May 2, 2018

TD5 Lab

Fernando Danilo González-Nilo

Full Professor and Director of the                                                              
Center for Bioinformatics and Integrative Biology (CBIB)
+56-2-770 3606

Dr. Fernando Danilo González Nilo, Ph.D. in Chemistry (47), is a full professor and Director of the Center for Bioinformatics and Integrative Biology (CBIB), at Universidad Andres Bello. The CBIB of the University Andres Bello houses a trans-disciplinary team whose main goal is to develop research strategies that bring together the benefits of computational and experimental validation methods.

The CBIB highly integrated approach favors an iterative research cycle based on observation, modeling, simulation, and validation. This approach is supported by a high performance computing system (SGI ICE 8400 with 1.536 cores and 3TB of RAM memory), enabling the development and use of high-performance molecular simulation and bioinformatics tools in areas as diverse as Molecular Design, Protein Engineering, and Omics-Technologies.

The computer system is tightly integrated to the Protein Engineering, Cell biology and Electron Microscopy laboratories. This arrangement in central to CBIB design for the development of multidisciplinary initiatives that allow exploring new questions in integrative biology.

CBIB team takes part in multiple theoretical-experimental projects through collaborative efforts with national and international groups specialized in biophysics, enzymatic catalysis, computer based drug design, transmembrane proteins and bio- and nano-technology, among others.

Other line of focus within the CBIB, is the development and implementation of advanced methods in Molecular Dynamics simulations for the analysis and characterization of the structural determinants that govern the activation and conductance of K channels (SHAKER, HSlo, TRPV1 and TRPM8).



Different Classes of Antidepressants Inhibit the Rat α7 Nicotinic Acetylcholine Receptor by Interacting within the Ion Channel: A Functional and Structural StudyYorley Duarte , Maximiliano Rojas, Jonathan Canan, Edwin G. Pérez, Fernando González-Nilo and Jesús García-Colunga .Molecules. 2021.
In Silico Study of Coumarins and Quinolines Derivatives as Potent Inhibitors of SARS-CoV-2 Main ProteaseOsvaldo Yañez, Manuel Isaías Osorio, Eugenio Uriarte, Carlos Areche, William Tiznado, José M. Pérez-Donoso , Olimpo García-Beltrán, Fernando González-NiloFrontiers in Chemistry. 2021.
Theobroma cacao L. compounds: Theoretical study and molecular modelling as inhibitors of main SARS-CoV-2 proteaseOsvaldo Yañez, Manuel Isaías Osorio, Carlos Areche, Alejandro Vasquez-Espinal, Jessica Bravo, Angélica Sandoval-Aldana, José M Pérez-Donoso , Fernando González-Nilo , Maria João Matos, Edison Osorio, Olimpo García-Beltrán, William TiznadoBiomedicine & Pharmacotherapy. 2021.
A physiologic rise in cytoplasmic calcium ion signal increases pannexin1 channel activity via a C-terminus phosphorylation by CaMKIIXimena López, Nicolás Palacios-Prado, Juan Güiza, Rosalba Escamilla, Paola Fernández, José L Vega, Maximiliano Rojas, Valeria Marquez-Miranda, Eduardo Chamorro, Ana M Cárdenas, María Constanza Maldifassi, Agustín D Martínez, Yorley Duarte, Fernando D González-Nilo, Juan C Sáez.Proceedings of the National Academy of Sciences. 2021.
Development of a PHBV nanoparticle as a peptide vehicle for NOD1 activationCabaña-Brunod, M., Herrera, P. A., Márquez-Miranda, V., Llancalahuen, F. M., Duarte, Y ., González-Nilo, D ., Fuentes, J. A., Vilos, C., Velásquez, L. & Otero, C.Drug Delivery. 2021.


A folding reaction at the C-terminal domain drives temperature sensing in TRPM8 channelsIgnacio Díaz-Franulic , Natalia Raddatza, Karen Castilloa, Fernando D. González-Nilo and Ramon LatorrePNAS Latest Articles. 2020.
Novel TRPV1 Channel Agonists With Faster and More Potent Analgesic Properties Than CapsaicinYorley Duarte , Javier Cáceres, Romina V. Sepúlveda, Diego Arriagada, Pedro Olivares, Ignacio Díaz-Franulic , Jimmy Stehberg and Fernando González-Nilo.Frontier in Pharmacology. 2020.
Cationic Carbosilane Dendritic Systems as Promising Anti‐Amyloid Agents in Type 2 DiabetesTania Lozano‐Cruz, Gema Alcarraz‐Vizán, F. Javier de la Mata, Sara de Pablo, Paula Ortega, Yorley Duarte , Fernado González-Nilo , Felipe Bravo‐Moraga … et al.Chemistry Europe, 2020.
Structural determinants of TRPV4 inhibition and identification of new antagonists with antiviral activityPablo Doñate-Macia, Yorley Duarte , Fanny Rubio-Moscardo, Fernando González-Nilo , Miguel A Valverde, et al.British Journal of Pharmacology. 2020. DOI: 10.1111/bph.15267
Stretch-Induced Activation of Pannexin 1 Channels Can Be Prevented by PKA-Dependent PhosphorylationXimena López, Rosalba Escamilla, Paola Fernández, Yorley Duarte, Fernando González-Nilo , Juan C Sáez, et al.International Journal of Molecular Sciences.2020. DOI: 10.3390/ijms21239180
Dynamin-2 R465W mutation induces long range perturbation in highly ordered oligomeric structuresHinostroza, F., Neely, A., Araya-Duran, I., Marabolí, V., Canan, J., Rojas, M., Aguayo , D ., Latorre, R., González-Nilo, F. D . & CárdenasScientific Reports.2020. DOI


Integration of target discovery, drug discovery and drug delivery: A review on computational strategiesYorley Duarte Q , Valeria Márquez-Miranda, Matthieu J. Miossec , Fernando González-NiloWires Nanomed Nanobiotechnol.. 2019 .
The molecular nature of the 17β-Estradiol binding site in the voltage- and Ca2+-activated K+ (BK) channel β1 subunitSara T. Granados, Karen Castillo, Felipe Bravo-Moraga, Romina V. Sepúlveda, Willy Carrasquel-Ursulaez, Maximiliano Rojas, Emerson Carmona, Yenisleidy Lorenzo-Ceballos, Fernando González-Nilo, Carlos González, Ramón Latorre & Yolima P. Torres Scientific Reports. 2019.
Odd Loop Regions of XenA and XenB Enzymes Modulate Their Interaction with Nitro-explosives Compounds and Provide Structural Support for Their RegioselectivityManuel I. Osorio, Ma. Angeles Cabrera, Fernando González-Nilo, José M. Pérez-Donoso.Journal of Chemical Information and Modeling. 2019. DOI: 10.1021/acs.jcim.9b00357
IDH1 and IDH2 mutants identified in cancer lose inhibition by isocitrate because of a change in their binding sitesJuan P. Bascur, Melissa Alegría-Arcos, Ingrid Araya-Durán, Ezequiel I. Juritz, Fernando D. González-Nilo, Daniel E. AlmonacidBioRxiv the preprint server for biology. 2019.


115Thermally activated TRP channels: molecular sensors for temperature detectionCastillo, K. ; Diaz-Franulic, I; Canan, J; Gonzalez-Nilo, F; Latorre, R.PHYSICAL BIOLOGY. 2018. DOI: 10.1088/1478-3975/aa9a6f
116IR and NMR spectroscopic correlation of enterobactin by DFTM. Moreno, A. Zacarias, A. Porzel,  L. Velasquez, G. Gonzalez, M. Alegría-Arcos, F. Gonzalez-Nilo, E.K.U. Grossb.Spectrochimica Acta. 2018. DOI: 10.1016/j.saa.2018.02.060
129Penicillium purpurogenum produces a novel endo-1,5-arabinanase, active on debranched arabinan, short arabinooligosaccharides and on the artificial substrate p-nitrophenyl arabinofuranoside.Vilches F, Ravanal MC, Bravo-Moraga F, Gonzalez-Nilo D, Eyzaguirre J.Carbohydrate Research. 2018. DOI: 10.1016/j.carres.2017.11.014.
134Engineering Atrazine Loaded Poly (lactic-co-glycolic Acid) Nanoparticles to Ameliorate Environmental ChallengesSchnoor, B ; Elhendawy, A.; Joseph, S. ; Putman, M.; Chacon-Cerdas, R.  ; Flores-Moraga, D. ; Bravo-Moraga, F.; Gonzalez-Nilo, F. ; Salvador-Morales, C.JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY. 2018. DOI: 10.1021/acs.jafc.8b01911
144Experimental and Computational Characterization of the Interaction between Gold Nanoparticles and Polyamidoamine DendrimersCamarada, MB; Comer, J ; Poblete, ; Singam, ERA ; Marquez-Miranda, V ; Morales-Verdejo, C; Gonzalez-Nilo.LANGMUIR. 2018. DOI: 10.1021/acs.langmuir.8b01809
145Experimental and theoretical structural/spectroscopical correlation of enterobactin and catecholamideMoreno, M ; Zacarias, A; Velasquez, L ; Gonzalez, G ; Alegria-Arcos, M; Gonzalez-Nilo, F ; Gross, EKU.DATA IN BRIEF. 2018. DOI: 10.1016/j.dib.2018.08.114


112Thermally-activated TRP channels: Molecular sensors for temperature detection.Castillo K, Díaz-Franulic I, Canan J,  Gonzalez-Nilo F , Latorre R.Physical Biology. 2017. DOI: 10.1088/1478-3975/aa9a6f
110Penicillium purpurogenum produces a novel endo-1,5-arabinanase, active on debranched arabinan, short arabinooligosaccharides and on the artificial substrate p-nitrophenyl arabinofuranoside.Vilches F, Ravanal MC, Bravo-Moraga F,  Gonzalez-Nilo D , Eyzaguirre J.Carbohydrate Research. 2017. DOI: 10.1016/j.carres.2017.11.014.
104Structure and application of antifreeze proteins from Antarctic bacteria.Munoz, Patricio A.; Marquez, Sebastian L.; Gonzalez-Nilo, Fernando D .; et ál.. Algal Reseach. 2017. DOI: 10.1186/s12934-017-0737-2
98Molecular determinants for cyclooligosaccharide-based nanoparticle-mediated effective siRNA transfectionManzanares, Dario; Araya-Duran, Ingrid; Gallego-Yerga, Laura; Jativa, Pablo; Marquez-Miranda, Valeria; Canan, Jonathan; Jimenez Blanco, Jose Luis; Ortiz Mellet, Carmen;  Gonzalez-Nilo, Fernando ; Garcia Fernandez, Jose Manuel; Cena, Valentin. NANOMEDICINE. 2017. DOI: 10.2217/nnm-2017-0123
97Increasing the intracellular isoprenoid pool in Saccharomyces cerevisiae by structural fine-tuning of a bifunctional farnesyl diphosphate synthaseRubat, Sebastian, Varas, Ignacio, Sepulveda, Romina, Almonacid, Daniel, Gonzalez-Nilo, Fernando , Agosin, Eduardo. FEMS Yeast Research. 2017. DOI: 10.1093/femsyr/fox032
86Structural analysis of binding functionality of folic acid-PEG dendrimers against folate receptor.Sampogna-Mireles, D.; Araya-Duran, ID.; Marquez-Miranda, V.; Valencia-Gallegos, JA. Gonzalez-Nilo, FD .Journal of Molecular Graphics & Modelling. 2017. DOI: 10.1016/j.jmgm.2017.01.004
85The complex of PAMAM-OH dendrimer with Angiotensin (1–7) prevented the disuse-induced skeletal muscle atrophy in mice.Marquez-Miranda, V.; Abrigo, J.; Rivera, JC.; Araya-Duran, I.; Aravena, J; Simon, F.; Pacheco, N.; Gonzalez-Nilo, FD ., Cabello-Verrugio, C.International Journal of Nanomedicine. 2017. DOI: 10.2147/IJN.S125521
84Intracellular trafficking and cellular uptake mechanism of PHBV nanoparticles for targeted delivery in epithelial cell lines.Penaloza, JP.; Marquez-Miranda, V.; Cabana-Brunod, M.; Reyes-Ramirez, R.; Llancalahuen, FM.; Vilos, C.; Maldonado-Biermann, F.; Velasquez, LA.; Fuentes, JA.; Gonzalez-Nilo, FD. ; Rodriguez-Diaz, M.; Otero, C.Journal of Nanobiotechnology. 2017. DOI: 10.1186/s12951-016-0241-6
83Molecular Determinants of BK Channel Functional Diversity and Functioning.Latorre R, Castillo K, Carrasquel-Ursulaez W, Sepulveda RV, Gonzalez-Nilo F , Gonzalez C, Alvarez O. Physiological Reviews. 2017. DOI: 10.1152/physrev.00001.2016


65beta 1-subunit-induced structural rearrangements of the Ca2+- and voltage-activated K+ (BK) channelCastillo JP., Sánchez-Rodríguez JE., Hyde HC., Zaelzer CA., Aguayo D., Sepúlveda RV., Luk LY., Kent SB., Gonzalez-Nilo FD., Bezanilla F., Latorre R.Proceedings of the National Academy of the Sciences of the United States of America. 2016. DOI: 10.1073/pnas.1606381113.
64Putative binding mode of Escherichia coli exopolyphosphatase and polyphosphates based on a hybrid in silico/biochemical approach.
Boetsch C., Aguayo-Villegas DR., Gonzalez-Nilo FD., Lisa ÁT., Beassoni PR.
Archives of Biochemistry Biophysics. 2016. DOI: 10.1016/
63Docking and Molecular Dynamics of Steviol Glycoside-Human Bitter Receptor InteractionsAcevedo, Waldo; Gonzalez-Nilo, Fernando; Agosin, Eduardo.Journal of Agricultural and Food Chemistry. 2016. DOI: 10.1021/acs.jafc.6b02840.
62Structure-Driven Pharmacology of Transient Receptor Potential Channel Vanilloid 1Diaz-Franulic, Ignacio; Caceres-Molina, Javier; Sepulveda, Romina V.; Gonzalez-Nilo, Fernando; Latorre, Ramon.
Molecular Pharmacology. 2016. DOI: 10.1124/mol.116.104430.
61Mechanistic Studies on the Self-Assembly of PLGA Patchy Particles and Their Potential Applications in Biomedical ImagingC. Salvador-Morales, Binal Brahmbhatt, V. Márquez-Miranda, I. Araya-Duran, J. Canan, F. Gonzalez-Nilo, C. Vilos,  J. Cebral, F. Mut, R. Lohner, B. Leong, G. Sundaresan, and J. Zweit.Langmuir. 2016. DOI: 10.1021/acs.langmuir.6b02177.
57Location of TEMPO derivatives in micelles: subtle effect of the probe orientation
Aliaga, Carolina; Bravo-Moraga, Felipe; Gonzalez-Nilo, Danilo; Marquez, Sebastian; Luehr, Susan; Mena, Geraldine; Caroli Rezende, Marcos.Food Chemistry. 2016. DOI: 10.1016/j.foodchem.2015.07.036
38Mechanistic Studies on the Self-Assembly of PLGA Patchy Particles and Their Potential Applications in Biomedical ImagingSalvador-Morales, C.; Brahmbhatt, B.; Marquez-Miranda, V.; Araya-Duran, I.; Canan, J.; Gonzalez-Nilo, F.; Vilos, C.; Cebral, J.; Mut, F.; Lohner, R.; Leong, B.; Sundaresan, G.; Zweit, J.LANGMUIR. DOI: 10.1021/acs.langmuir.6b02177.


28Nano-Detoxification of Organophosphate Agents by PAMAM DerivativesEsteban Durán-Lara; Fabian Ávila-Salas; Sebastian Galaz; Amalraj John; Adolfo Marican; Margarita Gutiérrez; Fabiane M. Nachtigall; Fernando D. Gonzalez-Nilo and Leonardo S. Santos. Journal of the Brazilian Chemical Society. 2015. DOI: 10.5935/0103-5053.20150013
27Synthesis, Biological Evaluation, and Molecular Simulation of Chalcones and Aurones as Selective MAO-B InhibitorsMorales-Camilo N, Salas CO, Sanhueza C, Espinosa-Bustos C, Sepúlveda-Boza S, Reyes-Parada M, Gonzalez-Nilo F, Caroli-Rezende M,Fierro A.Chemical Biology & Drug Design. 2015. DOI: 10.1111/cbdd.12458
25Development of a nanoparticle-based oral vaccine for Atlantic salmon against ISAV using an alphavirus replicon as adjuvantRivas-Aravena A, Fuentes Y, Cartagena J, Brito T, Poggio V, La Torre J, Mendoza H, Gonzalez-Nilo F, Sandino AM, Spencer E.Fish & Shellfish Inmunology. 2015. DOI: 10.1016/j.fsi.2015.03.033.


10The C-Terminal Regions Have an Important Role in the Activity of the Ferroxidase Center and the Stability of Chlorobium tepidum FerritinBrito, Cristian; Matias, Catalina; Gonzalez-Nilo, Fernando D.Protein Journal. 2014. DOI: 10.1007/s10930-014-9552-3


6Penicillium purpurogenum produces two GH family 43 enzymes with beta-xylosidase activity, one monofunctional and the other bifunctional: Biochemical and structural analyses explain the differenceCristina Ravanal, Maria; Alegria-Arcos, Melissa; Danilo Gonzalez-Nilo, Fernando.Archives of Biochemistry and Biophysics. 2013. DOI: 10.1016/
5Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics SimulationsComer, Jeffrey; Chipot, Christophe; Gonzalez-Nilo, Fernando D.Journal of Chemical Theory and Computation. 2013. DOI: 10.1021/ct300867e.


2Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force FieldAguayo, Daniel; Gonzalez-Nilo, Fernando D.; Chipot, Christophe.Journal of Chemical Theory and Computation. 2012. DOI: 10.1021/ct200849k.
1Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force FieldAguayo, Daniel; Gonzalez-Nilo, Fernando D.; Chipot, Christophe.Journal of Chemical Theory and Computation. 2012. DOI: 10.1021/ct200849k