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"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool.

ABSTRACT: The scaffold representation is widely employed to classify bioactive compounds on the basis of common core structures or correlate compound classes with specific biological activities. In this paper, we present a novel approach called "Molecular Anatomy" as a flexible and unbiased molecular scaffold-based metrics to cluster large set of compounds. We introduce a set of nine molecular representations at different abstraction levels, combined with fragmentation rules, to define a multi-dimensional network of hierarchically interconnected molecular frameworks. We demonstrate that the introduction of a flexible scaffold definition and multiple pruning rules is an effective method to identify relevant chemical moieties. This approach allows to cluster together active molecules belonging to different molecular classes, capturing most of the structure activity information, in particular when libraries containing a huge number of singletons are analyzed. We also propose a procedure to derive a network visualization that allows a full graphical representation of compounds dataset, permitting an efficient navigation in the scaffold's space and significantly contributing to perform high quality SAR analysis. The protocol is freely available as a web interface at https://ma.exscalate.eu .

SUBMITTER: Manelfi C

PROVIDER: S-EPMC8299179 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool.

Manelfi Candida C Gemei Marica M Talarico Carmine C Cerchia Carmen C Fava Anna A Lunghini Filippo F Beccari Andrea Rosario AR

Journal of cheminformatics 20210723

The scaffold representation is widely employed to classify bioactive compounds on the basis of common core structures or correlate compound classes with specific biological activities. In this paper, we present a novel approach called "Molecular Anatomy" as a flexible and unbiased molecular scaffold-based metrics to cluster large set of compounds. We introduce a set of nine molecular representations at different abstraction levels, combined with fragmentation rules, to define a multi-dimensional ...[more]

PMID: 34301327

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Project description:BackgroundThe role of bone tissue engineering in the field of regenerative medicine has been a main research topic over the past few years. There has been much interest in the use of three-dimensional (3D) engineered scaffolds (PLA) complexed with human gingival mesenchymal stem cells (hGMSCs) as a new therapeutic strategy to improve bone tissue regeneration. These devices can mimic a more favorable endogenous microenvironment for cells in vivo by providing 3D substrates which are able to support cell survival, proliferation and differentiation. The present study evaluated the in vitro and in vivo capability of bone defect regeneration of 3D PLA, hGMSCs, extracellular vesicles (EVs), or polyethyleneimine (PEI)-engineered EVs (PEI-EVs) in the following experimental groups: 3D-PLA, 3D-PLA + hGMSCs, 3D-PLA + EVs, 3D-PLA + EVs + hGMSCs, 3D-PLA + PEI-EVs, 3D-PLA + PEI-EVs + hGMSCs.MethodsThe structural parameters of the scaffold were evaluated using both scanning electron microscopy and nondestructive microcomputed tomography. Nanotopographic surface features were investigated by means of atomic force microscopy. Scaffolds showed a statistically significant mass loss along the 112-day evaluation.ResultsOur in vitro results revealed that both 3D-PLA + EVs + hGMSCs and 3D-PLA + PEI-EVs + hGMSCs showed no cytotoxicity. However, 3D-PLA + PEI-EVs + hGMSCs exhibited greater osteogenic inductivity as revealed by morphological evaluation and transcriptomic analysis performed by next-generation sequencing (NGS). In addition, in vivo results showed that 3D-PLA + PEI-EVs + hGMSCs and 3D-PLA + PEI-EVs scaffolds implanted in rats subjected to cortical calvaria bone tissue damage were able to improve bone healing by showing better osteogenic properties. These results were supported also by computed tomography evaluation that revealed the repair of bone calvaria damage.ConclusionThe re-establishing of the integrity of the bone lesions could be a promising strategy in the treatment of accidental or surgery trauma, especially for cranial bones.

Project description:ObjectivesThe features that contribute to the apparent effectiveness of three-dimensional visualisation technology [3DVT] in teaching anatomy are largely unknown. The aim of this study was to conduct a systematic review and meta-analysis of the role of stereopsis in learning anatomy with 3DVT.MethodsThe review was conducted and reported according to PRISMA Standards. Literature search of English articles was performed using EMBASE, MEDLINE, CINAHL EBSCOhost, ERIC EBSCOhost, Cochrane CENTRAL, Web of Science and Google Scholar databases until November 2019. Study selection, data extraction and study appraisal were performed independently by two authors. Articles were assessed for methodological quality using the Medical Education Research Study Quality Instrument and the Cochrane Collaboration's tool for assessing the risk of bias. For quantitative analysis, studies were grouped based on relative between-intervention differences in instructional methods and type of control conditions.ResultsA total of 3934 citations were obtained of which 67 underwent a full-text review. Ultimately, 13 randomised controlled trials were included in the meta-analysis. When interactive, stereoscopic 3D models were compared to interactive, monoscopic 3D models within a single level of instructional design, for example isolating stereopsis as the only true manipulated element in the experimental design, an effect size [ES] of 0.53 (95% confidence interval [CI] 0.26-0.80; P < .00001) was found. In comparison with 2D images within multiple levels of instructional design, an effect size of 0.45 (95% CI 0.10-0.81; P < .002) was found. Stereopsis had no effect on learning when utilised with non-interactive 3D images (ES = -0.87, 95% CI -2.09-0.35; P = .16).ConclusionStereopsis is an important distinguishing element of 3DVT that has a significant positive effect on acquisition of anatomical knowledge when utilised within an interactive 3D environment. A distinction between stereoscopic and monoscopic 3DVT is essential to make in anatomical education and research.

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"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool.

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"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool.

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