An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations.

/pdf/towards-the-sustainable-discovery-and-development-of-new-3ugkmuenu2.pdf

Towards the sustainable discovery and development of new antibiotics

Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in NP research around the world and in different application fields, therefore, over the years a multiplication of generalistic and thematic NP databases has been observed. However, there is, at this moment, no online resource regrouping all known NPs in just one place, which would greatly simplify NPs research and allow computational screening and other in silico applications. In this manuscript we present the online version of the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net
 .

/pdf/coconut-online-collection-of-open-natural-products-database-20bx7ti4q9.pdf

COCONUT online: Collection of Open Natural Products database

Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human gut, but also the chemistry of distant environments, such as other parts of the body. Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota, and to understand the functional role of these microbial metabolites. This Review provides a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis. Data analysis remains an obstacle; therefore, the emphasis is placed on data analysis approaches and integrative analysis, including the integration of microbiome sequencing data.

Mass spectrometry-based metabolomics in microbiome investigations.

Novel antibiotics are urgently needed to address the looming global crisis of antibiotic resistance. Historically, the primary source of clinically used antibiotics has been microbial secondary metabolism. Microbial genome sequencing has revealed a plethora of uncharacterized natural antibiotics that remain to be discovered. However, the isolation of these molecules is hindered by the challenge of linking sequence information to the chemical structures of the encoded molecules. Here, we present PRISM 4, a comprehensive platform for prediction of the chemical structures of genomically encoded antibiotics, including all classes of bacterial antibiotics currently in clinical use. The accuracy of chemical structure prediction enables the development of machine-learning methods to predict the likely biological activity of encoded molecules. We apply PRISM 4 to chart secondary metabolite biosynthesis in a collection of over 10,000 bacterial genomes from both cultured isolates and metagenomic datasets, revealing thousands of encoded antibiotics. PRISM 4 is freely available as an interactive web application at http://prism.adapsyn.com
 . Large-scale sequencing efforts have uncovered a large number of secondary metabolic pathways, but the chemicals they synthesise remain unknown. Here the authors present PRISM 4, which predicts the chemical structures encoded by microbial genome sequences, including all classes of bacterial antibiotics in clinical use.

/pdf/comprehensive-prediction-of-secondary-metabolite-structure-1jswgilst8.pdf

Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences.

Computational approaches such as genome and metabolome mining are becoming essential to natural products (NPs) research. Consequently, a need exists for an automated structure-type classification system to handle the massive amounts of data appearing for NP structures. An ideal semantic ontology for the classification of NPs should go beyond the simple presence/absence of chemical substructures, but also include the taxonomy of the producing organism, the nature of the biosynthetic pathway, and/or their biological properties. Thus, a holistic and automatic NP classification framework could have considerable value to comprehensively navigate the relatedness of NPs, and especially so when analyzing large numbers of NPs. Here, we introduce NPClassifier, a deep-learning tool for the automated structural classification of NPs from their counted Morgan fingerprints. NPClassifier is expected to accelerate and enhance NP discovery by linking NP structures to their underlying properties.

NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products.

Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced natural product structures. Lack of availability of these data is preventing the implementation of new technologies in natural products science. Specifically, development of new computational strategies for compound characterization and identification are being hampered by the lack of a comprehensive database of known compounds against which to compare experimental data. The creation of an open access, community-maintained database of microbial natural product structures would enable the development of new technologies in natural products discovery and improve the interoperability of existing natural products data resources. However, these data are spread unevenly throughout the historical scientific literature, including both journal articles and international patents. These documents have no standard format, are often not digitized as machine readable text, and are not publicly available. Further, none of these documents have associated structure files (e.g., MOL, InChI, or SMILES), instead containing images of structures. This makes extraction and formatting of relevant natural products data a formidable challenge. Using a combination of manual curation and automated data mining approaches we have created a database of microbial natural products (The Natural Products Atlas, www.npatlas.org) that includes 24 594 compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. This database is accompanied by an interactive web portal that permits searching by structure, substructure, and physical properties. The Web site also provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. These interactive tools offer a powerful knowledge base for natural products discovery with a central interface for structure and property-based searching and presents new viewpoints on structural diversity in natural products. The Natural Products Atlas has been developed under FAIR principles (Findable, Accessible, Interoperable, and Reusable) and is integrated with other emerging natural product databases, including the Minimum Information About a Biosynthetic Gene Cluster (MIBiG) repository, and the Global Natural Products Social Molecular Networking (GNPS) platform. It is designed as a community-supported resource to provide a central repository for known natural product structures from microorganisms and is the first comprehensive, open access resource of this type. It is expected that the Natural Products Atlas will enable the development of new natural products discovery modalities and accelerate the process of structural characterization for complex natural products libraries.

/pdf/the-natural-products-atlas-an-open-access-knowledge-base-for-41k50vym1e.pdf

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery.

Research Aims: Human resources are critical for success in the digital economy. However, IT human resources are predicted to be scarce and attracting IT talent is difficult for many enterprises. Currently, employer branding and social media advertising are possible solutions to these problems. This research aims to evaluate the influence of EVP and social media use on the intention to apply for an IT job. Design/Methodology/Approach: The quantitative research method is used to verify the research model. The sample includes 240 valid respondents from HCMC, Vietnam. The research model includes six independent variables (5 values of EVP and social media use) affecting the intention to apply for a job through organisational reputation. Some analysis methods used include Descriptive Statistics, Cronbach’s Alpha, EFA, Multiple Regression, and Bootstrap Analysis. Research Findings: The results show that 4/5 of the values (except management value) and social media use have positive impacts on reputation and, in turn, on the intention to apply for a job. Theoretical Contribution/Originality: This research clarifies the role of employer branding and social media use in attracting talent to the Vietnamese IT industry. The mediating role of organisational reputation is also confirmed using the bootstrapping method. Managerial Implication in the South East Asian Context: Based on the results, some recommendations have been made to improve the attractiveness of the IT industry in Vietnam and the ASEAN context. Research Limitations & Implications: Limitations of the study include the small sample size and lack of other aspects of employer branding. So, increasing the sample size and adding some other factors could be implications for future research directions.

/pdf/impact-of-employer-value-proposition-and-social-media-use-on-3ac5p5yy.pdf

Impact of Employer Value Proposition and Social Media Use on the Intention to Apply for a Job in the IT Industry of Vietnam

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The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery.

Impact of Employer Value Proposition and Social Media Use on the Intention to Apply for a Job in the IT Industry of Vietnam