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Article ; Online: PyRMD: A New Fully Automated AI-Powered Ligand-Based Virtual Screening Tool.

Amendola, Giorgio / Cosconati, Sandro

Journal of chemical information and modeling

2021 Volume 61, Issue 8, Page(s) 3835–3845

Abstract: Artificial intelligence (AI) algorithms are dramatically redefining the current drug discovery landscape by boosting the efficiency of its various steps. Still, their implementation often requires a certain level of expertise in AI paradigms and coding. ... ...

Abstract	Artificial intelligence (AI) algorithms are dramatically redefining the current drug discovery landscape by boosting the efficiency of its various steps. Still, their implementation often requires a certain level of expertise in AI paradigms and coding. This often prevents the use of these powerful methodologies by non-expert users involved in the design of new biologically active compounds. Here, the random matrix discriminant (RMD) algorithm, a high-performance AI method specifically tailored for the identification of new ligands, was implemented in a new fully automated tool, PyRMD. This ligand-based virtual screening tool can be trained using target bioactivity data directly downloaded from the ChEMBL repository without manual intervention. The software automatically splits the available training compounds into active and inactive sets and learns the distinctive chemical features responsible for the compounds' activity/inactivity. PyRMD was designed to easily screen millions of compounds in hours through an automated workflow and intuitive input files, allowing fine tuning of each parameter of the calculation. Additionally, PyRMD features a wealth of benchmark metrics, to accurately probe the model performance, which were used here to gauge its predictive potential and limitations. PyRMD is freely available on GitHub (https://github.com/cosconatilab/PyRMD) as an open-source tool.
MeSH term(s)	Algorithms ; Artificial Intelligence ; Drug Discovery ; Ligands ; Software
Chemical Substances	Ligands
Language	English
Publishing date	2021-07-16
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.1c00653
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Article ; Online: Streamlining Large Chemical Library Docking with Artificial Intelligence: the PyRMD2Dock Approach.

Roggia, Michele / Natale, Benito / Amendola, Giorgio / Di Maro, Salvatore / Cosconati, Sandro

Journal of chemical information and modeling

2023 Volume 64, Issue 7, Page(s) 2143–2149

Abstract: The present contribution introduces a novel computational protocol called PyRMD2Dock, which combines the Ligand-Based Virtual Screening (LBVS) tool PyRMD with the popular docking software AutoDock-GPU (AD4-GPU) to enhance the throughput of virtual ... ...

Abstract	The present contribution introduces a novel computational protocol called PyRMD2Dock, which combines the Ligand-Based Virtual Screening (LBVS) tool PyRMD with the popular docking software AutoDock-GPU (AD4-GPU) to enhance the throughput of virtual screening campaigns for drug discovery. By implementing PyRMD2Dock, we demonstrate that it is possible to rapidly screen massive chemical databases and identify those with the highest predicted binding affinity to a target protein. Our benchmarking and screening experiments illustrate the predictive power and speed of PyRMD2Dock and highlight its potential to accelerate the discovery of novel drug candidates. Overall, this study showcases the value of combining AI-powered LBVS tools with docking software to enable effective and high-throughput virtual screening of ultralarge molecular databases in drug discovery. PyRMD and the PyRMD2Dock protocol are freely available on GitHub (https://github.com/cosconatilab/PyRMD) as an open-source tool.
MeSH term(s)	Artificial Intelligence ; Molecular Docking Simulation ; Software ; Proteins/chemistry ; Drug Discovery ; Small Molecule Libraries ; Ligands
Chemical Substances	Proteins ; Small Molecule Libraries ; Ligands
Language	English
Publishing date	2023-08-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c00647
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Article: Interplay Between LOX Enzymes and Integrins in the Tumor Microenvironment.

Amendola, Pier Giorgio / Reuten, Raphael / Erler, Janine Terra

Cancers

2019 Volume 11, Issue 5

Abstract: Members of the lysyl oxidase (LOX) family are secreted copper-dependent amine oxidases that catalyze the covalent crosslinking of collagens and elastin in the extracellular matrix (ECM), an essential process for the structural integrity of all tissues. ... ...

Abstract	Members of the lysyl oxidase (LOX) family are secreted copper-dependent amine oxidases that catalyze the covalent crosslinking of collagens and elastin in the extracellular matrix (ECM), an essential process for the structural integrity of all tissues. LOX enzymes can also remodel the tumor microenvironment and have been implicated in all stages of tumor initiation and progression of many cancer types. Changes in the ECM can influence several cancer cell phenotypes. Integrin adhesion complexes (IACs) physically connect cells with their microenvironment. This review article summarizes the main findings on the role of LOX proteins in modulating the tumor microenvironment, with a particular focus on how ECM changes are integrated by IACs to modulate cells behavior. Finally, we discuss how the development of selective LOX inhibitors may lead to novel and effective therapies in cancer treatment.
Language	English
Publishing date	2019-05-26
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers11050729
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Article: The role of C5a-C5aR1 axis in bone pathophysiology: A mini-review.

Ruocco, Anna / Sirico, Anna / Novelli, Rubina / Iannelli, Silvia / Van Breda, Shane Vontelin / Kyburz, Diego / Hasler, Paul / Aramini, Andrea / Amendola, Pier Giorgio

Frontiers in cell and developmental biology

2022 Volume 10, Page(s) 957800

Abstract: Bone remodeling is a physiological, dynamic process that mainly depends on the functions of 2 cell types: osteoblasts and osteoclasts. Emerging evidence suggests that complement system is crucially involved in the regulation of functions of these cells, ... ...

Abstract	Bone remodeling is a physiological, dynamic process that mainly depends on the functions of 2 cell types: osteoblasts and osteoclasts. Emerging evidence suggests that complement system is crucially involved in the regulation of functions of these cells, especially during inflammatory states. In this context, complement component 5a (C5a), a powerful pro-inflammatory anaphylatoxin that binds the receptor C5aR1, is known to regulate osteoclast formation and osteoblast inflammatory responses, and has thus been proposed as potential therapeutic target for the treatment of inflammatory bone diseases. In this review, we will analyze the role of C5a-C5aR1 axis in bone physiology and pathophysiology, describing its involvement in the pathogenesis of some of the most frequent inflammatory bone diseases such as rheumatoid arthritis, and also in osteoporosis and bone cancer and metastasis. Moreover, we will examine C5aR1-based pharmacological approaches that are available and have been tested so far for the treatment of these conditions. Given the growing interest of the scientific community on osteoimmunology, and the scarcity of data regarding the role of C5a-C5aR1 axis in bone pathophysiology, we will highlight the importance of this axis in mediating the interactions between skeletal and immune systems and its potential use as a therapeutic target.
Language	English
Publishing date	2022-08-08
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2022.957800
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Article: Association of Indocyanine Green with Chitosan Oleate Coated PLGA Nanoparticles for Photodynamic Therapy.

Miele, Dalila / Sorrenti, Milena / Catenacci, Laura / Minzioni, Paolo / Marrubini, Giorgio / Amendola, Valeria / Maestri, Marcello / Giunchedi, Paolo / Bonferoni, Maria Cristina

Pharmaceutics

2022 Volume 14, Issue 8

Abstract: Indocyanine green (ICG) is a safe dye widely used in the biomedical field. Its photodynamic effect (PDT), originating from laser irradiation at 803 nm, opens interesting perspectives in theranostic applications. To overcome its low water stability, ICG ... ...

Abstract	Indocyanine green (ICG) is a safe dye widely used in the biomedical field. Its photodynamic effect (PDT), originating from laser irradiation at 803 nm, opens interesting perspectives in theranostic applications. To overcome its low water stability, ICG can be shielded with nanoparticles (NPs). In this work, previously developed NPs based on poly lactic-co-glycolic acid (PLGA) coated with chitosan oleate (CS-OA) and loaded with resveratrol as a hydrophobic model drug have been proposed as an ICG carrier. These systems have been selected for their observed immunostimulatory properties. The possible loading of the dye by adsorption onto NP surface by electrostatic interaction was studied here in comparison with the encapsulation into the PLGA core. The ICG-chitosan (CS) interaction has been characterized by spectrophotometry, spectroscopy and in-cell in vitro assays. Fluorescence quenching was observed due to the ionic interaction between ICG and CS and was studied considering the dye:polymer stoichiometry and the effect of the NP dilution in cell culture medium (DMEM). The NP systems have been compared in vitro, assessing their behaviour in Caco-2 cell lines. A reduction in cell viability was observed after irradiation of ICG associated with NPs, evident also for the samples loaded by adsorption. These findings open the opportunity to exploit the association of PDT's effect on ICG with the properties of CS-OA coated NPs, whose immunostimulatory effect can be associated with PDT mechanism in cancer therapy.
Language	English
Publishing date	2022-08-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527217-2
ISSN	1999-4923
ISSN	1999-4923
DOI	10.3390/pharmaceutics14081740
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Article ; Online: Ultrasound-guided percutaneous irreversible electroporation of hepatic and abdominal tumors not eligible for surgery or thermal ablation: a western report on safety and efficacy.

Giorgio, A / Amendola, F / Calvanese, A / Ingenito, E / Santoro, B / Gatti, P / Ciracì, E / Matteucci, P / Giorgio, V

Journal of ultrasound

2019 Volume 22, Issue 1, Page(s) 53–58

Abstract: Purpose: To report our first results on sixteen patients affected by liver and abdominal malignant tumors, unfit for surgery or thermal ablation, treated with US-guided percutaneous irreversible electroporation (IRE).: Methods: From June 2014 to ... ...

Abstract	Purpose: To report our first results on sixteen patients affected by liver and abdominal malignant tumors, unfit for surgery or thermal ablation, treated with US-guided percutaneous irreversible electroporation (IRE). Methods: From June 2014 to December 2016, all patients meeting the inclusion criteria (malignant hepatic or abdominal tumors not eligible for resection or thermal ablation) and not meeting the exclusion criteria (heart arrhythmia, pro-hemorrhagic hematological alterations, tumor size > 8 cm, presence of a biliary metallic stent) referred to our institutions were prospectively enrolled to undergo percutaneous US-guided irreversible electroporation (IRE). Sixteen patients (age range 59-68 years, mean 63; 7 females) with 18 tumors (diameter range 1.3-7.5 cm) fulfilled the inclusion criteria and were included in the study. Data concerning efficacy (tested by a 1-week CEUS and a 4-week enhanced CT and/or enhanced MRI) and safety were recorded during a 18-month follow up. Results: All patients completed a 35-50-min procedure without complications. One patient with 6 cm Klatskin tumor also underwent a second session for 1 month. A 1-week CEUS and a 4-week e-CT and/or e-MRI arterial phase contrast enhancement analysis showed an overall reduction of arterial flow with confirmation of unenhanced lesions for seven nodules. After 1-18 months of follow up, no major complications were recorded and no tumor-related death occurred. The lesions of two patients disappeared 3 and 6 months after their treatment, respectively. Conclusions: IRE is a promising ablation modality in the treatment of malignant hepatic and abdominal tumors unsuitable for resection or thermal ablation.
MeSH term(s)	Abdominal Neoplasms/diagnostic imaging ; Abdominal Neoplasms/therapy ; Aged ; Electroporation ; Female ; Follow-Up Studies ; Humans ; Liver Neoplasms/diagnostic imaging ; Liver Neoplasms/therapy ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Prospective Studies ; Tomography, X-Ray Computed ; Treatment Outcome ; Tumor Burden ; Ultrasonography, Interventional
Language	English
Publishing date	2019-03-06
Publishing country	Italy
Document type	Journal Article
ZDB-ID	2365426-0
ISSN	1876-7931 ; 1971-3495
ISSN (online)	1876-7931
ISSN	1971-3495
DOI	10.1007/s40477-019-00372-7
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Article ; Online: FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations.

Zavitsanou, Stamatia / Tsengenes, Alexandros / Papadourakis, Michail / Amendola, Giorgio / Chatzigoulas, Alexios / Dellis, Dimitris / Cosconati, Sandro / Cournia, Zoe

Journal of chemical information and modeling

2021 Volume 61, Issue 9, Page(s) 4131–4138

Abstract: Relative binding free energy calculations in drug design are becoming a useful tool in facilitating lead binding affinity optimization in a cost- and time-efficient manner. However, they have been limited by technical challenges such as the manual ... ...

Abstract	Relative binding free energy calculations in drug design are becoming a useful tool in facilitating lead binding affinity optimization in a cost- and time-efficient manner. However, they have been limited by technical challenges such as the manual creation of large numbers of input files to set up, run, and analyze free energy simulations. In this Application Note, we describe FEPrepare, a novel web-based tool, which automates the setup procedure for relative binding FEP calculations for the dual-topology scheme of NAMD, one of the major MD engines, using OPLS-AA force field topology and parameter files. FEPrepare provides the user with all necessary files needed to run a FEP/MD simulation with NAMD. FEPrepare can be accessed and used at https://feprepare.vi-seem.eu/.
MeSH term(s)	Entropy ; Internet ; Molecular Dynamics Simulation ; Physical Phenomena ; Thermodynamics
Language	English
Publishing date	2021-09-14
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.1c00215
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Article ; Online: Development of novel dipeptide nitriles as inhibitors of rhodesain of Trypanosoma brucei rhodesiense.

Di Chio, Carla / Previti, Santo / Amendola, Giorgio / Ravichandran, Rahul / Wagner, Annika / Cosconati, Sandro / Hellmich, Ute A / Schirmeister, Tanja / Zappalà, Maria / Ettari, Roberta

European journal of medicinal chemistry

2022 Volume 236, Page(s) 114328

Abstract: In this paper, we developed a new series of dipeptide nitriles that were demonstrated to be reversible rhodesain inhibitors at nanomolar level, with ... ...

Abstract	In this paper, we developed a new series of dipeptide nitriles that were demonstrated to be reversible rhodesain inhibitors at nanomolar level, with EC
MeSH term(s)	Cysteine Endopeptidases ; Cysteine Proteinase Inhibitors/chemistry ; Cysteine Proteinase Inhibitors/pharmacology ; Dipeptides/chemistry ; Dipeptides/pharmacology ; Nitriles/chemistry ; Nitriles/pharmacology ; Structure-Activity Relationship ; Trypanocidal Agents/chemistry ; Trypanocidal Agents/pharmacology ; Trypanosoma brucei rhodesiense/drug effects
Chemical Substances	Cysteine Proteinase Inhibitors ; Dipeptides ; Nitriles ; Trypanocidal Agents ; Cysteine Endopeptidases (EC 3.4.22.-) ; rhodesain (EC 3.4.22.-)
Language	English
Publishing date	2022-03-29
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.2022.114328
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Article ; Online: JMJD-1.2 controls multiple histone post-translational modifications in germ cells and protects the genome from replication stress.

Myers, Toshia R / Amendola, Pier Giorgio / Lussi, Yvonne C / Salcini, Anna Elisabetta

Scientific reports

2018 Volume 8, Issue 1, Page(s) 3765

Abstract: Post-translational modifications of histones, constitutive components of chromatin, regulate chromatin compaction and control all DNA-based cellular processes. C. elegans JMJD-1.2, a member of the KDM7 family, is a demethylase active towards several ... ...

Abstract	Post-translational modifications of histones, constitutive components of chromatin, regulate chromatin compaction and control all DNA-based cellular processes. C. elegans JMJD-1.2, a member of the KDM7 family, is a demethylase active towards several lysine residues on Histone 3 (H3), but its contribution in regulating histone methylation in germ cells has not been fully investigated. Here, we show that jmjd-1.2 is expressed abundantly in the germline where it controls the level of histone 3 lysine 9, lysine 23 and lysine 27 di-methylation (H3K9/K23/K27me2) both in mitotic and meiotic cells. Loss of jmjd-1.2 is not associated with major defects in the germ cells in animals grown under normal conditions or after DNA damage induced by UV or ionizing irradiation. However, jmjd-1.2 mutants are more sensitive to replication stress and the progeny of mutant animals exposed to hydroxyurea show increased embryonic lethality and mutational rate, compared to wild-type. Thus, our results suggest a role for jmjd-1.2 in the maintenance of genome integrity after replication stress and emphasize the relevance of the regulation of histone methylation in genomic stability.
MeSH term(s)	Animals ; Caenorhabditis elegans/cytology ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; DNA Damage/drug effects ; DNA Replication/genetics ; Genomic Instability ; Germ Cells/metabolism ; Histones/metabolism ; Jumonji Domain-Containing Histone Demethylases/genetics ; Jumonji Domain-Containing Histone Demethylases/metabolism ; Mutation ; Protein Processing, Post-Translational ; Protein Transport
Chemical Substances	Caenorhabditis elegans Proteins ; Histones ; JMJD-1.2 protein, C elegans (EC 1.14.11.-) ; Jumonji Domain-Containing Histone Demethylases (EC 1.14.11.-)
Language	English
Publishing date	2018-02-28
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/s41598-018-21914-9
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Article: Non-invasive estimation of

Frontiers in veterinary science

2023 Volume 10, Page(s) 1243325

Abstract: Biosensors applied in veterinary medicine serve as a noninvasive method to determine the health status of animals and, indirectly, their level of welfare. Near infrared spectroscopy (NIRS) has been suggested as a technology with this application. This ... ...

Abstract	Biosensors applied in veterinary medicine serve as a noninvasive method to determine the health status of animals and, indirectly, their level of welfare. Near infrared spectroscopy (NIRS) has been suggested as a technology with this application. This study presents preliminary
Language	English
Publishing date	2023-09-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2834243-4
ISSN	2297-1769
ISSN	2297-1769
DOI	10.3389/fvets.2023.1243325
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