Publications





Vera M. S., Sencanski M., Filipovic N., Santos D., Gasparovic A. C., Saraiva L., Afonso C., Rijo P.,* García-Sosa A. T.* "Activity to Breast Cancer Cell Lines of Different Malignancy and Predicted Interaction with Protein Kinase C Isoforms of Royleanones" International Journal of Molecular Sciences 2020, 20(10):3671 [HTML], [DOI], [PDF]

Dinic J., Efferth T., García-Sosa A. T. et al. "Repurposing Old Drugs to Fight Multidrug Resistant Cancers" Drug Resistance Updates 2020, 52:100713 [HTML], [DOI], [PDF]

Gütschow M. et al. "Breakthroughs in Medicinal Chemistry: New Targets and Mechanisms, New Drugs, New Hopes-7" Molecules 2020, 25(13):2968 [HTML], [DOI], [PDF]

Mansouri K. et al. "CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity" Environmental Health Perspectives 2020, 128(2):027002 [HTML], [DOI], [PDF]

Vanden Eynde J. J., Mangoni A. A., Rautio J., Leprince J., Azuma Y.- T., García-Sosa A. T. et al. "Breakthroughs in Medicinal Chemistry: New Targets and Mechanisms, New Drugs, New Hopes-6" Molecules 2020, 25(1):119 [HTML], [DOI], [PDF]

García-Sosa A. T.* "Benford's Law in Medicinal Chemistry: Implications for Drug Design" Future Medicinal Chemistry 2019, 11(17):2247-2253 [DOI], [HTML], [PDF], [Data]
[Data and Code on GitHub]

Stevanovic S., Sencanski M., Danel M., Menendez C., Belguedj R., Bouraiou A., Nikolic K., Cojean S., Loiseau P. M., Glisic S., Baltas M., García-Sosa, A. T.* "Synthesis, In Silico, and In Vitro Evaluation of Antileishmanial Activity of Oxadiazoles and Indolizine Containing Compounds Flagged Against Antitargets" Molecules 2019, 24(7):1282 [DOI], [HTML], [PDF]

Alcaro S., Bolognesi M. L., García-Sosa A. T., Rapposelli S. "Editorial: Multitarget Directed Ligands (MTDL) as Challenging Research Tools in Drug Discovery: From Design to Pharmacological Evaluation" Frontiers in Chemistry 2019, 7:71 [HTML], [DOI], [PDF]

Vacas A., Fernandez-Rubio C., Algarabel M., Peña-Guerrero J., Larrea E., Formiga F. R., García-Sosa A. T., Nguewa P. A. "A Novel Serine/Threonine Protein Kinase, 'LmjF.22.0810' from Leishmania major, May Be Involved in the Resistance to Drugs Such as Paromomycin" Biomolecules 2019, 9(11):723 [HTML], [PDF]

Acurcio R. A., Leonardo-Sousa C., García-Sosa A. T., Florindo H. F., Guedes R. C. "Structural Insights and Binding Analysis for Determining the Molecular Bases for Programmed Cell Death Protein Ligand-1 Inhibition" MedChemComm 2019, 10:1810-1818 [DOI], [HTML], [PDF]

Yosipof A., Guedes R. C., García-Sosa A. T.* "Data Mining and Machine Learning Models for Predicting Drug Likeness and their Disease or Organ Category" Frontiers in Chemistry 2018, 6:162 [DOI], [PDF]
Highlighted in the Specialty News
Technology Networks "Data Visualization in Biopharma: Leveraging AI, VR, and MR to Support Drug Discovery"


Borges A., Simões M., Todorovic T. R., Filipovic, N. R., García-Sosa A. T.* "Cobalt Complex with Thiazole_Based Ligand as New Pseudomonas aeruginosa Quorum Quencher, Biofilm Inhibitor, and Virulence Attenuator" Molecules 2018, 23:1385 [DOI], [HTML], [PDF]

Roman B. I., Guedes R. C., Stevens C. V., García-Sosa A. T.* "Recovering Actives in Multiantitarget and Target Design of Analogs of the Myosin II Inhibitor Blebbistatin" Frontiers in Chemistry 2018, 6:179 [DOI], [PDF]

García-Sosa A. T.* "Designing Ligands for Leishmania, Plasmodium, and Aspergillus N-Myristoyl Transferase with Specificity and Antitarget Safe Virtual Libraries" Current Computer-Aided Drug Design 2018, 14(2):131-141 [DOI], [PubMed]

Olsson M., García-Sosa A. T., Ryde U. "Binding Affinities of the Farnesoid X Receptor in the D3R Grand Challenge 2 Estimated by Free Energy Perturbation and Docking" Journal of Computer-Aided Molecular Design 2018, 32(1):211-224 [DOI], [HTML], [PDF]

Piir G., Kahn I., García-Sosa A. T., Sild S., Ahte P., Maran U. "Best Practices for QSAR Model Reporting: Physical and Chemical Properties, Ecotoxicity, Environmental Fate, Human Health, and Toxicokinetics Endpoints" Environmental Health Perspectives 2018, 126(12):126001 [DOI], [PDF]

Ivanova L., Tammiku-Taul J., García-Sosa A. T., Sidorova Y., Saarma M., Karelson M. "Molecular Dynamics Simulations of the Interactions between Glial Cell Line_Derived Neurotrophic Factor Family Receptor GFRalpha1 and Small_Molecule Ligands" ACS Omega 2018, 3(9):11407-11414 [DOI], [PDF]

Elshaflu H.; Todorovic T.; Nikolic M.; Lolic A.; Visnjevac A.; Hagenow S.; Padrón J. M.; García-Sosa A. T., Djordjevic I.; Grubisic S.; Stark H.; Filipovic N. "Selenazolyl Hydrazones as Novel Selective MAO Inhibitors with Antiproliferative and Antioxidant Activities: Experimental and In Silico Studies" Frontiers in Chemistry 2018, 6:247 [DOI], [PDF]

Viira B., García-Sosa A. T., Maran U. "Chemical Structure and Correlation Analysis of HIV 1 NNRT and NRT Inhibitors and Database Curated, Published Inhibition Constants with Chemical Structure in Diverse Datasets" Journal of Molecular Graphics and Modelling 2017, 76:205-223 [DOI], [PDF]

Glisic S., Sencanski M., Perovic V., Stevanovic S., García-Sosa A. T.* "Arginase Flavonoid Antileishmanial In Silico Inhibitors Flagged Against Antitargets" Molecules 2016, 21(5):589 [HTML], [DOI], [PDF]

Jakobson L., Vaahtera L., Tõldsepp K., Nuhkat M., Wang C., Wang Y.-S., Hõrak H., Valk E., Pechter P., Sindarovska Y., Tang J., Xiao C., Xu Y., Talas U. G., García-Sosa A. T., Kangasjärvi S., Maran U., Remm M., Roelfsema M. R. G., Hu H., Kangasjärvi J., Loog M., Schroeder J. I., Kollist H., Brosché M. "Natural Variation in Arabidopsis Cvi-0 Accession Reveals an Important Role of MPK12 in Guard Cell CO2 Signaling" PLoS Biology 2016, 14(12):e2000322 [DOI], [HTML], [PDF]
F1000 Prime Recommended Article
Maurel C: F1000Prime Recommendation of [Jakobson L et al., PLoS Biol 2016 14(12):e2000322]. In F1000Prime, 10 Jan 2017; 10.3410/f.727080912.793526875

Viira B., Selyutina A., García-Sosa A. T., Karonen M., Sinkkonen J., Merits A., Maran U. "Design, Discovery, Modelling, Synthesis, and Biological Evaluation of Novel and Small, Low Toxicity s-Triazine Derivatives as HIV 1 Nonnucleoside Reverse Transcriptase Inhibitors" Bioorganic & Medicinal Chemistry 2016, 24(11):2519-2529 B.V., A.S., and A.T.G.-S. contributed equally. [DOI], [PDF]

Freimann K., Arukuusk P., Kurrikoff K., Ferreira Vasconcelos L. D., Veiman K. -L., Uusna J., Margus H., García-Sosa A. T., Pooga M., Langel Ü. "Optimization of In Vivo DNA Delivery with NickFect Peptide Vectors" Journal of Controlled Release 2016, 241:134-143 [HTML], [DOI], [PDF]
Selected for Cover Figure and Editorial Comment
By the Journal of Controlled Release


Takkis K., García-Sosa A. T., Sild S. "Virtual Screening for HIV Protease Inhibitors Using a Novel Database Filtering Procedure" Molecular Informatics 2015, 34(6-7):485-492 [DOI], [Abstract], [PDF]

García-Sosa A. T.* "Role of Water Molecules and Hydration Properties in Modelling Ligand-Protein Interaction and Drug Design" Book Chapter, in "In Silico Drug Discovery and Design: Theory, Methods, Challenges and Applications" Cavasotto, C. (Ed.), CRC Press Ltd. 2015 393-410, ISBN 9781482217834, Taylor & Francis, USA.
[HTML]

García-Sosa A.T.* and Maran U., "Improving the Use of Ranking in Virtual Screening against HIV 1 Integrase with Triangular Numbers and Including Ligand Profiling with Antitargets" Journal of Chemical Information and Modeling 2014, 54(11):3172-3185 [DOI], [Abstract] [PDF]

García-Sosa A. T.,* Tulp I., Langel K., Langel Ü. "Peptide_Ligand Binding Modeling of siRNA with Cell_Penetrating Peptides" BioMed Research International 2014, 2014:257040 [DOI], [PDF]

García-Sosa A. T.* "Hydration Properties of Ligands and Drugs in Protein Binding Sites: Tightly_Bound, Bridging Water Molecules and their Effects and Consequences on Molecular Design Strategies" Journal of Chemical Information and Modeling 2013, 53(6):1388-1405 [DOI], [Abstract], [PDF]

García-Sosa A. T.* and Maran U. "Drugs, Nondrugs, and Disease Category Specificity: Organ Effects by Ligand Pharmacology" SAR and QSAR in Environmental Research 2013, 24(4):319-331 [DOI], [HTML], [PDF]

García-Sosa A. T.,* Oja M., Hetényi C., Maran U. "DrugLogit: Logistic Discrimination Between Drugs and Nondrugs Including Disease Specificity by Assigning Probabilities Based on Molecular Properties" Journal of Chemical Information and Modeling 2012, 52(8):2165-2180 [DOI], [Abstract], [PDF]

García-Sosa A. T., Oja M., Hetényi C., Maran U. "Disease Specific Differentiation between Drugs and Nondrugs using Principal Component Analysis of their Molecular Descriptor Space" Molecular Informatics 2012, 31:369-383 [DOI], [HTML], [PDF]

García-Sosa A. T., Maran U., Hetényi C. "Molecular Property Filters Describing Pharmacokinetics and Drug Binding" Current Medicinal Chemistry 2012, 19:1646-1662 [PubMed 22376034], [DOI], [PDF]

García-Sosa A. T.,* Sild S., Takkis K., Maran U. "Combined Approach using Ligand Efficiency, Cross Docking, and Antitarget Hits for Wild-Type and Drug-Resistant Y181C HIV 1 Reverse Transcriptase" Journal of Chemical Information and Modeling 2011, 51(10):2595-2611 [DOI], [HTML], [PDF]

García-Sosa A. T.* and Mancera R. L. "Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand_Protein Complex" Molecular Informatics 2010, 29(8-9):589-600 [DOI], [HTML], [PDF]
'Hot Article in Biochemistry 2011'
Named by Wiley-VCH

García-Sosa A. T.,* Hetényi C., Maran U. "Drug Efficiency Indices for Improvement of Molecular Docking Scoring Functions" Journal of Computational Chemistry 2010, 31(1):174-184 [DOI], [HTML], [PDF]

García-Sosa A. T.*, Sild S., Maran U. "Docking and Virtual Screening Using Distributed Grid Technology" QSAR & Combinatorial Science 2009, 28(8):815-821 [DOI], [HTML], [PDF]

García-Sosa A. T.*, Sild S., Maran U. "Design of Multibinding Site Inhibitors, Ligand Efficiency, and Consensus Screening of Avian Influenza H5N1 Wild_Type Neuraminidase and of the Oseltamivir_Resistant H274Y Variant" Journal of Chemical Information and Modeling 2008, 48:2074-2080 [DOI], [Supp. Info.], [PDF]

Hetényi C., Maran U., García-Sosa A. T., Karelson M. "Structure_Based Calculation of Drug Efficiency Indices" Bioinformatics 2007, 23(20):2678-2685 [HTML], [Suppl. data], [PDF]

García-Sosa A. T.* and Mancera R. L. "The Effect of a Tightly_Bound Water Molecule on Scaffold Diversity in the Computer_Aided De Novo Ligand Design of CDK2 Inhibitors" Journal of Molecular Modeling 2006, 12(4):422-431 [DOI], [PDF]

Park J. G., Sill P. C., Makiyi E. F., Garcia-Sosa A. T., Millard C. B., Schmidt J. J., Pang Y. P. "Serotype_Selective, Small_Molecule Inhibitors of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A" Bioorganic & Medicinal Chemistry 2006, 14:395-408 [DOI], [PDF]

García-Sosa A. T.*, Firth-Clark S., Mancera R. L. "Including Tightly_Bound Water Molecules in De Novo Drug Design: Exemplification Through the In Silico Generation of Poly (ADP Ribose) Polymerase Ligands" Journal of Chemical Information and Modeling 2005, 45:624-633 [DOI], [HTML], [PDF]

Lloyd D. G., García-Sosa A. T., Alberts I. L., Todorov N. P., Mancera R. L. "The Effect of Tightly Bound Water Molecules on the Structural Interpretation of Ligand_Derived Pharmacophore Models" Journal of Computer-Aided Molecular Design 2004, 18:89-100 [metapress], [DOI], [PDF]

García-Sosa A. T.*, Mancera R. L., Dean P. M. "WaterScore: A Novel Method for Distinguishing between Bound and Displaceable Water Molecules in the Crystal Structure of the Binding Site of Protein_Ligand Complexes" Journal of Molecular Modeling 2003, 9(3):172-182 [metapress], [DOI], [PDF]

García-Sosa A. T. and Castro M. "A Density Functional Study of FeO2, FeO2+, and FeO2- " International Journal of Quantum Chemistry 2000, 80(3):307-319 [DOI], [PDF], [TEX]

Ferri N. et al. "New Rac1 inhibitors as potential pharmacological agents for heart failure treatment" WO 2010119050 2010 [HTML], [PDF]

Ferri N. et al. "Preparation of pyrimidinylamine as Rac1 inhibitors for the treatment of heart failure" EP 2241555 2010 [HTML], [PDF]


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Please email me for a reprint of any of my papers, or click on the PDF links above

Reviewer for the peer-reviewed international journals:
ACS Medicinal Chemistry Letters, Antiviral Research, BioFactors, Bioinformatics, Biomolecules, Chemical Science (RSC), ChemMedChem, Chemosphere, Combinatorial Chemistry and High-Throughput Screening, Computer Methods and Programs in Biomedicine, Current Topics in Medicinal Chemistry, Drug Discovery Today, Frontiers in Chemistry: Theoretical and Computational Chemistry, Frontiers in Pharmacology: Experimental Pharmacology and Drug Discovery, Frontiers in Pharmacology: Medicinal and Pharmaceutical Chemistry, Future Medicinal Chemistry, International Journal of Antimicrobial Agents, International Journal of Molecular Sciences, Journal of Biomolecular Structure & Dynamics, Journal of Bionanotechnology, Journal of Chemical Information and Modeling, Journal of Computer-Aided Molecular Design, Journal of Computational Chemistry, Journal of the Mexican Chemical Society, Journal of Molecular Modeling, Journal of Molecular Structure, Medicinal Research Reviews, Molecular Informatics, Molecules MDPI, PLoS ONE, RSC Advances, and Scientific Reports (Nature Publishing Group)

ORCiD: 0000-0003-0542-4446, ResearcherID, Publons

2019 -> Management Committee member, EU COST Action CA17104 New diagnostic and therapeutic tools against multidrug resistant tumors (Stratagem)
2019 -> Management Committee member, EU COST Action CA17129 Catalysing transcriptomics research in cardiovascular disease
2018 -> Scientific Communication Manager, EU CA COST Action CA15135
2017 -> Management Committee member, EU CA COST Action CA16225 Realising the therapeutic potential of novel cardioprotective therapies
2016 -> Management Committee member, EU CA COST Action CA15135 Multi-target paradigm for innovative ligand identification in the drug discovery process (MuTaLig)
2013 -> 2018 Management Committee member, EU COST Action CM1307 Targeted chemotherapy towards diseases caused by endoparasites

Editorial Board Member of the WoS-indexed journals:
2019 -> Molecules
2016 -> Frontiers in Pharmacology, section Experimental Pharmacology and Drug Discovery
2015 -> Frontiers in Chemistry, section Medicinal and Pharmaceutical Chemistry
2014 -> Scientific Reports (Nature Publishing Group)
2013 -> Frontiers in Chemistry, section Theoretical and Computational Chemistry
2013 -> 2017 BioMed Research International
2011 -> Computational and Mathematical Methods in Medicine
2020 -> Molecules, Guest Editor, Issue Machine Learning and Data Science for Rare and Understudied Diseases
2019 -> Biomolecules, Guest Editor, Issue Biomolecular Structure and Drug Design. Advances in Therapy against Neglected Infectious Diseases
2018 -> Frontiers in Chemistry, Guest Associate Editor, Issue Muti-target directed ligands (MTDL) as challenging research tools in drug discovery: from design to pharmacological action

Scientific Evaluator for the Italian Ministry of Education, University, and Research (MIUR)
Scientific Reviewer/Monitor for the EU FET-Open research projects
Scientific Reviewer for the National Science Centre of Poland (NCN)
Reviewer for the Hungarian Scientific Research Fund (OTKA)
Reviewer/Rapporteur for the Executive Agency for Higher Education, Research, Development and Innovation Funding of Romania (UEFISCDI)
2015 -> EU COST Action External Evaluator
Evaluator for Research Projects, University of Parma, Italy

2016 Sentinel of Science award from Publons for being in the top 10% of reviewers in the Biochemistry, Genetics, and Molecular Biology field http://publons.com/community/awards/by-field/#biochemistry-genetics-and-molecular-biology

PhD University of Cambridge, UK
Overseas Research Scholarship Award by the Committee of Chancellors and Vice Chancellors of Universities in the UK
Post-doctoral Fellowship, Mayo Clinic, MN

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