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Article ; Online: Identification of Novel Non-Nucleoside Inhibitors of Zika Virus NS5 Protein Targeting MTase Activity.

Fiorucci, Diego / Meaccini, Micaela / Poli, Giulio / Stincarelli, Maria Alfreda / Vagaggini, Chiara / Giannecchini, Simone / Sutto-Ortiz, Priscila / Canard, Bruno / Decroly, Etienne / Dreassi, Elena / Brai, Annalaura / Botta, Maurizio

International journal of molecular sciences

2024 Volume 25, Issue 4

Abstract: Zika virus (ZIKV) is a positive-sense single-stranded virus member of ... ...

Abstract	Zika virus (ZIKV) is a positive-sense single-stranded virus member of the
MeSH term(s)	Humans ; Zika Virus/metabolism ; Zika Virus Infection/drug therapy ; Models, Molecular ; Antiviral Agents/chemistry ; Viral Nonstructural Proteins/metabolism
Chemical Substances	Antiviral Agents ; Viral Nonstructural Proteins
Language	English
Publishing date	2024-02-19
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/ijms25042437
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Discovery and Optimization of a Novel Macrocyclic Amidinourea Series Active as Acidic Mammalian Chitinase Inhibitors.

Balestri, Lorenzo Jacopo Ilic / Trivisani, Claudia Immacolata / Orofino, Francesco / Fiorucci, Diego / Truglio, Giuseppina Ivana / D'Agostino, Ilaria / Poggialini, Federica / Botta, Lorenzo / Docquier, Jean-Denis / Dreassi, Elena

ACS medicinal chemistry letters

2023 Volume 14, Issue 4, Page(s) 417–424

Abstract: Our research group has been involved for a long time in the development of macrocyclic amidinoureas (MCAs) as antifungal agents. The mechanistic investigation drove us to perform ... ...

Abstract	Our research group has been involved for a long time in the development of macrocyclic amidinoureas (MCAs) as antifungal agents. The mechanistic investigation drove us to perform an
Language	English
Publishing date	2023-03-21
Publishing country	United States
Document type	Journal Article
ISSN	1948-5875
ISSN	1948-5875
DOI	10.1021/acsmedchemlett.2c00472
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Book ; Online: Implicit neural representation for change detection

Naylor, Peter / Di Carlo, Diego / Traviglia, Arianna / Yamada, Makoto / Fiorucci, Marco

2023

Abstract: Identifying changes in a pair of 3D aerial LiDAR point clouds, obtained during two distinct time periods over the same geographic region presents a significant challenge due to the disparities in spatial coverage and the presence of noise in the ... ...

Abstract	Identifying changes in a pair of 3D aerial LiDAR point clouds, obtained during two distinct time periods over the same geographic region presents a significant challenge due to the disparities in spatial coverage and the presence of noise in the acquisition system. The most commonly used approaches to detecting changes in point clouds are based on supervised methods which necessitate extensive labelled data often unavailable in real-world applications. To address these issues, we propose an unsupervised approach that comprises two components: Implicit Neural Representation (INR) for continuous shape reconstruction and a Gaussian Mixture Model for categorising changes. INR offers a grid-agnostic representation for encoding bi-temporal point clouds, with unmatched spatial support that can be regularised to enhance high-frequency details and reduce noise. The reconstructions at each timestamp are compared at arbitrary spatial scales, leading to a significant increase in detection capabilities. We apply our method to a benchmark dataset comprising simulated LiDAR point clouds for urban sprawling. This dataset encompasses diverse challenging scenarios, varying in resolutions, input modalities and noise levels. This enables a comprehensive multi-scenario evaluation, comparing our method with the current state-of-the-art approach. We outperform the previous methods by a margin of 10% in the intersection over union metric. In addition, we put our techniques to practical use by applying them in a real-world scenario to identify instances of illicit excavation of archaeological sites and validate our results by comparing them with findings from field experts. Comment: Main article is 10 pages + 6 pages of supplementary. Conference style paper
Keywords	Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Image and Video Processing
Subject code	006
Publishing date	2023-07-28
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Computational drug repurposing for the identification of SARS-CoV-2 main protease inhibitors.

Fiorucci, Diego / Milletti, Eva / Orofino, Francesco / Brizzi, Antonella / Mugnaini, Claudia / Corelli, Federico

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 16, Page(s) 6242–6248

Abstract: Accepted 7 July 2020ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the known COVID-19 disease. Since currently no definitive therapies or vaccines for the SARS-CoV-2 virus are available, there is an ... ...

Abstract	Accepted 7 July 2020ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the known COVID-19 disease. Since currently no definitive therapies or vaccines for the SARS-CoV-2 virus are available, there is an urgent need to identify effective drugs against SARS-CoV-2 infection. One of the best-known targets available is the main protease of this virus, crucial for the processing of polyproteins codified by viral RNA. In this work, we used a computational virtual screening procedure for the repurposing of commercial drugs available in the DrugBank database as inhibitors of the SARS-CoV-2 main protease. Molecular docking calculations and molecular dynamics (MD) simulations have been applied. The computational model was validated through a self-docking procedure. The screening procedure highlighted five interesting drugs that showed a comparable or higher docking score compared to the crystallographic compound and maintained the protein binding during the MD runs. Amongst these drugs, Ritonavir has been used in clinical trials with patients affected by COVID-19 and Nelfinavir showed anti-SARS-CoV-2 activity. The five identified drugs could be evaluated experimentally as inhibitors of the SARS-CoV-2 main protease in view of a possible COVID-19 treatment. Communicated by Ramaswamy H. Sarma.
MeSH term(s)	COVID-19/drug therapy ; COVID-19 Vaccines ; Drug Repositioning ; Humans ; Molecular Docking Simulation ; Protease Inhibitors ; SARS-CoV-2
Chemical Substances	COVID-19 Vaccines ; Protease Inhibitors
Keywords	covid19
Language	English
Publishing date	2020-07-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1796805
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Article ; Online: Computational drug repurposing for the identification of SARS-CoV-2 main protease inhibitors

Fiorucci, Diego / Milletti, Eva / Orofino, Francesco / Brizzi, Antonella / Mugnaini, Claudia / Corelli, Federico

Journal of Biomolecular Structure and Dynamics

2020 , Page(s) 1–7

Keywords	Molecular Biology ; Structural Biology ; General Medicine ; covid19
Language	English
Publisher	Informa UK Limited
Publishing country	uk
Document type	Article ; Online
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1796805
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Article: Computational drug repurposing for the identification of SARS-CoV-2 main protease inhibitors

Fiorucci, Diego / Milletti, Eva / Orofino, Francesco / Brizzi, Antonella / Mugnaini, Claudia / Corelli, Federico

J Biomol Struct Dyn

Abstract: Accepted 7 July 2020ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the known COVID-19 disease. Since currently no definitive therapies or vaccines for the SARS-CoV-2 virus are available, there is an ... ...

Abstract	Accepted 7 July 2020ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the known COVID-19 disease. Since currently no definitive therapies or vaccines for the SARS-CoV-2 virus are available, there is an urgent need to identify effective drugs against SARS-CoV-2 infection. One of the best-known targets available is the main protease of this virus, crucial for the processing of polyproteins codified by viral RNA. In this work, we used a computational virtual screening procedure for the repurposing of commercial drugs available in the DrugBank database as inhibitors of the SARS-CoV-2 main protease. Molecular docking calculations and molecular dynamics (MD) simulations have been applied. The computational model was validated through a self-docking procedure. The screening procedure highlighted five interesting drugs that showed a comparable or higher docking score compared to the crystallographic compound and maintained the protein binding during the MD runs. Amongst these drugs, Ritonavir has been used in clinical trials with patients affected by COVID-19 and Nelfinavir showed anti-SARS-CoV-2 activity. The five identified drugs could be evaluated experimentally as inhibitors of the SARS-CoV-2 main protease in view of a possible COVID-19 treatment. Communicated by Ramaswamy H. Sarma.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #670348
Database	COVID19

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Article: Artemisinin Derivatives with Antimelanoma Activity Show Inhibitory Effect against Human DNA Topoisomerase 1.

Botta, Lorenzo / Filippi, Silvia / Zippilli, Claudio / Cesarini, Silvia / Bizzarri, Bruno Mattia / Cirigliano, Angela / Rinaldi, Teresa / Paiardini, Alessandro / Fiorucci, Diego / Saladino, Raffaele / Negri, Rodolfo / Benedetti, Pietro

ACS medicinal chemistry letters

2020 Volume 11, Issue 5, Page(s) 1035–1040

Abstract: Artesunic acid and artemisinin are natural substances with promiscuous anticancer activity against different types of cancer cell lines. The mechanism of action of these compounds is associated with the formation of reactive radical species by cleavage ... ...

Abstract	Artesunic acid and artemisinin are natural substances with promiscuous anticancer activity against different types of cancer cell lines. The mechanism of action of these compounds is associated with the formation of reactive radical species by cleavage of the sesquiterpene pharmacophore endoperoxide bridge. Here we suggested topoisomerase 1 as a possible molecular target for the improvement of the anticancer activity of these compounds. In this context, we report that novel hybrid and dimer derivatives of artesunic acid and artemisinin, bearing camptothecin and SN38 as side-chain biological effectors, can inhibit growth of yeast cells overexpressing human topoisomerase 1 and its enzymatic activity
Language	English
Publishing date	2020-04-10
Publishing country	United States
Document type	Journal Article
ISSN	1948-5875
ISSN	1948-5875
DOI	10.1021/acsmedchemlett.0c00131
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Article ; Online: In vitro characterization, ADME analysis, and histological and toxicological evaluation of BM1, a macrocyclic amidinourea active against azole-resistant Candida strains.

Orofino, Francesco / Truglio, Giuseppina I / Fiorucci, Diego / D'Agostino, Ilaria / Borgini, Matteo / Poggialini, Federica / Zamperini, Claudio / Dreassi, Elena / Maccari, Laura / Torelli, Riccardo / Martini, Cecilia / Bernabei, Micaela / Meis, Jacques F / Khandelwal, Nitesh Kumar / Prasad, Rajendra / Sanguinetti, Maurizio / Bugli, Francesca / Botta, Maurizio

International journal of antimicrobial agents

2019 Volume 55, Issue 3, Page(s) 105865

Abstract: Background: Candida species are one of the most common causes of nosocomial bloodstream infections among the opportunistic fungi. Extensive use of antifungal agents, most of which were launched on the market more than 20 years ago, led to the selection ... ...

Abstract	Background: Candida species are one of the most common causes of nosocomial bloodstream infections among the opportunistic fungi. Extensive use of antifungal agents, most of which were launched on the market more than 20 years ago, led to the selection of drug-resistant or even multidrug-resistant fungi. We recently described a novel class of antifungal macrocyclic compounds with an amidinourea moiety that is highly active against azole-resistant Candida strains. Objective: A compound from this family, BM1, was investigated in terms of in vitro activity against various Candida species, including C. auris isolates, interaction with the ABC transporter, CDR6, and in vivo distribution and safety. Methods: In vitro assays (CYP inhibition, microsomal stability, permeability, spot assays) were used to collect chemical and biological data; animal models (rat) paired with LC-MS analysis were utilised to evaluate in vivo toxicology, pharmacokinetics, and distribution. Results: The current research shows BM1 has a low in vivo toxicity profile, affinity for the renal system in rats, and good absorption, distribution, metabolism, and excretion (ADME). BM1 also has potent activity against azole-resistant fungal strains, including C. auris isolates and CDR6-overexpressing strains. Conclusions: The results confirmed low minimum inhibitory concentrations (MICs) against several Candida species, including preliminary data vs. C. auris. BM1 has good ADME and biochemical characteristics, is suitable and safe for daily administration and is particularly indicated for renal infections. These data indicate BM1 and its derivatives form a novel, promising antifungal class.
MeSH term(s)	Animals ; Antifungal Agents/pharmacology ; Antifungal Agents/therapeutic use ; Azoles/pharmacology ; Candida/drug effects ; Candidiasis/drug therapy ; Drug Resistance, Fungal/drug effects ; Guanidine/analogs & derivatives ; Guanidine/pharmacology ; Guanidine/therapeutic use ; Microbial Sensitivity Tests ; Rats ; Urea/analogs & derivatives ; Urea/pharmacology ; Urea/therapeutic use
Chemical Substances	Antifungal Agents ; Azoles ; guanidine carboxamide (141-83-3) ; Urea (8W8T17847W) ; Guanidine (JU58VJ6Y3B)
Language	English
Publishing date	2019-12-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1093977-5
ISSN	1872-7913 ; 0924-8579
ISSN (online)	1872-7913
ISSN	0924-8579
DOI	10.1016/j.ijantimicag.2019.105865
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Article ; Online: Design and synthesis of a novel inhibitor of T. Viride chitinase through an in silico target fishing protocol.

Maccari, Giorgio / Deodato, Davide / Fiorucci, Diego / Orofino, Francesco / Truglio, Giuseppina I / Pasero, Carolina / Martini, Riccardo / De Luca, Filomena / Docquier, Jean-Denis / Botta, Maurizio

Bioorganic & medicinal chemistry letters

2017 Volume 27, Issue 15, Page(s) 3332–3336

Abstract: In the last ten years, we identified and developed a new therapeutic class of antifungal agents, the macrocyclic amidinoureas. These compounds are active against several Candida species, including clinical isolates resistant to currently available ... ...

Abstract	In the last ten years, we identified and developed a new therapeutic class of antifungal agents, the macrocyclic amidinoureas. These compounds are active against several Candida species, including clinical isolates resistant to currently available antifungal drugs. The mode of action of these molecules is still unknown. In this work, we developed an in-silico target fishing procedure to identify a possible target for this class of compounds based on shape similarity, inverse docking procedure and consensus score rank-by-rank. Chitinase enzyme emerged as possible target. To confirm this hypothesis a novel macrocyclic derivative has been produced, specifically designed to increase the inhibition of the chitinase. Biological evaluation highlights a stronger enzymatic inhibition for the new derivative, while its antifungal activity drops probably because of pharmacokinetic issues. Collectively, our data suggest that chitinase represent at least one of the main target of macrocyclic amidinoureas.
MeSH term(s)	Antifungal Agents/chemical synthesis ; Antifungal Agents/chemistry ; Antifungal Agents/pharmacology ; Chitinases/antagonists & inhibitors ; Chitinases/metabolism ; Dose-Response Relationship, Drug ; Drug Design ; Enzyme Inhibitors/chemical synthesis ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Microbial Sensitivity Tests ; Models, Molecular ; Molecular Structure ; Structure-Activity Relationship ; Trichoderma/drug effects ; Trichoderma/enzymology
Chemical Substances	Antifungal Agents ; Enzyme Inhibitors ; Chitinases (EC 3.2.1.14)
Language	English
Publishing date	2017--01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2017.06.016
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Article: In vitro characterization, ADME analysis, and histological and toxicological evaluation of BM1, a macrocyclic amidinourea active against azole-resistant Candida strains

International journal of antimicrobial agents. 2020 Mar., v. 55, no. 3

2020

Abstract: Candida species are one of the most common causes of nosocomial bloodstream infections among the opportunistic fungi. Extensive use of antifungal agents, most of which were launched on the market more than 20 years ago, led to the selection of drug- ... ...

Abstract	Candida species are one of the most common causes of nosocomial bloodstream infections among the opportunistic fungi. Extensive use of antifungal agents, most of which were launched on the market more than 20 years ago, led to the selection of drug-resistant or even multidrug-resistant fungi. We recently described a novel class of antifungal macrocyclic compounds with an amidinourea moiety that is highly active against azole-resistant Candida strains.A compound from this family, BM1, was investigated in terms of in vitro activity against various Candida species, including C. auris isolates, interaction with the ABC transporter, CDR6, and in vivo distribution and safety.In vitro assays (CYP inhibition, microsomal stability, permeability, spot assays) were used to collect chemical and biological data; animal models (rat) paired with LC-MS analysis were utilised to evaluate in vivo toxicology, pharmacokinetics, and distribution.The current research shows BM1 has a low in vivo toxicity profile, affinity for the renal system in rats, and good absorption, distribution, metabolism, and excretion (ADME). BM1 also has potent activity against azole-resistant fungal strains, including C. auris isolates and CDR6-overexpressing strains.The results confirmed low minimum inhibitory concentrations (MICs) against several Candida species, including preliminary data vs. C. auris. BM1 has good ADME and biochemical characteristics, is suitable and safe for daily administration and is particularly indicated for renal infections. These data indicate BM1 and its derivatives form a novel, promising antifungal class.
Keywords	ABC transporters ; Candida ; absorption ; animal models ; antifungal agents ; blood flow ; cross infection ; excretion ; fungi ; histology ; kidney diseases ; liquid chromatography ; macrocyclic compounds ; markets ; mass spectrometry ; minimum inhibitory concentration ; moieties ; multiple drug resistance ; permeability ; pharmacokinetics ; rats ; toxicity ; toxicity testing
Language	English
Dates of publication	2020-03
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1093977-5
ISSN	1872-7913 ; 0924-8579
ISSN (online)	1872-7913
ISSN	0924-8579
DOI	10.1016/j.ijantimicag.2019.105865
Database	NAL-Catalogue (AGRICOLA)

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