1 Introduction

Antibiotics are used to fight bacterial infections in both humans and animals [1]. Antibiotics primarily inhibit bacteria growth by eradicating or stopping them from proliferating and spreading [2, 3]. Since there aren't many new classes of antibiotics in the pharmaceutical supply chain and antimicrobial medications are becoming steadily less effective, antimicrobial resistance is currently a severe danger to human health [4]. However, the issue of a decline in innovative therapeutic drugs to nurse numerous diseases in humans and animals is currently plaguing the world [5]. Due to resistance, current antibiotics are progressively losing their efficacy, and society may be transitioning into a post-antibiotic period. This poses serious risks to both national security and public health, such as pandemics and bioterrorism [6]. According to current estimates, antibiotic resistance is a growing problem that is claiming the lives of millions of people each year. If nothing is done to stop the trend towards rising AMR, 10 million lives may be at risk by 2050 [7]. Additionally, those who reside in developing nations, where infectious diseases account for a major portion of morbidity and mortality, will be the most severely affected [8]. More than a million deaths occur each year as a direct result of the six top infections causing resistance-associated mortality (Staphylococcus aureus, Acinetobacter baumannii, Klebsiella pneumoniae, Streptococcus pneumoniae, and Pseudomonas aeruginosa) [3, 9]. Complex microbial communities called biofilms are enclosed in an extracellular protein matrix, extracellular DNA (eDNA), lipids, and exo-polysaccharides [10, 11]. Since many illnesses produce biofilms as a form of resistance, they are more difficult to cure than their planktonic relatives [12].

Biofilms enable surface-attached microbes to endure adverse circumstances, such as the presence of inbuilt host defenses and antimicrobial substances [13]. As a result, one of the indirect processes through which bacteria develop antibiotic resistance is the development of biofilms [14], and it is also a mechanism by which, within the micro community of the biofilm, they disseminate resistance genes among the individuals [15]. Because they may form biofilms, several species of significant bacterial genera, which include Salmonella, Staphylococcus, Pasteurella, Bacillus, and Escherichia coli, etc., cause illnesses that are challenging to treat [16, 17], biofilms are responsible for two-thirds of all bacterial illnesses in humans, and they may be involved in over 60% of microbial illnesses [18, 19]. The necessity to address these issues and the shortage of new antimicrobials provide sufficient incentive to expand the hunt for viable medications and a variety of drug scaffolds [20]. Because a sizable portion of newly licensed antibacterials are either natural items in their original form or natural product derivatives, research efforts focusing on natural products provide a promising avenue for exploration [21]. Medicinal herbs have been used to treat a variety of human disorders since the dawn of time. Numerous plants have been shown to have antibacterial properties and to be employed in treating numerous infectious diseases in humans and animals [22]. It has been established that terpenoids and flavonoids are efficient against pathogens [23]. To examine their biological functions, separating and describing chemical constituents is a study area of interest. Molecular docking techniques have grown in importance for drug discovery today [24]. The biological effects of essential oils' and plant extracts' can be discovered through the phytochemical screening of plant components; however, the phytoconstituent that causes this impact is still unknown [25]. Silico docking studies are crucial in order to comprehend the compatibility and interaction of the identified compounds with the target proteins [26,27,28]. We chose Seriphidium kurramense (S. kurramense) as the subject of our investigation because of its intriguing antibacterial properties. It is a healing plant typically found in Pakistan's FATA region, which includes the upper Kurram organization, and in some areas of Afghanistan's border with Kurram office. The locals used this plant for a variety of uses. They mostly employed it as an anthelmintic, a remedy for stomach problems, and something harmful to people with diabetes. This study's goal was to identify the active ingredients of Seriphidium kurramense using the GC–MS method in order to analyze the bacteria's antibacterial and anti-biofilm properties further. Additionally, the draggability and pharmacokinetic characteristics of Seriphidium kurramense have been assessed utilizing ADME profiles and molecular docking methods.

2 Materials and methods

2.1 Plant collection and extraction

Plant was obtained from the Pewar Parachinar Kurram Agency ex FATA, it was shade-dried and ground into powder. Ethanolic extract of Seriphidium kurramense was prepared for the experiment.

2.2 Antibacterial evaluation by valves method

For this method, nutrient agar medium was prepared and autoclaved at 121 °C and 15psi for 15 min and was poured into sterile petri plates so that the 3/4th of the plate should be filled with the medium. The plates were placed into a laminar airflow cabinet to solidify. Inoculum of different bacteria was spread over the plate and then valves were made by 1 ml tips of micropipette which were also autoclaved. Four valves were made keeping the distance between them. Plates were incubated for 24 h at 37 °C. Zone of inhibitions was measured with a graduated ruler in millimeter scales. All assays were performed in continuous replicates, utilizing new agar plates. In situations where questionable results were observed, the assay was repeated in triplicate to confirm its activity and reliability [29].

2.3 Anti-biofilm activity through microtiter plate

For this purpose, microtiter plates with flat bottom containing 96 well were used. Fresh inoculum of those bacteria which produce biofilm was made. Nutrient broth media was prepared and autoclaved at 121 °C and 15 psi for 15 min. The microtiter plate was then labeled. Three positive controls and twelve negative controls totaled twelve valves. And the rest was used to check the antibiofilm activity of Seriphidium kurramense and some antibiotics. 200 µl of inoculum was added to all the wells with 20–200 µl micropipette. Antibiotics like penicillin, ceftriaxone, and gentamycin were used for the comparison of antibiofilm activity with plant extract. Antibiotics were diluted two folds. 50 µl antibiotics and plant extract were added in different valves while in positive control 50 µl sterilized nutrient broth was added. The total volume of each valve was 250 µl. The microtiter plate was maintained at 37 °C in an incubator for 24 h. Cells were discarded by flipping the plate over after incubation and tapped them separately to gently submerge in each well in a little tub of water. Water was tapped out and the process was repeated for a second time. The stain was removed till all excess liquid was removed. 0.1% crystal violet was added and the plates were kept for 15 min and then the stain was washed in the little tub of water and kept in open air to dry. Then 30% of acetic acid was added to the plates. They were incubated at room temperature for 10 to 15 min to allow the dye to solubilize. The supernatant of each well was briefly mixed by in–out pipetting. Optical density (OD) was estimated for each of these samples at a wavelength of 450 nm with the ELISA plate reader [30].

2.4 Analysis using GC–MS (gas chromatography–mass spectrometry)

We used a Thermo Scientific Trace GC1310-ISQ mass spectrometer with a direct capillary column TG-5MS (30 m 0.25 mm 0.25 m film thickness) to analyze the samples' chemical compositions. We started off keeping the temperature in the column oven at 50 °C; after that, we raised it by 15 °C/min to 150 °C, which we held for 3 min, and then by 30 °C/min to 220 °C, which we also held for 3 min. The MS transfer lines and injector temperatures were then maintained at 250 and 240 °C, respectively. As a carrier gas, helium was employed at a constant flow rate of 1 mL/min. We used the Autosampler AS1300 in split mode with a 3 min solvent delay, and we automatically injected 1 L of the diluted samples. We gathered EI mass spectra in full scan mode from m/z 40 to 1000 at 70 eV ionization voltages. The ion source temperature was then tuned to 200 °C. Finally, by comparing the components' retention times and mass spectra to those of the WILEY 09 and NIST 11 mass spectral databases, we were able to identify the constituent [31].

2.5 Fourier transform infrared spectroscopy FTIR analysis

For the structural identification of functional groups of various chemicals in extracts, Fourier transform infrared spectroscopy was used. The powdered samples were combined, and measurements of potassium bromide and the infrared spectrum were made at a temperature of 25 °C with a 4 cm−1 resolution. The IR spectra were measured using the OPUS program. The outcomes were contrasted with criteria for identifying active groups [32,33,34,35].

2.6 Molecular docking studies

Compounds found in Seriphidium kurramense were obtained from National Institute of Standards and Technology (NIST) Chemistry WebBook (https://webbook.nist.gov/chemistry/) in 3D.SDF format. Energy minimizations was carried out through MOE version 2019.0102 (Molecular Operating Environment) [36] for top ten Compounds and prepared for docking. Molecular docking studies were carried out through MOE for vital proteins of E.coli, Bacillus, Staphylococcus and Salmonella in order to further validate inhibitory studies. 3D crystal structures predicted through X-RAY diffraction technique were obtained from protein data bank (http://www.rcsb.org/pdb/) in.pdb format. MOE finds all possible binding geometries of receptor-ligand (binding affinities) based on a numerical score known as S-score. S-score is based on hydrogen bonds, salt bridges, hydrophobic interactions, cation-π, and solvent exposure [37]. Escherichia coli protein (PDB ID: 4MEE) is monomeric autotransporter AIDA-I (adhesin involved in diffuse adherence) bacterial protein which causes many gastrointestinal diseases via invasion, adhesion, and biofilm formation in host cells [36]. Bacillus spizizenii protein (PDB ID: 8AUR) is the major component of the biofilm matrix, by forming amyloid fibers which contribute to biofilm structure and stability [37]. Staphylococcus aureus protein (PDB ID: 7C7R) is Biofilm-associated surface protein (Baps) which is involved in mediating biofilm development and intercellular adhesion [38]. Salmonella protein (PDB ID: 5XP0) is bacterial adhesion to abiotic or biotic surfaces which regulate CsgD and switches planktonic growth to biofilm formation [39]. The rationale for selecting the proteins under investigation in this research stems from their significant contributions to various aspects of bacterial pathogenesis, including involvement in gastrointestinal diseases, modulation of biofilm structure and stability, facilitation of biofilm development, and mediation of intercellular adhesion. The exploration of these proteins is aimed at achieving a comprehensive understanding of the molecular mechanisms governing bacterial biofilm formation, with implications for the development of therapeutic interventions and strategies to address biofilm-associated infections. In MOE receptor structure were opened and prepared via quick prep module. The binding site was located using MOE site finder module.

2.7 In silico toxicity and drug-likeness predictions

Pharmacokinetics analysis was carried out for compounds found in Seriphidium kurramense which basically screen out compounds based on adsorption, distribution, metabolism, excretion, and toxicity (ADMET) within the body. In consideration of ADMET approximately 40% of drug candidates fails to pass clinical trials during in-silico study. So, it is necessary to eliminate highly reactive and unsuitable compounds [40]. ADMET analysis was done via QikProp Ligand-Based ADME/Tox Prediction Module in Schrodinger Maestro [41].

3 Results

3.1 Bacteria and its antibacterial activity

Four types of bacteria were isolated by streak plate technique which was also involved in making biofilm. The antibacterial activity was checked against all these four bacteria by using plant extract of Seriphidium kurramense and three different types of antibiotics (Penicillin, Gentamicin, Ceftriaxone). All antibiotics were diluted three folds. Then the inhibitory zones made by plant extract and the above-mentioned antibiotics were compared (Table 1, Fig. 1).

Table 1  Inhibitory zones made by plant extract and some antibiotics
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Fig. 1
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Measurement of Inhibitory zones by plant extract and antibiotics

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The graph displays the inhibitory zones formed by antibiotics and medicinal plant. The y-axis is the mm measurement of inhibitory zones formed by antibiotics and plant extract, while on the x-axis the microbes are listed. It can be clearly seen from the above graph that the maximum antibacterial activity by the plant extract was shown against Staphylococcus aureus which gave inhibitory zone of 28 mm. While among all the commercial antibiotics penicillin gave inhibitory zone of 30 mm which was also against Staphylococcus aureus which is a clear indication that this plant is as effective as all other antibiotics which are commercially synthesized.

3.2 Anti-biofilm activity through microtiter plate

Bacterial biofilms show a high expansive range of versatile anti-toxin obstruction and cause 66% of all contaminations, yet, there is an absence of supported anti-biofilm specialists. The microtiter plate (additionally called 96-well plate) examines for considering biofilm arrangement is a strategy that takes into account the perception of bacterial adherence to an abiotic surface. In this measure, microscopic organisms are brooded in vinyl "U"- base or different kinds of 96-well microtiter plates. The mean value of triplet sample is converted into percentage. Our results have showed. Ceftriaxone has been classic antibiotic for all the bacterial species. All bacterial species growth have been maximum inhibit by ceftriaxone and penicillin respectively. Gentamycin and plant extract have exhibit antimicrobial efficiency at minimum range (Table 2, Fig. 2).

Table 2 Biofilm growth inhibition by plant extract and commercial antibiotics on different bacteria
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Fig. 2
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Comparison of biofilm growth inhibition among plant extract and commercial antibiotics on different bacteria

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Antibiofilm activity is indicated with the help of above-mentioned bar graph. The horizontal axis features the cluster of bars that elaborate the effectivity of antibiotics for the specific microbe. While the vertical-axis describes the growth inhibition of microbes. The antibiofilm activity of plant extract against E.coli and Bacillus showed biofilm growth inhibition up to 15%, Staphylococcus aureus showed 14% and for Salmonella only 6% biofilm growth was inhibited. Ceftriaxone gave highest percentage (80%) of inhibition in anti-biofilm formation against Bacillus. Thus, we can culminate that the efficiency of anti-biofilm generation is dramatically decreasing from penicillin to plant extract.

3.3 Analysis using GC–MS (gas chromatography–mass spectrometry)

The GC/MS results show that the plant contains a number of different compounds, including eucalyptol, bicyclo [3.1.0] hexan-3-one, [+]-2-bornanone, bicyclo [2.2.1] heptan-2-ol, 1,2,2,3-tetramethylcyclopent-3-enol, bornyl acetate, caryophyllene, β-copaene, n-hexadecanoic acid, lumisantonin, phytol, 9,12,15-octadecatrienoic acid, α-santonin, and 3-oxo-10(14)-epoxyguai-11(13)-en-6,12-olide. The highest concentrations of these compounds are α-santonin (42.2%), eucalyptol (3.04%), and bicyclo [3.1.0] hexan-3-one (10.1%) (Tables 3, 4).

Table 3 Compounds found in plant under study
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Table 4 Compounds found in plant under study with PubChem CID and chemical structure
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3.4 FTIR analysis

Plant extract's FTIR spectrum revealed prominent peaks for the carbohydrate function groups –CH2, –CH, –C=O, –CH2 (bending), and –C–O, C–O at 2918, 2849, 1732, 1376, 1235, and 1026 cm−1, respectively. The vibrational intensities at 1732 cm−1 (C=O stretch), 2849 cm−1 (symmetric –CH2 stretch), and 2918 cm−1 (asymmetric –CH2 stretch). The vibration at 1732 cm−1 was attributed to the protein's amide bond's –C=O stretch, while the vibration at 1376 cm−1 was attributed to amide, which might result from the protein's amide group's –N–H bending and –C–N stretching (Fig. 3).

Fig. 3
figure 3

FTIR analysis of plant extract

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3.5 Molecular docking studies

In silico docking of all four-biofilm associated bacterial proteins against selected phytocompounds was performed using MOE against all the predicted active sites. The results showed that all selected inhibitors were in the pocket of the target protein exhibiting a possible interaction. The docking results were manipulated using the GBVI/WSA dG scoring function with the generalized Born solvation model (GBVI). The GBVI/WSA dG is a force field-based scoring function, which estimates the free energy of binding of the ligand from a given orientation. Interaction results were evaluated with the S score. Phytocompounds with the lowest S score tend to establish a strong interaction with all four-biofilm associated proteins on specific active sites (see Fig. 4 3D binding interaction with residues) (Tables 5, 6, 7).

Fig. 4
figure 4

Molecular docking of phytocompound Lumisantonin with biofilm associated bacterial proteins showing binding pocket and residue wise interactions. A Escherichia coli protein (PDB ID:4MEE). B Staphylococcus Aureus protein (PDB ID:7C7R). C Bacillus Spizizenii protein (PDB ID: 8AUR). D Salmonella protein (PDB ID: 5XP0)

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Table 5 Binding energy and molecular interactions of phytocompounds with Escherichia coli protein (PDB ID: 4MEE)
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Table 6 Binding energy and molecular interactions of phytocompounds with Staphylococcus Aureus protein (PDB ID: 7C7R)
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Table 7 Binding energy and molecular interactions of phytocompounds with Bacillus Spizizenii protein (PDB ID: 8AUR)
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Molecular interactions of phytocompounds with Escherichia coli protein fits well into binding pocket. Phytocompound 1,2,2,3-Tetramethylcyclopent-3-enol having S-score: − 7.7048 and RMSD: 0.8446 forms hydrogen bond interactions with ARG 1008, LYS 1247, and SER 1277 and other interactions such as van der waals with residue ARG 1008, LYS 1247, SER 1277, GLY 1278.[ +]-2-bornanone with S-score: − 7.5712, RMSD: 2.5391 forms hydrogen bond interactions with ARG 1008, THR 1010, ASP 984, and LEU 980 along with other interactions with ARG 1008, THR 1010. Bicyclo [2.2.1] heptan-2-ol, 1,7,7-trimethyl-, (1S-endo) with S-score: − 6.6380, RMSD: 1.6436 forms hydrogen bond interactions with ARG 1008 and interacts with LYS 1190, LEU 892. Bicyclo [3.1.0]hexan-3-one, 4-methyl-1-(1-methylethyl) with S-score: − 6.7841, RMSD: 0.8022 forms hydrogen bond interactions with ARG 1194, ARG 1008, TYR 1214. Bornyl acetate with S-score: − 8.3845, RMSD: 2.2656 forms hydrogen bond interactions with ARG 1008, LEU 982, and interacts with LEU 982, ILE 1031. Caryophyllene with S-score: − 8.3281, RMSD: 0.6765 forms hydrogen bond interactions with ARG 1008, LEU 892, and interacts with LYS 989, LEU 892, LEU 980. Eucalyptol with S-score: − 7.8073, RMSD: 1.3089 forms hydrogen bond interactions with LYS 989, ARG 1194, and interacts with ILE 1031, SER 1277, THR 1010. Lumisantonin with S-score: − 9.6711, RMSD: 0.6303 forms hydrogen bond interactions with LYS 1190, LEU 980, GLN 1029, LYS 989, and interacts with LYS 1190, GLN 1029, GLN 1267, LEU 980. n -Hexadecanoic acid with S-score: − 10.1233, RMSD: 2.2355 forms hydrogen bond interactions with ARG 1008, LYS 989, ARG 1194 (2), and interacts with ARG 1008, THR 1010, ARG 1194, LYS 989, LEU 892. All these molecular interactions, reflected in S-scores and RMSD values, highlight the favorable binding affinity of Lumisantonin, n-Hexadecanoic acid and ß-Copaene (See Table 4).

Staphylococcus Aureus protein (PDB ID: 7C7R) reveal significant interactions and binding affinities. Notably, Bornyl acetate exhibits the most favorable binding (S-score: − 9.7752) with hydrogen bonds involving GLN 361 and LYS 362, and van der Waals interactions with ASN 515, ASP 445, LEU 364, and LYS 362. Lumisantonin displays the highest binding affinity (S-score: − 10.5009), forming hydrogen bonds with GLN 361, LYS 362, ASN 443, and THR 451, along with van der Waals interactions with ASP 445, LEU 364, GLU 446, ASN 443, and THR 451 and n-Hexadecanoic acid with S-score: − 10.950, RMSD: 1.870 forms hydrogen bonds with ARG 741, ARG 738, GLN 506. Also, exhibits van der Waals interactions with LYS 415, ASP 452, ARG 738 making it highest binding score (see Table 5).

Bacillus Spizizenii protein (PDB ID: 8AUR), the top three compounds demonstrating notable binding affinities and interaction with 1,2,2,3-Tetramethylcyclopent-3-enoS-score of -8.0514 and an RMSD of 0.9320, forming hydrogen bonds with LYS 68 and VAL 55. Additionally, it engages in van der Waals interactions with ASN 56, LEU 224, LEU 57, ILE 222, and ILE 198. Lumisantonin exhibits a strong binding affinity with S-score of − 9.9751 and RMSD of 1.285 forming hydrogen bonds with ILE 222, PHE 109, and LEU 224. The van der Waals interactions include LEU 57, LEU 66, LEU 60, ILE 198, and ASN 56. Among all n-Hexadecanoic acid shows most significant binding affinity with S-score of -10.9172 and an RMSD of 2.4810. It forms hydrogen bonds with LYS 68 (2) and PHE 226 and engages in van der Waals interactions with ASN 59, LEU 224, LEU 57, ILE 222, SER 58, and ILE 198 (see Table 6).

Most favorable binding affinities of phytocompounds with Salmonella protein (PDB ID: 5XP0), based on S-score, are n-Hexadecanoic acid the highest S-score of − 9.8095, forms hydrogen bonds with LYS 18 and ALA 23 along with significant van der Waals interactions of multiple residues, including SER 20, GLN 22, LEU 26, GLN 114, THR 111, ASP 113, and GLU 62. ß-Copaene secures the second-highest S-score of − 9.2908, indicating a notable binding affinity. Although no hydrogen bonds are formed, the compound engages in substantial van der Waals interactions with LEU 26, ASP 113, THR 111, and LEU 87 followed by 1,2,2,3-Tetramethylcyclopent-3-enol, with an S-score of − 7.1322, represents the third-highest binding affinity among the phytocompounds. It forms hydrogen bonds with ASP 113 and engages in van der Waals interactions with ASP 113, GLN 114, ALA 110, and GLU 112 (see Table 7).

3.6 In silico toxicity and drug-likeness predictions

Seriphidium kurramense plant extracts were filtered compounds were taken for ADMET Analysis to find if they are possible drug like candidates. Pharmacokinetics analysis was conducted by QikProp which screen out compounds based on adsorption, distribution, metabolism, excretion, and toxicity (ADMET) [42]. In Table 8 mol-MW which is molecular weight of the compounds followed by Doner HB and Accept HB which is hydrogen doner and acceptor respectively. QPlogPo/w predicts octanol / water partition coefficient, which is basically distribution and absorption of drug in the body. QPPCaco predicts drug metabolism and its transport across membranes whereas QPlogBB predicts brain/blood partition coefficient also known as the blood–brain barrier. QPlogKhsa predicts binding to human serum albumin. Our results show molecular weight in range of 140 to 256 which acceptable. Values of hydrogen doner and acceptor, distribution and absorption, metabolism and its transport across membranes, and blood–brain barrier all lies between acceptable range. In addition to ADMET Analysis all our compounds pass Lipinski’s rule of five which is the rule of thumb for evaluating of drug-likeness and to determine certain properties to finds if drug can be taken orally by human (Table 9).

Table 8 Binding energy and molecular interactions of phytocompounds with Salmonella protein (PDB ID: 5XP0)
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Table 9 ADMET analysis by QikProp Schrodinger
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4 Discussion

The study highlights the significant antibacterial activity of Seriphidium kurramense against various bacterial strains, including Bacillus spizienii, Staphylococcus aureus, Salmonella, and E. coli. The inhibitory zones observed for the plant extract against these bacteria (26 mm, 28 mm, 24 mm, and 26 mm, respectively) suggest a robust antimicrobial potential. It's noteworthy that the antibacterial activity of Seriphidium kurramense is comparable to standard antibiotics like Penicillin, Gentamycin, and Ceftriaxone against the tested bacterial strains. This finding emphasizes the potential of Seriphidium kurramense as a natural alternative or supplement to conventional antibiotics. The discussion addresses the observed variations in inhibition zone widths when compared to other studies [43,44,45]. This variability can be attributed to differences in the chemical composition of the plant extract. Factors influencing the chemical makeup include the season of harvest, climate conditions, soil type, and plant age as study reported earlier [46]. These variables contribute to the complexity of studying plant-based antimicrobials.

To the best of our knowledge, Seriphidium kurramense's antibiofilm activity has not been documented in the literature. In this study, the plant's ability to prevent the growth of biofilms on the aforementioned bacteria was investigated for the first time by using microtiter plate method. The antibiofilm activity of plant compounds demonstrated biofilm growth suppression of up to 15% against E. coli and Bacillus, 14% against Staphylococcus aureus, and only 6% against Salmonella. The maximum percentage of inhibition (80%) in the anti-biofilm formation against Bacillus was provided by ceftriaxone. However, antibiofilm activity was found in previous studies for other species of Artemisia family [47, 48].

The in vitro activities of natural substances are frequently correlated with important target proteins involved in human diseases using computational research. In reality, in silico docking studies can give valuable information on the molecular underpinnings of natural goods' biological activity as well as probable mechanisms of action and modes of binding for active ingredients. Each component in the research plant extract was therefore docked with a particular target protein having antibacterial and antibiofilm capabilities [49, 50].

Docking studies were performed in MOE against Bacillus spizienii, Staphylococcus aureus, Salmonella, and E. coli important proteins that have been involved in biofilm activity. MOE produce binding scores based on binding configurations between the macromolecule and ligand molecules being in the three-dimensional box as discussed in a study [51]. Box is fixed and oriented on the selected atoms for docking. For finding configurations MOE uses molecular mechanics forcefields which is vary for different protocols and studies. All these molecular mechanics forcefields optimize the contacts and generate random changes to the ligand to make best fit to produce electrostatic interactions. The docking begins with user defined or random conformations along with torsion, distance, or using angle which produce binding energies also known as Gibbs free energy [51]. In our study it was calculated through London dG and GBVI/WSA dG (Generalized-Born Volume Integral/Weighted Surface area) scoring functions producing in the units of kcal/mol [52]. We desired negative Gibbs score from our MOE docking result.

The results of the molecular docking studies suggest that the selected phytocompounds exhibit strong interactions with the target bacterial proteins, indicating their potential as antimicrobial agents. The formation of hydrogen bonds and van der Waals interactions at specific active sites underscores the specificity and efficacy of these compounds. The observed variations in binding affinities among different phytocompounds highlight the importance of structural features and chemical properties in determining the strength of interactions. Lumisantonin, n-Hexadecanoic acid, and ß-Copaene consistently demonstrated high binding affinities across different bacterial proteins, suggesting their broad-spectrum inhibitory potential. It is essential to note that in silico docking studies provide valuable insights into potential interactions, but further experimental validation is crucial to confirm the inhibitory activity of these phytocompounds against biofilm-associated bacterial proteins. Additionally, considering the dynamic nature of protein–ligand interactions, molecular dynamics simulations and in vitro assays would complement the findings, offering a more comprehensive understanding of the inhibitory mechanisms. It works by interfering with the signaling and communication processes that bacteria use to coordinate biofilm formation. This disruption prevents the bacteria from adhering to surfaces and producing the protective matrix that constitutes the biofilm structure. As a result, the biofilm formation is inhibited, making the bacteria more susceptible to other antimicrobial agents. ß-Copaene is a sesquiterpene hydrocarbon found in our plant extract which shows antibacterial, same activity was reported for this compound from other plant species [53]. The saturated fatty acid n-Hexadecanoic acid, also known as palmitic acid, was identified in our plant and had an excellent binding score. Additionally, n-Hexadecanoic acid may prevent bacterial cells from sticking to surfaces, slowing the development of biofilms. Previous study reveals the antibacterial and antibiofilm activity of this compound from other plant [53]. These results imply that these phytoconstituents may be able to combat H3N2 influenza by acting as antiviral agents. Additionally, predictions of in silico toxicity and drug resemblance were made in order to evaluate the safety and potential of these phytoconstituents as possible drugs. Rumexoside and clicoemodin were shown to have favorable toxicity profiles and to adhere to drug-likeness standards, which made them attractive candidates for more study [54]. Every active phytocompound possesses drug-like qualities and is non-toxic and carcinogenic. These phytocompounds, either separately or in combination, have the potential to be developed into a potent COVID-19 treatment. We discovered that all three of the 6VYO complexes with anthrarufin, alizarin, and aloe-emodin were stable for up to 50 ns based on MD simulation data. These phytocompounds have the potential to be employed as a medication to treat SARS-CoV-2 infection and can be further investigated in vitro or in vivo [55, 56].

These docking scores and RMSD (Below 2) in all targets suggest that these compounds can be used in inhibitory studies against Bacillus spizienii, Staphylococcus aureus, Salmonella, and E. coli. The potential for these natural substances to prevent biofilm development by interfering with bacterial communication pathways is particularly interesting, as these findings collectively illustrate. Furthermore, the in silico ADMET analysis, covering molecular weight, hydrogen bonding, partition coefficients, and toxicity predictions, underscores the promising drug-likeness of compounds from Seriphidium kurramense. The favorable outcomes in these assessments position these phytocompounds as potential candidates for further drug development studies, warranting subsequent experimental validations as study earlier [57]. Overall, the research suggests that Seriphidium kurramense holds promise as a source of effective antimicrobial agents, with potential applications in combating bacterial infections and biofilm formation.

5 Conclusion

Seriphidium kurramense emerges as a promising botanical resource teeming with diverse phytochemicals of pharmacological significance. The extract from this plant exhibits robust antimicrobial activity against several antibiotic-resistant bacterial strains that pose formidable threats to human health. This research also delved into molecular docking studies, corroborating the in vitro findings by elucidating the binding of identified phyto-compounds to bacterial proteins. The computational assessment underscores the potent ADME (Absorption, Distribution, Metabolism, and Excretion) properties and exceptional binding affinities with the targeted proteins. These findings collectively substantiate the potential of Seriphidium kurramense's alternative application in the treatment of human ailments, owing to its efficacy and safety profile.

5.1 Future perspectives

Future research should focus on isolating and identifying specific bioactive compounds responsible for antibacterial activity. This can pave the way for developing novel antimicrobial agents. Additionally, exploring the clinical applications of Seriphidium kurramense in the context of antibiotic resistance is crucial for translating these findings into practical medical solutions.

5.2 Limitations

The study acknowledges certain limitations, including the need for further exploration of specific chemical constituents, and the complexity introduced by environmental factors. Standardization challenges in studying plant-based antimicrobials and the dynamic nature of protein–ligand interactions should be considered in future investigations. Addressing these limitations will enhance the robustness and applicability of the research findings. These considerations collectively underscore the potential of Seriphidium kurramense in the development of alternative antibacterial agents and provide a foundation for future research endeavors.