Computational Insights of Glucosamine-6-Phosphate Synthase- 2vf5 as Potential Inhibitors of Imidazole Derivatives

doi:10.21203/rs.3.rs-7576479/v1

Background

Bacterial infections pose a significant global health threat due to the increasing prevalence of antibiotic-resistant strains. Despite the availability of new antibacterial agents in India, some infections remain difficult to treat due to resistance and side effects. Glucosamine-6-phosphate synthase (2VF5) is an essential enzyme in bacterial cell wall formation, making it a promising target for novel drug development. This research focuses on molecular docking interactions and ADME (Absorption, Distribution, Metabolism, and Excretion) analysis of halogenated and electron-withdrawing/donating derivatives as potential inhibitors of 2VF5.

Materials and Methods

Computational molecular docking studies were performed to evaluate the binding affinity of selected derivatives with 2VF5. The antibacterial activity of these compounds was assessed using an in-vitro earthworm model, where 100 mg/mL concentrations were tested. Paralysis and mortality times were documented. ADME analysis was conducted to evaluate pharmacokinetic characteristics.

Results

Molecular docking findings revealed strong interactions between the tested compounds and 2VF5, suggesting their potential as inhibitors. In-vitro assays showed that the active compounds caused paralysis in earthworms within 20 minutes and death within 24 minutes. ADME analysis indicated favorable pharmacokinetic properties.

Conclusion

The results suggest that the tested compounds possess antibacterial potential by targeting glucosamine-6-phosphate synthase. Their strong molecular docking interactions and effective in-vitro performance support further research for potential clinical applications in antibacterial therapy.

Imidazole

Swiss ADME

Molecular docking

glucosamine-6-phosphate synthase

Structure-Based Drug Design

The essential heterocyclic nucleus imidazole is well known for having a diverse range of biological functions. The pharmacological effects of imidazole derivatives include antibacterial, anti-inflammatory and analgesic, anti-tubercular, cytotoxic, antiviral, and anti-muscarinic effects. Thus, in order to create potent agents with greater therapeutic efficacy, a novel series of imidazole and its derivatives were synthesized .One of the main criteria of heterocyclic chemistry is the simple and effective synthesis of heterocyclic molecules from easily available chemicals. Imidazole-indole fusion creates newer, more effective, and less reactive imidazoles. It has two equally strong tautomeric structures. Since both forms of imidazole have notable anticancer and antibacterial properties on their own, we developed a more modern synthetic method to create tetra aryl imidazole, which combines imidazole with indole. A review of the pertinent literature reveals that imidazole subordinates possess a range of biological functions independent of their synthetic benefits. The pharmacological activity they exhibit includes antibacterial, anthelmintic, cognitive enhancer, and anticancer properties.^1–3 These adaptable heterocycles are present in the centre structures of many of today's most effective therapies. Debus first described the interaction between glyoxal and smelling salts in 1858, long before this interaction became a fresh approach for the couplings of imidazole subsidiary. Following it, numerous articles depicted the unions of various imidazole subordinates. In light of these assumptions, the focus of this investigation is now on studying the in-vitro cytotoxicity and anthelmintic activities of mixed aryl imidazoles subsidiary. Based on several literature reviews, imidazole derivatives exhibit a variety of pharmacological properties. The most well-known heterocyclic agent is likely imidazole derivatives, which are a prevalent and significant component of many different natural goods and pharmaceuticals. In 1877, the imidazole nucleus was found. Imidazole has the chemical formula C₃H₄N₂. 2,4,5-Triphenylimidazole has the chemical formula C₂₁H₁₆N₂ and a molecular weight of 296.4. Certain imidazole derivatives, such as clonidine, ketoconazole, metronidazole, ornidazole, azamycin, oxiconazole, and ketomidate, are available in the Indian market for use in medication therapy. D-fructose-6-phosphate amido transferase is another term for glucosamine-6-phosphate synthase ^{4 –5}. Targeting this synthase in antimicrobial chemotherapy is a beneficial and efficient strategy. D-fructose-6-phosphate amido transferase is necessary for the conversion of D-fructose-6-phosphate (Fru-6-P) into D-glucosamine 6-phosphate (GlcN-6-P), which is catalysed by glucose-6-phosphate synthase.In the end, uridine 50-diphospho-N-acetyl-D-glucosamine (UDP-GlcNAc) is formed by employing glutamine as the ammonia source ^6–7. This complex plays a crucial role in metabolic regulation during the production of amino sugar-containing macromolecules, which is required for the building of bacterial and fungal cell walls. The several commercial examples are displayed in Fig. 1.The present work involves designing of some novel imidazole derivatives are given in Table 1. In this research; we study the various physicochemical properties, Molecular docking study against a bacterial target and evaluation of its in silico studies and ADMET properties ^{8– 9}.

In silico ADME (Absorption, Distribution, Metabolism and Excretion Studies):

The field known as ADME Studies explains how chemicals behave pharmacologically inside living things. ADME. Swiss ADME an online tool is used to identify new compounds of imidazole pharmacokinetic characteristics silico.We research the Lipinski rule.When two or more of the Lipinski's rules of five are broken, the molecules become inactive when taken orally.^10-12

Ligand Preparation:

The structures of Imidazole derivatives were drawn using Chemsketch software, which is a freeware programme available at http://www.acdlabs.com/download. The imidazole structure is provided in Table 1 and Fig. 2, respectively, and a 3D structure in PDB format is then generated. The proper binding orientations and conformations of several inhibitors into the binding pocket of glucosamine-6-phosphate synthase-2VF5 were determined using the automated docking approach.

Chemistry:

Using the procedures outlined in Scheme 1, the desired imidazole heterocyclic nucleus compounds were synthesised. Good yields of every chemical were obtained. All of the newly synthesised compounds' structures were verified using mass spectrum analysis, 1H-NMR, and FTIR analysis. An N-H peak appeared at d 12.54 and an O-H group was found at d 5.25 in the 1H NMR spectrum, confirming the functional group of 2,4,5-Triphenylimidazole derivatives of (SA6) with the amino group. The functional group of imidazole derivatives of (SA7) peaks with the amino group was confirmed by the appearance of an N-H peak appeared at d 12.1 peak. Bands appeared at 3310 cm-1 (NH2) and 3217 cm-1 (NH) spectra in analytical methods such FTIR. At 3310cm-1 (NH2), the N-H band configuration was visible. Moreover, there was a strong correlation between the assigned structures and the acquired mass values.

Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET)

Imidazole molecules found in all of the developed drugs have oral activity. Tables 1 and 2 present the ADME study results. The logarithm of the molar concentration represents the water solubility. The estimated oral bioavailability of proposed compounds is expected to be good, as their water solubility normally falls between -5.00 and -6.00. (Table 2 and 3) The percentage of the derivatives that were absorbed was computed, and the findings showed that the gastrointestinal tract from the human colon resembles intestinal epithelial cells, which is where most oral drug absorption happens. The blood-brain barrier permeability, % unbound, and volume of distribution (VD) were used to forecast the distribution of the substances in the body. Greater value VD indicates that medication distribution in tissues is superior to that in plasma. In tissues, all of the chemicals exhibit a moderate distribution. Medicines with lower percent bound efficacy are thought to be less bound to blood proteins. According to the plasma protein binding paradigm, an agent will bind firmly to the proteins that carry blood. Imidazole compounds have a percentage PPB that varies from 93% to 100%. Based on ADMT and Druglikeness evaluations, the proposed molecule has a high likelihood of readily achieving the intended targets. We computed the blood-brain barrier (BBB) permeability using Swiss ADME and pre ADMET technologies. Imidazole compounds all function as inhibitors or as substrates. With their favourable ADME and toxicity characteristics, all of the proposed compounds are likely lead molecules.

Molecular Docking study

Molecular docking studies of twelve imidazole derivatives and along with one standard drug i.e. Ciprofloxacin were carried out with the protein target Glucosamine-6-phosphate synthase using Autodock 4.0 to identify the binding mode..

The majority of imidazole derivatives interact differently with various amino acid residues and have strong docking scores. Table 4 displayed it. The derivatives with the greatest docking scores were those containing electron-withdrawing groups, such as NO2, on the phenyl ring, which demonstrated with amino acid residues. An understanding of amino acids was gained through the analysis of molecular docking experiments. Hydrogen bond interactions were demonstrated by Compound SA7 with LYS603, SER303, THR302, LEU484, VAL605, CYS300, UNL1, VAL605, and LEU601; by Compound SA10 with GLN348, GLN348, SER349, SER349, CYS300, CYS300, and LEU601; by Compound SA8 with CYS300, UNL1, VAL605, LYS603, SER604, CYS300.VAL606.All of the synthetic imidazole derivative molecules (SA1–SA10), including the standards, were put through molecular docking with the active site of glucosamine-6-phosphate synthase–2VF5 in order to determine the precise binding location of the ligands with the protein. They demonstrated strong binding interactions with the neighboring residues of amino acids. Table 4 lists the interacting amino acids along with the docking score. Complicated substances SA7 and SA8 can be shown in 3D in Figures 3 and 4.

Using the Swiss ADME model tool, a set of ten imidazole derivatives were created and evaluated in silico. Every developed chemical had a good oral bioavailability and complied with Lipinski's rule of five. We draw the conclusion that, like glucose-6-phosphate synthase, the majority of the docked imidazole derivatives showed good contact in the receptor sites and bonding and non-bonding interactions with the receptor's active site residues. Mixtures When compared to standard drug, 2-(2-(4-nitrophenyl)-4,5-diphenyl-1H-imidazol-1-yl)aniline SA7, 2-(2,4,5-triphenyl-1H-imidazol-1-yl)aniline SA8, 2-(2-(4-methoxyphenyl)-4,5-diphenyl-1H-imidazol-1-yl)aniline SA9, and 2-(2-(4-ethylphenyl)-4,5-diphenyl-1H-imidazol-1-yl)aniline SA10 demonstrated superior binding affinity. Based on that research paper, we conclude that these derivatives of imidazole may function as a strong inhibitor against the protein target, glucosamine-6-phosphate synthase. However, a promising ADME drug-like profile for the current compounds presents the opportunity to quickly add electron-donating and electron-withdrawing groups with certain modifications, which could result in lead structures with increased inhibitory activity towards the drug receptor target.

Sr.No.	Abbreviation	Full Name
1	mg/kg	Milligram/ kilograms
2	sec	seconds
3	kcal	kilocalorie
4	Mol.Wt	Molecular Weight
5	gm	Gram
6	LEU	Leucine
7	THR	Threonine
8	ALA	Alanine
9	MET	Methionine
10	PHE	Phenylalanine
11	CYP	Cytochrome P450
12	BBB	Blood Brain Barrier penetration
13	GI	Gastrointestinal absorption
14	Kp	Skin Permeation Coefficient

Funding Sources

This research, authorship, and publication received no financial assistance from any funding agency or organization.

Conflict of Interest

The authors declare that there are no conflicts of interest related to this work.

Data Availability

Data availability is not applicable to this article, as no datasets were generated or analyzed during the study.

Ethics Statement

Ethics declaration not applicable

Informed Consent Statement

As the study did not involve human participants, obtaining informed consent was not required.

Clinical Trial Registration

This study was not associated with any clinical trial and therefore does not require trial registration.

Author Contributions

Dr. Shinde Ganesh S, Dattaprasad Vikhe , Rahul Godge ,Shubham Khule was responsible for planning, conceptualization, data collection, and manuscript writing, while Ravindra S Jadhav contributed through supervision and project administration

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Tables 1 to 4 are available in the Supplementary Files section

No competing interests reported.

Tables.docx

Computational Insights of Glucosamine-6-Phosphate Synthase- 2vf5 as Potential Inhibitors of Imidazole Derivatives

Status:

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Abstract

Background

Materials and Methods

Results

Conclusion

Figures

Introduction

Materials and Methods

Results and Discussion

Conclusion

Abbreviations

Declarations

References

Tables

Additional Declarations

Supplementary Files

Status:

Version 1