PyMod 3: a complete suite for structural bioinformatics in PyMOL

Janson, Giacomo; Paiardini, Alessandro

doi:10.1093/bioinformatics/btaa849

Cited by 88 publications

(57 citation statements)

References 16 publications

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“…The final dataset was formed by four structures: 4J8M (Gustafson et al, 2014), 2X81 (Sloane et al, 2010), 2J4Z (Fancelli et al, 2006), 3UOH (Martin et al, 2012). The crystal structure of AURKA in complex with MLN8054 (PDB: 2X81) was used as a starting point to generate the model of AURKA in complex with Alisertib, using the “homology modeling” tool of PyMod 3.0 (Janson & Paiardini, 2020).…”

Section: Methodsmentioning

confidence: 99%

A Focused Small-Molecule Screen Identifies PHA-680626 as an Amphosteric Inhibitor Disrupting the Interaction between Aurora-A and N-Myc

Souvalidou

Montanari

et al. 2021

Preprint

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Neuroblastoma is a severe childhood disease, accounting for ≈10% of all infant cancers. The amplification of the MYCN gene, coding for the N-Myc transcriptional factor, is an essential marker correlated with tumor progression and poor prognosis. In neuroblastoma cells, the mitotic kinase Aurora-A (AURKA), which is another protein frequently overexpressed in cancer, prevents N-Myc degradation, by directly binding to a highly conserved N-Myc region, i.e. Myc Box I. As a result, elevated levels of N-Myc, which are required for the growth of MYCN amplified cells, are observed. During the last years, it has been demonstrated that the ATP competitive inhibitors of AURKA CD532, MLN8054 and Alisertib also cause essential conformational changes in the structure of the activation loop of the kinase that prevent N-Myc binding, thus impairing the formation of the AURKA /N-Myc complex. In this study, starting from a screening of crystal structures of AURKA in complex with known inhibitors, we identified additional compounds affecting the conformation of the kinase activation loop. We assessed the ability of such compounds to disrupt the interaction between AURKA and N-Myc in vitro, using Surface Plasmon Resonance competition assays, and in tumor cell lines overexpressing MYCN, by performing Proximity Ligation Assays. Finally, their effects on N-Myc cellular levels and cell viability were also investigated. Our results, identifying PHA-680626 as an amphosteric inhibitor both in vitro and MYCN overexpressing cell lines, expand the repertoire of known conformational disrupting inhibitors of the AURKA /N-Myc complex, and confirm that altering the conformation of the activation loop of AURKA with a small molecule is an effective strategy to destabilize the AURKA/N-Myc interaction in neuroblastoma cancer cells.

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Section: Methodsmentioning

confidence: 99%

A Focused Small-Molecule Screen Identifies PHA-680626 as an Amphosteric Inhibitor Disrupting the Interaction between Aurora-A and N-Myc

Souvalidou

Montanari

et al. 2021

Preprint

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“…To our knowledge, the crystal structure of eight CE4 enzymes acting on chitinous substrates are described so far, including AnCDA (2Y8U) 34 , ArCE4A (5LFZ) 33 , ClCDA (2IW0) 32 , SlCE4 (2CC0) 35 , VcCDA (4NY2) 22 , SpPgdA (2C1G) 44 , BsPdaC (6H8L) 27 and BmCDA8 (5Z34) 29 . All of them, except for BmCDA8, were used for a multiple structure alignment using the PyMOL plugin PyMod3 with SALIGN 45,46 . If multiple chains were present in the crystal structure, only chain A was used for the alignment.…”

Section: Multiple Structure Alignmentmentioning

confidence: 99%

In silico and in vitro analysis of an Aspergillus niger chitin deacetylase to decipher its subsite sugar preferences

Bonin

Hameleers

Hembach

et al. 2021

Journal of Biological Chemistry

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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“…The reference protein sequence Astrovirus VA1 capsid (accession number ASJ26376.1) was downloaded from Genbank; and HAstV-1 reference (CP core domain 5EWN and spike domain 5EWO [37]) was fetched in PyMOL (Version 2.0 Schrödinger, LLC). PyMOD3.0 [38] was used for the following analysis. Alignments of ASJ26376.1 with sequences of 5EWN and 5EWO were created separately using ClustalW [39].…”

Section: Capsid Structure Analysismentioning

confidence: 99%

Human Astroviruses: A Tale of Two Strains

Hargest

Davis

Tan

et al. 2021

Viruses

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Since the 1970s, eight closely related serotypes of classical human astroviruses (HAstV) have been associated with gastrointestinal illness worldwide. In the late 2000s, three genetically unique human astrovirus clades, VA1-VA3, VA2-VA4, and MLB, were described. While the exact disease associated with these clades remains to be defined, VA1 has been associated with central nervous system infections. The discovery that VA1 could be grown in cell culture, supports exciting new studies aimed at understanding viral pathogenesis. Given the association of VA1 with often lethal CNS infections, we tested its susceptibility to the antimicrobial drug, nitazoxanide (NTZ), which we showed could inhibit classical HAstV infections. Our studies demonstrate that NTZ inhibited VA1 replication in Caco2 cells even when added at 12 h post-infection, which is later than in HAstV-1 infection. These data led us to further probe VA1 replication kinetics and cellular responses to infection in Caco-2 cells in comparison to the well-studied HAstV-1 strain. Overall, our studies highlight that VA1 replicates more slowly than HAstV-1 and elicits significantly different cellular responses, including the inability to disrupt cellular junctions and barrier permeability.

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PyMod 3: a complete suite for structural bioinformatics in PyMOL

Cited by 88 publications

References 16 publications

A Focused Small-Molecule Screen Identifies PHA-680626 as an Amphosteric Inhibitor Disrupting the Interaction between Aurora-A and N-Myc

A Focused Small-Molecule Screen Identifies PHA-680626 as an Amphosteric Inhibitor Disrupting the Interaction between Aurora-A and N-Myc

In silico and in vitro analysis of an Aspergillus niger chitin deacetylase to decipher its subsite sugar preferences

Human Astroviruses: A Tale of Two Strains

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