LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 16

Search options

  1. Article: Exploring the Antioxidant Properties of Caffeoylquinic and Feruloylquinic Acids: A Computational Study on Hydroperoxyl Radical Scavenging and Xanthine Oxidase Inhibition.

    Boulebd, Houssem / Carmena-Bargueño, Miguel / Pérez-Sánchez, Horacio

    Antioxidants (Basel, Switzerland)

    2023  Volume 12, Issue 9

    Abstract: Caffeoylquinic (5-CQA) and feruloylquinic (5-FQA) acids, found in coffee and other plant sources, are known to exhibit diverse biological activities, including potential antioxidant effects. However, the underlying mechanisms of these phenolic compounds ... ...

    Abstract Caffeoylquinic (5-CQA) and feruloylquinic (5-FQA) acids, found in coffee and other plant sources, are known to exhibit diverse biological activities, including potential antioxidant effects. However, the underlying mechanisms of these phenolic compounds remain elusive. This paper investigates the capacity and mode of action of 5-CQA and 5-FQA as natural antioxidants acting as hydroperoxyl radical scavengers and xanthine oxidase (XO) inhibitors. The hydroperoxyl radical scavenging potential was investigated using thermodynamic and kinetic calculations based on the DFT method, taking into account the influence of physiological conditions. Blind docking and molecular dynamics simulations were used to investigate the inhibition capacity toward the XO enzyme. The results showed that 5-CQA and 5-FQA exhibit potent hydroperoxyl radical scavenging capacity in both polar and lipidic physiological media, with rate constants higher than those of common antioxidants, such as Trolox and BHT. 5-CQA carrying catechol moiety was found to be more potent than 5-FQA in both physiological environments. Furthermore, both compounds show good affinity with the active site of the XO enzyme and form stable complexes. The hydrogen atom transfer (HAT) mechanism was found to be exclusive in lipid media, while both HAT and SET (single electron transfer) mechanisms are possible in water. 5-CQA and 5-FQA may, therefore, be considered potent natural antioxidants with potential health benefits.
    Language English
    Publishing date 2023-08-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704216-9
    ISSN 2076-3921
    ISSN 2076-3921
    DOI 10.3390/antiox12091669
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Comparative assessment of different anti-CD147/Basigin 2 antibodies as a potential therapeutic anticancer target by molecular modeling and dynamic simulation.

    Besli, Nail / Bulut, Halil İbrahim / Onaran, İlhan / Carmena-Bargueño, Miguel / Pérez-Sánchez, Horacio

    Molecular diversity

    2024  

    Abstract: Cluster of differentiation 147 (CD147) is an attractive target for anticancer therapy since it is pivotal in developing and progressing several of malignant tumors in the context of its high expression levels. Although anti-CD147 antibodies by different ... ...

    Abstract Cluster of differentiation 147 (CD147) is an attractive target for anticancer therapy since it is pivotal in developing and progressing several of malignant tumors in the context of its high expression levels. Although anti-CD147 antibodies by different laboratories are designed for the Ig-like domains of CD147, there is a demand to provide priority among these anti-CD147 antibodies for developing of therapeutic anti-CD147 antibody before experimental validations. This study uses molecular docking and dynamic simulation techniques to compare the binding modes and affinities of nine antibody models against the Ig-like domains of CD147. After obtaining the model antibodies by homology modeling via Robetta, we predicted the CDRs of nine antibodies and the epitopes of CD147 to reach more accurate results for antigen affinity in molecular docking. Next, from HADDOCK 2.4., we meticulously handpicked the most superior model clusters (Z-Score: - 2.5 to - 1.2) and identified that meplazumab had higher affinities according to the success rate as the percentage of a scoring scale. We achieved stable simulations of CD147-antibody interaction. Our outcomes hold hypothetical importance for further experimental cancer research on the design and development of the relevant model antibodies.
    Language English
    Publishing date 2024-04-08
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1376507-3
    ISSN 1573-501X ; 1381-1991
    ISSN (online) 1573-501X
    ISSN 1381-1991
    DOI 10.1007/s11030-024-10832-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: ESSENCE-Dock: A Consensus-Based Approach to Enhance Virtual Screening Enrichment in Drug Discovery.

    Nelen, Jochem / Carmena-Bargueño, Miguel / Martínez-Cortés, Carlos / Rodríguez-Martínez, Alejandro / Villalgordo-Soto, José Manuel / Pérez-Sánchez, Horacio

    Journal of chemical information and modeling

    2024  Volume 64, Issue 5, Page(s) 1605–1614

    Abstract: Drug development is a complex, costly, and time-consuming endeavor. While high-throughput screening (HTS) plays a critical role in the discovery stage, it is one of many factors contributing to these challenges. In certain contexts, virtual screening can ...

    Abstract Drug development is a complex, costly, and time-consuming endeavor. While high-throughput screening (HTS) plays a critical role in the discovery stage, it is one of many factors contributing to these challenges. In certain contexts, virtual screening can complement the HTS, potentially offering a more streamlined approach in the initial stages of drug discovery. Molecular docking is an example of a popular virtual screening technique that is often used for this purpose; however, its effectiveness can vary greatly. This has led to the use of consensus docking approaches that combine results from different docking methods to improve the identification of active compounds and reduce the occurrence of false positives. However, many of these methods do not fully leverage the latest advancements in molecular docking. In response, we present ESSENCE-Dock (Effective Structural Screening ENrichment ConsEnsus Dock), a new consensus docking workflow aimed at decreasing false positives and increasing the discovery of active compounds. By utilizing a combination of novel docking algorithms, we improve the selection process for potential active compounds. ESSENCE-Dock has been made to be user-friendly, requiring only a few simple commands to perform a complete screening while also being designed for use in high-performance computing (HPC) environments.
    MeSH term(s) Molecular Docking Simulation ; Consensus ; Drug Discovery/methods ; Algorithms ; High-Throughput Screening Assays ; Ligands
    Chemical Substances Ligands
    Language English
    Publishing date 2024-02-28
    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.3c01982
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article: Identification of potent inhibitors of kynurenine-3-monooxygenase from natural products:

    Rebai, Redouane / Carmena-Bargueño, Miguel / Toumi, Mohammed Esseddik / Derardja, Imene / Jasmin, Luc / Pérez-Sánchez, Horacio / Boudah, Abdennacer

    Heliyon

    2024  Volume 10, Issue 9, Page(s) e30287

    Abstract: Existing inhibitors of kynurenine-3-monooxygenase (KMO) have side effects and poorly cross the blood-brain barrier. Therefore, the discovery of new molecules targeting KMO isnecessary.This study aims to develop a novel therapeutic drug targeting KMO ... ...

    Abstract Existing inhibitors of kynurenine-3-monooxygenase (KMO) have side effects and poorly cross the blood-brain barrier. Therefore, the discovery of new molecules targeting KMO isnecessary.This study aims to develop a novel therapeutic drug targeting KMO using computational methods and experimental validation of natural compounds.The results of our study show that the top four compounds, namely, 3'-Hydroxy-alpha-naphthoflavone exhibited the best docking scores with KMO (-10.0 kcal/mol), followed by 3'-Hydroxy-ss-naphthoflavone (-9.9 kcal/mol), genkwanin (-9.2 kcal/mol) and apigenin(-9.1 kcal/mol) respectively. Molecular dynamics was used to assess the stability of the primary target, KMO, and inhibitor complexes. We found stable interactions of 3'-Hydroxy-ss-naphthoflavone and apigenin with KMO up to 100 ns. Further, kinetic measurements showed that 3'-Hydroxy-alpha-naphthoflavone and 3'-Hydroxy-ss-naphthoflavone induce competitive inhibition with a good IC
    Language English
    Publishing date 2024-04-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2024.e30287
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article ; Online: Enhancing MD simulations: ASGARD's automated analysis for GROMACS.

    Rodríguez-Martínez, Alejandro / Nelen, Jochem / Carmena-Bargueño, Miguel / Martínez-Cortés, Carlos / Luque, Irene / Pérez-Sánchez, Horacio

    Journal of biomolecular structure & dynamics

    2024  , Page(s) 1–13

    Abstract: Molecular Dynamics (MD) simulations are essential in analyzing the physical movement of molecules, with GROMACS being a widely recognized open-source package for this purpose. However, conducting analyses individually in GROMACS can take excessive time ... ...

    Abstract Molecular Dynamics (MD) simulations are essential in analyzing the physical movement of molecules, with GROMACS being a widely recognized open-source package for this purpose. However, conducting analyses individually in GROMACS can take excessive time and effort. Addressing this challenge, we introduce ASGARD, an innovative workflow designed to streamline and automate the analysis of MD simulation of protein or protein-ligand complex. Unlike the traditional, manual approach, ASGARD enables researchers to generate comprehensive analyses with a single command line, significantly accelerating the research process and avoiding the laborious task of manual report generation. This tool automatically performs a range of analyses post-simulation, including system stability and flexibility assessments through RMSD Fluctuation and Distribution calculations. It further provides dynamic analysis using SASA, DSSP method graphs, and various interaction analyses. A key feature of ASGARD is its user-friendly design; it requires no additional installations or dependencies, making it highly accessible for researchers. In conclusion, ASGARD simplifies the MD simulation analysis process and substantially enhances efficiency and productivity in molecular research by providing an integrated, one-command analysis solution.Communicated by Ramaswamy H. Sarma.
    Language English
    Publishing date 2024-05-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2024.2349527
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: Effects of In Vitro Digestion of Polyphenols from Coffee on Binding Parameters to Human Topoisomerase II α.

    Grzelczyk, Joanna / Pérez-Sánchez, Horacio / Carmena-Bargueño, Miguel / Oracz, Joanna / Budryn, Grażyna

    Molecules (Basel, Switzerland)

    2023  Volume 28, Issue 16

    Abstract: Type II topoisomerase (TOPII) is an enzyme that influences the topology of DNA. DNA breaks generated by TOPII may result in mutagenic or cytotoxic changes in cancer cells. In this study, we characterized interactions of TOPIIα with coffee extracts and ... ...

    Abstract Type II topoisomerase (TOPII) is an enzyme that influences the topology of DNA. DNA breaks generated by TOPII may result in mutagenic or cytotoxic changes in cancer cells. In this study, we characterized interactions of TOPIIα with coffee extracts and individual chlorogenic acids (CHAs) from the extracts by performing isothermal titration calorimetry (ITC) and molecular docking (MD) simulations. The study showed that the highest affinity to TOPIIα was found in green coffee (ΔG = -38.23 kJ/mol) and monochlorogenic acids fraction of coffee extracts (ΔG = -35.80 kJ/mol), resulting from the high content of polyphenols, such as CHAs, which can bind to the enzyme in the active site. Coffee extracts and their fractions maintained a high affinity for TOPIIα after simulated digestion in the presence of probiotic bacteria. It can be concluded that coffee may be a potential TOPIIα inhibitor considered as a functional food for cancer prevention.
    MeSH term(s) Humans ; Polyphenols/pharmacology ; Molecular Docking Simulation ; DNA Topoisomerases, Type II ; Chlorogenic Acid/pharmacology ; Digestion
    Chemical Substances Polyphenols ; DNA Topoisomerases, Type II (EC 5.99.1.3) ; Chlorogenic Acid (318ADP12RI)
    Language English
    Publishing date 2023-08-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules28165996
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Evaluation of Activity of Sesquiterpene Lactones and Chicory Extracts as Acetylcholinesterase Inhibitors Assayed in Calorimetric and Docking Simulation Studies.

    Jaśkiewicz, Andrzej / Budryn, Grażyna / Carmena-Bargueño, Miguel / Pérez-Sánchez, Horacio

    Nutrients

    2022  Volume 14, Issue 17

    Abstract: The aim of the study was to explain the effects of sesquiterpene lactones (SLs) from chicory ( ...

    Abstract The aim of the study was to explain the effects of sesquiterpene lactones (SLs) from chicory (
    MeSH term(s) Acetylcholinesterase/metabolism ; Calorimetry ; Cichorium intybus/chemistry ; Cholinesterase Inhibitors/pharmacology ; Lactones/chemistry ; Lactones/pharmacology ; Ligands ; Molecular Docking Simulation ; Phytochemicals ; Plant Extracts/chemistry ; Plant Extracts/pharmacology ; Sesquiterpenes/chemistry ; Sesquiterpenes/pharmacology
    Chemical Substances Cholinesterase Inhibitors ; Lactones ; Ligands ; Phytochemicals ; Plant Extracts ; Sesquiterpenes ; Acetylcholinesterase (EC 3.1.1.7)
    Language English
    Publishing date 2022-09-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2518386-2
    ISSN 2072-6643 ; 2072-6643
    ISSN (online) 2072-6643
    ISSN 2072-6643
    DOI 10.3390/nu14173633
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article: Evaluation of Activity of Sesquiterpene Lactones and Chicory Extracts as Acetylcholinesterase Inhibitors Assayed in Calorimetric and Docking Simulation Studies

    Jaśkiewicz, Andrzej / Budryn, Grażyna / Carmena-Bargueño, Miguel / Pérez-Sánchez, Horacio

    Nutrients. 2022 Sept. 02, v. 14, no. 17

    2022  

    Abstract: The aim of the study was to explain the effects of sesquiterpene lactones (SLs) from chicory (Cichorium intybus L.) root extracts as inhibitors of acetylcholinesterase (AChE) at the molecular level and to determine the inhibition of AChE activity by ... ...

    Abstract The aim of the study was to explain the effects of sesquiterpene lactones (SLs) from chicory (Cichorium intybus L.) root extracts as inhibitors of acetylcholinesterase (AChE) at the molecular level and to determine the inhibition of AChE activity by specific SLs (lactucin and lactucopicrin) and different chicory extracts. The obtained SLs-rich extracts were purified by the countercurrent partition chromatography (CPC) technique. AChE inhibitors were analyzed using two models: isothermal titration calorimetry (ITC) and docking simulation. The results of ITC analysis of the enzyme and the ligands’ complexation showed strong interactions of SLs as well as extracts from chicory with AChE. In a test of enzyme activity inhibition after introducing acetylcholine into the model system with SL, a stronger ability to inhibit the hydrolysis of the neurotransmitter was observed for lactucopicrin, which is one of the dominant SLs in chicory. The inhibition of enzyme activity was more efficient in the case of extracts, containing different enzyme ligands, exhibiting complementary patterns of binding the AChE active site. The study showed the high potential of using chicory to decrease the symptoms of Alzheimer’s disease.
    Keywords Cichorium intybus ; acetylcholine ; acetylcholinesterase ; active sites ; calorimetry ; chicory ; chromatography ; enzyme activity ; hydrolysis ; ligands ; neurotransmitters ; sesquiterpenoid lactones ; titration
    Language English
    Dates of publication 2022-0902
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2518386-2
    ISSN 2072-6643
    ISSN 2072-6643
    DOI 10.3390/nu14173633
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  9. Article ; Online: Flavonoids improve the stability and function of P23H rhodopsin slowing down the progression of retinitis pigmentosa in mice.

    Ortega, Joseph Thomas / Parmar, Tanu / Carmena-Bargueño, Miguel / Pérez-Sánchez, Horacio / Jastrzebska, Beata

    Journal of neuroscience research

    2022  Volume 100, Issue 4, Page(s) 1063–1083

    Abstract: The balanced homeostasis of the G protein-coupled receptor (GPCR), rhodopsin (Rho), is required for vision. Misfolding mutations in Rho cause photoreceptor death, leading to retinitis pigmentosa (RP) and consequently blindness. With no cure currently ... ...

    Abstract The balanced homeostasis of the G protein-coupled receptor (GPCR), rhodopsin (Rho), is required for vision. Misfolding mutations in Rho cause photoreceptor death, leading to retinitis pigmentosa (RP) and consequently blindness. With no cure currently available, the development of efficient therapy for RP is an urgent need. Pharmacological supplementation with molecular chaperones, including flavonoids, improves stability, folding, and membrane targeting of the RP Rho mutants in vitro. Thus, we hypothesized that flavonoids by binding to P23H Rho and enhancing its conformational stability could mitigate detrimental effects of this mutation on retinal health. In this work, we evaluated the pharmacological potential of two model flavonoids, quercetin and myricetin, by using in silico, in vitro, and in vivo models of P23H Rho. Our computational analysis showed that quercetin could interact within the orthosteric binding pocket of P23H Rho and shift the conformation of its N-terminal loop toward the wild type (WT)-like state. Quercetin added to the NIH-3T3 cells stably expressing P23H Rho increased the stability of this receptor and improved its function. Systemic administration of quercetin to P23H Rho knock-in mice substantially improved retinal morphology and function, which was associated with an increase in levels of Rho and cone opsins. In addition, treatment with quercetin resulted in downregulation of the UPR signaling and oxidative stress-related markers. This study unravels the pharmacological potential of quercetin to slow down the progression of photoreceptor death in Rho-related RP and highlights its prospective as a lead compound to develop a novel therapeutic remedy to counter RP pathology.
    MeSH term(s) Animals ; Disease Models, Animal ; Mice ; Mutation ; Prospective Studies ; Quercetin/metabolism ; Quercetin/pharmacology ; Quercetin/therapeutic use ; Retina/metabolism ; Retinitis Pigmentosa/drug therapy ; Retinitis Pigmentosa/genetics ; Retinitis Pigmentosa/metabolism ; Rhodopsin/genetics ; Rhodopsin/metabolism
    Chemical Substances Rhodopsin (9009-81-8) ; Quercetin (9IKM0I5T1E)
    Language English
    Publishing date 2022-02-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 195324-2
    ISSN 1097-4547 ; 0360-4012
    ISSN (online) 1097-4547
    ISSN 0360-4012
    DOI 10.1002/jnr.25021
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article ; Online: Effect of Inhibiting Butyrylcholinesterase Activity Using Fractionated Coffee Extracts Digested In Vitro in Gastrointestinal Tract: Docking Simulation and Calorimetric and Studies.

    Grzelczyk, Joanna / Szwajgier, Dominik / Baranowska-Wójcik, Ewa / Pérez-Sánchez, Horacio / Carmena-Bargueño, Miguel / Sosnowska, Bożena / Budryn, Grażyna

    Nutrients

    2023  Volume 15, Issue 10

    Abstract: Butyrylcholinesterase (BChE) is a major enzyme from the alpha-glycoprotein family that catalyzes the hydrolysis of neurotransmitter acetylcholine (ACh), lowering the concentration of ACh in the nervous system, which could cause aggravation of Alzheimer's ...

    Abstract Butyrylcholinesterase (BChE) is a major enzyme from the alpha-glycoprotein family that catalyzes the hydrolysis of neurotransmitter acetylcholine (ACh), lowering the concentration of ACh in the nervous system, which could cause aggravation of Alzheimer's disease (AD). In select pathological conditions, it is beneficial to reduce the activity of this enzyme. The aim of this study was to evaluate the degree of BChE inhibition by coffee extracts fractionated into mono- and diesters of caffeic acid/caffeine, digested in vitro in the gastrointestinal tract. The bioactive compounds from coffee showed high affinity for BchE, -30.23--15.28 kJ/mol, and was the highest for the caffeine fraction from the green Arabica extract. The isolated fractions were highly effective in inhibiting BChE activity at all in vitro digestion phases. It has been shown that the fractionation of coffee extracts could be potentially used to obtain high prophylactic or even therapeutic effectiveness against AD.
    MeSH term(s) Humans ; Butyrylcholinesterase ; Caffeine/pharmacology ; Caffeine/therapeutic use ; Calorimetry ; Gastrointestinal Tract ; Alzheimer Disease/drug therapy ; Alzheimer Disease/prevention & control ; Cholinesterase Inhibitors/pharmacology ; Cholinesterase Inhibitors/chemistry ; Molecular Docking Simulation
    Chemical Substances Butyrylcholinesterase (EC 3.1.1.8) ; Caffeine (3G6A5W338E) ; Cholinesterase Inhibitors
    Language English
    Publishing date 2023-05-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2518386-2
    ISSN 2072-6643 ; 2072-6643
    ISSN (online) 2072-6643
    ISSN 2072-6643
    DOI 10.3390/nu15102366
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top