@article {559, title = {Isoxazole-containing 5' mRNA cap analogues as inhibitors of the translation initiation process}, journal = {Bioorganic Chemistry}, volume = {96}, year = {2020}, pages = {103583}, abstract = {Herein we describe a synthesis of new isoxazole-containing 5' mRNA cap analogues via a cycloaddition reaction. The obtained analogues show a capability to inhibit cap-dependent translation in vitro and are characterized by a new binding mode in which an isoxazolic ring, instead of guanine, is involved in the stacking effect. Our study provides valuable information toward designing new compounds that can be potentially used as anticancer therapeutics.}, keywords = {Cap analogue, Cycloaddition reaction, Isoxazol, mRNA, Translation initiation}, issn = {0045-2068}, doi = {https://doi.org/10.1016/j.bioorg.2020.103583}, url = {https://www.sciencedirect.com/science/article/pii/S004520681931819X}, author = {Karolina Piecyk and Maciej Lukaszewicz and Karol Kamel and Maria Janowska and Paulina Pietrow and Sebastian Kmiecik and Marzena Jankowska-Anyszka} } @article {528, title = {Protein-peptide docking: opportunities and challenges}, journal = {Drug Discovery Today}, volume = {23}, year = {2018}, pages = {1530-1537}, abstract = {Peptides have recently attracted much attention as promising drug candidates. Rational design of peptide-derived therapeutics usually requires structural characterization of the underlying protein-peptide interaction. Given that experimental characterization can be difficult, reliable computational tools are needed. In recent years, a variety of approaches have been developed for {\textquoteright}protein-peptide docking{\textquoteright}, that is, predicting the structure of the protein-peptide complex, starting from the protein structure and the peptide sequence, including variable degrees of information about the peptide binding site and/or conformation. In this review, we provide an overview of protein-peptide docking methods and outline their capabilities, limitations, and applications in structure-based drug design. Key challenges are also briefly discussed, such as modeling of large-scale conformational changes upon binding, scoring of predicted models, and optimal inclusion of varied types of experimental data and theoretical predictions into an integrative modeling process.}, doi = {10.1016/j.drudis.2018.05.006}, url = {https://www.sciencedirect.com/science/article/pii/S1359644617305937}, author = {Maciej Pawel Ciemny and Mateusz Kurcinski and Karol Kamel and Andrzej Koli{\'n}ski and Nawsad Alam and Ora Schueler-Furman and Sebastian Kmiecik} } @article {248, title = {Assessment of the free binding energy of 1,25-dihydroxyvitamin D3 and its analogs with the human VDR receptor model}, journal = {Acta Biochimica Polonica}, volume = {59}, year = {2012}, pages = {653-660}, abstract = {1,25-dihydroxyvitamin D(3) has quite significant anticancer properties, but its strong calcemic effect in principle excludes it as a potential anticancer drug. Currently, a lot of effort is being devoted to develop potent anticancer analogs of 1,25-dihydroxyvitamin D(3) that would not induce hypercalcemia during therapy. In this work, the free binding energy of the VDR receptor with 1,25-dihydroxyvitamin D(3) and its three potent analogs (EB 1089, KH 1060 and RO 25-9022) is calculated and compared with each other. With this approach, we could estimate the relative binding affinity of the most potent analog, RO 25-9022, and also revealed a quite distinct mechanism of its interaction with VDR.}, author = {Karol Kamel and Andrzej Koli{\'n}ski} } @article {Kamel2011, title = {Computational study of binding of epothilone A to β-tubulin}, journal = {Acta Biochimica Polonica}, volume = {58}, number = {2}, year = {2011}, month = {jan}, pages = {255{\textendash}60}, abstract = {Understanding the interactions of epothilones with β-tubulin is crucial for computer aided rational design of macrocyclic drugs based on epothilones and epothilone derivatives. Despite numerous structure-activity relationship investigations we still lack substantial knowledge about the binding mode of epothilones and their derivatives to β-tubulin. In this work, we reevaluated the electron crystallography structure of epothilone A/β-tubulin complex (PDB entry 1TVK) and proposed an alternative binding mode of epothilone A to β-tubulin that explains more experimental facts.}, keywords = {Animals, Binding Sites, Cattle, Computer Simulation, Epothilones, Epothilones: chemistry, Hydrogen Bonding, Models, Molecular, Protein Binding, Thermodynamics, Tubulin, Tubulin: chemistry}, issn = {1734-154X}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21633729}, author = {Karol Kamel and Andrzej Koli{\'n}ski} }