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Article ; Online: Human Glucosylceramide Synthase at Work as Provided by "

Canini, Giorgia / Lo Cascio, Ettore / Della Longa, Stefano / Cecconi, Francesco / Arcovito, Alessandro

ACS omega

2023 Volume 8, Issue 9, Page(s) 8755–8765

Abstract: Glucosylceramide synthase (GCS) is an enzyme that catalyzes the first reaction of ceramide glycosylation in sphingolipid metabolism. It represents a primary target in the pharmacological treatment of some lysosomal storage diseases (LSDs), such as ... ...

Abstract	Glucosylceramide synthase (GCS) is an enzyme that catalyzes the first reaction of ceramide glycosylation in sphingolipid metabolism. It represents a primary target in the pharmacological treatment of some lysosomal storage diseases (LSDs), such as Gaucher and Niemann-Pick syndromes. In this study, starting from the model reported in the AlphaFold Protein Structure Database, the location and conformations of GCS substrates and cofactors have been provided by a step-by-step
Language	English
Publishing date	2023-02-22
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.2c08219
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein.

Giacon, Noah / Lo Cascio, Ettore / Davidson, Darcy S / Polêto, Marcelo D / Lemkul, Justin A / Pennacchietti, Valeria / Pagano, Livia / Zamparelli, Carlotta / Toto, Angelo / Arcovito, Alessandro

Computational and structural biotechnology journal

2023 Volume 21, Page(s) 3259–3271

Abstract: The Envelope (E) protein of SARS-CoV-2 plays a key role in virus maturation, assembly, and virulence mechanisms. The E protein is characterized by the presence of a PDZ-binding motif (PBM) at its C-terminus that allows it to interact with several PDZ- ... ...

Abstract	The Envelope (E) protein of SARS-CoV-2 plays a key role in virus maturation, assembly, and virulence mechanisms. The E protein is characterized by the presence of a PDZ-binding motif (PBM) at its C-terminus that allows it to interact with several PDZ-containing proteins in the intracellular environment. One of the main binding partners of the SARS-CoV-2 E protein is the PDZ2 domain of ZO1, a protein with a crucial role in the formation of epithelial and endothelial tight junctions (TJs). In this work, through a combination of analytical ultracentrifugation analysis and equilibrium and kinetic folding experiments, we show that ZO1-PDZ2 domain is able to fold in a monomeric state, an alternative form to the dimeric conformation that is reported to be functional in the cell for TJs assembly. Importantly, surface plasmon resonance (SPR) data indicate that the PDZ2 monomer is fully functional and capable of binding the C-terminal portion of the E protein of SARS-CoV-2, with a measured affinity in the micromolar range. Moreover, we present a detailed computational analysis of the complex between the C-terminal portion of E protein with ZO1-PDZ2, both in its monomeric conformation (computed as a high confidence AlphaFold2 model) and dimeric conformation (obtained from the Protein Data Bank), by using both polarizable and nonpolarizable simulations. Together, our results indicate both the monomeric and dimeric states of PDZ2 to be functional partners of the E protein, with similar binding mechanisms, and provide mechanistic and structural information about a fundamental interaction required for the replication of SARS-CoV-2.
Language	English
Publishing date	2023-05-25
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2023.05.027
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Article ; Online: Spiropiperidine-Based Oligomycin-Analog Ligands To Counteract the Ischemia-Reperfusion Injury in a Renal Cell Model.

Turrin, Giulia / Lo Cascio, Ettore / Giacon, Noah / Fantinati, Anna / Cristofori, Virginia / Illuminati, Davide / Preti, Delia / Morciano, Giampaolo / Pinton, Paolo / Agyapong, Esther Densu / Trapella, Claudio / Arcovito, Alessandro

Journal of medicinal chemistry

2023 Volume 67, Issue 1, Page(s) 586–602

Abstract: Finding a therapy for ischemia-reperfusion injury, which consists of cell death following restoration of blood flowing into the artery affected by ischemia, is a strong medical need. Nowadays, only the use of broad-spectrum molecular therapies has ... ...

Abstract	Finding a therapy for ischemia-reperfusion injury, which consists of cell death following restoration of blood flowing into the artery affected by ischemia, is a strong medical need. Nowadays, only the use of broad-spectrum molecular therapies has demonstrated a partial efficacy in protecting the organs following reperfusion, while randomized clinical trials focused on more specific drug targets have failed. In order to overcome this problem, we applied a combination of molecular modeling and chemical synthesis to identify novel spiropiperidine-based structures active in mitochondrial permeability transition pore opening inhibition as a key process to enhance cell survival after blood flow restoration. Our results were confirmed by biological assay on an in vitro cell model on HeLa and human renal proximal tubular epithelial cells and pave the way to further investigation on an in vivo model system.
MeSH term(s)	Humans ; Mitochondrial Membrane Transport Proteins/metabolism ; Oligomycins ; Reperfusion Injury/drug therapy ; Mitochondrial Permeability Transition Pore ; Epithelial Cells/metabolism
Chemical Substances	Mitochondrial Membrane Transport Proteins ; Oligomycins ; Mitochondrial Permeability Transition Pore
Language	English
Publishing date	2023-11-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.3c01792
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Article: Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins.

Lo Cascio, Ettore / Toto, Angelo / Babini, Gabriele / De Maio, Flavio / Sanguinetti, Maurizio / Mordente, Alvaro / Della Longa, Stefano / Arcovito, Alessandro

Computational and structural biotechnology journal

2021 Volume 19, Page(s) 1838–1847

Abstract: Short Linear Motifs (SLiMs) are functional protein microdomains that typically mediate interactions between a short linear region in one protein and a globular domain in another. Surface Plasmon Resonance assays have been performed to determine the ... ...

Abstract	Short Linear Motifs (SLiMs) are functional protein microdomains that typically mediate interactions between a short linear region in one protein and a globular domain in another. Surface Plasmon Resonance assays have been performed to determine the binding affinity between PDZ domain of wild type human PALS1 protein and tetradecapeptides representing the SLiMs sequences of SARS-CoV-1 and SARS-CoV-2 E proteins (E-SLiMs). SARS-CoV-2 E-SLiM binds to the human target protein with a higher affinity compared to SARS-CoV-1, showing a difference significantly greater than previously reported using the F318W mutant of PALS1 protein and shorter target peptides. Moreover, molecular dynamics simulations have provided clear evidence of the structural determinants driving this binding process. Specifically, the Arginine 69 residue in the SARS-CoV-2 E-SLiM is the key residue able to both enhance the specific polar interaction with negatively charged pockets of the PALS1 PDZ domain and reduce significantly the mobility of the viral peptide. These experimental and computational data are reinforced by the comparison of the interaction between the PALS1 PDZ domain with the natural ligand CRB1, as well as the corresponding E-SLiMs of other coronavirus members such as MERS and OCF43. Our results provide a model at the molecular level of the strategies used to mimic the endogenous SLiM peptide in the binding of the tight junctions of the host cell, explaining one of the possible reasons of the severity of the infection and pulmonary inflammation by SARS-CoV-2.
Language	English
Publishing date	2021-03-18
Publishing country	Netherlands
Document type	Journal Article
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2021.03.014
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Article: Mother and Daughter Carrying of the Same Pathogenic Variant in FGFR2 with Discordant Phenotype

Lo Vecchio, Filomena / Tabolacci, Elisabetta / Nobile, Veronica / Pomponi, Maria Grazia / Pietrobono, Roberta / Neri, Giovanni / Amenta, Simona / Candida, Ettore / Grippaudo, Cristina / Lo Cascio, Ettore / Vita, Alessia / Tiberio, Federica / Arcovito, Alessandro / Lattanzi, Wanda / Genuardi, Maurizio / Chiurazzi, Pietro

Genes. 2022 June 27, v. 13, no. 7

2022

Abstract: Craniosynostosis are a heterogeneous group of genetic conditions characterized by the premature fusion of the skull bones. The most common forms of craniosynostosis are Crouzon, Apert and Pfeiffer syndromes. They differ from each other in various ... ...

Abstract	Craniosynostosis are a heterogeneous group of genetic conditions characterized by the premature fusion of the skull bones. The most common forms of craniosynostosis are Crouzon, Apert and Pfeiffer syndromes. They differ from each other in various additional clinical manifestations, e.g., syndactyly is typical of Apert and rare in Pfeiffer syndrome. Their inheritance is autosomal dominant with incomplete penetrance and one of the main genes responsible for these syndromes is FGFR2, mapped on chromosome 10, encoding fibroblast growth factor receptor 2. We report an FGFR2 gene variant in a mother and daughter who present with different clinical features of Crouzon syndrome. The daughter is more severely affected than her mother, as also verified by a careful study of the face and oral cavity. The c.1032G>A transition in exon 8, already reported as a synonymous p.Ala344 = variant in Crouzon patients, also activates a new donor splice site leading to the loss of 51 nucleotides and the in-frame removal of 17 amino acids. We observed lower FGFR2 transcriptional and translational levels in the daughter compared to the mother and healthy controls. A preliminary functional assay and a molecular modeling added further details to explain the discordant phenotype of the two patients.
Keywords	chromosomes ; exons ; face ; fibroblast growth factor receptor 2 ; mouth ; nucleotides ; penetrance ; phenotype ; skull ; transcription (genetics)
Language	English
Dates of publication	2022-0627
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13071161
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Mutated axon guidance gene PLXNB2 sustains growth and invasiveness of stem cells isolated from cancers of unknown primary.

Brundu, Serena / Napolitano, Virginia / Franzolin, Giulia / Lo Cascio, Ettore / Mastrantonio, Roberta / Sardo, Gabriele / Cascardi, Eliano / Verginelli, Federica / Sarnataro, Sergio / Gambardella, Gennaro / Pisacane, Alberto / Arcovito, Alessandro / Boccaccio, Carla / Comoglio, Paolo M / Giraudo, Enrico / Tamagnone, Luca

EMBO molecular medicine

2023 Volume 15, Issue 3, Page(s) e16104

Abstract: The genetic changes sustaining the development of cancers of unknown primary (CUP) remain elusive. The whole-exome genomic profiling of 14 rigorously selected CUP samples did not reveal specific recurring mutation in known driver genes. However, by ... ...

Abstract	The genetic changes sustaining the development of cancers of unknown primary (CUP) remain elusive. The whole-exome genomic profiling of 14 rigorously selected CUP samples did not reveal specific recurring mutation in known driver genes. However, by comparing the mutational landscape of CUPs with that of most other human tumor types, it emerged a consistent enrichment of changes in genes belonging to the axon guidance KEGG pathway. In particular, G842C mutation of PlexinB2 (PlxnB2) was predicted to be activating. Indeed, knocking down the mutated, but not the wild-type, PlxnB2 in CUP stem cells resulted in the impairment of self-renewal and proliferation in culture, as well as tumorigenic capacity in mice. Conversely, the genetic transfer of G842C-PlxnB2 was sufficient to promote CUP stem cell proliferation and tumorigenesis in mice. Notably, G842C-PlxnB2 expression in CUP cells was associated with basal EGFR phosphorylation, and EGFR blockade impaired the viability of CUP cells reliant on the mutated receptor. Moreover, the mutated PlxnB2 elicited CUP cell invasiveness, blocked by EGFR inhibitor treatment. In sum, we found that a novel activating mutation of the axon guidance gene PLXNB2 sustains proliferative autonomy and confers invasive properties to stem cells isolated from cancers of unknown primary, in EGFR-dependent manner.
MeSH term(s)	Animals ; Humans ; Mice ; Axon Guidance ; ErbB Receptors/genetics ; Mutation ; Neoplasm Recurrence, Local ; Neoplasms, Unknown Primary/genetics ; Nerve Tissue Proteins/genetics ; Neoplastic Stem Cells/pathology
Chemical Substances	ErbB Receptors (EC 2.7.10.1) ; PLXNB2 protein, human ; Plxnb2 protein, mouse ; Nerve Tissue Proteins
Language	English
Publishing date	2023-02-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2467145-9
ISSN	1757-4684 ; 1757-4676
ISSN (online)	1757-4684
ISSN	1757-4676
DOI	10.15252/emmm.202216104
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Article ; Online: Mother and Daughter Carrying of the Same Pathogenic Variant in

Genes

2022 Volume 13, Issue 7

Abstract	Craniosynostosis are a heterogeneous group of genetic conditions characterized by the premature fusion of the skull bones. The most common forms of craniosynostosis are Crouzon, Apert and Pfeiffer syndromes. They differ from each other in various additional clinical manifestations, e.g., syndactyly is typical of Apert and rare in Pfeiffer syndrome. Their inheritance is autosomal dominant with incomplete penetrance and one of the main genes responsible for these syndromes is FGFR2, mapped on chromosome 10, encoding fibroblast growth factor receptor 2. We report an FGFR2 gene variant in a mother and daughter who present with different clinical features of Crouzon syndrome. The daughter is more severely affected than her mother, as also verified by a careful study of the face and oral cavity. The c.1032G>A transition in exon 8, already reported as a synonymous p.Ala344 = variant in Crouzon patients, also activates a new donor splice site leading to the loss of 51 nucleotides and the in-frame removal of 17 amino acids. We observed lower FGFR2 transcriptional and translational levels in the daughter compared to the mother and healthy controls. A preliminary functional assay and a molecular modeling added further details to explain the discordant phenotype of the two patients.
MeSH term(s)	Acrocephalosyndactylia/genetics ; Craniosynostoses/genetics ; Female ; Humans ; Mothers ; Phenotype ; Receptor, Fibroblast Growth Factor, Type 2/genetics
Chemical Substances	FGFR2 protein, human (EC 2.7.10.1) ; Receptor, Fibroblast Growth Factor, Type 2 (EC 2.7.10.1)
Language	English
Publishing date	2022-06-27
Publishing country	Switzerland
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13071161
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Article ; Online: Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis.

De Maio, Flavio / Lo Cascio, Ettore / Babini, Gabriele / Sali, Michela / Della Longa, Stefano / Tilocca, Bruno / Roncada, Paola / Arcovito, Alessandro / Sanguinetti, Maurizio / Scambia, Giovanni / Urbani, Andrea

Microbes and infection

2020 Volume 22, Issue 10, Page(s) 592–597

Abstract: The Envelope (E) protein of SARS-CoV-2 is the most enigmatic protein among the four structural ones. Most of its current knowledge is based on the direct comparison to the SARS E protein, initially mistakenly undervalued and subsequently proved to be a ... ...

Abstract	The Envelope (E) protein of SARS-CoV-2 is the most enigmatic protein among the four structural ones. Most of its current knowledge is based on the direct comparison to the SARS E protein, initially mistakenly undervalued and subsequently proved to be a key factor in the ER-Golgi localization and in tight junction disruption. We compared the genomic sequences of E protein of SARS-CoV-2, SARS-CoV and the closely related genomes of bats and pangolins obtained from the GISAID and GenBank databases. When compared to the known SARS E protein, we observed a significant difference in amino acid sequence in the C-terminal end of SARS-CoV-2 E protein. Subsequently, in silico modelling analyses of E proteins conformation and docking provide evidences of a strengthened binding of SARS-CoV-2 E protein with the tight junction-associated PALS1 protein. Based on our computational evidences and on data related to SARS-CoV, we believe that SARS-CoV-2 E protein interferes more stably with PALS1 leading to an enhanced epithelial barrier disruption, amplifying the inflammatory processes, and promoting tissue remodelling. These findings raise a warning on the underestimated role of the E protein in the pathogenic mechanism and open the route to detailed experimental investigations.
MeSH term(s)	Amino Acid Sequence ; Animals ; COVID-19/genetics ; COVID-19/metabolism ; Chiroptera/virology ; Databases, Genetic ; Humans ; Membrane Proteins/chemistry ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Molecular Dynamics Simulation ; Nucleoside-Phosphate Kinase/chemistry ; Nucleoside-Phosphate Kinase/genetics ; Nucleoside-Phosphate Kinase/metabolism ; Pangolins/virology ; SARS Virus/chemistry ; SARS Virus/genetics ; SARS Virus/metabolism ; SARS-CoV-2/chemistry ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; SARS-CoV-2/pathogenicity ; Tight Junctions/chemistry ; Tight Junctions/metabolism ; Viral Envelope Proteins/chemistry ; Viral Envelope Proteins/genetics ; Viral Envelope Proteins/metabolism
Chemical Substances	Membrane Proteins ; Viral Envelope Proteins ; Nucleoside-Phosphate Kinase (EC 2.7.4.4) ; MPP5 protein, human (EC 2.7.4.8)
Keywords	covid19
Language	English
Publishing date	2020-09-04
Publishing country	France
Document type	Journal Article
ZDB-ID	1465093-9
ISSN	1769-714X ; 1286-4579
ISSN (online)	1769-714X
ISSN	1286-4579
DOI	10.1016/j.micinf.2020.08.006
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Article ; Online: Novel Mixed NOP/Opioid Receptor Peptide Agonists.

Journal of medicinal chemistry

2021 Volume 64, Issue 10, Page(s) 6656–6669

Abstract: The nociceptin/orphanin FQ (N/OFQ)/N/OFQ receptor (NOP) system controls different biological functions including pain and cough reflex. Mixed NOP/opioid receptor agonists elicit similar effects to strong opioids but with reduced side effects. In this ... ...

Abstract	The nociceptin/orphanin FQ (N/OFQ)/N/OFQ receptor (NOP) system controls different biological functions including pain and cough reflex. Mixed NOP/opioid receptor agonists elicit similar effects to strong opioids but with reduced side effects. In this work, 31 peptides with the general sequence [Tyr/Dmt
MeSH term(s)	Animals ; Binding Sites ; Cough/chemically induced ; Cough/drug therapy ; Disease Models, Animal ; Guinea Pigs ; Humans ; Hydrophobic and Hydrophilic Interactions ; Male ; Molecular Dynamics Simulation ; Peptides/chemistry ; Peptides/metabolism ; Peptides/therapeutic use ; Receptors, Opioid/agonists ; Receptors, Opioid/metabolism ; Receptors, Opioid, mu/agonists ; Receptors, Opioid, mu/genetics ; Receptors, Opioid, mu/metabolism ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/chemistry ; Recombinant Proteins/isolation & purification ; Structure-Activity Relationship
Chemical Substances	Peptides ; Receptors, Opioid ; Receptors, Opioid, mu ; Recombinant Proteins ; nociceptin receptor (DVO6VKD7IJ)
Language	English
Publishing date	2021-05-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.0c02062
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Article: Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis

Microbres infect

Abstract	The Envelope (E) protein of SARS-CoV-2 is the most enigmatic protein among the four structural ones. Most of its current knowledge is based on the direct comparison to the SARS E protein, initially mistakenly undervalued and subsequently proved to be a key factor in the ER-Golgi localization and in tight junction disruption. We compared the genomic sequences of E protein of SARS-CoV-2, SARS-CoV and the closely related genomes of bats and pangolins obtained from the GISAID and GenBank databases. When compared to the known SARS E protein, we observed a significant difference in amino acid sequence in the C-terminal end of SARS-CoV-2 E protein. Subsequently, in silico modelling analyses of E proteins conformation and docking provide evidences of a strengthened binding of SARS-CoV-2 E protein with the tight junction-associated PALS1 protein. Based on our computational evidences and on data related to SARS-CoV, we believe that SARS-CoV-2 E protein interferes more stably with PALS1 leading to an enhanced epithelial barrier disruption, amplifying the inflammatory processes, and promoting tissue remodelling. These findings raise a warning on the underestimated role of the E protein in the pathogenic mechanism and open the route to detailed experimental investigations.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #744191
Database	COVID19

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