Journal of Biomolecular Structure & Dynamics最新文献

Various carbonic anhydrase (CA) enzyme isoforms are known today. In addition to the use of CA inhibitors as diuretics, antiepileptics and antiglaucoma agents, the inhibition of other specific isoforms of CA was reported to have clinical benefits in cancers. In this study, two groups of 1,3,4-thiadiazole derivatives were designed and synthesized to act as human CA I and II (hCA I and hCA II) inhibitors. The activities of these compounds were tested in vitro and evaluated in silico studies. The activity of the synthesized compounds was also tested against acetylcholinesterase (AChE) to evaluate the relation of the newly designed structures to the activity against AChE. The synthesized compounds were analyzed by ¹H NMR,¹³C NMR and high-resolution mass spectroscopy (HRMS). The results displayed a better activity of all the synthesized compounds against hCA I than that of the commonly used standard drug, Acetazolamide (AAZ). The compounds also showed better activity against hCA II, except for compounds 5b and 6b. Only compounds 6a and 6c showed superior activity against AChE compared to the standard agent, tacrine (THA). In silico studies, including absorption, distribution, metabolism and excretion (ADME) and drug-likeness evaluation, molecular docking, molecular dynamic simulations (MDSs) and density functional theory (DFT) calculations, were compatible with the in vitro results and presented details regarding the structure-activity relationship.

The objective of research was to examine the likely anticancer effectiveness of distinct pillar[5] arene derivatives, ws-penta-P[5] and ws-deca-P[5], on breast and lung cancer cell lines in vitro. To achieve this goal, breast cancer (MCF7) cells, lung cancer (A549) cells, healthy cells (HEK293) were utilized. The IC₅₀ dose of ws-penta-P[5] and ws-deca-P[5] was determined using the MTT method. Both treatment (pillar[5] arene applied) and control (pillar[5] arene not applied) groups were established for all three cell lines. Real-time polymerase chain reaction (qPCR) was used to evaluate changes in gene expression following pillar[5] arene treatment. Flow cytometry analysis was used to determine apoptosis and cell cycle arrest. The treatment group and control group results were compared after the study. The results revealed that in both cell lines treated with ws-deca-P[5], proapoptotic gene expressions were upregulated, while antiapoptotic gene expressions and caspase activation gene expressions were down-regulated. The flow cytometry apoptosis and cell cycle analysis in treatment group compared to the control, it was observed that the apoptosis rate increased in the ws-deca-P[5] and ws-deca-P[5] were shown to cause G0/G1 phase arrest in both cell groups. Results from our study that pillar[5] arene derivatives had the potential for treating breast and lung cancer, and more research is required in this area.

In traditional medicine, potential anti-inflammatory and pain-relieving activity of Momordica charantia, Azadirachta indica, Nelumbo nucifera, Caesalpinia crista, Martynia annua and Erythrina variegate has been emphasized. In this study, we explored binding affinity of 36 bioactive compounds from these plants to cyclooxygenase-2 (COX-2) receptor using docking method. Six compounds namely, beta carotene, lycopene, lutein, momordicoside, rutin and azadirachtin showed excellent binding affinities (-10.29, -10.22, -10.03, -7.9, -8.81 and -7.88 kcal/mol, respectively) and stable interactions with COX-2 (greater than those of aspirin and diclofenac) and they were chosen for the molecular dynamics (MD) assessments done throughout a 100-ns time period. Based on the computed RMSD, RMSF, Rg, SASA and PCA, all ligands were found to form stable and adequate interactions with COX-2 protein; these findings were comparable to those of aspirin and diclofenac, indicating the potential inhibitory properties of these ligands on COX-2 protein. In addition, the toxicity of compounds was evaluated using Pred-hERG, Pred-Skin and ProTox-II. Since COX-2 inhibitors have been reported to activate the Nrf2 pathway, it is hypothesized that they may confer other health-promoting effects through triggering Nrf2 signaling.

Antimicrobial and plant defence elicitor peptides have received attention on last decades as novel tools to combat bacterial plant diseases. We previously reported a library of peptide conjugates resulting from the combination of an antimicrobial peptide (BP16, BP143, BP387 or BP475) and a plant defence elicitor sequence (flg15, BP13, Pep13 or PIP1). From this library, we selected a set of 14 peptide conjugates including both highly and poorly active sequences and we performed a structure-activity relationship study by NMR and MD simulations. Analysis of their structure by NMR in 30% TFE-d₃ and in zwitterionic DPC-d₃₈ and anionic SDS-d₂₅ micelles showed that the presence of an α-helix fragment together with a flexible random coil can be related to a high antibacterial activity and a low hemolysis. In contrast, the sequences with a rigid α-helix structure were low active and highly hemolytic. PRE-NMR experiments in presence of MnCl₂ and 16-DSA revealed that the highly active peptides flg15-BP475 and BP100-Pep13 interacted stronger with DPC-d₃₈ micelles than the low active peptide BP13-BP16. In the two former sequences this interaction took place through the α-helix region. From GaMD simulations of BP100-Pep13 conducted in membranes composed of anionic DPPG lipids, after its electrostatic interaction, the peptide flipped and the hydrophobic residues were faced to the membrane triggering its insertion and also causing membrane thinning. Thus, the flexibility and moderate cationicity of BP100-Pep13 seem to be crucial for its biological activity. These findings can help to establish the guidelines for future rational design of BP100 derivatives.

Kingella kingae is a Gram-negative bacterium that causes invasive infections in children and older or immunocompromised individuals, making it a significant public health concern. In this study, a pan-proteomic mediated vaccine target mining was attempted to identify potential vaccine targets in K. kingae. Currently, there is no vaccine available against this pathobiont. Therefore, we designed and validated an in silico vaccine construct by targeting the lactoferrin/transferrin-binding TonB-dependent receptor. Antigenic regions of the TonB receptor were mapped, and the predicted epitopes were anticipated to be effective in a broad range of the world population. Using their combinations with linkers and various adjuvants, 12 vaccine constructs were prepared. The best construct (C7) with no allergenicity and high antigenicity was subjected to molecular modeling, docking with important immune receptors of humans, and then molecular dynamics (MD) simulation. After binding validation and stability assessment, it was cloned into a pet-28a + plasmid vector. Immune response was also simulated, and the vaccine was observed to invoke B- and T-cell induction. These findings can help accelerate the development of a new vaccine against K. kingae or other pathogens targeting the homolog of TonB. Nevertheless, we propose additional testing of C7 construct for efficacy and safety in vitro and in vivo.

In the light of anticancer drug discovery and development, a new series of cyanochalcones incorporating indole moiety (5a-g) were efficiently synthesized and characterized by different spectral analysis. MTT assay was used to evaluate the antiproliferative activity of the synthesized compounds towards different cancer cells (Hela, MDA-MB-231, A375, and A549) in parallel with normal cells (HSF). Trimethoxy and diethoxy-containing derivatives (5d and 5e) displayed the most selective cytotoxic activities against cervical Hela cells with IC₅₀ values of 8.29 and 11.82 µM, respectively, with great safety pattern toward normal HSF cells (Selectivity index: 21.3 and 13.9, respectively). Therefore, 5d and 5e were chosen to study their effects on apoptosis, cell cycle arrest, and migration of Hela cells using flow cytometric analysis and wound healing assay. They induced apoptosis and cell cycle arrest at the S phase and impaired migration of HeLa cells. Regarding their effects on the expression profile of crucial genes related to the potential anticancer activities, 5d and 5e remarkably upregulated caspase 3 and Beclin1 and downregulated cyclin A1, CDK2, CDH2, MMP9, and HIF1A using qRT-PCR and ELISA techniques. UV-Vis spectral measurement demonstrated the ability of 5d and 5e to bind CT-DNA efficiently with K_b values of 3.7 × 10⁵ and 1 × 10⁵ M^-1, respectively. Moreover, in silico molecular docking was performed to assess the binding affinities of the compounds toward the active sites of Bcl2, CDK2, and DNA. Therefore, cyanochalcones 5d and 5e might be promising anticancer agents and could offer a scientific basis for intensive research into cancer chemotherapy.

Gambogic acid (GA), a xanthanoid compound, is derived from Garcinia Hanbury gamboge resin. Studying GA's DNA binding and targeting processes is crucial to understanding its tumor-targeting potentiality. This study used spectroscopic and in silico methods to investigate the GA-calf thymus DNA-binding interaction. The results of the UV-visible absorbance spectroscopy revealed that GA binds to DNA and forms a complex. Investigation of fluorescence quenching using ethidium bromide-DNA revealed that GA displaced ethidium bromide, and the type of quenching was static in nature, as determined by Stern-Volmer plot data. Thermodynamic analysis of the DNA-GA complex revealed a spontaneous, favorable interaction involving hydrogen bonding and hydrophobic interactions. Quenching experiments with potassium iodide, Acridine orange, and NaCl verified GA's groove-binding nature and the presence of weak electrostatic interactions. The thermal melting temperature of DNA in its native and bound states with GA did not differ significantly (69.27° C to 71.25° C), validating the binding of GA to the groove region. Furthermore, the groove-binding nature of GA was confirmed by studying its interaction with ssDNA and DNA viscosity. The methods of DSC, FT-IR, and CD spectroscopy have not revealed any structural aberrations in DNA bound with GA. Molecular docking and modeling studies revealed that GA has a groove-binding nature with DNA, which is consistent with prior experimental results. Finally, the findings shed information by which GA attaches to DNA and provide insights into its recognized anticancer effects via topoisomerase inhibition causing DNA cleavage, inhibition of cell proliferation and apoptosis.

Idiopathic pulmonary fibrosis (IPF) is a life-threatening disease with a survival rate of <5 years. The TGF-β plays a significant role in the progression and severity of IPF. The TGF-β receptor type1 TGFBR1 antagonists inhibit the process of fibrosis and may have a role in the treatment of IPF. The main objective of the study was to identify promising drug candidates against IPF using In-silico and In-vitro evaluation methods. An in-silico screening was carried out of the marketed Coxibs to find their TGFBR1 inhibitory potential considering their structural resemblance with the JZO-a co-crystalized ligand of the crystal structure of the TGFBR1. The virtual screening yielded rofecoxib as a TGFBR1 ligand with a significant docking score. To further validate the outcome of molecular docking studies, MD simulation of 200 ns was carried out followed by the determination of conformational stability, binding free energy calculation using MMPBSA/MMGBSA, and Free Energy Landscape (FEL). The therapeutic efficacy of rofecoxib was compared with that of nintedanib (a therapeutic agent used in the treatment of IPF) at equimolar concentrations (5 µM). The model of TGF-β1 (1 ng/ml)-induced EMT of A549 was used to determine the effect of rofecoxib on the EMT markers like cellular morphology, cytokine expressions, fibrosis associated protein, E-cadherin, and α-smooth muscle actin. In vitro results indicated that rofecoxib significantly suppresses the TGF-β1-induced EMT of A549 cells and validates the possible preventive/protective role of rofecoxib in pulmonary fibrosis. In conclusion, rofecoxib may be considered for repositioning as an anti-fibrotic agent.

Toxoplasma gondii, a worldwide prevalent parasite is responsible for causing toxoplasmosis in almost all warm-blooded animals, including humans. Golgi-resident T. gondii aspartic protease 5 (TgASP5) plays an essential role in the maturation and export of the effector proteins those modulate the host immune system to establish a successful infection. Hence, inhibiting this enzyme can be a possible therapeutic strategy against toxoplasmosis. This is the first report of the detailed structural investigations of the TgASP5 mature enzyme using molecular modeling and an all-atom simulation approach which provide in-depth knowledge of the active site architecture of TgASP5. The analysis of the binding mode of the TEXEL (Toxoplasma EXport Element) substrate to TgASP5 highlighted the importance of the active site residues. Ser505, Ala776 and Tyr689 in the S2 binding pocket are responsible for the specificity towards Arg at the P2 position of TEXEL substrate. The molecular basis of inhibition by the only known inhibitor RRL_Statine has been identified, and our results show that it blocks the active site by forming a hydrogen bond with a catalytic aspartate. Besides that, known aspartic protease inhibitors were screened against TgASP5 using docking, MD simulations and MM-PBSA binding energy calculations. The top-ranked inhibitors (SC6, ZY1, QBH) showed higher binding energy than RRL_Statine. Understanding the structural basis of substrate recognition and the binding mode of these inhibitors will help to develop potent mechanistic inhibitors against TgASP5. This study will also provide insights into the structural features of pepsin-like aspartic proteases from other apicomplexan parasites for developing antiparasitic agents.

Bacterium Halalkalibacterium halodurans is an industrially important alkalophilic bacteria. It is recognized as a producer of enzymes such as β-galactosidase, xylanase, amylase and protease which are able to function at higher pH values and thus can be used in textile, food, paper industry and more. This bacterium, as any other bacterium, requires a sensitive mechanism for regulation of homeostasis of manganese ions (Mn²⁺) in order to survive. The key protein regulating this mechanism in H. halodurans is MntR - a transcriptional factor that binds to DNA and regulates the transcription of genes for proteins involved in manganese homeostasis. Long range all-atom molecular dynamics (MD) simulations, from 500 ns up to 1.25 µs, were used to study different forms of H. halodurans MntR in order to investigate the differences in the protein's structural and dynamical properties upon Mn²⁺ binding. Simulations revealed an allosteric mechanism which is activated by Mn²⁺ binding. The results of simulations show that Mn²⁺ binding alters the non-covalent interaction network of the protein structure which leads to a conformational change that primarily affects the positions of the DNA binding domains and, consequently, the DNA binding affinity of H. halodurans MntR. The key amino acid residues of the proposed mechanism were identified and their role in the proposed mechanism was computationally confirmed by MD simulations of in silico mutants.