Docking and Molecular Dynamic of Microalgae Compounds as Potential Inhibitors of Beta-Lactamase

Antifungal activity and biocompatibility assessment with molecular docking and dynamic simulations of new pyrazole derivatives

BACKGROUND

Because of their many bioactivities, which include psychoanalytic, antifungal, antihypertensive, anti-inflammatory, and antiviral properties, pyrazoles and their derivatives are attracting interest in pharmacology and medicine, the pressing need for novel fungicides is increased for lessened by the growing microbiological resistance of illnesses to recognized antibiotics.

OBJECTIVE

The current work validates the results and pyrazole binding sites as potent antifungals by investigating many pyrazole derivatives as antifungal agents. The biocompatibility was assessed using an HFB4 normal human skin cell line.

METHODS

The biocompatibility was evaluated using an HFB4 normal human skin cell line and the findings of pyrazole binding sites were confirmed using molecular docking. The antifungal investigation was against 4 fungal pathogens: Aspergillus flavus ATCC 9643, A. niger ATCC 11414, Rhizopus oryzae ATCC 96382, and Penicillium chrysogenum ATCC 10106.

RESULTS

Among 20 different Pyrazole derivatives, Pyrazole 3b is the most effective compound against A. niger ATCC 11414 and A. flavus ATCC 9643 with IZDs and AIs of 32.0 mm (1.10) and 30.0 mm (1.0), respectively. Followed by compound 10b scored 28 and 20 mm for A. niger and P. chrysogenum ATCC 10106, respectively. While R. oryzae ATCC 96382 exhibited resistance with all pyrazole compounds. The study found that pyrazole 3b showed 100% antifungal activity between 1000 and 500 μg/ml, 50% at doses of 250 μg/ml, and no antifungal action at a dose of 125 μg/ml against the studied pathogenic fungal strains. The biocompatibility investigation showed that the 3b compound was completely safe with no IC50 dose obtained. The effectiveness of several pyrazole compounds against fungal targets was confirmed through molecular docking studies. The results highlighted that compounds 3b, 3g, 3h, 10b, 7, and 12 displayed strong binding energies, effectively engaging with the active sites of key proteins in various fungi such as FDC1 in A. niger, uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) in A. flavus, and Adenosine 5'-phosphosulfate kinase in P. chrysogenum. These interactions encompassed diverse molecular bonding types, suggesting these compounds' potential to hinder enzyme activity and demonstrate notable antifungal properties. Additionally, the computational ADMET "Absorption-distribution-metabolism-excretion-toxicity" analysis of these compounds revealed adherence to Lipinski's rules, indicating favorable physicochemical characteristics. The molecular dynamic simulations of Adenosine 5'-phosphosulfate kinase in P. chrysogenum, UDP-N-acetylglucosamine in A. flavus, and FDC1 in A. niger with 10b also demonstrated the formation of stable complexes with favorable values of Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Solvent Accessible Surface Area (SASA), and Radius of Gyration (Rg). These findings support the compounds' potential in ongoing therapeutic development projects.

CONCLUSION

The study found that pyrazole 3b was the most effective antifungal agent. The compounds' strong binding energies with fungi proteins suggest potential drug development.

Enhanced binding interaction and antibacterial inhibition for nanometal oxide particles activated with Aloe Vulgarize through one-pot ultrasonication techniques

The interaction of green zinc oxide nanoparticles (ZnO NPs) with bacterial strains are still scarcely reported. This work was conducted to study the green-one-pot-synthesized ZnO NPs from the Aloe Vulgarize (AV) leaf peel extract assisted with different sonication techniques followed by the physicochemical, biological activities and molecular docking studies. The NPs structure was analyzed using FTIR, UV-vis and EDX. The morphology, particle size and crystallinity of ZnO NPs were identified using FESEM and XRD. It was found that the formed flower-like structure with sharp edge and fine size of particulates in ZnO NPs/AV could enhance the bacterial inhibition. The minimum inhibitory concentration (MIC) for all the tested bacterial strains is at 3.125 µg/ml and the bacterial growth curve are dependent on the ZnO NPs dosage. The results of disc diffusion revealed that the ZnO NPs/AV possess better antibacterial effect with bigger ZOI due to the presence of AV active ingredient. The molecular docking between active ingredients of AV in the NPs with the protein of IFCM and 1MWU revealed that low binding energy (Ebind = -6.56 kcal/mol and -8.99 kcal/mol, respectively) attributes to the excessive hydrogen bond from AV that highly influenced their interaction with the amino acid of the selected proteins. Finally, the cytotoxicity test on the biosynthesized ZnO NPs with concentration below 20 µg/ml are found nontoxic on the HDF cell. Overall, ZnO NPs/20 % AV (probe sonication) is considered as the best synthesis option due to its efficient one-pot method, short sonication time but own the best antibacterial effect.

Unlocking bacterial defense: Exploring the potent inhibition of NorA efflux pump by coumarin derivatives in Staphylococcus aureus

The occurrence of bacterial resistance has been increasing, compromising the treatment of various infections. The high virulence of Staphylococcus aureus allows for the maintenance of the infectious process, causing many deaths and hospitalizations. The MepA and NorA efflux pumps are transporter proteins responsible for expelling antimicrobial agents such as fluoroquinolones from the bacterial cell. Coumarins are phenolic compounds that have been studied for their diverse biological actions, including against bacteria. A pharmacokinetic in silico characterization of compounds C10, C11, C13, and C14 was carried out according to the principles of Lipinski's Rule of Five, in addition to searching for similarity in ChemBL and subsequent search for publications in CAS SciFinder. All compounds were evaluated for their in vitro antibacterial and modulatory activity against standard and multidrug-resistant Gram-positive and Gram-negative strains. The effect of coumarins C9, C10, C11, C13, and C14 as efflux pump inhibitors in Staphylococcus aureus strains was evaluated using the microdilution method (MepA or NorA) and fluorimetry (NorA). The behavior of coumarins regarding the efflux pump was determined from their interaction properties with the membrane and coumarin-protein using molecular docking and molecular dynamics simulations. Only the isolated coumarin compound C13 showed antibacterial activity against standard strains of Staphylococcus aureus and Escherichia coli. However, the other tested coumarins showed modulatory capacity for fluoroquinolone and aminoglycoside antibacterials. Compounds C10, C13, and C14 were effective in reducing the MIC of both antibiotics for both multidrug-resistant strains, while C11 potentiated the effect of norfloxacin and gentamicin for Gram-positive and Gram-negative bacteria and only norfloxacin for Gram-negative. Only coumarin C14 produced synergistic effects when associated with ciprofloxacin in MepA-carrying strains. All tested coumarins have the ability to inhibit the NorA efflux pump present in Staphylococcus aureus, both in reducing the MIC and inducing increased ethidium bromide fluorescence emission in fluorimetry. The findings of this study offer an atomistic perspective on the potential of coumarins as active inhibitors of the NorA pump, highlighting their specific mode of action mainly targeting protein inhibition. In molecular docking, it was observed that coumarins are capable of interacting with various amino acid residues of the NorA pump. The simulation showed that coumarin C10 can cross the bilayer; however, the other coumarins interacted with the membrane but were unable to cross it. Coumarins demonstrated their potentiating role in the effect of norfloxacin through a dual mechanism: efflux pump inhibition through direct interaction with the protein (C9, C10, C11, and C13) and increased interaction with the membrane (C10 and C13). In the context of pharmacokinetic prediction studies, the studied structures have a suitable chemical profile for possible oral use. We suggest that coumarin derivatives may be an interesting alternative in the future for the treatment of resistant bacterial infections, with the possibility of a synergistic effect with other antibacterials, although further studies are needed to characterize their therapeutic effects and toxicity.

A Novel Tri-Hydroxy-Methylated Chalcone Isolated from Chromolaena tacotana with Anti-Cancer Potential Targeting Pro-Survival Proteins

Chromolaena tacotana (Klatt) R. M. King and H. Rob (Ch. tacotana) contains bioactive flavonoids that may have antioxidant and/or anti-cancer properties. This study investigated the potential anti-cancer properties of a newly identified chalcone isolated from the inflorescences of the plant Chromolaena tacotana (Klatt) R. M. King and H. Rob (Ch. tacotana). The chalcone structure was determined using HPLC/MS (QTOF), UV, and NMR spectroscopy. The compound cytotoxicity and selectivity were evaluated on prostate, cervical, and breast cancer cell lines using the MTT assay. Apoptosis and autophagy induction were assessed through flow cytometry by detecting annexin V/7-AAD, active Casp3/7, and LC3B proteins. These results were supported by Western blot analysis. Mitochondrial effects on membrane potential, as well as levels of pro- and anti-apoptotic proteins were analyzed using flow cytometry, fluorescent microscopy, and Western blot analysis specifically on a triple-negative breast cancer (TNBC) cell line. Furthermore, molecular docking (MD) and molecular dynamics (MD) simulations were performed to evaluate the interaction between the compounds and pro-survival proteins. The compound identified as 2',3,4-trihydroxy-4',6'-dimethoxy chalcone inhibited the cancer cell line proliferation and induced apoptosis and autophagy. MDA-MB-231, a TNBC cell line, exhibited the highest sensitivity to the compound with good selectivity. This activity was associated with the regulation of mitochondrial membrane potential, activation of the pro-apoptotic proteins, and reduction of anti-apoptotic proteins, thereby triggering the intrinsic apoptotic pathway. The chalcone consistently interacted with anti-apoptotic proteins, particularly the Bcl-2 protein, throughout the simulation period. However, there was a noticeable conformational shift observed with the negative autophagy regulator mTOR protein. Future studies should focus on the molecular mechanisms underlying the anti-cancer potential of the new chalcone and other flavonoids from Ch. tacotana, particularly against predominant cancer cell types.

Prediction of Phytochemicals for Their Potential to Inhibit New Delhi Metallo β-Lactamase (NDM-1)

The effectiveness of all antibiotics in the β-lactam group to cure bacterial infections has been impaired by the introduction of the New Delhi Metallo-β-lactamase (NDM-1) enzyme. Attempts have been made to discover a potent chemical as an inhibitor to this enzyme in order to restore the efficacy of antibiotics. However, it has been a challenging task to develop broad-spectrum inhibitors of metallo-β-lactamases. Lack of sequence homology across metallo-β-lactamases (MBLs), the rapidly evolving active site of the enzyme, and structural similarities between human enzymes and metallo-β-lactamases, are the primary causes for the difficulty in the development of these inhibitors. Therefore, it is imperative to concentrate on the discovery of an effective NDM-1 inhibitor. This study used various in silico approaches, including molecular docking and molecular dynamics simulations, to investigate the potential of phytochemicals to inhibit the NDM-1 enzyme. For this purpose, a library of about 59,000 phytochemicals was created from the literature and other databases, including FoodB, IMPPAT, and Phenol-Explorer. A physiochemical and pharmacokinetics analysis was performed to determine possible toxicity and mutagenicity of the ligands. Following the virtual screening, phytochemicals were assessed for their binding with NDM-1using docking scores, RMSD values, and other critical parameters. The docking score was determined by selecting the best conformation of the protein-ligand complex. Three phytochemicals, i.e., butein (polyphenol), monodemethylcurcumin (polyphenol), and rosmarinic acid (polyphenol) were identified as result of pharmacokinetics and molecular docking studies. Furthermore, molecular dynamics simulations were performed to determine structural stabilities of the protein-ligand complexes. Monodemethylcurcumin, butein, and rosmarinic acid were identified as potential inhibitors of NDM-1 based on their low RMSD, RMSF, hydrogen bond count, average Coulomb-Schrödinger interaction energy, and Lennard-Jones-Schrödinger interaction energy. The present investigation suggested that these phytochemicals might be promising candidates for future NDM-1 medication development to respond to antibiotic resistance.

Docking Studies on Biomolecules from Marine Microalga Skeletonema costatum Against Hemolysin Protein of Bioluminescence Disease-Causing Vibrio harveyi

Grow-out and hatchery units of shrimps are being impacted by disease-causing bacterial pathogens and predominantly marine Vibrios. The use of chemicals for governing bacterial pathogens in the aquaculture practices is developing resistance to bacteria. Henceforth, the application of bio-therapeutic agents from marine resources for controlling pathogens is most vital to be considered. Molecular docking is computer-assisted drug design tool to detect and counteract for drug-receptor interaction for known target protein of diseases. Therefore, an effort was made with the extract of the marine micro alga Skeletonema costatum against hemolysin protein of pathogenic bacteria Vibrio harveyi. The extract of S. costatum was tested against growth and virulence produced by V. harveyi during larviculture of Penaeus monodon. The extract was analyzed for phyto-constituents through GC-MS and used them as ligand molecule in docking. S. costatum extract at 200 µg mL-1 was found to decrease 35.20% of cumulative percentage mortality (CPM) in postlarvae of P. monodon against V. harveyi infections. The biomolecule Docasane, an alkane from the extract of S. costatum, exposed highest binding interaction than other compounds during docking analysis. The level of significance (P < 0.05) was found in CPM, growth, and virulence factors of V. harveyi studies. Thus, the present finding predicts that extract of S. costatum containing biomolecules can be recommended for use in the shrimp culture-based grow-out and hatchery units for eliminating bioluminescent V. harveyi.

Progress of the "Molecular Informatics" Section in 2022

This is the first Editorial of the "Molecular Informatics" Section (MIS) of the International Journal of Molecular Sciences (IJMS), which was created towards the end of 2018 (the first article was submitted on 27 September 2018) and has experienced significant growth from 2018 to now [...].

A review on the mechanistic details of OXA enzymes of ESKAPE pathogens

The production of β-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum β-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D β-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current β-lactamase inhibitors for conventional treatments of 'OXA' mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.