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  1. Article: MBC and ECBL libraries: outstanding tools for drug discovery.

    Ginex, Tiziana / Madruga, Enrique / Martinez, Ana / Gil, Carmen

    Frontiers in pharmacology

    2023  Volume 14, Page(s) 1244317

    Abstract: Chemical libraries have become of utmost importance to boost drug discovery processes. It is widely accepted that the quality of a chemical library depends, among others, on its availability and chemical diversity which help in rising the chances of ... ...

    Abstract Chemical libraries have become of utmost importance to boost drug discovery processes. It is widely accepted that the quality of a chemical library depends, among others, on its availability and chemical diversity which help in rising the chances of finding good hits. In this regard, our group has developed a source for useful chemicals named Medicinal and Biological Chemistry (MBC) library. It originates from more than 30 years of experience in drug design and discovery of our research group and has successfully provided effective hits for neurological, neurodegenerative and infectious diseases. Moreover, in the last years, the European research infrastructure for chemical biology EU-OPENSCREEN has generated the European Chemical Biology library (ECBL) to be used as a source of hits for drug discovery. Here we present and discuss the updated version of the MBC library (MBC v.2022), enriched with new scaffolds and containing more than 2,500 compounds together with ECBL that collects about 100,000 small molecules. To properly address the improved potentialities of the new version of our MBC library in drug discovery, up to 44 among physicochemical and pharmaceutical properties have been calculated and compared with those of other well-known publicly available libraries. For comparison, we have used ZINC20, DrugBank, ChEMBL library, ECBL and NuBBE along with an approved drug library. Final results allowed to confirm the competitive chemical space covered by MBC v.2022 and ECBL together with suitable drug-like properties. In all, we can affirm that these two libraries represent an interesting source of new hits for drug discovery.
    Language English
    Publishing date 2023-08-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2023.1244317
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Searching for effective antiviral small molecules against influenza A virus: A patent review.

    Ginex, Tiziana / Luque, F Javier

    Expert opinion on therapeutic patents

    2020  Volume 31, Issue 1, Page(s) 53–66

    Abstract: Introduction: ...

    Abstract Introduction:
    MeSH term(s) Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; COVID-19/drug therapy ; Drug Discovery ; Humans ; Influenza A virus/drug effects ; Influenza, Human/drug therapy ; Influenza, Human/virology ; Patents as Topic ; Small Molecule Libraries
    Chemical Substances Antiviral Agents ; Small Molecule Libraries
    Keywords covid19
    Language English
    Publishing date 2020-10-19
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1186201-4
    ISSN 1744-7674 ; 0962-2594 ; 1354-3776
    ISSN (online) 1744-7674
    ISSN 0962-2594 ; 1354-3776
    DOI 10.1080/13543776.2020.1831471
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits.

    Vázquez, Javier / Ginex, Tiziana / Herrero, Albert / Morisseau, Christophe / Hammock, Bruce D / Luque, F Javier

    Journal of chemical information and modeling

    2023  Volume 63, Issue 10, Page(s) 3209–3225

    Abstract: The human soluble epoxide hydrolase (sEH) is a bifunctional enzyme that modulates the levels of regulatory epoxy lipids. The hydrolase activity is carried out by a catalytic triad located at the center of a wide L-shaped binding site, which contains two ... ...

    Abstract The human soluble epoxide hydrolase (sEH) is a bifunctional enzyme that modulates the levels of regulatory epoxy lipids. The hydrolase activity is carried out by a catalytic triad located at the center of a wide L-shaped binding site, which contains two hydrophobic subpockets at both sides. On the basis of these structural features, it can be assumed that desolvation is a major factor in determining the maximal achievable affinity that can be attained for this pocket. Accordingly, hydrophobic descriptors may be better suited to the search of novel hits targeting this enzyme. This study examines the suitability of quantum mechanically derived hydrophobic descriptors in the discovery of novel sEH inhibitors. To this end, three-dimensional quantitative structure-activity relationship (3D-QSAR) pharmacophores were generated by combining electrostatic and steric or alternatively hydrophobic and hydrogen-bond parameters in conjunction with a tailored list of 76 known sEH inhibitors. The pharmacophore models were then validated by using two external sets chosen (i) to rank the potency of four distinct series of compounds and (ii) to discriminate actives from decoys, using in both cases datasets taken from the literature. Finally, a prospective study was performed including a virtual screening of two chemical libraries to identify new potential hits, which were subsequently experimentally tested for their inhibitory activity on human, rat, and mouse sEH. The use of hydrophobic-based descriptors led to the identification of six compounds as inhibitors of the human enzyme with IC
    MeSH term(s) Mice ; Humans ; Rats ; Animals ; Epoxide Hydrolases/chemistry ; Pharmacophore ; Prospective Studies ; Quantitative Structure-Activity Relationship ; Enzyme Inhibitors/metabolism ; Hydrophobic and Hydrophilic Interactions
    Chemical Substances Epoxide Hydrolases (EC 3.3.2.-) ; Enzyme Inhibitors
    Language English
    Publishing date 2023-05-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; 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.3c00301
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Computational Study of the Aza-Michael Addition of the Flavonoid (+)-Taxifolin in the Inhibition of β-Amyloid Fibril Aggregation.

    Ginex, Tiziana / Trius, Marta / Luque, F Javier

    Chemistry (Weinheim an der Bergstrasse, Germany)

    2018  Volume 24, Issue 22, Page(s) 5813–5824

    Abstract: Inhibition of abnormal protein self-aggregation is an attractive strategy against amyloidogenic diseases, but has found limited success due to the complexity of protein self-assembly, the absence of fully reproducible aggregation assays, and the scarce ... ...

    Abstract Inhibition of abnormal protein self-aggregation is an attractive strategy against amyloidogenic diseases, but has found limited success due to the complexity of protein self-assembly, the absence of fully reproducible aggregation assays, and the scarce knowledge of the inhibition mechanisms by small molecules. In this context, catechol-containing compounds may lead to covalent adducts with amyloid fibrils that interfere with the aggregation process. In particular, the covalent adduct formed between the oxidized form of (+)-taxifolin and an β-amyloid (Aβ42) suggests the involvement of a specific recognition motif that enables the chemical reaction with Aβ42. In this study, we have examined the mechanisms implicated in the aza-Michael addition of the o-quinone species of (+)-taxifolin with Aβ42 fibrils. The results support the binding of (+)-taxifolin to the hydrophobic groove delimited by the edges defined by Lys16 and Glu22 residues in the fibril. The chemical reaction proceeds through the nucleophilic attack of the deprotonated amino group of a Lys16 residue in a process activated by the interaction between the o-quinone ring with a vicinal Lys16 residue, as well as by a water-assisted proton transfer, which is the rate-limiting step of the reaction. This specific inhibition mechanism, which may explain the enhanced anti-aggregating activity of oxidized flavonoids compared to fresh compounds, holds promise for developing disease-modifying therapies.
    MeSH term(s) Amyloid/chemistry ; Amyloid beta-Peptides/chemistry ; Amyloid beta-Peptides/drug effects ; Computational Biology ; Flavonoids/chemistry ; Flavonoids/pharmacology ; Glutamine/chemistry ; Lysine/chemistry ; Quercetin/analogs & derivatives ; Quercetin/chemistry ; Stereoisomerism
    Chemical Substances Amyloid ; Amyloid beta-Peptides ; Flavonoids ; Glutamine (0RH81L854J) ; Quercetin (9IKM0I5T1E) ; taxifolin (9SOB9E3987) ; Lysine (K3Z4F929H6)
    Language English
    Publishing date 2018-04-17
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1478547-x
    ISSN 1521-3765 ; 0947-6539
    ISSN (online) 1521-3765
    ISSN 0947-6539
    DOI 10.1002/chem.201706072
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: N

    Garcia-Rubia, Alfonso / Lasala, Fátima / Ginex, Tiziana / Morales-Tenorio, Marcos / Olal, Catherine / Heung, Michelle / Oquist, Paola / Galindo, Inmaculada / Cuesta-Geijo, Miguel Ángel / Casasnovas, José M / Campillo, Nuria E / Canales, Ángeles / Alonso, Covadonga / Martínez, Ana / Muñoz-Fontela, César / Delgado, Rafael / Gil, Carmen

    Journal of medicinal chemistry

    2023  Volume 66, Issue 8, Page(s) 5465–5483

    Abstract: Ebola virus (EBOV) is a single-strand RNA virus belonging to ... ...

    Abstract Ebola virus (EBOV) is a single-strand RNA virus belonging to the
    MeSH term(s) Humans ; Hemorrhagic Fever, Ebola ; Ebolavirus ; Molecular Dynamics Simulation ; Mutagenesis ; Virus Replication
    Language English
    Publishing date 2023-04-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.2c01785
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Inhibition of β-Amyloid Aggregation in Alzheimer's Disease: The Key Role of (Pro)electrophilic Warheads.

    Basagni, Filippo / Naldi, Marina / Ginex, Tiziana / Luque, F Javier / Fagiani, Francesca / Lanni, Cristina / Iurlo, Matteo / Marcaccio, Massimo / Minarini, Anna / Bartolini, Manuela / Rosini, Michela

    ACS medicinal chemistry letters

    2022  Volume 13, Issue 11, Page(s) 1812–1818

    Abstract: Catechols have been largely investigated as antiaggregating agents toward β-amyloid peptide. Herein, as a follow up of a previous series of hydroxycinnamic derivatives, we synthesized a small set of dihydroxy isomers for exploring the role of the ... ...

    Abstract Catechols have been largely investigated as antiaggregating agents toward β-amyloid peptide. Herein, as a follow up of a previous series of hydroxycinnamic derivatives, we synthesized a small set of dihydroxy isomers for exploring the role of the reciprocal position of the two hydroxyl functions at a molecular level.
    Language English
    Publishing date 2022-10-10
    Publishing country United States
    Document type Journal Article
    ISSN 1948-5875
    ISSN 1948-5875
    DOI 10.1021/acsmedchemlett.2c00410
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Lipophilicity in drug design: an overview of lipophilicity descriptors in 3D-QSAR studies.

    Ginex, Tiziana / Vazquez, Javier / Gilbert, Enric / Herrero, Enric / Luque, Francisco J

    Future medicinal chemistry

    2019  Volume 11, Issue 10, Page(s) 1177–1193

    Abstract: The pharmacophore concept is a fundamental cornerstone in drug discovery, playing a critical role in determining the success ... ...

    Abstract The pharmacophore concept is a fundamental cornerstone in drug discovery, playing a critical role in determining the success of
    MeSH term(s) Computer Simulation ; Drug Design ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Models, Chemical ; Pharmaceutical Preparations/chemistry ; Quantitative Structure-Activity Relationship ; Quantum Theory
    Chemical Substances Ligands ; Pharmaceutical Preparations
    Language English
    Publishing date 2019-02-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ISSN 1756-8927
    ISSN (online) 1756-8927
    DOI 10.4155/fmc-2018-0435
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Potential pharmacological strategies targeting the Niemann-Pick C1 receptor and Ebola virus glycoprotein interaction.

    Morales-Tenorio, Marcos / Ginex, Tiziana / Cuesta-Geijo, Miguel Ángel / Campillo, Nuria E / Muñoz-Fontela, César / Alonso, Covadonga / Delgado, Rafael / Gil, Carmen

    European journal of medicinal chemistry

    2021  Volume 223, Page(s) 113654

    Abstract: Niemann-Pick C1 (NPC1) receptor is an intracellular protein located in late endosomes and lysosomes whose main function is to regulate intracellular cholesterol trafficking. Besides being postulated as necessary for the infection of highly pathogenic ... ...

    Abstract Niemann-Pick C1 (NPC1) receptor is an intracellular protein located in late endosomes and lysosomes whose main function is to regulate intracellular cholesterol trafficking. Besides being postulated as necessary for the infection of highly pathogenic viruses in which the integrity of cholesterol transport is required, this protein also allows the entry of the Ebola virus (EBOV) into the host cells acting as an intracellular receptor. EBOV glycoprotein (EBOV-GP) interaction with NPC1 at the endosomal membrane triggers the release of the viral material into the host cell, starting the infective cycle. Disruption of the NPC1/EBOV-GP interaction could represent an attractive strategy for the development of drugs aimed at inhibiting viral entry and thus infection. Some of the today available EBOV inhibitors were proposed to interrupt this interaction, but molecular and structural details about their mode of action are still preliminary thus more efforts are needed to properly address these points. Here, we provide a critical discussion of the potential of NPC1 and its interaction with EBOV-GP as a therapeutic target for viral infections.
    MeSH term(s) Antibodies/immunology ; Antibodies/pharmacology ; Ebolavirus/metabolism ; Glycoproteins/chemistry ; Glycoproteins/metabolism ; Hemorrhagic Fever, Ebola/drug therapy ; Hemorrhagic Fever, Ebola/pathology ; Humans ; Molecular Docking Simulation ; Niemann-Pick C1 Protein/chemistry ; Niemann-Pick C1 Protein/immunology ; Niemann-Pick C1 Protein/metabolism ; Protein Binding ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/metabolism ; Small Molecule Libraries/pharmacology ; Small Molecule Libraries/therapeutic use ; Virus Internalization/drug effects
    Chemical Substances Antibodies ; Glycoproteins ; Niemann-Pick C1 Protein ; Small Molecule Libraries
    Language English
    Publishing date 2021-06-19
    Publishing country France
    Document type Journal Article ; Review
    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.2021.113654
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Host-Directed FDA-Approved Drugs with Antiviral Activity against SARS-CoV-2 Identified by Hierarchical In Silico/In Vitro Screening Methods.

    Ginex, Tiziana / Garaigorta, Urtzi / Ramírez, David / Castro, Victoria / Nozal, Vanesa / Maestro, Inés / García-Cárceles, Javier / Campillo, Nuria E / Martinez, Ana / Gastaminza, Pablo / Gil, Carmen

    Pharmaceuticals (Basel, Switzerland)

    2021  Volume 14, Issue 4

    Abstract: The unprecedent situation generated by the COVID-19 global emergency has prompted us to actively work to fight against this pandemic by searching for repurposable agents among FDA approved drugs to shed light into immediate opportunities for the ... ...

    Abstract The unprecedent situation generated by the COVID-19 global emergency has prompted us to actively work to fight against this pandemic by searching for repurposable agents among FDA approved drugs to shed light into immediate opportunities for the treatment of COVID-19 patients. In the attempt to proceed toward a proper rationalization of the search for new antivirals among approved drugs, we carried out a hierarchical in silico/in vitro protocol which successfully combines virtual and biological screening to speed up the identification of host-directed therapies against COVID-19 in an effective way. To this end a multi-target virtual screening approach focused on host-based targets related to viral entry, followed by the experimental evaluation of the antiviral activity of selected compounds, has been carried out. As a result, five different potentially repurposable drugs interfering with viral entry-cepharantine, clofazimine, metergoline, imatinib and efloxate-have been identified.
    Language English
    Publishing date 2021-04-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph14040332
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  10. Article ; Online: Structure-Based Design and Discovery of Pyridyl-Bearing Fused Bicyclic HIV-1 Inhibitors: Synthesis, Biological Characterization, and Molecular Modeling Studies.

    Huang, Boshi / Ginex, Tiziana / Luque, F Javier / Jiang, Xiangyi / Gao, Ping / Zhang, Jian / Kang, Dongwei / Daelemans, Dirk / De Clercq, Erik / Pannecouque, Christophe / Zhan, Peng / Liu, Xinyong

    Journal of medicinal chemistry

    2021  Volume 64, Issue 18, Page(s) 13604–13621

    Abstract: Two series of new pyridyl-bearing fused bicyclic analogues designed to target the dual-tolerant regions of the non-nucleoside reverse transcriptase inhibitor (NNRTI)-binding pocket were synthesized and evaluated for their anti-HIV activities. Several ... ...

    Abstract Two series of new pyridyl-bearing fused bicyclic analogues designed to target the dual-tolerant regions of the non-nucleoside reverse transcriptase inhibitor (NNRTI)-binding pocket were synthesized and evaluated for their anti-HIV activities. Several compounds, such as
    MeSH term(s) Anti-HIV Agents/chemical synthesis ; Anti-HIV Agents/metabolism ; Anti-HIV Agents/pharmacology ; Cell Line ; Drug Design ; HIV Reverse Transcriptase/chemistry ; HIV Reverse Transcriptase/genetics ; HIV Reverse Transcriptase/metabolism ; HIV-1/drug effects ; Heterocyclic Compounds, 2-Ring/chemical synthesis ; Heterocyclic Compounds, 2-Ring/metabolism ; Heterocyclic Compounds, 2-Ring/pharmacology ; Humans ; Microsomes, Liver/metabolism ; Molecular Dynamics Simulation ; Molecular Structure ; Mutation ; Protein Binding ; Pyridines/chemical synthesis ; Pyridines/metabolism ; Pyridines/pharmacology ; Reverse Transcriptase Inhibitors/chemical synthesis ; Reverse Transcriptase Inhibitors/metabolism ; Reverse Transcriptase Inhibitors/pharmacology ; Structure-Activity Relationship
    Chemical Substances Anti-HIV Agents ; Heterocyclic Compounds, 2-Ring ; Pyridines ; Reverse Transcriptase Inhibitors ; HIV Reverse Transcriptase (EC 2.7.7.49)
    Language English
    Publishing date 2021-09-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.1c00987
    Database MEDical Literature Analysis and Retrieval System OnLINE

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