Mind your prevalence!

Multiple metrics are used when assessing and validating the performance of quantitative structure-activity relationship (QSAR) models. In the case of binary classification, balanced accuracy is a metric to assess the global performance of such models. In contrast to accuracy, balanced accuracy does not depend on the respective prevalence of the two categories in the test set that is used to validate a QSAR classifier. As such, balanced accuracy is used to overcome the effect of imbalanced test sets on the model's perceived accuracy. Matthews' correlation coefficient (MCC), an alternative global performance metric, is also known to mitigate the imbalance of the test set. However, in contrast to the balanced accuracy, MCC remains dependent on the respective prevalence of the predicted categories. For simplicity, the rest of this work is based on the positive prevalence. The MCC value may be underestimated at high or extremely low positive prevalence. It contributes to more challenging comparisons between experiments using test sets with different positive prevalences and may lead to incorrect interpretations. The concept of balanced metrics beyond balanced accuracy is, to the best of our knowledge, not yet described in the cheminformatic literature. Therefore, after describing the relevant literature, this manuscript will first formally define a confusion matrix, sensitivity and specificity and then present, with synthetic data, the danger of comparing performance metrics under nonconstant prevalence. Second, it will demonstrate that balanced accuracy is the performance metric accuracy calibrated to a test set with a positive prevalence of 50% (i.e., balanced test set). This concept of balanced accuracy will then be extended to the MCC after showing its dependency on the positive prevalence. Applying the same concept to any other performance metric and widening it to the concept of calibrated metrics will then be briefly discussed. We will show that, like balanced accuracy, any balanced performance metric may be expressed as a function of the well-known values of sensitivity and specificity. Finally, a tale of two MCCs will exemplify the use of this concept of balanced MCC versus MCC with four use cases using synthetic data. SCIENTIFIC CONTRIBUTION: This work provides a formal, unified framework for understanding prevalence dependence in model validation metrics, deriving balanced metric expressions beyond balanced accuracy, and demonstrating their practical utility for common use cases. In contrast to prior literature, it introduces the derived confusion matrix to express metrics as functions of sensitivity, specificity and prevalence without needing additional coefficients. The manuscript extends the concept of balanced metrics to Matthews' correlation coefficient and other widely used performance indicators, enabling robust comparisons under prevalence shifts.

Umbelliferyloxymethyl phosphonate compounds-weakly binding zinc ionophores with neuroprotective properties.

Umbelliferone is a member of the coumarin family of compounds which are known for diverse pharmacological activity including in targets relevant to Alzheimers disease, AD. The toxicity associated with some forms of the amyloid protein, Aß, and the role of Zn2+ (and other biometals) dyshomeostasis in this, are of great interest in AD and make metal ionophore capability desirable in so called multi target drug ligands MTDLs. A new series of umbelliferyloxymethyl phosphonic acid diethylester compounds (umbelliferyloxymethyl phosphonates) bearing a phosphonate at the 7-position (compounds 1, 3-6), hydrolysis products 2, 2a and 2b from 1 and analogues 7 and 8 of 1 with 7-O to 7-S and 1-O to 1-NH substitutions, are reported. Single crystal X-ray structures of compounds 1, 2 and 2a were determined. In terms of neuroprotective properties, the compounds 1, 2, 3, 4, 5 and 6 at 1 µM concentration, inhibited the toxicity of Aß1-42 (Aß42) in both toxic Amyloid Derived Diffusible Ligand (ADDL) and fibrillar (fibril) forms towards rat hippocampal cells. Compound 7 displayed cytotoxicity and 8 failed to inhibit Aß42 toxicity. Concerning compound-metal ionophore activity (assessed using chemical experiments), despite weak binding to Zn2+ determined from 31P NMR titration of 1 and 2 by ZnCl2, compounds 1, 3, 4, 5 and 6 demonstrated ionophore assisted partition of Zn2+ from water to octanol at micromolar concentrations with efficacy on a par with or better than the chelator MTDL clioquinol (5-chloro-7-iodo-8-hydroxyquinoline). Partition was assessed using furnace Atomic Absorption Spectroscopy (AAS). In further experiments interaction of compound 1 with Zn2+ or it's pathways was inferred by (i) delayed fluorescence response with added Zn2+ in cells treated with FluoZin-3 and (ii) by suppression of Zn2+ promoted aggregation of Aß42.

Extrapolation of in vitro structural alerts for mutagenicity to the in vivo endpoint.

As part of the hazard and risk assessment of chemicals in man, it is important to assess the ability of a chemical to induce mutations in vivo. Because of the commonalities in the molecular initiating event, mutagenicity in vitro can correlate well to the in vivo endpoint for certain compound classes; however, the difficulty lies in identifying when this correlation holds true. In silico alerts for in vitro mutagenicity may therefore be used as the basis for alerts for mutagenicity in vivo where an expert assessment is carried out to establish the relevance of the correlation. Taking this into account, a data set of publicly available transgenic rodent gene mutation assay data, provided by the National Institute of Health Sciences of Japan, was processed in the expert system Derek Nexus against the in vitro mutagenicity endpoint. The resulting predictivity was expertly reviewed to assess the validity of the observed correlations in activity and mechanism of action between the two endpoints to identify suitable in vitro alerts for extension to the in vivo endpoint. In total, 20 alerts were extended to predict in vivo mutagenicity, which has significantly improved the coverage of this endpoint in Derek Nexus against the data set provided. Updating the Derek Nexus knowledge base in this way led to an increase in sensitivity for this data set against this endpoint from 9% to 66% while maintaining a good specificity of 89%.

The Asymmetric Aza-silyl-Prins Reaction: Synthesis of Enantiopure Piperidines.

The design and development of the first asymmetric aza-silyl-Prins reaction is reported, giving rise to valuable and diverse piperidines and pipecolic acid derivatives in both high yields and as single enantiomers. The creation of a novel chiral auxiliary-homoallylic amine for the aza-silyl-Prins reaction is essential to its success.

Utility of published DNA reactivity alerts.

The identification of impurities with mutagenic potential is required for any potential pharmaceutical. The ICH M7 guidelines state that two complementary in silico toxicity prediction tools may be used to predict the mutagenic potential of pharmaceutical impurities. An expert review of the resulting in silico predictions is required, and numerous publications have been released to guide the expert review process. One such publication suggests that literature-based structural alerts (LBSAs) may provide a suitable aid in the expert review process. This publication provides a study of the effect of using one such set of LBSAs for the expert review of mutagenicity predictions from two complementary in silico tools. The analysis was performed using an Ames test dataset of 2619 compounds, and required interpretation of the LBSAs which proved to be a subjective process. Globally the LBSAs produced many more false positives than the in silico systems; whilst some exhibited a predictive performance comparable to the in silico systems, the majority were overly sensitive at the cost of accuracy. Use of LBSAs as part of an expert review process, without considering mitigating factors, could result in many more false positives and potentially the need to carry out additional and unnecessary Ames tests.

Synthesis of Azabicycles via Cascade Aza-Prins Reactions: Accessing the Indolizidine and Quinolizidine Cores.

The first detailed studies of intramolecular aza-Prins and aza-silyl-Prins reactions, starting from acyclic materials, are reported. The methods allow rapid and flexible access toward an array of [6,5] and [6,6] aza-bicycles, which form the core skeletons of various alkaloids. On the basis of our findings on the aza-Prins and aza-silyl-Prins cyclizations, herein we present simple protocols for the intramolecular preparation of the azabicyclic cores of the indolizidines and quinolizidines using a one-pot cascade process of N-acyliminium ion formation followed by aza-Prins cyclization and either elimination or carbocation trapping. It is possible to introduce a range of different substituents into the heterocycles through a judicial choice of Lewis acid and solvent(s), with halo-, phenyl-, and amido-substituted azabicyclic products all being accessed through these highly diastereoselective processes.

Conception and evolution of stereocontrolled strategies toward functionalized 8-aryloctanoic acids related to the total synthesis of aliskiren.

A detailed account is given describing the approaches used toward the total synthesis of aliskiren. In particular, ring-closing metathesis with the Hoveyda-Grubbs catalyst accelerates the formation of a 9-membered lactone from an (R)-ester. The diastereomeric (S)-ester leads to the formation of dimeric dilactones, which were characterized by X-ray analysis and chemical conversions.

Total synthesis of "aliskiren": the first Renin inhibitor in clinical practice for hypertension.

We report a "macrocycle route" toward aliskiren, a drug presently marketed for the treatment of hypertension, using a highly stereocontrolled approach starting from a common "isopropyl chiron". Highlights of the synthesis include a challenging RCM reaction to produce a nine-membered unsaturated lactone, a highly stereoselective catalytic Du Bois aziridination, and a regio- and diastereoselective aziridine ring-opening to a vicinal amino alcohol.

A detailed investigation of the aza-Prins reaction.

The development of a Lewis acid-promoted aza-Prins reaction to form piperidines and pyrrolidines is described. Indium trichloride has been found to be a highly successful and mild Lewis acid for promoting this reaction. A thorough mechanistic investigation is described, including the factors that influence the formation of the 5- or 6-membered ring product(s).

Targeting ACE and ECE with dual acting inhibitors.

A series of urea analogues related to SA6817 and a GSK phosphonic acid with reported ACE inhibitory activity were prepared and tested for dual ACE and ECE activities. Although excellent ACE and NEP inhibition was achieved, only modest ECE inhibition was observed with one analogue.

A versatile indium trichloride mediated Prins-type reaction to unsaturated heterocycles.

A versatile and high-yielding indium trichloride mediated cyclization reaction of silylated homoallylic alcohols, thiols, or amines with aldehydes or epoxides is described as a rapid route to a range of unsaturated heterocycles. The excellent diastereoselectivity observed offers a method of wide scope and generality.