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  1. Article ; Online: Optimal HTS Fingerprint Definitions by Using a Desirability Function and a Genetic Algorithm.

    Cortes Cabrera, Alvaro / Petrone, Paula M

    Journal of chemical information and modeling

    2018  Volume 58, Issue 3, Page(s) 641–646

    Abstract: The use of compound biological fingerprints built on data from high-throughput screening (HTS) campaigns, or HTS fingerprints, is a novel cheminformatics method of representing compounds by integrating chemical and biological activity data that is ... ...

    Abstract The use of compound biological fingerprints built on data from high-throughput screening (HTS) campaigns, or HTS fingerprints, is a novel cheminformatics method of representing compounds by integrating chemical and biological activity data that is gaining momentum in its application to drug discovery, including hit expansion, target identification, and virtual screening. HTS fingerprints present two major limitations, noise and missing data, which are intrinsic to the high-throughput data acquisition technologies and to the assay availability or assay selection procedure used for their construction. In this work, we present a methodology to define an optimal set of HTS fingerprints by using a desirability function that encodes the principles of maximum biological and chemical space coverage and minimum redundancy between HTS assays. We used a genetic algorithm to optimize the desirability function and obtained an optimal fingerprint that was evaluated for performance in a test set of 33 diverse assays. Our results show that the optimal HTS fingerprint represents compounds in chemical biology space using 25% fewer assays. When used for virtual screening, the optimal HTS fingerprint obtained equivalent performance, in terms of both area under the curve and enrichment factors, to full fingerprints for 27 out of 33 test assays, while randomly assembled fingerpints could achieve equivalent performance in only 23 test assays.
    MeSH term(s) Algorithms ; Drug Discovery/methods ; High-Throughput Screening Assays/methods ; Humans ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/pharmacology
    Chemical Substances Small Molecule Libraries
    Language English
    Publishing date 2018-02-22
    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.7b00447
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  2. Article ; Online: Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule.

    Sánchez-Murcia, Pedro A / Mills, Alberto / Cortés-Cabrera, Álvaro / Gago, Federico

    Journal of computer-aided molecular design

    2019  Volume 33, Issue 7, Page(s) 627–644

    Abstract: Many natural products target mammalian tubulin but only a few can form a covalent bond and hence irreversibly affect microtubule function. Among them, zampanolide (ZMP) and taccalonolide AJ (TAJ) stand out, not only because they are very potent antitumor ...

    Abstract Many natural products target mammalian tubulin but only a few can form a covalent bond and hence irreversibly affect microtubule function. Among them, zampanolide (ZMP) and taccalonolide AJ (TAJ) stand out, not only because they are very potent antitumor agents but also because the adducts they form with β-tubulin have been structurally characterized in atomic detail. By applying model building techniques, molecular orbital calculations, molecular dynamics simulations and hybrid QM/MM methods, we have gained insight into the 1,2- and 1,4-addition reactions of His229 and Asp226 to ZMP and TAJ, respectively, in the taxane-binding site of β-tubulin. The experimentally inaccessible precovalent complexes strongly suggest a water-mediated proton shuttle mechanism for ZMP adduct formation and a direct nucleophilic attack by the carboxylate of Asp226 on C22 of the C22R,C23R epoxide in TAJ. The M-loop, which is crucially important for interprotofilament interactions, is structured into a short helix in both types of complexes, mostly as a consequence of the fixation of the phenol ring of Tyr283 and the guanidinium of Arg284. As a side benefit, we obtained evidence supporting the existence of a commonly neglected intramolecular disulfide bond between Cys241 and Cys356 in β-tubulin that contributes to protein compactness and is absent in the β
    MeSH term(s) Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; Humans ; Macrolides/chemistry ; Macrolides/pharmacology ; Microtubules/chemistry ; Microtubules/metabolism ; Molecular Dynamics Simulation ; Protein Binding ; Steroids/chemistry ; Steroids/pharmacology ; Thermodynamics ; Tubulin/chemistry ; Tubulin/metabolism ; Tubulin Modulators/chemistry ; Tubulin Modulators/pharmacology
    Chemical Substances Antineoplastic Agents ; Macrolides ; Steroids ; Tubulin ; Tubulin Modulators ; taccalonolide AJ ; zampanolide
    Language English
    Publishing date 2019-05-31
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 808166-9
    ISSN 1573-4951 ; 0920-654X
    ISSN (online) 1573-4951
    ISSN 0920-654X
    DOI 10.1007/s10822-019-00208-w
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  3. Article ; Online: Structural rationale for the cross-resistance of tumor cells bearing the A399V variant of elongation factor eEF1A1 to the structurally unrelated didemnin B, ternatin, nannocystin A and ansatrienin B.

    Sánchez-Murcia, Pedro A / Cortés-Cabrera, Álvaro / Gago, Federico

    Journal of computer-aided molecular design

    2017  Volume 31, Issue 10, Page(s) 915–928

    Abstract: At least four classes of structurally distinct natural products with potent antiproliferative activities target the translation elongation factor eEF1A1, which is best known as the G-protein that delivers amino acyl transfer RNAs (aa-tRNAs) to ribosomes ... ...

    Abstract At least four classes of structurally distinct natural products with potent antiproliferative activities target the translation elongation factor eEF1A1, which is best known as the G-protein that delivers amino acyl transfer RNAs (aa-tRNAs) to ribosomes during mRNA translation. We present molecular models in atomic detail that provide a common structural basis for the high-affinity binding of didemnin B, ternatin, ansatrienin B and nannocystin A to eEF1A1, as well as a rationale based on molecular dynamics results that accounts for the deleterious effect of replacing alanine 399 with valine. The proposed binding site, at the interface between domains I and III, is eminently hydrophobic and exists only in the GTP-bound conformation. Drug binding at this site is expected to disrupt neither loading of aa-tRNAs nor GTP hydrolysis but would give rise to stabilization of this particular conformational state, in consonance with reported experimental findings. The experimental solution of the three-dimensional structure of mammalian eEF1A1 has proved elusive so far and the highly homologous eEF1A2 from rabbit muscle has been crystallized and solved only as a homodimer in a GDP-bound conformation. Interestingly, in this dimeric structure the large interdomain cavity where the drugs studied are proposed to bind is occupied by a mostly hydrophobic α-helix from domain I of the same monomer. Since binding of this α-helix and any of these drugs to domain III of eEF1A(1/2) is, therefore, mutually exclusive and involves two distinct protein conformations, one intriguing possibility that emerges from our study is that the potent antiproliferative effect of these natural products may arise not only from inhibition of protein synthesis, which is the current dogma, but also from interference with some other non-canonical functions. From this standpoint, this type of drugs could be considered antagonists of eEF1A1/2 oligomerization, a hypothesis that opens up novel areas of research.
    Language English
    Publishing date 2017-10
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 808166-9
    ISSN 1573-4951 ; 0920-654X
    ISSN (online) 1573-4951
    ISSN 0920-654X
    DOI 10.1007/s10822-017-0066-x
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  4. Article ; Online: Making sense of the past: hyperstability of ancestral thioredoxins explained by free energy simulations.

    Cortés Cabrera, Álvaro / Sánchez-Murcia, Pedro A / Gago, Federico

    Physical chemistry chemical physics : PCCP

    2017  Volume 19, Issue 34, Page(s) 23239–23246

    Abstract: Thioredoxin (Trx), a small and globular protein, is present in all kinds of organisms, from Archea to higher mammals. Throughout evolution, the Trx sequence has undergone subtle modifications to adapt to varying environmental conditions. The high degree ... ...

    Abstract Thioredoxin (Trx), a small and globular protein, is present in all kinds of organisms, from Archea to higher mammals. Throughout evolution, the Trx sequence has undergone subtle modifications to adapt to varying environmental conditions. The high degree of sequence conservation makes Trx very amenable to ancestral protein reconstruction techniques. In this work, we address the study of the structural and energetic determinants of thermostability in E. coli Trx using a dataset of mutations inspired by ancestral reconstruction. We compute, from first principles, the expected contribution of 19 different amino acid substitutions to the stability (ΔΔG) and the melting temperature (ΔT
    Language English
    Publishing date 2017-08-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c7cp03659k
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  5. Article: Application of Artificial Intelligence to the Prediction of the Antimicrobial Activity of Essential Oils.

    Daynac, Mathieu / Cortes-Cabrera, Alvaro / Prieto, Jose M

    Evidence-based complementary and alternative medicine : eCAM

    2015  Volume 2015, Page(s) 561024

    Abstract: Essential oils (EOs) are vastly used as natural antibiotics in Complementary and Alternative Medicine (CAM). Their intrinsic chemical variability and synergisms/antagonisms between its components make difficult to ensure consistent effects through ... ...

    Abstract Essential oils (EOs) are vastly used as natural antibiotics in Complementary and Alternative Medicine (CAM). Their intrinsic chemical variability and synergisms/antagonisms between its components make difficult to ensure consistent effects through different batches. Our aim is to evaluate the use of artificial neural networks (ANNs) for the prediction of their antimicrobial activity. Methods. The chemical composition and antimicrobial activity of 49 EOs, extracts, and/or fractions was extracted from NCCLS compliant works. The fast artificial neural networks (FANN) software was used and the output data reflected the antimicrobial activity of these EOs against four common pathogens: Staphylococcus aureus, Escherichia coli, Candida albicans, and Clostridium perfringens as measured by standardised disk diffusion assays. Results. ANNs were able to predict >70% of the antimicrobial activities within a 10 mm maximum error range. Similarly, ANNs were able to predict 2 or 3 different bioactivities at the same time. The accuracy of the prediction was only limited by the inherent errors of the popular antimicrobial disk susceptibility test and the nature of the pathogens. Conclusions. ANNs can be reliable, fast, and cheap tools for the prediction of the antimicrobial activity of EOs thus improving their use in CAM.
    Language English
    Publishing date 2015-09-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2171158-6
    ISSN 1741-4288 ; 1741-427X
    ISSN (online) 1741-4288
    ISSN 1741-427X
    DOI 10.1155/2015/561024
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  6. Article ; Online: A computational fragment-based de novo design protocol guided by ligand efficiency indices (LEI).

    Cortés-Cabrera, Álvaro / Gago, Federico / Morreale, Antonio

    Methods in molecular biology (Clifton, N.J.)

    2015  Volume 1289, Page(s) 89–100

    Abstract: We present a new protocol aimed at the structure-based design of drug-like molecules using a fragment approach. It starts from a suitably placed and well-defined "base fragment" and then uses an incremental construction algorithm and a scoring function ... ...

    Abstract We present a new protocol aimed at the structure-based design of drug-like molecules using a fragment approach. It starts from a suitably placed and well-defined "base fragment" and then uses an incremental construction algorithm and a scoring function to grow the molecule into prioritized candidates. The selection of the most promising solutions for synthesis and validation is guided by the optimization of the calculated ligand efficiency indices known as binding efficiency index (BEI) and surface efficiency index (SEI), which allow the user to navigate proficiently in chemico-biological space. A test case for the protocol is exemplified here using published data for inhibitors of protein kinase B, aka AKT, a key enzyme in several signal transduction pathways. Our procedure was able to identify the main features responsible for the binding of inhibitors and guided the selection process towards molecules that included or resembled those shown as the most active in the original studies.
    MeSH term(s) Binding Sites/genetics ; Drug Design ; Ligands ; Models, Molecular ; Molecular Structure ; Protein Binding ; Proteins/genetics ; Proteins/metabolism ; Proto-Oncogene Proteins c-akt/antagonists & inhibitors ; Proto-Oncogene Proteins c-akt/chemistry ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/metabolism ; Software
    Chemical Substances Ligands ; Proteins ; Small Molecule Libraries ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1)
    Language English
    Publishing date 2015
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-2486-8_8
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  7. Article ; Online: Identification of NEK3 and MOK as novel targets for lithium.

    Bravo, Ana / de Lucio, Héctor / Sánchez-Murcia, Pedro A / Jiménez-Ruiz, Antonio / Petrone, Paula M / Gago, Federico / Cortés Cabrera, Alvaro

    Chemical biology & drug design

    2019  Volume 93, Issue 5, Page(s) 965–969

    Abstract: Lithium ion, commonly used as the carbonate salt in the treatment of bipolar disorders, has been identified as an inhibitor of several kinases, including Glycogen Synthase Kinase-3β, for almost 20 years. However, both the exact mechanism of enzymatic ... ...

    Abstract Lithium ion, commonly used as the carbonate salt in the treatment of bipolar disorders, has been identified as an inhibitor of several kinases, including Glycogen Synthase Kinase-3β, for almost 20 years. However, both the exact mechanism of enzymatic inhibition and its apparent specificity for certain metalloenzymes are still a matter of debate. A data-driven hypothesis is presented that accounts for the specificity profile of kinase inhibition by lithium in terms of the presence of a unique protein environment in the magnesium-binding site. This hypothesis has been validated by the discovery of two novel potential targets for lithium, namely NEK3 and MOK, which are related to neuronal function.
    MeSH term(s) Antigens, Neoplasm/chemistry ; Antigens, Neoplasm/metabolism ; Binding Sites ; Glycogen Synthase Kinase 3 beta/chemistry ; Glycogen Synthase Kinase 3 beta/metabolism ; Humans ; Inhibitory Concentration 50 ; Ions/chemistry ; Lithium/chemistry ; Lithium/metabolism ; Magnesium/chemistry ; Magnesium/metabolism ; Mitogen-Activated Protein Kinases/chemistry ; Mitogen-Activated Protein Kinases/metabolism ; Molecular Dynamics Simulation ; NIMA-Related Kinases/chemistry ; NIMA-Related Kinases/metabolism ; Protein Structure, Tertiary
    Chemical Substances Antigens, Neoplasm ; Ions ; Lithium (9FN79X2M3F) ; Glycogen Synthase Kinase 3 beta (EC 2.7.11.1) ; NEK3 protein, human (EC 2.7.11.1) ; NIMA-Related Kinases (EC 2.7.11.1) ; MOK protein, human (EC 2.7.11.22) ; Mitogen-Activated Protein Kinases (EC 2.7.11.24) ; Magnesium (I38ZP9992A)
    Language English
    Publishing date 2019-02-12
    Publishing country England
    Document type Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 2216600-2
    ISSN 1747-0285 ; 1747-0277
    ISSN (online) 1747-0285
    ISSN 1747-0277
    DOI 10.1111/cbdd.13487
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  8. Article ; Online: A reverse combination of structure-based and ligand-based strategies for virtual screening.

    Cortés-Cabrera, Alvaro / Gago, Federico / Morreale, Antonio

    Journal of computer-aided molecular design

    2012  Volume 26, Issue 3, Page(s) 319–327

    Abstract: A new approach is presented that combines structure- and ligand-based virtual screening in a reverse way. Opposite to the majority of the methods, a docking protocol is first employed to prioritize small ligands ("fragments") that are subsequently used ... ...

    Abstract A new approach is presented that combines structure- and ligand-based virtual screening in a reverse way. Opposite to the majority of the methods, a docking protocol is first employed to prioritize small ligands ("fragments") that are subsequently used as queries to search for similar larger ligands in a database. For a given chemical library, a three-step strategy is followed consisting of (1) contraction into a representative, non-redundant, set of fragments, (2) selection of the three best-scoring fragments docking into a given macromolecular target site, and (3) expansion of the fragments' structures back into ligands by using them as queries to search the library by means of fingerprint descriptions and similarity criteria. We tested the performance of this approach on a collection of fragments and ligands found in the ZINC database and the directory of useful decoys, and compared the results with those obtained using a standard docking protocol. The new method provided better overall results and was several times faster. We also studied the chemical diversity that both methods cover using an in-house compound library and concluded that the novel approach performs similarly but at a much smaller computational cost.
    MeSH term(s) Ligands ; Molecular Structure ; Structure-Activity Relationship
    Chemical Substances Ligands
    Language English
    Publishing date 2012-03-07
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 808166-9
    ISSN 1573-4951 ; 0920-654X
    ISSN (online) 1573-4951
    ISSN 0920-654X
    DOI 10.1007/s10822-012-9558-x
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  9. Article ; Online: AtlasCBS: a web server to map and explore chemico-biological space.

    Cortés-Cabrera, Alvaro / Morreale, Antonio / Gago, Federico / Abad-Zapatero, Celerino

    Journal of computer-aided molecular design

    2012  Volume 26, Issue 9, Page(s) 995–1003

    Abstract: New approaches are needed that can help decrease the unsustainable failure in small-molecule drug discovery. Ligand Efficiency Indices (LEI) are making a great impact on early-stage compound selection and prioritization. Given a target-ligand database ... ...

    Abstract New approaches are needed that can help decrease the unsustainable failure in small-molecule drug discovery. Ligand Efficiency Indices (LEI) are making a great impact on early-stage compound selection and prioritization. Given a target-ligand database with chemical structures and associated biological affinities/activities for a target, the AtlasCBS server generates two-dimensional, dynamical representations of its contents in terms of LEI. These variables allow an effective decoupling of the chemical (angular) and biological (radial) components. BindingDB, PDBBind and ChEMBL databases are currently implemented. Proprietary datasets can also be uploaded and compared. The utility of this atlas-like representation in the future of drug design is highlighted with some examples. The web server can be accessed at http://ub.cbm.uam.es/atlascbs and https://www.ebi.ac.uk/chembl/atlascbs.
    MeSH term(s) Databases, Protein ; Drug Discovery ; Internet ; Ligands ; Small Molecule Libraries ; User-Computer Interface
    Chemical Substances Ligands ; Small Molecule Libraries
    Language English
    Publishing date 2012-07-14
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 808166-9
    ISSN 1573-4951 ; 0920-654X
    ISSN (online) 1573-4951
    ISSN 0920-654X
    DOI 10.1007/s10822-012-9587-5
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  10. Article ; Online: ALFA: automatic ligand flexibility assignment.

    Klett, Javier / Cortés-Cabrera, Álvaro / Gil-Redondo, Rubén / Gago, Federico / Morreale, Antonio

    Journal of chemical information and modeling

    2014  Volume 54, Issue 1, Page(s) 314–323

    Abstract: ALFA is a fast computational tool for the conformational analysis of small molecules that uses a custom-made iterative algorithm to provide a set of representative conformers in an attempt to reproduce the diversity of states in which small molecules can ...

    Abstract ALFA is a fast computational tool for the conformational analysis of small molecules that uses a custom-made iterative algorithm to provide a set of representative conformers in an attempt to reproduce the diversity of states in which small molecules can exist, either isolated in solution or bound to a target. The results shown in this work prove that ALFA is fast enough to be integrated into massive high-throughput virtual screening protocols with the aim of incorporating ligand flexibility and also that ALFA reproduces crystallographic X-ray structures of bound ligands with great accuracy. Furthermore, the application includes a graphical user interface that allows its use through the popular molecular graphics program PyMOL to make it accessible to nonexpert users. ALFA is distributed free of charge upon request from the authors.
    MeSH term(s) Algorithms ; Computational Biology ; Computer Graphics ; Crystallography, X-Ray ; High-Throughput Screening Assays ; Ligands ; Molecular Conformation ; Software ; Static Electricity ; User-Computer Interface
    Chemical Substances Ligands
    Language English
    Publishing date 2014-01-27
    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/ci400453n
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