Publications 2015

1. Czarnecki, W.M.; Podlewska, S.; Bojarski, A.J. Extremely Randomized Machine Learning Methods for Compound Activity Prediction. Molecules, 201511, 20107-20117 (http://www.ncbi.nlm.nih.gov/pubmed/26569196).

2. Kurczyk, A.; Warszycki, D.; Musiol, R.; Kafel, R.; Bojarski, A.J.; Polanski, J. Ligand-Based Virtual Screening in a Search for Novel Anti-HIV-1 Chemotypes. J. Chem. Inf. Model. 201510, 2168-2177 (http://www.ncbi.nlm.nih.gov/pubmed/26431196).

3. Deau, E.; Robin, E.; Voinea, R.; Percina, N.; Satała, G.; Finaru, A.L.; Chartier, A.; Tamagnan, G.; Alagille, D.; Bojarski, A.J.; Morisset-Lopez, S.; Suzenet, F.; Guillaumet, G. Rational Design, Pharmacomodulation, and Synthesis of Dual 5-Hydroxytryptamine 7 (5-HT7)/5-Hydroxytryptamine 2A (5-HT2A) Receptor Antagonists and Evaluation by [(18)F]-PET Imaging in a Primate Brain. J. Med. Chem. 201520, 8066-8096 (http://www.ncbi.nlm.nih.gov/pubmed/26348247)

4. Czarnecki, W.M., Jastrzebski, S., Sieradzki, I., Podlewska, S. Active Learning of Compounds Activity – Towards Scientifically Sound Simulation of Drug Candidates Identification. Proceedings of 2nd Workshop on Machine Learning in Life Sciences, 2015, ISBN: 978-83-943803-0-4, 40–51 (http://issuu.com/paweksieniewicz/docs/mlls_2015_proceedings/3?e=6403122/31441344).

5. Czarnecki, W. M. Rataj, K. Compounds Activity Prediction in Large Imbalanced Datasets with Substructural Relations Fingerprint and EEM. IEEE Trustcom/BigDataSE/ISPA, 2015, 2, 192–197 (http://wojciechczarnecki.com/pdfs/preprint-eem-chem.pdf)

6. Staroń, J.; Boroń, B.; Karcz, D.; Szczygieł, M.; Fiedor, L. Recent progress in chemical modifications of chlorophylls and bacteriochlorophylls for the application in photodynamic therapy. Curr. Med. Chem. 201522, 3054-3074 (http://www.ncbi.nlm.nih.gov/pubmed/26282940).

7. Grychowska, K.; Masurier, N.; Verdie, P. Satała, G.; Bojarski, A.J.; Martinez, J.; Pawłowski, M.; Subra, G.; Zajdel, P. Solid-Supported Synthesis and 5-HT7/5-HT1A Receptor Affinity of Arylpiperazinylbutyl Derivatives of 4,5-dihydro-1,2,4-triazine-6-(1H)-one. Chem. Biol. Drug. Des. 201586, 697-703 (http://www.ncbi.nlm.nih.gov/pubmed/25684690).

8. Canale, V.; Kurczab, R.; Partyka, A.; Satala, G.; Witek, J.; Jastrzebska-Wiesek, M.; Pawlowski, M.; Bojarski, A. J.; Wesolowska, A.; Zajdel, P. Towards novel 5-HT7 versus 5-HT1A receptor ligands among LCAPs with cyclic amino acid amide fragments: Design, synthesis, and antidepressant properties. Part II. Eur. J Med. Chem. 2015, 92, 202-211 (http://www.ncbi.nlm.nih.gov/pubmed/25555143).

9. Zmudzki, P.; Satala, G.; Chłoń-Rzepa, G.; Bojarski, A. J.; Popik, P.; Zajdel, P. N-(4-Arylpiperazinoalkyl) acetamide derivatives of 1,3- and 3,7-dimethyl-1H-purine-2,6(3H,7H)-diones and their 5-HT6, 5-HT7, and D2 receptors affinity. Heterocycl. Comm. 2015, 21, 13-18 (http://www.degruyter.com/view/j/hc.2015.21.issue-1/hc-2014-0200/hc-2014-0200.xml).

10. Waszkielewicz, A. M.; Pytka, K.; Rapacz, A.; Welna, E.; Jarzyna, M.; Satala, G.; Bojarski, A.; Sapa, J.; Zmudzki, P.; Filipek, B.; Marona, H. Synthesis and Evaluation of Antidepressant-like Activity of Some 4-Substituted 1-(2-methoxyphenyl)Piperazine Derivatives. Chem. Biol. Drug Des. 2015, 85, 326-335 (http://www.ncbi.nlm.nih.gov/pubmed/25048712).

11. Staroń, J.; Warszycki, D.; Kalinowska-Tłuścik, J.; Satała, G.; Bojarski, A. J. Rational design of 5-HT6R ligands using a bioisosteric strategy: synthesis, biological evaluation and molecular modelling. RSC Advances 2015, 5, 25806-25815 (http://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra00054h#!divAbstract).

12. Zajdel, P.; Canale, V.; Partyka, A.; Marciniec, K.; Kurczab, R.; Satala, G. ; Siwek, A.; Jastrzebska-Wiesek, M.; Wesolowska, A.; Kos, T. ; Popik, P.; Bojarski, A. J. Arylsulfonamide derivatives of (aryloxy)ethylpiperidines as 5-HT7 receptor antagonists and their psychotropic properties. Med. Chem. Commun. 2015, 6, 2172-2177  (http://pubs.rsc.org/en/content/articlelanding/2015/md/c5md00166h#!divAbstract).

13. Czarnecki, W. M.; Podlewska, S.; Bojarski, A. J. Robust optimization of SVM hyperparameters in the classification of bioactive compounds. J. Cheminform. 2015, 7:38, 1-15 (http://www.jcheminf.com/content/7/1/38).

14. Lewkowski, J.; Jóźwiak, A.; Tokarz, P.; Zagórski, P. M.; Hamera, R.; Cal, D.; Satala, G.; Bojarski, A. J. Synthesis of Some Aminophosphonates Bearing N-(Fluorophenyl)-piperazynyl Moiety and Their Activity toward Serotonin Receptors. Heteroatom Chem. 2015, 26, 290-298 (http://onlinelibrary.wiley.com/doi/10.1002/hc.21259/abstract).

15. Chilmonczyk, Z.; Bojarski, A.J.; Pilc, A.; Sylte, I. Functional Selectivity and Antidepressant Activity of Serotonin 1A Receptor Ligands. Int. J. Mol. Sci., 2015, 16, 18474-18506 (http://www.ncbi.nlm.nih.gov/pubmed/26262615).

16. Matys, A.; Podlewska, S.; Witek, K.; Witek, J.; Bojarski, A.J.; Schabikowski, J.; Otrębska-Machaj, E.; Latacz, G.; Szymańska, E.; Kieć-Kononowicz, K.; Molnar, J.; Amaral, L.; Handzlik, J. Imidazolidine-4-one derivatives in the search for novel chemosensitizers of Staphylococcus aureus MRSA: Synthesis, biological evaluation and molecular modeling studies. Eur. J. Med. Chem. 2015, 101, 313-325 (http://www.ncbi.nlm.nih.gov/pubmed/26160112)

17. Gomółka, A.; Ciesielska, A.; Wróbel, M.Z.; Chodkowski, A.; Kleps, J.; Dawidowski, M.; Siwek, A.; Wolak, M.; Stachowicz, K.; Sławińska, A.; Nowak, G.; Satała, G; Bojarski, A.J.; Belka, M.; Ulenberg, S.; Bączek, T.; Skowronek, P.; Turło, J.; Herold, F. Novel 4-aryl-pyrido[1,2-c]pyrimidines with dual SSRI and 5-HT1A activity. Part 5. Eur. J. Med.Chem. 2015, 98, 221-236 (http://www.ncbi.nlm.nih.gov/pubmed/26043160)

18. Warszycki, D.; Mordalski, S.; Staroń, J.; Bojarski, A.J. Bioisosteric matrices for ligands of serotonin receptors.  ChemMedChem. 2015 10, 601-605. (http://www.ncbi.nlm.nih.gov/pubmed/25772514)

19. Żmudzki, P.; Chłoń-Rzepa, G.; Bojarski, A.J.; Zygmunt, M.; Kazek, G.; Mordyl, B.; Pawłowski M. Structure-5-HT receptor affinity relationship in a new group of 7-arylpiperazynylalkyl and 7-tetrahydroisoquinolinylalkyl derivatives of 8-amino-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione. Arch Pharm (Weinheim). 2015, 348, 229-41. (http://www.ncbi.nlm.nih.gov/pubmed/25773578)

20. Chłoń-Rzepa, G.; Zagórska, A.; Bucki, A.; Kołaczkowski, M.; Pawłowski, M.; Satała, G.; Bojarski, A.J.; Partyka, A.; Wesołowska, A.; Pękala, E.; Słoczyńska, K. New arylpiperazinylalkyl derivatives of 8-alkoxy-purine-2,6-dione and dihydro[1,3]oxazolo[2,3-f]purinedione targeting the serotonin 5-HT1A /5-HT2A /5-HT7 and dopamine D2 receptors. Arch Pharm (Weinheim). 2015, 348, 242-253. (http://www.ncbi.nlm.nih.gov/pubmed/25773907)

21. Smusz, S.; Mordalski, S.; Witek, J.; Rataj, K.; Kafel, R.; Bojarski, A.J.  Multi-Step Protocol for Automatic Evaluation of Docking Results Based on Machine Learning Methods-A Case Study of Serotonin Receptors 5-HT6 and 5-HT7. J. Chem. Inf. Model. 2015, 55, 823-832. (http://www.ncbi.nlm.nih.gov/pubmed/25806997)

22. Smusz, S.; Kurczab, R.; Satała, G.; Bojarski, A. J. Fingerprint-based consensus virtual screening towards structurally new 5-HT6R ligands. Bioorg Med Chem Lett. 2015, 25, 1827-1830 (http://www.ncbi.nlm.nih.gov/pubmed/25866241)

23. Czopek, A.; Kołaczkowski, M.; Bucki, A.; Byrtus, H.; Pawłowski, M.; Kazek, G.; Bojarski, A.J.; Piaskowska, A.; Kalinowska-Tłuścik, J.; Partyka, A.; Wesołowska, A. Novel spirohydantoin derivative as a potent multireceptor-active antipsychotic and antidepressant agent. Bioorg Med Chem. 2015, 13, 3436-47 (http://www.ncbi.nlm.nih.gov/pubmed/25936259)

24. Mordalski, S.; Witek, J.; Smusz, S.; Rataj, K.; Bojarski, A.J. Multiple conformational states in retrospective virtual screening – homology models vs. crystal structures: beta-2 adrenergic receptor case study. J. Cheminform. 2015, 9, 7:13.  (http://www.ncbi.nlm.nih.gov/pubmed/25949744)

25. Zagórska, A.; Kołaczkowski, M.; Bucki. A.; Siwek, A.; Kazek, G.; Satała, G.; Bojarski, A.J.; Partyka, A.; Wesołowska, A.; Pawłowski, M. Structure-activity relationships and molecular studies of novel arylpiperazinylalkyl purine-2,4-diones and purine-2,4,8-triones with antidepressant and anxiolytic-like activity. Eur J Med Chem. 2015,  97, 142-154 (http://www.ncbi.nlm.nih.gov/pubmed/25965777).

26. Isberg, V.; de Graaf, C.; Bortolato, A.; Cherezov, V. ; Katritch, V.; Marshall, F. H.; Mordalski, S.; Pin, J.;  Stevens, R. C.; Vriend, G.; Gloriam, D. E. Generic GPCR residue numbers – aligning topology maps while minding the gaps. Trends Pharmacol. Sci. 2015, 36, 22-31 (http://www.ncbi.nlm.nih.gov/pubmed/25541108).

27. Partyka, A.; Chlon-Rzepa, G.; Wasik, A.; Jastrzebska-Wiesek, M.; Bucki, A.; Kolaczkowski, M.; Satala, G.; Bojarski, A. J. ; Wesołowska, A. Antidepressant- and anxiolytic-like activity of 7-phenylpiperazinylalkyl-1,3-dimethyl-purine-2,6-dione derivatives with diversified 5-HT1A receptor functional profile. Bioorg. Med. Chem. 2015, 23, 212-221 (http://www.ncbi.nlm.nih.gov/pubmed/25435254).

28. Fidom, K.; Isberg, V.; Hauser, A. S.; Mordalski, S.; Lehto, T.; Bojarski, A. J.; Gloriam, D. E. A new crystal structure fragment-based pharmacophore method for G protein-coupled receptors. Methods 2015, 71, 104-112 (http://www.ncbi.nlm.nih.gov/pubmed/25286328).

29. Smusz, S.; Czarnecki, W. M.; Warszycki, D.; Bojarski, A. J. Exploiting uncertainty measures in compounds activity prediction using support vector machines. Bioorg. Med. Chem. Lett. 2015, 25, 100-105 (http://www.ncbi.nlm.nih.gov/pubmed/25466199).