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Article ; Online: Detection of HIV-1 matrix protein p17 in sera of viremic and aviremic patients.

Zani, Alberto / Messali, Serena / Uggeri, Matteo / Bonfanti, Carlo / Caruso, Arnaldo / Caccuri, Francesca

2023 Volume 324, Page(s) 114858

Abstract: People living with human immunodeficiency virus type 1 (HIV-1), even if successfully treated with a combined antiretroviral therapy, display a persistent inflammation and chronic immune activation, and an increasing risk of developing cardiovascular and ... ...

Abstract	People living with human immunodeficiency virus type 1 (HIV-1), even if successfully treated with a combined antiretroviral therapy, display a persistent inflammation and chronic immune activation, and an increasing risk of developing cardiovascular and thrombotic events, cancers, and neurologic disorders. Accumulating evidence reveals that biologically active HIV-1 proteins may play a role in the development of these HIV-1-associated conditions. The HIV-1 matrix protein p17 (p17) is released and accumulates in different organs and tissue where it may exert multiple biological activities on different target cells. To assess a role of p17 in different HIV-1-related pathological processes, it is central to definitively ascertain and quantitate its expression in a large number of sera obtained from HIV-1-infected (HIV-1
MeSH term(s)	Humans ; HIV-1 ; gag Gene Products, Human Immunodeficiency Virus/metabolism ; HIV Antigens/metabolism ; Viremia ; HIV Infections
Chemical Substances	gag Gene Products, Human Immunodeficiency Virus ; HIV Antigens
Language	English
Publishing date	2023-11-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2023.114858
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Article ; Online: Molecular mechanisms behind the generation of pro-oncogenic HIV-1 matrix protein p17 variants.

Zani, Alberto / Messali, Serena / Bugatti, Antonella / Uggeri, Matteo / Rondina, Alessandro / Sclavi, Leonardo / Caccuri, Francesca / Caruso, Arnaldo

The Journal of general virology

2024 Volume 105, Issue 4

Abstract: HIV-1 matrix protein p17 variants (vp17s), characterized by amino acid insertions at the COOH-terminal region of the viral protein, have been recently identified and studied for their biological activity. Different from their wild-type counterpart ( ... ...

Abstract	HIV-1 matrix protein p17 variants (vp17s), characterized by amino acid insertions at the COOH-terminal region of the viral protein, have been recently identified and studied for their biological activity. Different from their wild-type counterpart (refp17), vp17s display a potent B cell growth and clonogenic activity. Recent data have highlighted the higher prevalence of vp17s in people living with HIV-1 (PLWH) with lymphoma compared with those without lymphoma, suggesting that vp17s may play a key role in lymphomagenesis. Molecular mechanisms involved in vp17 development are still unknown. Here we assessed the efficiency of HIV-1 Reverse Transcriptase (RT) in processing this genomic region and highlighted the existence of hot spots of mutation in
MeSH term(s)	gag Gene Products, Human Immunodeficiency Virus/genetics ; gag Gene Products, Human Immunodeficiency Virus/metabolism ; Humans ; HIV-1/genetics ; HIV Antigens/genetics ; HIV Antigens/metabolism ; HIV Reverse Transcriptase/genetics ; HIV Reverse Transcriptase/metabolism ; Mutation ; HIV Infections/virology ; HIV Infections/genetics ; Cell Line
Chemical Substances	p17 protein, Human Immunodeficiency Virus Type 1 ; gag Gene Products, Human Immunodeficiency Virus ; HIV Antigens ; HIV Reverse Transcriptase (EC 2.7.7.49) ; reverse transcriptase, Human immunodeficiency virus 1 (EC 2.7.7.-)
Language	English
Publishing date	2024-04-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/jgv.0.001982
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Article ; Online: Germline

Colombo, Elisa Adele / Valiante, Michele / Uggeri, Matteo / Orro, Alessandro / Majore, Silvia / Grammatico, Paola / Gentilini, Davide / Finelli, Palma / Gervasini, Cristina / D'Ursi, Pasqualina / Larizza, Lidia

International journal of molecular sciences

2023 Volume 24, Issue 4

Abstract: Two adult siblings born to first-cousin parents presented a clinical phenotype reminiscent of Rothmund-Thomson syndrome (RTS), implying fragile hair, absent eyelashes/eyebrows, bilateral cataracts, mottled pigmentation, dental decay, hypogonadism, and ... ...

Abstract	Two adult siblings born to first-cousin parents presented a clinical phenotype reminiscent of Rothmund-Thomson syndrome (RTS), implying fragile hair, absent eyelashes/eyebrows, bilateral cataracts, mottled pigmentation, dental decay, hypogonadism, and osteoporosis. As the clinical suspicion was not supported by the sequencing of
MeSH term(s)	Humans ; Nuclear Pore Complex Proteins/chemistry ; Nuclear Pore Complex Proteins/genetics ; Rothmund-Thomson Syndrome/genetics ; Siblings ; Germ-Line Mutation ; Male ; Female ; Protein Conformation
Chemical Substances	Nuclear Pore Complex Proteins ; Nup98 protein, human
Language	English
Publishing date	2023-02-16
Publishing country	Switzerland
Document type	Case Reports ; Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24044028
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Article ; Online: Virtual Drug Repositioning as a Tool to Identify Natural Small Molecules That Synergize with Lumacaftor in F508del-CFTR Binding and Rescuing.

Fossa, Paola / Uggeri, Matteo / Orro, Alessandro / Urbinati, Chiara / Rondina, Alessandro / Milanesi, Maria / Pedemonte, Nicoletta / Pesce, Emanuela / Padoan, Rita / Ford, Robert C / Meng, Xin / Rusnati, Marco / D'Ursi, Pasqualina

International journal of molecular sciences

2022 Volume 23, Issue 20

Abstract: Cystic fibrosis is a hereditary disease mainly caused by the deletion of the Phe 508 (F508del) of the cystic fibrosis transmembrane conductance regulator (CFTR) protein that is thus withheld in the endoplasmic reticulum and rapidly degraded by the ... ...

Abstract	Cystic fibrosis is a hereditary disease mainly caused by the deletion of the Phe 508 (F508del) of the cystic fibrosis transmembrane conductance regulator (CFTR) protein that is thus withheld in the endoplasmic reticulum and rapidly degraded by the ubiquitin/proteasome system. Cystic fibrosis remains a potentially fatal disease, but it has become treatable as a chronic condition due to some CFTR-rescuing drugs that, when used in combination, increase in their therapeutic effect due to a synergic action. Also, dietary supplementation of natural compounds in combination with approved drugs could represent a promising strategy to further alleviate cystic fibrosis symptoms. On these bases, we screened by in silico drug repositioning 846 small synthetic or natural compounds from the AIFA database to evaluate their capacity to interact with the highly druggable lumacaftor binding site of F508del-CFTR. Among the identified hits, nicotinamide (NAM) was predicted to accommodate into the lumacaftor binding region of F508del-CFTR without competing against the drug but rather stabilizing its binding. The effective capacity of NAM to bind F508del-CFTR in a lumacaftor-uncompetitive manner was then validated experimentally by surface plasmon resonance analysis. Finally, the capacity of NAM to synergize with lumacaftor increasing its CFTR-rescuing activity was demonstrated in cell-based assays. This study suggests the possible identification of natural small molecules devoid of side effects and endowed with the capacity to synergize with drugs currently employed for the treatment of cystic fibrosis, which hopefully will increase the therapeutic efficacy with lower doses.
MeSH term(s)	Humans ; Cystic Fibrosis Transmembrane Conductance Regulator/metabolism ; Cystic Fibrosis/drug therapy ; Cystic Fibrosis/genetics ; Cystic Fibrosis/metabolism ; Drug Repositioning ; Proteasome Endopeptidase Complex/metabolism ; Benzodioxoles/pharmacology ; Benzodioxoles/therapeutic use ; Aminopyridines/pharmacology ; Aminopyridines/therapeutic use ; Niacinamide/therapeutic use ; Ubiquitins/metabolism ; Mutation
Chemical Substances	Cystic Fibrosis Transmembrane Conductance Regulator (126880-72-6) ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Benzodioxoles ; Aminopyridines ; Niacinamide (25X51I8RD4) ; Ubiquitins ; CFTR protein, human
Language	English
Publishing date	2022-10-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms232012274
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Article ; Online: Recent Strategic Advances in CFTR Drug Discovery: An Overview.

Rusnati, Marco / D'Ursi, Pasqualina / Pedemonte, Nicoletta / Urbinati, Chiara / Ford, Robert C / Cichero, Elena / Uggeri, Matteo / Orro, Alessandro / Fossa, Paola

International journal of molecular sciences

2020 Volume 21, Issue 7

Abstract: Cystic fibrosis transmembrane conductance regulator (CFTR)-rescuing drugs have already transformed cystic fibrosis (CF) from a fatal disease to a treatable chronic condition. However, new-generation drugs able to bind CFTR with higher specificity/ ... ...

Abstract	Cystic fibrosis transmembrane conductance regulator (CFTR)-rescuing drugs have already transformed cystic fibrosis (CF) from a fatal disease to a treatable chronic condition. However, new-generation drugs able to bind CFTR with higher specificity/affinity and to exert stronger therapeutic benefits and fewer side effects are still awaited. Computational methods and biosensors have become indispensable tools in the process of drug discovery for many important human pathologies. Instead, they have been used only piecemeal in CF so far, calling for their appropriate integration with well-tried CF biochemical and cell-based models to speed up the discovery of new CFTR-rescuing drugs. This review will give an overview of the available structures and computational models of CFTR and of the biosensors, biochemical and cell-based assays already used in CF-oriented studies. It will also give the reader some insights about how to integrate these tools as to improve the efficiency of the drug discovery process targeted to CFTR.
MeSH term(s)	Biosensing Techniques ; Computational Biology ; Cystic Fibrosis/drug therapy ; Cystic Fibrosis Transmembrane Conductance Regulator/chemistry ; Cystic Fibrosis Transmembrane Conductance Regulator/drug effects ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; Drug Discovery/methods ; Humans ; Models, Molecular ; Protein Conformation
Chemical Substances	CFTR protein, human ; Cystic Fibrosis Transmembrane Conductance Regulator (126880-72-6)
Language	English
Publishing date	2020-03-31
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21072407
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Article ; Online: In silico drug repositioning on F508del-CFTR: A proof-of-concept study on the AIFA library.

Orro, Alessandro / Uggeri, Matteo / Rusnati, Marco / Urbinati, Chiara / Pedemonte, Nicoletta / Pesce, Emanuela / Moscatelli, Marco / Padoan, Rita / Cichero, Elena / Fossa, Paola / D'Ursi, Pasqualina

European journal of medicinal chemistry

2021 Volume 213, Page(s) 113186

Abstract: Computational drug repositioning is of growing interest to academia and industry, for its ability to rapidly screen a huge number of candidates in silico (exploiting comprehensive drug datasets) together with reduced development cost and time. The ... ...

Abstract	Computational drug repositioning is of growing interest to academia and industry, for its ability to rapidly screen a huge number of candidates in silico (exploiting comprehensive drug datasets) together with reduced development cost and time. The potential of drug repositioning has not been fully evaluated yet for cystic fibrosis (CF), a disease mainly caused by deletion of Phe 508 (F508del) of the cystic fibrosis transmembrane conductance regulator (CFTR) protein. F508del-CFTR is thus withheld in the endoplasmic reticulum and rapidly degraded by the ubiquitin/proteasome system. CF is still a fatal disease. Nowadays, it is treatable by some CFTR-rescuing drugs, but new-generation drugs with stronger therapeutic benefits and fewer side effects are still awaited. In this manuscript we report about the results of a pilot computational drug repositioning screening in search of F508del-CFTR-targeted drugs performed on AIFA library by means of a dedicated computational pipeline and surface plasmon resonance binding assay to experimentally validate the computational findings.
MeSH term(s)	Cystic Fibrosis Transmembrane Conductance Regulator/antagonists & inhibitors ; Cystic Fibrosis Transmembrane Conductance Regulator/metabolism ; Datasets as Topic ; Dose-Response Relationship, Drug ; Drug Repositioning ; Humans ; Molecular Structure ; Phenylalanine/antagonists & inhibitors ; Phenylalanine/metabolism ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/pharmacology ; Structure-Activity Relationship
Chemical Substances	CFTR protein, human ; Small Molecule Libraries ; Cystic Fibrosis Transmembrane Conductance Regulator (126880-72-6) ; Phenylalanine (47E5O17Y3R)
Language	English
Publishing date	2021-01-13
Publishing country	France
Document type	Journal Article
ZDB-ID	188597-2
ISSN	1768-3254 ; 0009-4374 ; 0223-5234
ISSN (online)	1768-3254
ISSN	0009-4374 ; 0223-5234
DOI	10.1016/j.ejmech.2021.113186
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Zs.B 784: Show issues

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Article ; Online: Evolution toward beta common chain receptor usage links the matrix proteins of HIV-1 and its ancestors to human erythropoietin.

Caccuri, Francesca / D'Ursi, Pasqualina / Uggeri, Matteo / Bugatti, Antonella / Mazzuca, Pietro / Zani, Alberto / Filippini, Federica / Salmona, Mario / Ribatti, Domenico / Slevin, Mark / Orro, Alessandro / Lu, Wuyuan / Liò, Pietro / Gallo, Robert C / Caruso, Arnaldo

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 118, Issue 2

Abstract: The HIV-1 matrix protein p17 (p17) is a pleiotropic molecule impacting on different cell types. Its interaction with many cellular proteins underlines the importance of the viral protein as a major determinant of human specific adaptation. We previously ... ...

Abstract	The HIV-1 matrix protein p17 (p17) is a pleiotropic molecule impacting on different cell types. Its interaction with many cellular proteins underlines the importance of the viral protein as a major determinant of human specific adaptation. We previously showed the proangiogenic capability of p17. Here, by integrating functional analysis and receptor binding, we identify a functional epitope that displays molecular mimicry with human erythropoietin (EPO) and promotes angiogenesis through common beta chain receptor (βCR) activation. The functional EPO-like epitope was found to be present in the matrix protein of HIV-1 ancestors SIV originated in chimpanzees (SIVcpz) and gorillas (SIVgor) but not in that of HIV-2 and its ancestor SIVsmm from sooty mangabeys. According to biological data, evolution of the EPO-like epitope showed a clear differentiation between HIV-1/SIVcpz-gor and HIV-2/SIVsmm branches, thus highlighting this epitope on p17 as a divergent signature discriminating HIV-1 and HIV-2 ancestors. P17 is known to enhance HIV-1 replication. Similarly to other βCR ligands, p17 is capable of attracting and activating HIV-1 target cells and promoting a proinflammatory microenvironment. Thus, it is tempting to speculate that acquisition of an epitope on the matrix proteins of HIV-1 ancestors capable of triggering βCR may have represented a critical step to enhance viral aggressiveness and early human-to-human SIVcpz/gor dissemination. The hypothesis that the p17/βCR interaction and βCR abnormal stimulation may also play a role in sustaining chronic activation and inflammation, thus marking the difference between HIV-1 and HIV-2 in term of pathogenicity, needs further investigation.
MeSH term(s)	Cells, Cultured ; Epitopes/immunology ; Erythropoietin/genetics ; Erythropoietin/metabolism ; Evolution, Molecular ; HIV Antigens/genetics ; HIV Antigens/metabolism ; HIV Seropositivity ; HIV-1/genetics ; HIV-1/metabolism ; HIV-2 ; Humans ; Molecular Mimicry ; Simian Immunodeficiency Virus ; gag Gene Products, Human Immunodeficiency Virus/genetics ; gag Gene Products, Human Immunodeficiency Virus/metabolism
Chemical Substances	EPO protein, human ; Epitopes ; HIV Antigens ; gag Gene Products, Human Immunodeficiency Virus ; p17 protein, Human Immunodeficiency Virus Type 1 ; Erythropoietin (11096-26-7)
Language	English
Publishing date	2020-12-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2021366118
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Zs.A 1148: Show issues

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Article ; Online: Heparin and heparan sulfate proteoglycans promote HIV-1 p17 matrix protein oligomerization: computational, biochemical and biological implications.

Bugatti, Antonella / Paiardi, Giulia / Urbinati, Chiara / Chiodelli, Paola / Orro, Alessandro / Uggeri, Matteo / Milanesi, Luciano / Caruso, Arnaldo / Caccuri, Francesca / D'Ursi, Pasqualina / Rusnati, Marco

Scientific reports

2019 Volume 9, Issue 1, Page(s) 15768

Abstract: p17 matrix protein released by HIV+ cells interacts with leukocytes heparan sulfate proteoglycans (HSPGs), CXCR1 and CXCR2 exerting different cytokine-like activities that contribute to AIDS pathogenesis. Since the bioactive form of several cytokines is ... ...

Abstract	p17 matrix protein released by HIV+ cells interacts with leukocytes heparan sulfate proteoglycans (HSPGs), CXCR1 and CXCR2 exerting different cytokine-like activities that contribute to AIDS pathogenesis. Since the bioactive form of several cytokines is represented by dimers/oligomers and oligomerization is promoted by binding to heparin or HSPGs, here we evaluated if heparin/HSPGs also promote p17 oligomerization. Heparin favours p17 dimer, trimer and tetramer assembly, in a time- and biphasic dose-dependent way. Heparin-induced p17 oligomerization is of electrostatic nature, being it prevented by NaCl, by removing negative sulfated groups of heparin and by neutralizing positive lysine residues in the p17 N-terminus. A new computational protocol has been implemented to study heparin chains up to 24-mer accommodating a p17 dimer. Molecular dynamics show that, in the presence of heparin, two p17 molecules undergo conformational modifications creating a continuous "electropositive channel" in which heparin sulfated groups interact with p17 basic amino acids, promoting its dimerization. At the cell surface, HSPGs induce p17 oligomerization, as demonstrated by using B-lymphoblastoid Namalwa cells overexpressing the HSPG Syndecan-1. Also, HSPGs on the surface of BJAB and Raji human B-lymphoblastoid cells are required to p17 to induce ERK
MeSH term(s)	Acquired Immunodeficiency Syndrome/metabolism ; Cell Line, Tumor ; HIV Antigens/chemistry ; HIV Antigens/metabolism ; HIV-1/chemistry ; HIV-1/metabolism ; Heparin/chemistry ; Heparin/metabolism ; Humans ; MAP Kinase Signaling System ; Protein Multimerization ; Syndecan-1/chemistry ; Syndecan-1/metabolism ; gag Gene Products, Human Immunodeficiency Virus/chemistry ; gag Gene Products, Human Immunodeficiency Virus/metabolism
Chemical Substances	HIV Antigens ; SDC1 protein, human ; Syndecan-1 ; gag Gene Products, Human Immunodeficiency Virus ; p17 protein, Human Immunodeficiency Virus Type 1 ; Heparin (9005-49-6)
Language	English
Publishing date	2019-10-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-52201-w
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Article ; Online: Detection of HIV-1 matrix protein p17 in sera of viremic and aviremic patients.

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Article ; Online: Molecular mechanisms behind the generation of pro-oncogenic HIV-1 matrix protein p17 variants.

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Article ; Online: Germline

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Article ; Online: Virtual Drug Repositioning as a Tool to Identify Natural Small Molecules That Synergize with Lumacaftor in F508del-CFTR Binding and Rescuing.

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Article ; Online: Recent Strategic Advances in CFTR Drug Discovery: An Overview.

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Article ; Online: In silico drug repositioning on F508del-CFTR: A proof-of-concept study on the AIFA library.

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Article ; Online: Evolution toward beta common chain receptor usage links the matrix proteins of HIV-1 and its ancestors to human erythropoietin.

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Article ; Online: Heparin and heparan sulfate proteoglycans promote HIV-1 p17 matrix protein oligomerization: computational, biochemical and biological implications.

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