Identification of SARS-CoV-2 surface therapeutic targets and drugs using molecular modeling methods for inhibition of the virus entry

Investigation of self-assembly mechanism of gluten protein amyloid fibrils and molecular characterization of structure units

The mechanism of peptides self-assembly into gluten amyloid fibrils was explored through bond-breaking experiments and molecular dynamics (MD) simulations, verified through fibrillation experiments using synthetic peptides. The disruption of hydrogen bonds reduced thioflavin T fluorescence intensity and average particle size of gluten amyloid fibrils by 24 % and 81 %, respectively, causing a breakdown of internal structure. Disruption of electrostatic and hydrophobic forces induced further aggregation of fibrils. MD simulation revealed that peptides transitioned from a dispersed state to aggregation, followed by changes in secondary structure, culminating in the formation of stacked β-sheets structure units. Hydrogen bonding emerged as the primary driver of self-assembly with contributions from hydrophobic and electrostatic interactions. The synthetic single or hybrid peptide systems selected by MD formed ribbon- or fiber-like amyloid fibrils with inter-strand distance of 4.7 Å and respective inter-sheet distances of 10.2 Å and 10.8 Å, suggesting that the structure and morphology of eventual amyloid fibrils were affected by the peptide sequence and cross β-sheet structure units.

Deciphering the molecular interaction between Vitamin D3 and pepsin by in vitro and in silico perspectives

The current study explored the molecular interaction between Vitamin D3 (Vit D3) and pepsin using multi-spectroscopic, molecular dynamic simulation (MDS), and molecular docking. The fluorescence emission spectra discovered Vit D3 interacted with pepsin in a static quenching manner due to the formation of the steady-state complex. Thermodynamic data revealed the spontaneous binding of Vit D3 on pepsin. The formation of the Pepsin-Vit D3 complex was also validated by circular dichroism (CD) spectroscopy. The fluorescence and CD spectroscopy results revealed Vit D3 altered the tertiary and secondary structure of pepsin, respectively. Meanwhile, FTIR spectroscopy results revealed a hypochromic shift in the amide I and II peaks. Kinetic parameters showed Vit D3 inhibited the activity of pepsin by the uncompetitive process. Applied spectroscopic methods disclosed that Vit D3 binding to pepsin caused microenvironmental modifications around the aromatic residues of protein and changed its structure and function. Moreover, MD simulation and molecular docking were done to analyze the formation of Pepsin-Vit D3 complexes. Molecular docking findings demonstrated the interaction of Vit D3 with pepsin mainly involved van der Waals forces and hydrogen bonds that were in good agreement with the fluorescence results. Finally, MDS findings including RMSD, RMSF, and RG confirmed all the experimental data.

Inhibitory effect of chlorogenic acid on tannase-mediated astringency removal and its mechanism

BACKGROUND

Phenolic acids, such as chlorogenic acid (CGA) and rosmarinic acid (RA), are added to plant-based beverages as nutritional supplements to enhance their health benefits. However, these compounds can also interfere with the astringency-reducing effect of tannase. This study employed electronic tongue analysis, enzyme inhibition kinetics, spectroscopy, molecular docking and molecular dynamics simulations to investigate the inhibitory mechanisms of CGA and RA on tannase-mediated deastringency.

RESULTS

Our research results indicate that CGA can inhibit tannase-mediated deastringency. It, along with RA, inhibits tannase activity in a non-competitive manner and quenches its intrinsic fluorescence through static quenching. The binding of CGA and RA to tannase led to the exposure of aromatic amino acid residues and a more polar microenvironment. Fourier transform infrared spectroscopy showed that CGA and RA reduced the α-helix and β-turn content in tannase, while increasing the unordered coil content. Molecular docking and dynamics simulations revealed that CGA and RA bind tightly to tannase primarily through hydrogen bonds and van der Waals interactions, occupying the substrate-binding site and thus inhibiting tannase's astringency-reducing activity. Additionally, other polyphenols, such as epicatechin, hesperidin and naringin, were also found to inhibit tannase activity.

CONCLUSION

The study demonstrated that CGA and RA inhibit the astringency-removal activity of tannase, offering important mechanistic insights for the development of plant-based beverages and deastringency techniques. © 2025 Society of Chemical Industry.

Investigating Plasma-Activated Water (PAW) on Aspergillus flavus in Almonds and the Study of Its Effect on the GPI Receptor of the Fungus

Plasma-activated water (PAW) represents an innovative application of non-thermal plasma technology that can potentially enhance water treatment processes. A recent study investigated the efficacy of plasma-activated water in inhibiting Aspergillus flavus in almonds. The Study demonstrated that the duration of plasma-activated water treatment most significantly diminished fungal presence, followed by water flow rate and the argon-to-combined gas ratio. Plasma-activated water eliminated 2.6 logarithmic units of fungi across multiple experimental regimens. Plasma diminished water flow, further reducing A. flavus fungus. Extending activated water application from 1 to 10 min diminished A. flavus by 1.17 logs. The research revealed that 1O2, NO3-, and H2O2 influenced the GPI receptor in distinct manners. The quantity of hydrogen bonds between molecular GPI and the solvent in H2O2 exhibited a wider variety of effects than the two free radicals. The Study indicates that plasma-activated water eradicates A. flavus fungus by targeting the GPI receptor.

Molecular and technical aspects on the interaction of bovine serum albumin with pyrazine derivatives: From molecular docking to spectroscopy study

In order to better understand the transport and action mechanism of flavor substance and proteins in human body, the interaction mechanism between pyrazine derivatives and bovine serum albumin (BSA) was studied by molecular dynamics simulation and a series of spectroscopic methods. In molecular docking, it was observed that the small molecules were surrounded by hydrophobic amino acid residues of the protein, and the main amino acid residues formed π-π interaction and hydrogen bond interaction with BSA. The results of fluorescence emission spectroscopy combined with thermodynamic analysis showed that static quenching was the main mechanism of the interaction between three pyrazine derivatives and BSA, which was dominated by hydrophobic interaction. Synchronous fluorescence spectroscopy and three-dimensional fluorescence spectroscopy combined with molecular dynamics simulation proved that the pyrazine derivatives changed the conformation of BSA. In summary, pyrazine derivatives can interact with BSA, and the complexation of the complex changes its spatial conformation. The research in this paper has positive significance for understanding the binding, transport, and metabolism of pyrazine compounds in the process of blood circulation and provides key data for the metabolism of pyrazine compounds in vivo. PRACTICAL APPLICATION: The interaction of pyrazine derivatives-BSA is studied by multi-spectra and MD. The fluorescence quenching of pyrazine derivatives-BSA is static quenching. The main force between pyrazine derivatives and BSA is hydrophobic force. There is only one site of association between pyrazine derivatives and BSA. Pyrazine derivatives have effects on conformation of BSA.

Mechanistic Insights into the interaction between aldehyde aroma compounds and β-Casein through Multi-Spectroscopy and molecular dynamics

The interaction between proteins and aroma compounds significantly impacts cheese flavor retention during processing. However, it is still unknown how cheese proteins and the aldehyde aroma compounds (AACs) interact. This study aims to clarify the interaction mechanisms between the AACs (benzaldehyde, 2-methylpropanal, 2-methylbutanal and 3-methylbutanal) and β-casein (β-CN) using SPME-GC/MS, multi-spectroscopy techniques, and molecular dynamics simulations. The results reveal notable variations in the binding abilities of the four AACs and β-CN, with the strongest binding observed for 3-methylbutanal. Specifically, the binding affinity (Ka) values between β-casein and benzaldehyde, 2-methylpropanal, 2-methylbutanal, and 3-methylbutanal are 2.26 × 103, 1.78 × 103, 2.03 × 103, and 2.52 × 103 M-1, respectively, indicating moderate binding affinity. Additionally, the quenching rate constants (Kq) for interactions with these compounds are 2.57 × 1011, 2.92 × 1011, 3.74 × 1011, and 4.81 × 1011 M-1s-1, significantly exceeding the collisional quenching limit, suggesting specific interactions. The interactions between the four AACs and β-CN occur through irreversible covalent bonding, primarily involving hydrogen bonds and hydrophobic interactions. The quenching mechanism of β-CN and the four AACs is static, which leads to changes in the secondary structure and microenvironment of β-CN. Molecular docking and dynamics simulations confirm that hydrogen bonds and hydrophobic interactions are the key driving forces for the binding of β-CN with the four AACs, and contribute to the stability of the composite system.

EpiMed Coronabank Chemical Collection: Compound selection, ADMET analysis, and utilisation in the context of potential SARS-CoV-2 antivirals

Antiviral drugs are important for the coronavirus disease 2019 (COVID-19) response, as vaccines and antibodies may have reduced efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Antiviral drugs that have been made available for use, albeit with questionable efficacy, include remdesivir (Veklury®), nirmatrelvir-ritonavir (Paxlovid™), and molnupiravir (Lagevrio®). To expand the options available for COVID-19 and prepare for future pandemics, there is a need to investigate new uses for existing drugs and design novel compounds. To support these efforts, we have created a comprehensive library of 750 molecules that have been sourced from in vitro, in vivo, and in silico studies. It is publicly available at our dedicated website (https://epimedlab.org/crl/). The EpiMed Coronabank Chemical Collection consists of compounds that have been divided into 10 main classes based on antiviral properties, as well as the potential to be used for the management, prevention, or treatment of COVID-19 related complications. A detailed description of each compound is provided, along with the molecular formula, canonical SMILES, and U.S. Food and Drug Administration approval status. The chemical structures have been obtained and are available for download. Moreover, the pharmacokinetic properties of the ligands have been characterised. To demonstrate an application of the EpiMed Coronabank Chemical Collection, molecular docking was used to evaluate the binding characteristics of ligands against SARS-CoV-2 nonstructural and accessory proteins. Overall, our database can be used to aid the drug repositioning process, and for gaining further insight into the molecular mechanisms of action of potential compounds of interest.

Exploring the structural, photophysical and optoelectronic properties of a diaryl heptanoid curcumin derivative and identification as a SARS-CoV-2 inhibitor

Developing modifiable natural products those having antiviral activities against SARS-CoV-2 is a key research area which is popular in current scenario of COVID pandemic. A diaryl heptanoid curcumin and its derivatives are already presenting promising candidates for anti-viral drug development. We have synthesized single crystals of a dimethylamino derivative of natural curcumin and structural characterization was done by single crystal XRD analysis. Using steady-state absorption and emission spectra and guided by complimentary ab initio calculations, we unraveled the solvent effects on the photophysical properties of the dimethyl amino curcumin derivative. Chemical reactivity of the compound has investigated using frontier molecular orbitals and molecular electrostatic potential surface. High stability of the curcumin derivative in water environment has evaluated by Radial Distributions Functions (RDF) calculated via Molecular Dynamics (MD) simulations. The inhibitory activity of the title compound was evaluated by in silico methods and the stability of the protein-ligand complexes were studied using Molecular Dynamics simulations and MM-PBSA analysis. With this detailed study, we hope to motivate scientific community to develop new curcumin derivatives against SARS-CoV-2 virus.

Repurposing of drugs against methyltransferase as potential Zika virus therapies

In recent years, the outbreak of infectious disease caused by Zika Virus (ZIKV) has posed a major threat to global public health, calling for the development of therapeutics to treat ZIKV disease. Several possible druggable targets involved in virus replication have been identified. In search of additional potential inhibitors, we screened 2895 FDA-approved compounds using Non-Structural Protein 5 (NS5) as a target utilizing virtual screening of in-silco methods. The top 28 compounds with the threshold of binding energy -7.2 kcal/mol value were selected and were cross-docked on the three-dimensional structure of NS5 using AutoDock Tools. Of the 2895 compounds screened, five compounds (Ceforanide, Squanavir, Amcinonide, Cefpiramide, and Olmesartan_Medoxomil) ranked highest based on filtering of having the least negative interactions with the NS5 and were selected for Molecular Dynamic Simulations (MDS) studies. Various parameters such as RMSD, RMSF, Rg, SASA, PCA and binding free energy were calculated to validate the binding of compounds to the target, ZIKV-NS5. The binding free energy was found to be -114.53, -182.01, -168.19, -91.16, -122.56, and -150.65 kJ mol^-1 for NS5-SFG, NS5-Ceforanide, NS5-Squanavir, NS5-Amcinonide, NS5-Cefpiramide, and NS5-Ol_Me complexes respectively. The binding energy calculations suggested Cefpiramide and Olmesartan_Medoxomil (Ol_Me) as the most stable compounds for binding to NS5, indicating a strong rationale for their use as lead compounds for development of ZIKV inhibitors. As these drugs have been evaluated on pharmacokinetics and pharmacodynamics parameters only, in vitro and in vivo testing and their impact on Zika viral cell culture may suggest their clinical trials on ZIKV patients.

Structural change study of pepsin in the presence of spermidine trihydrochloride: Insights from spectroscopic to molecular dynamics methods

Spermidine is an aliphatic polyamine that directs a set of biological processes. This work aimed to use UV-Vis spectroscopy, fluorescence spectroscopy, thermal stability, kinetic methods, docking, and molecular dynamic simulations to examine the influence of spermidine trihydrochloride (SP) on the structure and function of pepsin. The results of the fluorescence emission spectra indicated that spermidine could quench pepsin's intrinsic emission in a static quenching process, resulting in the formation of the pepsin-spermidine complex. The results discovered that spermidine had a strong affinity to the pepsin structure because of its high binding constant. The obtained results from spectroscopy and molecular dynamic approaches showed the binding interaction between spermidine and pepsin, induced micro-environmental modifications around tryptophan residues that caused a change in the tertiary and secondary structure of the enzyme. FTIR analysis showed hypochromic effects in the spectra of amide I and II and redistribution of the helical structure. Moreover, the molecular dynamic (MD) and docking studies confirmed the experimental data. Both experimental and molecular dynamics simulation results clarified that electrostatic bond interactions were dominant forces.

Copper(II) and Cobalt(II) Complexes Based on Abietate Ligands from Pinus Resin: Synthesis, Characterization and Their Antibacterial and Antiviral Activity against SARS-CoV-2

Co-abietate and Cu-abietate complexes were obtained by a low-cost and eco-friendly route. The synthesis process used Pinus elliottii resin and an aqueous solution of CuSO₄/CoSO₄ at a mild temperature (80 °C) without organic solvents. The obtained complexes are functional pigments for commercial architectural paints with antipathogenic activity. The pigments were characterized by Fourier-transform infrared spectroscopy (FTIR), mass spectrometry (MS), thermogravimetry (TG), near-edge X-ray absorption fine structure (NEXAFS), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and colorimetric analysis. In addition, the antibacterial efficiency was evaluated using the minimum inhibitory concentration (MIC) test, and the antiviral tests followed an adaptation of the ISO 21702:2019 guideline. Finally, virus inactivation was measured using the RT-PCR protocol using 10% (w/w) of abietate complex in commercial white paint. The Co-abietate and Cu-abietate showed inactivation of >4 log against SARS-CoV-2 and a MIC value of 4.50 µg·mL^-1 against both bacteria Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). The results suggest that the obtained Co-abietate and Cu-abietate complexes could be applied as pigments in architectural paints for healthcare centers, homes, and public places.

A comprehensive insight into the effects of caffeic acid (CA) on pepsin: Multi-spectroscopy and MD simulations methods

The interaction between caffeic acid (CA) and pepsin was investigated using multi-spectroscopy approaches and molecular dynamic simulations (MDS). The effects of CA on the structure, stability, and activity of pepsin were studied. Fluorescence emission spectra and UV-vis absorption peaks all represented the static quenching mechanism of pepsin by CA. Moreover, the fluorescence spectra displayed that the interaction of CA exposed the tryptophan chromophores of pepsin to a more hydrophilic micro-environment. Consistent with the simulation results, thermodynamic parameters revealed that CA was bound to pepsin with a high binding affinity. The Van der Waals force and Hydrogen bond interaction were the dominant driving forces during the binding process. The circular dichroism (CD) spectroscopy analysis showed that the CA binding to pepsin decreased the contents of α-Helix and Random Coil but increased the content of β-sheet in the pepsin structure. Accordingly, MD simulations confirmed all the experimental results. As a result, CA is considered an inhibitor with adverse effects on pepsin activity.

The interaction mechanism of candidone with calf thymus DNA: A multi-spectroscopic and MD simulation study

In this investigation, the effects of candidone on the structure and conformation of DNA were evaluated by spectroscopic methods, molecular dynamics simulation, and molecular docking studies. Fluorescence emission peaks, ultraviolet-visible spectra, and molecular docking exhibited the complex formation between candidone and DNA in a groove-binding mode. Fluorescence spectroscopy results also showed a static quenching mechanism of DNA in the presence of candidone. Moreover, thermodynamic parameters demonstrated that candidone spontaneously bound to DNA with a high binding affinity. The hydrophobic interactions were the dominant forces over the binding process. Based on the Fourier transform infrared data candidone tended to attach to the A-T base pairs of the minor grooves of DNA. The thermal denaturation and circular dichroism measurements displayed that candidone caused a slight change in the DNA structure, which was confirmed by the molecular dynamics simulation results. According to the obtained findings from the molecular dynamic simulation, the structural flexibility and dynamics of DNA were altered to a more extended structure.

Adsorption of cationic surfactant as a probe of the montmorillonite surface reactivity in the alginate hydrogel composites

Adsorption of a cationic surfactant allowed to probe the surface reactivity of montmorillonite encapsulated in a composite of alginate hydrogels (A-MMT). Dodecylbenzyldimethylammonium chloride (BAC-12) was the surfactant used for these studies. BAC-12 is part of the widely used surfactant mixture known as benzalkonium chloride. XRD showed that up to three different types of basal spacing (d 001) were present within the composite indicating that as the concentration of adsorbed BAC-12 increases, populations with different adsorption conformational arrangements are present, even unexpanded clay remains. From the SEM-EDS spectra it is observed that the clay is distributed in the whole composite. In addition, the effect of the presence of cationic and anionic biocides on BAC-12 adsorption was studied. Cationic biocides such as tetradecyllbenzyldimethylammonium chlorides (BAC-14) and paraquat (PQ) show a competitive behavior for the clay adsorption sites at BAC-12 low concentration indicating an electrostatic adsorption mechanism. However, the presence of anionic contaminants such as 2,4-D and metsulfuron methyl do not affect surfactant adsorption. In all scenarios is observed an abrupt increase of BAC-12 adsorbed amount reaching values higher than the clay CEC suggesting strong tail-tail interactions. This occurs at concentrations 10 times lower than the CMC of BAC-12 promoted by clay encapsulation in the composite. In these composites the alginate does not affect the surface reactivity of the clay, but the formation of the hydrogel allows it to be easily extracted from aqueous media which makes it an interesting material with a potential use in water remediation.

SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate Optimization Algorithm (QAOA) Based MaxCut with ZDOCK

The pulmonary surfactant protein A (SP-A) is a constitutively expressed immune-protective collagenous lectin (collectin) in the lung. It binds to the cell membrane of immune cells and opsonizes infectious agents such as bacteria, fungi, and viruses through glycoprotein binding. SARS-CoV-2 enters airway epithelial cells by ligating the Angiotensin Converting Enzyme 2 (ACE2) receptor on the cell surface using its Spike glycoprotein (S protein). We hypothesized that SP-A binds to the SARS-CoV-2 S protein and this binding interferes with ACE2 ligation. To study this hypothesis, we used a hybrid quantum and classical in silico modeling technique that utilized protein graph pruning. This graph pruning technique determines the best binding sites between amino acid chains by utilizing the Quantum Approximate Optimization Algorithm (QAOA)-based MaxCut (QAOA-MaxCut) program on a Near Intermediate Scale Quantum (NISQ) device. In this, the angles between every neighboring three atoms were Fourier-transformed into microwave frequencies and sent to a quantum chip that identified the chemically irrelevant atoms to eliminate based on their chemical topology. We confirmed that the remaining residues contained all the potential binding sites in the molecules by the Universal Protein Resource (UniProt) database. QAOA-MaxCut was compared with GROMACS with T-REMD using AMBER, OPLS, and CHARMM force fields to determine the differences in preparing a protein structure docking, as well as with Goemans-Williamson, the best classical algorithm for MaxCut. The relative binding affinity of potential interactions between the pruned protein chain residues of SP-A and SARS-CoV-2 S proteins was assessed by the ZDOCK program. Our data indicate that SP-A could ligate the S protein with a similar affinity to the ACE2-Spike binding. Interestingly, however, the results suggest that the most tightly-bound SP-A binding site is localized to the S2 chain, in the fusion region of the SARS-CoV-2 S protein, that is responsible for cell entry Based on these findings we speculate that SP-A may not directly compete with ACE2 for the binding site on the S protein, but interferes with viral entry to the cell by hindering necessary conformational changes or the fusion process.