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

Publicaciones

1) Aguayo-Ortiz, R.; Dominguez, L. Generation of amyloid-β peptides by γ-secretase. Isr. J. Chem. 2017, 57 (7), 574–585. (doi: 10.1002/ijch.201600073)
o IF: 3.333
2) Aguayo-Ortiz, R.; Cano-González, L.; Hernández-Campos, A.; Castillo, R.; Dominguez, L. Structure-based approaches for the design of benzimidazole-2-carbamate derivatives as tubulin polymerization inhibitors. Chem. Biol. Drug Des. 2017, 90 (1), 40–51. (doi: 10.1111/cbdd.12926)
o IF: 2.817
3) Gutiérrez-Gutiérrez, F.; Palomo-Ligas, L.; Hernández-Hernández, J. M.; Pérez-Rangel, A.; Aguayo-Ortiz, R.; Hernández-Campos, A.; Castillo, R.; González-Pozos, S.; Cortés-Zárate, R.; Ramírez-Herrera, M. A.; Mendoza-Magaña, M. L.; Castillo-Romero, A. Curcumin alters the cytoskeleton and microtubule organization on trophozoites of Giardia lamblia. Acta Trop. 2017, 172, 113–121. (doi: 10.1016/j.actatropica.2017)
o IF: 3.112
4) Flores-Carrillo, P.; Velázquez-López, J. M.; Aguayo-Ortiz, R.; Hernández-Campos, A.; Trejo-Soto, P. J.; Yépez-Mulia, L.; Castillo R. Synthesis, antiprotozoal activity and chemoinformatic analysis of novel 2-(methylthio)-1H-benzimidazole-5-carboxamide derivatives: Identification of new selective giardicide and trichomonicide compounds. Eur. J. Med. Chem. 2017, 132, 211–220. (doi: 10.1016/j.ejmech.2017.05.058)
o IF: 6.510
5) Aguayo-Ortiz, R.; Chávez-García, C.; Straub, JE.; Dominguez, L. Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach. Chem. Sci. 2017, 8 (8), 5576–5584. (doi: 10.1039/c7sc00980a)
o IF: 9.969
6) Aguayo-Ortiz, R.; Meza-Cervantez, P.; Castillo, R.; Hernández-Campos, A.; Dominguez, L.; Yépez-Mulia, L. Insights into the Giardia intestinalis enolase and human plasminogen interaction. Mol. Biosyst. 2017, 13 (10), 2015–2023. (doi: 10.1039/c7mb00252a)
o IF: 3.781
7) Guzmán-Ocampo, D. C.; Aguayo-Ortiz, R.; Cano-González, L.; Castillo, R.; Hernández-Campos, A.; Dominguez, L. Effects of the protonation state of titratable residues and the presence of water molecules on the nocodazole binding to β-tubulin. ChemMedChem 2018, 13 (1), 20–24. (doi: 10.1002/cmdc.201700530)
o IF: 3.540
8) López-Méndez, L. J.; González-Méndez, I.; Aguayo-Ortiz, R.; Dominguez, L.; Alcaraz-Estrada, L.; Guadarrama, P.; Rojas-Aguirre, Y. Synthesis of a poly(ester) dendritic β-cyclodextrin derivative by ‘click’ chemistry: Combining the best of two worlds for complexation enhancement. Carbohydr. Polym. 2018, 184, 20–29. (doi: 10.1016/j.carbpol.2017.12.049)
o IF: 10.723
9) Tabatabaei-Dakhili, S. A.; Aguayo-Ortiz, R.; Dominguez, L.; Velázquez-Martínez, C. A. Untying the knot of transcription factor druggability: molecular modeling study of FOXM1 inhibitors. J. Mol. Graph. Model. 2018, 80, 197–201. (doi: 10.1016/j.jmgm.2018.01.009)
o IF: 2.942
10) Aguayo-Ortiz, R and Dominguez, L. Simulating the γ-secretase enzyme: recent advances and future directions. Biochimie. 2018, 147, 130–135. (doi: 10.1016/j.biochi.2018.01.007)
o IF: 4.372
11) Salla, M.; Aguayo-Ortiz, R.; Ibrahim, D. G.; Zare, A.; Said, A.; Moore, J.; Pandya, V.; Manaloor, R.; Fong, S.; Blankstein, A. R.; Gibson, S.; Ramos Garcia, L.; Meier, P.; Bhullar, K. S.; Hubbard, B. P.; Fiteh, Y.; Vliagoftis, H.; Goping, I. S.; Brocks, D.; Hwang, P.; Velázquez-Martínez, C. A.; and Baksh, S. Identification and characterization of novel Receptor Interacting Serine/threonine‐Protein Kinase 2 (RIPK2) inhibitors using structural similarity analysis. J. Pharmacol. Exp. Ther. 2018, 365 (2), 354–367. (doi: 10.1124/jpet.117.247163)
o IF: 4.400
12) Aguayo-Ortiz, R.; Straub, JE.; Dominguez, L. Influence of membrane lipid composition on the structure and activity of γ-secretase. Phys. Chem. Chem. Phys. 2018, 20 (43), 27294–27304. (doi: 10.1039/c8cp04138e)
o IF: 3.567
13) Chávez-García, C.; Aguayo-Ortiz, R.; Dominguez, L. Quantifying correlations between mutational sites in the catalytic subunit of γ-secretase. J. Mol. Graph. Model. 2019, 88, 221–227. (doi: 10.1016/j.jmgm.2019.02.002)
o IF: 2.942
14) Aguayo-Ortiz, R.; Guzmán-Ocampo, D. C.; Dominguez, L. Toward the characterization of DAPT interaction with γ‐secretase. ChemMedChem, 2019, 14 (10), 1005–1010. (doi: 10.1002/cmdc.201900106)
o IF: 3.540
15) Aguayo-Ortiz, R.; Dominguez, L. APH-1A component of γ-secretase forms an internal water and ion-containing cavity. ACS Chem. Neurosci. 2019, 10 (6), 2931–2938. (doi: 10.1021/acschemneuro.9b00150)
o IF: 4.418
16) Aguayo-Ortiz, R.; González-Navejas, A.; Palomino-Vizcaino, G.; Rodriguez-Meza, O.; Costas, M.; Quintanar, L.; Dominguez, L. Thermodynamic stability of human γD-crystallin mutants using alchemical free energy calculations. J. Phys. Chem. B 2019, 123 (27), 5671–5677. (doi: 10.1021/acs.jpcb.9b01818)
o IF: 3.466
17) González-Hernández, I.; Palomares-Alonso, F.; Becerril-Vega, J.; Melchor-Doncel de la Torre, S.; Hernández-Luis, F.; Rodriguez-Morales, S.; Aguayo-Ortiz, R.; Dominguez, L.; Rodríguez-Balderas, CA.; González-Maciel, A.; Rojas-Tomé, I. S.; Castro, N.; Jung-Cook, H. Evaluation of new benzimidazole derivatives as cysticidal agents: in vitro, in vivo and docking studies. Chem. Pharm. Bull. 2019, 67 (12), 1293–1300. (doi: 10.1248/cpb.c19-00574)
o IF: 1.645
18) 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
19) 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
20) 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
21) 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
22) 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
23) 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
24) 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
25) 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
26) 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
27) 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
28) 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
29) 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
30) 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
31) 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
32) 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
33) 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
34) 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
35) 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
36) 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
37) 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
38) 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
39) 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
40) 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
41) 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, In press. (doi: 10.1016/j.abb.2022.109398)
o IF: 4.013

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

55 5623 7006
mdcbq@posgrado.unam.mx