Lysozyme and Human Serum Albumin Proteins as Potential Nitric Oxide Cardiovascular Drug Carriers: Theoretical and Experimental Investigation

Identification of potential MMP-8 inhibitors through virtual screening of natural product databases

Matrix metalloproteinase-8 (MMP-8), a type II collagenase, is a key enzyme in the degradation of collagens and is implicated in various pathological processes, making it a promising target for drug discovery. Despite advancements in the development of MMP-8 inhibitors, concerns over potential adverse effects persist. This study aims to address these concerns by focusing on the development of novel compounds with improved safety profiles while maintaining efficacy. In this study, we employed a computational approach to screen potent and safe inhibitors of MMP-8 from the Natural Product Activity and Species Source Database (NPASS). Initially, we constructed a pharmacophore model based on the crystal structure of the MMP-8-FIN complex (PDB ID: 4EY6) utilizing the Pharmit tool. This model then guided the selection of 44 promising molecules from NPASS, setting the stage for further analysis and evaluation. We comprehensively evaluated their drug-likeness and toxicity profiles. Molecules 21, 4, and 44 were identified as potentially effective MMP-8 inhibitors through a robust pipeline that included ADMET profiling, molecular docking, and molecular dynamics simulations. Notably, molecule 21 stood out for its low toxicity, high binding stability, and favorable ADMET profile, while molecule 44 demonstrated excellent affinity. These compounds offer structural novelty compared to known MMP-8 inhibitors. These computational results can be combined with in vitro experiments in the future to validate their activity and safety. These findings provide an important reference for drug design of MMP-8 inhibitors.

Computational Evaluation of Fusarium nygamai Compounds as AcrD Efflux Pump Protein Inhibitors of Salmonella Typhimurium

In Salmonella Typhimurium, efflux pump proteins, such as AcrD actively expel drugs and hazardous chemicals from bacterial cells, resulting in treatment failure and the emergence of antibiotic-resistant variants. Focusing on AcrD may lead to the development of novel antimicrobials against multidrug-resistant bacteria. However, challenges persist in achieving high selectivity, low toxicity, and effective bacterial penetration. Natural products, particularly microbial secondary metabolites, possess distinct chemical structures that may target the efflux pump systems. The efflux pump inhibitor capabilities of Fusarium nygamai compounds in Salmonella have not been previously investigated. This study employed molecular docking and molecular dynamics simulations to evaluate 25 F. nygamai compounds as potential inhibitors of AcrD. Additionally, the pharmacological characteristics of these substances were examined. Molecular docking results revealed that 3,6-Dimethoxy-2,5-dinitrobenzonitrile, methyl (2-oxo-3-phenylquinoxalin-1(2H)-yl)acetate, and 7-Methyl-5-nitro-1,4-dihydro-quinoxaline-2,3-dione exhibited the highest binding energies with AcrD. Furthermore, molecular dynamics simulations indicated stable ligand-receptor complex variations over time. This study contributes to the efforts against antibiotic resistance and the improvement of Salmonella infection treatment outcomes globally by facilitating the development of novel therapeutic approaches and enhancing antibiotic efficacy.

Triple-Action Therapy: Combining Machine Learning, Docking, and Dynamics to Combat BRCA1-Mutated Breast Cancer

Breast cancer dominates women's mortality, and among other factors, mutations in the BRCA1 gene are significant risk factors. Several approaches are followed to treat the BRCA1 affected cancer patients. However, specific BRCA1 inhibitors are not available till date due to its structural complexity. In addition, there are several limitations associated with the existing drugs used to treat BRCA1-related breast cancer and some side effects. The side effects include symptoms such as hot flashes, joint pain, nausea, fatigue, hair loss, diarrhea, chills, fever, and others. Therefore, advanced approaches needed that can overcome all the limitations and side effects of the current inhibitors. In this study, we adopted a multistep approach to identify potential inhibitors for BRCA1-mutated breast cancer. We used our developed machine learning models to screen potential inhibitors. Molecular docking approach was carried out for the screened hit compounds with BRCA1 and its mutated forms. Two ligands, β-amyrin and Narirutin, has shown significant performance in multiple scoring schemes such as molecular docking and RF score calculations. Molecular dynamics simulations demonstrated the stability of the complexes formed by β-amyrin and Narirutin with BRCA1, with lower RMSD values and less RMSF fluctuations at the binding site locations. Principal component analysis (PCA) and free energy landscape (FEL) further confirmed the compactness and favorable binding of β-Amyrin and Narirutin to BRCA1. These findings suggest that β-amyrin and Narirutin have potential as therapeutic agents against BRCA1-mutated breast cancer.

Integrating Blood Biomarkers and Marine Brown Algae-Derived Inhibitors in Parkinson's Disease: A Multi-scale Approach from Interactomics to Quantum Mechanics

Parkinson's disease (PD) involves alpha-synuclein accumulation according to Braak's pattern, with diverse clinical progressions that complicate diagnosis and treatment. We aimed to correlate Braak's pattern with rapid progressive PD to identify blood-based biomarkers and therapeutic targets exploiting brown algae-derived bioactives for potential treatment. We implemented a systematic workflow of transcriptomic profiling, co-expression networks, cluster profiling, transcriptional regulator identification, molecular docking, quantum calculations, and dynamic simulations. The transcriptomic analyses exhibited highly expressed genes at each Braak's stage and in rapidly progressive PD. Co-expression networks for Braak's stages were built, and the top five clusters from each stage displayed significant overlap with differentially expressed genes in rapidly progressive PD, indicating shared biomarkers between the blood and the PD brain. Further investigation showed, NF-kappa-B p105 as the master transcriptional regulator of these biomarkers. Molecular docking screened phlorethopentafuhalol-A from brown algae, exhibiting a superior inhibitory effect with p105 (- 7.51 kcal/mol) by outperforming PD drugs and anti-inflammatory compounds (- 5.73 to - 4.38 kcal/mol). Quantum mechanics and molecular mechanics (QM/MM) calculations and dynamic simulations have confirmed the interactive stability of phlorethopentafuhalol-A with p105. Overall, our combined computational study shows that phlorethopentafuhalol-A derived from brown algae, may have healing properties that could help treat PD.

Interaction of the lysozyme with anticoagulant drug warfarin: Spectroscopic and computational analyses

Warfarin is a cardiovascular drug, used to treat or inhibit the coagulation of the blood. In this paper, we have studied the interaction of lysozyme with warfarin using several experimental (fluorescence, UV-visible and circular dichroism spectroscopies) and computational (molecular docking, molecular dynamics and DFT) approaches. Experimental studies have suggested that there was a strong interaction between lysozyme and warfarin. Inner filter effect played important role in fluorescence experimental data which show that the emission intensity of lysozyme decreased on the addition of warfarin, however, after inner filter effect correction the actual outcome turned out be the fluorescence enhancement. The extent of binding, increased with temperature rise. The interaction was primarily taken place via the dominance of hydrophobic forces. Small amount of warfarin didn't influence the secondary structure of lysozyme; however, the higher concentration of warfarin caused a decrease in the helicity of the protein and a consequent partial unfolding. Molecular docking studies were also performed which revealed that warfarin binds with lysozyme mainly with hydrophobic forces along with a significant contribution of hydrogen bonding. The flexibility of warfarin played important role in fitting the molecule into the binding pocket of lysozyme. Frontier molecular orbitals of warfarin, using DFT, in free as well as complexed form have also been calculated and discussed. Molecular dynamics simulations of unbound and warfarin bound lysozyme reveal a stable complex with slightly higher RMSD values in the presence of warfarin. Despite slightly increased RMSF values, the overall compactness and folding properties remain consistent, emphasizing strong binding towards lysozyme through the results obtained from intermolecular hydrogen bonding analysis. Essential dynamics analysis suggests warfarin induces slight structural changes without significantly altering the conformation, additionally supported by SASA patterns. Aside from the examination of global and essential motion, the MM/PBSA-based analysis of binding free energy elucidates the significant binding of warfarin to lysozyme, indicating a binding free energy of -13.3471 kcal/mol.

Probing the interaction of cephalosporin antibiotic "cefoperazone" with lysozyme using spectroscopic and in silico methods: Effect of paracetamol on binding

The interaction of lysozyme with cefoperazone was studied by means of spectroscopic and computational approaches. The change in the UV-visible spectrum of lysozyme in presence of cefoperazone was an indication of the complex formation between them. Fluorescence spectroscopy suggested that there was a fair interaction between the protein and drug which was taken place via dynamic quenching mechanism and the binding ratio was approximately 1:1. The binding was energetically feasible and principally supported by the hydrophobic forces. CD spectroscopic studies have shown that cefoperazone induced the secondary structure of lysozyme by increasing the α-helical contents of the latter. In silico studies revealed that the large nonpolar cavity was the preferred binding site of cefoperazone within lysozyme and the interaction was taken place mainly through hydrophobic forces with small involvement of hydrogen bonding and electrostatic interactions which is in good agreement with the experimental analyses. Effect of paracetamol was also seen on the binding and it was found that paracetamol had a negative influence on the binding between cefoperazone and lysozyme.

Unraveling the Interaction of Diflunisal with Cyclodextrin and Lysozyme by Fluorescence Spectroscopy

Understanding the interaction between the drug:carrier complex and protein is essential for the development of a new drug-delivery system. However, the majority of reports are based on an understanding of interactions between the drug and protein. Here, we present our findings on the interaction of the anti-inflammatory drug diflunisal with the drug carrier cyclodextrin (CD) and the protein lysozyme, utilizing steady-state and time-resolved fluorescence spectroscopy. Our findings reveal a different pattern of molecular interaction between the inclusion complex of β-CD (β-CD) or hydroxypropyl-β-CD (HP-β-CD) (as the host) and diflunisal (as the guest) in the presence of protein lysozyme. The quantum yield for the 1:2 guest:host complex is twice that of the 1:1 guest:host complex, indicating a more stable hydrophobic microenvironment created in the 1:2 complex. Consequently, the nonradiative decay pathway is significantly reduced. The interaction is characterized by ultrafast solvation dynamics and time-resolved fluorescence resonance energy transfer. The solvation dynamics of the lysozyme becomes 10% faster under the condition of binding with the drug, indicating a negligible change in the polar environment after binding. In addition, the fluorescence lifetime of diflunisal (acceptor) is increased by 50% in the presence of the lysozyme (donor), which indicates that the drug molecule is bound to the binding pocket on the surface of the protein, and the average distance between active tryptophan in the hydrophobic region and diflunisal is calculated to be approximately 50 Å. Excitation and emission matrix spectroscopy reveals that the tryptophan emission increases 3-5 times in the presence of both diflunisal and CD. This indicates that the tryptophan of lysozyme may be present in a more hydrophobic environment in the presence of both diflunisal and CD. Our observations on the interaction of diflunisal with β-CD and lysozyme are well supported by molecular dynamics simulation. Results from this study may have an impact on the development of a better drug-delivery system in the future. It also reveals a fundamental molecular mechanism of interaction of the drug-carrier complex with the protein.

Deciphering the molecular details of interactions between anti-COVID drugs and functional human proteins: in silico approach

The molecular docking calculations have been employed to investigate the interactions a set of proteins with the repurposed anti-COVID drugs. The position of the therapeutic agents within the protein structure was dependent on a particular drug-protein system and varied from the binding cleft to the periphery of the polypeptide chain. Interactions involved in the drug-protein complexation includes predominantly hydrogen bonding and hydrophobic contacts. The obtained results may be of particular importance while developing the anti-COVID strategies as well as for deeper understanding of the drug pharmacodynamics and pharmacokinetics.

In Vitro Interaction of a C-Terminal Fragment of TDP-43 Protein with Human Serum Albumin Modulates Its Aggregation

An increased level of naturally occurring anti-TDP-43 antibodies was observed in the serum and cerebrospinal fluid (CSF) of amyotrophic lateral sclerosis patients. Human serum albumin (HSA), the most abundant protein in blood plasma and CSF, is found to interact with pathological proteins like Aβ and α-synuclein. Therefore, we examined the effect on the in vitro aggregation of a C-terminal fragment of TDP-43 in the presence of HSA. We found that the lag phase in TDP-43^2C aggregation is abrogated in the presence of HSA, but there is an overall decreased aggregation as examined by thioflavin-T fluorescence spectroscopy and microscopy. An early onset of TDP-43^2C oligomer formation in the presence of HSA was observed using atomic force microscopy and transmission electron microscopy. Also, a known chemical inhibitor of TDP-43^2Caggregation, AIM4, abolishes the HSA-induced early formation of TDP-43^2C oligomers. Notably, the aggregates of TDP-43^2C formed in the presence of HSA are more stable against sarkosyl detergent. Using affinity copurification, we observed that HSA can bind to TDP-43^2C, and biolayer interferometry further supported their physical interaction and suggested the binding affinity to be in sub-micromolar range. Taken together, the data support that HSA can interact with TDP-43^2C in vitro and affect its aggregation.

Diffusion of small molecule drugs is affected by surface interactions and crowder proteins

Crowded environments are known to affect the diffusion of macromolecules, but their effects on the diffusion of small molecules are largely uncharacterized. We investigate how three protein crowders, bovine serum albumin (BSA), hen egg-white lysozyme, and myoglobin, influence the diffusion rates and interactions of four small molecules: fluorescein, and three drugs, doxorubicin, glycogen synthase kinase-3 inhibitor SB216763, and quinacrine. Using Line-FRAP measurements, Brownian dynamics simulations, and molecular docking, we find that the diffusion rates of the small molecules are highly affected by self-aggregation, interactions with the proteins, and surface adsorption. The diffusion of fluorescein is decreased because of its interactions with the protein crowders and their surface adsorption. Protein crowders increase the diffusion rates of doxorubicin and SB216763 by reducing surface interactions and self-aggregation, respectively. Quinacrine diffusion was not affected by protein crowders. The mechanistic insights gained here may assist in optimization of compounds for higher mobility in complex macromolecular environments.

Solvent-Free Synthesis, In Vitro and In Silico Studies of Novel Potential 1,3,4-Thiadiazole-Based Molecules against Microbial Pathogens

A new series of 1,3,4-thiadiazoles was synthesized by the reaction of methyl 2-(4-hydroxy-3-methoxybenzylidene) hydrazine-1-carbodithioate (2) with selected derivatives of hydrazonoyl halide by grinding method at room temperature. The chemical structures of the newly synthesized derivatives were resolved from correct spectral and microanalytical data. Moreover, all synthesized compounds were screened for their antimicrobial activities using Escherichia coli, Pseudomonas aeruginosa, Proteus vulgaris, Bacillus subtilis, Staphylococcus aureus, and Candida albicans. However, compounds 3 and 5 showed significant antimicrobial activity against all tested microorganisms. The other prepared compounds exhibited either only antimicrobial activity against Gram-positive bacteria like compounds 4 and 6, or only antifungal activity like compound 7. A molecular docking study of the compounds was performed against two important microbial enzymes: tyrosyl-tRNA synthetase (TyrRS) and N-myristoyl transferase (Nmt). The tested compounds showed variety in binding poses and interactions. However, compound 3 showed the best interactions in terms of number of hydrogen bonds, and the lowest affinity binding energy (−8.4 and −9.1 kcal/mol, respectively). From the in vitro and in silico studies, compound 3 is a good candidate for the next steps of the drug development process as an antimicrobial drug.

Interaction of Carrier Protein with Potential Metallic Drug Candidate N-Glycoside 'GATPT': Validation by Multi-Spectroscopic and Molecular Docking Approaches

Lysozyme is often used as a model protein to study interaction with drug molecules and to understand biological processes which help in illuminating the therapeutic effectiveness of the drug. In the present work, in vitro interaction studies of 1-{(2-hydroxyethyl)amino}-2-amino-1,2-dideoxy-d-glucose triphenyl tin (IV) (GATPT) complex with lysozyme were carried out by employing various biophysical methods such as absorption, fluorescence, and circular dichroism (CD) spectroscopies. The experimental results revealed efficient binding affinity of GATPT with lysozyme with intrinsic binding (Kb) and binding constant (K) values in the order of 105 M-1. The number of binding sites and thermodynamic parameters ΔG, ΔH, and ΔS at four different temperatures were also calculated and the interaction of GATPT with lysozyme was found to be enthalpy and entropy driven. The CD spectra revealed alterations in the population of α-helical content within the secondary structure of lysozyme in presence of GATPT complex. The morphological analysis of the complex with lysozyme and lysozyme-DNA condensates was carried out by employing confocal and SEM studies. Furthermore, the molecular docking studies confirmed the interaction of GATPT within the larger hydrophobic pocket of the lysozyme via several non-covalent interactions.