Manuel A. Llanos

A complete list of publications (20) can be found at https://tinyurl.com/3jz28y53. Also, scientific presentations (26) at congresses and international conferences can be found at https://tinyurl.com/5n8njn2a.

Selected publications:

• CosolvKit: a versatile tool for cosolvent MD preparation and analysis. Bruciaferri, Niccolò; Eberhardt, Jerome; Llanos, Manuel; Loeffler, Johannes; Holcomb, Matthew; Fernández-Quintero, Monica; Santos-Martins, Diogo; Ward, Andrew; Forli, Stefano. JCIM, 2024. https://pubs.acs.org/doi/10.1021/acs.jcim.4c01398.
• Structure-Based Virtual Screening Identifies Novobiocin, Montelukast, and Cinnarizine as TRPV1 Modulators with Anticonvulsant Activity In Vivo. Llanos et al., JCIM, 2022. https://doi.org/10.1021/acs.jcim.2c00312.
• A Combined Ligand- and Structure-Based Virtual Screening To Identify Novel NaV1.2 Blockers: In Vitro Patch Clamp Validation and In Vivo Anticonvulsant Activity. Llanos et al., JCIM, 2023. https://doi.org/10.1021/acs.jcim.3c00645.
• Strengths and weaknesses of docking simulations in the SARS-CoV-2 era: the main protease (MPro) case study. Llanos et al., JCIM, 2021. https://doi.org/10.1021/acs.jcim.1c00404.

Publications submitted/in-press: 

• Post-Translational Modifications Remodel Proteome-Wide Ligandability. Weichao Li*; Qijia Wei*; Paolo Governa; Manuel Llanos; Tzu-Yuan Chiu; Jacob M. Wozniak; Appaso M. Jadhav; Clara Gathmann; Matthew Holcomb; Jacob Cravatt; Ashok Dongre; Mia L. Huang; Stefano Forli; Christopher G. Parker. Nature, 2025. Submitted.
• Structure-based rational design of covalent probes. Holcomb, Matthew; Llanos, Manuel; Hansel-Harris, Althea; Forli, Stefano. Nature Communications Chemistry, 2025. In press.

• Center for Antiviral Medicines and Pandemic Preparedness (CAMPP).

Multidisciplinary center with focus on development of antiviral drugs to combat coronaviruses and other viruses with pandemic potential. CAMPP was one of nine NIAID-sponsored Antiviral Drug Discovery (AViDD) Centers for Pathogens of Pandemic Concern. As part of the Core E - Structural Biology and Computational Modeling, we provided support during the hit identification and optimization phases. Funded by NIAID-NIH. https://www.campp.org/

• Target validation and AI-guided identification of Trypanosoma cruzi phosphodiesterase inhibitors for the treatment of Chagas disease.

Project coordinator: Eisai Co., Ltd. - Japan. Funded by Global Health Innovative Technology (GHIT) Fund. This multicentric project aims to validate PDEs as drug targets for Chagas disease and identify selective inhibitors using a computationally-enhanced screening cascade. Our lab provided modelling support during the hit identification phase of the project. https://www.ghitfund.org/investment/portfoliodetail/detail/171

• REpeat protein Function Refinement, Annotation and Classification of Topologies (REFRACT).

Project coordinator: Dr. Silvio Tosatto. Università degli Studi di Padova - Italy. Funded by Marie Skłodowska-Curie Action-RISE action (H2020 EU GA N 823886). International research consortium on Tandem Repeat Proteins. In the context of this project, I completed a six-month research exchange at the Laboratoire de Bioinformatique Structurale et Modélisation Moléculaire (BiSMM) - CNRS - Montpellier, France., under the supervision of Dr. Andrey Kajava. https://refract-rise.eu/

• Drug Discovery Against the Major Protease of SARS-CoV-2 (DaMPro-CoV-2).

Project coordinator: Dr. Marcelo Comini. Institut Pasteur Montevideo – Uruguay. Funded by Institut Pasteur International Network.

Multicentric and multidisciplinary drug discovery project aiming the identification and full characterization of inhibitors of the SARS-CoV-2 cysteine-dependent viral proteases. In this project I provided ligand/structure-based modelling support during the hit identification stage.

• Rational discovery of novel therapeutic agents to treat refractory epilepsy.

Project coordinator: Prof. Dr. Alan Talevi. LIDeB – National University of La Plata. This project sought to discover more efficacious and better-tolerated drugs to treat refractory epilepsy. My doctoral thesis was conducted within the framework of this project and, as a result, I identified three repurposing candidates with proved in vitro activity against TRPV1 and NaV1.2 and anticonvulsant activity in vivo.

Computational Skills:

• Molecular modeling using the Rosetta Suite/AlphaFold.
• Extensive experience in MD simulations of Ion Channels/GPCRs, soluble proteins, and small peptides. Protein-ligand complexes and RBFE (OpenFE).
• Enhanced sampling and conformational dynamics. GaMD, Metadynamics, Steered MD. Markov State modeling.
• Extensive experience in Virtual Screening, combining ligand and structure-based techniques, such as QSAR/QSPR, docking and MD.
• Docking methods development and application within the AutoDock suite.
• Active Learning and exploration of ultra-large chemical libraries.
• Proficient in Python, Linux and Bash scripting. Scientific libraries including RDKit, Scikit-Learn, and PyTorch. Version control Git/GitHub.

Wet lab Experience:

• Electrophysiological recordings of ion channels using the Patch-Clamp technique.
• Organic synthesis and purification of drug standards for public pharmaceutical laboratories.

• Distinguished Graduate Student UNLP 2022

Biological Sciences Graduate Program, College of Exact Sciences. Issued by the National University of La Plata · December 2023.

• Dr. Enrique Herrero Ducloux Award 2023

Best doctoral thesis 2022 in the fields of inorganic chemistry, physical chemistry, theoretical chemistry, and analytical chemistry. Issued by the Argentine Chemical Society · November 2023.

• Tony B. Academic Travel Award

Three time awardee: SLAS2019 Europe Barcelona, Spain; SLAS2019 Washington DC, USA.; SLAS2018 San Diego, CA, USA. Issued by the Society for Laboratory Automation and Screening (SLAS).