl fluoride intermediate which then reacts with the nucleophilic arene. The reaction tolerates a wide variety of functional groups including unprotected polar functionality and has been applied to the late-stage benzylation of several biologically relevant molecules.

Can e-learning improve the performance of undergraduate medical students in Clinical Microbiology examinations?

BACKGROUND: Clinical Microbiology is a core subject in medical undergraduate curricula. However, students struggle to cover the content and clinically contextualise basic microbiology. Our aim was to evaluate student engagement with new e-learning material and to investigate the impact it had on examination performance in a Clinical Microbiology module. METHODS: An online resource was designed to support didactic teaching in a Fundamentals of Clinical Microbiology module. One cohort of students had access to the online material (2017/2018 class) and the other did not (2016/2017 class). Each cohort sat the same multiple-choice question (MCQ) and short-note question (SNQ) examination papers and the impact of engagement with the online resource and examination performance was analysed. RESULTS: Both groups were of the same academic standard prior to beginning the module. In the 2017/2018 cohort, 227/309 (73.5%) students had ≥80% engagement with the content. Students engaged most with the index of pathogens and pathogen focused clinical cases related to diverse genera and families of clinically important microorganisms. A statistically higher difference in the mean percentage grade in both the MCQ and SNQ examinations was seen for 2017/2018 compared to 2016/2017 cohort. For the MCQ examination, the 2017/2018 cohort were on average 5.57% (95% confidence interval (CI): 3.92 to 7.24%; P < 0.001) higher, and for the SNQ examination the 2017/2018 cohort were on average 2.08% (95% CI: 0.74 to 3.41%; P = 0.02) higher. When the results were adjusted for previous examination performance, for every percentage increase in online engagement the grade in the SNQ examination only increased by 0.05% (95% CI: 0.02 to 0.08) on average. CONCLUSIONS: These findings suggest students engage with e-learning when studying and that such activities may help students perform better in assessments.

Enabling synthesis in fragment-based drug discovery by reactivity mapping: photoredox-mediated cross-dehydrogenative heteroarylation of cyclic amines.

In fragment-based drug discovery (FBDD), a weakly binding fragment hit is elaborated into a potent ligand by bespoke functionalization along specific directions (growth vectors) from the fragment core in order to complement the 3D structure of the target protein. This structure-based design approach can present significant synthetic challenges, as growth vectors often originate on sp2 or sp3 ring carbons which are not the most synthetically accessible points on the fragment. To address this issue and expedite synthesis in FBDD, we established a nanogram-to-gram workflow for the development of enabling synthetic transformations, such as the direct C-H functionalization of heterocycles. This novel approach deploys high-throughput experimentation (HTE) in 1536-well microtiter plates (MTPs) facilitated by liquid handling robots to screen reaction conditions on the nanomolar scale; subsequently the reaction is upscaled in a continuous flow to generate gram-quantities of the material. In this paper, we disclose the use of this powerful workflow for the development of a photoredox-mediated cross-dehydrogenative coupling of fragments and medicinally relevant heterocyclic precursors via Minisci-type addition of α-amino radicals to electron-deficient heteroarenes. The optimized reaction conditions were employed on the milligram-scale on a diverse set of 112 substrates to map out structure-reactivity relationships (SRRs) of the transformation. The coupling exhibits excellent tolerance to a variety of functional groups and N-rich heteroarenes relevant to FBDD and was upscaled in a continuous flow to afford gram-quantities of pharmaceutically relevant sp2-sp3 privileged architectures.

Photocatalytic Three-Component Umpolung Synthesis of 1,3-Diamines.

A visible-light-mediated photocatalytic umpolung synthesis of 1,3-diamines from in situ-generated imines and dehydroalanine derivatives is described. Pivoting on a key nucleophilic addition of photocatalytically generated α-amino radicals to electron-deficient alkenes, this three-component coupling reaction affords 1,3-diamines efficiently and diastereoselectively. The mild protocol tolerates a wide variety of functionalities including heterocycles, pinacol boronates, and aliphatic chains. Application to biologically relevant α-amino-γ-lactam synthesis and extension to 1,3-aminoalcohols is also demonstrated.

IVIG Associated Aseptic Meningitis in a Renal Transplant Patient.

The management of antibody-mediated rejection in renal transplant recipients involves plasmapheresis with IVIG. Aseptic meningitis is a rare adverse effect of IVIG therapy and is a diagnosis of exclusion. We report a case of a renal transplant patient who developed IVIG associated aseptic meningitis in the context of management of antibody-mediated rejection, four years after transplantation.

The ortho-substituent effect on the Ag-catalysed decarboxylation of benzoic acids.

A combined experimental and computational investigation on the Ag-catalysed decarboxylation of benzoic acids is reported herein. The present study demonstrates that a substituent at the ortho position exerts dual effects in the decarboxylation event. On one hand, ortho-substituted benzoic acids are inherently destabilised starting materials compared to their meta- and para-substituted counterparts. On the other hand, the presence of an ortho-electron-withdrawing group results in an additional stabilisation of the transition state. The combination of both effects results in an overall reduction of the activation energy barrier associated with the decarboxylation event. Furthermore, the Fujita-Nishioka linear free energy relationship model indicates that steric bulk of the substituent can also exert a negative effect by destabilising the transition state of decarboxylation.

Interventions for preventing the spread of infestation in close contacts of people with scabies.

BACKGROUND: Scabies, caused by Sarcoptes scabiei variety hominis or the human itch mite, is a common parasitic infection. While anyone can become infected, it causes significant morbidity in immunocompromised hosts and it spreads easily between human hosts where there is overcrowding or poor sanitation. The most common symptom reported is itch which is worse at night. As the symptoms are attributed to an allergic reaction to the mite, symptoms usually develop between four to six weeks after primary infection. Therefore, people may be infected for some time prior to developing symptoms. During this time, while asymptomatic, they may spread infection to others they are in close contact with. Consequently, it is usually recommended that when an index case is being treated, others who have been in close contact with the index case should also be provided with treatment. OBJECTIVES: To assess the effects of prophylactic interventions for contacts of people with scabies to prevent infestation in the contacts. SEARCH METHODS: We searched electronic databases (Cochrane Occupational Safety and Health Review Group Specialised Register, CENTRAL (The Cochrane Library), MEDLINE (Ovid), Pubmed, EMBASE, LILACS, CINAHL, OpenGrey and WHO ICTRP) up to November 2013. SELECTION CRITERIA: Randomised controlled trials (RCTs) or cluster RCTs which compared prophylactic interventions which were given to contacts of index cases with scabies infestation. Interventions could be compared to each other, or to placebo or to no treatment. Both drug treatments and non-drug treatments were acceptable. DATA COLLECTION AND ANALYSIS: Two authors intended to extract dichotomous data (developed infection or did not develop infection) for the effects of interventions and report this as risk ratios with 95% confidence intervals. We intended to report any adverse outcomes similarly. MAIN RESULTS: We did not include any trials in this review. Out of 29 potentially-relevant studies, we excluded 16 RCTs as the data for the contacts were either not reported or were reported only in combination with the outcomes for the index cases. We excluded a further 11 studies as they were not RCTs. We also excluded one study as not all subjects were examined at baseline and follow-up, and another as it was a case study. AUTHORS' CONCLUSIONS: The effects of providing prophylactic treatments for contacts of people with scabies to prevent infestation are unknown. We need well-designed RCTs of the use of prophylactic measures to prevent the transmission of scabies conducted with people who had the opportunity for prolonged skin contact with an index case, such as family members, healthcare workers or residential care personnel, within the previous six weeks.

Selective deuteration of (hetero)aromatic compounds via deutero-decarboxylation of carboxylic acids.

A practical, mild and highly selective protocol for the monodeuteration of a variety of arenes and heteroarenes is presented. Catalytic amounts of Ag(I) salts in DMSO/D(2)O are shown to facilitate the deutero-decarboxylation of ortho-substituted benzoic and heteroaromatic α-carboxylic acids in high yields with excellent levels of deuterium incorporation.