Diseño de fármacos asistido por computadora. Dinámica molecular de complejos proteína-ligando y proteína-proteína. Caracterización estructural y dinámica de blancos terapéuticos.

Publicaciones

01) Aguayo-Ortiz, R.; Dominguez, L. Effects of mutating Trp42 residue on γD-crystallin stability. J. Chem. Inf. Model. 2020, 60 (2), 777–785. (doi: 10.1021/acs.jcim.9b00747)
o IF: 4.956
02) Fernández-de Gortari, E.; Aguayo-Ortiz, R.; Autry, J.; Espinoza-Fonseca, L. M. A hallmark of phospholamban functional divergence is located in the N-terminal phosphorylation domain. Comput. Struct. Biotechnol. J. 2020, 18, 705–713. (doi: 10.1016/j.csbj.2020.02.016)
o IF: 7.271
03) González-Méndez, I.; Aguayo-Ortiz, R.; Sorroza-Martínez, K.; Solano, J. D.; Porcu, P.; Rivera E.; Dominguez L. Conformational analysis by NMR and molecular dynamics of Adamantane-Doxorubicin prodrugs and their assemblies with β-cyclodextrin: A focus on the design of platforms for controlled drug delivery. Bioorg. Med. Chem. 2020, 28 (13), 115510. (doi: 10.1016/j.bmc.2020.115510)
o IF: 3.641
04) Uriostegui-Arcos, M.; Aguayo-Ortiz, R.; Valencia-Morales, M. P.; Melchy-Pérez, E.; Rosenstein, Y.; Dominguez, L.; Zurita, M. Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer. Open Biol. 2020, 10 (6), 200050. (doi: 10.1098/rsob.200050)
o IF: 6.41
05) Aguayo-Ortiz, R.; Espinoza-Fonseca, L. M. Linking biochemical and structural states of SERCA: achievements, challenges, and new opportunities. Int. J. Mol. Sci. 2020, 21 (11), 4146. (doi: 10.3390/ijms21114146)
o IF: 5.923
06) Aguayo-Ortiz, R.; Fernández-de Gortari, E.; Espinoza-Fonseca, L. M. Conserved luminal C-terminal domain dynamically controls interdomain communication in sarcolipin. J. Chem. Inf. Model. 2020, 60 (8), 3985–3991. (doi: 10.1021/acs.jcim.0c00418)
o IF: 4.956
07) Herrera-Vázquez, F. S.; Matadamas-Martínez, F.; Aguayo-Ortiz, R.; Dominguez, L.; Ramírez-Apan, T.; Yépez-Mulia, L.; Hernández-Luis, F. Design, synthesis and evaluation of 2,4-diaminoquinazoline derivatives as potential tubulin polymerization inhibitors. ChemMedChem, 2020, 15, 1802 –1812. (doi: 10.1002/cmdc.202000185)
o IF: 3.466
08) Raguimova, O. N.; Aguayo-Ortiz, R.; Robia, S. L.; Espinoza-Fonseca, L. M. Dynamics-driven allostery underlies Ca2+-mediated release of SERCA inhibition by Phospholamban. Biophys. J. 2020, 119, 1–10. (doi: 10.1016/j.bpj.2020.09.014)
o IF: 4.003
09) Aguayo-Ortiz, R.; Espinoza-Fonseca, L. M. Atomistic structure and dynamics of the Ca2+-ATPase bound to phosphorylated phospholamban. Int. J. Mol. Sci. 2020, 21 (19), 7261. (doi: 10.3390/ijms21197261)
o IF: 5.923
10) Fisher, M. L.; Bovo, E.; Aguayo-Ortiz, R.; Cho, E. E.; Pribadi, M. P.; Rathod, N.; Lemieux, M. J.; Espinoza-Fonseca, L. M.; Robia, S. L.; Zima, A. V.; Young, H. S. Dwarf open reading frame (DWORF) is a direct activator of the sarcoplasmic reticulum calcium pump SERCA. eLife. 2021, 10, e65545. (doi: 10.7554/eLife.65545)
o IF: 8.14
11) Martínez-Ortega, U.; Figueroa-Figueroa, D. I.; Hernández-Luis, F.; Aguayo-Ortiz, R.* In silico characterization of masitinib interaction with SARS-CoV-2 main protease. ChemMedChem. 2021, 16 (15), 2339-2344. (doi: 10.1002/cmdc.202100375)
o IF: 3.466
12) Santiago, Á.; Guzmán-Ocampo, D. C.; Aguayo-Ortiz, R.*; Dominguez, L.* Characterizing the chemical space of γ-secretase inhibitors and modulators. ACS Chem. Neurosci. 2021, 12 (15), 2765-2775. (doi: 10.1021/acschemneuro.1c00313)
o IF: 4.418
13) Aguayo-Ortiz, R.; Creech, J.; Jiménez-Vázquez, E. N.; Guerrero-Serna, G.; Wang, N.; da Rocha, A. M.; Herron, T. J.; & Espinoza-Fonseca. A multiscale approach for bridging the gap between potency, efficacy, and safety of small molecules directed at membrane proteins. Sci. Rep. 2021, 11 (1), 16580. (doi: 10.1038/s41598-021-96217-7)
o IF: 4.380
14) Hernández-Ochoa, B.; Navarrete-Vázquez, G.; Aguayo-Ortiz, R.; Ortiz-Ramírez, P.; Morales-Luna, L.; Martínez-Rosas, V.; González-Valdez, A.; Gómez-Chávez, F.; Enriquez-Flores, S.; Wong-Baeza, C.; Baeza-Ramírez, I.; Pérez de la Cruz, V.; Gómez-Manzo, S. Identification and in silico characterization of novel Helicobacter pylori glucose-6-phosphate dehydrogenase inhibitors. Molecules. 2021, 26 (16), 4955. (doi: 10.3390/molecules26164955)
o IF: 4.411
15) Ramos-Orea, A.; Ramírez-Apan, M.; Chávez-Santos, R.; Aguayo-Ortiz, R.; Espitia, C.; Silva Miranda, M.; Torres-Ochoa, R.; Martinez, R. Total syntheses and antiproliferative activities of prenostodione and its analogues. Org. Biomol. Chem. 2021, 19 (38), 8272-8280. (doi: 10.1039/D1OB00897H)
o IF: 3.876
16) Pretelín-Castillo, G.; Silva Miranda, M.; Espitia, C.; Chávez-Santos, R. M.; Suárez-Castro, A.; Chacón-García, L.; Aguayo-Ortiz, R.; Martínez, R. (2Z)-3-hydroxy-3-(4-R-phenyl)-prop-2-enedithioic acids as new antituberculosis compounds. Infection and Drug Resistance. 2021, 14, 4323. (doi: 10.2147/IDR.S328132)
o IF: 4.028
17) Aguayo-Ortiz, R.; Guzmán-Ocampo, D. C.; Dominguez, L. Insights into the binding of morin to human γD-crystallin. Biophys. Chem. 2022, 282, 106750. (doi: 10.1016/j.bpc.2021.106750)
o IF: 2.352
18) Liu, A. Y.; Aguayo-Ortiz, R.; Guerrero-Serna, G.; Wang, N.; Blin, M. G.; Goldstein, D. R.; Espinoza-Fonseca, L. M. Homologous cardiac calcium pump regulators phospholamban and sarcolipin adopt distinct oligomeric states in the membrane. Comput. Struct. Biothecnol. J. 2022, 20, 380-384. (doi: 10.1016/j.csbj.2021.12.031)
o IF: 7.271
19) Martínez-Rosas, V.; Hernández-Ochoa, B.; Navarrete-Vázquez, G.; Martínez-Conde, C.; Gómez-Chávez, F.; Morales-Luna, L.; González-Valdez, A.; Arreguin-Espinosa, R.; Enríquez-Flores, S.; Pérez de la Cruz, V.; Aguayo-Ortiz, R.; Wong-Baeza, C.; Baeza-Ramírez, I.; Gómez-Manzo, S. Kinetic and molecular docking studies to determine the effect of inhibitors on the activity and structure of fused G6PD::6PGL protein from Trichomonas vaginalis. Molecules. 2022, 27 (4), 1174. (doi: 10.3390/molecules27041174)
o IF: 4.411
20) Bibian-García, J.A.; Ortiz-Ramírez, J.A.; Amazan-Villegas, L.M.; Aguayo-Ortiz, R.; Cano-Cachola, C.; Cuéllar-Cruz, Mayra, López-Romero, E. A GDPase/UDPase bifunctional enzyme from Candida albicans: purification and biochemical characterization. Antonie van Leeuwenhoek. 2022, 115 (4), 505-519.
o IF: 2.271
21) Madrigal-Angulo, J.L.; Menez-Guerrero, C.; Estrada-Soto, S.; Ramirez-Espinosa, J.J.; Almanza-Pérez, J.C.; Leon-Rivera, I.; Hernadez-Nuñez, E.; Aguirre-Vidal, Y.; Flores-León, C.D.; Aguayo-Ortiz, R.; Navarrete-Vázquez, G. Synthesis, in vitro, in silico and in vivo hypoglycemic and lipid-lowering effects of 4-benzyloxy-5-benzylidene-1,3-thiazolidine-2,4-diones mediated by dual PPAR α/γ modulation. Bioorg. Med. Chem. Lett. 2022, 70, 128804. (doi: 10.1016/j.bmcl.2022.128804)
o IF: 2.823
22) Aguayo-Ortiz, R.*; Dominguez, L. Unveiling the possible oryzalin-binding site in the α-tubulin of Toxoplasma gondii. ACS Omega. 2022, 7 (22), 18434-18442. (doi: 10.1021/acsomega.2c00729)
o IF: 3.512
23) Bak, J.J.; Aguayo-Ortiz, R.; Rathod, N.; Primeau, J.O.; Khan, M.B.; Robia, S.L.; Lemieux, M.J.; Espinoza-Fonseca, M.; Young H.S. Primitive phospholamban-and sarcolipin-like peptides inhibit the sarcoplasmic reticulum calcium pump SERCA. Biochemistry. 2022, 61 (14): 1419-1430.
o IF: 3.162
24) Flores-León, C.D.; Dominguez, L.; Aguayo-Ortiz, R*. Molecular basis of Toxoplasma gondii oryzalin resistance from a novel α-tubulin binding site model. Arch. Biochem. Biophys. 2022, 730, 109398.
o IF: 4.013
25) Guzmán-Ocampo, D.C.; Aguayo-Ortiz, R.; Velasco-Bolom, J.L., Gupta, P.L.; Roitberg, A.E.; Dominguez, L. Elucidating the protonation state of the γ-secretase catalytic dyad. ACS Chem. Neurosci. 2023, 14: 261-269.
o IF: 4.20
26) Flores-León, C.D.; Colorado-Pablo, L.F.; Santos-Contreras, M.Á.; Aguayo-Ortiz, R.* Determination of nucleoside DOT1L inhibitors' residence times by τRAMD simulations. Front. Drug Des. Discov. 2023, 2, 1-7.
o IF: N/D
27) Cruz-Cortés, C.; Velasco-Saavedra, M.A.; Fernández-de Gortari, E.; Guerrero-Serna, G.; Aguayo-Ortiz, R.; Espinoza-Fonseca, L.M. A novel machine learning-based screening identifies statins as inhibitors of the calcium pump SERCA. J. Biol. Chem. 2023, 299(5), 104681.
o IF: 4.00
28) Vázquez-López, N.A.; Aguayo-Ortiz, R.; Cuéllar-Cruz, M. Molecular modeling of the phosphoglycerate kinase and fructose-bisphosphate aldolase proteins from Candida glabrata and Candida albicans. Med. Chem. Res. 2023, 32, 2356-2369.
o IF: 2.60
29) Lopez-Sanchez, M.A.; Garcia-Rodriguez, M. del C.; Aguayo-Ortiz, R.; Hernandez-Cruz, E.; Figueroa-Figueroa, D.I.; Hernandez-Luis, F. Synthesis of quinazolin-2,4,6-triamine derivatives as non-purine Xanthine oxidase inhibitors and exploration of their toxicological potential. ChemMedChem, 2023, 18(20), e202300184.
o IF: 3.54
30) Velasco-Saavedra, M.A.; Mar-Antonio, E.; Aguayo-Ortiz, R.* Molecular insights into the covalent binding of zoxamide to the β-tubulin of Botrytis cinerea. J. Chem. Inf. Model. 2023, 63 (20), 6386-6395.
o IF: 5.70
31) Martínez-Conde, C.; Colín-Lozano, B.; Gutiérrez-Hernández, A.; Hernández-Núñez, E.; Yépez-Mulia, L.; Colorado-Pablo, L.F.; Aguayo-Ortiz, R.; Escalante, J.; Rivera-Leyva, J.; Sánchez-Carranza, J.N.; Barbosa-Cabrera, E.; Navarrete-Vázquez, G. Enhancing giardicidal activity and aqueous solubility through the development of “RetroABZ”, a regioisomer of albendazole: in vitro, in vivo, and in silico studies. Int. J. Mol. Sci. 2023, 24(19), 14949.
o IF: 4.90
32) Díaz-Rojas, M.; González-Andrade, M.; Aguayo-Ortiz, R.; Rodríguez-Sotres, R.; Pérez-Vásquez, A.; Madariaga-Mazón, A.; Mata, R. Discovery of inhibitors of protein tyrosine phosphatase 1B contained in a natural products library from Mexican medicinal plants and fungi using a combination of enzymatic and in silico methods. Front. Pharmacol. 2023, 14, 1281045.
o IF: 4.40
33) Martínez-Rodríguez, O.P.; García-Contreras, R.; Aguayo-Ortiz, R.; Figueroa, M. Antimicrobial and antibiofilm activity of fungal metabolites on methicillin-resistant Staphylococcus aureus (ATCC 43300) mediated by SarA and AgrA. Biofouling. 2023, 39 (8), 830-837.
o IF: 2.60
34) Cano-González, L.; Espinosa-Mendoza, J.D.; Matadamas-Martínez, F.; Romero-Velásquez, A.; Flores-Ramos, M.; Colorado-Pablo, L.F.; Cerbón-Cervantes, M. A.; Castillo, R.; González-Sánchez, I.; Yépez-Mulia, L.*; Hernández-Campos, A.*; Aguayo-Ortiz, R.* Structure-based optimization of carbendazim-derived tubulin polymerization inhibitors through alchemical free energy calculations. J. Chem. Inf. Model. 2023, 63 (22), 7228-7238.
o IF: 5.70
35) Padilla-Mayne, S.; Ovalle-Magallanes, B.; Figueroa, M.; Linares, E.; Bye, R.; Rivero-Cruz, I.; González-Andrade, M.; Aguayo-Ortiz, R.; Mata, R. Chemical analysis and antidiabetic potential of a decoction from Stevia serrata roots. J. Nat. Prod. 2024, 87 (3), 501-513.
o IF: 3.40
36) Guzmán-Ocampo, D.C.; Aguayo-Ortiz, R.; Dominguez, L. Understanding the modulatory role of E2012 on the γ-secretase-substrate interaction. J. Chem. Inf. Model. 2024, 64, 3855-3864.
o IF: 5.70
37) Gutiérrez-Aguilar, M.; Klutho, P.J.; Aguayo-Ortiz, R.; Song, L.; Baines, C.P. Endogenous complement 1q binding protein (C1qbp) regulates mitochondrial permeability transition and post-myocardial infarction remodeling and dysfunction. J. Mol. Cell. Cardiol. 2024, 196, 1-11.
o IF: 4.9

Circuito de Posgrado, Ciudad Universitaria
Alcaldía Coyoacán, C.P. 04510, México, CDMX

55 5623 7006
mdcbq@posgrado.unam.mx