المؤلفون: Arafet Cruz, Kemel

المساهمون: University/Department: Universitat Jaume I. Departament de Química Física i Analítica

مرشدي الرسالة: Moliner Ibáñez, Vicente, Ferrer Castillo, Silvia

المصدر: TDX (Tesis Doctorals en Xarxa)

مصطلحات موضوعية: Cysteine Proteases, Inhibition, Catalytic, Cruzain, Falcipain-2, Química

وصف الملف: application/pdf

الوصول الحر: http://hdl.handle.net/10803/436898Test

المؤلفون: Medrano Martin, Francisco Javier, de la hoz rodriguez, Sergio, Martí, Sergio, Arafet Cruz, Kemel, Schirmeister, Tanja, Hammerschmidt, Stefan Josef, Müller-Ruttloff, Christin, González-Martínez, Águeda, Santillana Heras, Elena, Ziebuhr, John, Romero Garrido, Antonio, Zimmer, Collin, Weldert, Annabelle Carolin, Zimmermann, Robert, Lodola, Alessio, Świderek, Katarzyna, Moliner, Vicent, González, Florenci

مصطلحات موضوعية: COVID-19, antiviral drugs, peptidyl nitroalkene, protease, 3. Salud y bienestar

وصف الملف: application/pdf

العلاقة: SomUJIcontracovid crowdfunding campaign; Medrano, F.J., de la Hoz-Rodríguez, S., Martí, S. et al. Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2. Commun Chem 7, 15 (2024). https://doi.org/10.1038/s42004-024-01104-7Test; http://hdl.handle.net/10234/206159Test; https://doi.org/10.1038/s42004-024-01104-7Test

الإتاحة: https://doi.org/10.1038/s42004-024-01104-7Test
http://hdl.handle.net/10234/206159Test

المؤلفون: Arafet Cruz, Kemel, Royo, Santiago, Schirmeister, Tanja, Barthels, Fabian, González, Florenci, Moliner, Vicent

مصطلحات موضوعية: cysteine proteases, cathepsin L, cruzain, dipeptidyl nitroalkenes, inhibitory activities, QM/MM, free energy surfaces, in vitro activities, 3. Salud y bienestar

وصف الملف: application/pdf

العلاقة: ACS catalysis, 2023, vol. 13, no 9; https://figshare.com/collections/Impact_of_the_Recognition_Part_of_Dipeptidyl_Nitroalkene_Compounds_on_the_Inhibition_Mechanism_of_Cysteine_Proteases_Cruzain_and_Cathepsin_L/6613814Test; Arafet, K.; Royo, S.; Schirmeister, T.; Barthels, F.; González, F. V.; Moliner, V.Impact of the Recognition Part of Dipeptidyl Nitroalkene Compounds on the Inhibition Mechanism of Cysteine Proteases Cruzain and Cathepsin L. ACS Catal. 2023, 13, 9, 6289–6300. DOI: https://doi.org/10.1021/acscatal.3c01035Test; http://hdl.handle.net/10234/202767Test; https://doi.org/10.1021/acscatal.3c01035Test

الإتاحة: https://doi.org/10.1021/acscatal.3c01035Test
http://hdl.handle.net/10234/202767Test

المؤلفون: Martí, Sergio, Arafet Cruz, Kemel, Lodola, Alessio, Mulholland, Adrian, Świderek, Katarzyna, Moliner, Vicent

مصطلحات موضوعية: SARS-CoV-2 Mpro, COVID-19, inhibition, ketone-based Michael acceptor inhibitors, QM/MM, MD, methyl oxo-enoate based inhibitors

وصف الملف: application/pdf

العلاقة: ACS Catal. 2022, 12, 1; Marti S, Arafet K, Lodola A, Mulholland A, Swiderek K, Moliner V. Impact of warhead modulations on the covalent inhibition of SARS-CoV-2 Mpro explored by QM/MM simulations. ACS Catal. 2022, 12, 1, 698–708; http://hdl.handle.net/10234/196445Test; https://doi.org/10.1021/acscatal.1c04661Test

الإتاحة: https://doi.org/10.1021/acscatal.1c04661Test
http://hdl.handle.net/10234/196445Test

المؤلفون: Kholodar, Svetlana, Finer-Moore, Janet, Świderek, Katarzyna, Arafet Cruz, Kemel, Moliner, Vicent, Stroud, Robert M., Kohen, Amnon

مصطلحات موضوعية: peptides and proteins, monomers, crystal structure, chemical structure, inhibitors

وصف الملف: application/pdf

العلاقة: Biochemistry, 2021, vol. 60, no 16; Svetlana A. Kholodar, Janet S. Finer-Moore, Katarzyna Świderek, Kemel Arafet, Vicent Moliner, Robert M. Stroud, and Kohen, A. (2021) Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog. Biochemistry 2021 60 (16), 1243-1247, DOI:10.1021/acs.biochem.1c00063; http://hdl.handle.net/10234/194857Test; https://doi.org/10.1021/acs.biochem.1c00063Test

الإتاحة: https://doi.org/10.1021/acs.biochem.1c00063Test
http://hdl.handle.net/10234/194857Test

المؤلفون: Arafet Cruz, Kemel, Serrano Aparicio, Natalia, Lodola, Alessio, Mulholland, Adrian J., González, Florenci, Świderek, Katarzyna, Moliner, Vicent

المساهمون: This work was supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (Grant PGC2018-094852-B-C21 and PID2019-107098RJ-I00), Generalitat Valenciana (Grant AICO/2019/195 and SEJI/2020/007) Universitat Jaume I (UJI B2017-31, UJI B2018-41, UJI-A2019-04 and SomUJIContraCovid crowdfunding campaign), KŚ thanks the Spanish Ministerio de Ciencia, Innovación y Universidades for a Juan de la Cierva – Incorporación (ref. IJCI-2016-27503) contract. K. A. thanks Universitat Jaume I (POSDOC-A/2018/30) and Generalitat Valenciana (APOSTD/2020/015) for post-doctoral contracts. NS thanks the MINECO for doctoral FPI grant (BES-2016-078029). The authors thankfully acknowledge the computer resources at Pirineus and the technical support provided at Pirineus and by Barcelona Supercomputing Center (QSB-2020-2-0004), as well as the local computational resources of the Servei d’Informàtica of Universitat Jaume I. AJM thanks EPSRC for support (CCP-BioSim, grant number EP/M022609/1) and also the British Society for Antimicrobial Chemotherapy (grant number BSAC-COVID-30).

مصطلحات موضوعية: SARS-CoV-2, COVID-19, main protease

وصف الملف: application/pdf

العلاقة: Chemical Science, 2021; https://pubs.rsc.org/en/content/articlehtml/2021/sc/d0sc06195fTest; K. Arafet, N. Serrano-Aparicio, A. Lodola, A. J. Mulholland, F. V. González, K. Świderek and V. Moliner. Mechanism of inhibition of SARS-CoV-2 Mpro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity. , Chem. Sci., 2021, 2041-6520; http://hdl.handle.net/10234/191528Test; https://doi.org/10.1039/D0SC06195FTest

الإتاحة: https://doi.org/10.1039/D0SC06195FTest
http://hdl.handle.net/10234/191528Test

المؤلفون: Arafet Cruz, Kemel, González, Florenci, Moliner, Vicent

مصطلحات موضوعية: rhodesain, free energy surfaces, inhibition mechanism, molecular dynamics, dipeptidyl enoates, QM/MM

وصف الملف: application/pdf

العلاقة: Chem. Eur. J. 2021, 27; ARAFET, Kemel; GONZÁLEZ, Florenci V.; MOLINER, Vicent. Elucidating the dual mode of action of dipeptidyl enoates in the inhibition of rhodesain cysteine proteases. Chem. Eur. J. 2021, 27; http://hdl.handle.net/10234/193658Test; https://doi.org/10.1002/chem.202100892Test

الإتاحة: https://doi.org/10.1002/chem.202100892Test
http://hdl.handle.net/10234/193658Test

المؤلفون: Boneta, Sergio, Arafet Cruz, Kemel, Moliner, Vicent

مصطلحات موضوعية: QM/MM, free energy surfaces, computational chemistry, enzyme catalysis, catalytic mechanism, poly(ethylene terephthalate) (PET), plastic recycling, biodegradation, Ideonalla sakaiensis, PET hydrolase (PETase), leaf-branch compost cutinase (LCC)

وصف الملف: application/pdf

العلاقة: J Chem Inf Model . 2021 Jun 28;61(6):3041-3051.; https://pubs.acs.org/journal/jcisd8Test; Boneta S, Arafet K, Moliner V. QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate. J Chem Inf Model. 2021 Jun 28;61(6):3041-3051. doi:10.1021/acs.jcim.1c00394. Epub 2021 Jun 4. PMID: 34085821.; http://hdl.handle.net/10234/194903Test; https://doi.org/10.1021/acs.jcim.1c00394Test

الإتاحة: https://doi.org/10.1021/acs.jcim.1c00394Test
http://hdl.handle.net/10234/194903Test

المؤلفون: Arafet Cruz, Kemel, Świderek, Katarzyna, Moliner, Vicent

مصطلحات موضوعية: biochemistry, enzyme kinetics, free energy, molecular dynamics, molecular dynamics simulation, molecular mechanics, potential energy, proteins, reaction mechanism

وصف الملف: application/pdf

العلاقة: ACS Omega, 2018, vol. 3, no 12; Spanish Ministerio de Economia y Competitividad: CTQ2015-66223-C2; FEDER funds: CTQ2015-66223-C2; Universitat Jaume I: UJI.B2017-31; Spanish Ministerio de Economia y Competitividad for a Juan de la Cierva -Incorporacion: IJCI-2016-27503; ARAFET, Kemel; ŚWIDEREK, Katarzyna; MOLINER, Vicent. Computational Study of the Michaelis Complex Formation and the Effect on the Reaction Mechanism of Cruzain Cysteine Protease. ACS Omega, 2018, vol. 3, no 12, p. 18613-18622; http://hdl.handle.net/10234/181927Test; http://dx.doi.org/10.1021/acsomega.8b03010Test

الإتاحة: https://doi.org/10.1021/acsomega.8b03010Test
http://hdl.handle.net/10234/181927Test

المؤلفون: Arafet Cruz, Kemel, Ferrer Castillo, Silvia, Moliner, Vicent

مصطلحات موضوعية: Chagas disease, PHK inhibitors, QM/MM, Molecular Dynamics, PMF

وصف الملف: application/pdf

العلاقة: Biochemistry, 2015, vol. 54, no 21; ARAFET, Kemel; FERRER, Silvia; MOLINER, Vicent. First Quantum Mechanics/Molecular Mechanics Studies of the Inhibition Mechanism of Cruzain by Peptidyl Halomethyl Ketones. Biochemistry, 2015, vol. 54, no 21, p. 3381-3391.; http://hdl.handle.net/10234/154786Test; http://dx.doi.org/10.1021/bi501551gTest

الإتاحة: https://doi.org/10.1021/bi501551gTest
http://hdl.handle.net/10234/154786Test