Binding Energy Values Research Articles

Aluminum and Mild Steel Inhibition Investigation Using Trithiocyanuric Acid: Insights from Density Functional Theory (DFT)

<p>The study investigates the corrosion inhibition properties of Trithiocyanuric Acid (TTCA) on Aluminum and mild steel using Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations. The electronic properties of TTCA, including the highest occupied molecular orbital (E<sub>HOMO</sub>) of -7.617 eV and the lowest unoccupied molecular orbital (E<sub>LUMO</sub>) of -4.301 eV, yield an energy gap of 3.316 eV. The calculated absolute electronegativity was 5.959 eV, global hardness obtained was 1.658 eV, global softness was 0.603136 eV, global electrophilicity index was 1.449891 eV, and nucleophilicity was 0.689707 eV. The energy of back donation was also 0.689707 eV. The charge transfer parameters, ΔNFe and ΔNAl, are also 0.862989 eV and -0.21653 eV, respectively, indicating effective interaction with both metal surfaces. Functional groups in TTCA contribute significantly to its corrosion inhibition performance by facilitating alignment on the metal surfaces. The interaction mechanism is characterized as physisorption, with binding energy values falling within the range typical for this adsorption type. The results suggest that TTCA is a suitable corrosion inhibitor for Aluminum and mild steel, making it a promising molecule for industrial applications where metal protection is essential.</p>

Evaluation of suppressor behavior of guanidine-derived metformin and galegine as novel potential drugs for cancer treatment: an in silico study.

There are some natural products from plants that can prevent and treat disease. Metformin, a derivative of galegine, is the basic drug to treat diabetes. Moreover, this molecule has anticancer properties that inhibit cancer cell growth and proliferation. In this study, the main interactions of galegine and metformin with various cancer-involved proteins, including mitochondrial alpha-glycerophosphate dehydrogenase, yeast NADH dehydrogenase, and transforming growth factor-β1, were surveyed by molecular docking and molecular dynamics simulations. The results showed that each of the proteins makes complexes with the ligands via favorable non-bonded interactions, especially hydrogen bond interactions. There is greater stability for complexes containing galegine based on the root mean square deviation results. The higher structure compactness is also found in galegine receptors than in metformin receptors. Calculation of ΔGbinding, using the MM/PBSA methodology, shows that the binding energy values for metformin and galegine in interaction with each of the receptors are almost the same, and galegine has similar binding properties with metformin in interaction with the studied protein receptors. Therefore, galegine, a natural ingredient with better binding properties to cancer-involved proteins than metformin (with various side effects), can be applied as a new drug for cancer treatment.

Molecular docking aided machine learning for the identification of potential VEGFR inhibitors against renal cell carcinoma.

Renal cell carcinoma is a highly vascular tumor associated with vascular endothelial growth factor (VEGF) expression. The Vascular Endothelial Growth Factor -2 (VEGF-2) and its receptor was identified as a potential anti-cancer target, and it plays a crucial role in physiology as well as pathology. Inhibition of angiogenesis via blocking the signaling pathway is considered an attractive target. In the present study, 150 FDA-approved drugs have been screened using the concept of drug repurposing against VEGFR-2 by employing the molecular docking, molecular dynamics, grouping data with Machine Learning algorithms, and density functional theory (DFT) approaches. The identified compounds such as Pazopanib, Atogepant, Drosperinone, Revefenacin and Zanubrutinib shown the binding energy - 7.0 to - 9.5kcal/mol against VEGF receptor in the molecular docking studies and have been observed as stable in the molecular dynamic simulations performed for the period of 500ns. The MM/GBSA analysis shows that the value ranging from -44.816 to -82.582kcal/mol. Harnessing the machine learning approaches revealed that clustering with K = 10 exhibits the relevance through high binding energy and satisfactory logP values, setting them apart from compounds in distinct clusters. Therefore, the identified compounds are found to be potential to inhibit the VEGFR-2 and the present study will be a benchmark to validate the compounds experimentally.

The impact of nanoparticle surface topography on the interfacial mechanical behavior and microstructure of polyvinyl alcohol composites

The interfacial mechanical strength between nanoparticle and matrix is one of the key factors affecting the mechanical properties of nanoparticulate-polymer composites. Based on the structural composition of a nanoscale iron particle/polyvinyl alcohol composite, this study employed molecular dynamics simulations to investigate the stress-response behavior and microstructural evolution of Fe/PVA/Fe interface models with different surface morphologies under both tensile and shear deformations. The results indicate that when the particle surfaces exhibit different rough structures, the interfacial tensile strength significantly increases with the absolute value of the interfacial binding energy. The order of tensile strength is Type-cube > Type-pyramid > Type-plane. Furthermore, during the shearing process, the protruding structures on the particle surfaces significantly hinder the deformation and unfolding of the matrix molecular chains. As the volume of the protruding structures increases, the interfacial shear strength decreases markedly. The research findings illuminate the mechanisms by which nanoparticle surface morphology at the microscopic molecular scale influences the mechanical properties of nanoparticle-polymer composite materials. These discoveries aid in selecting nanoparticle fillers that enhance the mechanical performance of polymer nanocomposites to a measurable extent.

A Theoretical Investigation for Exploring the Potential Performance of Non-Fullerene Organic Solar Cells Through Side-Chain Engineering Having Diphenylamino Groups to Enhance Photovoltaic Properties.

The development of ecofriendly fabrication phenomenon is essential requirement for commercialization of non-fullerene acceptors. Recently, end-capped modeling is employed for computational design of five non-fullerene acceptors to elevate various photovoltaic properties. All new molecules are formulated by altering the peripheral acceptors of CH3-2F and DFT methodology is employed to explore the opto-electronic, morphological and charge transfer analysis. From the computational investigation, all reported molecules manifested red shifted absorption with remarkable reduced band gap. Among investigated molecules, FA1-FA3 evinced effectively decreased value of band gaps and designed molecules have low excitation energy justifying proficient charge transference. The lower values of binding energy of FA1 and FA2 suggest their facile exciton dissociation leading to improved charge mobility. By blending with J61 donor, FA4 have sufficiently enhanced value of VOC (1.72eV) and fill factor (0.9228). Energy loss of the model (R) is 0.57eV and statistical calculation demonstrate that all our modified molecules except FA3 has profoundly reduced energy loss compelling in its pivotal utilization. From accessible supportive outcomes of recent investigation, it is recommended that our modified chromophore exhibit remarkable noteworthy applications in solar cells for forthcoming innovations.

Tuning the photovoltaic potential of thiazole based materials via incorporation of selenophene and electron acceptors rings at peripheral positions: A DFT approach

The non-fullerene acceptor (NFA) chromophores have sparked scientific and economic interest, due to their rapid advancements in power conversion efficiencies. Therefore, a series of new chlorothiazole based compounds (STM1-STM6) with A1–π–A2–π–A1 configuration was designed using reference chromophore (STMR). Structural modifications were made via incorporating selenophene and extended acceptor units, to enhance photovoltaic response in the designed materials. Density functional theory/time dependent-density functional theory (DFT/TD-DFT) calculations were executed at M06/6-311G (d,p) level to investigate key electronic and photovoltaic properties of STM1-STM6. So, various analyses such as UV–Visible, frontier molecular orbitals (FMOs), transition density matrix (TDM), density of states (DOS), open circuit voltage (Voc) and binding energy (Eb) were conducted to comprehend the photovoltaic properties. The designing in structural aspects with terminal acceptors and π-linker induced a reduction in energy gaps (ΔE = 2.078–2.237 eV) with an enhancement in the bathochromic shift (λmax = 744.650–798.250 nm in chloroform) than reference compound. A higher exciton dissociation rate was observed in all the compounds due to lower binding energy values (Eb = 0.525–0.572 eV). Additionally, TDM and DOS findings further endorsed the effective charge delocalization from HOMO to LUMO. Among all the examined compounds, STM3 exhibited the smallest band gap (2.078 eV), highest absorption maxima (798.250 nm), and the lowest exciton binding energy (0.525 eV), indicating significant electronic properties. Moreover, Voc analysis was conducted with respect to HOMOPBDBT-LUMOacceptor for all the designed chromophores; consequently, STM2 demonstrated a substantial Voc value of 1.647 V. Similarly, electron hole analysis was also conducted and significant electron and hole density was observed in all the investigated compounds, especially in STM2. The entitled compounds with photovoltaic potential would be considered as promising materials for the development of solar energy devices.

Exploring anti-diabetic potential of compounds from roots of Dendrobium polyanthum Wall. ex Lindl. through inhibition of carbohydrate-digesting enzymes and glycation inhibitory activity

Eight compounds, including one anthraquinone, two bibenzyls, one phenanthrene, three dihydrophenanthrenes, and one flavonoid, were isolated from the roots of Dendrobium polyanthum Wall. ex Lindl. Among these, six compounds were investigated for inhibitory activities against alpha-glucosidase, alpha-amylase, and advanced glycation end products (AGEs) production. Additionally, molecular docking was conducted to analyze the interactions of the test compounds with alpha-glucosidase. Moscatin, the only isolated phenanthrene, displayed the strongest anti–alpha-glucosidase activity with an IC50 of 32.45 ± 1.04 μM, approximately 10-fold smaller than that of acarbose. Furthermore, moscatilin most strongly inhibited alpha-amylase and AGEs production with IC50 values of 256.94 ± 9.87 and 67.89 ± 9.42 μM, respectively. Molecular docking analysis revealed the effective binding of all substances to alpha-glucosidase with smaller lowest binding energy values than acarbose. Moscatin was selected for kinetics studies, and it was identified as a non-competitive inhibitor with approximately 9-fold greater inhibitory capability than acarbose. This study represents the first report on the phytochemical constituents and antidiabetic potential of compounds derived from the roots of D. polyanthum Wall. ex Lindl.

Anticancer activity of Aucklandia costus Falc. terpenes: Targeting MDM2 protein inhibition for therapeutic advancements

Context: Protein 53 (p53) is a well-known tumor suppressor protein, while murine double minute 2 (MDM2) acts as a negative regulator of p53, leading to p53 inactivation and cancer development. Aucklandia costus Falc. or Saussurea lappa contains bioactive compounds, particularly terpenoids, known for their anticancer activity against various cancer cells. Targeting the p53-MDM2 protein interaction and inhibiting MDM2 are crucial strategies in cancer therapy. Aims: To analyze the anticancer properties of A. costus terpenes against MDM2 protein. Methods: The compounds costunolide, dehydrocostus lactone, lappadilactone, and cynaropicrin were docked with MDM2 (PDB ID: 4HG7) using AutoDockTools 1.5.6. Additionally, the physicochemical, pharmacokinetic, and toxicity properties were predicted using pkCSM. Results: Lappadilactone exhibited the highest binding energy value, surpassing both the control and the native ligand. Following lappadilactone, cynaropicrin, costunolide, and dehydrocostus lactone displayed decreasing binding energies. When assessing ADMET properties with pkCSM, all compounds exhibited good permeability, suggesting their ability to penetrate intestinal cell membranes, and showed no signs of hepatotoxicity. Conclusions: Lappadilactone emerges as a promising candidate with high intestinal absorption, distinctive distribution characteristics, and a lack of mutagenic or hepatotoxic effects.

Synthesis, characterisation, and in vitro antiparasitic activity of new flavanoidal tetrazinan-6′-ones and their binding study with calf thymus DNA using molecular modelling and spectroscopic techniques

With the developing resistance to traditional antiparasitic medications, the purpose of this study was to efficiently develop a series of six noble flavanoidal tetrazinane-6′-one derivatives by a one-pot reaction pathway. FT-IR, 1HNMR, 13CNMR, and Mass spectra were employed for the structural elucidation of the synthesized compounds (7–12). Clinostomum complanatum, a parasite infection model that has been well-established, demonstrated that all the synthesized compounds are potent antiparasitic agents. DNA is the main target for various medicinal compounds. As a result, thestudy of how small molecules attach to DNA has received a lot of attention. In the present study, we have performed various biophysical techniques to determine the mode of binding of synthesized compounds (7–12) with calf thymus DNA (ct-DNA). It was observed from the UV–visible absorbance and fluorescence spectra that all synthesized compounds (7–12) form complexes with the ct-DNA. The value of binding constant (Kb) was obtained to be in the range of 4.36–––24.50 × 103 M - 1 at 298 K. Competitive displacement assay with ethidium bromide (EB), CD spectral analysis, viscosity measurements, and in silico molecular docking confirmed that ligands (7–12) incorporate with ct-DNA through groove binding only. Molecular docking studies were performed for all synthesized compounds with the calf thymus DNA and it was found that all the newly synthesized compounds strongly bind with the chain B of DNA in the minor groove with the value of binding energy in the range of −8.54 to −9.04 kcal per mole and several hydrogen bonding interactions.

Hybrid approach predicts a lower binding energy for benzene on water ice

ABSTRACT In this paper, we provide a highly accurate value for the binding energy of benzene to proton-ordered crystalline water ice (XIh), as a model for interstellar ices. We compare our computed value to the latest experimental data available from temperature-programmed desorption experiments and find that our binding energy value agrees well with data obtained from binding to either crystalline or amorphous ice. Importantly, our new value is lower than that used in most astrochemical networks by about nearly half its value. We explore the impact of this revised binding energy value for both an asymptotic giant branch (AGB) outflow and a protoplanetary disc. We find that the lower value of the binding energy predicted here compared with values used in the literature (4050 K versus 7587 K) leads to less depletion of gas-phase benzene in an AGB outflow, and leads to a shift outwards in the benzene snowline in the mid-plane of a protoplanetary disc. Using this new value, the AGB model predicts lower abundances of benzene in the solid phase throughout the outflow. The disc model also predicts a larger reservoir of gas-phase benzene in the inner disc, which is consistent with the recent detections of benzene for the first time in protoplanetary discs with JWST.

IN VITRO AND IN SILICO INHIBITORY ACTIVITY OF ANGIOTENSIN-CONVERTING ENZYME II AND ANTI-INFLAMMATORY EFFECTS OF NATURAL COMPOUNDS FROM RHEUM OFFICINALE ROOTS

Rhubarb roots (Rheum officinale), a common medicinal plant in folk remedies, and their chemical compositions were investigated for their inhibitory activity of angiotensin-converting enzyme II and anti-inflammatory effects by inhibiting NO production and IL-6 expression. Four natural compounds, including two anthraquinones, chrysophanol (2) and emodin (3), and two stilbenes, rhapontigenin (1) and trans-piceatannol (4), were isolated from the roots of Rhubarb. The results showed that rhapontigenin (1) exhibited an inhibitory effect on the ACE-2 enzyme with an IC50 value of 132 mM. In an in silico study, rhapotigenin (1) had a binding energy value of -9.32 kcal/mol, lower than MLN-4760, on ACE-2. Both rhapontigenin (1) and emodin (3) exhibited inhibitory activity on NO production in primary cultures of macrophages RAW264.7, with IC50 values ranging from 5.65 to 32.3 µg/mL. This is the first study of the anti-ACE-2 and anti-inflammatory activity of Rhubarb root extract and its constituents.

Synthesis and characterization of newly phthalocyanine molecules: Their enzyme inhibition and antioxidant properties, in silico and in vitro

Pcs exhibiting maximum absorption in the phototherapeutic window continue to shine as a beacon of hope in the treatment of cancer. In particular, they maintain skin sensitivity after treatment and can treat deep-seated tumors by stimulating them with broad-spectrum radiation. This makes them advantageous compared to their counterparts. In this study, Novel 1,2,3-triazole schiff base (5a), its methoxy homolog (5b), and their silicon complexes (SiPc-6a and SiPc-6b) were synthesized. Their proposed structures were confirmed by FT-IR, NMR, UV–vis and MS instrumental techniques. Compound (6b) showed inhibitory activity on amylase and glucosidase enzymes. Moreover, considering the glucosidase activity, compound (6b) (IC50, 22.4 ± 1.0 µM) was observed to be more effective than the standard compound (IC50, 186.1 ± 5.8 µM). Molecular docking studies showed that the synthesized compounds bind to the same enzymes with high affinity. The binding energy of SiPc-6a compound with α-amylase, α-glucosidase and tyrosinase enzymes are -10.28, -11.31 and -11.9 kcal/mol, respectively. And another compound, SiPc-6b, has a binding energy of -11.46, -10.11 and -10.27 kcal/mol with a-amylase, a-glucosidase and tyrosinase enzymes, respectively. Based on experimental results that support each other with binding energy values in quality and quantity indicating efficient binding, it is concluded that these compounds can be used in candidate drug discovery. Beside these, as a result of the studies, it was understood that all molecules have antioxidant activity. Additionally, molecular electrostatic potentials, frontier orbital analysis, natural bond orbital (NBO) properties of compounds calculated with DFT and TD-DFT methods and these properties associated with structural properties.

In silico analysis: Fulleropyrrolidine derivatives against HIV-PR mutants and SARS-CoV-2 Mpro

Abstract Approximately 37.9 million people living with HIV (PLWH) are at risk of severe consequences from COVID-19. Urgent development of tailored treatments for PLWH, who have historically been excluded from vaccine trials, is crucial. The present study introduces some modified fulleropyrrolidine derivatives with chalcogen atoms (O, S, or Se) and hydroxymethylcarbonyl (HMC) groups to target 11 single and double HIV-1 protease (HIV-PR) mutations and the main protease of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2 Mpro). The inhibitory activities of these derivatives are computationally examined through molecular docking, molecular dynamic simulations for 200 ns, and Lipinski’s rule of five (RO5). Fourier-transform infrared spectroscopy spectra and thermodynamic properties are calculated and analyzed using Density Functional Theory B88-PW91 method. The results indicate that the suggested O-compounds obey three parameters of the RO5 and HMC forms hydrogen bonds with studied viral proteases. Compounds with O and S additives display a high binding affinity with negative binding energy values for HIV-PR mutations (A71V-I84V, V77I-I84V, and I84V-L90M) and SARS-CoV-2 Mpro. The compounds with S and Se additives shift to lower frequencies of the major vibrational bands. Specifically, compound 1, with two oxygen additives, emerges as the most effective in inhibiting both HIV-PR mutations and SARS-CoV-2 Mpro.

Rational Approach toward COVID-19's Main Protease Inhibitors: A Hierarchical Biochemoinformatics Analysis.

This study investigated the potential of selected compounds as inhibitors of SARS-CoV-2 Mpro through pharmacokinetic and toxicological analyses, molecular docking, and molecular dynamics simulations. In silico molecular docking simulations revealed promising ligands with favorable binding affinities for Mpro, ranging from -6.2 to -9.5 kcal/mol. Moreover, molecular dynamics simulations demonstrated the stability of protein-ligand complexes over 200 ns, maintaining protein secondary structures. MM-PBSA analysis revealed favorable interactions between ligands and Mpro, with negative binding energy values. Hydrogen bond formation capacity during molecular dynamics was confirmed, indicating consistent interactions with Mpro catalytic residues. Based on these findings, selected ligands show promise for future studies in developing COVID-19 treatments.

Interaction of HIV-1 Gag matrix domain with plasma membrane from coarse-grained molecular dynamics simulations

We performed coarse-grained simulations with explicit solvent to analyse the role of myristoyl in the matrix domain of the HIV-1 protein Gag that interacts with three models of the lipid bilayer. These models were chosen to represent:(a) the inner membrane of the mammalian plasma membrane, (b) the lipid-raft domains, and (c) a generic cholesterol-free bilayer. The inner plasma membrane is the target for the Gag protein when forming the HIV-1 capsid. The other two models permit investigations of the effects of bilayer composition on the interaction between the matrix domain and the lipid bilayer. Our coarse-grained simulations allow sampling over several hundreds of microseconds, in contrast to other atomistic-detail simulations that can only cover a few microseconds. We measured the probability distributions associated with position and orientation of the myristoyl interacting with the plasma membrane models and quantified the orientational order of the myristoyl inserted into the membrane. We determined the Gibbs free energies (potentials of mean force and torque) associated with the observed probability distributions and determined binding energy values of the order of 8 kT , equivalent to ∼ 5 kcal mol − 1 at physiological temperature. Our methods can be applied to other acylated proteins interacting with the plasma membrane.

Exploring the twin potential of nanostructured TiO2:SeO2 as a promising visible light photocatalyst and selective fluorosensing platform

The present work describes the development of TiO2/SeO2 nanostructure as a potential candidate for visible light photocatalysis as well as selective fluorophore for the sensing of picric acid. The obtained nanostructure consists of uniform globular nanoparticles having approximate size of 170 nm and possess an optical band gap of 2.33 eV with absorption maxima at 473 nm. The photocatalyst was able to achieve 90.34% degradation efficiency for 2, 4-dichlorophenol (2,4-DCP) with rate constant of 0.0046 min−1 in the visible region. Further the nanostructure was able to serve as a selective fluorophore for sensing of Picric acid portraying more than 95% of fluorescence quenching when the concentration of PA is 10–4 M. Theoretical calculations indicate the interaction of organic pollutants with the nanostructure and reveal that both picric acid (− 66.21 kcal/mol) and 2,4-DCP (− 12.31 kcal/mol) possess more negative binding energy values demonstrating a strong interaction of both with the nanostructure, making it suitable for the degradation as well as sensing of organic pollutants. Thus this study explains the potential of prepared catalyst for waste water treatment.

In vitro and in silico anticancer potential of binuclear silver (I) N-heterocyclic carbene (NHCs) complexes: Investigation of interaction with surfactants

N-heterocyclic carbene (NHCs) silver complexes are getting tremendous attention for appealing biological potentials. The present study is planned to synthesize silver-NHC complexes to investigate their anticancer potential against breast, colon and ovarian cancer cell lines. The synthesized benzimidazolium salts (C1-C2) and their binuclear silver complexes (C3-C4) were assured through spectroscopy (UV–visible, FTIR, NMR and FLR), HPLC-DAD (high performance liquid chromatography), elemental analysis as well as mass spectrometry. Molecular docking studies indicated that compound C4 has lower binding energy values of −4.49, −1.95 and −2.95 kcal/mol for Bruton’s tyrosine kinase, Human topoisomerase II alpha and Aromatase cytochrome P450 protein targets respectively. The In Vitro cytotoxicity assay confirmed the C4 is better cytotoxic agent from other studied compounds of present study having lower IC50 values of 0.996 ± 0.04, 0.97 5 ± 0.04, 0.872 ± 0.05 and 0.987 ± 0.05 µg/mL against MCF-7, A-549, A-2780 and HCT-116 cell lines. Stability of compounds in solution form studied through spectroscopy and all compounds were found stable for studied course of time. Interactions of C3-C4 with surfactants (SDS, tween-20, tween-80) have confirmed the substantial interaction to improve aqueous solubility. Interaction of C3-C4 with surfactants indicates that there is potential affinity among test compounds and surfactants for complex formation spontaneously, having strongest binding affinity for SDS (sodium dodecyl sulfate) as compared to Tween-20 and Tween-80.

Quantum Chemical Computations, Molecular Docking, and ADMET Predictions of Cynarin

Cynarin (1,3-o-dicaffeoylquinic acid) is one of the biologically active functional food components which is the most well-known caffeoylquinic acid derivative found in artichoke. The structural and electronic features of cynarin compound were investigated theoretically using density functional theory (DFT). The highest occupied molecular orbital (HOMO) and the least occupied molecular orbital (LUMO) are the most significant orbitals in molecules, these orbitals are quite helpful to know several molecular features such as the chemical reactivity, kinetic stability, electronegativity, chemical potential, electrophilicity index, chemical hardness and softness and electronegativity. Molecular orbital analysis HOMO-LUMO was used to explore the stability of the molecule. Moreover, physicochemical properties, drug-likeness, and toxicity estimation of the cynarin compound were appraised owing to ADMET (including absorption, distribution, metabolism, excretion, and toxicology). Molecular docking was carried out to examine the biological activity of the cynarin compound. 5A19, a liver cancer biomarker, is human methionine adenosyl-transferase enzymes. Cynarin-methionine adenosyl-transferase enzyme binding energy value was calculated as -7.9 kcal/mol. As a result, this in silico study confirmed that cynarin has the potential to be a drug by revealing its protective effect against liver diseases.

<i>In Silico</i> Study of Aptamer Specificity for Detection of Insulin as Development for Diabetes Mellitus Diagnosis

Diabetes mellitus (DM) is a metabolic disorder characterized by elevated blood glucose levels. There are 2 types of DM where molecular-level diagnosis becomes very important because both have different treatments to avoid treatment errors. An electrochemical aptasensor as a type 2 DM detector with insulin target has been developed. This study aims to determine the interaction and specificity based on the values of RMSD, RMSF, and binding energy between aptamer and insulin when it reaches stability in silico compared to HbA1c and glucose. Docking simulations were performed on the HDOCK webserver and dynamics simulations for 1000 ns on the aptamer and protein molecular models used. The simulation results were analyzed to see the stability and visualized using VMD to see the conformation of the aptamer-ligand complex. The docking result showed higher binding energy between aptamer-insulin compared to other molecules, namely −221.87 kcal/mol. The results of RMSF and RMSD analysis of molecular dynamics simulations show that the system is stable, has the best binding energy value of −9.9510 kcal/mol. The aptamer complex with insulin showed better specificity compared to glucose and HbA1c based on RMSD, RMSF, and binding energy.

Evaluation of suitability and biodegradability of the organophosphate insecticides to mitigate insecticide pollution in onion farming

Organophosphates constitute a major class of pesticides widely employed in agriculture to manage insect pests. Their toxicity is attributed to their ability to inhibit the functioning of acetylcholinesterase (AChE), an essential enzyme for normal nerve transmission. Organophosphates, especially chlorpyrifos, have been a key component of the integrated pest management (IPM) in onions, effectively controlling onion maggot Delia antiqua, a severe pest of onions. However, the growing concerns over the use of this insecticide on human health and the environment compelled the need for an alternative organophosphate and a potential microbial agent for bioremediation to mitigate organophosphate pesticide pollution. In the present study, chloropyrifos along with five other organophosphate insecticides, phosmet, primiphos-methyl, isofenphos, iodofenphos and tribuphos, were screened against the target protein AChE of D. antiqua using molecular modeling and docking techniques. The results revealed that iodofenphos showed the best interaction, while tribuphos had the lowest interaction with the AChE based on comparative binding energy values. Further, protein-protein interaction analysis conducted using the STRING database and Cytoscap software revealed that AChE is linked with a network of 10 different proteins, suggesting that the function of AChE is disrupted through interaction with insecticides, potentially leading to disruption within the network of associated proteins. Additionally, an in silico study was conducted to predict the binding efficiency of two organophosphate degrading enzymes, organophosphohydrolase (OpdA) from Agrobacterium radiobacter and Trichoderma harzianum paraoxonase 1 like (ThPON1-like) protein from Trichoderma harzianum, with the selected insecticides. The analysis revealed their potential to degrade the pesticides, offering a promising alternative before going for cumbersome onsite remediation.