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  1. Artikel ; Online: Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations.

    Coimbra, João T S / Fernandes, Pedro A / Ramos, Maria J

    Journal of chemical information and modeling

    2023  Band 63, Heft 20, Seite(n) 6354–6365

    Abstract: Due to the emergence of antibiotic resistance, the need to explore novel antibiotics and/or novel strategies to counter antibiotic resistance is of utmost importance. In this work, we explored the molecular and mechanistic details of the degradation of a ...

    Abstract Due to the emergence of antibiotic resistance, the need to explore novel antibiotics and/or novel strategies to counter antibiotic resistance is of utmost importance. In this work, we explored the molecular and mechanistic details of the degradation of a streptogramin B antibiotic by virginiamycin B (Vgb) lyase of
    Mesh-Begriff(e) Virginiamycin/chemistry ; Virginiamycin/metabolism ; Molecular Dynamics Simulation ; Lyases/metabolism ; Anti-Bacterial Agents/chemistry ; Catalysis
    Chemische Substanzen Virginiamycin (11006-76-1) ; Lyases (EC 4.-) ; Anti-Bacterial Agents
    Sprache Englisch
    Erscheinungsdatum 2023-10-04
    Erscheinungsland United States
    Dokumenttyp 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.3c00962
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: The antioxidant activity of polysaccharides: A structure-function relationship overview.

    Fernandes, Pedro A R / Coimbra, Manuel A

    Carbohydrate polymers

    2023  Band 314, Seite(n) 120965

    Abstract: Over the last years, polysaccharides have been linked to antioxidant effects using both in vitro chemical and biological models. The reported structures, claimed to act as antioxidants, comprise chitosan, pectic polysaccharides, glucans, mannoproteins, ... ...

    Abstract Over the last years, polysaccharides have been linked to antioxidant effects using both in vitro chemical and biological models. The reported structures, claimed to act as antioxidants, comprise chitosan, pectic polysaccharides, glucans, mannoproteins, alginates, fucoidans, and many others of all type of biological sources. The structural features linked to the antioxidant action include the polysaccharide charge, molecular weight, and the occurrence of non-carbohydrate substituents. The establishment of structure/function relationships can be, however, biased by secondary phenomena that tailor polysaccharides behavior in antioxidant systems. In this sense, this review confronts some basic concepts of polysaccharides chemistry with the current claim of carbohydrates as antioxidants. It critically discusses how the fine structure and properties of polysaccharides can define polysaccharides as antioxidants. Polysaccharides antioxidant action is highly dependent on their solubility, sugar ring structure, molecular weight, occurrence of positive or negatively charged groups, protein moieties and covalently linked phenolic compounds. However, the occurrence of phenolic compounds and protein as contaminants leads to misleading results in methodologies often used for screening and characterization purposes, as well as in vivo models. Despite falling in the concept of antioxidants, the role of polysaccharides must be well defined according with the matrices where they are involved.
    Mesh-Begriff(e) Antioxidants/pharmacology ; Antioxidants/chemistry ; Polysaccharides/pharmacology ; Polysaccharides/chemistry ; Glucans ; Pectins ; Structure-Activity Relationship
    Chemische Substanzen Antioxidants ; Polysaccharides ; Glucans ; Pectins (89NA02M4RX)
    Sprache Englisch
    Erscheinungsdatum 2023-04-29
    Erscheinungsland England
    Dokumenttyp Journal Article ; Review
    ZDB-ID 1501516-6
    ISSN 1879-1344 ; 0144-8617
    ISSN (online) 1879-1344
    ISSN 0144-8617
    DOI 10.1016/j.carbpol.2023.120965
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  3. Artikel ; Online: Viper Venom Phospholipase A2 Database: The Structural and Functional Anatomy of a Primary Toxin in Envenomation.

    de Oliveira, Ana L Novo / Lacerda, Miguel T / Ramos, Maria J / Fernandes, Pedro A

    Toxins

    2024  Band 16, Heft 2

    Abstract: Viper venom phospholipase A2 enzymes (vvPLA2s) and phospholipase A2-like (PLA2-like) proteins are two of the principal toxins in viper venom that are responsible for the severe myotoxic and neurotoxic effects caused by snakebite envenoming, among other ... ...

    Abstract Viper venom phospholipase A2 enzymes (vvPLA2s) and phospholipase A2-like (PLA2-like) proteins are two of the principal toxins in viper venom that are responsible for the severe myotoxic and neurotoxic effects caused by snakebite envenoming, among other pathologies. As snakebite envenoming is the deadliest neglected tropical disease, a complete understanding of these proteins' properties and their mechanisms of action is urgently needed. Therefore, we created a database comprising information on the holo-form, cofactor-bound 3D structure of 217 vvPLA2 and PLA2-like proteins in their physiologic environment, as well as 79 membrane-bound viper species from 24 genera, which we have made available to the scientific community to accelerate the development of new anti-snakebite drugs. In addition, the analysis of the sequenced, 3D structure of the database proteins reveals essential aspects of the anatomy of the proteins, their toxicity mechanisms, and the conserved binding site areas that may anchor universal interspecific inhibitors. Moreover, it pinpoints hypotheses for the molecular origin of the myotoxicity of the PLA2-like proteins. Altogether, this study provides an understanding of the diversity of these toxins and how they are conserved, and it indicates how to develop broad, interspecies, efficient small-molecule inhibitors to target the toxin's many mechanisms of action.
    Mesh-Begriff(e) Humans ; Viper Venoms/chemistry ; Snake Bites ; Phospholipases A2/chemistry ; Myotoxicity ; Binding Sites
    Chemische Substanzen Viper Venoms ; Phospholipases A2 (EC 3.1.1.4)
    Sprache Englisch
    Erscheinungsdatum 2024-02-01
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2518395-3
    ISSN 2072-6651 ; 2072-6651
    ISSN (online) 2072-6651
    ISSN 2072-6651
    DOI 10.3390/toxins16020071
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel: Evolution of the Quinoline Scaffold for the Treatment of Leishmaniasis: A Structural Perspective.

    Silva, Carlos F M / Pinto, Diana C G A / Fernandes, Pedro A / Silva, Artur M S

    Pharmaceuticals (Basel, Switzerland)

    2024  Band 17, Heft 3

    Abstract: Since the beginning of the XXI century, Leishmaniasis has been integrated into the World Health Organization's list of the 20 neglected tropical diseases, being considered a public health issue in more than 88 countries, especially in the tropics, ... ...

    Abstract Since the beginning of the XXI century, Leishmaniasis has been integrated into the World Health Organization's list of the 20 neglected tropical diseases, being considered a public health issue in more than 88 countries, especially in the tropics, subtropics, and the Mediterranean area. Statistically, this disease presents a world prevalence of 12 million cases worldwide, with this number being expected to increase shortly due to the 350 million people considered at risk and the 2-2.5 million new cases appearing every year. The lack of an appropriate and effective treatment against this disease has intensified the interest of many research groups to pursue the discovery and development of novel treatments in close collaboration with the WHO, which hopes to eradicate it shortly. This paper intends to highlight the quinoline scaffold's potential for developing novel antileishmanial agents and provide a set of structural guidelines to help the research groups in the medicinal chemistry field perform more direct drug discovery and development programs. Thus, this review paper presents a thorough compilation of the most recent advances in the development of new quinoline-based antileishmanial agents, with a particular focus on structure-activity relationship studies that should be considerably useful for the future of the field.
    Sprache Englisch
    Erscheinungsdatum 2024-02-22
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Review
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph17030285
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  5. Artikel ; Online: Rational Engineering of (

    De Sousa, João P M / Oliveira, Nuno C S A / Fernandes, Pedro A

    Molecules (Basel, Switzerland)

    2023  Band 28, Heft 11

    Abstract: ...

    Abstract (
    Mesh-Begriff(e) Benzylisoquinolines ; Alkaloids/metabolism ; Carbon-Nitrogen Ligases/genetics ; Carbon-Nitrogen Ligases/metabolism ; Codeine ; Papaver/genetics ; Papaver/metabolism
    Chemische Substanzen Benzylisoquinolines ; norcoclaurine synthase (EC 6.3.3.-) ; Alkaloids ; Carbon-Nitrogen Ligases (EC 6.3.-) ; Codeine (UX6OWY2V7J)
    Sprache Englisch
    Erscheinungsdatum 2023-05-23
    Erscheinungsland Switzerland
    Dokumenttyp 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/molecules28114265
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  6. Artikel ; Online: Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics.

    Neves, Rui P P / Fernandes, Pedro A / Ramos, Maria J

    Journal of chemical information and modeling

    2022  Band 62, Heft 15, Seite(n) 3638–3650

    Abstract: We assessed enzyme:substrate conformational dynamics and the rate-limiting glycosylation step of a human pancreatic α-amylase:maltopentose complex. Microsecond molecular dynamics simulations suggested that the distance of the catalytic Asp197 nucleophile ...

    Abstract We assessed enzyme:substrate conformational dynamics and the rate-limiting glycosylation step of a human pancreatic α-amylase:maltopentose complex. Microsecond molecular dynamics simulations suggested that the distance of the catalytic Asp197 nucleophile to the anomeric carbon of the buried glucoside is responsible for most of the enzyme active site fluctuations and that both Asp197 and Asp300 interact the most with the buried glucoside unit. The buried glucoside binds either in a
    Mesh-Begriff(e) Carbon ; Catalysis ; Catalytic Domain ; Glucosides ; Humans ; Molecular Dynamics Simulation ; Oxygen ; Quantum Theory ; Water ; alpha-Amylases/chemistry
    Chemische Substanzen Glucosides ; Water (059QF0KO0R) ; Carbon (7440-44-0) ; alpha-Amylases (EC 3.2.1.1) ; Oxygen (S88TT14065)
    Sprache Englisch
    Erscheinungsdatum 2022-07-26
    Erscheinungsland United States
    Dokumenttyp 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.2c00691
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel: Necessity is the Mother of Invention: A Remote Molecular Bioinformatics Practical Course in the COVID-19 Era.

    Fernandes, Pedro A / Passos, Óscar / Ramos, Maria J

    Journal of chemical education

    2022  Band 99, Heft 5, Seite(n) 2147–2153

    Abstract: The COVID-19 pandemic has brought many challenges to human beings, related to not only health and way of life but also teaching because of the interruption of the standard training at universities imposed by lockdowns. Concerning the latter, the academic ...

    Abstract The COVID-19 pandemic has brought many challenges to human beings, related to not only health and way of life but also teaching because of the interruption of the standard training at universities imposed by lockdowns. Concerning the latter, the academic community had to reinvent itself, in many ways, to carry on with prepandemic education. This article focuses on the use of modern technology and software to create a virtual, highly interactive classroom where a remote but still hands-on course on molecular bioinformatics can be taught, motivating the university students and helping them learn the course contents without significant compromises imposed by successive lockdowns. We implemented such a virtual hands-on molecular bioinformatics course in the second semester of the 2020/2021 academic year. Furthermore, we compared the learning outcomes with those for the earlier editions of the same course in the pre-COVID-19 era, in which the more traditional teaching method was used where all teaching was delivered with physically present lecturers. The virtual classroom proposed here allowed the students to develop skills close to, although slightly below, those obtained with physically present learning.
    Sprache Englisch
    Erscheinungsdatum 2022-04-21
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 218164-2
    ISSN 1938-1328 ; 0021-9584
    ISSN (online) 1938-1328
    ISSN 0021-9584
    DOI 10.1021/acs.jchemed.1c01195
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  8. Artikel ; Online: Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis.

    Neves, Rui P P / Ramos, Maria J / Fernandes, Pedro A

    Journal of chemical information and modeling

    2022  Band 63, Heft 1, Seite(n) 20–26

    Abstract: We describe an approach to identify enzyme mutants with increased turnover using the enzyme DszC as a case study. Our approach is based on recalculating the barriers of alanine mutants through single-point energy calculations at the hybrid QM/MM level in ...

    Abstract We describe an approach to identify enzyme mutants with increased turnover using the enzyme DszC as a case study. Our approach is based on recalculating the barriers of alanine mutants through single-point energy calculations at the hybrid QM/MM level in the wild-type reactant and transition state geometries. We analyze the difference in the electron density between the reactant and transition state to identify sites/residues where electrostatic interactions stabilize the transition state over the reactants. We also assess the insertion of a unit probe charge to identify positions in which the introduction of charged residues lowers the barrier.
    Mesh-Begriff(e) Catalysis
    Sprache Englisch
    Erscheinungsdatum 2022-12-19
    Erscheinungsland United States
    Dokumenttyp 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.2c01337
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  9. Artikel ; Online: Modern Strategies for the Diversification of the Supply of Natural Compounds: The Case of Alkaloid Painkillers.

    Sousa, João P M / Ramos, Maria J / Fernandes, Pedro A

    Chembiochem : a European journal of chemical biology

    2022  Band 23, Heft 10, Seite(n) e202100623

    Abstract: Plant-derived natural compounds have been used for treating diseases since prehistorical times. The supply of many plant-derived natural compounds for medicinal purposes, such as thebaine, morphine, and codeine, is primarily dependent on opium poppy crop ...

    Abstract Plant-derived natural compounds have been used for treating diseases since prehistorical times. The supply of many plant-derived natural compounds for medicinal purposes, such as thebaine, morphine, and codeine, is primarily dependent on opium poppy crop harvesting. This dependency adds an extra risk factor to ensuring the supply chain because crops are highly susceptible to environmental conditions. Emerging technologies, such as biocatalysis, might help to solve this problem by diversifying the sources of supply of these compounds. Here we review the first committed step in the production of alkaloid painkillers, the production of S-norcoclaurine, and the enzymes involved. The improvement of these enzymes can be carried out experimentally by directed evolution and rational design strategies, supported by computational methods, to create variants that produce the S-norcoclaurine precursor for alkaloid painkillers in heterologous organisms, meeting the pharmaceutical industry standards and needs without depending on opium poppy crops.
    Mesh-Begriff(e) Alkaloids ; Papaver
    Chemische Substanzen Alkaloids
    Sprache Englisch
    Erscheinungsdatum 2022-01-19
    Erscheinungsland Germany
    Dokumenttyp Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020469-3
    ISSN 1439-7633 ; 1439-4227
    ISSN (online) 1439-7633
    ISSN 1439-4227
    DOI 10.1002/cbic.202100623
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  10. Artikel ; Online: DszA Catalyzes C-S Bond Cleavage through N

    Ferreira, Pedro / Neves, Rui P P / Miranda, Filipa P / Cunha, Ana V / Havenith, Remco W A / Ramos, Maria J / Fernandes, Pedro A

    Journal of chemical information and modeling

    2024  

    Abstract: Due to its detrimental impact on human health and the environment, regulations demand ultralow sulfur levels on fossil fuels, in particular in diesel. However, current desulfurization techniques are expensive and cannot efficiently remove heteroaromatic ... ...

    Abstract Due to its detrimental impact on human health and the environment, regulations demand ultralow sulfur levels on fossil fuels, in particular in diesel. However, current desulfurization techniques are expensive and cannot efficiently remove heteroaromatic sulfur compounds, which are abundant in crude oil and concentrate in the diesel fraction after distillation. Biodesulfurization
    Sprache Englisch
    Erscheinungsdatum 2024-04-29
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.4c00301
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