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  1. Article ; Online: A comprehensive review of synthetic strategies and SAR studies for the discovery of PfDHODH inhibitors as antimalarial agents. Part 1: triazolopyrimidine, isoxazolopyrimidine and pyrrole-based (DSM) compounds.

    Sharma, Manmohan / Pandey, Vinita / Poli, Giulio / Tuccinardi, Tiziano / Lolli, Marco L / Vyas, Vivek K

    Bioorganic chemistry

    2024  Volume 146, Page(s) 107249

    Abstract: One of the deadliest infectious diseases, malaria, still has a significant impact on global morbidity and mortality. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) catalyzes the fourth step in de novo pyrimidine nucleotide biosynthesis and ... ...

    Abstract One of the deadliest infectious diseases, malaria, still has a significant impact on global morbidity and mortality. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) catalyzes the fourth step in de novo pyrimidine nucleotide biosynthesis and has been clinically validated as an innovative and promising target for the development of novel targeted antimalarial drugs. PfDHODH inhibitors have the potential to significantly slow down parasite growth at the blood and liver stages. Several PfDHODH inhibitors based on various scaffolds have been explored over the past two decades. Among them, triazolopyrimidines, isoxazolopyrimidines, and pyrrole-based derivatives known as DSM compounds showed tremendous potential as novel antimalarial agents, and one of the triazolopyrimidine-based compounds (DSM265) was able to reach phase IIa clinical trials. DSM compounds were synthesized as PfDHODH inhibitors with various substitutions based on structure-guided medicinal chemistry approaches and further optimised as well. For the first time, this review provides an overview of all the synthetic approaches used for the synthesis, alternative synthetic routes, and novel strategies involving various catalysts and chemical reagents that have been used to synthesize DSM compounds. We have also summarized SAR study of all these PfDHODH inhibitors. In an attempt to assist readers, scientists, and researchers involved in the development of new PfDHODH inhibitors as antimalarials, this review provides accessibility of all synthetic techniques and SAR studies of the most promising triazolopyrimidines, isoxazolopyrimidines, and pyrrole-based PfDHODH inhibitors.
    MeSH term(s) Antimalarials/chemistry ; Plasmodium falciparum ; Oxidoreductases Acting on CH-CH Group Donors/chemistry ; Pyrroles/pharmacology ; Dihydroorotate Dehydrogenase ; Enzyme Inhibitors/pharmacology ; Enzyme Inhibitors/chemistry
    Chemical Substances Antimalarials ; Oxidoreductases Acting on CH-CH Group Donors (EC 1.3.-) ; Pyrroles ; Dihydroorotate Dehydrogenase ; Enzyme Inhibitors
    Language English
    Publishing date 2024-03-03
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 120080-x
    ISSN 1090-2120 ; 0045-2068
    ISSN (online) 1090-2120
    ISSN 0045-2068
    DOI 10.1016/j.bioorg.2024.107249
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: An update on antibacterial AlkylGuanidino Ureas: Design of new derivatives, synergism with colistin and data analysis of the whole library.

    Ardino, Claudia / Sannio, Filomena / Poli, Giulio / Galati, Salvatore / Dreassi, Elena / Botta, Lorenzo / Docquier, Jean-Denis / D'Agostino, Ilaria

    European journal of medicinal chemistry

    2024  Volume 270, Page(s) 116362

    Abstract: Antimicrobial resistance (AMR) represents one of the most challenging global Public Health issues, with an alarmingly increasing rate of attributable mortality. This scenario highlights the urgent need for innovative medicinal strategies showing activity ...

    Abstract Antimicrobial resistance (AMR) represents one of the most challenging global Public Health issues, with an alarmingly increasing rate of attributable mortality. This scenario highlights the urgent need for innovative medicinal strategies showing activity on resistant isolates (especially, carbapenem-resistant Gram-negative bacteria, methicillin-resistant S. aureus, and vancomycin-resistant enterococci) yielding new approaches for the treatment of bacterial infections. We previously reported AlkylGuanidino Ureas (AGUs) with broad-spectrum antibacterial activity and a putative membrane-based mechanism of action. Herein, new tetra- and mono-guanidino derivatives were designed and synthesized to expand the structure-activity relationships (SARs) and, thereby, tested on the same panel of Gram-positive and Gram-negative bacteria. The membrane-active mechanism of selected compounds was then investigated through molecular dynamics (MD) on simulated bacterial membranes. In the end, the newly synthesized series, along with the whole library of compounds (more than 70) developed in the last decade, was tested in combination with subinhibitory concentrations of the last resort antibiotic colistin to assess putative synergistic or additive effects. Moreover, all the AGUs were subjected to cheminformatic and machine learning analyses to gain a deeper knowledge of the key features required for bioactivity.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Colistin/pharmacology ; Methicillin-Resistant Staphylococcus aureus ; Gram-Negative Bacteria ; Gram-Positive Bacteria ; Bacteria ; Data Analysis ; Microbial Sensitivity Tests
    Chemical Substances Anti-Bacterial Agents ; Colistin (Z67X93HJG1)
    Language English
    Publishing date 2024-03-28
    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.2024.116362
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: MolBook UNIPI─Create, Manage, Analyze, and Share Your Chemical Data for Free.

    Galati, Salvatore / Di Stefano, Miriana / Macchia, Marco / Poli, Giulio / Tuccinardi, Tiziano

    Journal of chemical information and modeling

    2023  Volume 63, Issue 13, Page(s) 3977–3982

    Abstract: Here, we present MolBook UNIPI, freely available and user-friendly software specifically designed for medicinal chemists as a powerful tool for the easy management of virtual libraries of chemical compounds. With MolBook UNIPI, it is possible to create, ... ...

    Abstract Here, we present MolBook UNIPI, freely available and user-friendly software specifically designed for medicinal chemists as a powerful tool for the easy management of virtual libraries of chemical compounds. With MolBook UNIPI, it is possible to create, store, handle, and share molecular databases in a very simple and intuitive way. The software allows users to rapidly generate libraries of bioactive ligands, building blocks, or commercial compounds by either manually creating single molecules or automatically importing compounds from public databases and pre-existing libraries. MolBook UNIPI databases can be enriched with all kinds of data and can be filtered based on molecular structures or properties, allowing the desired molecules, along with their structures and features, to be easily accessible in just a few clicks. Moreover, new molecular properties and potential toxicological effects of compounds can be rapidly and reliably predicted. Notably, all of these functions can be easily mastered even by inexperienced users, with no prior cheminformatics knowledge or programming skills, which makes MolBook UNIPI an invaluable tool for medicinal chemists. MolBook UNIPI can be downloaded free of charge from the project web page https://molbook.farm.unipi.it/.
    MeSH term(s) Software ; Databases, Factual ; Databases, Chemical ; Ligands
    Chemical Substances Ligands
    Language English
    Publishing date 2023-06-26
    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.3c00278
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Application of MM-PBSA Methods in Virtual Screening.

    Poli, Giulio / Granchi, Carlotta / Rizzolio, Flavio / Tuccinardi, Tiziano

    Molecules (Basel, Switzerland)

    2020  Volume 25, Issue 8

    Abstract: Computer-aided drug design techniques are today largely applied in medicinal chemistry. In particular, receptor-based virtual screening (VS) studies, in which molecular docking represents the gold standard in silico approach, constitute a powerful ... ...

    Abstract Computer-aided drug design techniques are today largely applied in medicinal chemistry. In particular, receptor-based virtual screening (VS) studies, in which molecular docking represents the gold standard in silico approach, constitute a powerful strategy for identifying novel hit compounds active against the desired target receptor. Nevertheless, the need for improving the ability of docking in discriminating true active ligands from inactive compounds, thus boosting VS hit rates, is still pressing. In this context, the use of binding free energy evaluation approaches can represent a profitable tool for rescoring ligand-protein complexes predicted by docking based on more reliable estimations of ligand-protein binding affinities than those obtained with simple scoring functions. In the present review, we focused our attention on the Molecular Mechanics-Poisson Boltzman Surface Area (MM-PBSA) method for the calculation of binding free energies and its application in VS studies. We provided examples of successful applications of this method in VS campaigns and evaluation studies in which the reliability of this approach has been assessed, thus providing useful guidelines for employing this approach in VS.
    MeSH term(s) Binding Sites ; Drug Design ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; Structure-Activity Relationship
    Chemical Substances Ligands
    Language English
    Publishing date 2020-04-23
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules25081971
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Three-Dimensional Interactions Analysis of the Anticancer Target c-Src Kinase with Its Inhibitors.

    Jha, Vibhu / Macchia, Marco / Tuccinardi, Tiziano / Poli, Giulio

    Cancers

    2020  Volume 12, Issue 8

    Abstract: Src family kinases (SFKs) constitute the biggest family of non-receptor tyrosine kinases considered as therapeutic targets for cancer therapy. An aberrant expression and/or activation of the proto-oncogene c-Src kinase, which is the oldest and most ... ...

    Abstract Src family kinases (SFKs) constitute the biggest family of non-receptor tyrosine kinases considered as therapeutic targets for cancer therapy. An aberrant expression and/or activation of the proto-oncogene c-Src kinase, which is the oldest and most studied member of the family, has long been demonstrated to play a major role in the development, growth, progression and metastasis of numerous human cancers, including colon, breast, gastric, pancreatic, lung and brain carcinomas. For these reasons, the pharmacological inhibition of c-Src activity represents an effective anticancer strategy and a few compounds targeting c-Src, together with other kinases, have been approved as drugs for cancer therapy, while others are currently undergoing preclinical studies. Nevertheless, the development of potent and selective inhibitors of c-Src aimed at properly exploiting this biological target for the treatment of cancer still represents a growing field of study. In this review, the co-crystal structures of c-Src kinase in complex with inhibitors discovered in the past two decades have been described, highlighting the key ligand-protein interactions necessary to obtain high potency and the features to be exploited for addressing selectivity and drug resistance issues, thus providing useful information for the design of new and potent c-Src kinase inhibitors.
    Language English
    Publishing date 2020-08-18
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers12082327
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Sirtuin 1-activating derivatives belonging to the anilinopyridine class displaying

    Bononi, Giulia / Citi, Valentina / Martelli, Alma / Poli, Giulio / Tuccinardi, Tiziano / Granchi, Carlotta / Testai, Lara / Calderone, Vincenzo / Minutolo, Filippo

    RSC medicinal chemistry

    2023  Volume 15, Issue 1, Page(s) 267–282

    Abstract: Sirtuin 1 (SIRT1) is an enzyme that relies on ... ...

    Abstract Sirtuin 1 (SIRT1) is an enzyme that relies on NAD
    Language English
    Publishing date 2023-12-05
    Publishing country England
    Document type Journal Article
    ISSN 2632-8682
    ISSN (online) 2632-8682
    DOI 10.1039/d3md00489a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Identification of New GSK3β Inhibitors through a Consensus Machine Learning-Based Virtual Screening.

    Galati, Salvatore / Di Stefano, Miriana / Bertini, Simone / Granchi, Carlotta / Giordano, Antonio / Gado, Francesca / Macchia, Marco / Tuccinardi, Tiziano / Poli, Giulio

    International journal of molecular sciences

    2023  Volume 24, Issue 24

    Abstract: Glycogen synthase kinase-3 beta (GSK3β) is a serine/threonine kinase that plays key roles in glycogen metabolism, Wnt/β-catenin signaling cascade, synaptic modulation, and multiple autophagy-related signaling pathways. GSK3β is an attractive target for ... ...

    Abstract Glycogen synthase kinase-3 beta (GSK3β) is a serine/threonine kinase that plays key roles in glycogen metabolism, Wnt/β-catenin signaling cascade, synaptic modulation, and multiple autophagy-related signaling pathways. GSK3β is an attractive target for drug discovery since its aberrant activity is involved in the development of neurodegenerative diseases such as Alzheimer's and Parkinson's disease. In the present study, multiple machine learning models aimed at identifying novel GSK3β inhibitors were developed and evaluated for their predictive reliability. The most powerful models were combined in a consensus approach, which was used to screen about 2 million commercial compounds. Our consensus machine learning-based virtual screening led to the identification of compounds
    MeSH term(s) Molecular Docking Simulation ; Consensus ; Glycogen Synthase Kinase 3 beta ; Reproducibility of Results ; Wnt Signaling Pathway
    Chemical Substances Glycogen Synthase Kinase 3 beta (EC 2.7.11.1)
    Language English
    Publishing date 2023-12-07
    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/ijms242417233
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: An in silico toolbox for the prediction of the potential pathogenic effects of missense mutations in the dimeric region of

    Poli, Giulio / Demontis, Gian Carlo / Sodi, Andrea / Saba, Alessandro / Rizzo, Stanislao / Macchia, Marco / Tuccinardi, Tiziano

    Journal of enzyme inhibition and medicinal chemistry

    2023  Volume 38, Issue 1, Page(s) 2162047

    Abstract: ... ...

    Abstract h
    MeSH term(s) Humans ; Mutation, Missense ; cis-trans-Isomerases/genetics ; Computational Biology
    Chemical Substances retinoid isomerohydrolase (EC 3.1.1.64) ; cis-trans-Isomerases (EC 5.2.-)
    Language English
    Publishing date 2023-01-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2082578-X
    ISSN 1475-6374 ; 1475-6366
    ISSN (online) 1475-6374
    ISSN 1475-6366
    DOI 10.1080/14756366.2022.2162047
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: VenomPred 2.0: A Novel

    Di Stefano, Miriana / Galati, Salvatore / Piazza, Lisa / Granchi, Carlotta / Mancini, Simone / Fratini, Filippo / Macchia, Marco / Poli, Giulio / Tuccinardi, Tiziano

    Journal of chemical information and modeling

    2023  Volume 64, Issue 7, Page(s) 2275–2289

    Abstract: The application of artificial intelligence and machine learning (ML) methods is becoming increasingly popular in computational toxicology and drug design; it is considered as a promising solution for assessing the safety profile of compounds, ... ...

    Abstract The application of artificial intelligence and machine learning (ML) methods is becoming increasingly popular in computational toxicology and drug design; it is considered as a promising solution for assessing the safety profile of compounds, particularly in lead optimization and ADMET studies, and to meet the principles of the 3Rs, which calls for the replacement, reduction, and refinement of animal testing. In this context, we herein present the development of VenomPred 2.0 (http://www.mmvsl.it/wp/venompred2/), the new and improved version of our free of charge web tool for toxicological predictions, which now represents a powerful web-based platform for multifaceted and human-interpretable
    MeSH term(s) Animals ; Humans ; Artificial Intelligence ; Machine Learning
    Language English
    Publishing date 2023-09-07
    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.3c00692
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. 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
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