Using Bibliometric Analysis and Machine Learning to Identify Compounds Binding to Sialidase-1

Machine learning combines atomistic simulations to predict SARS-CoV-2 Mpro inhibitors from natural compounds

To date, the COVID-19 pandemic has still been infectious around the world, continuously causing social and economic damage on a global scale. One of the most important therapeutic targets for the treatment of COVID-19 is the main protease (Mpro) of SARS-CoV-2. In this study, we combined machine-learning (ML) model with atomistic simulations to computationally search for highly promising SARS-CoV-2 Mpro inhibitors from the representative natural compounds of the National Cancer Institute (NCI) Database. First, the trained ML model was used to scan the library quickly and reliably for possible Mpro inhibitors. The ML output was then confirmed using atomistic simulations integrating molecular docking and molecular dynamic simulations with the linear interaction energy scheme. The results turned out to show that there was evidently good agreement between ML and atomistic simulations. Ten substances were proposed to be able to inhibit SARS-CoV-2 Mpro. Seven of them have high-nanomolar affinity and are very potential inhibitors. The strategy has been proven to be reliable and appropriate for fast prediction of SARS-CoV-2 Mpro inhibitors, benefiting for new emerging SARS-CoV-2 variants in the future accordingly.

Learning from COVID-19: How drug hunters can prepare for the next pandemic

Over 3 years, the SARS-CoV-2 pandemic killed nearly 7 million people and infected more than 767 million globally. During this time, our very small company was able to contribute to antiviral drug discovery efforts through global collaborations with other researchers, which enabled the identification and repurposing of multiple molecules with activity against SARS-CoV-2 including pyronaridine tetraphosphate, tilorone, quinacrine, vandetanib, lumefantrine, cetylpyridinium chloride, raloxifene, carvedilol, olmutinib, dacomitinib, crizotinib, and bosutinib. We highlight some of the key findings from this experience of using different computational and experimental strategies, and detail some of the challenges and strategies for how we might better prepare for the next pandemic so that potential antiviral treatments are available for future outbreaks.

The Impact of Artificial Intelligence in the Odyssey of Rare Diseases

Emerging machine learning (ML) technologies have the potential to significantly improve the research and treatment of rare diseases, which constitute a vast set of diseases that affect a small proportion of the total population. Artificial Intelligence (AI) algorithms can help to quickly identify patterns and associations that would be difficult or impossible for human analysts to detect. Predictive modeling techniques, such as deep learning, have been used to forecast the progression of rare diseases, enabling the development of more targeted treatments. Moreover, AI has also shown promise in the field of drug development for rare diseases with the identification of subpopulations of patients who may be most likely to respond to a particular drug. This review aims to highlight the achievements of AI algorithms in the study of rare diseases in the past decade and advise researchers on which methods have proven to be most effective. The review will focus on specific rare diseases, as defined by a prevalence rate that does not exceed 1-9/100,000 on Orphanet, and will examine which AI methods have been most successful in their study. We believe this review can guide clinicians and researchers in the successful application of ML in rare diseases.

Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches

Computational approaches, including physics- and knowledge-based methods, have commonly been used to determine the ligand-binding affinity toward SARS-CoV-2 main protease (Mpro or 3CLpro). Strong binding ligands can thus be suggested as potential inhibitors for blocking the biological activity of the protease. In this context, this paper aims to provide a short review of computational approaches that have recently been applied in the search for inhibitor candidates of Mpro. In particular, molecular docking and molecular dynamics (MD) simulations are usually combined to predict the binding affinity of thousands of compounds. Quantitative structure-activity relationship (QSAR) is the least computationally demanding and therefore can be used for large chemical collections of ligands. However, its accuracy may not be high. Moreover, the quantum mechanics/molecular mechanics (QM/MM) method is most commonly used for covalently binding inhibitors, which also play an important role in inhibiting the activity of SARS-CoV-2. Furthermore, machine learning (ML) models can significantly increase the searching space of ligands with high accuracy for binding affinity prediction. Physical insights into the binding process can then be confirmed via physics-based calculations. Integration of ML models into computational chemistry provides many more benefits and can lead to new therapies sooner.

The Commoditization of AI for Molecule Design

Anyone involved in designing or finding molecules in the life sciences over the past few years has witnessed a dramatic change in how we now work due to the COVID-19 pandemic. Computational technologies like artificial intelligence (AI) seemed to become ubiquitous in 2020 and have been increasingly applied as scientists worked from home and were separated from the laboratory and their colleagues. This shift may be more permanent as the future of molecule design across different industries will increasingly require machine learning models for design and optimization of molecules as they become "designed by AI". AI and machine learning has essentially become a commodity within the pharmaceutical industry. This perspective will briefly describe our personal opinions of how machine learning has evolved and is being applied to model different molecule properties that crosses industries in their utility and ultimately suggests the potential for tight integration of AI into equipment and automated experimental pipelines. It will also describe how many groups have implemented generative models covering different architectures, for de novo design of molecules. We also highlight some of the companies at the forefront of using AI to demonstrate how machine learning has impacted and influenced our work. Finally, we will peer into the future and suggest some of the areas that represent the most interesting technologies that may shape the future of molecule design, highlighting how we can help increase the efficiency of the design-make-test cycle which is currently a major focus across industries.

MegaSyn: Integrating Generative Molecular Design, Automated Analog Designer, and Synthetic Viability Prediction

Generative machine learning models have become widely adopted in drug discovery and other fields to produce new molecules and explore molecular space, with the goal of discovering novel compounds with optimized properties. These generative models are frequently combined with transfer learning or scoring of the physicochemical properties to steer generative design, yet often, they are not capable of addressing a wide variety of potential problems, as well as converge into similar molecular space when combined with a scoring function for the desired properties. In addition, these generated compounds may not be synthetically feasible, reducing their capabilities and limiting their usefulness in real-world scenarios. Here, we introduce a suite of automated tools called MegaSyn representing three components: a new hill-climb algorithm, which makes use of SMILES-based recurrent neural network (RNN) generative models, analog generation software, and retrosynthetic analysis coupled with fragment analysis to score molecules for their synthetic feasibility. We show that by deconstructing the targeted molecules and focusing on substructures, combined with an ensemble of generative models, MegaSyn generally performs well for the specific tasks of generating new scaffolds as well as targeted analogs, which are likely synthesizable and druglike. We now describe the development, benchmarking, and testing of this suite of tools and propose how they might be used to optimize molecules or prioritize promising lead compounds using these RNN examples provided by multiple test case examples.

Exploring machine learning: a scientometrics approach using bibliometrix and VOSviewer

Machine Learning has found application in solving complex problems in different fields of human endeavors such as intelligent gaming, automated transportation, cyborg technology, environmental protection, enhanced health care, innovation in banking and home security, and smart homes. This research is motivated by the need to explore the global structure of machine learning to ascertain the level of bibliographic coupling, collaboration among research institutions, co-authorship network of countries, and sources coupling in publications on machine learning techniques. The Hierarchical Density-Based Spatial Clustering of Applications with Noise (HDBSCAN) was applied to clustering prediction of authors dominance ranking in this paper. Publications related to machine learning were retrieved and extracted from the Dimensions database with no language restrictions. Bibliometrix was employed in computation and visualization to extract bibliographic information and perform a descriptive analysis. VOSviewer (version 1.6.16) tool was used to construct and visualize structure map of source coupling networks of researchers and co-authorship. About 10,814 research papers on machine learning published from 2010 to 2020 were retrieved for the research. Experimental results showed that the highest degree of betweenness centrality was obtained from cluster 3 with 153.86 from the University of California and Harvard University with 24.70. In cluster 1, the national university of Singapore has the highest degree betweenness of 91.72. Also, in cluster 5, the University of Cambridge (52.24) and imperial college London (4.52) having the highest betweenness centrality manifesting that he could control the collaborative relationship and that they possessed and controlled a large number of research resources. Findings revealed that this work has the potential to provide valuable guidance for new perspectives and future research work in the rapidly developing field of machine learning.

Phase-In to Phase-Out—Targeted, Inclusive Strategies Are Needed to Enable Full Replacement of Animal Use in the European Union

Simple Summary

In the European Union (and elsewhere), the overall use of animals in laboratories has failed to undergo any significant decline, despite six decades of purported adherence to the “3Rs” principles of replacement, reduction, and refinement. In the EU, the 1986 adoption of a legal requirement to use scientific methods not entailing the use of live animals, rising public opinion against the use of animals and the almost exponential rise in development and application of non-animal new approach methodologies (NAMs) signals a readiness to end animal testing. Indeed, the European Parliament recently carried an almost unanimous vote to adopt an action plan to phase out the use of animals in research and testing. This article explores what is needed to make this action plan a success, considering all stakeholders and their needs.

Abstract

In September 2021, the European Parliament voted overwhelmingly in favour of a resolution to phase out animal use for research, testing, and education, through the adoption of an action plan. Here we explore the opportunity that the action plan could offer in developing a more holistic outlook for fundamental and biomedical research, which accounts for around 70% of all animal use for scientific purposes in the EU. We specifically focus on biomedical research to consider how mapping scientific advances to patient needs, taking into account the ambitious health policies of the EU, would facilitate the development of non-animal strategies to deliver safe and effective medicines, for example. We consider what is needed to help accelerate the move away from animal use, taking account of all stakeholders and setting ambitious but realistic targets for the total replacement of animals. Importantly, we envisage this as a ‘phase-in’ approach, encouraging the use of human-relevant NAMs, enabling their development and application across research (with applications for toxicology testing). We make recommendations for three pillars of activity, inspired by similar efforts for making the shift to renewable energy and reducing carbon emissions, and point out where investment—both financial and personnel—may be needed.

Berberine Alleviates Gastroesophageal Reflux-Induced Airway Hyperresponsiveness in a Transient Receptor Potential A1-Dependent Manner

BACKGROUND

To investigate the beneficial effect of berberine on gastroesophageal reflux-induced airway hyperresponsiveness (GERAHR) and explore the underlying mechanism.

METHODS

Coword cluster analysis and strategic coordinates were used to identify hotspots for GERAHR research, and an online tool (STRING, https://string-db.org/) was used to predict the potential relationships between proteins. Guinea pigs with chemically induced GERAHR received PBS or different berberine-based treatments to evaluate the therapeutic effect of berberine and characterize the underlying mechanism. Airway responsiveness was assessed using a plethysmography system, and protein expression was evaluated by western blotting, immunohistochemical staining, and quantitative PCR analysis.

RESULTS

Bioinformatics analyses revealed that TRP channels are hotspots of GERAHR research, and TRPA1 is related to the proinflammatory neuropeptide substance P (SP). Berberine, especially at the middle dose tested (MB, 150 mg/kg), significantly improved lung function, suppressed inflammatory cell infiltration, and protected inflammation-driven tissue damage in the lung, trachea, esophagus, and nerve tissues in GERAHR guinea pigs. MB reduced the expression of TRPA1, SP, and tumor necrosis factor-alpha (TNF-α) in evaluated organs and tissues. Meanwhile, the MB-mediated protective effects were attenuated by simultaneous TRPA1 activation.

CONCLUSIONS

Mechanistically, berberine was found to suppress GERAHR-induced upregulation of TRPA1, SP, and TNF-α in many tissues. Our study has highlighted the potential therapeutic value of berberine for the treatment of GERAHR.