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Chinellato M, Perin S, Carli A, Lastella L, Biondi B, Borsato G, Di Giorgio E, Brancolini C, Cendron L, Angelini A. Folding of Class IIa HDAC Derived Peptides into α-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA. J Mol Biol 2024; 436:168541. [PMID: 38492719 DOI: 10.1016/j.jmb.2024.168541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Interaction of transcription factor myocyte enhancer factor-2 (MEF2) family members with class IIa histone deacetylases (HDACs) has been implicated in a wide variety of diseases. Though considerable knowledge on this topic has been accumulated over the years, a high resolution and detailed analysis of the binding mode of multiple class IIa HDAC derived peptides with MEF2D is still lacking. To fulfil this gap, we report here the crystal structure of MEF2D in complex with double strand DNA and four different class IIa HDAC derived peptides, namely HDAC4, HDAC5, HDAC7 and HDAC9. All class IIa HDAC derived peptides form extended amphipathic α-helix structures that fit snugly in the hydrophobic groove of MEF2D domain. Binding mode of class IIa HDAC derived peptides to MEF2D is very similar and occur primarily through nonpolar interactions mediated by highly conserved branched hydrophobic amino acids. Further studies revealed that class IIa HDAC derived peptides are unstructured in solution and appear to adopt a folded α-helix structure only upon binding to MEF2D. Comparison of our peptide-protein complexes with previously characterized structures of MEF2 bound to different co-activators and co-repressors, highlighted both differences and similarities, and revealed the adaptability of MEF2 in protein-protein interactions. The elucidation of the three-dimensional structure of MEF2D in complex with multiple class IIa HDAC derived peptides provide not only a better understanding of the molecular basis of their interactions but also have implications for the development of novel antagonist.
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Affiliation(s)
- Monica Chinellato
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy
| | - Stefano Perin
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy
| | - Alberto Carli
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy
| | - Luana Lastella
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Via Marzolo 1, 35131 Padova, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Via Marzolo 1, 35131 Padova, Italy
| | - Giuseppe Borsato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy
| | - Eros Di Giorgio
- Department of Medicine, Università Degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Department of Medicine, Università Degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Laura Cendron
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy.
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy; European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy.
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2
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Nielsen AL, Bognar Z, Mothukuri GK, Zarda A, Schuttel M, Merz ML, Ji X, Will E, Chinellato M, Bartling CRO, Stromgaard K, Cendron L, Angelini A, Heinis C. Large Libraries of Structurally Diverse Macrocycles Suitable for Membrane Permeation. Angew Chem Int Ed Engl 2024:e202400350. [PMID: 38602024 DOI: 10.1002/anie.202400350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/11/2024] [Accepted: 04/09/2024] [Indexed: 04/12/2024]
Abstract
Macrocycles offer an attractive format for drug development due to their good binding properties and potential to cross cell membranes. To efficiently identify macrocyclic ligands for new targets, methods for the synthesis and screening of large combinatorial libraries of small cyclic peptides were developed, many of them using thiol groups for efficient peptide macrocyclization. However, a weakness of these libraries is that invariant thiol-containing building blocks such as cysteine are used, resulting in a region that does not contribute to library diversity but increases molecule size. Herein, we synthesized a series of structurally diverse thiol-containing elements and used them for the combinatorial synthesis of a 2,688-member library of small, structurally diverse peptidic macrocycles with unprecedented skeletal complexity. We then used this library to discover potent thrombin and plasma kallikrein inhibitors, some also demonstrating favorable membrane permeability. X-ray structure analysis of macrocycle-target complexes showed that the size and shape of the newly developed thiol elements are key for binding. The strategy and library format presented in this work significantly enhance structural diversity by allowing combinatorial modifications to a previously invariant region of peptide macrocycles, which may be broadly applied in the development of membrane permeable therapeutics.
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Affiliation(s)
| | - Zsolt Bognar
- EPFL Institute of Chemical Sciences and Engineering, ISIC, SWITZERLAND
| | | | - Anne Zarda
- EPFL Institute of Chemical Sciences and Engineering, ISIC, SWITZERLAND
| | - Mischa Schuttel
- EPFL Institute of Chemical Sciences and Engineering, ISIC, SWITZERLAND
| | - Manuel L Merz
- EPFL Institute of Chemical Sciences and Engineering, ISIC, SWITZERLAND
| | - Xinjian Ji
- EPFL Institute of Chemical Sciences and Engineering, ISIC, SWITZERLAND
| | - Edward Will
- EPFL Institute of Chemical Sciences and Engineering, ISIC, SWITZERLAND
| | | | | | | | | | - Alessandro Angelini
- Ca' Foscari University of Venice, Department of Molecular Sciences and Nanosystems, ITALY
| | - Christian Heinis
- Ecole Polytechnique Federale de Lausanne EPFL, Institute of Chemical Sciences and Engineering, BCH 5305, 1015, Lausanne, SWITZERLAND
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3
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Villano G, Novo E, Turato C, Quarta S, Ruvoletto M, Biasiolo A, Protopapa F, Chinellato M, Martini A, Trevellin E, Granzotto M, Cannito S, Cendron L, De Siervi S, Guido M, Parola M, Vettor R, Pontisso P. The protease activated receptor 2 - CCAAT/enhancer-binding protein beta - SerpinB3 axis inhibition as a novel strategy for the treatment of non-alcoholic steatohepatitis. Mol Metab 2024; 81:101889. [PMID: 38307387 PMCID: PMC10864841 DOI: 10.1016/j.molmet.2024.101889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/11/2024] [Accepted: 01/26/2024] [Indexed: 02/04/2024] Open
Abstract
OBJECTIVE The serine protease inhibitor SerpinB3 has been described as critical mediator of liver fibrosis and it has been recently proposed as an additional hepatokine involved in NASH development and insulin resistance. Protease Activated Receptor 2 has been identified as a novel regulator of hepatic metabolism. A targeted therapeutic strategy for NASH has been investigated, using 1-Piperidine Propionic Acid (1-PPA), since this compound has been recently proposed as both Protease Activated Receptor 2 and SerpinB3 inhibitor. METHODS The effect of SerpinB3 on inflammation and fibrosis genes was assessed in human macrophage and stellate cell lines. Transgenic mice, either overexpressing SerpinB3 or carrying Serpinb3 deletion and their relative wild type strains, were used in experimental NASH models. Subgroups of SerpinB3 transgenic mice and their controls were also injected with 1-PPA to assess the efficacy of this compound in NASH inhibition. RESULTS 1-PPA did not present significant cell and organ toxicity and was able to inhibit SerpinB3 and PAR2 in a dose-dependent manner. This effect was associated to a parallel reduction of the synthesis of the molecules induced by endogenous SerpinB3 or by its paracrine effects both in vitro and in vivo, leading to inhibition of lipid accumulation, inflammation and fibrosis in experimental NASH. At mechanistic level, the antiprotease activity of SerpinB3 was found essential for PAR2 activation, determining upregulation of the CCAAT Enhancer Binding Protein beta (C/EBP-β), another pivotal regulator of metabolism, inflammation and fibrosis, which in turn determined SerpinB3 synthesis. CONCLUSIONS 1-PPA treatment was able to inhibit the PAR2 - C/EBP-β - SerpinB3 axis and to protect from NASH development and progression, supporting the potential use of a similar approach for a targeted therapy of NASH.
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Affiliation(s)
- Gianmarco Villano
- Dept. of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Italy
| | - Erica Novo
- Dept. of Clinical and Biological Sciences, University of Torino, Italy
| | | | | | | | | | | | | | | | | | | | - Stefania Cannito
- Dept. of Clinical and Biological Sciences, University of Torino, Italy
| | | | | | - Maria Guido
- Dept. of Medicine, University of Padova, Italy
| | - Maurizio Parola
- Dept. of Clinical and Biological Sciences, University of Torino, Italy
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4
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De Felice S, Romanyuk Z, Chinellato M, Zoia G, Linciano S, Kumada Y, Pardon E, Steyaert J, Angelini A, Cendron L. Crystal structure of human serum albumin in complex with megabody reveals unique human and murine cross-reactive binding site. Protein Sci 2024; 33:e4887. [PMID: 38152025 PMCID: PMC10804666 DOI: 10.1002/pro.4887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/22/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023]
Abstract
The pharmacokinetic properties of small biotherapeutics can be enhanced via conjugation to cross-reactive albumin-binding ligands in a process that improves their safety and accelerates testing through multiple pre-clinical animal models. In this context, the small and stable heavy-chain-only nanobody NbAlb1, capable of binding both human and murine albumin, has recently been successfully applied to improve the stability and prolong the in vivo plasma residence time of multiple small therapeutic candidates. Despite its clinical efficacy, the mechanism of cross-reactivity of NbAlb1 between human and murine serum albumins has not yet been investigated. To unveil the molecular basis of such an interaction, we solved the crystal structure of human serum albumin (hSA) in complex with NbAlb1. The structure was obtained by harnessing the unique features of a megabody chimeric protein, comprising NbAlb1 grafted onto a modified version of the circularly permutated and bacterial-derived protein HopQ. This structure showed that NbAlb1 contacts a yet unexplored binding site located in the peripheral region of domain II that is conserved in both human and mouse serum albumin proteins. Furthermore, we show that the binding of NbAlb1 to both serum albumin proteins is retained even at acidic pH levels, thus explaining its extended in vivo half-life. The elucidation of the molecular basis of NbAlb1 cross-reactivity to human and murine albumins might guide the design of novel nanobodies with broader reactivity toward a larger panel of serum albumins, thus facilitating the pre-clinical and clinical phases in humans.
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Affiliation(s)
| | - Zhanna Romanyuk
- Department of Molecular Sciences and NanosystemsCa’ Foscari University of VeniceVeniceItaly
| | | | - Giulia Zoia
- Department of Molecular Sciences and NanosystemsCa’ Foscari University of VeniceVeniceItaly
| | - Sara Linciano
- Department of Molecular Sciences and NanosystemsCa’ Foscari University of VeniceVeniceItaly
| | - Yoichi Kumada
- Department of Functional Chemistry and EngineeringKyoto Institute of TechnologyKyotoJapan
| | - Els Pardon
- VIB‐VUB Center for Structural Biology, VIBBrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Jan Steyaert
- VIB‐VUB Center for Structural Biology, VIBBrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Alessandro Angelini
- Department of Molecular Sciences and NanosystemsCa’ Foscari University of VeniceVeniceItaly
- European Centre for Living Technology (ECLT), Ca’ BottacinVeniceItaly
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5
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Marchesan E, Nardin A, Mauri S, Bernardo G, Chander V, Di Paola S, Chinellato M, von Stockum S, Chakraborty J, Herkenne S, Basso V, Schrepfer E, Marin O, Cendron L, Medina DL, Scorrano L, Ziviani E. Activation of Ca 2+ phosphatase Calcineurin regulates Parkin translocation to mitochondria and mitophagy in flies. Cell Death Differ 2024; 31:217-238. [PMID: 38238520 PMCID: PMC10850161 DOI: 10.1038/s41418-023-01251-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 02/09/2024] Open
Abstract
Selective removal of dysfunctional mitochondria via autophagy is crucial for the maintenance of cellular homeostasis. This event is initiated by the translocation of the E3 ubiquitin ligase Parkin to damaged mitochondria, and it requires the Serine/Threonine-protein kinase PINK1. In a coordinated set of events, PINK1 operates upstream of Parkin in a linear pathway that leads to the phosphorylation of Parkin, Ubiquitin, and Parkin mitochondrial substrates, to promote ubiquitination of outer mitochondrial membrane proteins. Ubiquitin-decorated mitochondria are selectively recruiting autophagy receptors, which are required to terminate the organelle via autophagy. In this work, we show a previously uncharacterized molecular pathway that correlates the activation of the Ca2+-dependent phosphatase Calcineurin to Parkin translocation and Parkin-dependent mitophagy. Calcineurin downregulation or genetic inhibition prevents Parkin translocation to CCCP-treated mitochondria and impairs stress-induced mitophagy, whereas Calcineurin activation promotes Parkin mitochondrial recruitment and basal mitophagy. Calcineurin interacts with Parkin, and promotes Parkin translocation in the absence of PINK1, but requires PINK1 expression to execute mitophagy in MEF cells. Genetic activation of Calcineurin in vivo boosts basal mitophagy in neurons and corrects locomotor dysfunction and mitochondrial respiratory defects of a Drosophila model of impaired mitochondrial functions. Our study identifies Calcineurin as a novel key player in the regulation of Parkin translocation and mitophagy.
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Affiliation(s)
| | - Alice Nardin
- Department of Biology, University of Padova, Padova, Italy
| | - Sofia Mauri
- Department of Biology, University of Padova, Padova, Italy
| | - Greta Bernardo
- Department of Biology, University of Padova, Padova, Italy
| | - Vivek Chander
- Department of Biology, University of Padova, Padova, Italy
| | - Simone Di Paola
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Institute for Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Napoli, Italy
| | | | | | | | | | | | - Emilie Schrepfer
- Department of Biology, University of Padova, Padova, Italy
- Dulbecco-Telethon Institute, Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Oriano Marin
- Department of Biomedical Sciences (DSB), University of Padova, Padova, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Padova, Italy
| | - Diego L Medina
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, Padova, Italy
- Dulbecco-Telethon Institute, Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Elena Ziviani
- Department of Biology, University of Padova, Padova, Italy.
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6
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Chinellato M, Gasparotto M, Quarta S, Ruvoletto M, Biasiolo A, Filippini F, Spiezia L, Cendron L, Pontisso P. 1-Piperidine Propionic Acid as an Allosteric Inhibitor of Protease Activated Receptor-2. Pharmaceuticals (Basel) 2023; 16:1486. [PMID: 37895957 PMCID: PMC10610151 DOI: 10.3390/ph16101486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
In the last decades, studies on the inflammatory signaling pathways in multiple pathological contexts have revealed new targets for novel therapies. Among the family of G-protein-coupled Proteases Activated Receptors, PAR2 was identified as a driver of the inflammatory cascade in many pathologies, ranging from autoimmune disease to cancer metastasis. For this reason, many efforts have been focused on the development of potential antagonists of PAR2 activity. This work focuses on a small molecule, 1-Piperidine Propionic Acid (1-PPA), previously described to be active against inflammatory processes, but whose target is still unknown. Stabilization effects observed by cellular thermal shift assay coupled to in-silico investigations, including molecular docking and molecular dynamics simulations, suggested that 1-PPA binds PAR2 in an allosteric pocket of the receptor inactive conformation. Functional studies revealed the antagonist effects on MAPKs signaling and on platelet aggregation, processes mediated by PAR family members, including PAR2. Since the allosteric pocket binding 1-PPA is highly conserved in all the members of the PAR family, the evidence reported here suggests that 1-PPA could represent a promising new small molecule targeting PARs with antagonistic activity.
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Affiliation(s)
- Monica Chinellato
- Department of Medicine, University of Padova, 35121 Padova, Italy; (M.C.); (S.Q.); (M.R.); (A.B.)
| | - Matteo Gasparotto
- Department of Biology, University of Padova, 35121 Padova, Italy; (M.G.); (F.F.); (L.C.)
| | - Santina Quarta
- Department of Medicine, University of Padova, 35121 Padova, Italy; (M.C.); (S.Q.); (M.R.); (A.B.)
| | - Mariagrazia Ruvoletto
- Department of Medicine, University of Padova, 35121 Padova, Italy; (M.C.); (S.Q.); (M.R.); (A.B.)
| | - Alessandra Biasiolo
- Department of Medicine, University of Padova, 35121 Padova, Italy; (M.C.); (S.Q.); (M.R.); (A.B.)
| | - Francesco Filippini
- Department of Biology, University of Padova, 35121 Padova, Italy; (M.G.); (F.F.); (L.C.)
| | - Luca Spiezia
- Department of Medicine, University of Padova, 35121 Padova, Italy; (M.C.); (S.Q.); (M.R.); (A.B.)
| | - Laura Cendron
- Department of Biology, University of Padova, 35121 Padova, Italy; (M.G.); (F.F.); (L.C.)
| | - Patrizia Pontisso
- Department of Medicine, University of Padova, 35121 Padova, Italy; (M.C.); (S.Q.); (M.R.); (A.B.)
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7
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Cassari L, Pavan A, Zoia G, Chinellato M, Zeni E, Grinzato A, Rothenberger S, Cendron L, Dettin M, Pasquato A. SARS-CoV-2 S Mutations: A Lesson from the Viral World to Understand How Human Furin Works. Int J Mol Sci 2023; 24:4791. [PMID: 36902222 PMCID: PMC10003014 DOI: 10.3390/ijms24054791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the etiological agent responsible for the worldwide pandemic and has now claimed millions of lives. The virus combines several unusual characteristics and an extraordinary ability to spread among humans. In particular, the dependence of the maturation of the envelope glycoprotein S from Furin enables the invasion and replication of the virus virtually within the entire body, since this cellular protease is ubiquitously expressed. Here, we analyzed the naturally occurring variation of the amino acids sequence around the cleavage site of S. We found that the virus grossly mutates preferentially at P positions, resulting in single residue replacements that associate with gain-of-function phenotypes in specific conditions. Interestingly, some combinations of amino acids are absent, despite the evidence supporting some cleavability of the respective synthetic surrogates. In any case, the polybasic signature is maintained and, as a consequence, Furin dependence is preserved. Thus, no escape variants to Furin are observed in the population. Overall, the SARS-CoV-2 system per se represents an outstanding example of the evolution of substrate-enzyme interaction, demonstrating a fast-tracked optimization of a protein stretch towards the Furin catalytic pocket. Ultimately, these data disclose important information for the development of drugs targeting Furin and Furin-dependent pathogens.
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Affiliation(s)
- Leonardo Cassari
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Angela Pavan
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Giulia Zoia
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Monica Chinellato
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Elena Zeni
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Alessandro Grinzato
- European Synchrotron Radiation Facility, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Sylvia Rothenberger
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Monica Dettin
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Antonella Pasquato
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
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8
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Minisini M, Di Giorgio E, Kerschbamer E, Dalla E, Faggiani M, Franforte E, Meyer-Almes FJ, Ragno R, Antonini L, Mai A, Fiorentino F, Rotili D, Chinellato M, Perin S, Cendron L, Weichenberger CX, Angelini A, Brancolini C. Transcriptomic and genomic studies classify NKL54 as a histone deacetylase inhibitor with indirect influence on MEF2-dependent transcription. Nucleic Acids Res 2022; 50:2566-2586. [PMID: 35150567 PMCID: PMC8934631 DOI: 10.1093/nar/gkac081] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/25/2022] [Indexed: 12/23/2022] Open
Abstract
In leiomyosarcoma class IIa HDACs (histone deacetylases) bind MEF2 and convert these transcription factors into repressors to sustain proliferation. Disruption of this complex with small molecules should antagonize cancer growth. NKL54, a PAOA (pimeloylanilide o-aminoanilide) derivative, binds a hydrophobic groove of MEF2, which is used as a docking site by class IIa HDACs. However, NKL54 could also act as HDAC inhibitor (HDACI). Therefore, it is unclear which activity is predominant. Here, we show that NKL54 and similar derivatives are unable to release MEF2 from binding to class IIa HDACs. Comparative transcriptomic analysis classifies these molecules as HDACIs strongly related to SAHA/vorinostat. Low expressed genes are upregulated by HDACIs, while abundant genes are repressed. This transcriptional resetting correlates with a reorganization of H3K27 acetylation around the transcription start site (TSS). Among the upregulated genes there are several BH3-only family members, thus explaining the induction of apoptosis. Moreover, NKL54 triggers the upregulation of MEF2 and the downregulation of class IIa HDACs. NKL54 also increases the binding of MEF2D to promoters of genes that are upregulated after treatment. In summary, although NKL54 cannot outcompete MEF2 from binding to class IIa HDACs, it supports MEF2-dependent transcription through several actions, including potentiation of chromatin binding.
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Affiliation(s)
- Martina Minisini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Emanuela Kerschbamer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck. Via Galvani 31, 39100 Bolzano, Italy
| | - Emiliano Dalla
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Massimo Faggiani
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Elisa Franforte
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Science, Haardtring 100, 64295 Darmstadt, Germany
| | - Rino Ragno
- Rome Center for Molecular Design, Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Lorenzo Antonini
- Rome Center for Molecular Design, Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Antonello Mai
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Francesco Fiorentino
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Dante Rotili
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Monica Chinellato
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121 Padova, Italy
| | - Stefano Perin
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy.,European Centre for Living Technology (ECLT), Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121 Padova, Italy
| | - Christian X Weichenberger
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck. Via Galvani 31, 39100 Bolzano, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy.,European Centre for Living Technology (ECLT), Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
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9
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Linciano S, Wong EL, Mazzocato Y, Chinellato M, Scaravetti T, Caregnato A, Cacco V, Romanyuk Z, Angelini A. Guidelines, Strategies, and Principles for the Directed Evolution of Cross-Reactive Antibodies Using Yeast Surface Display Technology. Methods Mol Biol 2022; 2491:251-262. [PMID: 35482195 DOI: 10.1007/978-1-0716-2285-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The ability of cross-reactive antibodies to bind multiple related or unrelated targets derived from different species provides not only superior therapeutic efficacy but also a better assessment of treatment toxicity, thereby facilitating the transition from preclinical models to human clinical studies. This chapter provides some guidelines for the directed evolution of cross-reactive antibodies using yeast surface display technology. Cross-reactive antibodies are initially isolated from a naïve library by combining highly avid magnetic bead separations followed by multiple cycles of flow cytometry sorting. Once initial cross-reactive clones are identified, sequential rounds of mutagenesis and two-pressure selection strategies are applied to engineer cross-reactive antibodies with improved affinity and yet retained or superior cross-reactivity.
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Affiliation(s)
- Sara Linciano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Ee Lin Wong
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Ylenia Mazzocato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Monica Chinellato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
- Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Tiziano Scaravetti
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Alberto Caregnato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Veronica Cacco
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Zhanna Romanyuk
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy.
- European Centre for Living Technology (ECLT), Ca' Bottacin, Venice, Italy.
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Chinellato M, Lenay Caruelle F, Chinellato É. Syndrome cannabinoïde. Ann Fr Med Urgence 2017. [DOI: 10.1007/s13341-017-0703-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Chinellato M, Chinellato E. Filariose lymphatique (éléphantiasis). Ann Fr Med Urgence 2016. [DOI: 10.1007/s13341-016-0689-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Chinellato M. Luxation post-traumatique de la hanche chez un enfant. Ann Fr Med Urgence 2015. [DOI: 10.1007/s13341-014-0495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Valle R, Chinellato M, Milani L. Impact of a guideline-based management on outcomes of very old persons with heart failure living in nursing homes. Arch Intern Med 2001; 161:2264-5; author reply 2265. [PMID: 11575990 DOI: 10.1001/archinte.161.18.2264-a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Valle R, Chinellato M, Gallo G, Milani L. [Heart failure in nursing homes: prevalence, hospitalization, compliance to guidelines]. Ital Heart J Suppl 2001; 2:772-4. [PMID: 11508295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
BACKGROUND The prevalence of heart failure, the hospitalization rates for DRG 127 and the adherence to the recommendations included in the guidelines on pharmacological treatment among very old persons are poorly known. METHODS We screened 141 very old subjects (75% females, aged 87+/-4 years), living in 2 nursing homes. Heart failure was defined according to clinical criteria and on the basis of administrative databases and chart reviews. The latter were also used to collect data on hospitalization rates and pharmacological therapy. RESULTS We found that: 1) 23% of the subjects were affected by heart failure; 2) with regard to such patients, 26 hospital admissions for DRG 127 occurred in 1999 (18 admissions and 8 readmissions; 3) ACE-inhibitors have been prescribed to 54% of patients with a diagnosis of heart failure. CONCLUSIONS Heart failure affects a huge number of very old persons living in nursing homes. These patients have high hospitalization rates for DRG 127. The adherence to the recommendations included in the guidelines on the pharmacological therapy for very old persons is poor.
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Affiliation(s)
- R Valle
- Unità Operativa di Cardiologia, Ospedale Civile, ASL 10 Veneto Orientale, San Donà di Piave (VE).
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