Home Physical Sciences Molecular docking analysis of subtilisin-like alkaline serine protease (SLASP) and laccase with natural biopolymers
Article Open Access

Molecular docking analysis of subtilisin-like alkaline serine protease (SLASP) and laccase with natural biopolymers

  • Radhakrishnan Narayanaswamy ORCID logo EMAIL logo , Vasantha-Srinivasan Prabhakaran , Fatimah Oleyan Al-Otibi , Raedah Ibrahim Alharbi and Kalibulla Syed Ibrahim
Published/Copyright: September 30, 2024
Download Article (PDF)
Open Chemistry
From the journal Open Chemistry Volume 22 Issue 1

Abstract

Alkaline serine proteases (ASPs) and laccases (Lacs) have been reported to possess several industrial applications, particularly in the food, cosmetic, and leather industries. Thus, in the present study, eighteen natural biopolymers, including agar, agarose, alginate, kappa carrageenan, cellulose, chitosan pentamer, chitosan oligosaccharide, chondroitin sulfate, dextran, fucoidan, heparin, hyaluronan, lignin, mannan, pectin, phytic acid, pullulan and starch soluble, were studied for their docking behavior, such as subtilisin-like alkaline serine protease (SLASP) KP-43 and Bacillus subtilis laccase (Bs Lac), using the SwissDock method. Additionally, the toxicity toward honey bees and human liver was determined by utilizing the free Bee-Tox and pkCSM web servers, respectively. Bee-Tox analysis demonstrated that four ligands (namely, agar, cellulose, lignin, and pullulan) exhibited acute oral toxicity toward honey bees (Apis mellifera). The docking study revealed that chitosan pentamer and lignin exhibited maximum binding energies of −9.67 and −11.37 kcal/mol against the target proteins SLASP (KP-43) and Lac (Bs Lac), respectively. Interestingly, in the present study, agarose was shown to interact with the His68 and Ser255 amino acid residues of SLASP (KP-43) from KSM-KP43 Bacillus sp. Thus, the current investigation showed the potential of eighteen natural biopolymers as immobilizing agents to prepare ASP and Lac nanoparticles for biomedical applications.

Graphical abstract

Keywords: molecular docking; natural biopolymer; subtilisin-like alkaline serine protease; Bacillus subtilis laccase; chitosan; nanoparticles; MD simulation

1 Introduction

Enzymes are proteins in nature that serve as biocatalysts by enhancing biochemical reactions in living organisms. For a long time, it has been utilized in the production of various products, such as beer, cheese, sourdough, vinegar, and wine, and in the manufacturing of materials, including indigo, leather, and linen. Enzymes from microbial sources are involved in various metabolic reactions and are utilized in different industrial applications. Currently, enzymes, especially those utilized in manufacturing, are hydrolytic in nature and are utilized for the breakdown of large substances into smaller substances [1]. For instance, microbial proteases catalyze protein hydrolysis into polypeptides and oligopeptides along with amino acids (AAs). Proteases are classified into three types on the basis of pH: (i) acidic, (ii) neutral, and (iii) alkaline protease (AlP). AlP is a widely utilized industrial enzyme owing to its relatively high activity and high stability at basic pH [2]. Moreover, proteases alone contribute to approximately 60% of the global enzyme sales. Furthermore, Bacillus species serve as major enzyme producers [3]. Similarly, proteases are distinguished into four important groups on the basis of AA active site residues along with catalytic actions: (i) aspartic, (ii) cysteine, (iii) metallo, and (iv) serine proteases. Among them, serine proteases are a widespread group of proteolytic enzymes from microbial and animal sources [4]. Moreover, alkaline serine proteases (ASPs) are a widely utilized group of commercial manufacturing enzymes, especially in meat, detergent, and leather production. Furthermore, ASPs are recognized as microbial enzymes with greater market value (>35%) [5]. Macquarrie and Bacheva have reported that subtilisin immobilized in chitosan has shown high catalytic activity and good stability nature [6]. Eser and Aydemir have demonstrated that subtilisin immobilized in magnetic chitosan has been utilized for eco-friendly leather preparation process [7]. Shettar et al. have reported that subtilisin entrapped in calcium alginate beads has exhibited superior storage longevity, recyclability, and confirming its practical viability. Thus, in the present study, subtilisin-like alkaline serine protease (SLASP) from Bacillus sp. strain KSM-KP43 was chosen as the first enzyme target [8].

Laccases (Lacs) (copper-containing enzymes) are involved in (i) the biodegradation of organic pollutants, (ii) bioremediation, (iii) cosmetics, (iv) the food sector, (v) the paper and pulp sector, and (vi) synthetic chemistry applications. In recent years, the Lac enzyme has been shown to play a vital role in nanobiotechnology owing to its unique characteristic ability to catalyze electron transfer reactions (rxs) without any additional cofactors. Lac has been immobilized using different immobilization agents, such as carbon fibers, ceramics, and pyrolytic graphite [9]. Ping et al. have reported that Lac immobilized in alginate/gelatin mixed with polyethylene glycol has been applied in decolorization of reactive dyes [10]. Unal and Pazarlioglu have demonstrated that Lac immobilized in gelatin has been utilized for analysis of phenolic contents present in commercially prepared fruit juices [11]. Mogharabi et al. have reported that Lac immobilized in alginate-gelatin mixed gel has been used for the decolorization of synthetic dyes [12]. Rocasalbas et al. have demonstrated that Lac entrapped in chitosan/gelatin hydrogel has exhibited antibacterial activity against both Pseudomonas aeruginosa and Staphylococcus aureus [13]. Khalighi et al. have reported that Lac immobilized in sugar beet fiber (fibrex) gel has been applied in pharmaceutical and several other industrial sectors [14]. Harguindeguy et al. have demonstrated that Lac immobilized in gelatin has been employed as biocatalyst for waste water treatment process [15]. Therefore, in the present study, Bacillus subtilis laccase (Bs Lac) was selected as the second target enzyme.

Natural biopolymers are biologically acceptable substances or biomaterials that can be utilized as structures in tissue engineering applications and regenerative medicine. Natural biopolymers such as chitosan, collagen, fibrin, gelatin, and silk fibroin have been utilized as biocompatible scaffolds (platforms) to fulfill the relevant biological and mechanical properties required for tissue engineering and regenerative medicine applications [16]. Similarly, natural biopolymers such as (i) albumin (protein), (ii) alginate (polysaccharide), (iii) apoferritin (protein), (iv) beta-glucan (polysaccharide), (v) casein (protein), (vi) chitosan (polysaccharide), (vii) collagen (protein), (viii) cyclodextrin (oligosaccharide), (ix) dextran (polysaccharide), (x) fibrinogen (glycoprotein), (xi) fucoidan (polysaccharide), (xii) gelatin (protein), (xiii) heparin (polysaccharide), (xiv) hyaluronic acid (polysaccharide), (xv) lectin (glycoprotein), (xvi) mannan (polysaccharide), (xvii) pullulan (polysaccharide), (xviii) starch (polysaccharide), and (xix) zein (protein) have been commonly utilized for the preparation of nanoparticles [17].

The current investigation aims to impart an understanding of the mechanistic basics for the in silico binding of eighteen natural biopolymers with two target enzymes from Bacillus species. And, moreover, the present investigation objective was to reveal insights about the binding efficiency of the two target enzymes (SLASP and Bs Lac) with eighteen selected natural biopolymers which include agar, agarose, alginate, kappa carrageenan, cellulose, chitosan pentamer, chitosan oligosaccharide, chondroitin sulfate, dextran, fucoidan, heparin, hyaluronan, lignin, mannan, pectin, phytic acid, pullulan, and starch soluble by utilizing molecular docking approaches which in turn pave way for biomedical applications.

2 Materials and methods

2.1 Ligand preparation

The biochemical structures of selected ligands, namely, (i) agar (ID 71571511), (ii) agarose (ID 11966011), (iii) alginate (ID 131704328), iv) kappa carrageenan (ID 11966249), (v) cellulose (ID 14055602), (vi) chitosan pentamer* (0C09269), (vii) chitosan oligosaccharide (ID 3458144), (viii) chondroitin sulfate (ID 24766), (ix) dextran (ID 4125253), (x) fucoidan (ID 129532628), (xi) heparin (ID 22833565), (xii) hyaluronan (ID 24759), (xiii) lignin (ID 73555271), (xiv) mannan (ID 25147451), (xv) pectin (441476), (xvi) phytic acid (ID 890), (xvii) pullulan (ID 131636581), and (xviii) starch soluble (ID 51003661), were downloaded from the PubChem (www.pubchem.com) and Biosynth* (www.biosynth.com) databases. These ligands were selected as adapted from previous research [18]. Mol2 files are given for each ligand (natural biopolymer), Chemistry at Harvard Macromolecular Mechanics (CHARMM) topology, parameters, and coordinates; files proceed spontaneously from the Merck Molecular Force Field (MMFF). These prepared structures were used for further study (SwissDock).

2.2 Prediction of bee toxicity

Bee-Tox (www.beetoxai.labmol.com.br) is a free web server based on artificial intelligence technology that is currently utilized to predict the acute “oral and contact” toxicity of ligands/chemicals to honey bees [19]. In the present research, the toxicity of 18 selected chemicals (natural biopolymers) toward honey bees (Apis mellifera) and human liver was assessed using the Bee-Tox (LabMol) and pkCSM (www.biosig.lab.uq.edu.au/pkcsm/) free web servers, respectively [20].

2.3 Identification and preparation of target enzymes

The three-dimensional structures of the SLASP from the KP-43 strains of the Bacillus species KSM-KP43 (Protein Data Bank [PDB] ID: 1WME) and Bs Lac (PDB ID: 3ZDW) were obtained from the PDB. The “A” chains of both enzymes were prepared separately by eliminating ligands and crystallographic water molecules (water deprived of hydrogen bonds), as observed by utilizing UCSF Chimera software [21].

2.4 Docking investigation

Docking investigations were carried out for eighteen selected natural biopolymers using the SwissDock online server. The SwissDock web server is executed with open-source technologies (Apache web server, Hypertext Preprocessor) and, moreover, it uses the EADock DSS engine. Calculations are currently accomplished on 32 computing nodes with Dual Xeon E5440 2.83 GHz and 16 GB of RAM, computing for a total of 256 CPU and 512Go of RAM, which pertain to the Molecular Modeling group of the Swiss Institute of Bioinformatics and are integrated into the Vital-IT cluster. The docking assays are performed in the Chemistry at Harvard Macromolecular Mechanics (CHARMM22/27) all-hydrogen force field [22]. Finally, interaction site investigation was carried out by using PyMOL software.

2.5 Molecular dynamics (MD) simulation

The MD simulation of the protein-ligand complex was performed with GROMACS using NMRbox virtual machines [23,24] simulation and OPLS-AA/M force field. The molecular topology file of the ligand compatible with the OPLS-AA/M force field was obtained from LigParGen web service [25]. The protein-ligand complex was solvated with Simple Point Charge water (SPC) and the complete system was neutralized with the addition of chlorine (Cl− ions) by replacing the water molecules. The energy minimization of the system was performed with the steepest gradient algorithms (5,000 cycles), which was then followed by equilibration of the system using two consecutive NVT (constant number of particles (NPT), volume, and temperature) and (NPT, pressure, and temperature are all constant) runs. Finally, the complex was subjected to a 100 ns MD simulation. The simulation trajectories were then analyzed based on the root mean square deviations, the root mean square fluctuations, solvent accessible surface area (SASA), and radius of gyration [26].

3 Results and discussion

Proteases usually play a key role in enhancing wash performance parameters in the formulation of detergents [27]. These proteases (detergent) fit into the serine protease family, which cleaves peptide bonds in proteins, and they catalyze biochemical reactions using a catalytic triad covering histidine (His), aspartate (Asp), and serine (Ser). The presence of individual AAs (Asp–His–Ser) in the catalytic triad plays a specific role in the catalytic process [28]. The considerable production of microbial ASP on an industrial or large scale could be achieved by suitable downstream processing and extraction methods. However, in some cases, it is tedious and difficult to achieve good enzyme yield. The immobilization of ASPs on different nanomatrices or nanoparticles will be able to resolve the abovementioned problems by (i) enhancing the product yield, (ii) improving the shelf life, (iii) preventing the agglutination, self-decomposition, and denaturation of ASPs, and (iv) ensuring the long-lasting shelf life/stability of immobilized ASPs over nanoparticles or nanomatrices [29].

Lac (a copper-containing enzyme) is an extensively studied enzyme worldwide. Moreover, Lac is recognized as a “green tool” owing to its potential to carry out catalytic reactions by utilizing molecular oxygen as a co-substrate [30].

Thus, natural biopolymers such as alginate, cellulose, chitosan pentamer, chitosan oligosaccharide, chondroitin sulfate, dextran, fucoidan, hyaluronan, mannan, pullulan, and starch soluble (as shown in Table 1) were chosen for the present research to assess the behavior of docking on ASP and Lac.

Table 1

The “simplified molecular input line entry system” (SMILES) of eighteen selected natural biopolymers is shown

Ligand name “Simplified molecular input line entry system” (SMILES)
Agar “CC1C(C2C(C(O1)CO2)OC3C(C(C(C(O3)CO)O)OC)O)O”
Agarose “C1C2C(C(O1)C(C(O2)O)O)OC3C(C(C(C(O3)CO)O)OC4C(C5C(C(O4)CO5)OC6C(C(C(C(O6)CO)O)O)O)O)O”
Alginate “C1(C(C(OC(C1OC2C(C(C(C(O2)C(═O)O)P)O)O)C(═O)O)OP)O)O”
Kappa carrageenan “C1C2C(C(O1)C(C(O2)O)O)OC3C(C(C(C(O3)CO)OS(═O)(═O)[O])OC4C(C5C(C(O4)CO5)OC6C(C(C(C(O6)CO)OS(═O)(═O)[O-])O)O)O)O”
Cellulose “COC1C(OC(C(C1O)O)OC2C(OC(C(C2O)O)OC)CO)CO”
Chitosan pentamer “Cl.Cl.Cl.Cl.Cl.NC1C(O)OC(CO)C(OC2OC(CO)C(OC3OC(CO)C(OC4OC(CO)C(OC5OC(CO)C(O)C(O)C5N)C(O)C4N)C(O)C3N)C(O)C2N)C1O”
Chitosan oligosaccharide “C(C1C(C(C(C(O1)OC2C(OC(C(C2O)N)O)CO)N)O)O)O”
Chondroitin sulfate “CC(═O)NC1C(C(C(OC1O)OS(═O)(═O)O)O)OC2C(C(C(C(O2)C(═O)O)O)O)O”
Dextran “C(C1C(C(C(C(O1)OCC2C(C(C(C(O2)OCC(C(C(C(C═O)O)O)O)O)O)O)O)O)O)O)O”
Fucoidan “CC1C(C(C(C(O1)C)OS(═O)(═O)O)O)OC”
Heparin “CC(═O)NC1C(C(C(OC1OC2C(C(C(OC2C(═O)O)OC3C(C(C(OC3O)OC4C(C(C(OC4C(═O)O)O)OS(═O)(═O)O)O)OS(═O)(═O)O)CS(═O)(═O)O)O)O)COS(═O)(═O)O)O)O”
Hyaluronan “CC(═O)NC1C(C(C(OC1O)CO)O)OC2C(C(C(C(O2)C(═O)O)OC3C(C(C(C(O3)CO)O)OC4C(C(C(C(O4)C(═O)O)O)O)O)NC(═O)C)O)O”
Lignin “CC(C(C1═CC2═C(C(═C1)OC)OC(C2CO)C3═CC(═C(C═C3)OC(CO)C(C4═CC(═C(C═C4)O)OC)OC5═C(C═C(C═C5OC)C(C(CO)OC6═C(C═C(C═C6)C7C8COCC8C(O7)C9═CC(═C(C(═C9)OC)O)OC)OC)OC1═C(C═C(C═C1)C(C(CO)OC1═C(C═C(C═C1)C═CCO)OC)O)OC)O)OC)O)O”
Mannan “C(C1C(C(C(C(O1)OC2C(OC(C(C2O)O)OC3C(OC(C(C3O)O)OC4C(OC(C(C4O)O)O)CO)CO)CO)O)O)O)O”
Pectin “C1(C(C(OC(C1O)O)C(═O)O)O)O”
Phytic acid “C1(C(C(C(C(C1OP(═O)(O)O)OP(═O)(O)O)OP(═O)(O)O)OP(═O)(O)O)OP(═O)(O)O)OP(═O)(O)O”
Pullulan “COCC1C(C(C(C(O1)OC2C(OC(C(C2O)O)OC3C(OC(C(C3O)O)OC)CO)CO)O)O)O”
Starch soluble “C(C1C(C(C(C(O1)OC2C(OC(C(C2O)O)O)CO)O)O)O)O”

Bee-Tox analysis demonstrated that four ligands (namely, agar, cellulose, lignin and pullulan) exhibited acute oral toxicity toward honey bees. However, none of the eighteen selected natural biopolymers (ligands) exhibited any acute contact toxicity toward honey bees. Similarly, none of the eighteen chosen natural biopolymers (ligands) have shown any hepatotoxicity activity (as shown in Table 2).

Table 2

The honey bee (A. mellifera) and human liver toxicity analysis of eighteen selected natural biopolymers using Bee-Tox (LabMol) and pkCSM (Biosig Lab) free web servers

Ligand name Acute oral toxicity (LD50◊) Acute contact toxicity Hepatotoxicity
Agar Toxic (7.37 µg/bee◊) NT■ NT■
Agarose NT■ NT■ NT■
Alginate NT■ NT■ NT■
Kappa carrageenan NT■ NT■ NT■
Cellulose Toxic (15.69 µg/bee◊) NT■ NT■
Chitosan pentamer NT■ NT■ NT■
Chitosan oligosaccharide NT■ NT■ NT■
Chondroitin sulfate NT■ NT■ NT■
Dextran NT■ NT■ NT■
Fucoidan NT■ NT■ NT■
Heparin NT■ NT■ NT■
Hyaluronan NT■ NT■ NT■
Lignin Toxic (13.14 µg/bee◊) NT■ NT■
Mannan NT■ NT■ NT■
Pectin NT■ NT■ NT■
Phytic acid NT■ NT■ NT■
Pullulan Toxic (24.58 µg/bee◊) NT■ NT■
Starch soluble NT■ NT■ NT■

Note: LD50◊ – expressed in micrograms/bee, NT■ – nontoxic.

A numerous studies have been carried out to understand the binding efficiency of the modeled protease (enzyme), especially from Bacillus species with various substrates by molecular docking approaches [28,31]. The present docking investigation and binding energy [BE] (Table 3) showed that the chitosan pentamer exhibited the maximum BE (−9.67 kcal/mol); additionally, pectin had the least energy binding (−6.54 kcal/mol) against the targeted protein (SLASP KP-43). The BE analysis of the current investigation showed the following order: chitosan pentamer (−9.67 kcal/mol), <agarose (−9.52 kcal/mol), <dextran (−9.42 kcal/mol), <kappa carrageenan (−8.82 kcal/mol), <phytic acid (−8.81 kcal/mol), <lignin (−8.63 kcal/mol), <hyaluronan (−8.38 kcal/mol), <heparin (−8.29 kcal/mol), <alginate (−8.23 kcal/mol), <pullulan (−8.03 kcal/mol), <chondroitin sulfate (−8.01 kcal/mol), <chitosan oligosaccharide (−7.90 kcal/mol), <mannan (−7.73 kcal/mol), <starch soluble (−7.59 kcal/mol), <cellulose (−7.42 kcal/mol), <agar (−7.17 kcal/mol), fucoidan (−7.04 kcal/mol), and <pectin (−6.54 kcal/mol). Previously, we reported that natural biopolymers, including (i) alginate, (ii) albumin, (iii) apoferritin, (iv) beta-glucan, (v) chitosan, (vi) casein, (vii) cyclodextrin, (viii) collagen, (ix) dextra, (x) fucoidan, (xi) fibrinogen, (xii) gelatin, (xiii) hyaluronic acid, (xiv) heparin, (xv) lectin, (xvi) mannan, (xvii) pullulan, (xviii) starch, and (xix) zein, have been utilized as contrast agents for magnetic resonance (MR) imaging [17]. According to Rezakhani et al., the protease immobilized in alginate-chitosan beads (A–C) exhibited fairly stable and significant enzyme activity [32].

Table 3

Interaction energy analysis of eighteen selected natural biopolymers with SLASP KP-43 from the Bacillus species KSM-KP43 using the SwissDock method

Ligand name SwissDock interaction energy (−kcal/mol) Interaction amino acid (AA) residue Bond distance (Å)
Agar 7.17 Gly214 2.3
Trp393 2.3 and 2.4
Gly395 3.1
Asn397 3.4
Agarose 9.52 His68 3.2
Asn162 2.5, 3.1 and 3.3
Glu163 1.8
Ser239 2.2
Trp241 3.3 and 3.4
Ser255 3.2 and 3.4
Alginate 8.23 Asn383 2.4
Asp394 1.9 and 3.4
Kappa carrageenan 8.82 Ala293 3.3
Asp295 3.5
Arg309 3.1
Lys314 3.2 and 3.3
Lys343 3.4
Lys346 3.0
Cellulose 7.42 Asn405 2.1 and 3.0
Chitosan pentamer 9.67 Asp295 2.1
Tyr300 3.4
Tyr389 3.2
Phe403 2.7
Asn405 2.0, 3.1 and 3.5
Ala406 2.4
Chitosan oligosaccharide 7.90 Gly214 2.2 and 2.3
Asn383 2.7
Trp393 2.2
Asp394 2.0
Gly395 3.0
Asp397 3.4
Chondroitin sulfate 8.01 Leu104 3.2
Ser129 2.7
Gly131 3.2
Asn162 3.1
Glu163 1.9 and 1.9
Ser171 2.0 and 3.5
Dextran 9.42 Asp295 1.8
Lys346 3.3
Phe385 2.0
Tyr389 2.2, 3.0 and 3.4
Phe403 2.0
Asn405 3.4 and 3.4
Ala406 2.9
Fucoidan 7.04 Asp384 2.5
Thr386 3.2 and 3.5
Heparin 8.29 Tyr300 3.2
Asn376 3.1
Thr378 3.5 and 3.6
Tyr380 2.0, 3.3 and 3.4
Tyr389 3.0
Asn405 3.4
Ala406 2.2
Glm408 3.2
Hyaluronan 8.38 Asp295 2.1
Leu298 2.3
Tyr380 2.9
Phe403 2.1
Asn405 3.3
Lignin 8.63 Lys343 3.0 and 3.3
Asn434 2.0 and 2.9
Mannan 7.73 Tyr300 2.1
Tyr380 2.0 and 3.0
Phe403 2.2
Asn405 3.4
Gln408 3.1
Pectin 6.54 Leu364 1.9 and 2.0
Asp367 1.9 and 3.3
Asn420 3.3
Phytic acid 8.81 Asn383 1.9 and 3.2
Phe385 3.1
Trp393 2.1
Asp394 2.0
Asn397 3.3
Pullulan 8.03 Gly131 2.2
Ala133 3.2 and 3.2
Asn162 3.0, 3.2 and 3.3
Glu163 2.1
Ser171 3.4
Starch soluble 7.59 Gly214 1.8 and 2.2
Asn383 2.0
Asp384 2.1
Phe385 3.0
Thr386 2.5 and 3.3
Asn397 3.1

Alnoch et al. reported the use of biomaterials, including cellulose, agarose, chitin, cellulose, chitosan, and starch, for lipase immobilization [33]. Prokopijevic reported that natural biopolymers (alginate, cellulose, chitosan, collagen, xylan, and pectin) can be utilized as carriers for enzyme immobilization processes [34]. Sharma et al. reported the utilization of natural polysaccharides such as alginate, carrageenan, cellulose, chitin, pectin, and starch in various enzyme immobilization processes [35]. Similarly, Lyu et al. reported the use of natural polymers such as alginate, agarose (lyoxylagarose, amino-glyoxylagarose, carboxy-glyoxylagarose, and chelate-glyoxylagarose), cellulose, chitosan, dextran and pectin in various enzyme immobilization processes [36]. In recent years, computational techniques have been utilized for analyzing nanoparticle interactions with biomolecules, including enzymes [37]. Borkotoky et al. reported that heparin (mucopolysaccharide) and low molecular weight derivatives of heparin interact with the T7 RNA polymerase enzyme [38]. Narayanaswamy reported that alginate oligosaccharides (Alg2–Alg6) interact with bacterial collagenase enzymes [39]. Maksimenko et al. reported that glycosaminoglycan ligands, namely, chondroitin sulfate (trimer) and heparin (tetramer), interact with the enzyme bovine testicular hyaluronidase [40]. Franco and Mesa utilized an in silico approach to analyze the interactions of chitosan and carboxy methyl chitosan with the beta-galactosidase enzyme [41]. Omar et al. reported that biopolymers (such as cellulose, chitosan, gelatin, and starch), as well as their blends (such as chitosan/cellulose, chitosan/gelatin, and chitosan/starch), interact with the HIV protease enzyme [42]. Thus, the current investigation demonstrated the potential of eighteen selected natural biopolymers as immobilizing agents for the preparation of ASP nanoparticles.

Two ligands, namely, fucoidan and starch soluble, interact with the Asp384 and Thr386 amino acid residues (AAR) of the protein (SLASP KP-43), respectively. Similarly, three other ligands, agarose, chondroitin sulfate, and pullulan, interact with the AARs Asn162 and Glu163 of the protein (SLASP KP-43). Furthermore, four ligands (chitosan pentamer, dextran, hyaluronan, and mannan) interact with the AAR Phe403 of the protein (SLASP KP-43). According to Nonaka et al., calcium ions (Ca2+) assist in the thermal stability of subtilisins, and thus far, three calcium ion (Ca2+)-binding sites have been reported in the SLASP KP-43 [43]. Moreover, calcium-II and calcium-III ions existing in the C-terminal domain of KP-43 have been reported to stabilize a loop section (from aspartic acid 384 to asparagine 398) in the domain [43]. Interestingly, in the present study, nine ligands, namely, agar, alginate, chitosan pentamer, chitosan oligosaccharide, dextran, fucoidan, heparin, phytic acid, and starch soluble, exhibited AA interactions in the above calcium ion (Ca2+)-binding region, i.e., between aspartic acid 384 and asparagine 398 in the target protein. The N-domain of KP-43 has been reported to contain residues of the catalytic triad, such as His68, Ser255, and Asp30 [43,44]. Interestingly, in the present study, agarose showed AA interactions with both the His68 and Ser255 residues of SLASP KP-43 (as shown in Table 3). Okuda et al. have reported that the hydrophobicity of AAR (especially AARs like Tyr195, Phe192, Phe205, Phe226, and Trp241) in the flexible loop of KP-43 protease has altered catalytic activity towards a macromolecule substrate (casein) [45]. In the present study, agarose (natural biopolymer) has shown interaction with Trp241 AAR of SLAP KP-43. Mahmoud et al. have reported that AARs like Leu188, Ser361, Trp393, Thr419, and Asn420 have shown interaction with macromolecule substrate (casein) [46]. In the current investigation, agar (Figure 1), chitosan oligosaccharide and phytic acid (natural biopolymers) have exhibited interaction with Trp393 AAR of SLAP KP-43. Mahmoud et al. have demonstrated that the AARs namely Asp155, His187, and Ser384 as catalytic triad of AKD9 protease [46]. In the present investigation, fucoidan and starch soluble (natural biopolymers) have shown interaction with Asp384 AAR of SLAP KP-43, instead of Ser384 AAR of AKD9 protease.

Figure 1 The interaction energy analysis of agar (a natural biopolymer) with the Bacillus species KSM-KP43 SLASP KP-43 was performed using the SwissDock method. Note: ↓ (down arrow) indicates the Trp393 amino acid residue, and ↑ (up arrow) indicates the Gly395 amino acid residue.
Figure 1

The interaction energy analysis of agar (a natural biopolymer) with the Bacillus species KSM-KP43 SLASP KP-43 was performed using the SwissDock method. Note: ↓ (down arrow) indicates the Trp393 amino acid residue, and ↑ (up arrow) indicates the Gly395 amino acid residue.

The docking investigation and BE (Table 4) showed that lignin exhibited the highest BE (−11.37 kcal/mol); additionally, pectin had the lowest energy of binding (−6.50 kcal/mol) to the targeted enzyme (Bs Lac). The BE analysis of the current investigation showed the following order: lignin (−11.37 kcal/mol), <kappa carrageenan (−10.01 kcal/mol), <hyaluronan (−9.25 kcal/mol), <chitosan pentamer (−9.00 kcal/mol), <heparin (−8.91 kcal/mol), <agarose (−8.58 kcal/mol), <pullulan (−8.50 kcal/mol), <phytic acid (−8.41 kcal/mol), <mannan (−8.27 kcal/mol), <chondroitin sulfate (−8.18 kcal/mol), <alginate (−8.04 kcal/mol), <dextran (−7.96 kcal/mol), <starch soluble (−7.59 kcal/mol), <cellulose (−7.48 kcal/mol), <agar (−7.36 kcal/mol), <fucoidan (−7.29 kcal/mol), <chitosan oligosaccharide (−7.23 kcal/mol), and <pectin (−6.50 kcal/mol). Singh et al. utilized a docking method to predict the binding potential of seven pharmaceutical pollutants with both bacterial and fungal Lacs [47].

Table 4

The interaction energy analysis of eighteen selected natural biopolymers with Bs Lac using the SwissDock method

Ligand name SwissDock interaction energy (−kcal/mol) Interaction amino acid (AA) residue Bond distance (Å)
Agar 7.36 Thr260 2.1
Thr262 3.0
Thr415 3.1
Gly417 3.3
His419 3.4
Agarose 8.58 Thr262 3.0
Gly321 2.0
Gly323 3.3
Gly324 3.5
Arg416 3.5
Thr418 3.5
Alginate 8.04 Thr262 3.2
Gly321 2.6
Thr415 3.5
Gly417 3.3
Thr418 3.0 and 3.3
His419 3.1
His497 3.4
Kappa carrageenan 10.01 Thr262 3.0
Gly321 3.2
Arg416 2.9 and 3.1
His497 3.1
Cellulose 7.48 Gly321 2.0
Thr418 2.0, 2.0, 3.1 and 3.2
Chitosan pentamer 9.00 Ala227 2.3
Chitosan oligosaccharide 7.23 Gly323 3.4
Thr418 1.9 and 2.1
Chondroitin sulfate 8.18 Thr260 3.0
Thr262 3.0 and 3.3
Gly321 2.2
Thr415 3.4
Thr418 2.9
His419 2.2
Dextran 7.96 Gly323 3.4
His497 3.2
Fucoidan 7.29 Thr415 3.1
Gly417 3.2
Thr418 2.0
His419 2.1
Heparin 8.91 Thr260 2.7
Thr262 2.9 and 3.4
Gly323 3.4
Gly417 3.0
Thr418 3.3
Hyaluronan 9.25 Thr262 2.8
Gly323 3.2
His497 2.2 and 2.3
Lignin 11.37 Ala227 2.2
Gly323 3.0
Gly324 3.5
Arg416 3.2
Thr418 2.4, 3.1 and 3.1
Mannan 8.27 Thr260 2.5
Thr262 3.4
Gly323 3.1
Gly376 2.4
Thr418 2.7, 3.1 and 3.4
Pectin 6.50 Gly230 2.5
Arg261 3.1
Cys322 1.9
Asp325 1.8
Asn327 3.3
Thr330 3.4
Phytic acid 8.41 Pro414 3.4
Thr415 3.4
Arg416 3.2 and 3.4
Gly417 3.0
His419 3.4
Pullulan 8.50 Gly417 3.3
His419 3.2
Starch soluble 7.59 Thr260 2.0
Thr262 3.1 and 3.3
Thr418 2.5

Rivera-Hoyos et al. have demonstrated that the AARs namely Pro226, Ala227, His319, Cys322, Gly323, Pro384, Arg416, Gly417, and His497 of Lac have exhibited interaction towards 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) substrate [48]. In the current investigation, chitosan pentamer and lignin have shown interaction with Ala227 AAR of Lac. Similarly, pectin (natural biopolymer) has exhibited interaction with Cys322 AAR of Bs Lac. Moreover, agarose, kappa carrageenan, lignin, and phytic acid have shown interaction with Arg416 AAR of Bs Lac. Similarly, agar (Figure 2) alginate, fucoidan, heparin, phytic acid, and pullulan have exhibited interaction with Gly417 AAR of Lac. Furthermore, alginate, kappa carrageenan, dextran and hyaluronan (natural biopolymers) have shown interaction with His497 AAR of Bs Lac.

Figure 2 The interaction energy analysis of agar (a natural biopolymer) with Bs Lac using the SwissDock method. Note: ↓ (down arrow) indicates the Gly417 amino acid residue, and ↑ (up arrow) indicates the His419 amino acid residue.
Figure 2

The interaction energy analysis of agar (a natural biopolymer) with Bs Lac using the SwissDock method. Note: ↓ (down arrow) indicates the Gly417 amino acid residue, and ↑ (up arrow) indicates the His419 amino acid residue.

Xie et al. have demonstrated that the AARs namely Pro226, Pro384, Leu386, Thr415, Arg416, His419, Cys492, and His497 of Lac have exhibited interaction towards sinapic acid [SA] substrate [49]. In the current investigation, agar, alginate, chondroitin sulfate, fucoidan, and phytic acid have shown interaction with Thr415 AAR of Bs Lac.

Six ligands (agarose, chitosan oligosaccharide, heparin, hyaluronan, lignin and mannan) interact with the Gly323 AAR of the enzyme (Bs Lac). This finding was on par with a previous report in which Gly323 was reported as a binding pocket-1 AAR of Lac [50].

During the docking process, the interaction between the ligands and the protein are instantaneous and may be unstable. The MD simulation on the other hand provides us with information about the stability of the molecular interactions of the complexes over a period of time [51]. In this study, root-mean-square deviations (RMSD) of the C-alpha atoms of the complexes were evaluated with respect to the atoms in starting structures. However, it can be noted that the complex had lower RMSD ranges during the whole simulation periods (100 ns) which correlates with the complex’s stability. Figure 3a illustrates the plotting of the RMSD values of Target (in red) and ligand (in black), indicating that the complexes were stabilized after 30 ns. Also, the root-mean-square fluctuations (RMSF) of the complexes were analyzed to understand the flexibility across the AARs of the complexes [51]. Figure 3b clearly indicates that almost every residue has a lower RMSF than 2.5 Å which defines the complex’s stability. The stability of those complexes was further evaluated by plotting radius of gyration (R g) to understand the mobility of the complexes where the higher R g defines the higher flexibility [51]. The rise observed in the target is due to the higher flexibility of the target. The calculated R g value over the simulation time scale is demonstrated in Figure 3c, where complexes exhibit a stable R g profile across the simulation trajectories. Additionally, SASA predicts the surface area of a target protein that is accessible by the solvent molecules which is defined as the extent to which atoms on the surface of a protein can form contact with the solvent [52]. Generally, it is measured in squared nanometers (nm2). Figure 3d shows the predicted SASA of the target (SLASP KP-43) which indicated lower fluctuations.

Figure 3 Represents the result of 100 nanoseconds (ns) MD simulation of SLASP KP-43 and chitosan pentamer complex (a) RMSD (root mean square deviation) values of docked complexes from C-α atoms. The structural changes of receptor protein by means of: (b) RMSF (root mean fluctuation), (c) R g (radius of gyration), and (d) SASA respectively. Note: Red color plot in Figure 3a indicates the target protein (SLASP KP-43), similarly black color plot indicates the selected ligand (chitosan pentamer).
Figure 3

Represents the result of 100 nanoseconds (ns) MD simulation of SLASP KP-43 and chitosan pentamer complex (a) RMSD (root mean square deviation) values of docked complexes from C-α atoms. The structural changes of receptor protein by means of: (b) RMSF (root mean fluctuation), (c) R g (radius of gyration), and (d) SASA respectively. Note: Red color plot in Figure 3a indicates the target protein (SLASP KP-43), similarly black color plot indicates the selected ligand (chitosan pentamer).

The present in silico analysis can be further confirmed by performing detailed in vitro analyses against the target enzymes, particularly for those natural biopolymers with the highest BE. Moreover, the natural biopolymer with the highest BE was not investigated by using a cell-based assay or an animal model for assessing their pharmacokinetic and toxicokinetic properties.

4 Conclusion

In the present study, all eighteen selected natural biopolymers were found to dock with both target proteins (SLASP KP-43 from the Bacillus species KSM-KP43 and Bs Lac). In the present study, nine ligands, namely, agar, alginate, chitosan pentamer, chitosan oligosaccharide, dextran, fucoidan, heparin, phytic acid, and starch soluble, were shown to participate in AA interactions between aspartic acid 384 and asparagine 398 in the target protein (SLASP). The MD simulation results reveal that SLASP KP-43 and chitosan pentamer complex remain stable in nature. Similarly, six ligands, namely, agarose, chitosan oligosaccharide, heparin, hyaluronan, lignin and mannan, interact with the glycine 323 position of the protein (Bs Lac). Thus, the current study demonstrated the potential of eighteen selected natural biopolymers as immobilizing agents to prepare SLASP and Lac nanoparticles. Furthermore, wet laboratory studies are required to improve our knowledge of eighteen selected natural biopolymers as immobilizing agents to prepare SLASP and Lac nanoparticles for biomedical applications.

Acknowledgments

The authors acknowledge the Researchers Supporting Project number (RSP2024R114), King Saud University, Riyadh, Saudi Arabia, for funding this research work.

  1. Funding information: The authors extend their appreciation to the Researchers Supporting Project number (RSP2024R114), King Saud University, Riyadh, Saudi Arabia.

  2. Author contributions: Conceptualization, R.N.; methodology, R.N. and K.S.I.; software, R.N. and K.S.I; validation, R.N. and K.S.I; formal analysis, R.N., M.R., and K.S.I; investigation, V.S.P. and R.N.; resources, F.O.Al.-O.; data curation, R.N., V.S.P., and K.S.I; visualization, R.N., V.S.P., F.O.Al.-O., and K.S.I; supervision, R.N.; project administration, R.N., V.S.P., and R.I.A.; funding acquisition, R.N., F.O.Al.-O., and R.I.A.; writing-original draft preparation, R.N., V.S.P., and K.S.I; writing-review and editing, R.N., V.S.P., F.O.Al.-O., R.I.A, and K.S.I.; all authors have read and agreed to the published version of the manuscript.

  3. Conflict of interest: The authors declare that they have no conflicts of interest.

  4. Data availability statement: The data that support the findings of this study are available from the corresponding author upon reasonable request.

References

[1] Sharma M, Gat Y, Arya S, Kumar V, Panghal A, Kumar A. A review on microbial alkaline protease: an essential tool for various industrial approaches. Ind Biotechnol. 2019;15(2):69–78.10.1089/ind.2018.0032Search in Google Scholar

[2] Guleria S, Walia A, Chauhan A, Shirkot CK. Purification and characterization of detergent stable alkaline protease from Bacillus amyloliquefaciens SP1 isolated from apple rhizosphere. J Basic Microbiol. 2016;56(2):38–52.10.1002/jobm.201500341Search in Google Scholar PubMed

[3] Bouacem K, Bouanane-Darenfed A, Laribi-Habchi H, Elhoul MB, Hmida-Sayari A, Hacene H, et al. Biochemical characterization of a detergent-stable serine alkaline protease from Caldicoprobacter guelmensis. Int J Biol Macromol. 2015;81:299–307.10.1016/j.ijbiomac.2015.08.011Search in Google Scholar PubMed

[4] Ellaiah P, Srinivasulu B, Adinarayana K. A review on microbial alkaline proteases. J Sci Ind Res. 2002;61:690–704.Search in Google Scholar

[5] Bhunia B, Basak B, Dey A. A review on production of serine alkaline protease by Bacillus spp. J Biochem Technol. 2012;3(4):448–57.Search in Google Scholar

[6] Macquarrie DJ, Bacheva A. Efficient subtilisin immobilization in chitosan, and peptide synthesis using chitosan–subtilisin biocatalytic films. Green Chem. 2008;10(6):692–5.10.1039/b800584bSearch in Google Scholar

[7] Eser A, Aydemir T. Subtilisin Carlsberg immobilization and its application for eco-friendly leather processing. J Clean Prod. 2022;377:134296.10.1016/j.jclepro.2022.134296Search in Google Scholar

[8] Shettar SS, Bagewadi ZK, Khan TY, Shamsudeen SM, Kolvekar HN. Biochemical characterization of immobilized recombinant subtilisin and synthesis and functional characterization of recombinant subtilisin capped silver and zinc oxide nanoparticles. Saudi J Biol Sci. 2024;31(7):104009.10.1016/j.sjbs.2024.104009Search in Google Scholar PubMed PubMed Central

[9] Shekher R, Sehgal S, Kamthania M, Kumar A. Laccase: microbial sources, production, purification, and potential biotechnological applications. Enzyme Res. 2011;2011:217861.10.4061/2011/217861Search in Google Scholar PubMed PubMed Central

[10] Ping W, Xuerong F, Li C, Qiang W, Aihui Z. Decolorization of reactive dyes by laccase immobilized in alginate/gelatin blent with PEG. J Environ Sci. 2008;20(12):1519–22.10.1016/S1001-0742(08)62559-0Search in Google Scholar

[11] Unal YD, Pazarlioglu NK. Production and gelatin entrapment of laccase from Trametes versicolor and its application to quantitative determination of phenolic contents of commercial fruit juices. Food Biotechnol. 2011;25(4):351–68.10.1080/08905436.2011.617258Search in Google Scholar

[12] Mogharabi M, Nassiri-Koopaei N, Bozorgi-Koushalshahi M, Nafissi-Varcheh N, Bagherzadeh G, Faramarzi MA. Immobilization of laccase in alginate‐gelatin mixed gel and decolorization of synthetic dyes. Bioinorg Chem Appl. 2012;2012(1):823830.10.1155/2012/823830Search in Google Scholar PubMed PubMed Central

[13] Rocasalbas G, Francesko A, Touriño S, Fernández-Francos X, Guebitz GM, Tzanov T. Laccase-assisted formation of bioactive chitosan/gelatin hydrogel stabilized with plant polyphenols. Carbohydr Polym. 2013;92(2):989–96.10.1016/j.carbpol.2012.10.045Search in Google Scholar PubMed

[14] Khalighi S, Berger RG, Ersoy F. Cross-linking of fibrex gel by fungal laccase: Gel rheological and structural characteristics. Processes. 2019;8(1):16.10.3390/pr8010016Search in Google Scholar

[15] Harguindeguy M, Antonelli C, Belleville MP, Sanchez‐Marcano J, Pochat‐Bohatier C. Gelatin supports with immobilized laccase as sustainable biocatalysts for water treatment. J Appl Polym Sci. 2021;138(2):49669.10.1002/app.49669Search in Google Scholar

[16] Nosrati H, Pourmotabed S, Sharifi E. A review on some natural biopolymers and their applications in angiogenesis and tissue engineering. J Appl Biotechnol Rep. 2018;5(3):81–91.10.29252/JABR.05.03.01Search in Google Scholar

[17] Narayanaswamy R, Kanagesan S, Pandurangan A, Padmanabhan P. Basics to different imaging techniques, different nanobiomaterials for image enhancement. In: Grumezescu A, editor. Nanobiomaterials in medical imaging. New York, USA: William Andrew Publishing; 2016. p. 101–29.10.1016/B978-0-323-41736-5.00004-2Search in Google Scholar

[18] Ragavan V, Ramesh A, Narayanaswamy R. Molecular docking analysis of Gossypol analogs as human neutrophil elastase (HNE), matrix metalloproteinases (MMP 2 and 9) and tyrosinase inhibitors. Rasayan J Chem. 2020;13(1):469–75.10.31788/RJC.2020.1315541Search in Google Scholar

[19] Moreira-Filho JT, Braga RC, Lemos JM, Alves VM, Borba JV, Costa WS, et al. BeeToxAI: An artificial intelligence-based web app to assess acute toxicity of chemicals to honey bees. Artif Intell Life Sci. 2021;1:100013.10.1016/j.ailsci.2021.100013Search in Google Scholar

[20] Narayanaswamy R, Prabhakaran VS, Al-Ansari MM, Al-Humaid LA, Tiwari P. An In Silico analysis of synthetic and natural compounds as inhibitors of Nitrous oxide reductase (N2OR) and Nitrite reductase (NIR). Toxics. 2023;11(8):660.10.3390/toxics11080660Search in Google Scholar PubMed PubMed Central

[21] Santhakumaran I, Narayanaswamy R, Arumugam G. Bioinformatic insights into the biochemical efficacy of a fungal metabolite: asperyellone. New J Chem. 2021;45(38):17941–50.10.1039/D1NJ02938JSearch in Google Scholar

[22] Grosdidier A, Zoete V, Michielin O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 2011;39(2):W270–7.10.1093/nar/gkr366Search in Google Scholar PubMed PubMed Central

[23] Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics. 2013;29(7):845–54.10.1093/bioinformatics/btt055Search in Google Scholar PubMed PubMed Central

[24] Maciejewski MW, Schuyler AD, Gryk MR, Moraru II, Romero PR, Ulrich EL, et al. NMRbox: a resource for biomolecular NMR computation. Biophys J. 2017;112:1529–34.10.1016/j.bpj.2017.03.011Search in Google Scholar PubMed PubMed Central

[25] Dodda LS, Cabeza de Vaca I, Tirado-Rives J, Jorgensen WL. LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands. Nucleic Acids Res. 2017;45(W1):W331–6.10.1093/nar/gkx312Search in Google Scholar PubMed PubMed Central

[26] Ghahremanian S, Rashidi MM, Raeisi K, Toghraie D. Molecular dynamics simulation approach for discovering potential inhibitors against SARS-CoV-2: A structural review. J Mol Liq. 2022;354:118901.10.1016/j.molliq.2022.118901Search in Google Scholar PubMed PubMed Central

[27] Grbavcic S, Bezbradica D, Izrael-Zivkovic L, Avramovic N, Milosavic N, Karadzic I, et al. Production of lipase and protease from an indigenous Pseudomonas aeruginosa strain and their evaluation as detergent additives: compatibility study with detergent ingredients and washing performance. Bioresour Technol. 2011;102(24):11226–33.10.1016/j.biortech.2011.09.076Search in Google Scholar PubMed

[28] Baweja M, Tiwari R, Singh PK, Nain L, Shukla P. An alkaline protease from Bacillus pumilus MP 27: functional analysis of its binding model toward its applications as detergent additive. Front Microbiol. 2016;7:1195.10.3389/fmicb.2016.01195Search in Google Scholar PubMed PubMed Central

[29] Tanwar M, Debnath M, Debnath S, Sharma P, Mukhopadhay A, Kakar N, et al. Exploring the utility of nanoprotease as environmentally friendly benign laundry detergent fabric cleaner. J Clean Prod. 2022;334:130243.10.1016/j.jclepro.2021.130243Search in Google Scholar

[30] Mayolo-Deloisa K, Gonzalez-Gonzalez M, Rito-Palomares M. Laccases in food industry: Bioprocessing, potential industrial and biotechnological applications. Front Bioeng Biotechnol. 2020;8:222.10.3389/fbioe.2020.00222Search in Google Scholar PubMed PubMed Central

[31] Kandasamy S, Duraisamy S, Chinnappan S, Balakrishnan S, Thangasamy S, Muthusamy G, et al. Molecular modeling and docking of protease from Bacillus sp. for the keratin degradation. Biocatal Agric Biotechnol. 2018;13:95–104.10.1016/j.bcab.2017.11.016Search in Google Scholar

[32] Rezakhani N, Parivar K, Khayati M, Etemadzade S. Immobilization of protease in biopolymers (mixture of alginate-chitosan). Arch Adv Biosci. 2014;5(4):108–13.Search in Google Scholar

[33] Alnoch RC, Alves dos Santos L, Marques de Almeida J, Krieger N, Mateo C. Recent trends in biomaterials for immobilization of lipases for application in nonconventional media. Catalysts. 2020;10(6):697.10.3390/catal10060697Search in Google Scholar

[34] Prokopijevic M. Natural polymers: suitable carriers for enzyme immobilization. Biol Serb. 2021;43(1):43–9.Search in Google Scholar

[35] Sharma A, Thatai KS, Kuthiala T, Singh G, Arya SK. Employment of polysaccharides in enzyme immobilization. React Funct Polym. 2021;167:105005.10.1016/j.reactfunctpolym.2021.105005Search in Google Scholar

[36] Lyu X, Gonzalez R, Horton A, Li T. Immobilization of enzymes by polymeric materials. Catalysts. 2021;11(10):1211.10.3390/catal11101211Search in Google Scholar

[37] Abdelsattar AS, Dawoud A, Helal MA. Interaction of nanoparticles with biological macromolecules: A review of molecular docking studies. Nanotoxicology. 2021;15(1):66–95.10.1080/17435390.2020.1842537Search in Google Scholar PubMed

[38] Borkotoky S, Meena CK, Murali A. Interaction analysis of T7 RNA polymerase with heparin and its low molecular weight derivatives–an In silico approach. Bioinform Biol Insight. 2016;10:155–66.10.4137/BBI.S40427Search in Google Scholar PubMed PubMed Central

[39] Narayanaswamy R. Molecular docking analysis of Alginate oligosaccharides (Alg2-Alg6) as bacterial collagenase inhibition. J Appl Cosmetol. 2017;35(3/4):105–13.Search in Google Scholar

[40] Maksimenko AV, Sakharova YS, Beabealashvilli RS. Experimental and computational study of hyaluronidase interactions with glycosaminoglycans and their ligands. Curr Mol Med. 2022;22(8):675–90.10.2174/1566524021666211018113204Search in Google Scholar PubMed

[41] Franco YN, Mesa M. Complementary experimental/docking approach for determining chitosan and carboxymethylchitosan ability for the formation of active polymer-β-galactosidase adducts. Int J Biol Macromol. 2021;192:736–44.10.1016/j.ijbiomac.2021.10.020Search in Google Scholar PubMed

[42] Omar A, Ezzat H, Elhaes H, Ibrahim MA. Molecular modeling analyses for modified biopolymers. Biointerface Res Appl Chem. 2021;11(1):7847–59.10.33263/BRIAC111.78477859Search in Google Scholar

[43] Nonaka T, Fujihashi M, Kita A, Saeki K, Ito S, Horikoshi K, et al. The crystal structure of an oxidatively stable subtilisin-like alkaline serine protease, KP-43, with a C-terminal β-barrel domain. J Biol Chem. 2004;279(45):47344–51.10.1074/jbc.M409089200Search in Google Scholar PubMed

[44] Siezen RJ, Leunissen JA. Subtilases: the superfamily of subtilisin‐like serine proteases. Protein Sci. 1997;6(3):501–23.10.1002/pro.5560060301Search in Google Scholar PubMed PubMed Central

[45] Okuda M, Ozawa T, Kawahara A, Takimura Y. The hydrophobicity of an amino acid residue in a flexible loop of KP-43 protease alters activity toward a macromolecule substrate. Appl Microbiol Biotechnol. 2020;104:8339–49.10.1007/s00253-020-10826-2Search in Google Scholar PubMed PubMed Central

[46] Mahmoud A, Kotb E, Alqosaibi AI, Al-Karmalawy AA, Al-Dhuayan IS, Alabkari H. In vitro and in silico characterization of alkaline serine protease from Bacillus subtilis D9 recovered from Saudi Arabia. Heliyon. 2021;7(10):e08148.10.1016/j.heliyon.2021.e08148Search in Google Scholar PubMed PubMed Central

[47] Singh A, Kumari S, Pal TK. In silico analysis for laccase-mediated bioremediation of the emerging pharmaceutical pollutants. Int J Bioautom. 2015;19:423–32.Search in Google Scholar

[48] Rivera-Hoyos CM, Morales-Alvarez ED, Poveda-Cuevas SA, Reyes-Guzman EA, Poutou-Pinales RA, Reyes-Montano EA, et al. Computational analysis and low-scale constitutive expression of laccases synthetic genes GlLCC1 from Ganoderma lucidum and POXA 1B from Pleurotus ostreatus in Pichia pastoris. PLoS One. 2015;10(1):e0116524.10.1371/journal.pone.0116524Search in Google Scholar PubMed PubMed Central

[49] Xie T, Liu Z, Liu Q, Wang G. Structural insight into the oxidation of sinapic acid by CotA laccase. J Struct Biol. 2015;190(2):155–61.10.1016/j.jsb.2015.03.005Search in Google Scholar PubMed

[50] Kumar A, Mishra T, Kulshreshtha A. Binding interaction of laccases from Bacillus subtilis after industrial dyes exposure: Molecular docking and molecular dynamics simulation studies. Indian J Biochem Biophys. 2023;60(4):320–30.Search in Google Scholar

[51] Hollingsworth SA, Dror RO. Molecular dynamics simulation for all. Neuron. 2018;99(6):1129–43.10.1016/j.neuron.2018.08.011Search in Google Scholar PubMed PubMed Central

[52] Durham E, Dorr B, Woetzel N, Staritzbichler R, Meiler J. Solvent accessible surface area approximations for rapid and accurate protein structure prediction. J Mol Model. 2009;15(9):1093–108.10.1007/s00894-009-0454-9Search in Google Scholar PubMed PubMed Central

Received: 2024-04-01
Revised: 2024-07-26
Accepted: 2024-09-03
Published Online: 2024-09-30

© 2024 the author(s), published by De Gruyter

This work is licensed under the Creative Commons Attribution 4.0 International License.

Articles in the same Issue

  1. Regular Articles
  2. Porous silicon nanostructures: Synthesis, characterization, and their antifungal activity
  3. Biochar from de-oiled Chlorella vulgaris and its adsorption on antibiotics
  4. Phytochemicals profiling, in vitro and in vivo antidiabetic activity, and in silico studies on Ajuga iva (L.) Schreb.: A comprehensive approach
  5. Synthesis, characterization, in silico and in vitro studies of novel glycoconjugates as potential antibacterial, antifungal, and antileishmanial agents
  6. Sonochemical synthesis of gold nanoparticles mediated by potato starch: Its performance in the treatment of esophageal cancer
  7. Computational study of ADME-Tox prediction of selected phytochemicals from Punica granatum peels
  8. Phytochemical analysis, in vitro antioxidant and antifungal activities of extracts and essential oil derived from Artemisia herba-alba Asso
  9. Two triazole-based coordination polymers: Synthesis and crystal structure characterization
  10. Phytochemical and physicochemical studies of different apple varieties grown in Morocco
  11. Synthesis of multi-template molecularly imprinted polymers (MT-MIPs) for isolating ethyl para-methoxycinnamate and ethyl cinnamate from Kaempferia galanga L., extract with methacrylic acid as functional monomer
  12. Nutraceutical potential of Mesembryanthemum forsskaolii Hochst. ex Bioss.: Insights into its nutritional composition, phytochemical contents, and antioxidant activity
  13. Evaluation of influence of Butea monosperma floral extract on inflammatory biomarkers
  14. Cannabis sativa L. essential oil: Chemical composition, anti-oxidant, anti-microbial properties, and acute toxicity: In vitro, in vivo, and in silico study
  15. The effect of gamma radiation on 5-hydroxymethylfurfural conversion in water and dimethyl sulfoxide
  16. Hollow mushroom nanomaterials for potentiometric sensing of Pb2+ ions in water via the intercalation of iodide ions into the polypyrrole matrix
  17. Determination of essential oil and chemical composition of St. John’s Wort
  18. Computational design and in vitro assay of lantadene-based novel inhibitors of NS3 protease of dengue virus
  19. Anti-parasitic activity and computational studies on a novel labdane diterpene from the roots of Vachellia nilotica
  20. Microbial dynamics and dehydrogenase activity in tomato (Lycopersicon esculentum Mill.) rhizospheres: Impacts on growth and soil health across different soil types
  21. Correlation between in vitro anti-urease activity and in silico molecular modeling approach of novel imidazopyridine–oxadiazole hybrids derivatives
  22. Spatial mapping of indoor air quality in a light metro system using the geographic information system method
  23. Iron indices and hemogram in renal anemia and the improvement with Tribulus terrestris green-formulated silver nanoparticles applied on rat model
  24. Integrated track of nano-informatics coupling with the enrichment concept in developing a novel nanoparticle targeting ERK protein in Naegleria fowleri
  25. Cytotoxic and phytochemical screening of Solanum lycopersicum–Daucus carota hydro-ethanolic extract and in silico evaluation of its lycopene content as anticancer agent
  26. Protective activities of silver nanoparticles containing Panax japonicus on apoptotic, inflammatory, and oxidative alterations in isoproterenol-induced cardiotoxicity
  27. pH-based colorimetric detection of monofunctional aldehydes in liquid and gas phases
  28. Investigating the effect of resveratrol on apoptosis and regulation of gene expression of Caco-2 cells: Unravelling potential implications for colorectal cancer treatment
  29. Metformin inhibits knee osteoarthritis induced by type 2 diabetes mellitus in rats: S100A8/9 and S100A12 as players and therapeutic targets
  30. Effect of silver nanoparticles formulated by Silybum marianum on menopausal urinary incontinence in ovariectomized rats
  31. Synthesis of new analogs of N-substituted(benzoylamino)-1,2,3,6-tetrahydropyridines
  32. Response of yield and quality of Japonica rice to different gradients of moisture deficit at grain-filling stage in cold regions
  33. Preparation of an inclusion complex of nickel-based β-cyclodextrin: Characterization and accelerating the osteoarthritis articular cartilage repair
  34. Empagliflozin-loaded nanomicelles responsive to reactive oxygen species for renal ischemia/reperfusion injury protection
  35. Preparation and pharmacodynamic evaluation of sodium aescinate solid lipid nanoparticles
  36. Assessment of potentially toxic elements and health risks of agricultural soil in Southwest Riyadh, Saudi Arabia
  37. Theoretical investigation of hydrogen-rich fuel production through ammonia decomposition
  38. Biosynthesis and screening of cobalt nanoparticles using citrus species for antimicrobial activity
  39. Investigating the interplay of genetic variations, MCP-1 polymorphism, and docking with phytochemical inhibitors for combatting dengue virus pathogenicity through in silico analysis
  40. Ultrasound induced biosynthesis of silver nanoparticles embedded into chitosan polymers: Investigation of its anti-cutaneous squamous cell carcinoma effects
  41. Copper oxide nanoparticles-mediated Heliotropium bacciferum leaf extract: Antifungal activity and molecular docking assays against strawberry pathogens
  42. Sprouted wheat flour for improving physical, chemical, rheological, microbial load, and quality properties of fino bread
  43. Comparative toxicity assessment of fisetin-aided artificial intelligence-assisted drug design targeting epibulbar dermoid through phytochemicals
  44. Acute toxicity and anti-inflammatory activity of bis-thiourea derivatives
  45. Anti-diabetic activity-guided isolation of α-amylase and α-glucosidase inhibitory terpenes from Capsella bursa-pastoris Linn.
  46. GC–MS analysis of Lactobacillus plantarum YW11 metabolites and its computational analysis on familial pulmonary fibrosis hub genes
  47. Green formulation of copper nanoparticles by Pistacia khinjuk leaf aqueous extract: Introducing a novel chemotherapeutic drug for the treatment of prostate cancer
  48. Improved photocatalytic properties of WO3 nanoparticles for Malachite green dye degradation under visible light irradiation: An effect of La doping
  49. One-pot synthesis of a network of Mn2O3–MnO2–poly(m-methylaniline) composite nanorods on a polypyrrole film presents a promising and efficient optoelectronic and solar cell device
  50. Groundwater quality and health risk assessment of nitrate and fluoride in Al Qaseem area, Saudi Arabia
  51. A comparative study of the antifungal efficacy and phytochemical composition of date palm leaflet extracts
  52. Processing of alcohol pomelo beverage (Citrus grandis (L.) Osbeck) using saccharomyces yeast: Optimization, physicochemical quality, and sensory characteristics
  53. Specialized compounds of four Cameroonian spices: Isolation, characterization, and in silico evaluation as prospective SARS-CoV-2 inhibitors
  54. Identification of a novel drug target in Porphyromonas gingivalis by a computational genome analysis approach
  55. Physico-chemical properties and durability of a fly-ash-based geopolymer
  56. FMS-like tyrosine kinase 3 inhibitory potentials of some phytochemicals from anti-leukemic plants using computational chemical methodologies
  57. Wild Thymus zygis L. ssp. gracilis and Eucalyptus camaldulensis Dehnh.: Chemical composition, antioxidant and antibacterial activities of essential oils
  58. 3D-QSAR, molecular docking, ADMET, simulation dynamic, and retrosynthesis studies on new styrylquinolines derivatives against breast cancer
  59. Deciphering the influenza neuraminidase inhibitory potential of naturally occurring biflavonoids: An in silico approach
  60. Determination of heavy elements in agricultural regions, Saudi Arabia
  61. Synthesis and characterization of antioxidant-enriched Moringa oil-based edible oleogel
  62. Ameliorative effects of thistle and thyme honeys on cyclophosphamide-induced toxicity in mice
  63. Study of phytochemical compound and antipyretic activity of Chenopodium ambrosioides L. fractions
  64. Investigating the adsorption mechanism of zinc chloride-modified porous carbon for sulfadiazine removal from water
  65. Performance repair of building materials using alumina and silica composite nanomaterials with electrodynamic properties
  66. Effects of nanoparticles on the activity and resistance genes of anaerobic digestion enzymes in livestock and poultry manure containing the antibiotic tetracycline
  67. Effect of copper nanoparticles green-synthesized using Ocimum basilicum against Pseudomonas aeruginosa in mice lung infection model
  68. Cardioprotective effects of nanoparticles green formulated by Spinacia oleracea extract on isoproterenol-induced myocardial infarction in mice by the determination of PPAR-γ/NF-κB pathway
  69. Anti-OTC antibody-conjugated fluorescent magnetic/silica and fluorescent hybrid silica nanoparticles for oxytetracycline detection
  70. Curcumin conjugated zinc nanoparticles for the treatment of myocardial infarction
  71. Identification and in silico screening of natural phloroglucinols as potential PI3Kα inhibitors: A computational approach for drug discovery
  72. Exploring the phytochemical profile and antioxidant evaluation: Molecular docking and ADMET analysis of main compounds from three Solanum species in Saudi Arabia
  73. Unveiling the molecular composition and biological properties of essential oil derived from the leaves of wild Mentha aquatica L.: A comprehensive in vitro and in silico exploration
  74. Analysis of bioactive compounds present in Boerhavia elegans seeds by GC-MS
  75. Homology modeling and molecular docking study of corticotrophin-releasing hormone: An approach to treat stress-related diseases
  76. LncRNA MIR17HG alleviates heart failure via targeting MIR17HG/miR-153-3p/SIRT1 axis in in vitro model
  77. Development and validation of a stability indicating UPLC-DAD method coupled with MS-TQD for ramipril and thymoquinone in bioactive SNEDDS with in silico toxicity analysis of ramipril degradation products
  78. Biosynthesis of Ag/Cu nanocomposite mediated by Curcuma longa: Evaluation of its antibacterial properties against oral pathogens
  79. Development of AMBER-compliant transferable force field parameters for polytetrafluoroethylene
  80. Treatment of gestational diabetes by Acroptilon repens leaf aqueous extract green-formulated iron nanoparticles in rats
  81. Development and characterization of new ecological adsorbents based on cardoon wastes: Application to brilliant green adsorption
  82. A fast, sensitive, greener, and stability-indicating HPLC method for the standardization and quantitative determination of chlorhexidine acetate in commercial products
  83. Assessment of Se, As, Cd, Cr, Hg, and Pb content status in Ankang tea plantations of China
  84. Effect of transition metal chloride (ZnCl2) on low-temperature pyrolysis of high ash bituminous coal
  85. Evaluating polyphenol and ascorbic acid contents, tannin removal ability, and physical properties during hydrolysis and convective hot-air drying of cashew apple powder
  86. Development and characterization of functional low-fat frozen dairy dessert enhanced with dried lemongrass powder
  87. Scrutinizing the effect of additive and synergistic antibiotics against carbapenem-resistant Pseudomonas aeruginosa
  88. Preparation, characterization, and determination of the therapeutic effects of copper nanoparticles green-formulated by Pistacia atlantica in diabetes-induced cardiac dysfunction in rat
  89. Antioxidant and antidiabetic potentials of methoxy-substituted Schiff bases using in vitro, in vivo, and molecular simulation approaches
  90. Anti-melanoma cancer activity and chemical profile of the essential oil of Seseli yunnanense Franch
  91. Molecular docking analysis of subtilisin-like alkaline serine protease (SLASP) and laccase with natural biopolymers
  92. Overcoming methicillin resistance by methicillin-resistant Staphylococcus aureus: Computational evaluation of napthyridine and oxadiazoles compounds for potential dual inhibition of PBP-2a and FemA proteins
  93. Exploring novel antitubercular agents: Innovative design of 2,3-diaryl-quinoxalines targeting DprE1 for effective tuberculosis treatment
  94. Drimia maritima flowers as a source of biologically potent components: Optimization of bioactive compound extractions, isolation, UPLC–ESI–MS/MS, and pharmacological properties
  95. Estimating molecular properties, drug-likeness, cardiotoxic risk, liability profile, and molecular docking study to characterize binding process of key phyto-compounds against serotonin 5-HT2A receptor
  96. Fabrication of β-cyclodextrin-based microgels for enhancing solubility of Terbinafine: An in-vitro and in-vivo toxicological evaluation
  97. Phyto-mediated synthesis of ZnO nanoparticles and their sunlight-driven photocatalytic degradation of cationic and anionic dyes
  98. Monosodium glutamate induces hypothalamic–pituitary–adrenal axis hyperactivation, glucocorticoid receptors down-regulation, and systemic inflammatory response in young male rats: Impact on miR-155 and miR-218
  99. Quality control analyses of selected honey samples from Serbia based on their mineral and flavonoid profiles, and the invertase activity
  100. Eco-friendly synthesis of silver nanoparticles using Phyllanthus niruri leaf extract: Assessment of antimicrobial activity, effectiveness on tropical neglected mosquito vector control, and biocompatibility using a fibroblast cell line model
  101. Green synthesis of silver nanoparticles containing Cichorium intybus to treat the sepsis-induced DNA damage in the liver of Wistar albino rats
  102. Quality changes of durian pulp (Durio ziberhinus Murr.) in cold storage
  103. Study on recrystallization process of nitroguanidine by directly adding cold water to control temperature
  104. Determination of heavy metals and health risk assessment in drinking water in Bukayriyah City, Saudi Arabia
  105. Larvicidal properties of essential oils of three Artemisia species against the chemically insecticide-resistant Nile fever vector Culex pipiens (L.) (Diptera: Culicidae): In vitro and in silico studies
  106. Design, synthesis, characterization, and theoretical calculations, along with in silico and in vitro antimicrobial proprieties of new isoxazole-amide conjugates
  107. The impact of drying and extraction methods on total lipid, fatty acid profile, and cytotoxicity of Tenebrio molitor larvae
  108. A zinc oxide–tin oxide–nerolidol hybrid nanomaterial: Efficacy against esophageal squamous cell carcinoma
  109. Research on technological process for production of muskmelon juice (Cucumis melo L.)
  110. Physicochemical components, antioxidant activity, and predictive models for quality of soursop tea (Annona muricata L.) during heat pump drying
  111. Characterization and application of Fe1−xCoxFe2O4 nanoparticles in Direct Red 79 adsorption
  112. Torilis arvensis ethanolic extract: Phytochemical analysis, antifungal efficacy, and cytotoxicity properties
  113. Magnetite–poly-1H pyrrole dendritic nanocomposite seeded on poly-1H pyrrole: A promising photocathode for green hydrogen generation from sanitation water without using external sacrificing agent
  114. HPLC and GC–MS analyses of phytochemical compounds in Haloxylon salicornicum extract: Antibacterial and antifungal activity assessment of phytopathogens
  115. Efficient and stable to coking catalysts of ethanol steam reforming comprised of Ni + Ru loaded on MgAl2O4 + LnFe0.7Ni0.3O3 (Ln = La, Pr) nanocomposites prepared via cost-effective procedure with Pluronic P123 copolymer
  116. Nitrogen and boron co-doped carbon dots probe for selectively detecting Hg2+ in water samples and the detection mechanism
  117. Heavy metals in road dust from typical old industrial areas of Wuhan: Seasonal distribution and bioaccessibility-based health risk assessment
  118. Phytochemical profiling and bioactivity evaluation of CBD- and THC-enriched Cannabis sativa extracts: In vitro and in silico investigation of antioxidant and anti-inflammatory effects
  119. Investigating dye adsorption: The role of surface-modified montmorillonite nanoclay in kinetics, isotherms, and thermodynamics
  120. Antimicrobial activity, induction of ROS generation in HepG2 liver cancer cells, and chemical composition of Pterospermum heterophyllum
  121. Study on the performance of nanoparticle-modified PVDF membrane in delaying membrane aging
  122. Impact of cholesterol in encapsulated vitamin E acetate within cocoliposomes
  123. Review Articles
  124. Structural aspects of Pt(η3-X1N1X2)(PL) (X1,2 = O, C, or Se) and Pt(η3-N1N2X1)(PL) (X1 = C, S, or Se) derivatives
  125. Biosurfactants in biocorrosion and corrosion mitigation of metals: An overview
  126. Stimulus-responsive MOF–hydrogel composites: Classification, preparation, characterization, and their advancement in medical treatments
  127. Electrochemical dissolution of titanium under alternating current polarization to obtain its dioxide
  128. Special Issue on Recent Trends in Green Chemistry
  129. Phytochemical screening and antioxidant activity of Vitex agnus-castus L.
  130. Phytochemical study, antioxidant activity, and dermoprotective activity of Chenopodium ambrosioides (L.)
  131. Exploitation of mangliculous marine fungi, Amarenographium solium, for the green synthesis of silver nanoparticles and their activity against multiple drug-resistant bacteria
  132. Study of the phytotoxicity of margines on Pistia stratiotes L.
  133. Special Issue on Advanced Nanomaterials for Energy, Environmental and Biological Applications - Part III
  134. Impact of biogenic zinc oxide nanoparticles on growth, development, and antioxidant system of high protein content crop (Lablab purpureus L.) sweet
  135. Green synthesis, characterization, and application of iron and molybdenum nanoparticles and their composites for enhancing the growth of Solanum lycopersicum
  136. Green synthesis of silver nanoparticles from Olea europaea L. extracted polysaccharides, characterization, and its assessment as an antimicrobial agent against multiple pathogenic microbes
  137. Photocatalytic treatment of organic dyes using metal oxides and nanocomposites: A quantitative study
  138. Antifungal, antioxidant, and photocatalytic activities of greenly synthesized iron oxide nanoparticles
  139. Special Issue on Phytochemical and Pharmacological Scrutinization of Medicinal Plants
  140. Hepatoprotective effects of safranal on acetaminophen-induced hepatotoxicity in rats
  141. Chemical composition and biological properties of Thymus capitatus plants from Algerian high plains: A comparative and analytical study
  142. Chemical composition and bioactivities of the methanol root extracts of Saussurea costus
  143. In vivo protective effects of vitamin C against cyto-genotoxicity induced by Dysphania ambrosioides aqueous extract
  144. Insights about the deleterious impact of a carbamate pesticide on some metabolic immune and antioxidant functions and a focus on the protective ability of a Saharan shrub and its anti-edematous property
  145. A comprehensive review uncovering the anticancerous potential of genkwanin (plant-derived compound) in several human carcinomas
  146. A study to investigate the anticancer potential of carvacrol via targeting Notch signaling in breast cancer
  147. Assessment of anti-diabetic properties of Ziziphus oenopolia (L.) wild edible fruit extract: In vitro and in silico investigations through molecular docking analysis
  148. Optimization of polyphenol extraction, phenolic profile by LC-ESI-MS/MS, antioxidant, anti-enzymatic, and cytotoxic activities of Physalis acutifolia
  149. Phytochemical screening, antioxidant properties, and photo-protective activities of Salvia balansae de Noé ex Coss
  150. Antihyperglycemic, antiglycation, anti-hypercholesteremic, and toxicity evaluation with gas chromatography mass spectrometry profiling for Aloe armatissima leaves
  151. Phyto-fabrication and characterization of gold nanoparticles by using Timur (Zanthoxylum armatum DC) and their effect on wound healing
  152. Does Erodium trifolium (Cav.) Guitt exhibit medicinal properties? Response elements from phytochemical profiling, enzyme-inhibiting, and antioxidant and antimicrobial activities
  153. Integrative in silico evaluation of the antiviral potential of terpenoids and its metal complexes derived from Homalomena aromatica based on main protease of SARS-CoV-2
  154. 6-Methoxyflavone improves anxiety, depression, and memory by increasing monoamines in mice brain: HPLC analysis and in silico studies
  155. Simultaneous extraction and quantification of hydrophilic and lipophilic antioxidants in Solanum lycopersicum L. varieties marketed in Saudi Arabia
  156. Biological evaluation of CH3OH and C2H5OH of Berberis vulgaris for in vivo antileishmanial potential against Leishmania tropica in murine models
https://doi.org/10.1515/chem-2024-0090
Keywords for this article
molecular docking; natural biopolymer; subtilisin-like alkaline serine protease; Bacillus subtilis laccase; chitosan; nanoparticles; MD simulation
Creative Commons
BY 4.0

Articles in the same Issue

  1. Regular Articles
  2. Porous silicon nanostructures: Synthesis, characterization, and their antifungal activity
  3. Biochar from de-oiled Chlorella vulgaris and its adsorption on antibiotics
  4. Phytochemicals profiling, in vitro and in vivo antidiabetic activity, and in silico studies on Ajuga iva (L.) Schreb.: A comprehensive approach
  5. Synthesis, characterization, in silico and in vitro studies of novel glycoconjugates as potential antibacterial, antifungal, and antileishmanial agents
  6. Sonochemical synthesis of gold nanoparticles mediated by potato starch: Its performance in the treatment of esophageal cancer
  7. Computational study of ADME-Tox prediction of selected phytochemicals from Punica granatum peels
  8. Phytochemical analysis, in vitro antioxidant and antifungal activities of extracts and essential oil derived from Artemisia herba-alba Asso
  9. Two triazole-based coordination polymers: Synthesis and crystal structure characterization
  10. Phytochemical and physicochemical studies of different apple varieties grown in Morocco
  11. Synthesis of multi-template molecularly imprinted polymers (MT-MIPs) for isolating ethyl para-methoxycinnamate and ethyl cinnamate from Kaempferia galanga L., extract with methacrylic acid as functional monomer
  12. Nutraceutical potential of Mesembryanthemum forsskaolii Hochst. ex Bioss.: Insights into its nutritional composition, phytochemical contents, and antioxidant activity
  13. Evaluation of influence of Butea monosperma floral extract on inflammatory biomarkers
  14. Cannabis sativa L. essential oil: Chemical composition, anti-oxidant, anti-microbial properties, and acute toxicity: In vitro, in vivo, and in silico study
  15. The effect of gamma radiation on 5-hydroxymethylfurfural conversion in water and dimethyl sulfoxide
  16. Hollow mushroom nanomaterials for potentiometric sensing of Pb2+ ions in water via the intercalation of iodide ions into the polypyrrole matrix
  17. Determination of essential oil and chemical composition of St. John’s Wort
  18. Computational design and in vitro assay of lantadene-based novel inhibitors of NS3 protease of dengue virus
  19. Anti-parasitic activity and computational studies on a novel labdane diterpene from the roots of Vachellia nilotica
  20. Microbial dynamics and dehydrogenase activity in tomato (Lycopersicon esculentum Mill.) rhizospheres: Impacts on growth and soil health across different soil types
  21. Correlation between in vitro anti-urease activity and in silico molecular modeling approach of novel imidazopyridine–oxadiazole hybrids derivatives
  22. Spatial mapping of indoor air quality in a light metro system using the geographic information system method
  23. Iron indices and hemogram in renal anemia and the improvement with Tribulus terrestris green-formulated silver nanoparticles applied on rat model
  24. Integrated track of nano-informatics coupling with the enrichment concept in developing a novel nanoparticle targeting ERK protein in Naegleria fowleri
  25. Cytotoxic and phytochemical screening of Solanum lycopersicum–Daucus carota hydro-ethanolic extract and in silico evaluation of its lycopene content as anticancer agent
  26. Protective activities of silver nanoparticles containing Panax japonicus on apoptotic, inflammatory, and oxidative alterations in isoproterenol-induced cardiotoxicity
  27. pH-based colorimetric detection of monofunctional aldehydes in liquid and gas phases
  28. Investigating the effect of resveratrol on apoptosis and regulation of gene expression of Caco-2 cells: Unravelling potential implications for colorectal cancer treatment
  29. Metformin inhibits knee osteoarthritis induced by type 2 diabetes mellitus in rats: S100A8/9 and S100A12 as players and therapeutic targets
  30. Effect of silver nanoparticles formulated by Silybum marianum on menopausal urinary incontinence in ovariectomized rats
  31. Synthesis of new analogs of N-substituted(benzoylamino)-1,2,3,6-tetrahydropyridines
  32. Response of yield and quality of Japonica rice to different gradients of moisture deficit at grain-filling stage in cold regions
  33. Preparation of an inclusion complex of nickel-based β-cyclodextrin: Characterization and accelerating the osteoarthritis articular cartilage repair
  34. Empagliflozin-loaded nanomicelles responsive to reactive oxygen species for renal ischemia/reperfusion injury protection
  35. Preparation and pharmacodynamic evaluation of sodium aescinate solid lipid nanoparticles
  36. Assessment of potentially toxic elements and health risks of agricultural soil in Southwest Riyadh, Saudi Arabia
  37. Theoretical investigation of hydrogen-rich fuel production through ammonia decomposition
  38. Biosynthesis and screening of cobalt nanoparticles using citrus species for antimicrobial activity
  39. Investigating the interplay of genetic variations, MCP-1 polymorphism, and docking with phytochemical inhibitors for combatting dengue virus pathogenicity through in silico analysis
  40. Ultrasound induced biosynthesis of silver nanoparticles embedded into chitosan polymers: Investigation of its anti-cutaneous squamous cell carcinoma effects
  41. Copper oxide nanoparticles-mediated Heliotropium bacciferum leaf extract: Antifungal activity and molecular docking assays against strawberry pathogens
  42. Sprouted wheat flour for improving physical, chemical, rheological, microbial load, and quality properties of fino bread
  43. Comparative toxicity assessment of fisetin-aided artificial intelligence-assisted drug design targeting epibulbar dermoid through phytochemicals
  44. Acute toxicity and anti-inflammatory activity of bis-thiourea derivatives
  45. Anti-diabetic activity-guided isolation of α-amylase and α-glucosidase inhibitory terpenes from Capsella bursa-pastoris Linn.
  46. GC–MS analysis of Lactobacillus plantarum YW11 metabolites and its computational analysis on familial pulmonary fibrosis hub genes
  47. Green formulation of copper nanoparticles by Pistacia khinjuk leaf aqueous extract: Introducing a novel chemotherapeutic drug for the treatment of prostate cancer
  48. Improved photocatalytic properties of WO3 nanoparticles for Malachite green dye degradation under visible light irradiation: An effect of La doping
  49. One-pot synthesis of a network of Mn2O3–MnO2–poly(m-methylaniline) composite nanorods on a polypyrrole film presents a promising and efficient optoelectronic and solar cell device
  50. Groundwater quality and health risk assessment of nitrate and fluoride in Al Qaseem area, Saudi Arabia
  51. A comparative study of the antifungal efficacy and phytochemical composition of date palm leaflet extracts
  52. Processing of alcohol pomelo beverage (Citrus grandis (L.) Osbeck) using saccharomyces yeast: Optimization, physicochemical quality, and sensory characteristics
  53. Specialized compounds of four Cameroonian spices: Isolation, characterization, and in silico evaluation as prospective SARS-CoV-2 inhibitors
  54. Identification of a novel drug target in Porphyromonas gingivalis by a computational genome analysis approach
  55. Physico-chemical properties and durability of a fly-ash-based geopolymer
  56. FMS-like tyrosine kinase 3 inhibitory potentials of some phytochemicals from anti-leukemic plants using computational chemical methodologies
  57. Wild Thymus zygis L. ssp. gracilis and Eucalyptus camaldulensis Dehnh.: Chemical composition, antioxidant and antibacterial activities of essential oils
  58. 3D-QSAR, molecular docking, ADMET, simulation dynamic, and retrosynthesis studies on new styrylquinolines derivatives against breast cancer
  59. Deciphering the influenza neuraminidase inhibitory potential of naturally occurring biflavonoids: An in silico approach
  60. Determination of heavy elements in agricultural regions, Saudi Arabia
  61. Synthesis and characterization of antioxidant-enriched Moringa oil-based edible oleogel
  62. Ameliorative effects of thistle and thyme honeys on cyclophosphamide-induced toxicity in mice
  63. Study of phytochemical compound and antipyretic activity of Chenopodium ambrosioides L. fractions
  64. Investigating the adsorption mechanism of zinc chloride-modified porous carbon for sulfadiazine removal from water
  65. Performance repair of building materials using alumina and silica composite nanomaterials with electrodynamic properties
  66. Effects of nanoparticles on the activity and resistance genes of anaerobic digestion enzymes in livestock and poultry manure containing the antibiotic tetracycline
  67. Effect of copper nanoparticles green-synthesized using Ocimum basilicum against Pseudomonas aeruginosa in mice lung infection model
  68. Cardioprotective effects of nanoparticles green formulated by Spinacia oleracea extract on isoproterenol-induced myocardial infarction in mice by the determination of PPAR-γ/NF-κB pathway
  69. Anti-OTC antibody-conjugated fluorescent magnetic/silica and fluorescent hybrid silica nanoparticles for oxytetracycline detection
  70. Curcumin conjugated zinc nanoparticles for the treatment of myocardial infarction
  71. Identification and in silico screening of natural phloroglucinols as potential PI3Kα inhibitors: A computational approach for drug discovery
  72. Exploring the phytochemical profile and antioxidant evaluation: Molecular docking and ADMET analysis of main compounds from three Solanum species in Saudi Arabia
  73. Unveiling the molecular composition and biological properties of essential oil derived from the leaves of wild Mentha aquatica L.: A comprehensive in vitro and in silico exploration
  74. Analysis of bioactive compounds present in Boerhavia elegans seeds by GC-MS
  75. Homology modeling and molecular docking study of corticotrophin-releasing hormone: An approach to treat stress-related diseases
  76. LncRNA MIR17HG alleviates heart failure via targeting MIR17HG/miR-153-3p/SIRT1 axis in in vitro model
  77. Development and validation of a stability indicating UPLC-DAD method coupled with MS-TQD for ramipril and thymoquinone in bioactive SNEDDS with in silico toxicity analysis of ramipril degradation products
  78. Biosynthesis of Ag/Cu nanocomposite mediated by Curcuma longa: Evaluation of its antibacterial properties against oral pathogens
  79. Development of AMBER-compliant transferable force field parameters for polytetrafluoroethylene
  80. Treatment of gestational diabetes by Acroptilon repens leaf aqueous extract green-formulated iron nanoparticles in rats
  81. Development and characterization of new ecological adsorbents based on cardoon wastes: Application to brilliant green adsorption
  82. A fast, sensitive, greener, and stability-indicating HPLC method for the standardization and quantitative determination of chlorhexidine acetate in commercial products
  83. Assessment of Se, As, Cd, Cr, Hg, and Pb content status in Ankang tea plantations of China
  84. Effect of transition metal chloride (ZnCl2) on low-temperature pyrolysis of high ash bituminous coal
  85. Evaluating polyphenol and ascorbic acid contents, tannin removal ability, and physical properties during hydrolysis and convective hot-air drying of cashew apple powder
  86. Development and characterization of functional low-fat frozen dairy dessert enhanced with dried lemongrass powder
  87. Scrutinizing the effect of additive and synergistic antibiotics against carbapenem-resistant Pseudomonas aeruginosa
  88. Preparation, characterization, and determination of the therapeutic effects of copper nanoparticles green-formulated by Pistacia atlantica in diabetes-induced cardiac dysfunction in rat
  89. Antioxidant and antidiabetic potentials of methoxy-substituted Schiff bases using in vitro, in vivo, and molecular simulation approaches
  90. Anti-melanoma cancer activity and chemical profile of the essential oil of Seseli yunnanense Franch
  91. Molecular docking analysis of subtilisin-like alkaline serine protease (SLASP) and laccase with natural biopolymers
  92. Overcoming methicillin resistance by methicillin-resistant Staphylococcus aureus: Computational evaluation of napthyridine and oxadiazoles compounds for potential dual inhibition of PBP-2a and FemA proteins
  93. Exploring novel antitubercular agents: Innovative design of 2,3-diaryl-quinoxalines targeting DprE1 for effective tuberculosis treatment
  94. Drimia maritima flowers as a source of biologically potent components: Optimization of bioactive compound extractions, isolation, UPLC–ESI–MS/MS, and pharmacological properties
  95. Estimating molecular properties, drug-likeness, cardiotoxic risk, liability profile, and molecular docking study to characterize binding process of key phyto-compounds against serotonin 5-HT2A receptor
  96. Fabrication of β-cyclodextrin-based microgels for enhancing solubility of Terbinafine: An in-vitro and in-vivo toxicological evaluation
  97. Phyto-mediated synthesis of ZnO nanoparticles and their sunlight-driven photocatalytic degradation of cationic and anionic dyes
  98. Monosodium glutamate induces hypothalamic–pituitary–adrenal axis hyperactivation, glucocorticoid receptors down-regulation, and systemic inflammatory response in young male rats: Impact on miR-155 and miR-218
  99. Quality control analyses of selected honey samples from Serbia based on their mineral and flavonoid profiles, and the invertase activity
  100. Eco-friendly synthesis of silver nanoparticles using Phyllanthus niruri leaf extract: Assessment of antimicrobial activity, effectiveness on tropical neglected mosquito vector control, and biocompatibility using a fibroblast cell line model
  101. Green synthesis of silver nanoparticles containing Cichorium intybus to treat the sepsis-induced DNA damage in the liver of Wistar albino rats
  102. Quality changes of durian pulp (Durio ziberhinus Murr.) in cold storage
  103. Study on recrystallization process of nitroguanidine by directly adding cold water to control temperature
  104. Determination of heavy metals and health risk assessment in drinking water in Bukayriyah City, Saudi Arabia
  105. Larvicidal properties of essential oils of three Artemisia species against the chemically insecticide-resistant Nile fever vector Culex pipiens (L.) (Diptera: Culicidae): In vitro and in silico studies
  106. Design, synthesis, characterization, and theoretical calculations, along with in silico and in vitro antimicrobial proprieties of new isoxazole-amide conjugates
  107. The impact of drying and extraction methods on total lipid, fatty acid profile, and cytotoxicity of Tenebrio molitor larvae
  108. A zinc oxide–tin oxide–nerolidol hybrid nanomaterial: Efficacy against esophageal squamous cell carcinoma
  109. Research on technological process for production of muskmelon juice (Cucumis melo L.)
  110. Physicochemical components, antioxidant activity, and predictive models for quality of soursop tea (Annona muricata L.) during heat pump drying
  111. Characterization and application of Fe1−xCoxFe2O4 nanoparticles in Direct Red 79 adsorption
  112. Torilis arvensis ethanolic extract: Phytochemical analysis, antifungal efficacy, and cytotoxicity properties
  113. Magnetite–poly-1H pyrrole dendritic nanocomposite seeded on poly-1H pyrrole: A promising photocathode for green hydrogen generation from sanitation water without using external sacrificing agent
  114. HPLC and GC–MS analyses of phytochemical compounds in Haloxylon salicornicum extract: Antibacterial and antifungal activity assessment of phytopathogens
  115. Efficient and stable to coking catalysts of ethanol steam reforming comprised of Ni + Ru loaded on MgAl2O4 + LnFe0.7Ni0.3O3 (Ln = La, Pr) nanocomposites prepared via cost-effective procedure with Pluronic P123 copolymer
  116. Nitrogen and boron co-doped carbon dots probe for selectively detecting Hg2+ in water samples and the detection mechanism
  117. Heavy metals in road dust from typical old industrial areas of Wuhan: Seasonal distribution and bioaccessibility-based health risk assessment
  118. Phytochemical profiling and bioactivity evaluation of CBD- and THC-enriched Cannabis sativa extracts: In vitro and in silico investigation of antioxidant and anti-inflammatory effects
  119. Investigating dye adsorption: The role of surface-modified montmorillonite nanoclay in kinetics, isotherms, and thermodynamics
  120. Antimicrobial activity, induction of ROS generation in HepG2 liver cancer cells, and chemical composition of Pterospermum heterophyllum
  121. Study on the performance of nanoparticle-modified PVDF membrane in delaying membrane aging
  122. Impact of cholesterol in encapsulated vitamin E acetate within cocoliposomes
  123. Review Articles
  124. Structural aspects of Pt(η3-X1N1X2)(PL) (X1,2 = O, C, or Se) and Pt(η3-N1N2X1)(PL) (X1 = C, S, or Se) derivatives
  125. Biosurfactants in biocorrosion and corrosion mitigation of metals: An overview
  126. Stimulus-responsive MOF–hydrogel composites: Classification, preparation, characterization, and their advancement in medical treatments
  127. Electrochemical dissolution of titanium under alternating current polarization to obtain its dioxide
  128. Special Issue on Recent Trends in Green Chemistry
  129. Phytochemical screening and antioxidant activity of Vitex agnus-castus L.
  130. Phytochemical study, antioxidant activity, and dermoprotective activity of Chenopodium ambrosioides (L.)
  131. Exploitation of mangliculous marine fungi, Amarenographium solium, for the green synthesis of silver nanoparticles and their activity against multiple drug-resistant bacteria
  132. Study of the phytotoxicity of margines on Pistia stratiotes L.
  133. Special Issue on Advanced Nanomaterials for Energy, Environmental and Biological Applications - Part III
  134. Impact of biogenic zinc oxide nanoparticles on growth, development, and antioxidant system of high protein content crop (Lablab purpureus L.) sweet
  135. Green synthesis, characterization, and application of iron and molybdenum nanoparticles and their composites for enhancing the growth of Solanum lycopersicum
  136. Green synthesis of silver nanoparticles from Olea europaea L. extracted polysaccharides, characterization, and its assessment as an antimicrobial agent against multiple pathogenic microbes
  137. Photocatalytic treatment of organic dyes using metal oxides and nanocomposites: A quantitative study
  138. Antifungal, antioxidant, and photocatalytic activities of greenly synthesized iron oxide nanoparticles
  139. Special Issue on Phytochemical and Pharmacological Scrutinization of Medicinal Plants
  140. Hepatoprotective effects of safranal on acetaminophen-induced hepatotoxicity in rats
  141. Chemical composition and biological properties of Thymus capitatus plants from Algerian high plains: A comparative and analytical study
  142. Chemical composition and bioactivities of the methanol root extracts of Saussurea costus
  143. In vivo protective effects of vitamin C against cyto-genotoxicity induced by Dysphania ambrosioides aqueous extract
  144. Insights about the deleterious impact of a carbamate pesticide on some metabolic immune and antioxidant functions and a focus on the protective ability of a Saharan shrub and its anti-edematous property
  145. A comprehensive review uncovering the anticancerous potential of genkwanin (plant-derived compound) in several human carcinomas
  146. A study to investigate the anticancer potential of carvacrol via targeting Notch signaling in breast cancer
  147. Assessment of anti-diabetic properties of Ziziphus oenopolia (L.) wild edible fruit extract: In vitro and in silico investigations through molecular docking analysis
  148. Optimization of polyphenol extraction, phenolic profile by LC-ESI-MS/MS, antioxidant, anti-enzymatic, and cytotoxic activities of Physalis acutifolia
  149. Phytochemical screening, antioxidant properties, and photo-protective activities of Salvia balansae de Noé ex Coss
  150. Antihyperglycemic, antiglycation, anti-hypercholesteremic, and toxicity evaluation with gas chromatography mass spectrometry profiling for Aloe armatissima leaves
  151. Phyto-fabrication and characterization of gold nanoparticles by using Timur (Zanthoxylum armatum DC) and their effect on wound healing
  152. Does Erodium trifolium (Cav.) Guitt exhibit medicinal properties? Response elements from phytochemical profiling, enzyme-inhibiting, and antioxidant and antimicrobial activities
  153. Integrative in silico evaluation of the antiviral potential of terpenoids and its metal complexes derived from Homalomena aromatica based on main protease of SARS-CoV-2
  154. 6-Methoxyflavone improves anxiety, depression, and memory by increasing monoamines in mice brain: HPLC analysis and in silico studies
  155. Simultaneous extraction and quantification of hydrophilic and lipophilic antioxidants in Solanum lycopersicum L. varieties marketed in Saudi Arabia
  156. Biological evaluation of CH3OH and C2H5OH of Berberis vulgaris for in vivo antileishmanial potential against Leishmania tropica in murine models
Sign up now to receive a 20% welcome discount
Institutional Access
How does access work?
Have an idea on how to improve our website?
Please write us.
© 2025 De Gruyter Brill
Downloaded on 6.12.2025 from https://www.degruyterbrill.com/document/doi/10.1515/chem-2024-0090/html
Scroll to top button