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Article

Structure, Antimicrobial Activity, Hirshfeld Analysis, and Docking Studies of Three Silver(I) Complexes-Based Pyridine Ligands

by
Ahmed M. A. Badr
1,*,
Assem Barakat
2,*,
Jörg H. Albering
3,
Mona M. Sharaf
4,
Zaheer Ul-Haq
5 and
Saied M. Soliman
1,*
1
Department of Chemistry, Faculty of Science, Alexandria University, P.O. Box 426, Ibrahimia, Alexandria 21321, Egypt
2
Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
3
Technische Universität Graz, A-8010 Graz, Austria
4
Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technological Applications, Borg El-Arab, Alexandria 21321, Egypt
5
Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
*
Authors to whom correspondence should be addressed.
Appl. Sci. 2020, 10(14), 4853; https://doi.org/10.3390/app10144853
Submission received: 30 June 2020 / Revised: 10 July 2020 / Accepted: 13 July 2020 / Published: 15 July 2020
(This article belongs to the Section Chemical and Molecular Sciences)
Browse Figures
Versions Notes

Abstract

:
Three broad spectrum Ag(I) complexes against MDR (multi drug resistance) and ATCC standard bacteria as well as the fungus C. albicans were presented. The three well-known structurally-related Ag(I) complexes, [Ag(pyridine-3-carboxaldhyde)2NO3], 1, [Ag3(2-pyridone)3(NO3)3]n, 2, and [Ag(3-hydroxypyridine)2]NO3, 3, were prepared by the direct combination of AgNO3 with the corresponding pyridine ligands in a water-ethanol mixture. 1 and 3 are molecular compounds while, 2 is a 2D coordination polymer with sheets bridged by strong homoleptic R2,2(8) hydrogen bonds between ligands giving the ins topology. Different contacts affecting the molecular packing in their crystal structures were computed by employing Hirshfeld analysis. Charge transferences from the ligand groups to Ag(I) were analyzed using natural population analysis. The effect of protonation and metal coordination on the tautomerism of 2-pyridone was analyzed using data from the Cambridge Structure Database (CSD). It was found that Lewis acid attachment to both N and O sites favor a state in between the two formal tautomers. All compounds were significantly more active than 17 tested commercial antibiotics against three clinically isolated strains of Ps. Aeruginosa, with 2 and 3 performing best on average against all ten tested bacterial strains but with 3 containing less Ag per weight. Finally, docking studies were carried out to unravel the inhibition mechanism of the synthesized silver(I) complexes.

Graphical Abstract

1. Introduction

Silver-containing compounds continue to attract academic attention for their antimicrobial properties [1,2,3,4,5,6,7,8] but also for the immense variety of its coordination polymers, [9] and sometimes the two coincide [10]. A recent review is optimistic of the future role of silver in medicine, [11] while clinical studies are still not of sufficient quality to judge the practical usefulness of different silver based wound healing materials, the most common medical application [12].
The attractiveness lies in the low human toxicity of silver and silver ions, combined with the in-vitro antimicrobial properties that are on par, or better than conventional antibiotics. The difficulties lie in the yet sketchy knowledge of the mode(s) of action, [12] the variability of the Ag(I) coordination modes, and the solution chemistry that likely will be dominated by chlorine interactions, such as the precipitation and dissolution of AgCl(s), in biological fluids.
Silver(I) ion, and its complexes as well as their nanoparticles, have been proven to have anti-inflammatory [7], antiseptic [13], and anti-cancer activities [14]. For example, silver(I) sulfadiazine is used for treating infections during burn wounds treatment but it has been observed that silver(I) sulfadiazine has major side effects such as slowing the rate of wound healing [15,16]. In the literature, many Ag(I) complexes with N-heterocylic ligands that have significant anti-microbial actions were reported. The results disclosed that the complexes of silver(I)-N-heteroclyles (e.g., pyridine, pyrimidine, pyridazine, pyrazine, pyrazole, phthalazine, quinoxaline, quinazoline, and tricyclic phenazine) have high anti-microbial activity towards several strains including Pseudomonas aeruginosa, Candida albican, etc. [17,18,19,20].
The mechanism of action of the silver metal complexes as anti-microbial agent is multi-directional [21,22,23,24]. The advantage of the different pathways of the activity of silver(I) may lead to a slowdown of the bacterial drug resistance development [21,22,23,24]. One of the multi-directional activities is that silver can interact with the cell surface of the bacteria, which help it to penetrate into the cell, subsequently binding with the amino acid (thiol group in the cysteine as an example) in the DNA which interrupts the replication and transcription processes leading to death of bacteria [21,22,23,24]. An alternative pathway is that silver(I) ion can induce reactive oxygen species (ROS) production, that are known to target nucleic acids, proteins, and lipids leading to the cell death via malfunction of these biomolecules.
There is thus a good reason to continue to study the antimicrobial properties of Ag(I) compounds, while at the same time exploring their fascinating and diverse solid state and coordination chemistry [25]. In this paper we present a study of three well-known silver(I) complexes [26,27,28] with the closely related pyridine-type ligands pyridine-3-carboxaldehyde (also known as nicotinaldehyde), 2-pyridone (keto form of 2-hydroxy-pyridine), and 3-hydroxypyridine (3-pyridinol), see Figure 1. Synthesis, characterizations, single crystal X-ray structures, and antimicrobial screening in comparison to 17 commercial antibiotics are also described. Moreover, network topology analysis [29,30,31] was applied to describe the structure of the synthesized complex with 2-pyridone. In addition, the intermolecular interactions such as hydrogen bonding, C-H…π interactions, π-π stacking, etc. play very crucial role in molecular packing of building blocks in the crystal. Hirshfeld calculations are important for quantifying these intermolecular interactions in the crystal [32,33,34,35,36,37]. In this regard, Hirshfeld quantitative analysis for the three complexes was performed.

2. Materials and Methods

2.1. General Methods

All reagents used in this research are technical grade and utilized without purification. All physicochemical measurements are provided in the supplementary information.

2.2. Synthesis

All silver(I) complexes were synthesized by employing a self-assembly approach. To a solution of AgNO3 (0.17 g, 1.0 mmol) in H2O (10 Ml, deionized), then, an ethanolic solution of pyridine-3-carboxaldhyde (0.19 mL, ~2.0 mmol), 2-pyridone (0.095 g, 1.0 mmol) or 3-hydroxypyridine (0.19 g, 2.0 mmol) added drop by drop with stirring. The solution was kept at ambient for few days to give colorless crystals of the target complexes. The crystals were filtered off, washed with small amount of ethanol, and dried in air. FTIR and NMR spectra of the three complexes are given in Figures S1 and Figure S2 (Supplementary data), respectively.
[Ag(pyridine-3-carboxaldhyde)2NO3], 1 [26], Yield: 0.15 g, 80% with respect to the ligand. (%): Calc.: C, 37.52; H, 2.62; N, 10.94; Ag, 28.08. Found: C, 37.49; H, 2.63; N, 10.94; Ag, 28.10. 1H NMR (DMSO-d6, 500 MHz): δ 7.64 (t, 1H at C-5), 8.24 (d, 1H at C-4), 8.82 (d, 1H at C-6), 9.06 (s, 1H at C-2) and 10.08 (s, 1H at C-7). 13C NMR (DMSO-d6, 125 MHz): δ 125.16, 125.18 (C-5), 131.90, 131.95 (C-3), 136.89, 137.14 (C-4), 152.10, 152.22 (C-2), 155.40, 155.40 (C-6), 192.23, 192.24, 193.17, 193.82 (C-7 of aldehyde).
[Ag3(2-pyridone)3(NO3)3]n, 2 [27], Yield: 0.196 g, 74% with respect to the ligand. (%): Calc.: C, 22.66; H, 1.90; N, 10.57; Ag, 40.71. Found: C, 22.67; H, 1.91; N, 10.57; Ag, 40.70.
1H NMR (DMSO-d6, 500 MHz): δ 6.20 (t, 1 H, H-4), 6.33 (d, 1 H, H-3), 7.39–7.41 (m, 2 H, H–5, H-6), 11.61 (s, 1 H, NH, exchangeable with D2O); 13C NMR (DMSO-d6, 125 MHz): δ 106.57, 106.81 (C-5), 119.59, 119.83 (C-3), 137.04, 137.33 (C-6), 141.65, 141.89(C-4), 163.16 (C=O).
[Ag(3-hydroxypyridine)2]NO3, 3 [28], Yield: 0.31 g, 86% with respect to the ligand. (%): Calc.: C, 33.36; H, 2.80; N, 11.67; Ag, 29.96. Found: C, 33.36; H, 2.81; N, 11.66; Ag, 29.97. 1H NMR (DMSO-d6, 500 MHz): δ 7.2–7.4 (m, 2 H, H–4, H–5), 8.01 (d, 1 H, H-5), 8.12 (d, H, H–2), 10.05 (s, 1 H, OH, exchangeable with D2O); 13C NMR (DMSO-d6, 125 MHz):δ 123.26, 123.68 (C-4), 125.00, 125.37 (C-5), 139.82, 139.09 (C-2), 141.25, 141.49 (C-6), 154.50 (C-3).

2.3. X-Ray Crystallography

Experimental details of the crystallographic measurements for the studied complexes are provided in the supplementary information [38,39,40]. The low temperature crystallographic structural data at 100(2) K for the studied Ag(I) complexes were deposited at CCDC with numbers 1,062,878–1,062,880. The topology analyses were performed using Crystal Explorer 17.5 program [41].

2.4. Computational Details

The amount of charge transferred from the ligand groups to the Ag(I) in complexes 1–3 were calculated using NBO 3.1 [42] program with the aid of Gaussian 09 program package [43]. For this task, the ωB97XD DFT method in combination with 6-311G(d,p) basis sets for nonmetal atoms and LANL2DZ basis set for Ag were used.

2.5. Testing of Antimicrobial Activity

The full details about the anti-microbial protocol are provided in the supplementary information [44].

2.6. Methodology for Molecular Docking

The binding mechanism of the three silver(I) complexes was investigated at molecular level using molecular docking. To validate and specify the target for anti-bacterial and anti-fungal potential of these compounds, seven different protein targets i.e., N-myristoyl transferase (PDB ID 1IYL) [45], dihydrofolate reductase (DHFR) (PDB ID 4HOF) [46] from C. albicans were selected as fungal targets, while dihydrofolate reductase (PDB ID 3FYV) [47], gyrase B (PDB ID 4URM) [48] from S. aureus, DNA (PDB ID 1BNA) [49] thymidylate kinase of P. Aeruginosa (PDB ID 3UWK) [50], and undecaprenyl diphosphate synthase (PDB ID 4H2M) [51] from E. coli were selected based on their direct role in the drug resistance. Crystal structures of all these proteins in complex with their cognate ligand were retrieved from the Protein Data Bank. All proteins were prepared, protonated, charged, and minimized by structure preparation module in MOE [52]. Solvent molecules were removed as required. The compounds were built using the builder module in MOE. Complexes were further charged and minimized by MMFF94x forcefield [53]. For docking, an induced fit docking protocol was used with default MOE docking parameters i.e., Triangle Matcher Algorithm with two rescoring functions London dG and GBVI/WSA dG. For each complex a total thirty conformations were generated and saved in mdb format.

3. Results and Discussion

3.1. Crystal Structures

All crystallographic measurements were performed using graphite monochromated MoKa radiation at 100(2) K. The structure of complexes 1 and 3 agrees well with the previously reported X-ray data shown in Figure 2 [26,28]. All relevant crystallographic data as well as selected interatomic distances and bond angles can be taken from Tables S1–S4 (Supplementary data). Interestingly, the low temperature X-ray structure of [Ag(2-pyridone)NO3]n; (2) complex showed some variations compared to the previously reported room temperature (293(2) K) data [27]. Hence, its structure will be described in some details in this publication. The asymmetric unit of [Ag(2-pyridone)NO3]n; (2) contains three independent AgL(NO3) complexes (Figure 2), which differ slightly by their Ag-O(NO2) bond distances and O-Ag-O bond angles. The coordination geometry of Ag(I) have one short Ag-O bond (2.307–2.316(4) Å) to the organic ligand and longer bonds (2.533(4) Å, Ag3-O9, to 2.666(5) Å, Ag2-O12) to the nitrate anions. On other hand, the main difference between the newly reported structure of 2 with the previously reported data by Bowmaker and coworkers is that the asymmetric unit of the latter comprised one AgL(NO3) unit in which the corresponding Ag-O distances are 2.315(6) and 2.588(8) to 2.715(10) Ǻ, respectively.
The crystal structure of [Ag(2-pyridone)NO3]n is built up by a strongly folded 2D-infinite network of silver cations and nitrate anions parallel to the ab plane of the unit cell (Figure S3; Supplementary data) where the coordination geometry of the Ag(I) could be simply described as distorted tetrahedral as shown in Figure S4 (Supplementary data). These are interconnected by the 2-pyridone ligands by formation of two strong hydrogen bonds with the R2,2(8) pattern between two neighboring ligands (N-H...O distances: N-H: 0.879 Å, H...O: 1.922 Å for O3-H1, 1.924 Å for O2-H3B and 1.932 Å for O1-H2B) as shown in Figure 3. This is a common motif for lactam dimers [54]. The structure is best understood as a 3D net with the ins-topology, illustrated in Figure 4. The topology is binodal, containing one type of 3-connected node and one type of 4-connected node. This topology is rather rare, but has also been found in the coordination polymer [Ag3(hexamethylenetetramine)2][ClO4]3·2H2O [55].
Indeed, the ADDSYM option of the software package PLATON suggests a transformation to another unit cell with only 1/3 of the initial volume and thus only one formula unit per asymmetric unit [27]. However, even if this may correspond to the network topology, this is not the correct description of the symmetry of the studied complex. A refinement with the smaller unit cell led to implausible atomic displacement parameters, high standard deviations of the positional parameters, and much higher R-values.

3.2. Tautomerism in 2-Pyridone/2-Hydroxy-Pyridine Systems

It has been agreed for quite some time that it is the 2-pyridone form and not the tautomer 2-hydroxy-pyridine that is the most stable form of this molecule in the solid state, but in the gas phase 2-hydroxy-pyridine is favored and in solution sometime delicate equilibriums exist [56,57]. Depending on substitution pattern, similar molecules may prefer either forms, but a search of the Cambridge Structure Database (CSD) showed that the 2-pyridone form is prevalent, as illustrated in the plot of C1-O1 versus C1-C2 shown in Figure 5.
It is clear that there is a preference for C-C distance of 1.48 Å with a C-O distance of 1.22 Å, thus the 2-pyridone form, but there is also a much smaller minimum at C-C distance of 1.39 Å with a C-O distance of 1.35 Å corresponding to the 2-hydroxy-pyridine form. In [Ag(2-pyridone)NO3]n complex, both N and O are connected to Lewis acids (H+ and Ag+) and also the C-C distances: 1.425–1.436Å; and C-O distances: 1.266–1.273 Å, give no clear clue about whether this is the keto- or enol-form. In fact, looking at Figure 5 it seems that it falls right in the area that could be considered to correspond to the transition state and indeed the transition state of the tautomerization has been shown theoretically to go through a similar dimerization [57].

3.3. Analysis of Molecular Packing

The different Hirshfeld surfaces of the three complexes are collected in Figure 6. In the studied Ag(I) complexes, the molecules are packed differently in the crystal structure and the possible contacts are presented in Figure 7.
It is clear from Figure 7 that the O…H interactions contributed heavily in the molecular packing of the three complexes. The parentages of the O…H interactions are 43.7, 43.8, and 35.6% for complexes 1–3, respectively. The decomposed dnorm maps and fingerprint plots shown in Figure 8 revealed the importance of these interactions in the molecular packing.
The π-π stacking interactions are another interesting feature of molecular packing that was observed using Hirshfeld surface analysis. It is clear from Figure 9 that all evidences for the π-π contacts such as red spots in dnorm and blue/red triangles in the shape index map were achieved. In addition, there is appropriate amount of C…C contacts in the three complexes as indicated from the fingerprint plot. The C…C contact percentages are 6.4, 2.8, and 2.6% for complexes 1–3, respectively.
In addition to these intermolecular interactions, the Hirshfeld surfaces detected very well the polymeric nature of complex 2 via Ag-O bonding with the neighboring complex units (Figure 10B). Also, complex 1 showed significant amount of short Ag…N interactions (3.9%) with the neighboring complex units (Figure 10A), while in complex 3 some significant Ag…C (1.7%) and Ag…O (5.7%) interactions were detected (Figure 10C,D). It is worth to note that the Ag…C interactions have less significance in complexes 1 and 2 compared to 3.

3.4. Natural Charge Analysis

The calculated natural charges of Ag and ligand groups for the [Ag(pyridine-3-carboxaldhyde)2NO3]; (1), [Ag3(2-pyridone)3(NO3)3]; (2), and [Ag(3-hydroxypyridine)2]NO3; (3) complex units are listed in Table 1. It is clear that the net charge of the nitrate group is close to −1 in complex 3 which comprised an ionic nitrate, which is weakly coordinated to Ag(I) ion. The amount of electrons transferred to Ag(I) in this case is only 0.0358 e. In contrast, the amount of electrons transferred from the nitrate group to Ag(I) ion in complexes 1 and 2 are higher. The amounts of electron density transferred are 0.1635 and 0.1936 e, respectively indicating strongly coordinated nitrate to the silver ion. The pyridine ligand groups transferred 0.1071, 0.0762, and 0.1395 e in complexes 1–3, respectively. As a result, the charges at silver atom were reduced to 0.6222, 0.7284, and 0.6852, respectively.

3.5. Antimicrobial Activity

Previous studies showed that silver(I) metal complexes-based different N-heterocycles such as imidazole, 1,2,4-triazole and tetrazole were active against two strains including Ps. aeruginosa and S. aureus and more potent (ca. 4–8 folds) better than the silver nitrate (AgNO3) as positive control [58]. Also, silver(I)-imidazole and silver(I)-L-histidine polymer complexes were shown to have an equal potency of the studied microbial strains S. aureus and Ps. aeruginosa (MIC 15.7 and 12.5 μg/mL), on the other hands, silver(I)-1,2,3-triazole polymer complex had no effect on the bacteria [59]. Several examples of the silver metal complexes based on nicotinate compounds have been explored by our research group previously [60], where [Ag(isonicotinamide)2-μ-O,O’(NO3)]2 and [Ag2-μ-O,O’(2-aminonicotinium)2-(NO3)2]n exhibited a remarkable effect towards Ps. aeruginosa with MIC ranged 2–8 μg/mL, another example for the silver metal complex such as [Ag(ethylnicotinate)2](NO3) showed against two strains including S. aureus and S. pyogenes (MIC = 4–16 and 2–4 μg/mL, respectively). [Ag(ethylisonicotinate)2(NO3)], [Ag(methylisonicotinate)2(H2O)](NO3), and[Ag(ethylnicotinate)2](NO3) possessed high efficacy towards P. mirabilis (MIC 1–16 μg/mL). Also, we have explored silver(I)-based pyridine complexes and the anti-microbial activity against S. lutea and M. lutea, which provided interesting and promising results with the MIC = 2 and 4 μg/mL, respectively [44].
In this paper we introduced another group of silver(I) pyridine complexes with relatively high biological activity against a broad spectrum of MDR (multi drug resistance) and ATCC standard bacteria as well as the fungus C. albicans. The Minimum Inhibition Concentrations (MIC) of the tested compounds were tested and 17 antibiotics were used for the activity comparison. The detailed results are given in Table 2 and presented graphically in Figure 11. One of the advantages of this set of silver complexes is its broad-spectrum activity against MDR (multi drug resistance) bacteria isolated from diabetic foot ulcers as well as the ATCC standard bacteria with different action ranging from MIC = 4 μg/mL for compound 2 against Ps. Aeruginosa to MIC = 64 μg/mL for compound 1 against K. pneumoniae and E. Coli. An additional advantage of silver compounds is that they, in contrast with antibiotics in general, are active against fungi. Thus complexes 1–3 were active against the yeast C. albicans (See Table 2). When looking to these data, we also need to consider the different silver contents of the three compounds. These being by weight 28% for 1, 41% for 2 and 30% for 3. The best action is for 2 against Ps. Aeruginosa with MIC value of 4 μg/mL.

3.6. Molecular Docking Studies

The analysis of the docking results revealed that among all seven targets, only thymidylate kinase (TMK) from P. aeruginosa showed good binding affinity and docking interactions with studied complexes. The results of the docking scores of control inhibitor and silver complexes against the target proteins are mentioned in the Table 3. Figure 12D presents the alignment of different silver complexes in the active site of TMK. As shown in the Figure 12A–C, all the complexes fit well into the active site of TMK. The coordinates of these compounds overlap in the crystal structure of the template plate, mimicking some of its interactions with the macromolecule.
The binding mode of complex 1 with thymidylate kinase displayed number of prominent interactions including hydrophobic, hydrophilic, salt bridges, and π- stacking interactions. Figure 12A presented that O3 of the nitrate anion that directly ligated to the silver metal involved in hydrogen bond interaction with the side chain of Arg50 (2.73 and 2.95 Å), Arg96 (3.23 Å), and Arg151 (2.85 Å), respectively. While Tyr104 mediate strong hydrogen bond interaction with the carbonyl of pyridine-3-carboxaldehyde at a distance of 2.07 Å. The hydrophobic contact of pyridine ring with Glu12, Arg96, Phe155, and Glu156 might also contribute in the observed activity of this complex. Further protein-ligand interactions are stabilized by the formation of a salt bridge between complex and Glu12 and Asp153. Moreover, the geometry of the silver metal interaction retained by making contact with Asp153 at a distance of 2.78 Å.
In case of most active complex 2, a network of strong hydrogen bond interactions with the residues of the active site of TMK has been observed that rationalize the inhibitory potential of the complex. The nitrate ion of the complex involved in three hydrogen bond interactions with Tyr104, side chain of Glu12, and Arg96 at a distance of 1.88, 2.19, and 2.46 Å, respectively. Both of the nitrate ions that ligated with silver metal mediated bidentate hydrogen bond interactions with the residues Glu12 (3.02 Å), Arg50 (2.99 Å), Arg96 (2.66 Å), Arg149 (2.80 and 2.88 Å), and Glu156 (3.41 Å). The hydrophobic contact of pyridone rings with the hydrophobic patch of Pro11, Ala100, Tyr104, Ala146, Arg151, Phe155, and Phe163 provided further anchorage to the active site. Complex 2 was further stabilized by special type of electrostatic interactions i.e., salt bridges between pyridone of the complex with Glu12, Asp153, and Glu156 (Figure 12B).
In contrast to complexes 1 and 2, complex 3 (Figure 12C) mainly stabilized by hydrophobic interactions with Glu12, Ala100, Tyr104, Phe155, and Glu156. Additionally, the contacts were further stabilized by hydrophilic interactions between Glu12 and Phe155 with 3-hydroxypyridine at a distance of 3.30 and 31.9 Å, respectively.

4. Conclusions

Three Ag(I) complexes with pyridine ligands were synthesized and well characterized using X-ray single crystal diffraction analysis, elemental analysis and NMR spectra. The solid state structure of [Ag(2-pyridone)NO3]n is peculiar and best understood using network topology analysis giving the unusual ins-net. Their antimicrobial properties were compared with 17 antibiotics. [Ag(2-pyridone)NO3]n has specific activity against three clinically isolated strains of Ps. Aeruginosa compared to the tested antibiotics. This group of silver(I) pyridine complexes have relatively high biological activity against a broad spectrum of MDR (multi drug resistance) and ATCC standard bacteria as well as the fungus C. albicans. We hope to find promising substances to be used in wound dressing applications. Also, molecular packing analyses for complexes 1–3 were performed with the aid of Hirshfeld analysis. The net charges at silver atom are 0.6222, 0.7284, and 0.6852 instead of 1.0000 due to the interactions with the ligand groups coordinating it. The molecular docking of the studied complexes shows several types of interactions with the pocket including hydrophilic, hydrophobic, salt bridges, and π- stacking interactions.

Supplementary Materials

The following are available online at https://www.mdpi.com/2076-3417/10/14/4853/s1, Figures S1–S3: 1H and 13C NMR spectra of complexes 1–3. Figure S4: Distorted tetrahedral coordination of the silver atoms in [Ag(2-pyridone)NO3]n. Figure S5: Hydrogen bond interactions. Figure S6: X-ray structure with atom numbering for complexes 1–3. Tables S1–S4: X-ray crystal data for the complexes 1–3.

Author Contributions

Conceptualization, A.M.A.B. and S.M.S.; data curation, A.M.A.B., A.B., J.H.A., M.M.S., and Z.U.-H.; formal analysis, J.H.A., M.M.S., Z.U.-H., and S.M.S.; funding acquisition, A.B.; investigation, S.M.S.; methodology, M.M.S. and S.M.S.; software, J.H.A. and Z.U.-H.; supervision, S.M.S.; writing—original draft, A.M.A.B., A.B., Z.U.-H., and S.M.S.; writing—review and editing, A.M.A.B., A.B., and S.M.S. All authors have read and agreed to the published version of the manuscript.

Funding

The research was funded by King Saud University, Researchers Supporting Project Number (RSP-2020/64).

Acknowledgments

The authors would like to extend their sincere appreciation to Researchers Supporting Project Number (RSP-2020/64), King Saud University, Riyadh, Saudi Arabia.

Conflicts of Interest

The authors declare no conflicts of interest.

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Applsci 10 04853 g001 550
Figure 1. The representative schematic presentation for the synthesis of the target complexes 1–3.
Figure 1. The representative schematic presentation for the synthesis of the target complexes 1–3.
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Figure 2. The X-ray structure of complexes 1–3.
Figure 2. The X-ray structure of complexes 1–3.
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Figure 3. Projection of the structure of [Ag(2-pyridone)NO3]n along the crystallographic a-axis.
Figure 3. Projection of the structure of [Ag(2-pyridone)NO3]n along the crystallographic a-axis.
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Figure 4. Node assignment (top) and resulting ins-net in [Ag(2-pyridone)NO3]n; 2 (center) and the ideal ins-net (bottom).
Figure 4. Node assignment (top) and resulting ins-net in [Ag(2-pyridone)NO3]n; 2 (center) and the ideal ins-net (bottom).
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Figure 5. Analysis of the 2-pyridone/2-hydroxy-pyridine tautomerism in purely organic compounds in the Cambridge Structure Database (CSD). Using the atom numbering in Figure 1, we have plotted the distances of C1-O1 versus C1-C2 and the colors represent number of hits in the database.
Figure 5. Analysis of the 2-pyridone/2-hydroxy-pyridine tautomerism in purely organic compounds in the Cambridge Structure Database (CSD). Using the atom numbering in Figure 1, we have plotted the distances of C1-O1 versus C1-C2 and the colors represent number of hits in the database.
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Figure 6. Hirshfeld analyses of [Ag(pyridine-3-carboxaldhyde)2NO3]; (1), [Ag3(2-pyridone)3(NO3)3]; (2), and [Ag(3-hydroxypyridine)2]NO3; (3) complexes.
Figure 6. Hirshfeld analyses of [Ag(pyridine-3-carboxaldhyde)2NO3]; (1), [Ag3(2-pyridone)3(NO3)3]; (2), and [Ag(3-hydroxypyridine)2]NO3; (3) complexes.
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Figure 7. Different contacts in [Ag(pyridine-3-carboxaldhyde)2NO3]; (1), [Ag3(2-pyridone)3(NO3)3]; (2) and [Ag(3-hydroxypyridine)2]NO3; (3) complexes.
Figure 7. Different contacts in [Ag(pyridine-3-carboxaldhyde)2NO3]; (1), [Ag3(2-pyridone)3(NO3)3]; (2) and [Ag(3-hydroxypyridine)2]NO3; (3) complexes.
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Figure 8. The fingerprint (upper) and dnorm maps (lower) of the O…H contacts. Sharp spikes in the fingerprint plot and red spots in dnorm maps are strong pieces of evidence on the importance of O…H contacts in the molecular packing.
Figure 8. The fingerprint (upper) and dnorm maps (lower) of the O…H contacts. Sharp spikes in the fingerprint plot and red spots in dnorm maps are strong pieces of evidence on the importance of O…H contacts in the molecular packing.
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Figure 9. The fingerprint (upper), dnorm maps (middle), and shape index (lower) of the C…C contacts.
Figure 9. The fingerprint (upper), dnorm maps (middle), and shape index (lower) of the C…C contacts.
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Figure 10. The rest of the most important contacts in complexes 1–3.
Figure 10. The rest of the most important contacts in complexes 1–3.
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Figure 11. Overview of the antibacterial test showing Minimum Inhibitory Concentrations (MIC) in µg/mL, thus lowest values corresponding to the most active compounds.
Figure 11. Overview of the antibacterial test showing Minimum Inhibitory Concentrations (MIC) in µg/mL, thus lowest values corresponding to the most active compounds.
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Figure 12. Binding patterns of (A) Complex 1, (B) Complex 2, and (C) Complex 3 with thymidylate kinase (TMK) of P. aeruginosa demonstrated from the top ranked dock pose. Red dashed lines represent H-bonds, while (D) presents the superimposition of all the compounds.
Figure 12. Binding patterns of (A) Complex 1, (B) Complex 2, and (C) Complex 3 with thymidylate kinase (TMK) of P. aeruginosa demonstrated from the top ranked dock pose. Red dashed lines represent H-bonds, while (D) presents the superimposition of all the compounds.
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Table
Table 1. The net natural charges at ligand groups and Ag.
Table 1. The net natural charges at ligand groups and Ag.
Metal/Ligand123
Ag0.62220.72840.6852
Py-ligand0.10710.07620.1395
NO3−−0.8365−0.8046−0.9642
Table
Table 2. Minimum inhibitory concentration (MIC) for complexes 1–3 compared with reference antibiotic drugs. (MIC ≥ 256 indicated no activity).
Table 2. Minimum inhibitory concentration (MIC) for complexes 1–3 compared with reference antibiotic drugs. (MIC ≥ 256 indicated no activity).
AntibioticGram-Positive BacteriaGram-Negative BacteriaFungi
MIC (µg/mL)
S. lutea1M. luteus2S. aureus3E. coli4K. pneumoniae2Ps. aeruginosa1Ps. aeruginosa2Ps. aeruginosa3P. mirablis2E. cloacae2C. albicans2
Amikacin4848>2561232>25664>256-
Gentamicin161616432242496192>256-
Streptomycin1664126641612128128>256-
Amoxicillin824832>256>25616192192128-
Ampicillin6416424>256889612896-
Cephradinei4864162419212832192192>256-
Cefuroximeii3232816128641612896128-
Cefoperazoneiii161661296816963248-
Cefepimeiv2484464328482432-
Imipenem83223>256>2566496>25616-
Meropenem321622192128486412812-
Azithromycin1616121264128641284864-
Clarithromycin2424168329648963232-
Nalidixic acidi8322441286448128>256>256-
Ciprofloxacinii424463248246464128-
Levofloxaciniii161638163216323232-
Vancomycin322432412864321284864-
132832166488832646
21216832324441688
31216161632888163232
1 ATCC 10,031 2 Clinical 3 ATCC 6538p, 4 ATCC 8739; Roman superscript numbers indicate the generation of the antibiotic. Lower values indicate higher activity.
Table
Table 3. Root-mean-square deviation (RMSD) and predicted binding affinity (docking scores in kcal/mol) of control inhibitor and silver complexes against target proteins.
Table 3. Root-mean-square deviation (RMSD) and predicted binding affinity (docking scores in kcal/mol) of control inhibitor and silver complexes against target proteins.
PDB ID Codes Docking Scores
RMSD of Control Ligand Silver (I) Complexes
(Å)Control Ligand123
1IYL1.85−11.6752−7.224−10.1026−7.7626
1BNA --−5.7922−7.2206−4.3620
3FYV1.23−8.4286−6.8618−9.6077−5.3467
3UWK0.9−10.9856−8.1865−11.4224−6.2362
4HOF1.5−8.6736−5.9142−7.8969−4.9028
4URM1.9−9.4327−6.7318−8.0604−4.881
4H2M2.0−10.6792−5.7233−9.2959−4.8587

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Badr, A.M.A.; Barakat, A.; Albering, J.H.; Sharaf, M.M.; Ul-Haq, Z.; Soliman, S.M. Structure, Antimicrobial Activity, Hirshfeld Analysis, and Docking Studies of Three Silver(I) Complexes-Based Pyridine Ligands. Appl. Sci. 2020, 10, 4853. https://doi.org/10.3390/app10144853

AMA Style

Badr AMA, Barakat A, Albering JH, Sharaf MM, Ul-Haq Z, Soliman SM. Structure, Antimicrobial Activity, Hirshfeld Analysis, and Docking Studies of Three Silver(I) Complexes-Based Pyridine Ligands. Applied Sciences. 2020; 10(14):4853. https://doi.org/10.3390/app10144853

Chicago/Turabian Style

Badr, Ahmed M. A., Assem Barakat, Jörg H. Albering, Mona M. Sharaf, Zaheer Ul-Haq, and Saied M. Soliman. 2020. "Structure, Antimicrobial Activity, Hirshfeld Analysis, and Docking Studies of Three Silver(I) Complexes-Based Pyridine Ligands" Applied Sciences 10, no. 14: 4853. https://doi.org/10.3390/app10144853

APA Style

Badr, A. M. A., Barakat, A., Albering, J. H., Sharaf, M. M., Ul-Haq, Z., & Soliman, S. M. (2020). Structure, Antimicrobial Activity, Hirshfeld Analysis, and Docking Studies of Three Silver(I) Complexes-Based Pyridine Ligands. Applied Sciences, 10(14), 4853. https://doi.org/10.3390/app10144853

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