Materials 2021, 14, 5401. https://doi.org/10.3390/ma14185401 www.mdpi.com/journal/materials Article Pyridine Derivatives—A New Class of Compounds That Are Toxic to E. coli K12, R2–R4 Strains Dominik Koszelewski 1 , Ryszard Ostaszewski 1 , Paweł Śmigielski 1 , Anastasiia Hrunyk 1 , Karol Kramkowski 2 , Łukasz Laskowski 3 , Magdalena Laskowska 3 , Rafał Lizut 4 , Mateusz Szymczak 5 , Jacek Michalski 6 , Kamil Gawin 6 and Paweł Kowalczyk 6, * 1 Institute of Organic Chemistry PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland; d.koszelewski@icho.edu.pl (D.K.); r.ostaszewski@icho.edu.pl (R.O.); p.smigielski@icho.edu.pl (P.Ś.); a.hrunyk@icho.edu.pl (A.H.) 2 Department of Physical Chemistry, Medical University of Bialystok, Kilińskiego 1 Str., 15-089 Białystok, Poland; kkramk@wp.pl 3 Institute of Nuclear Physics Polish Academy of Sciences, 31-342 Krakow, Poland; lukasz.laskow- ski@ifj.edu.pl (Ł.L.); magdalena.laskowska@ifj.edu.pl (M.L.) 4 The John Paul II Catholic University of Lublin, Institute of Mathematics, Informatics and Landscape Architecture ul. Konstantynów 1 H, 20-708 Lublin, Poland; lizut@kul.pl 5 Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; mszymczak@biol.uw.edu.pl 6 Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, 05-110 Jabłonna, Poland; j.michalski@ifzz.pl (J.M.); k.gawin@ifzz.pl (K.G.) * Correspondence: p.kowalczyk@ifzz.pl Abstract: A preliminary study of 2-amino-4-aryl-3,5-dicarbonitrile-6-thiopyridines as new potential antimicrobial drugs was performed. Special emphasis was placed on the selection of the structure of target pyridine derivatives with the highest biological activity against different types of Gram- stained bacteria by lipopolysaccharide (LPS). Herein, Escherichia coli model strains K12 (without LPS in its structure) and R2–R4 (with different lengths of LPS in its structure) were used. Studied target compounds were provided with yields ranging from 53% to 91% by the lipase-catalyzed one pot multicomponent reaction of various aromatic aldehydes with malononitrile, and thiols. The pre- sented work showed that the antibacterial activity of the studied pyridines depends on their struc- ture and affects the LPS of bacteria. Moreover, the influence of the pyridines on bacteria possessing smooth and rough LPS and oxidative damage to plasmid DNA caused by investigated compounds was indicated. Additionally, the modification of the bacterial DNA with the tested compounds was performed to detect new potential oxidative damages, which are recognized by the Fpg protein. The obtained damage modification values of the analyzed compounds were compared with the modifications after antibiotics were used in this type of research. The presented studies demonstrate that 2-amino-4-aryl-3,5-dicarbonitrile-6-thiopyridines can be used as substitutes for known antibi- otics. The observed results are especially important in the case of the increasing resistance of bacte- ria to various drugs and antibiotics. Keywords: pyridine derivatives; E. coli strains; oxidative stress; antibiotics; lipopolysaccharide 1. Introduction The pyridine ring system can be found in a number of natural products and in several pharmacologically relevant compounds. Among others, 2-amino-4-aryl-3,5-dicarboni- trile-6-thiopyridines have gained considerable attention due to their wide-ranging biolog- ical activities (Figure 1) [1]. Citation: Koszelewski, D.; Ostaszewski, R.; Śmigielski, P.; Hrunyk, A.; Kramkowski, K.; Laskowski, Ł.; Laskowska, M.; Lizut, R.; Szymczak, M.; Michalski, J.; et al. Pyridine Derivatives—A New Class of Compounds That Are Toxic to E. coli K12, R2–R4 Strains. Materials 2021, 14, 5401. https://doi.org/10.3390/ ma14185401 Academic Editors: Jordi Marti and Abdelwahab Omri Received: 17 July 2021 Accepted: 16 September 2021 Published: 18 September 2021 Publisher’s Note: MDPI stays neu- tral with regard to jurisdictional claims in published maps and institu- tional affiliations. Copyright: © 2021 by the authors. Li- censee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and con- ditions of the Creative Commons At- tribution (CC BY) license (http://crea- tivecommons.org/licenses/by/4.0/).