Edubiotik : Jurnal Pendidikan.
Biologi dan Terapan ISSN 2528-679X .
ISSN 2597-9833 .
Vol.
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November 2025, 11.
496 Ae 506 Available online at:
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php/edubiotik Research Article In silico analysis of bioactive compounds from Strobilanthes crispus as MurE inhibitors in Escherichia coli Yoga Aria Aditama 1,a .
Indah Rakhmawati Afrida 1,b,* .
Kukuh Munandar 1,c .
Riyanto 2,d 1 Biology Education Program.
Universitas Muhammadiyah Jember.
Jember.
Indonesia 2 Biology Education Department.
Insan Budi Utomo University.
Malang.
Indonesia Email: yhogaaja1123@gmail.
com 1,a , indahrakhmawatiafrida@unmuhjember.
id 1, b, * , kukuhmunandar@unmuhjember.
id 1, c , riyanto@uibu.
id 2,d * Corresponding author Article Information Article History:
Submitted: 2025-06-23 Revised: 2025-11-12 Accepted: 2025-12-30 Published: 2025-12-30 Keywords:
Escherichia coli.
molecular docking.
MurE enzyme.
Strobilanthes crispus.
urinary tract infection Publisher Biology Education Department.
Insan Budi Utomo University.
Malang.
Indonesia
ABSTRACT
Urinary Tract Infection (UTI) is one of the most common infectious diseases, predominantly caused by Escherichia coli.
Increasing antibiotic resistance has driven the search for new antibacterial agents from natural sources.
This study aims to evaluate the potential of bioactive compounds from Strobilanthes crispus as inhibitors of the E.
coli MurE enzyme using an in-silico approach.
Molecular docking, toxicity prediction, and pharmacokinetic analysis were performed.
The docking results demonstrated that apigenin 7-O-beta-D-glucuronide exhibited the highest binding affinity toward MurE with a binding energy of -9,5 kcal/mol, followed by acteoside (-9,4 kcal/mo.
and isoacteoside (-9,2 kcal/mo.
, outperforming ciprofloxacin (-7,1 kcal/mo.
Pharmacokinetic analysis indicated that all tested compounds showed good solubility and acceptable safety profiles, althought they exhibited los gastrointestinal absorption and poor oral These findings suggest that S.
crispus bioactive compounds possess promising potential as MurE inhibitors and warrant further optimization and experimental validation as antibacterial candidates against E.
How to Cite Aria Aditama .
Rakhmawati Afrida .
Munandar.
, & Riyanto.
In silico analysis of bioactive compounds from Strobilanthes crispus as MurE inhibitors in Escherichia coli.
Edubiotik : Jurnal Pendidikan.
Biologi Dan Terapan, 10.
https://doi.
org/10.
33503/ebio.
Copyright A 2025.
Aria Aditama et al.
This is an open-access article under the C C-BY-SA license INTRODUCTION Urinary tract infection (UTI) remains a major global public health issue, with Escherichia coli (E.
recognized as the primary causative pathogen.
UTI commonly affects the kidneys, ureters, bladder, and urethra, and disproportionately occurs among women of reproductive age (Brookes-Howell et al.
Sher et al.
, 2.
In Indonesia, the estimated incidence reaches 90-100 cases per 100,000 population per year, underscoring the need for effective therapeutic strategies in both global and local Risk factors for UTI include poor personal hygiene, sexual activity, urinary catheterization, and edubiotic@uibu.
: https://doi.
org/10.
33503/ebio.
Edubiotics : Journal of Education.
Biology and Applied Vol.
No.
, 11.
496 Ae 506 comorbidities such as diabetes mellitus, which contribute to increased susceptibility and severity (Du et , 2024.
Sinha et al.
, 2025.
Soiza et al.
, 2.
Antibiotics remain the standard therapy for UTI.
however, irrational and excessive antibiotic use has accelerated antimicrobial resistance (AMR), particularly in E.
Increasing resistance to commonly used antibiotics such as ciprofloxacin poses a major clinical challenge, making previously manageable infections difficult to treat.
The World Health Organization (WHO, 2.
has identified AMR as a global health emergency, emphasizing the urgent need for alternative therapeutic agents with novel mechanisms of action.
Medicinal plants have gained significant attention as promising sources of new bioactive compounds due to their diverse pharmacological properties and relatively low side-effect profiles.
Strobilanthes crispus, traditionally used in several Asian countries including Indonesia, exhibits various biological activities, including anti-inflammatory, anticancer (Baraya et al.
, 2022.
Bataya et al.
, 2021.
et al.
, 2.
, antioxidant (Tan et al.
, 2.
, and antimicrobial effects (Adibi et al.
, 2017.
Adriana et al.
Ban et al.
, 2022.
Dwi Pramesti et al.
, 2.
Bioactive constituents of S.
crispus, such as flavonoids, phenolic compounds, saponins, and tannins, have demonstrated antibacterial potential against several pathogenic bacteria (Adriana et al.
, 2023.
Suboh et al.
, 2.
Although previous studies have reported the antibacterial activity of Strobilanthes crispus extracts, the molecular mechanisms underlying its activity against Escherichia coli, particularly uropathogenic strains, remain poorly understood.
Several essential bacterial enzymes, such as DNA gyrase.
MurA, and penicillin-binding proteins, have been extensively investigated as antibacterial targets.
however, these targets are frequently associated with the development of antibiotic resistance due to their long-term clinical use.
In contrast, the MurE enzyme, a cytosolic ligase involved in the incorporation of mesodiaminopimelic acid into the peptidoglycan precursor, plays a critical role in bacterial cell wall biosynthesis and remains comparatively underexplored as a therapeutic target (Kumar et al.
, 2023.
Sangshetti et al.
Previous in silico studies on plant-derived antibacterials have largely focused on well-established targets or evaluated crude extracts without elucidating specific enzymeAeligand interactions.
Therefore, this study contributes a target-specific and mechanistic in silico investigation by evaluating the interaction of individual S.
crispus bioactive compounds with the MurE enzyme.
Moreover, this work integrates molecular docking with pharmacokinetic and toxicity predictions, providing a more comprehensive assessment than docking-only studies.
By comparing the binding affinity of S.
compounds with a reference antibiotic, this study offers new insights into MurE inhibition and highlights the potential of S.
crispus as a source of alternative antibacterial agents against E.
Advances in computational biology enable in silico approaches such as molecular docking to efficiently predict ligandprotein interactions and assess potential antibacterial activity (Afrida et al.
, 2021.
Bullock et al.
, 2020.
Paramita et al.
, 2024.
Widhiastuti et al.
, 2.
This method provides insights into binding affinity and inhibition mechanisms and can be complemented by toxicity and pharmacokinetic analysis to evaluate drug-likeness properties.
Therefore, this study aims to assess the antibacterial potential of S.
crispus bioactive compounds against the MurE enzyme of E.
coli through molecular docking analysis, supported by toxicity and pharmacokinetic evaluation.
The findings are expected to contribute to the early development of plantbased therapeutic candidates to address E.
coli-associated UTI and the increasing burden of antibiotic Aditama et al.
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RESEARCH METHODS
This study employed an exploratory descriptive research design based on an in-silico approach to investigate the antibacterial potential of bioactive compounds from S.
crispus against E.
The entire research process was conducted computationally without wet-laboratory experiments, utilizing bioinformatics software and publicly accessible online databases.
The research workflow comprised several stages, including identification of bioactive compounds, selection and preparation of the target protein, molecular preparation of ligands, docking simulation, and pharmacokinetic and toxicity evaluation.
Bioactive compounds of S.
crispus were identified from the PubChem database.
The threedimensional crystal structure of the MurE enzyme of E.
uramyl ligase.
PDB ID: 7B9E) was retrieved from the Protein Data Bank and prepared by removing water molecules and non-essential heteroatoms, followed by the addition of polar hydrogen atoms.
Ligand structures were energy-minimized prior to Molecular docking simulations were performed using AutoDock Vina with a rigid receptor and flexible ligands.
The docking grid box was defined as encompassing the MurE active site region to ensure coverage of key catalytic residues, and the exhaustiveness parameter was set to 8.
Docking poses were ranked based on binding affinity values .
cal/mo.
, and the optimal binding conformation was selected according to the lowest binding energy and favorable proteinAeligand interaction profiles.
The population in this study comprised all bioactive compounds reported from S.
Five compounds were selected as samples based on a predicted antibacterial probability (Pa valu.
greater According to the PASS (Prediction of Activity Spectra for Substance.
approach, compounds with Pa values above 0.
5 are considered to have a meaningful probability of exhibiting biological activity.
therefore, a Pa threshold of >0.
6 was applied to prioritize compounds with promising antibacterial potential for exploratory in silico analysis (Filimonov et al.
, 2.
These compounds included apigenin 7-O--Dglucuronide (CID: 5319.
, acteoside (CID: 5281.
, isoacteoside (CID: 6476.
, quercetin 3rutinoside (CID: 5280.
, and calceolarioside (CID: 11284.
Ciprofloxacin (CID: 2.
was used as a reference compound due to its well-established antibacterial activity against Gram-negative and Grampositive bacteria.
Computational analyses were conducted using PyMOL for visualization and structure preparation.
Discovery Studio 2024 for active site identification and interaction analysis, and PyRx integrated with AutoDock Vina for molecular docking simulations (Mawaddani et al.
, 2.
Pharmacokinetic properties and toxicity profiles of the top-ranked compounds were predicted using SwissADME and ProTox-II online Data collection involved retrieving compound and protein structures from public databases and generating molecular interaction data from docking simulations, including binding affinity values, hydrogen bond interactions, and key interacting residues.
Data analysis employed a descriptive-comparative approach by comparing the molecular docking results and pharmacokineticAetoxicological profiles of the tested compounds with those of the reference compound .
The results were interpreted to evaluate the antibacterial potential and drug-likeness of S.
crispus bioactive compounds based on their molecular interaction characteristics.
FINDING AND DISCUSSION
The muramyl ligase (MurE) enzyme is an essential component of the peptidoglycan biosynthesis pathway, which is vital for the survival of bacteria, including E.
coli the main pathogen responsible for urinary tract infections (UTI.
(Hervin et al.
, 2.
MurE catalyzes the addition of meso-diaminopimelic acid .
-DAP) to the growing peptidoglycan precursor, a key step in bacterial cell wall synthesis (Rohde.
Since this process does not occur in eukaryotic cells.
MurE serves as a specific and strategic target Aditama et al.
Ae In silico analysis of bioactive compounds from Strobilanthes A Edubiotics : Journal of Education.
Biology and Applied Vol.
No.
, 11.
496 Ae 506 for the development of novel antibacterial agents.
In this study, the bioactive compounds from S.
were evaluated for their potential antibacterial activity through inhibition of the E.
coli MurE enzyme using an in silico molecular docking approach (Table .
Table 1.
Binding affinity and amino acid residues between ligands and proteins Binding Affinity Complex Interacting Residues Interaction Types .
cal/mo.
Apigenin 7-O-beta-D-9.
GLN370.
PHE307.
MET343,
Hydrogen bonds, glucuronide_MurE ASN308.
ALA371.
LYS367.
THR121.
LYS120.
ARG342 Acteoside_MurE THR117.
THR122.
ASN118.
Hydrogen bonds.
ASN308.
GLU357.
LYS367.
GLN370.
ALA306.
PHE307, hydrophobic, nonALA364.
ALA371.
ASP357.
TYR358 Isoacteoside_MurE SER29.
ASN91.
LEU27.
Hydrogen bonds.
VAL41.
ASP28.
ASP164.
VAL163.
THR26.
MET25 Quercetin 3-9.
THR143.
THR121.
MET347,
Hydrogen bonds.
Rutinoside_MurE ALA371.
ARG342.
LYS367.
THR112.
LYS120.
GLY119, hydrophobic, nonTYR358 Calceolarioside_MurE ASP357.
ARG342.
THR121.
Hydrogen bonds.
ALA371.
PHE307.
ALA306.
MET343.
LYS367 Ciprofloxacin_MurE THR122.
ASN308.
ALA368.
Hydrogen bonds, .
LYS367.
TYR358 Bond Distance .
I) 7 Ae 4.
6 Ae 4.
7 Ae 4.
7 Ae 4.
7 Ae 4.
2 Ae 4.
The molecular docking results demonstrated that the S.
crispus bioactive compounds were able to interact effectively with the active site of the E.
coli MurE enzyme, forming hydrogen bonds, hydrophobic interactions, and electrostatic contacts with several amino acid residues.
The binding affinity values ranged from Ae8.
2 to Ae9.
5 kcal/mol, reflecting varying binding strengths among the compounds.
Apigenin 7-O--D-glucuronide exhibited the strongest interaction (Ae9.
5 kcal/mo.
, forming hydrogen bonds with GLN370 and THR121, electrostatic interactions with LYS120 and ARG342, and hydrophobic contacts with MET343 and ALA371 (Figure .
The short bond distances .
7Ae4.
1 yI) indicatea stable and energetically favorable ligandAeprotein complex.
Similarly, acteoside and isoacteoside showed strong binding affinities of Ae9.
4 kcal/mol and Ae9.
2 kcal/mol, respectively.
Acteoside interacted with 13 amino acid residues, including ASN118.
GLU357.
ASP357, and TYR358 (Figure .
, suggesting stable and synergistic binding, while isoacteoside formed hydrogen bonds with SER29 and THR26 and electrostatic interactions with ASP28 and ASP164 near the MurE active site (Figure .
Quercetin 3-rutinoside also demonstrated a high binding potential (Ae9.
0 kcal/mo.
, forming hydrogen and electrostatic interactions with ARG342.
LYS367, and TYR358 (Figure .
, whereas calceolarioside exhibited a lower binding affinity (Ae8.
2 kcal/mo.
and interacted mainly with ASP357.
ARG342, and LYS367 (Figure .
For comparison, ciprofloxacin formed key interactions with residues THR122.
ASN308.
ALA368.
LYS367, and TYR358 at the MurE catalytic site (Figure .
, consistent with previous reports (Moreira da Silva et al.
, 2017.
Rambaher et al.
, 2.
These findings suggest that ciprofloxacin, in condition to its Aditama et al.
Ae In silico analysis of bioactive compounds from Strobilanthes A Edubiotics : Journal of Education.
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, 11.
496 Ae 506 established inhibition of DNA gyrase and topoisomerase IV, may also interact with MurE, indicating potential drug repurposing effects against bacterial cell wall biosynthesis (Ogbuagu et al.
, 2.
To further interpret these docking results, the involvement of MurE catalytic residues was analyzed based on recent structural studies.
MurE is an ATP-dependent ligase responsible for the incorporation of D-glutamate into the UDP-N-acetylmuramoyl peptide during peptidoglycan biosynthesis.
Structural and functional analyses have identified several conserved catalytic and substrate-binding residues in E.
MurE, including ARG342.
LYS367.
ASP357, and TYR358, which play essential roles in ATP binding, substrate stabilization, and peptide bond formation.
These residues are highly conserved among Gramnegative bacteria and absent in mammalian cells, making MurE an attractive antibacterial target.
The direct interactions observed between S.
crispus bioactive compounds, and these key catalytic residues suggest a plausible inhibitory mechanism through competitive occupation of the MurE active site, potentially disrupting ATP utilization and peptide ligation.
Similar inhibitory patterns have been reported for flavonoids such as apigenin and quercetin, which exert antibacterial effects through enzyme inhibition and interference with bacterial metabolic pathways (Saqallah et al.
, 2022.
Shamsudin et al.
, 2.
Figure 1.
Interaction between the apigenin 7-O-beta-D-glucuronide_MurE complex and the amino acid residues Figure 2.
Interaction between the acteoside_MurE complex and the amino acid residues Figure 3.
Interaction between the isoacteoside_MurE complex and amino acid residues Aditama et al.
Ae In silico analysis of bioactive compounds from Strobilanthes A Edubiotics : Journal of Education.
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496 Ae 506 Figure 4.
Interaction between the quercetin 3-rutinoside_MurE complex and the amino acid residues Figure 5.
Interaction between the calceolarioside_MurE complex and the amino acid residues Figure 6.
Interaction between the ciprofloxacin_MurE complex and the amino acid residues Following the molecular docking analysis, pharmacokinetic evaluation was conducted to assess the drug-likeness of the tested compounds (Table .
The pharmacokinetic profiles revealed notable differences between ciprofloxacin and the five S.
crispus bioactive compounds.
Ciprofloxacin exhibited the lowest molecular weight .
34 g/mo.
and the smallest topological polar surface area (TPSA: 74.
yIA), supporting its high gastrointestinal absorption, optimal bioavailability, and high solubility (Moradpour et al.
, 2.
It also complied with all major drug-likeness rules (Lipinski.
Ghose.
Veber.
Egan, and Muegg.
and achieved the highest bioavailability score .
, indicating an ideal oral drug profile.
Conversely, all S.
crispus compounds had high molecular weights (>446 g/mo.
and large TPSA values (>187 yIA to 289.
43 yIA), limiting membrane permeability and gastrointestinal absorption.
Consequently, these compounds violated two or more oral drug-likeness criteria and showed low bioavailability scores .
11Ae0.
The low consensus logP values (Ae1.
51 to 0.
reflected strong hydrophilicity, favoring solubility but restricting membrane diffusion.
Aditama et al.
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496 Ae 506 Table 2.
Results of pharmacokinetic analysis of test compounds Parameter Apigenin 7Acteoside Isoacteoside Quercetin 3O-beta-Drutinoside Glucuronide Molecular Weight .
/mo.
TPSA .
IA) LogP (Consensu.
Solubility Class
(ESOL)
GI Absorption Low Low Low Low Lipinski's Violation Ghose's Violation Veber Violation Egan's Violation Muegge's Violation Bioavailability Score PAINS Alert 1 alert 1 alert 1 alert .
atechol_A) .
atechol_A) .
atechol_A) Brenk Alert 3 alerts 2 alerts 1 alert Leadlikeness did not pass did not pass did not pass did not pass Calceolarioside Ciprofloxacin very soluble Low High 1 alert .
atechol_A) 2 alerts did not pass Several S.
crispus compounds also triggered PAINS and Brenk alerts, including acteoside, isoacteoside, and calceolarioside, suggesting the presence of structural motifs that may cause assay interference or chemical instability (Capuzzi et al.
, 2.
Although these characteristics indicate potential limitations for direct oral administration, they do not preclude the possibility that these compounds may act as potential MurE inhibitors.
Instead, formulation optimization strategies, such as nanoparticle encapsulation, prodrug desain, or chemical modification may enhance their pharmacokinetic behavior and biological performance (Ogbuagu et al.
, 2022.
Saqallah et al.
, 2.
To complement the pharmacokinetic analysis, toxicity predictions were performed to estimate the safety profiles of the tested compounds (Table .
The results indicated that all S.
crispus bioactive compounds exhibited lower predicted acute toxicity than ciprofloxacin.
Each of the five compounds showed a predicted LD50 value of 5000 mg/kg body weight, corresponding to toxicity class 5 under the Globally Harmonized System (GHS), which suggests a low risk of acute toxicity based on computational In comparison, ciprofloxacin displayed a predicted LD50 value of 2000 mg/kg .
The toxicity prediction models yielded confidence levels above 70% for all compounds, indicating acceptable reliability of the predictions.
however, experimental validation is required to confirm these findings.
Overall, the integrated in silico analysis combining molecular docking, pharmacokinetic profiling, and toxicity prediction suggests that S.
crispus bioactive compounds particularly apigenin 7-O-beta-Dglucuronide and acteoside may act as potential MurE inhibitors in E.
MurE plays a critical role in the ATP-dependent ligation of D-glutamate to UDP-N-acetylmuramoyl-L-alanine, a key step in the formation of the peptide stem that ultimately incorporates meso-diaminopimelic acid .
-DAP) during bacterial peptidoglycan biosynthesis.
Disruption of this pathway can compromise cell wall integrity and bacterial Aditama et al.
Ae In silico analysis of bioactive compounds from Strobilanthes A Edubiotics : Journal of Education.
Biology and Applied Vol.
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496 Ae 506 Table 3.
Analysis of predicted toxicity of test compounds Apigenin 7-O-betaActeoside Isoacteoside D-Glucuronide Predicted LD50 Predicted Toxicity Average Similarity Prediction Accuracy Quercetin 3-rutinoside Calceolarioside Ciprofloxacin The docking results demonstrated that these compounds interact strongly with conserved catalytic and substrate-binding residues within the MurE active site, including ARG342.
LYS367.
ASP357, and TYR358, which are known to be essential for ATP utilization and peptide bond formation in the m-DAPAe dependent peptidoglycan synthesis pathway.
The observed high binding affinities, together with favorable predicted toxicity profiles, suggest that these compounds may competitively occupy the MurE catalytic pocket and interfere with the ligation process required for proper cell wall assembly.
Although their predicted oral bioavailability is limited, these findings highlight the potential of S.
crispus bioactive compounds as lead molecules for further optimization and development of natural productAebased antibacterial agents targeting the m-DAPAeMurE axis in E.
CONCLUSION
This study conceptually supports the potential of S.
crispus bioactive compounds .
pigenin 7-Obeta-D-glucuronide, acteoside, isoacteoside, quercetin 3-rutinoside, and calceolariosid.
as potential antibacterial agents against E.
coli through inhibition of the MurE enzyme, a crucial catalyst in bacterial cell wall biosynthesis.
The molecular docking results revealed that these compounds formed stable interactions with the active residues of MurE, suggesting their ability to interfere with its catalytic function.
Toxicological analysis indicated that all compounds belong to toxicity class 5 .
redicted LDCICA = 5000 mg/k.
, reflecting lower predicted acute toxicity compared to ciprofloxacin .
However, pharmacokinetic evaluation showed limitations related to high molecular weight, large polar surface area, and low gastrointestinal absorption, which may restrict oral bioavailability.
Importantly, this study contributes to the development of herbal-based antibacterial candidates by providing an integrated in silico framework that links bioactive compound selection.
MurE-targeted mechanistic analysis, and preliminary safety evaluation to support early-stage screening of natural products.
Overall, these findings provide a conceptual basis for the development of S.
crispus-derived antibacterial agents as natural product leads, while further in vitro and in vivo validation, as well as formulation optimization .
nanoparticle or prodrug strategie.
, are recommended to enhance their pharmacological effectiveness and clinical applicability.
ACKNOWLEDGEMENT
The author would like to thank the LPPM of Universitas Muhammadiyah Jember for the funding provided for the implementation of this research with contract number 469/II.
AU/LPPM/Riset/2024 dated December 9, 2024.
Aditama et al.
Ae In silico analysis of bioactive compounds from Strobilanthes A Edubiotics : Journal of Education.
Biology and Applied Vol.
No.
, 11.
496 Ae 506
REFERENCES