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Medicinal chemistry strategies towards the development of non-covalent SARS-CoV-2 Mpro inhibitors

Acta Pharmaceutica Sinica B 2024年第1期14卷 87-109页

作者： Letian Song Shenghua Gao Bing Ye Mianling Yang Yusen Cheng Dongwei Kang Fan Yi Jin-Peng Sun Luis Menéndez-Arias Johan Neyts Xinyong Liu Peng Zhan Department of Medicinal Chemistry Key Laboratory of Chemical Biology(Ministry of Education)School of Pharmaceutical SciencesCheeloo College of MedicineShandong UniversityJinan 250012China Shenzhen Research Institute of Shandong University Shenzhen 518057China The Key Laboratory of Infection and Immunity of Shandong Province Department of PharmacologySchool of Basic Medical SciencesShandong UniversityJinan 250012China Key Laboratory Experimental Teratology of the Ministry of Education Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinan 250012China Centro de Biologı´a Molecular“Severo Ochoa”(Consejo Superior de Investigaciones Cientı´ficas&Autonomous University of Madrid) Madrid 28049Spain KU Leuven Department of Microbiology and ImmunologyRega Institute for Medical ResearchLaboratory of Virology and ChemotherapyLeuven 3000Belgium

The main protease(M^(pro))of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life *** covalent M^(pro)inhibitor nirmatrelvir(in combination with ritonavir,a pharmacokinetic enhancer)and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic *** antiviral drugs are needed to fight the pandemic,while non-covalent M^(pro)inhibitors could be promising alternatives due to their high selectivity and favorable *** non-covalent M^(pro)inhibitors with desirable properties have been developed based on available crystal structures of M^(pro).In this article,we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent M^(pro)inhibitors,followed by a general overview and critical analysis of the available *** viewpoints and insights into current strategies for the development of non-covalent M^(pro)inhibitors are also discussed.

关键词： COVID-19 SARS-CoV-2 Main protease Non-covalent inhibitors Medicinal chemistry strategies

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A higher-order porous thermoelastic problem with microtemperatures

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Applied Mathematics and Mechanics(English Edition) 2023年第11期44卷 1911-1926页

作者： J.R.fernández R.QUINTANILLA Department of Applied Mathematics I University of VigoETSI de Telecomunicacion Campus As Lagoas Marcosende s/nVigo 36310Spain Department of Mathematics Polytechnical University of CatalunyaTerrassa 08222BarcelonaSpain

In this paper,we study a porous thermoelastic problem with microtemperatures assuming parabolic higher order in time derivatives for the thermal *** model is derived and written as a coupled linear ***,a uniqueness result is proved by using the logarithmic convexity method in the case that we do not assume that the mechanical energy is positive ***,the existence of the solution is obtained by introducing an energy function and applying the theory of linear semigroups.

关键词： higher order thermoelasticity microtemperature logarithmic convexity method existence and uniqueness

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Artificial muscles driven by the cooperative actuation of electrochemical molecular *** discrepancies and challenges

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International Journal of Smart and Nano Materials 2017年第4期8卷 125-143页

作者： Toribio fernández Otero Laboratory of Electrochemistry Intelligent Materials and DevicesUniversidad Politécnica de Cartagena.Aulario IIICampus Alfonso XIIICartagenaSpain

Here we review the persisting conceptual discrepancies between different research groups working on artificial muscles based on conducting polymers and other electroactive *** basic question is if they can be treated as traditional electro-mechanical(physical)actuators driven by electric fields and described by some adaptation of their physical models or if,replicating natural muscles,they are electro-chemo-mechanical actuators driven by electrochemical reaction of the constitutive molecular machines:the polymeric *** that case the charge consumed by the reaction will control the volume variation of the muscular material and the motor displacement,following the basic and single Faraday’s laws:the charge consumed by the reaction determines the number of exchanged ions and solvent,the film volume variation to lodge/expel them and the amplitude of the *** from the linear relationships are due to the osmotic exchange of solvent and to the presence of parallel reactions from the electrolyte,which originate creeping *** and limitations are underlined.

关键词： Electromechanical actuator electro-chemo-mechanical artificial muscle molecular machines creeping osmotic effects

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DNA metabarcoding reveals seasonal changes in diet composition across four arthropod-eating lizard species(Phrynosomatidae:Sceloporus)

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Integrative Zoology 2024年第3期19卷 480-495页

作者： Mauricio HERNÁndez Stephanie HEREIRA-PACHECO Antton ALBERDI Aníbal H.DÍAZ DE LA VEGA-PÉREZ Arturo ESTRADA-TORRES Sergio ANCONA Yendi E.NAVARRO-NOYA Doctorado en Ciencias Biológicas Centro Tlaxcala de Biología de la ConductaUniversidad Autónoma de TlaxcalaTlaxcalaMexico Estación Científica La Malinche Centro Tlaxcala de Biología de la ConductaUniversidad Autónoma de TlaxcalaTlaxcalaMexico Center for Evolutionary Hologenomics The Globe InstituteUniversity of CopenhagenCopenhagenDenmark Consejo Nacional de Ciencia y Tecnología-Centro Tlaxcala de Biología de la Conducta Universidad Autónoma de TlaxcalaTlaxcalaMexico Departamento de Ecología Evolutiva Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico Laboratorio de Interacciones Bióticas Centro de Investigación en Ciencias BiológicasUniversidad Autónoma de TlaxcalaSan Felipe IxtacuixtlaTlaxcalaMexico

Diet composition and its ecological drivers are rarely investigated in coexisting closely related *** used a molecular approach to characterize the seasonal variation in diet composition in four spiny lizard species inhabiting a mountainous *** metabarcoding revealed that the lizards Sceloporus aeneus,***,***,and *** mostly consumed arthropods of the orders Hemiptera,Araneae,Hymenoptera,and *** terrestrial lizards *** and *** mostly predated ants and spiders,whereas the arboreal–saxicolous *** and saxicolous *** largely consumed grasshoppers and *** taxonomic and phylogenetic diversity of the prey was higher during the dry season than the rainy season,likely because reduced prey availability in the dry season forced lizards to diversify their diets to meet their nutritional *** and phylogenetic composition varied seasonally depending on the species,but only dietary composition varied with *** dietary turnover was greater in *** than in ***,suggesting site-specific seasonal variability in prey availability;no other differences among species were ***,which lives at the highest altitude in our study site,displayed interseasonal variation in diet *** differences were correlated with the species’feeding strategies and elevational distribution,which likely contributed to the coexistence of these lizard species in the studied geographic area and beyond.

关键词： arthropod-eating lizards diet breadth environmental barcoding mountainous ecosystem seasonal dietary shifts

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On the Estimation of the Functional Size of Software from Requirements Specifications

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Journal of Computer Science & Technology 2007年第3期22卷 358-370页

作者： Nelly Condori-fernández Silvia Abrahao Oscar Pastor Department of Information Systems and Computation Valencia University of TechnologyCamino de Vera s/n46020 ValenciaSpain

This paper introduces a measurement procedure, called RmFFP, which describes a set of operations for modelling and estimating the size of object-oriented software systems from high-level specifications using the OO-Method Requirement Model. OO-Method is an automatic software production method. The contribution of this work is to systematically define a set of rules that allows estimating the functional size at an early stage of the software production process, in accordance with COSMIC-FFP. To do this, we describe the design, the application, and the analysis of the proposed measurement procedure following the steps of a process model for software measurement. We also report initial results on the evaluation of RmFFP in terms of its reproducibility.

关键词： requirement specification product metrics measurement technique

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A building energy models calibration methodology based on inverse modelling approach

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Building Simulation 2022年第11期15卷 1883-1898页

作者： Vicente Gutiérrez González Carlos fernández Bandera Installations construction and structuresSchool of ArchitectureUniversity of NavarraCampus UniversitarioPamplona31009NavarraSpain

Nowadays,building energy models(BEMs)are widely used,particularly in the assessment of energy consumption in buildings to address the potential savings that can be *** realisation of a dynamic energy model based on high-fidelity physics(white-box models)requires a tuning process to fit the model to reality,due to many uncertainties *** some research trends try to reduce this performance gap by modulating different types of experimental parameters such as:capacitances or *** EnergyPlus simulation software,in its latest versions,has implemented an object:HybridModel:Zone that calculates the infiltration and internal mass of buildings using an inverse modelling approach that employs only the measured indoor temperature data to invert the heat balance equation for the zone under *** main objective of this paper is to reduce the execution time and uncertainties in the development of quality energy models by generating a new calibration methodology that implements this *** uses,as a starting point,a research created by the authors of this study,which was empirically and comparatively validated against the energy models developed by the participants in Annex *** is also worth highlighting the empirical validation of the HybridModel:Zone object,since it was activated in all scenarios where its execution is possible:periods of seven days or more of free oscillation and periods in which the building is under *** findings are *** data generated with the new methodology,if compared with those produced by the baseline model,improve their resemblance to the real ones by 22.9%.While those of its predecessor did it by 15.6%.For this study,the two dwellings foreseen in Annex 58 of the IEA ECB project have been modelled and their real monitoring data have been used.

关键词： internal thermal mass energy simulation EnergyPlus inverse model Annex 58 infiltration

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Deep optics preconditioner for modulation-free pyramid wavefront sensing

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Photonics Research 2024年第2期12卷 301-312页

作者： FELIPE GUZMÁN JORGE TAPIA CAMILO WEINBERGER NICOLÁS HERNÁndez JORGE BACCA BENOIT NEICHEL ESTEBAN VERA School of Electrical Engineering Pontificia Universidad Católica de Valparaı´soValparaı´soChile Department of Systems Engineering Universidad Industrial de SantanderBucaramangaColombia Laboratoire d’Astrophysique de Marseille MarseilleFrance

The pyramid wavefront sensor(PWFS)can provide the sensitivity needed for demanding adaptive optics applications,such as imaging exoplanets using the future extremely large telescopes of over 30 m of diameter(D).However,its exquisite sensitivity has a limited linear range of operation,or dynamic range,although it can be extended through the use of beam modulation—despite sacrificing sensitivity and requiring additional optical *** by artificial intelligence techniques,this work proposes to train an optical layer—comprising a passive diffractive element placed at a conjugated Fourier plane of the pyramid prism—to boost the linear response of the pyramid sensor without the need for cumbersome *** develop an end-2-end simulation to train the diffractive element,which acts as an optical preconditioner to the traditional least-square modal phase estimation *** results with a large range of turbulence conditions show a noticeable improvement in the aberration estimation performance equivalent to over 3λ∕D of modulation when using the optically preconditioned deep PWFS(DPWFS).Experimental results validate the advantages of using the designed optical layer,where the DPWFS can pair the performance of a traditional PWFS with 2λ∕D of *** and adding an optical preconditioner to the PWFS is just the tip of the iceberg,since the proposed deep optics methodology can be used for the design of a completely new generation of wavefront sensors that can better fit the demands of sophisticated adaptive optics applications such as ground-to-space and underwater optical communications and imaging through scattering media.

关键词： process optics pyramid

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New determinants of prognosis in bacterial infections in cirrhosis

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World Journal of Gastroenterology 2014年第23期20卷 7252-7259页

作者： Juan Acevedo Javier fernández Department of Gastroenterology and Hepatology Hospital of Calella08370 BarcelonaCatalunyaSpain Liver Unit Hospital ClínicUniversity of Barcelona08150 BarcelonaCatalunyaSpain Institut d’Investigacions Biomèdiques August-Pi-Sunyer (IDIBAPS) 08036 BarcelonaSpain Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHED) 08150 BarcelonaSpain

Despite major advances in the knowledge and management of liver diseases achieved in recent decades,decompensation of cirrhosis still carries a high burden of morbidity and *** infections are one of the main causes of *** is very important for clinical management to be aware of the population with the highest risk of poor *** review deals with the new determinants of prognosis in patients with cirrhosis and bacterial infections reported *** of multiresistant bacteria has led to an increasing failure rate of the standard empirical antibiotic therapy recommended by international ***,it has been recently reported that endothelial dysfunction is associated with the degree of liver dysfunction and,in infected patients,with the degree of *** has also been reported that relative adrenal insufficiency is frequent in the non-critically ill cirrhotic population and it is associated with a higher risk of developing infection,severe sepsis,hepatorenal syndrome and *** advise a change in the standard empirical antibiotic therapy in patients with high risk for multiresistant infections and also to take into account endothelial and adrenal dysfunction in prognostic models in hospitalized patients with decompensated cirrhosis.

关键词： Bacterial infections Liver cirrhosis Drug resistance Bacterial Endothelial dysfunction Relative adrenal insufficiency

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The movement dynamics of autotomized lizards and their tails reveal functional costs of caudal autotomy

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Integrative Zoology 2020年第6期15卷 511-521页

作者： Irene fernÁndez-RODRÍGUEZ Florentino BRAÑA Department of Organisms and Systems Biology(Zoology) University of OviedoOviedoSpain Research Unit of Biodiversity(UMIB UO/CSIC/PA)University of OviedoMieresSpain

Autotomy has evolved independently several times in different animal *** frequently involves immediate functional costs,so regeneration evolved in many instances to restore the functionality of that body *** autotomy is a widespread antipredator strategy in lizards,although it may affect energy storage,locomotion dynamics,or survival in future encounters with ***,we assessed the effect of tail loss on the locomotor performance of wall lizards(Podarcis muralis),as well as the recovery of locomotor functionality of lizards with regenerated tails,and the movement dynamics of shed tails that were either intact or having regenerated *** loss had no effect on locomotion over unhindered spaces,possibly due to compensation between a negative effect on the stride of front limbs,and a positive effect of losing mass and friction *** found a clear negative impact of tail loss on locomotion in spaces with interspersed obstacles,in which tailed lizards jumped larger distances when leaving the ***,lizards that used the tail to push off the ground were able to approach the obstacles from further,so that the tail seemed to be useful when used during *** fully restores lizard’s locomotor capacities,but tail antipredator value,as indicated by the intensity of post-autotomic movements,is only partially *** these results,we propose that,together with the recovery of post-autotomy antipredator capacities,the restoration of the organismal locomotor performance may have been an important,yet frequently neglected factor in the evolution of lizard’s regeneration ability.

关键词： autotomy locomotor performance regeneration tail wall lizard

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The reversed intra- and extracellular pH in tumors as a unified strategy to chemotherapeutic delivery using targeted nanocarriers

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Acta Pharmaceutica Sinica B 2021年第8期11卷 2243-2264页

作者： Edgar Pérez-Herrero Alberto fernández-Medarde Departamento de Ingeniería Química y Tecnología Farmacéutica Universidad de La LagunaLa Laguna 38206TenerifeSpain Instituto Universitario de Bio-Orgánica Antonio González Universidad de La LagunaLa Laguna 38206TenerifeSpain Instituto Universitario de Tecnologías Biomédicas Universidad de La LagunaLa Laguna 38200TenerifeSpain Instituto de Biología Molecular y Celular Del Cáncer Centro de Investigación Del Cáncer(USAL-CSIC)Salamanca 37007Spain

Solid tumors are complex entities,comprising a wide variety of malignancies with very different molecular *** this,they share a set of characteristics known as"hallmarks of cancer"that can be used as common therapeutic ***,every tumor needs to change its metabolism in order to obtain the energy levels required for its high proliferative rates,and these adaptations lead to alterations in extra-and intracellular *** changes in p H are common to all solid tumors,and can be used either as therapeutic targets,blocking the cell proton transporters and reversing the pH changes,or as means to specifically deliver anticancer *** this review we will describe how proton transport inhibitors in association with nanocarriers have been designed to block the pH changes that are needed for cancer cells to survive after their metabolic *** will also describe studies aiming to decrease intracellular pH in cancer using nanoparticles as molecular cages for protons which will be released upon UV or IR light ***,we will comment on several studies that have used the extracellular pH in cancer for an enhanced cell internalization and tumor penetration of nanocarriers and a controlled drug delivery,describing how nanocarriers are being used to increase drug stability and specificity.

关键词： pH-Gradient inversion Metabolism of glucose Proton transport inhibitors Proton-caged carriers Chemotherapy Targeted drug delivery pH-Sensitive nanocarriers Warburg effect Cancer

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