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Scrutinizing Coronaviruses Using Publicly Available Bioinformatic Tools: The Viral Structural Proteins as a Case Study.

ABSTRACT: Since early 2020, the world suffers from a new beta-coronavirus, called SARS-CoV-2, that has devastating effects globally due to its associated disease, Covid-19. Until today, Covid-19, which not only causes life-threatening lung infections but also impairs various other organs and tissues, has killed hundreds of thousands of people and caused irreparable damage to many others. Since the very onset of the pandemic, huge efforts were made worldwide to fully understand this virus and numerous studies were, and still are, published. Many of these deal with structural analyses of the viral spike glycoprotein and with vaccine development, antibodies and antiviral molecules or immunomodulators that are assumed to become essential tools in the struggle against the virus. This paper summarizes knowledge on the properties of the four structural proteins (spike protein S, membrane protein M, envelope protein E and nucleocapsid protein N) of the SARS-CoV-2 virus and its relatives, SARS-CoV and MERS-CoV, that emerged few years earlier. Moreover, attention is paid to ways to analyze such proteins using freely available bioinformatic tools and, more importantly, to bring these proteins alive by looking at them on a computer/laptop screen with the easy-to-use but highly performant and interactive molecular graphics program DeepView. It is hoped that this paper will stimulate non-bioinformaticians and non-specialists in structural biology to scrutinize these and other macromolecules and as such will contribute to establishing procedures to fight these and maybe other forthcoming viruses.

SUBMITTER: Beeckmans S

PROVIDER: S-EPMC8181738 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThere is an increasing number of interactive web-based advance care planning (ACP) support tools, which are web-based aids in any format encouraging reflection, communication, and processing of publicly available information, most of which cannot be found in the peer-reviewed literature.ObjectiveThis study aims to conduct a systematic review of web-based ACP support tools to describe the characteristics, readability, and quality of content and investigate whether and how they are evaluated.MethodsWe systematically searched the web-based gray literature databases OpenGrey, ClinicalTrials.gov, ProQuest, British Library, Grey Literature in the Netherlands, and Health Services Research Projects in Progress, as well as Google and app stores, and consulted experts using the following eligibility criteria: web-based, designed for the general population, accessible to everyone, interactive (encouraging reflection, communication, and processing of information), and in English or Dutch. The quality of content was evaluated using the Quality Evaluation Scoring Tool (score 0-28-a higher score indicates better quality). To synthesize the characteristics of the ACP tools, readability and quality of content, and whether and how they were evaluated, we used 4 data extraction tables.ResultsA total of 30 tools met the eligibility criteria, including 15 (50%) websites, 10 (33%) web-based portals, 3 (10%) apps, and 2 (7%) with a combination of formats. Of the 30 tools, 24 (80%) mentioned a clear aim, including 7 (23%) that supported reflection or communication, 8 (27%) that supported people in making decisions, 7 (23%) that provided support to document decisions, and 2 (7%) that aimed to achieve all these aims. Of the 30 tools, 7 (23%) provided information on the development, all of which were developed in collaboration with health care professionals, and 3 (10%) with end users. Quality scores ranged between 11 and 28, with most of the lower-scoring tools not referring to information sources.ConclusionsA variety of ACP support tools are available on the web, varying in the quality of content. In the future, users should be involved in the development process of ACP support tools, and the content should be substantiated by scientific evidence.Trial registrationPROSPERO CRD42020184112; https://tinyurl.com/mruf8b43.

Project description:The molecular initiating event for many mechanisms of toxicological action comprise the reactive, covalent binding between an exogenous electrophile and an endogenous nucleophile. The target sites for electrophiles are typically peptides, proteins, enzymes or DNA. Of these, the formation of covalent adducts with proteins and DNA are perhaps the most established as they are most closely associated with skin sensitisation and genotoxicity endpoints. As such, being able to identify electrophilic features within a chemical structure provides a starting point to characterise its reactivity profile. There are a number of software tools that have been developed to help identify structural features indicative of electrophilic reactive potential to address various purposes, including: 1) to facilitate category formation for read-across of toxicity effects such as skin sensitisation potential, as well as 2) to profile substances to identify potential confounding factors to rationalise their activity in high-throughput screening (HTS) assays. Here, three such schemes that have been published in the literature as collections of SMARTS patterns and their associated chemical-biological reaction domains have been compared. The goals are 1) to better understand their scope and coverage, and 2) to assess their performance relative to a published skin sensitisation dataset where manual annotations to assign likely mechanistic domains based on expert judgement were already available. The 3 schemes were then applied to the Tox21 library and the consensus outcome was reported to highlight the proportion of chemicals likely to exhibit a reactivity response, specific to a mechanistic reaction domain, but non-specific with respect to target-tissue based activity. ToxPrint fingerprints were computed and activity enrichments computed to compare the structural features identified for the skin sensitisation dataset and Tox21 chemicals for each 'consensus' reaction domain. Enriched ToxPrints were also used to identify ToxCast assays potentially informative for reactivity.

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Scrutinizing Coronaviruses Using Publicly Available Bioinformatic Tools: The Viral Structural Proteins as a Case Study.

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