Journal of Biomolecular Structure & Dynamics最新文献

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.

The Japanese encephalitis virus, (JEV), is a flavivirus mostly transmitted by Culex mosquitoes mostly present in Southeast Asia and the Western Pacific region. Ardeid-wading birds are the natural reservoir of JEV; nonetheless, pigs are frequently a key amplifying host during epidemics in human populations. Although more domestic animals and wildlife are JEV hosts, it is unclear how these animals fit into the ecology and epidemiology of the virus. Even though there is no specific therapy, vaccines are available to prevent this infection. However, current vaccinations do not work against every clinical isolate and can cause neurological problems in certain people. In this study, we have screened 501 phytochemical compounds from various plants from the Zingeberaceae family against the RdRp protein of JEV. Based on this, the top five compounds (IMPHY014466, IMPHY004928, IMPHY007097, IMPHY014179 and IMPHY005010) were selected based on the obtained docking scores, which was above -8.0 Kcal/mol. Further, the binding affinity of these selected ligands was also analysed using molecular interaction, and the presence of interactions like hydrogen bonds, hydrophobic bonds and polar bonds with respective active residues were identified and studied elaborately. Furthermore, the dynamic stability of the docked RdRp protein with these selected phytochemicals was studied using Molecular dynamic simulation and essential dynamics. The free energy landscape analysis also provided information about the energy transition responsible stability of the complex. The results obtained advocated phytochemical compounds from the zingeberaceae family for future experimental validation, as these compounds exhibited significant potential as JEV antagonists.

Spike glycoprotein has a significant role in the entry of SARS-CoV-2 to host cells, which makes it a potential drug target. Continued accumulation of non-synonymous mutations in the receptor binding domain of spike protein poses great challenges in identifying antiviral drugs targeting this protein. This study aims to identify potential entry inhibitors of SARS-CoV-2 using virtual screening and molecular dynamics (MD) simulations from three distinct chemical libraries including Pandemic Response Box, Drugbank and DrugCentral, comprising 6971 small molecules. The molecules were screened against a binding pocket identified in the receptor-binding domain (RBD) region of the spike protein which is known as the linoleic acid binding pocket, a highly conserved motif among several SARS-CoV-2 variants. Through virtual screening and binding free energy calculations, we identified four top-scoring compounds, MMV1579787 ([2-Oxo-2-[2-(3-phenoxyphenyl)ethylamino]ethyl]phosphonic acid), Tretinoin, MMV1633963 ((2E,4E)-5-[3-(3,5-dichlorophenoxy)phenyl]penta-2,4-dienoic acid) and Polydatin, which were previously reported to have antibacterial, antifungal or antiviral properties. These molecules showed stable binding on MD simulations over 100 ns and maintained stable interactions with TYR365, PHE338, PHE342, PHE377, TYR369, PHE374 and LEU368 of the spike protein RBD that are found to be conserved among SARS-CoV-2 variants. Our findings were further validated with free energy landscape, principal component analysis and dynamic cross-correlation analysis. Our in silico analysis of binding mode and MD simulation analyses suggest that the identified compounds may impede viral entrance by interacting with the linoleic acid binding site of the spike protein of SARS-CoV-2 regardless of its variants, and they thus demand for further in vitro and in vivo research.

The current research focuses on exploring tautomerism in uracil. 47 tautomers were found that varied in significance in RNA and stability. To discover these molecules, diverse potential energy levels were explored, and corresponding transition states were found in these pathways. But the imperative thing that was taken note in this investigation is that for the first time, a method was detailed for the probability of forming distinctive molecules relative to each other. In this method, the conversion of uracil and its tautomers, which together turn into 47 molecules, was composed as a Markov chain. Then, the transition matrix was explained using its support, whose components are the probability of creating molecules from each step. At last, by multiplying this matrix by n times, the probability of forming different molecules was obtained. Moreover, by solving this matrix at different times, it is conceivable to appear which molecules can be converted to uracil sooner. It was appeared that a few tautomers act as transitory absorption point or temporary terminal states and other molecules, to begin with convert to these molecules before turning into uracil.

Lung adenocarcinoma is highly heterogeneous at the molecular level between different stages; therefore, understanding molecular mechanisms contributing to such heterogeneity is needed. In addition, multiple stages of progression are critical factors for lung adenocarcinoma treatment. However, previous studies showed that cancer progression is associated with altered lncRNA expression, highlighting the tissue-specific and developmental stage-specific nature of lncRNAs in various diseases. Therefore, a study using an integrated network approach to explore the role of lncRNA in carcinogenesis was done using expression profiles revealing stage-specific and conserved lncRNA biomarkers in lung adenocarcinoma. We constructed ceRNA networks for each stage of lung adenocarcinoma and analysed them using network topology, differential co-expression network, protein-protein interaction network, functional enrichment, survival analysis, genomic analysis and deep learning to identify potential lncRNA biomarkers. The co-expression networks of healthy and three successive stages of lung adenocarcinoma have shown different network properties. One conserved and four stage-specific lncRNAs are identified as genome regulatory biomarkers. These lncRNAs can successfully identify lung adenocarcinoma and different stages of progression using deep learning. In addition, we identified five mRNAs, four miRNAs and twelve novel carcinogenic interactions associated with the progression of lung adenocarcinoma. These lncRNA biomarkers will provide a novel perspective into the underlying mechanism of adenocarcinoma progression and may be further helpful in early diagnosis, treatment and prognosis of this deadly disease.

Kirsten rat sarcoma (KRAS) stands out as the most prevalent mutated oncogene, playing a crucial role in the initiation and progression of various cancer types, including colorectal, lung and pancreatic cancer. The oncogenic modifications of KRAS are intricately linked to tumor development and are identified in 22% of cancer patients. This has spurred the necessity to explore inhibition mechanisms, with the aim of investigating and repurposing existing drugs for diagnosing cancers dependent on KRAS G12C In this investigation, 26 nucleoside-based drugs were collected from literature to assess their effectiveness against KRAS G12C. The study incorporates in-silico molecular simulations and molecular docking examinations of these nucleoside-derived drugs with the KRAS G12C protein using Protein Data Bank (PDB) ID: 5V71. The docking outcomes indicated that two drugs, Azacitidine and Ribavirin, exhibited substantial binding affinities of -8.7 and -8.3 kcal/mol, respectively. These drugs demonstrated stability in binding to the active site of the protein during simulation studies. Root mean square deviation (RMSD) analyses indicated that the complexes closely adhered to an equilibrium RMSD value ranging from 0.17 to 0.2 nm. Additionally, % occupancies, bond angles and the length of hydrogen bonds were calculated. These findings suggest that Azacitidine and Ribavirin may potentially serve as candidates for repurposing in individuals with KRAS-dependent cancers.

A polymeric compound formulized as [Cu(µ-dipic)₂{Na₂(µ-H₂O)₄]_n.2nH₂O (I), where dipic is 2,6-pyridine dicarboxylic acid (dipicolinic acid, H₂dipic), was synthesized by sonochemical irradiation. The initial in-vitro cytotoxic activity of this complex compared with renowned anticancer drugs like cisplatin, versus HCT116 colon cell lines, shows promising results. This study investigated the interaction mode between compound (I) and calf-thymus DNA utilizing a range of analytical techniques including spectrophotometry, fluorimetry, partition coefficient analysis, viscometry, gel electrophoresis and molecular docking technique. The results obtained from experimental methods reveal complex (I) could bind to CT-DNA via hydrogen bonding and van der Waals forces and the theoretical methods support it. Also, complex (I) indicates nuclease activity in the attendance of H₂O₂ and can act as an artificial nuclease to cleave DNA with high efficiency.