- Computational (nano)toxicology

- Consultations and activities on
computational chemistry

- Virtual library screening

- Computer aided molecular design

NanoTox Group

Alfanet OÜ
Jakobi 52, Tartu 51005, Estonia
Kaido Tämm, PhD
e-mail: kaido@nanotox.ee

Fe-doped ZnO nanoparticle toxicity: assessment by a new generation of nanodescriptors

Jaanus Burk, Lauri Sikk, Peeter Burk, Bella Manshian, Stefaan J. Soenen, Janeck Scott-Fordsmand, Tarmo Tamm, Kaido Tämm
Nanoscale, 2018, 10, 21985.  DOI: 10.1039/C8NR05220D.

Parametrization of Nanoparticles: Development of Full-particle Nanodescriptors

Kaido Tämm, Lauri Sikk, Jaanus Burk, Robert Rallo,  Suman Pokhrel, Lutz Mädler, Janeck J Scott-Fordsmand, Peeter Burk, Tarmo Tamm
Nanoscale, 2016, 8, 16243.

• Burk, Jaanus; Adamson, Aiko; Sikk, Lauri; Tämm, Kaido; Pupart, Anni; Burk, Peeter (2020). DFT study of 2,9-bis(1,2,4-triazin-3-yl)-1,10-phenanthroline (BTPhen) and its derivatives complexation with lanthanide series. Computational and Theoretical Chemistry, 1175, 112729.10.1016/j.comptc.2020.112729.
• Liiv, J.; Zekker, Ivar; Zekker; Tämm, K., Rikmann, E. (2020). Greenhouse gases emissions and climate change - beyond mainstream. MOJ Bioorganic & Organic Chemistry, 4 (1), 11−16.10.15406/mojboc.2020.04.00104.
• Afantitis, Antreas; Melagraki, Georgia; Isigonis, Panagiotis; Tsoumanis, Andreas; Varsou, Dimitra Danai; Valsami-Jones, Eugenia; Papadiamantis, Anastasios; Ellis, Laura-Jayne A.; Sarimveis, Haralambos; Doganis, Philip; Karatzas, Pantelis; Tsiros, Periklis; Liampa, Irene; Lobaskin, Vladimir; Greco, Dario; Serra, Angela; Kinaret, Pia Anneli Sofia; Saarimäki, Laura Aliisa; Grafström, Roland; Kohonen, Pekka ... Lynch, Iseult (2020). NanoSolveIT Project: Driving Nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment. Computational and Structural Biotechnology Journal, 18, 583−602.10.1016/j.csbj.2020.02.023.
• Zekker, Ivar; Bhowmick, Gourav Dhar; Priks, Hans; Nath, Dibyojyoty; Rikmann, Ergo; Jaagura, Madis; Tenno, Taavo; Tämm, Kaido; Ghangrekar, Makarand Madhao (2020). ANAMMOX-denitrification biomass in microbial fuel cell to enhance the electricity generation and nitrogen removal efficiency. Biodegradation, dx.doi.org/10.1007/s10532-020-09907-w
• Papadiamantis, Anastasios G.; Jänes, Jaak; Voyiatzis, Evangelos; Sikk, Lauri; Burk, Jaanus; Burk, Peeter; Tsoumanis, Andreas; Ha, My Kieu; Yoon, Tae Hyun; Valsami-Jones, Eugenia; Lynch, Iseult; Melagraki, Georgia; Tämm, Kaido; Afantitis, Antreas (2020). Predicting cytotoxicity of metal oxide nanoparticles using Isalos Analytics platform. Nanomaterials, 10.10.3390/nano10102017.
• Kallip, S.; Oliveira, M.P.; Bastos, AC.; Sikk, L.; Tämm, K. (2019). Inhibition of galvanic corrosion by synergistic corrosion inhibitor combinations. EUROCORR 2019, September 9 – 13, 2019, Sevilla, Spain.. DECHEMA, Gesellschaft für Chemische Technik und Biotechnologie.
• Luhaste, Liisa; Tämm, Kaido; Sikk, Lauri; Pupart, Anni; Toomsalu, Eve; Burk, Peeter (2018). Comparison of prominent methods for computational studies of lanthanoid cation complexation. Proceedings of the Estonian Academy of Sciences, 67 (1), 106−113.10.3176/proc.2018.1.06.
• Burk, J.; Sikk, L.; Burk, P.; Manshian, B.; Soenen, S. J.; Scott-Fordsmand, J. J.; Tamm, T.; Tämm, K. (2018). Fe-doped ZnO nanoparticle toxicity: assessment by a new generation of nanodescriptors. Nanoscale, 10, 21985−21993.10.1039/C8NR05220D.
• Toots, Mart; Ustav, Mart Jr.; Männik, Andres; Mumm, Karl; Tämm, Kaido; Tamm, Tarmo; Ustav, Ene; Ustav, Mart. (2017). Identification of several high-risk HPV inhibitors and drug targets with a novel high-throughput screening assay. PLoS Pathogens, 13 (2), e1006168.10.1371/journal.ppat.1006168.
• Manshian, Bella B.; Pokhrel, Suman; Himmelreich, Uwe; Tämm, Kaido; Sikk, Lauri; Fernández, Alberto; Rallo, Robert; Tamm, Tarmo; Mädler, Lutz; Soenen, Stefaan J. (2017). In Silico Design of Optimal Dissolution Kinetics of Fe-Doped ZnO Nanoparticles Results in Cancer-Specific Toxicity in a Preclinical Rodent Model. Advanced Healthcare Materials, 1601379.10.1002/adhm.201601379.
• Brehm, Martin; Kafka, Alexander; Bamler, Markus; Kühne, Ralph; Schüürmann, Gerrit; Sikk, Lauri; Burk, Jaanus; Burk, Peeter; Tamm, Tarmo; Tämm, Kaido; Pokhrel, Suman; Mädler, Lutz; Kahru, Anne; Aruoja, Villem; Sihtmäe, Mariliis; Scott-Fordsmand, Janeck; Sorensen, Peter B.; Escorihuela, Laura; Roca, Carlos P.; Fernández, Alberto ... (2017). An Integrated Data-Driven Strategy for Safe-by-Design Nanoparticles: The FP7 MODERN Project. In: Lang Tran, Miguel A. Bañares, Robert Rallo (Ed.). Modelling the Toxicity of Nanoparticles (257−301). springer Link.
• Kalvet, I.; Tammiku-Taul, J.; Mäeorg, U.; Tämm, K.; Burk, P.; Sikk, L. (2016). NMR and DFT Study of the Copper(I)-Catalyzed Cycloaddition Reaction: H/D Scrambling of Alkynes and Variable Reaction Order of the Catalyst. ChemCatChem, 8 (10), 1804−1808, 10.1002/cctc.201600176.
• Tämm, K.; Sikk, L.; Burk, J.; Rallo, R.; Pokhrel, S.; Mädler, L.; Scott-Fordsmand, J.J.; Burk, P.; Tamm, T. (2016). Parametrization of nanoparticles: development of full-particle nanodescriptors. Nanoscale, 8, 16243-16250.
• Pillai, G.G.; Mederos, L.; Panda, C.S.; Gronski, A.; Burk, P.; Hall, C.D.; Katritzky, A.R.; Tämm, K.; Karelson, M. (2016). Robust Modeling and Scaffold Hopping: Case Study based on HIV Reverse Transcriptase Inhibitors Type-1 Data. Medicinal Chemistry, x−x, 1573406411666151005110141 [ilmumas].
• Ibrahim, M.A.; Panda, S.S.; Oliferenko, A.; Oliferenko, P.V.; Girgis, A., Elagawany, M.; Küçükbay, F.Z.; Panda, C.S.; Pillai, G.G.; Samir, A.; Tämm, K.; Hall, C.D.; Katritzky, A.R. (2015). Macrocyclic peptidomimetics with antimicrobial activity: synthesis, bioassay, and molecular modeling studies. Organic and Biomolecular Chemistry, 13 (36), 9492−9503, C5OB01400J.
• Kipper, Andi; Kalvet, Iindrek; Tämm, Kaido; Sikk, Lauri; Burk, Peeter; Kõiv, Kuldar; Mäeorg, Uno (2015). Synthesis of Unprotected CH2-Skipped Piperazine-Pyridine Alternating Cycles with Azide End-Group. Heterocycles, 90 (1), 625−630.
• Pillai, Girinath G.; Sikk, Lauri; Tamm, Tarmo; Karelson, Mati; Burk, Peeter; Tamm, Kaido. (2015). Theoretical Modeling of HPV: QSAR and Novodesign with Fragment Approach. Current Computer Aided-Drug Design, 10 (4), 303−314, 1574886309666141126145756 .
• Dobchev, D. A.; Tulp, I.; Karelson, G.; Tamm, T.; Tämm, K.; Karelson, M. (2013). Subchronic Oral and Inhalation Toxicities: a Challenging Attempt for Modeling and Prediction. Molecular Informatics, 32, 793−801, minf.201300033.
• Tämm, K.; Mayeux, C.; Sikk, L.; Gal, J-F.; Burk, P. (2013). Theoretical modeling of sensitivity factors of Bayard-Alpert ionization gauges. International Journal of Mass Spectrometry, 341, 52−58, j.ijms.2013.02.014.
• Karelson, M.; Dobchev, D.A.; Karelson, G.; Tamm, T.; Tämm, K.; Nikonov, A.; Mutso, M.; Merits, A. (2012). Fragment-based development of HCV protease inhibitors for the treatment of hepatitis C. Current Computer-Aided Drug Design, 8 (1), 55−61, 10.2174/157340912799218516.
• Katritzky, A.R.; Stoyanova-Slavova, I.B.; Tämm, K.; Tamm, T.; Karelson, M. (2011). Application of the QSPR Approach to the Boiling Points of Azeotropes. Journal of Physical Chemistry A, 115 (15), 3475−3479, jp104287p.
• Katritzky, A.R.; Kasemets, K.; Slavov, S.; Radzvilovits, M.; Tämm, K.; Karelson, M. (2010). Estimating the toxicities of organic chemicals in activated sludge process. Water Research, 44 (8), 2451−2460, j.watres.2010.01.009.
• Dobchev, D. A.; Mäger, I.; Tulp, I.; Karelson, G.; Tamm, T.; Tämm, T.; Jänes, J.; Langel, Ü.; Karelson, M. (2010). Prediction of Cell-Penetrating Peptides Using Artificial Neural Networks. Current Computer-Aided Drug Design, 6 (2), 79−89.
• Katritzky, A.R.; Radzvilovits, M.; Slavov, S.; Kasemets, K.; Tamm, K.; Karelson, M. (2010). Quantitative structure-activity relationship modeling of bioconcentration factors of polychlorinated biphenyls. Toxicological and Environmental Chemistry, 92 (7), 1233−1247.
• Karelson, M.; Karelson, G.; Tamm, T.; Tulp, I.; Jänes, J.; Tämm, K.; Lomaka, A.; Savchenko, D.; Dobchev, D.A. (2009). QSAR study of pharmacological permeabilities. Arkivoc, 2, 218−238.
• Karelson, M; Dobchev, D; Tamm, T; Tulp, I; Jänes, J; Tämm, K; Lomaka, A; Savchenko, D; Karelson, G (2008). Correlation of Blood-Brain Penetration and Human Serum Albumin Binding with Theoretical Descriptors. Arkivoc, xvi, 38−60.
• Tämm, K.; Burk, P. (2006). QSPR Analysis for Infinite Dilution Activity Coefficients of Organic Compounds. Journal of Molecular Modeling, 12 (4), 417−421.
• Katritzky, A. R.; Dobchev, D. A.; Fara, D. C.; Hur, E.; Tämm, K.; Kurunczi, L.; Karelson, M.; Varnek, A.; Solov'ev, V. P. (2006). Skin Permeation Rate as a Function of Chemical Structure. Journal of Medicinal Chemistry, 49 (11), 3305−3314, jm051031d S0022-2623(05)01031-9 .
• Tulp, I.; Tämm, K.; Burk, P.; Trummal, A.; Koppel, I.A.; Karelson, M.; Maran, U. (2006). The quantum chemical modeling of solvent effect in the QSPR analysis of pKa of phenols in the H2O and DMSO. The 12th International Workshop on Quantitative Structure-Activity Relationships in Environmental Toxicology; 2006; France.
• Tämm, K.; Fara, DC.; Katritzky, AR.; Burk, P.; Karelson, M. (2004). A quantitative structure-property relationship study of lithium cation basicities. Journal of Physical Chemistry A, 108 (21), 4812−4818.
• Katritzky, A.R.; Tämm, K.; Kuanar, M.; Fara, D.C.; Oliferenko, A.; Oliferenko, P.; Huddleston, J.G.; Rogers, R.D. (2004). Aqueous Biphasic Systems. Partitioning of Organic Molecules: A QSPR Treatment. Journal of Chemical Information and Computer Sciences, 44 (1), 136−142.
• Katritzky, AR.; Fara, DC.; Yang, HF.; Tamm, K.; Tamm, T.; Karelson, M. (2004). Quantitative measures of solvent polarity. Chemical Reviews, 104 (1), 175−198.
• Burk, P.; Mölder, U.; Tämm, K. (2001). Gas-Phase Basicities and Proton Affinities of Alkali Metal Oxides and Hydroxides. A Theoretical Study. Proceedings of the Estonian Academy of Sciences. Chemistry, 50 (4), 241−253.