Coumarin structure as a lead scaffold for antibacterial agents - molecular docking study BIOLOGICA NYSSANA 7 (2)  December 2016: 167-170 Veselinović, J.B. et al.  Coumarin structure as a lead scaffold… 167 Original Article Received: 30 October 2016 Revised: 14 November 2016 Accepted: 24 November 2016 Coumarin structure as a lead scaffold for antibacterial agents - molecular docking study Jovana B. Veselinović1*, Jelena S. Matejić2, Aleksandar M. Veselinović2, Dušan Sokolović2 1Health Institution Filly Farm, Pharmacy Filly 63, Cara Dušana 31, 18000 Niš, Serbia 2Faculty of Medicine, University of Niš, Bulevar Dr Zorana Ðinđića 81, 18000 Niš, Serbia * E-mail: milosavljevic.jovana@hotmail.com Abstract: Veselinović, J.B., Matejić, J.S., Veselinović, A.M., Sokolović, D.: Coumarin structure as a lead scaffold for antibacterial agents - molecular docking study. Biologica Nyssana, 7 (2), December 2016: 167-170. Coumarins owe their class name to “Coumarou”, the vernacular name of the tonka bean (Dipteryx odorata Willd, Fabaceae), from which coumarin was isolated in 1820. Many molecules based on the coumarin structure have been synthesized utilizing innovative synthetic techniques. Various synthetic routes have led to interesting derivatives including the furanocoumarins, pyranocoumarins and coumarinsulfamates which have been found to be useful in photochemotherapy, antitumor and anti-HIV therapy, as stimulants for central nervous system, antiinflammatory therapy, as anti-coagulants, etc. One of important pharmacological activity of coumarin molecules is their potential as antibacterial agents since they show inhibitory activity toward isoleucyl-transfer RNA (tRNA) synthetase. In the presented research molecular docking studies of selected coumarin compounds inside isoleucyltransfer RNA (tRNA) synthetase active site were performed. Molecular docking scores of all studied compounds were obtained through score functions. Presented results indicate that from all studied coumarin compounds the strongest interactions with studied enzyme has 7,8-dihydroxy-4-phenyl coumarin followed by 5,7-dihydroxy-4-phenyl coumarin. Presented results are in accordance with in vitro obtained results for their antibacterial activity. Presented findings suggest that 4-phenyl hydroxycoumarins may be considered as good molecular templates for potential antibacterial agents and can be used for further chemical modifications for improving their antibacterial activity. Key words: Verbascum davidoffii, endemic species, genetic diversity, conservation Apstrakt: Veselinović, J.B., Matejić, J.S., Veselinović, A.M., Sokolović, D.: Coumarin structure as a lead scaffold for antibacterial agents - molecular docking study. Biologica Nyssana, 7 (2), Decembar 2016: 167-170. Kumarini su dobili ime od reči "Coumarou", narodnom nazivu za tonku (Dipterix odorata Willd, Fabaceae) iz koje je kumarin izolovan 1820. godine. Mnogi molekuli bazirani na kumarinskoj strukturi su sintetisani primenom inovativnih hemijskih tehnika. Razičiti putevi sinteze su doveli do interesantnih derivata koji uključuju furanokumarine, piranokumarine i kumarinsulfamate koji imaju primenu u fitohemoterapiji, antitumorskoj i anti-HIV terapiji, kao stimulanti za centralni nervni sistem, kao antinflamatorni i antikoagulativni agensi, itd. Jedna od važnih farmakoloških aktivnosti kumarinskih jedinjenja je njihov potencijal kao antibakterijskih agenasa, jer pokazuju inhibitornu aktivnost prema izoleucil-transfer RNK sintetazi (tRNK). U predstavljenom istraživanju studija molekularnog dokinga unutar aktivnog mesta izoleucil- 7 (2) • December 2016: 167-170 12th SFSES • 16-19 June 2016, Kopaonik Mt DOI: 10.5281/zenodo.200417 BIOLOGICA NYSSANA 7 (2)  December 2016: 167-170 Veselinović, J.B. et al.  Coumarin structure as a lead scaffold… 168 transfer RNK sintetaze (tRNK) je primenjena za odabrana kumarinska jedinjena. Vrednosti molekularnog dokinga za sva ispitivana jedinjenja su dobijene primenom odgovarajućih skoring funkcija. Predstavljeni rezultati ukazuju da od svih ispitivanih kumarinskih jedinjenja najviše interakcija sa ispitivanim enzimom ima 7,8-dihidroksi-4-fenil kumarin, a zatim 5,7-dihidroksi-4-fenil kumarin. Predstavljeni rezultati su u skladu sa in vitro dobijenim rezultima za njihovu antibakterijsku aktivnost. Prikazani rezultati ukazuju da se 4-fenil hidroksikumarini mogu smatrati dobrim molekuskim osnovama za potencijalne antibakterijske agense i da se mogu koristiti za dalje hemijske modifikacije u cilju poboljšanja antibakterijske aktivnosti. Key words: 4-fenil hidroksikumarini, antibakterijska aktivnost, molekularni doking Introduction Great hopes that the discovery and the application of penicillin and other antibiotics would forever solve the problem of bacterial infections lasted for a relatively short time period. Seven decades after antibiotics were introduced, infectious diseases as a cause of mortality are in third place in Europe. In the European Union (EU) around 2 million people are hospitalized and around 200,000 die from some infectious diseases annually. As a gloom example in South Asia in every 2 minutes one infant dies due to resistance to existing antibiotics. It is considered that the main reason for this "failure" of the treatment is a large percentage of drug-resistant and multidrug- resistant bacteria. Today, antibacterial resistance is a growing public health threat of major concern around the world. A post-antibiotic era (in which common infections and minor injuries can kill), far from being an apocalyptic fantasy, is instead a very real possibility for the 21st century (WHO, 2014). Bacterial resistance is a natural biological phenomenon that can be associated with their fight for survival. Mechanisms of bacterial resistance to antibiotics are very different and complex and depend both on the bacteria and the structure of antibiotics. Also, it involves a range of resistance mechanisms acting an ever-widening range of bacteria, most of which can cause a wide spectrum of diseases in humans and animals. Factors that favor the development of bacterial resistance are: overusing prescribing antibiotics, improper use - the compliance, inadvertent application of antibiotics and slow development of new effective antibiotics. Of all identified bacterial strains resistant to antibiotics of particular concern are methicillin- resistant Staphylococcus aureus (MRSA), penicillin- resistant Streptococcus pneumoniae, vancomycin- resistant Enterococcus, and Mycobacterium tuberculosis, since many of these organisms are resistant to several classes of established antibiotics and they can cause infections which are very difficult to treat. Above stated facts are forcing the search for novel antibacterial agents which affect targets that are essential to bacteria (P a y n e et al., 2007; B o l l e n b a c h , 2015). In this regard, the aminoacyl- tRNA synthetase (AaRS) enzymes have been a focus of recent antibacterial drug research. Inhibition of these enzymes halts protein biosynthesis which in turn results in the attenuation of bacterial growth under both in vitro and infectious conditions and for this reason bacterial AaRSs present a vast number of opportunities for the identification of novel inhibitors that can be considered as candidates for development as antibiotics (O c h s n e r et al., 2007). Today resistant bacterial strains occur significantly faster than the synthesis and the release of new effective antibiotics. It is well known fact that the development of new drugs in recent decades has become extremely expensive and time-consuming process. For this reason novel computational methods like molecular docking are used to speed up the process of drug design and development. The main aim of molecular docking is the determination of a suitable geometry and binding affinity of the tested molecule (ligand) to the active site of the target macromolecules (receptors) with the application of the “scoring” functions (K r o e m e r , 2007). Coumarins are a group of molecules found extensively in plants and they show various biological and pharmacological activities including anticoagulant, estrogenic, vasodilator, hypothermic, anthelmintic, sedative, analgesic, anti-inflammatory and antiulcer. Further, coumarin derivates have a wide range of structural modifications (B o r g e s et al., 2005) and they can serve as molecular templates for new drugs. Coumarin derivates are also considered as potential antibacterial agents (V e s e l i n o v i ć et al., 2015). Main goal of presented research was to establish the influence of 4-phenyl group addition and the number and position of hydroxyl groups within main coumarine structure on the interaction with isoleucyl-transfer RNA (tRNA) synthetase using molecular docking study. Studied interactions are considered as main influence on enzyme inhibition which can lead to antibacterial activity. Material and methods Molecular docking. In order to gain insight into the plausible mechanism of antibacterial action docking simulations were performed. The crystal structure of isoleucyl-transfer RNA (tRNA) synthetase (IleRS) BIOLOGICA NYSSANA 7 (2)  December 2016: 167-170 Veselinović, J.B. et al.  Coumarin structure as a lead scaffold… 169 was obtained from the Brookhaven Protein Data Bank http://www.rcsb.org/pdb (PDB entry: 1QU3). The compounds were docked into enzyme binding sites using the MolegroVirtual Docker (MVD) and published methodology [7]. Three dimensional structures of compounds (7-hydroxy-4-phenyl coumarin (7C), B) 5,7-dihydroxy-4-phenyl coumarin (57C) and C) 7,8-dihydroxy-4-phenyl coumarin (78C)) used for docking simulation were constructed using MarvinSketch 6.1.0, 2013, ChemAxon (http://www. chemaxon.com). Geometry optimization was carried out by employing MMFF94 molecular force field. Fig. 1. Above: Chemical structures of investigated compounds: A) 7-hydroxy-4-phenyl coumarin (7C), B) 5,7-dihydroxy-4-phenyl coumarin (57C) and C) 7,8-dihydroxy-4-phenyl coumarin (78C). Bellow: The structure of IleRS with best docking poses for all investigated coumarins inside enzyme binding pocket. Results and discussion Chemical structures of investigated coumarines are presented in Fig. 1. The least energy binding mode of compounds has been studied and best docking poses for all investigated coumarins inside enzyme binding pocket is presented in Fig. 1. Binding affinity of a ligand to the active site of the enzyme can be estimated based on the score values obtained using scoring functions form the molecular docking method. Table 1 presents score values for all studied compounds. Presented results indicate that of all studied compounds the highest interactions with enzyme has 78C followed by 57C. According to presented results the difference between their interaction energies is not as big as difference between their interaction energies and 7C interaction energy. It is of great importance that presented results are in accordance with in vitro obtained results for antibacterial activity. Interesting result was obtained with molecular docking study – that 7C don’t form any hydrogen bond with the active site of studied enzyme. This can be one of the reasons why 7C show the lowest antibacterial activity, because number, bond length, and bond energy of hydrogen bonds formed between ligand and enzyme have an important role in ligand effect on investigated activity. Two dimensional representations of formed hydrogen bonds for 57C and 78C are presented in Fig. 2. It was observed from in silico studies that 57C forms one hydrogen bond - oxygen atom from carbonyl group from the lacton part of molecule with Lys-71 (2.80 Å). 78C forms four hydrogen bonds. Oxygen atom from carbonyl group from the lacton part of molecule forms one hydrogen bond with Lys71 (2.79 Å). Hydroxyl group at position 7 forms Fig. 2. Two dimensional representations of the best docking pose for A) 5,7-dihydroxy-4-phenyl coumarin, and B) 7,8-dihydroxy-4-phenyl coumarin inside isoleucyl-transfer RNA (tRNA) synthetase active site. BIOLOGICA NYSSANA 7 (2)  December 2016: 167-170 Veselinović, J.B. et al.  Coumarin structure as a lead scaffold… 170 one hydrogen bond with His585 (3.23 Å). Hydroxyl group at position 8 forms two hydrogen bonds with His585 (3.19 Å) and Gly66 (2.60 Å). Conclusion Molecular docking simulations against IleRS were performed and correlation between the observed inhibitory activity and the in silico molecular docking scores of the compounds was obtained through hydrogen bonding interactions. These findings suggest that 4-phenyl hydroxycoumarins may be considered as good molecular templates for potential antibacterial agents and can be used for further chemical modifications for improving antibacterial activity what will be the main goal of our further research. Acknowledgements. This work has been financially supported by Ministry of Education and Science, Republic of Serbia, under Project Number 43012.. 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Veselinović, J.B, Veselinović, A.M., Nikolić, G.M., Pešić, S.Z., Stojanović, D.B., Matejić, J.S., Mihajilov-Krstev, T.M. 2015: Antibacterial potential of selected 4-phenyl hydroxycoumarins integrated in vitro and molecular docking studies. Medicinal Chemistry Research, 24 (4): 1626- 1634. WHO. 2014: Antimicrobial resistance: global report on surveillance. World Health Organization WHO Library Cataloguing-in-Publication Data. Table 1. Score values (kcal/mol) for all studied coumarin compounds. MolDock ReRank Interaction Inter. HBond Docking Score 78C -125.476 -108.328 -138.994 13.517 -6.0007 -127.625 57C -118.820 -101.209 -130.653 11.832 -3.8847 -124.704 7C -106.467 -88.612 -116.639 10.172 0 -104.336