Molecular Property Diagnostic Suite for COVID-19 (MPDS^COVID-19): An open access disease specific drug discovery portal

Abstract

Computational drug discovery is intrinsically interdisciplinary and has to deal with the multifarious factors which are often dependent on the type of disease. Molecular Property Diagnostic Suite (MPDS) is a Galaxy based web portal which was conceived and developed as a disease specific web portal, originally developed for tuberculosis (MPDSTB). As specific computational tools are often required for a given disease, developing a disease specific web portal is highly desirable. This paper emphasises on the development of the customised web portal for COVID-19 infection and is referred to as MPDSCOVID-19. Expectedly, the MPDS suites of programs have modules which are essentially independent of a given disease, whereas some modules are specific to a particular disease. In the MPDSCOVID-19 portal, there are modules which are specific to COVID-19, and these are clubbed in SARS-COV-2 disease library. Further, the new additions and/or significant improvements were made to the disease independent modules, besides the addition of tools from galaxy toolshed. This manuscript provides a latest update on the disease independent modules of MPDS after almost 6 years, as well as provide the contemporary information and tool-shed necessary to engage in the drug discovery research of COVID-19. The disease independent modules include file format converter and descriptor calculation under the data processing module; QSAR, pharmacophore, scaffold analysis, active site analysis, docking, screening, drug repurposing tool, virtual screening, visualisation, sequence alignment, phylogenetic analysis under the data analysis module; and various machine learning packages, algorithms and in-house developed machine learning antiviral prediction model are available. The MPDS suite of programs are expected to bring a paradigm shift in computational drug discovery, especially in the academic community, guided through a transparent and open innovation approach. The MPDSCOVID-19 can be accessed at http://mpds.neist.res.in:8085.

Molecular Property Diagnostic Suite Compound Library (MPDS-CL): A Structure based Classification of the Chemical Space

“…At that time, using the 6 most popular and abundant chemical databases, around 110 million unique non-redundant set of compounds, with 31 classes, was reported. Over the period of time, various disease-speci c MPDS portals including MPDS TB [15], MPDS DM [34], MPDS COVID−19 [41] were developed, and other portals like MPDS NAFLD and MPDS HIV are under development. The modules in MPDS are categorized into (i) data library (that consists of information on genes and targets speci c to a disease or disorder, a molecular repository, druglike fragments, literature, etc.,) (ii) data processing (computation of molecular descriptors/ ngerprints, le format converter) (iii) data analysis (QSAR, docking, drug-likeness lter, and visualization tool), (iv) Advanced modules (which include various predictive modules for disease-disease interaction, big data analysis, and machine learning tools).…”

“…The modules in MPDS are categorized into (i) data library (that consists of information on genes and targets speci c to a disease or disorder, a molecular repository, druglike fragments, literature, etc.,) (ii) data processing (computation of molecular descriptors/ ngerprints, le format converter) (iii) data analysis (QSAR, docking, drug-likeness lter, and visualization tool), (iv) Advanced modules (which include various predictive modules for disease-disease interaction, big data analysis, and machine learning tools). MPDS is also equipped with a work ow management system that enables the users to easily integrate multiple tools from the available modules and customize the existing work ows as per the requirements [32][33][34]41]. The utility and scope of open-source packages are well documented in the literature [42][43].…”