Manuel A. Llanos, Ph.D.

I like molecules 💊 👨‍🔬 🧉 🇦🇷
Drug discovery | Computational Biophysics

[23] I. Taneja, M. A. Llanos, M. L. Fernández-Quintero, J. R. Loeffler, M. Holcomb, A. B. Ward, S. Forli. “AlphaFold-RandomWalk and AlphaFold-Ensemble: Sampling Alternative Protein Conformations with Perturbed Versions of AlphaFold.” Journal of Chemical Information and Modeling. 2026, 66, 152–166. https://doi.org/10.1021/acs.jcim.5c02004

[22] W. Li*, Q. Wei*, P. Governa*, M. A. Llanos*, T.-Y. Chiu, J. M. Wozniak, A. M. Jadhav, C. Gathmann, M. Holcomb, J. Cravatt, A. Dongre, M. L. Huang, S. Forli, C. G. Parker. “Post-Translational Modifications Remodel Proteome-Wide Ligandability.” Nature Chemical Biology. 2025. https://doi.org/10.1101/2025.07.31.667978 (bioRxiv preprint) * Equal contribution

[21] D. Santos-Martins, Y. He, J. Eberhardt, P. Sharma, N. Bruciaferri, M. Holcomb, M. A. Llanos, et al., S. Forli. “Meeko: Molecule Parametrization and Software Interoperability for Docking and Beyond.” Journal of Chemical Information and Modeling. 2025, 65, 13045–13050. https://doi.org/10.1021/acs.jcim.5c02271

[20] M. Holcomb, M. A. Llanos, A. Hansel-Harris, S. Forli. “Structure-Based Rational Design of Covalent Probes.” Communications Chemistry (Nature Portfolio). 2025, 8:242. https://doi.org/10.1038/s42004-025-01606-y — 2025 Editors’ Highlights

[19] S. Wang, E. C. Woods, J. Jo, J. Zhu, A. Hansel-Harris, M. Holcomb, M. A. Llanos, N. J. Pedowitz, T. Upadhyay, J. Bennett, M. Fellner, K. W. Park, A. Zhang, T. A. Valdez, S. Forli, A. I. Chan, C. N. Cunningham, M. Bogyo. “An mRNA Display Approach for Covalent Targeting of a Staphylococcus aureus Virulence Factor.” Journal of the American Chemical Society. 2025, 147, 8312–8325. https://doi.org/10.1021/jacs.4c15713

[18] D. N. Prada Gori, E. M. Barrionuevo, L. N. Alberca, M. L. Sbaraglini, M. A. Llanos, S. Giovannuzzi, F. Carta, M. I. Marchetto, C. T. Supuran, C. D. Alba Soto, L. Gavernet, A. Talevi. “Discovery of Trypanosoma cruzi Carbonic Anhydrase Inhibitors by a Combination of Ligand- and Structure-Based Virtual Screening.” Journal of Chemical Information and Modeling. 2025, 65, 4980–4993. https://doi.org/10.1021/acs.jcim.5c00279

[17] N. Bruciaferri, J. Eberhardt, M. A. Llanos, J. R. Loeffler, M. Holcomb, M. L. Fernandez-Quintero, D. Santos-Martins, A. B. Ward, S. Forli. “CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis.” Journal of Chemical Information and Modeling. 2024, 64, 8227–8235. https://doi.org/10.1021/acs.jcim.4c01398

[16] E. M. Barrionuevo, E. Peralta, A. Manzur De Nardi, J. Monat, M. J. Fallico, M. A. Llanos, L. Gavernet, E. R. Mustafá, P. Martin, A. Talevi. “In Silico Screening Identification of Fatty Acids and Fatty Acid Derivatives with Antiseizure Activity: In Vitro and In Vivo Validation.” Pharmaceutics. 2024, 16, 996. https://doi.org/10.3390/pharmaceutics16080996

[15] M. A. Llanos, N. Enrique, V. Esteban-López, S. Scioli-Montoto, D. Sánchez-Benito, M. E. Ruiz, V. Milesi, D. E. López, A. Talevi, P. Martín, L. Gavernet. “A Combined Ligand- and Structure-Based Virtual Screening To Identify Novel NaV1.2 Blockers: In Vitro Patch Clamp Validation and In Vivo Anticonvulsant Activity.” Journal of Chemical Information and Modeling. 2023, 63, 7083–7096. https://doi.org/10.1021/acs.jcim.3c00645

[14] S. M. Ruatta, D. N. Prada Gori, M. Fló Díaz, F. Lorenzelli, K. Perelmuter, L. N. Alberca, C. L. Bellera, A. Medeiros, G. V. López, M. Ingold, …, M. A. Llanos, …, A. Talevi, M. A. Comini. “Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro.” Frontiers in Pharmacology. 2023. https://doi.org/10.3389/fphar.2023.1193282

[13] M. A. Llanos, N. Enrique, M. L. Sbaraglini, F. M. Garofalo, A. Talevi, L. Gavernet, P. Martín. “Structure-Based Virtual Screening Identifies Novobiocin, Montelukast, and Cinnarizine as TRPV1 Modulators with Anticonvulsant Activity In Vivo.” Journal of Chemical Information and Modeling. 2022. https://doi.org/10.1021/acs.jcim.2c00312

[12] M. A. Llanos, C. Ventura, P. Martín, N. Enrique, J. I. Felice, L. Gavernet, V. Milesi. “Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect.” Journal of Chemical Information and Modeling. 2022, 62, 3200–3212. https://doi.org/10.1021/acs.jcim.1c01396

[11] M. A. Llanos, L. N. Alberca, S. C. Vilchez Larrea, A. C. Schoijet, G. D. Alonso, C. L. Bellera, L. Gavernet, A. Talevi. “Homology Modeling and Molecular Dynamics Simulations of Trypanosoma cruzi Phosphodiesterase b1.” Chemistry & Biodiversity. 2022, 19, e202100712. https://doi.org/10.1002/cbdv.202100712

[10] M. A. Llanos, L. N. Alberca, M. D. Ruiz, M. L. Sbaraglini, C. Miranda, A. Pino-Martinez, L. Fraccaroli, C. Carrillo, C. D. Alba Soto, L. Gavernet, A. Talevi. “A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity.” Journal of Computer-Aided Molecular Design. 2022. https://doi.org/10.1007/s10822-022-00491-0

[9] M. E. Gantner, D. N. Prada Gori, M. A. Llanos, A. Talevi, A. Angeli, D. Vullo, C. T. Supuran, L. Gavernet. “Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening.” Journal of Chemical Information and Modeling. 2022. https://doi.org/10.1021/acs.jcim.2c00910

[8] D. N. Prada Gori, L. N. Alberca, S. Rodriguez, J. I. Alice, M. A. Llanos, C. L. Bellera, A. Talevi. “LIDeB Tools: A Latin American resource of freely available, open-source cheminformatics apps.” Artificial Intelligence in the Life Sciences. 2022, 2, 100049. https://doi.org/10.1016/j.ailsci.2022.100049

[7] D. N. Prada Gori, M. A. Llanos, C. L. Bellera, A. Talevi, L. N. Alberca. “iRaPCA and SOMoC: Development and Validation of Web Applications for Clustering of Small Molecules.” Journal of Chemical Information and Modeling. 2022. https://doi.org/10.1021/acs.jcim.2c00265

[6] C. L. Bellera, M. A. Llanos, M. E. Gantner, S. Rodriguez, L. Gavernet, M. Comini, A. Talevi. “Can drug repurposing strategies be the solution to the COVID-19 crisis?” Expert Opinion on Drug Discovery. 2021, 16, 605–612. https://doi.org/10.1080/17460441.2021.1863943

[5] M. A. Llanos, M. E. Gantner, S. Rodriguez, L. N. Alberca, C. L. Bellera, A. Talevi, L. Gavernet. “Strengths and Weaknesses of Docking Simulations in the SARS-CoV-2 Era: the Main Protease (Mpro) Case Study.” Journal of Chemical Information and Modeling. 2021. https://doi.org/10.1021/acs.jcim.1c00404

[4] M. E. Gantner, M. A. Llanos, F. M. Garofalo, M. L. Villalba, L. Gavernet. “Computational and Synthetic Target-based Approaches to the Discovery of Novel Anticonvulsant Compounds.” Current Medicinal Chemistry. 2021, 28. https://doi.org/10.2174/0929867328666210506161234

[3] M. A. Llanos, M. L. Sbaraglini, M. L. Villalba, M. D. Ruiz, C. Carrillo, C. Alba Soto, A. Talevi, A. Angeli, S. Parkkila, C. T. Supuran, L. Gavernet. “A structure-based approach towards the identification of novel antichagasic compounds: Trypanosoma cruzi carbonic anhydrase inhibitors.” Journal of Enzyme Inhibition and Medicinal Chemistry. 2020, 35, 21–30. https://doi.org/10.1080/14756366.2019.1677638

[2] M. A. Castro, M. A. Llanos, B. E. Rodenak-Kladniew, L. Gavernet, M. E. Galle, R. Crespo. “Citrus reticulata peel oil as an antiatherogenic agent: Hypolipogenic effect in hepatic cells, lipid storage decrease in foam cells, and prevention of LDL oxidation.” Nutrition, Metabolism and Cardiovascular Diseases. 2020, 30, 1590–1599. https://doi.org/10.1016/j.numecd.2020.04.033

[1] A. I. Sulatskaya, S. A. Bondarev, M. I. Sulatsky, N. P. Trubitsina, M. V. Belousov, G. A. Zhouravleva, M. A. Llanos, A. V. Kajava, I. M. Kuznetsova, K. K. Turoverov. “Point mutations affecting yeast prion propagation change the structure of its amyloid fibrils.” Journal of Molecular Liquids. 2020, 314, 113618. https://doi.org/10.1016/j.molliq.2020.113618