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Article ; Online: Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation.

Rinaldi, Silvia / Moroni, Elisabetta / Rozza, Riccardo / Magistrato, Alessandra

Journal of chemical theory and computation

2024 Volume 20, Issue 3, Page(s) 993–1018

Abstract: Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute 98-99% of the human genome. Non-coding RNAs encompass diverse functional classes, including microRNAs, small interfering RNAs, PIWI-interacting RNAs, small nuclear RNAs, ...

Abstract	Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute 98-99% of the human genome. Non-coding RNAs encompass diverse functional classes, including microRNAs, small interfering RNAs, PIWI-interacting RNAs, small nuclear RNAs, small nucleolar RNAs, and long non-coding RNAs. With critical involvement in gene expression and regulation across various biological and physiopathological contexts, such as neuronal disorders, immune responses, cardiovascular diseases, and cancer, non-coding RNAs are emerging as disease biomarkers and therapeutic targets. In this review, after providing an overview of non-coding RNAs' role in cell homeostasis, we illustrate the potential and the challenges of state-of-the-art computational methods exploited to study non-coding RNAs biogenesis, function, and modulation. This can be done by directly targeting them with small molecules or by altering their expression by targeting the cellular engines underlying their biosynthesis. Drawing from applications, also taken from our work, we showcase the significance and role of computer simulations in uncovering fundamental facets of ncRNA mechanisms and modulation. This information may set the basis to advance gene modulation tools and therapeutic strategies to address unmet medical needs.
MeSH term(s)	Humans ; RNA, Untranslated/genetics ; MicroRNAs/genetics ; RNA, Small Interfering ; Neoplasms
Chemical Substances	RNA, Untranslated ; MicroRNAs ; RNA, Small Interfering
Language	English
Publishing date	2024-01-30
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.3c01239
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Article ; Online: The dynamics of t1 adenosine binding on human Argonaute 2: Understanding recognition with conformational selection.

Rinaldi, Silvia / Colombo, Giorgio / Paladino, Antonella

Protein science : a publication of the Protein Society

2022 Volume 31, Issue 8, Page(s) e4377

Abstract: The control of expression in genetic regulation is a fundamental process for cell life. In RNA-mediated silencing, human Argonaute-2 protein (hAgo2) uses sequence information encoded in small RNAs (guide) to identify complementary sites in messenger RNAs ...

Abstract	The control of expression in genetic regulation is a fundamental process for cell life. In RNA-mediated silencing, human Argonaute-2 protein (hAgo2) uses sequence information encoded in small RNAs (guide) to identify complementary sites in messenger RNAs (target) for repression. The specificity of this molecular recognition lies at the basis of the mechanisms that control the expression of thousands of genes, which necessarily requires a fine tuning of complex events. Among these, the binding of the first nucleotide of the target RNA (t1) is emerging as an important modulator of hAgo2-mediated machinery. Using atomistic molecular dynamics-derived analyses, we address the mechanism behind t1-dependent regulation and study the impact of different t1 nucleotides (t1A, t1C, t1G, t1U) on the conformational dynamics of both hAgo2 and guide-target RNAs. Only when an adenine is found at this position, t1 directly interacts with a specific hAgo2 binding pocket, favoring the stabilization of target binding. Our findings show that hAgo2 exploits a dynamic recognition mechanism of the t1-target thanks to a modulation of RNA conformations. Here, t1-adenine is the only nucleobase endowed with a dual binding mode: a T-shape and a co-planar conformation, respectively, orthogonal and parallel to the following base-pairs of guide-target duplex. This triggers a composite set of molecular interactions that stabilizes distinctive conformational ensembles. Our comparative analyses show characteristic traits of local and global dynamic interplay between hAgo2 and the RNA molecules and highlight how t1A binding acts as a molecular switch for target recognition and complex stabilization. Implications for future mechanistic studies are discussed.
MeSH term(s)	Adenine ; Adenosine ; Humans ; Nucleotides ; Protein Binding ; RNA ; RNA Interference ; RNA, Messenger/genetics
Chemical Substances	Nucleotides ; RNA, Messenger ; RNA (63231-63-0) ; Adenine (JAC85A2161) ; Adenosine (K72T3FS567)
Language	English
Publishing date	2022-07-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4377
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Mechanistic Model for the Hsp90-Driven Opening of Human Argonaute.

Rinaldi, Silvia / Colombo, Giorgio / Paladino, Antonella

Journal of chemical information and modeling

2020 Volume 60, Issue 3, Page(s) 1469–1480

Abstract: The assembly of RNA-induced silencing complex (RISC) is a key process in small RNA-mediated gene silencing. Loading of small RNAs into Argonaute (Ago), the key player protein in the process, has been shown to depend on the Hsp90 chaperone machinery. ... ...

Abstract	The assembly of RNA-induced silencing complex (RISC) is a key process in small RNA-mediated gene silencing. Loading of small RNAs into Argonaute (Ago), the key player protein in the process, has been shown to depend on the Hsp90 chaperone machinery. Experimental single-molecule data indicate that ATP binding to the chaperone facilitates the conformational changes leading to the open state of Ago essential to form a complex with small-RNA duplexes. Yet, no atomic-level description of the dynamic mechanisms and protein-protein interactions underpinning Hsp90-mediated Ago conformational activation is available. Here we investigate the functionally oriented structural and dynamic features of Hsp90-human Ago (hAgo2) complexes in different ligand states by integrating protein-protein docking techniques, all-atom MD simulations, and novel methods of analysis of protein internal dynamics and energetics. On this basis, we develop a structural-dynamic model of the mechanisms underlying the chaperone-assisted human RISC assembly. Our approach unveils the large conformational variability displayed by hAgo2 in the unbound vs the Hsp90-bound states. In this context, several hAgo2 states are found to coexist in isolation, while Hsp90 selects and stabilizes the active form. Hsp90 binding modulates the conformational plasticity of hAgo2 (favoring its opening) by modifying the patterns of hAgo2 intramolecular interactions. Finally, we identify a series of experimentally verifiable key sites that can be mutated to modulate Hsp90-mediated hAgo2 conformational response and ability to bind RNA.
MeSH term(s)	Argonaute Proteins/metabolism ; HSP90 Heat-Shock Proteins/metabolism ; Humans ; Protein Binding ; RNA Interference ; RNA-Induced Silencing Complex/metabolism
Chemical Substances	Argonaute Proteins ; HSP90 Heat-Shock Proteins ; RNA-Induced Silencing Complex
Language	English
Publishing date	2020-03-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.0c00053
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Article: Lung cancer prognosis: can histological patterns and morphological features have a role in the management of lung cancer patients?

Rinaldi, Silvia / Berardi, Rossana

Annals of translational medicine

2017 Volume 5, Issue 17, Page(s) 353

Language	English
Publishing date	2017-09-07
Publishing country	China
Document type	Editorial ; Comment
ZDB-ID	2893931-1
ISSN	2305-5847 ; 2305-5839
ISSN (online)	2305-5847
ISSN	2305-5839
DOI	10.21037/atm.2017.05.18
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Article: The role of an immune checkpoint score in resected non-small cell lung cancer patients' prognosis.

Berardi, Rossana / Rinaldi, Silvia

Journal of thoracic disease

2017 Volume 9, Issue 10, Page(s) 3480–3482

Language	English
Publishing date	2017-12-18
Publishing country	China
Document type	Editorial ; Comment
ZDB-ID	2573571-8
ISSN	2077-6624 ; 2072-1439
ISSN (online)	2077-6624
ISSN	2072-1439
DOI	10.21037/jtd.2017.09.130
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Article ; Online: Label-Free SERS and MD Analysis of Biomarkers for Rapid Point-of-Care Sensors Detecting Head and Neck Cancer and Infections.

Farnesi, Edoardo / Rinaldi, Silvia / Liu, Chen / Ballmaier, Jonas / Guntinas-Lichius, Orlando / Schmitt, Michael / Cialla-May, Dana / Popp, Juergen

Sensors (Basel, Switzerland)

2023 Volume 23, Issue 21

Abstract: For the progress of point-of-care medicine, where individual health status can be easily and quickly monitored using a handheld sensor, saliva serves as one of the best-suited body fluids thanks to its availability and abundance of physiological ... ...

Abstract	For the progress of point-of-care medicine, where individual health status can be easily and quickly monitored using a handheld sensor, saliva serves as one of the best-suited body fluids thanks to its availability and abundance of physiological indicators. Salivary biomarkers, combined with rapid and highly sensitive detection tools, may pave the way to new real-time health monitoring and personalized preventative therapy branches using saliva as a target matrix. Saliva is increasing in importance in liquid biopsy, a non-invasive approach that helps physicians diagnose and characterize specific diseases in patients. Here, we propose a proof-of-concept study combining the unique specificity in biomolecular recognition provided by surface-enhanced Raman spectroscopy (SERS) in combination with molecular dynamics (MD) simulations, which give leave to explore the biomolecular absorption mechanism on nanoparticle surfaces, in order to verify the traceability of two validated salivary indicators, i.e., interleukin-8 (IL-8) and lysozyme (LYZ), implicated in oropharyngeal squamous cell carcinoma (OSCC) and oral infection. This strategy simultaneously assures the detection and interpretation of protein biomarkers in saliva, ultimately opening a new route for the evolution of fast and accurate point-of-care SERS-based sensors of interest in precision medicine diagnostics.
MeSH term(s)	Humans ; Mouth Neoplasms/diagnosis ; Point-of-Care Systems ; Carcinoma, Squamous Cell/diagnosis ; Head and Neck Neoplasms/diagnosis ; Biomarkers/analysis ; Saliva/chemistry ; Spectrum Analysis, Raman ; Biomarkers, Tumor/analysis
Chemical Substances	Biomarkers ; Biomarkers, Tumor
Language	English
Publishing date	2023-11-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s23218915
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Article ; Online: SARS-CoV-2 inhibitory activity of a short peptide derived from internal fusion peptide of S2 subunit of spike glycoprotein

Stincarelli, Maria Alfreda / Quagliata, Michael / Di Santo, Andrea / Pacini, Lorenzo / Fernandez, Feliciana Real / Arvia, Rosaria / Rinaldi, Silvia / Papini, Anna Maria / Rovero, Paolo / Giannecchini, Simone

Virus Research. 2023 Sept., v. 334 p.199170-

2023

Abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has posed a great concern in human population. To fight coronavirus emergence, we have dissected the conserved amino acid region of the internal fusion peptide in the S2 subunit of Spike ... ...

Abstract	Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has posed a great concern in human population. To fight coronavirus emergence, we have dissected the conserved amino acid region of the internal fusion peptide in the S2 subunit of Spike glycoprotein of SARS-CoV-2 to design new inhibitory peptides. Among the 11 overlapping peptides (9-23-mer), PN19, a 19-mer peptide, exhibited a powerful inhibitory activity against different SARS-CoV-2 clinical isolate variants in absence of cytotoxicity. The PN19 inhibitory activity was found to be dependent on conservation of the central Phe and C-terminal Tyr residues in the peptide sequence. Circular dichroism spectra of the active peptide exhibited an alpha-helix propensity, confirmed by secondary structure prediction analysis. The PN19 inhibitory activity, exerted in the first step of virus infection, was reduced after peptide adsorption treatment with virus-cell substrate during fusion interaction. Additionally, PN19 inhibitory activity was reduced by adding S2 membrane-proximal region derived peptides. PN19 showed binding ability to the S2 membrane proximal region derived peptides, confirmed by molecular modelling, playing a role in the mechanism of action. Collectively, these results confirm that the internal fusion peptide region is a good candidate on which develop peptidomimetic anti SARS-CoV-2 antivirals.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; adsorption ; amino acid sequences ; amino acids ; antiviral agents ; circular dichroism spectroscopy ; cytotoxicity ; glycoproteins ; human population ; mechanism of action ; peptides ; prediction ; research ; viruses ; Coronavirus ; SARS-CoV-2 ; S2 Spike glycoprotein ; internal fusion peptide region ; synthetic peptide ; antiviral activity ; CD ; SPR ; COVID-19 ; ACE2 ; NTD ; RBD ; FP ; IFP ; HR1-2 ; MPER ; TM ; FBS ; MW-SPPS ; DMEM ; TMPRSS2 ; PRA ; PFU ; MOI ; IC50 ; BSL3 ; MTT
Language	English
Dates of publication	2023-09
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2023.199170
Database	NAL-Catalogue (AGRICOLA)

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Zs.A 1965: Show issues

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Article ; Online: Management of lung cancer patients during COVID-19 pandemic: dos, don'ts and don't knows.

Torniai, Mariangela / Agostinelli, Veronica / Cantini, Luca / Liguori, Carolina / Morgese, Francesca / Rinaldi, Silvia / Scortichini, Laura / Berardi, Rossana

Exploration of targeted anti-tumor therapy

2022 Volume 3, Issue 3, Page(s) 321–336

Abstract: Aim: During the coronavirus disease 2019 (COVID-19) pandemic two needs have overlapped: on one hand continuing to provide the best care for patients with lung cancer and preventing the spread of the virus between patients and healthcare professionals on ...

Abstract	Aim: During the coronavirus disease 2019 (COVID-19) pandemic two needs have overlapped: on one hand continuing to provide the best care for patients with lung cancer and preventing the spread of the virus between patients and healthcare professionals on the other hand. Due to the pandemic's unpredictable duration, physicians had to evaluate the risk/benefit ratio of anti-cancer therapeutic strategy to do the best for their patients and to protect patients themselves, as well as healthcare workers. Methods: Systematic literature research was performed with the aim to assess the available guidelines for the management of lung cancer patients during the COVID-19 pandemic. Thirteen potentially relevant articles were selected and recommendations have been divided into three main categories: dos, don'ts and don't knows. Results: All guidelines and recommendations highlighted the relevance of being able to delay, if possible and based on risk stratification, and curative interventions. The selected recommendations should be considered adaptable and flexible because they might be contextualized on the basis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection prevalence and the availability of diagnostic-therapeutic resources. Conclusions: It remains of fundamental importance to discuss each diagnostic and therapeutic decision with the patient taking into account risks and benefits that might vary from case to case.
Language	English
Publishing date	2022-06-10
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2692-3114
ISSN (online)	2692-3114
DOI	10.37349/etat.2022.00085
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Article ; Online: Outpatient surgery is the solution at hand for reducing costs and hospital stays for pediatric surgery too: a hospital trial.

Caredda, Emanuele / Guolo, Stefano / Rinaldi, Silvia / Brusco, Carla / Raponi, Massimiliano

Minerva pediatrica

2019 Volume 72, Issue 2, Page(s) 101–108

Abstract: Background: Outpatient management has proven to be the most useful method of treatment for various minimally complex surgical specialties compared to day-hospital management or ordinary inpatient processes, a fact confirmed by numerous technical ... ...

Abstract	Background: Outpatient management has proven to be the most useful method of treatment for various minimally complex surgical specialties compared to day-hospital management or ordinary inpatient processes, a fact confirmed by numerous technical documents and works in the literature. Methods: We analyzed 27,713 surgical interventions carried out in our hospital between 2005 and 2017. This analysis included all interventions for which the indication of the level of care has moved, over the years, to an outpatient setting. We evaluated the direct costs of these services, comparing them by year and by treatment setting. Results: From the analysis of costs in general, for the same number of services, a reduction of 56.6% can be seen in the comparison between 2005 and 2017. In addition, the analysis of the length of stay shows an average reduction in the number of days of hospitalization from 2.9 to 1.2 between 2005 and 2017. On the basis of a large quantity of data, our study confirms that outpatient surgery can have a significant impact in reducing costs and days of hospitalization, even in a pediatric setting, demonstrating that it is the best choice in terms of saving resources and, above all, clinical and organizational appropriateness. Conclusions: Outpatient surgery is in fact a valuable solution that provides an advantage for both the patient and his/her family, especially in the pediatric field, for the hospital and more generally for the health system as a whole.
MeSH term(s)	Ambulatory Surgical Procedures/classification ; Ambulatory Surgical Procedures/economics ; Ambulatory Surgical Procedures/statistics & numerical data ; Ambulatory Surgical Procedures/trends ; Analysis of Variance ; Child ; Cost Savings/economics ; Direct Service Costs ; Female ; History, 20th Century ; Hospital Costs ; Humans ; Length of Stay ; Male ; Surgicenters/history
Language	English
Publishing date	2019-05-23
Publishing country	Italy
Document type	Historical Article ; Journal Article
ZDB-ID	123571-0
ISSN	1827-1715 ; 0026-4946
ISSN (online)	1827-1715
ISSN	0026-4946
DOI	10.23736/S0026-4946.19.05426-4
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Article: Benefits and Limitations of a Multidisciplinary Approach in Cancer Patient Management.

Berardi, Rossana / Morgese, Francesca / Rinaldi, Silvia / Torniai, Mariangela / Mentrasti, Giulia / Scortichini, Laura / Giampieri, Riccardo

Cancer management and research

2020 Volume 12, Page(s) 9363–9374

Abstract: Over the years, a growing body of literature has confirmed as beneficial the implementation of a multidisciplinary approach in the so-often-intricate scenario of cancer patients' management. Together with the consolidation of tumor-board experience in ... ...

Abstract	Over the years, a growing body of literature has confirmed as beneficial the implementation of a multidisciplinary approach in the so-often-intricate scenario of cancer patients' management. Together with the consolidation of tumor-board experience in clinical practice, certain aspects have emerged as controversial and a source of current debate. In this systematic literature review, we focused our attention on the impact of multidisciplinary tumor boards, assessing benefits and limitations as a result of the dissemination of such approaches. On the bright side, adherence to clinical guidelines, treatment outcomes, and overall improvement in decision-making processes have been recognized as advantages. On the other side, our analysis highlights a few limitations that should be taken into account to optimize cancer patients' management. Of note, some issues, such as costs, legal responsibility, geographic barriers, and treatment delays, have yet to be resolved. In order partly to address this matter, software platforms and novel methods of computational analysis may provide the needed support. Therefore, the aim of our analysis was to describe the multidisciplinary approach in cancer care in terms of adherence to clinical guidelines, treatment outcomes, and overall improvement in decision-making processes through a systematic review of the literature.
Language	English
Publishing date	2020-09-30
Publishing country	New Zealand
Document type	Journal Article ; Review
ZDB-ID	2508013-1
ISSN	1179-1322
ISSN	1179-1322
DOI	10.2147/CMAR.S220976
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