Comprehensive Data-Driven Assessment of Non-Kinase Targets of Inhibitors of the Human Kinome.

Protein kinases (PKs) are involved in many intracellular signal transduction pathways through phosphorylation cascades and have become intensely investigated pharmaceutical targets over the past two decades. Inhibition of PKs using small-molecular inhibitors is a premier strategy for the treatment of diseases in different therapeutic areas that are caused by uncontrolled PK-mediated phosphorylation and aberrant signaling. Most PK inhibitors (PKIs) are directed against the ATP cofactor binding site that is largely conserved across the human kinome comprising 518 wild-type PKs (and many mutant forms). Hence, these PKIs often have varying degrees of multi-PK activity (promiscuity) that is also influenced by factors such as single-site mutations in the cofactor binding region, compound binding kinetics, and residence times. The promiscuity of PKIs is often-but not always-critically important for therapeutic efficacy through polypharmacology. Various in vitro and in vivo studies have also indicated that PKIs have the potential of interacting with additional targets other than PKs, and different secondary cellular targets of individual PKIs have been identified on a case-by-case basis. Given the strong interest in PKs as drug targets, a wealth of PKIs from medicinal chemistry and their activity data from many assays and biological screens have become publicly available over the years. On the basis of these data, for the first time, we conducted a systematic search for non-PK targets of PKIs across the human kinome. Starting from a pool of more than 155,000 curated human PKIs, our large-scale analysis confirmed secondary targets from diverse protein classes for 447 PKIs on the basis of high-confidence activity data. These PKIs were active against 390 human PKs, covering all kinase groups of the kinome and 210 non-PK targets, which included other popular pharmaceutical targets as well as currently unclassified proteins. The target distribution and promiscuity of the 447 PKIs were determined, and different interaction profiles with PK and non-PK targets were identified. As a part of our study, the collection of PKIs with activity against non-PK targets and the associated information are made freely available.

Chemoinformatic approaches for navigating large chemical spaces.

INTRODUCTION: Large chemical spaces (CSs) include traditional large compound collections, combinatorial libraries covering billions to trillions of molecules, DNA-encoded chemical libraries comprising complete combinatorial CSs in a single mixture, and virtual CSs explored by generative models. The diverse nature of these types of CSs require different chemoinformatic approaches for navigation. AREAS COVERED: An overview of different types of large CSs is provided. Molecular representations and similarity metrics suitable for large CS exploration are discussed. A summary of navigation of CSs in generative models is provided. Methods for characterizing and comparing CSs are discussed. EXPERT OPINION: The size of large CSs might restrict navigation to specialized algorithms and limit it to considering neighborhoods of structurally similar molecules. Efficient navigation of large CSs not only requires methods that scale with size but also requires smart approaches that focus on better but not necessarily larger molecule selections. Deep generative models aim to provide such approaches by implicitly learning features relevant for targeted biological properties. It is unclear whether these models can fulfill this ideal as validation is difficult as long as the covered CSs remain mainly virtual without experimental verification.

Advancing Cheminformatics-A Theme Issue in Honor of Professor Jürgen Bajorath.

While cheminformatics problems have been actively researched since the early 1960s, as witnessed by the QSAR approaches developed by Toshio Fujita and Corwin Hansch [...].

Using deep neural networks to explore chemical space.

INTRODUCTION: The popularity and success of advanced AI methods like deep neural networks has led to novel ways for exploring chemical space. Their opaque nature poses challenges for model evaluation regarding novelty, uniqueness, and distribution of the chemical space covered. However, these methods also promise to be able to explore uncharted chemical space in novel ways that do not rely directly on structural similarity. AREAS COVERED: This review provides an overview of popular deep learning methods for chemical space exploration. Crucial aspects like choice of molecular representation, training for focused chemical space exploration, and criteria for assessing and validating chemical space coverage are discussed. EXPERT OPINION: Deep learning offers great potential for chemical space exploration beyond conventional fragment-based methods. Given the rarity of prospective applications and considering the difficulty in assessing representativeness and comprehensiveness of chemical space covered, developing criteria for assessing and validating generative models is of great significance. Latent space models like variational autoencoders are conceptually appealing for inverse QSAR/QSPR approaches as neighborhood relationships in latent space can be trained to reflect property similarities. Future research in understanding and interpreting generative models might lead to a better understanding of biologically relevant properties of molecules.

Set-Theoretic Formalism for Treating Ligand-Target Datasets.

Data on ligand-target (LT) interactions has played a growing role in drug research for several decades. Even though the amount of data has grown significantly in size and coverage during this period, most datasets remain difficult to analyze because of their extreme sparsity, as there is no activity data whatsoever for many LT pairs. Even within clusters of data there tends to be a lack of data completeness, making the analysis of LT datasets problematic. The current effort extends earlier works on the development of set-theoretic formalisms for treating thresholded LT datasets. Unlike many approaches that do not address pairs of unknown interaction, the current work specifically takes account of their presence in addition to that of active and inactive pairs. Because a given LT pair can be in any one of three states, the binary logic of classical set-theoretic methods does not strictly apply. The current work develops a formalism, based on ternary set-theoretic relations, for treating thresholded LT datasets. It also describes an extension of the concept of data completeness, which is typically applied to sets of ligands and targets, to the local data completeness of individual ligands and targets. The set-theoretic formalism is applied to the analysis of simple and joint polypharmacologies based on LT activity profiles, and it is shown that null pairs provide a means for determining bounds to these values. The methodology is applied to a dataset of protein kinase inhibitors as an illustration of the method. Although not dealt with here, work is currently underway on a more refined treatment of activity values that is based on increasing the number of activity classes.

X-ray imaging: A potential enabler of automated particulate detection and cake-structure analysis in lyophilized products?

The presence of particulate matter in parenteral products is a major concern since it affects the patients' safety and is one of the main reasons for product recalls. Conventional quality control is based on a visual inspection, which is a labour-intensive task. Limited to clear solutions and the surface of lyophilised products, it cannot be applied to opaque containers. This study assesses the application of X-ray imaging for detecting the particulate matter in a pharmaceutical lyophilized product. The most common types of particulates (i.e., steel, glass, lyo stopper, polymers and organics in different size classes) were intentionally spiked in vials. After optimizing all relevant parameters of the X-ray set-up, all classes of particulates were detected. At the same time, due to contrast enhancement, the inherent structures of lyophilized cake became obvious. This work addresses the potential and limits of X-ray technology in that regard, paving the way for automated image-based particulate matter detection. Moreover, this paper discusses using this approach to predict critical quality attributes (CQAs) of the drug product based on the cake structure attributes.

Automatic Identification of Analogue Series from Large Compound Data Sets: Methods and Applications.

Analogue series play a key role in drug discovery. They arise naturally in lead optimization efforts where analogues are explored based on one or a few core structures. However, it is much harder to accurately identify and extract pairs or series of analogue molecules in large compound databases with no predefined core structures. This methodological review outlines the most common and recent methodological developments to automatically identify analogue series in large libraries. Initial approaches focused on using predefined rules to extract scaffold structures, such as the popular Bemis-Murcko scaffold. Later on, the matched molecular pair concept led to efficient algorithms to identify similar compounds sharing a common core structure by exploring many putative scaffolds for each compound. Further developments of these ideas yielded, on the one hand, approaches for hierarchical scaffold decomposition and, on the other hand, algorithms for the extraction of analogue series based on single-site modifications (so-called matched molecular series) by exploring potential scaffold structures based on systematic molecule fragmentation. Eventually, further development of these approaches resulted in methods for extracting analogue series defined by a single core structure with several substitution sites that allow convenient representations, such as R-group tables. These methods enable the efficient analysis of large data sets with hundreds of thousands or even millions of compounds and have spawned many related methodological developments.

Prediction of activity cliffs on the basis of images using convolutional neural networks.

An activity cliff (AC) is formed by a pair of structurally similar compounds with a large difference in potency. Accordingly, ACs reveal structure-activity relationship (SAR) discontinuity and provide SAR information for compound optimization. Herein, we have investigated the question if ACs could be predicted from image data. Therefore, pairs of structural analogs were extracted from different compound activity classes that formed or did not form ACs. From these compound pairs, consistently formatted images were generated. Image sets were used to train and test convolutional neural network (CNN) models to systematically distinguish between ACs and non-ACs. The CNN models were found to predict ACs with overall high accuracy, as assessed using alternative performance measures, hence establishing proof-of-principle. Moreover, gradient weights from convolutional layers were mapped to test compounds and identified characteristic structural features that contributed to successful predictions. Weight-based feature visualization revealed the ability of CNN models to learn chemistry from images at a high level of resolution and aided in the interpretation of model decisions with intrinsic black box character.

Predicting Isoform-Selective Carbonic Anhydrase Inhibitors via Machine Learning and Rationalizing Structural Features Important for Selectivity.

Carbonic anhydrases (CAs) catalyze the physiological hydration of carbon dioxide and are among the most intensely studied pharmaceutical target enzymes. A hallmark of CA inhibition is the complexation of the catalytic zinc cation in the active site. Human (h) CA isoforms belonging to different families are implicated in a wide range of diseases and of very high interest for therapeutic intervention. Given the conserved catalytic mechanisms and high similarity of many hCA isoforms, a major challenge for CA-based therapy is achieving inhibitor selectivity for hCA isoforms that are associated with specific pathologies over other widely distributed isoforms such as hCA I or hCA II that are of critical relevance for the integrity of many physiological processes. To address this challenge, we have attempted to predict compounds that are selective for isoform hCA IX, which is a tumor-associated protein and implicated in metastasis, over hCA II on the basis of a carefully curated data set of selective and nonselective inhibitors. Machine learning achieved surprisingly high accuracy in predicting hCA IX-selective inhibitors. The results were further investigated, and compound features determining successful predictions were identified. These features were then studied on the basis of X-ray structures of hCA isoform-inhibitor complexes and found to include substructures that explain compound selectivity. Our findings lend credence to selectivity predictions and indicate that the machine learning models derived herein have considerable potential to aid in the identification of new hCA IX-selective compounds.

From Qualitative to Quantitative Analysis of Activity and Property Landscapes.

Activity or, more generally, property landscapes (PLs) have been considered as an attractive way to visualize and explore structure-property relationships (SPRs) contained in large data sets of chemical compounds. For graphical analysis, three-dimensional representations reminiscent of natural landscapes are particularly intuitive. So far, the use of such landscape models has essentially been confined to qualitative assessment. We describe recent efforts to analyze PLs in a more quantitative manner, which make it possible to calculate topographical similarity values for comparison of landscape models as a measure of relative SPR information content.

Computational Method for Quantitative Comparison of Activity Landscapes on the Basis of Image Data.

Activity landscape (AL) models are used for visualizing and interpreting structure-activity relationships (SARs) in compound datasets. Therefore, ALs are designed to present chemical similarity and compound potency information in context. Different two- or three-dimensional (2D or 3D) AL representations have been introduced. For SAR analysis, 3D AL models are particularly intuitive. In these models, an interpolated potency surface is added as a third dimension to a 2D projection of chemical space. Accordingly, AL topology can be associated with characteristic SAR features. Going beyond visualization and a qualitative assessment of SARs, it would be very helpful to compare 3D ALs of different datasets in more quantitative terms. However, quantitative AL analysis is still in its infancy. Recently, it has been shown that 3D AL models with pre-defined topologies can be correctly classified using machine learning. Classification was facilitated on the basis of AL image feature representations learned with convolutional neural networks. Therefore, we have further investigated image analysis for quantitative comparison of 3D ALs and devised an approach to determine (dis)similarity relationships for ALs representing different compound datasets. Herein, we report this approach and demonstrate proof-of-principle. The methodology makes it possible to computationally compare 3D ALs and quantify topological differences reflecting varying SAR information content. For SAR exploration in drug design, this adds a quantitative measure of AL (dis)similarity to graphical analysis.

Role of Formulation Parameters on Intravitreal Dosing Accuracy Using 1 mL Hypodermic Syringes.

PURPOSE: Evaluation of product viscosity, density and aeration on the dose delivery and accuracy for intravitreal injections with commonly used commercially available hypodermic 1 mL syringes. METHODS: Six commercially available hypodermic 1 mL syringes with different specifications were used for the study. Syringes were filled with the test solutions with different densities and viscosities. Syringes were also subjected to shaking stress to introduce aeration in the test solutions in the presence of different surfactant concentrations with and without high antibody concentration. Target intravitreal volumes of 100 µL, 50 µL and 30 µL were tested to assess dosing accuracy in a controlled simulated administration setup using DIN ISO 11040-4 guidelines and Zwick/Roell Z010 TN instrument. RESULTS: With increasing product viscosity, higher volumes and hence doses were delivered especially for very low volumes like 50 µL and 30 µL. No impact of increasing product density was found on the delivered dose. The presence of surfactants or high protein concentration can lead to aeration, which also negatively affects the dose accuracy and precision. CONCLUSION: Formulation parameters like viscosity can have an impact on dose delivery using hypodermic syringes for intravitreal injections and on the resulting glide force.

Quantitative Comparison of Three-Dimensional Activity Landscapes of Compound Data Sets Based upon Topological Features.

Visualization of structure-activity relationships (SARs) in compound data sets substantially contributes to their systematic analysis. For SAR visualization, different types of activity landscape (AL) representations have been introduced. Three-dimensional (3D) AL models in which an activity hypersurface is constructed in chemical space are particularly intuitive because these 3D ALs are reminiscent of "true" (geographical) landscapes. Accordingly, the topologies of 3D AL representations can be immediately associated with different SAR characteristics of compound data sets. However, the comparison of 3D ALs has thus far been confined to visual inspection and qualitative analysis. We have focused on image analysis as a possible approach to facilitate a quantitative comparison of 3D ALs, which would further increase their utility for SAR exploration. Herein, we introduce a new computational methodology for quantifying topological relationships between 3D ALs. Images of color-coded 3D ALs were converted into top-down views of these ALs. From transformed images, different categories of shape features were systematically extracted, and multilevel shape correspondence was determined as a measure of AL similarity. This made it possible to differentiate between 3D ALs in quantitative terms.

Determining Maximum Allowable Rubber Stopper Displacement for Container Closure Integrity (CCI).

Sterile pharmaceuticals require they be developed and manufactured using suitable container closure systems to maintain sterility until product opening. Characterizing container closure integrity (CCI) in relation to rubber stopper displacement was controversially discussed during the Annex 1 revision process. An automated inspection system can reject units with displaced rubber stoppers, and the related acceptance criteria for such in-process testing can be established by adequate studies. In this manuscript, we describe a novel helium leak CCI testing method to study the relation of rubber stopper displacement and CCI. Ten different commonly used vial-rubber stopper combinations were characterized, which led to robust test results. Pronounced differences between the different vial-rubber stopper combinations were observed, clearly showing that the combination of different stoppers, vials, and caps led to significant differences in allowable stopper displacement for routine manufacture.

Characterization of Polymeric Syringes Used for Intravitreal Injection.

Intravitreal (IVT) injection is currently the state of the art for drug delivery to the back of the eye. Drug Products (DP) intended for IVT injections usually pose challenges such as a very low injection volume (e.g. 50 µL) and high injection forces. DPs in vials are typically transferred and injected using disposable polymer syringes, which can feature a silicone oil (SO) coating. In our syringe in-use study, we compared dead volume, total SO content and SO layer distributions of three IVT transfer injection syringes. We assessed multiple potential impact factors such as protein concentration, needle gauge, injection speed, surfactant type and the impact of the in-use hold time on sub-visible particle (SvP) formation and injection forces. Pronounced differences were observed between the syringes regarding SvP generation. Siliconized syringes showed higher SvP counts as compared to non-siliconized syringes. In some cases injection forces exceeded 20 N, which caused needles to burst off during injection. The syringes also showed relevant differences in total SO content and dead volume. In conclusion, specific consideration in the selection of an adequate transfer injection syringe are required. This includes extensive testing and characterization under intended and potential in-use conditions and the development of in-use handling procedures.

From SAR Diagnostics to Compound Design: Development Chronology of the Compound Optimization Monitor (COMO) Method.

In medicinal chemistry, compound optimization largely depends on chemical knowledge, experience, and intuition, and progress in hit-to-lead and lead optimization projects is difficult to estimate. Accordingly, approaches are sought after that aid in assessing the odds of success with an optimization project and making decisions whether to continue or discontinue work on an analog series at a given stage. However, currently there are only very few approaches available that are capable of providing decision support. We introduce a computational methodology designed to combine the assessment of chemical saturation of analog series and structure-activity relationship (SAR) progression. The current endpoint of these development efforts, the compound optimization monitor (COMO), further extends lead optimization diagnostics to compound design and activity prediction. Hence, COMO plays dual role in supporting lead optimization campaigns.

Evaluation of Different Quality-Relevant Aspects of Closed System Transfer Devices (CSTDs).

PURPOSE: Health care professionals can be exposed to hazardous drugs such as cytostatics during preparation of drugs for administration. Closed sytem transfer devices (CSTDs) were introduced to provide protection for healthcare professional against unintended exposure to hazardous drugs. The interest in CSTDs has significantly increased after USP <800> monograph was issued. The majority of the studies published so far on CSTDs have focused on their "containment" function. However, other important attributes for CSTDs with potential importance for product quality impact are not yet fully evaluated. METHODS: In the current study, we evaluated four sytems from different suppliers, in combination with different container closure systems (CCS), using solutions of different viscosity and surface tension. The different CSTD / CCS combinations were tested for (a) containment (integrity) using a highly sensitive helium leak test, (b) the force required for mounting the vial adaptor, (c) contribution to visible and subvisible particles as well as (d) the hold-up volume. RESULTS: Results show that the majority of CSTDs may have leaks varying in size, and that some of them generated visible particles due to stopper coring and subvisible particles, both due to silicon oil and particulate contaminations of the Devices. Finally, the holdup volume was up to 1 mL depending on the CSTD type, vial size and solution viscosity. CONCLUSION: These results show that there is a need to evaluate the compatibility of CSTD systems to select the best system for the intended use and that CSTDs may adversely impact product quality and delivered dose.

ccbmlib - a Python package for modeling Tanimoto similarity value distributions.

The ccbmlib Python package is a collection of modules for modeling similarity value distributions based on Tanimoto coefficients for fingerprints available in RDKit. It can be used to assess the statistical significance of Tanimoto coefficients and evaluate how molecular similarity is reflected when different fingerprint representations are used. Significance measures derived from p-values allow a quantitative comparison of similarity scores obtained from different fingerprint representations that might have very different value ranges. Furthermore, the package models conditional distributions of similarity coefficients for a given reference compound. The conditional significance score estimates where a test compound would be ranked in a similarity search. The models are based on the statistical analysis of feature distributions and feature correlations of fingerprints of a reference database. The resulting models have been evaluated for 11 RDKit fingerprints, taking a collection of ChEMBL compounds as a reference data set. For most fingerprints, highly accurate models were obtained, with differences of 1% or less for Tanimoto coefficients indicating high similarity.

Activity landscape image analysis using convolutional neural networks.

Activity landscapes (ALs) are graphical representations that combine compound similarity and activity data. ALs are constructed for visualizing local and global structure-activity relationships (SARs) contained in compound data sets. Three-dimensional (3D) ALs are reminiscent of geographical maps where differences in landscape topology mirror different SAR characteristics. 3D AL models can be stored as differently formatted images and are thus amenable to image analysis approaches, which have thus far not been considered in the context of graphical SAR analysis. In this proof-of-concept study, 3D ALs were constructed for a variety of compound activity classes and 3D AL image variants of varying topology and information content were generated and classified. To these ends, convolutional neural networks (CNNs) were initially applied to images of original 3D AL models with color-coding reflecting compound potency information that were taken from different viewpoints. Images of 3D AL models were transformed into variants from which one-dimensional features were extracted. Other machine learning approaches including support vector machine (SVM) and random forest (RF) algorithms were applied to derive models on the basis of such features. In addition, SVM and RF models were trained using other features obtained from images through edge filtering. Machine learning was able to accurately distinguish between 3D AL image variants with different topology and information content. Overall, CNNs which directly learned feature representations from 3D AL images achieved highest classification accuracy. Predictive performance for CNN, SVM, and RF models was highest for image variants emphasizing topological elevation. In addition, SVM models trained on rudimentary images from edge filtering classified such images with high accuracy, which further supported the critical role of altitude-dependent topological features for image analysis and predictions. Taken together, the findings of our proof-of-concept investigation indicate that image analysis has considerable potential for graphical SAR exploration to systematically infer different SAR characteristics from topological features of 3D ALs.