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At least 379 records · Page 21Linked to original sources

Unraveling cellular dynamic changes in tumor evolution induced by long-term low dose-rate radiation.

BACKGROUND: In recent years, there has been a steady increase in professionals engaged in radioactive work. The biological impacts of long-term exposure to low dose-rate radiation remain elusive, as there is a dearth of systematic research in this field. METHODS: BEAS-2B cells were used to establish a cell model with continuous passaging after radiation exposure, which was subsequently subjected to in vivo tumorigenesis assays and in vitro malignant phenotype experiments. By scRNA-seq, we conducted copy number variation analysis, cell trajectory analysis, and cell communication analysis. Furthermore, we used FACS, molecular docking, multiplex immunohistochemistry, qRT-PCR, and co-immunoprecipitation to validate and further explore the molecular mechanisms driving tumor evolution. RESULTS: Long-term low dose-rate exposure is associated with a higher degree of malignancy, as evidenced by the induction of more CNV and EMT events, as well as the delayed activation of DNA repair pathways, which trigger increased genomic instability. The long-term low dose-rate specific ligand-receptor pair, ANGPTL4-SDC4, enhances cell malignancy by promoting angiogenesis in newly formed lung tumor cells. CONCLUSIONS: This study not only provides the first evidence and mechanistic explanation that long-term low dose-rate radiation leads to increased cellular malignancy but also offers valuable theoretical insights into the dynamic processes of early tumor evolution in lung cancer within the realm of tumor biology.

Humans↗

Prediction of the multimeric assembly of staphylococcal enterotoxin A with cell-surface protein receptors.

Staphylococcal enterotoxin A (SEA) cross-links two class II major histocompatibility complex (MHC) molecules and forms a multimeric assembly with T-cell receptors (TcRs). The X-ray crystal structure of SEA has been solved, yet details describing molecular recognition and association remain unclear. We present a structural model for the interactions of SEA with cell-surface proteins. Molecular docking calculations predicting SEA association with the class II MHC molecule HLA-DR1 were performed by using a rigid-body docking method. Docked orientations were evaluated by a Poisson-Boltzmann model for the electrostatic free energy of binding and the hydrophobic effect calculated from molecular surface areas. We found that the best-scoring SEA conformers for the DR1alpha interface display a binding mode similar to that determined crystallographically for staphylococcal enterotoxin B bound to HLA-DR1. For the zinc-binding site of SEA, docking DR1beta yielded several orientations exhibiting tetrahedral-like coordination geometries. Combining the two interfaces, tetramers were modeled by docking an alphabeta TcR with trimolecular complexes DR1beta-SEA-DR1alpha and SEA-betaDR1alpha-SEA. Our results indicate that the complex DR1beta-SEA-DR1alpha provides a more favorable assembly for the engagement of TcRs, forming SEA molecular contacts that are in accord with reported mutagenesis studies. In contrast, the cooperative association of two SEA molecules on a single DR1 molecule sterically inhibits interactions with TcRs. We suggest that signal transduction stimulated by SEA through large-scale assembly is limited to four or five TcR-(DR1beta-SEA-DR1alpha) tetramers and requires the dimerization of class II MHC molecules, while TcR dimerization is unlikely.

Enterotoxins↗

Influence of Major Histocompatibility Complex (MHC) Diversity on Immune Modulation, Pathogenesis, and Control of Lumpy Skin Disease Virus.

INTRODUCTION: Lumpy Skin Disease Virus (LSDV), a member of the genus Capripoxvirus within the family Poxviridae, is an economically important transboundary viral pathogen affecting cattle and water buffalo. The disease causes severe production losses through decreased milk yield, infertility, hide damage, reduced growth performance, and occasional mortality. The rapid geographic spread of LSDV, together with its vectorborne transmission and emerging recombinant strains, has intensified the need for improved understanding of viral pathogenesis, host immune responses, and effective prevention strategies. In particular, the role of the bovine Major Histocompatibility Complex (BoLA/MHC) in regulating antiviral immunity, disease susceptibility, and vaccine responsiveness has gained increasing scientific attention. METHODS: This review summarises the published literature related to the epidemiology, transmission, structure, pathogenesis, diagnosis, prevention, and control of LSDV, with special emphasis on the immunological and molecular role of bovine MHC molecules. Relevant studies concerning BoLA-mediated antigen presentation, immunoinformaticsbased epitope prediction, vaccine development, antiviral drug repurposing, molecular docking, genomic surveillance, and diagnostic approaches, including PCR- and ELISAbased assays, were critically evaluated. Recent advances in computational biology, molecular virology, and host-pathogen interaction studies were also reviewed. RESULTS: The reviewed studies demonstrate that Lumpy Skin Disease Virus (LSDV) possesses a complex double-stranded DNA genome enabling immune modulation and efficient transmission through arthropod vectors such as mosquitoes, ticks, and biting flies. Disease progression involves systemic viral replication, vascular injury, dermal necrosis, and inflammatory skin lesions. Real-time PCR remains the most sensitive diagnostic method for early detection, while ELISA supports surveillance. Evidence highlights the central role of bovine Major Histocompatibility Complex (BoLA) molecules in antigen presentation and T-cell activation. Computational studies identified promising BoLA-binding epitopes and repurposed antiviral candidates, including ivermectin, theaflavin, canagliflozin, and tepotinib, for future therapeutic development. DISCUSSION: Current evidence indicates that effective LSDV control requires integration of molecular diagnostics, vector management, vaccination, and host immunogenetics. BoLAguided immunoinformatics provides promising opportunities for developing multi-epitope vaccines, although experimental validation remains essential. Similarly, repurposed antiviral candidates require comprehensive in vivo and pharmacological evaluation before clinical application. Future research should focus on elucidating viral immune-evasion mechanisms, validating predicted epitopes, and translating computational findings into practical vaccines and therapeutics for sustainable disease control. CONCLUSION: Lumpy Skin Disease continues to pose a major threat to global cattle health and livestock economies. Advances in molecular diagnostics, genomic surveillance, antiviral drug discovery, and BoLA-guided vaccine design provide promising opportunities for improved disease control. Understanding the interaction between LSDV and the bovine MHC system is essential for developing next-generation vaccines, immunotherapeutics, and precision disease-management strategies. Future research should prioritise experimental validation of predicted epitopes, large-scale vaccine trials, and mechanistic studies on host-virus immune interactions to establish effective and sustainable global control programs for LSDV.

BoLA↗

Novel broad-spectrum thiourea non-nucleoside inhibitors for the prevention of mucosal HIV transmission.

Non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTI) are an integral part of combination therapy comprising three classes of antiretroviral drugs for the management of HIV/AIDS. NNRTIs are chemically diverse compounds that bind to a common allosteric site of HIV-1 RT and noncompetitively inhibit DNA polymerization. Resistance to NNRTIs arises rapidly upon drug treatment and results from mutation of the amino acids lining the HIV-1 RT binding pocket. Nevertheless, rationally designed NNRTIs deduced from changes in binding pocket size, shape, and residue character that result from clinically observed NNRTI resistance mutations exhibit broad-spectrum anti-HIV-1 activity. Notably, membrane permeable tight binding NNRTIs have utility as topical microbicides since they are capable of blocking cell-free and cell-associated mucosal HIV-1 infection without metabolic activation. This review summarizes the discovery of highly potent tight binding phenethyl-thiazolyl-thiourea (PETT) derivatives targeting the NNI binding pocket of HIV-1 RT. These NNRTIs were rationally designed by molecular docking using a composite binding pocket constructed by superimposing the crystal structure coordinate data of several NNI/RT ligand-binding site complexes. Molecular modeling and score functions such as molecular surface area, the buried surface, and binding affinity values were used to analyze how drug-resistant mutations would change the RT binding pocket shape, volume, and chemical make-up of these NNRTIs, and how these changes could affect drug binding. Several ligand derivatization sites were identified for docked compounds that fit the binding pocket. The best fit was determined by calculating an inhibition constant (Ludi Ki) of the docked compound for the composite binding pocket. Compounds with a Ludi Ki of <1 microM were identified as the most promising tight binding NNRTIs. This review highlights novel lipophilic thiourea NNRTIs that display high binding affinity and selective indices with robust anti-HIV-1 activity against the wild type as well as drug-resistant isolates carrying multiple RT gene mutations. The increasing prevalence of drug-escape mutants among recent HIV seroconverters makes the discovery of these broad-spectrum thiourea NNRTIs useful as a component of topical microbicide for the prevention of mucosal HIV transmission.

Acquired Immunodeficiency Syndrome↗

Molecular modelling probes: docking and scoring.

A general introduction to molecular modelling techniques in the area of protein-ligand interactions is given. Methods covered range from binding-site analysis to statistical treatment of sets of ligands. The main focus of this paper is on docking and scoring. After an outline of the main concepts, two specific application examples are given.

Algorithms↗

Comparison of two implementations of the incremental construction algorithm in flexible docking of thrombin inhibitors.

A set of 32 known thrombin inhibitors representing different chemical classes has been used to evaluate the performance of two implementations of incremental construction algorithms for flexible molecular docking: DOCK 4.0 and FlexX 1.5. Both docking tools are able to dock 10-35% of our test set within 2 A of their known, bound conformations using default sampling and scoring parameters. Although flexible docking with DOCK or FlexX is not able to reconstruct all native complexes, it does offer a significant improvement over rigid body docking of single, rule-based conformations, which is still often used for docking of large databases. Docking of sets of multiple conformers of each inhibitor, obtained with a novel protocol for diverse conformer generation and selection, yielded results comparable to those obtained by flexible docking. Chemical scoring, which is an empirically modified force field scoring method implemented in DOCK 4.0, outperforms both interaction energy scoring by DOCK and the Böhm scoring function used by FlexX in rigid and flexible docking of thrombin inhibitors. Our results indicate that for reliable docking of flexible ligands the selection of anchor fragments, conformational sampling and currently available scoring methods still require improvement.

Algorithms↗

Docking studies on PARP-1 inhibitors: insights into the role of a binding pocket water molecule.

The binding mode of a series of competitive PARP-1 inhibitors was investigated employing a molecular docking approach by using Autodock 3.0. A particular attention was given to the role played by a water molecule present in some but not all the so far available crystal structures of the catalytic domain of PARP-1. Good correlation between calculated binding energies and experimental inhibitory activities was obtained either by including (r2=0.87) or not (r2=0.84) the structural water molecule. Closer inspection of our results suggested that this water molecule should be considered part of the hydration shell of polar inhibitors and not as a structural water.

Catalytic Domain↗

Development and evaluation of a generic evolutionary method for protein-ligand docking.

We have developed a generic evolutionary method with an empirical scoring function for the protein-ligand docking, which is a problem of paramount importance in structure-based drug design. This approach, referred to as the GEMDOCK (Generic Evolutionary Method for molecular DOCKing), combines both continuous and discrete search mechanisms. We tested our approach on seven protein-ligand complexes, and the docked lowest energy structures have root-mean-square derivations ranging from 0.32 to 0.99 A with respect to the corresponding crystal ligand structures. In addition, we evaluated GEMDOCK on crossdocking experiments, in which some complexes with an identical protein used for docking all crystallized ligands of these complexes. GEMDOCK yielded 98% docked structures with RMSD below 2.0 A when the ligands were docked into foreign protein structures. We have reported the validation and analysis of our approach on various search spaces and scoring functions. Experimental results show that our approach is robust, and the empirical scoring function is simple and fast to recognize compounds. We found that if GEMDOCK used the RMSD scoring function, then the prediction accuracy was 100% and the docked structures had RMSD below 0.1 A for each test system. These results suggest that GEMDOCK is a useful tool, and may systematically improve the forms and parameters of a scoring function, which is one of major bottlenecks for molecular recognition.

Drug Design↗

Guided docking approaches to structure-based design and screening.

With the number of protein-ligand complexes available in the Protein Data Bank constantly growing, structure-based approaches to drug design and screening have become increasingly important. Alongside this explosion of structural information, a number of molecular docking methods have been developed over the last years with the aim of maximally exploiting all available structural and chemical information that can be derived from proteins, from ligands, and from protein-ligand complexes. In this respect, the term 'guided docking' is introduced to refer to docking approaches that incorporate some degree of chemical information to actively guide the orientation of the ligand into the binding site. To reflect the focus on the use of chemical information, a classification scheme for guided docking approaches is proposed. In general terms, guided docking approaches can be divided into indirect and direct approaches. Indirect approaches incorporate chemical information implicitly, having an effect on scoring but not on orienting the ligand during sampling. In contrast, direct approaches incorporate chemical information explicitly, thus actively guiding the orientation of the ligand during sampling. Direct approaches can be further divided into protein-based, mapping-based, and ligand-based approaches to reflect the source used to derive the features capturing the chemical information inside the protein cavity. Within each category, a representative list of docking approaches is discussed. In view of the limitations of current scoring functions, it was generally found that making optimal use of chemical information represents an efficient knowledge-based strategy for improving binding affinity estimations, ligand binding-mode predictions, and virtual screening enrichments obtained from protein-ligand docking.

Binding Sites↗

Irreversible inhibition of glucose-6-phosphate dehydrogenase by the coenzyme A conjugate of ketoprofen: a key to oxidative stress induced by non-steroidal anti-inflammatory drugs?

Oxidative damage by non-steroidal anti-inflammatory drugs (NSAIDs) has been considered relevant to the occurrence of gastro-intestinal side-effects. In the case of chiral arylpropionate derivatives like ketoprofen (KPF), this mechanism has been evidenced for the R-enantiomer, especially when chiral inversion was observed, and lets us suppose the involvement of CoA conjugates. Glucose-6-phosphate dehydrogenase (G6PD) is the crucial enzyme to regenerate the GSH pool and maintain the intracellular redox potential. This enzyme is known to be down-regulated by palmitoyl-CoA thioester. We hypothesised then that G6PD is the target of carboxylic NSAIDs, via their CoA metabolites. We used molecular docking to localise a putative site in the human G6PD then we chose the Yeast orthologue, as the most suitable species to study experimentally the precise molecular interaction. KPF-CoA was effectively shown to bind covalently to the unique cysteine residue of the yeast enzyme. Binding was found to occur in the same site as palmitoyl-CoA. It was decreased in the presence of an allosteric inhibitor of G6PD, phospho(enol)pyruvate, and was not detected with G6PD of Leuconostoc mesenteroides, which does not possess the allosteric site. This site is distinct from the catalytic site, and probably allosteric, explaining the observed non-competitive inhibition of its activity by KPF-CoA. KPF-CoA was shown to induce the production of reactive oxygen species in Caco-2 cells, where its inhibition of G6PD activity was observed.

Amino Acid Sequence↗

Molecular modeling and molecular dynamics simulation of the human A2B adenosine receptor. The study of the possible binding modes of the A2B receptor antagonists.

A molecular model of the human A(2B) adenosine receptor containing seven transmembrane alpha helices connected by three intracellular and three extracellular hydrophilic loops had been constructed. A molecular docking of seven structurally diverse xanthine antagonists of the A(2B) receptor was performed, and the differences in their binding modes were investigated. The 1 ns molecular dynamics (MD) simulations of several obtained ligand-receptor complexes inserted into the phospholipid bilayer were carried out. The conformational changes of the A(2B) receptor occurring during MD simulations were explored, and the stable binding modes of the studied antagonists were determined. According to the models presented in this work, the involvement of the His251, Asn282, Ser92, Thr89, and some aromatic residues in ligand recognition was determined. The obtained binding modes of the A(2B) antagonists demonstrate good agreement with the site-directed mutagenesis data.

Adenosine A2 Receptor Antagonists↗

Modified AutoDock for accurate docking of protein kinase inhibitors.

Protein kinases are an important class of enzymes controlling virtually all cellular signaling pathways. Consequently, selective inhibitors of protein kinases have attracted significant interest as potential new drugs for many diseases. Computational methods, including molecular docking, have increasingly been used in the inhibitor design process [1]. We have considered several docking packages in order to strengthen our kinase inhibitor work with computational capabilities. In our experience, AutoDock offered a reasonable combination of accuracy and speed, as opposed to methods that specialize either in fast database searches or detailed and computationally intensive calculations. However, AutoDock did not perform well in cases where extensive hydrophobic contacts were involved, such as docking of SB203580 to its target protein kinase p38. Another shortcoming was a hydrogen bonding energy function, which underestimated the attraction component and, thus, did not allow for sufficiently accurate modeling of the key hydrogen bonds in the kinase-inhibitor complexes. We have modified the parameter set used to model hydrogen bonds, which increased the accuracy of AutoDock and appeared to be generally applicable to many kinase-inhibitor pairs without customization. Binding to largely hydrophobic sites, such as the active site of p38, was significantly improved by introducing a correction factor selectively affecting only carbon and hydrogen energy grids, thus, providing an effective, although approximate, treatment of solvation.

Adenosine Diphosphate↗

Research on anti-HIV-1 agents. Investigation on the CD4-Suradista binding mode through docking experiments.

Sulfonated distamycin (Suradista) derivatives exhibit anti-HIV-1 activity by inhibiting the binding of the viral envelope glycoprotein gp120 to its receptor (CD4). With the aim to propose a possible binding mode between Suradistas and the CD4 macromolecule, molecular docking experiments, followed by energy minimization of the complexes thus obtained, were performed. Computational results show that ligand binding at the CD4 surface involves two or three positively charged regions of the macromolecule, in agreement with the results of X-ray crystallographic analysis of a ternary complex (CD4/gp120/neutralizing antibody) recently reported in the literature. Our findings account well for the structure-activity relationship found for Suradista compounds.

Anti-HIV Agents↗

Computational screening of phthalate monoesters for binding to PPARgamma.

Phthalate esters are ubiquitous environmental contaminants that interact with peroxisome proliferator-activated receptors (PPARs), a family of nuclear receptors. Molecular docking and free energy calculations were performed in an effort to identify novel phthalate ligands of PPARgamma, a subtype expressed in a wide range of human tissues. The method was validated using several agonists and partial agonists of PPARgamma, whose binding orientations were correctly reproduced; however, reduced accuracy in docking was observed with ligands of increasing size and flexibility. Improved results were obtained by introduction of a more accurate scoring function based on the all-atom molecular mechanics potential CHARMM and a generalized Born/surface area solvation term ACE (analytical continuum electrostatics). Comparison of the lowest CHARMM/ACE energy of each phthalate vs the logarithm of the experimentally determined EC(50) value for PPARgamma trans-activation yielded a good correlation (R(2) = 0.82). Thus, we can reliably distinguish phthalates that bind and activate PPARgamma from those that do not, with the computational method predicting relative PPARgamma binding activities with some degree of accuracy. We have applied this method to screen a series of 73 mono-ortho-phthalate esters listed in the Available Chemicals Directory. Several putative PPARgamma binding phthalates were identified, including compounds that are known PPARgamma agonists. These findings support the use of computational methods to identify environmental chemicals that warrant further experimental evaluation for PPAR binding and trans-activation potential in cell-based models.

Binding, Competitive↗

New leads for selective GSK-3 inhibition: pharmacophore mapping and virtual screening studies.

Glycogen Synthase Kinase-3 is a regulatory serine/threonine kinase, which is being targeted for the treatment of a number of human diseases including type-2 diabetes mellitus, neurodegenerative diseases, cancer and chronic inflammation. Selective GSK-3 inhibition is an important requirement owing to the possibility of side effects arising from other kinases. A pharmacophore mapping strategy is employed in this work to identify new leads for selective GSK-3 inhibition. Ligands known to show selective GSK-3 inhibition were employed in generating a pharmacophore map using distance comparison method (DISCO). The derived pharmacophore map was validated using (i) important interactions involved in selective GSK-3 inhibitions, and (ii) an in-house database containing different classes of GSK-3 selective, non-selective and inactive molecules. New Lead identification was carried out by performing virtual screening using validated pharmacophoric query and three chemical databases namely NCI, Maybridge and Leadquest. Further data reduction was carried out by employing virtual filters based on (i) Lipinski's rule of 5 (ii) van der Waals bumps and (iii) restricting the number of rotatable bonds to seven. Final screening was carried out using FlexX based molecular docking study.

Computational Biology↗

QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR.

The recent wide spreading of the H5N1 avian influenza virus (AIV) in Asia, Europe and Africa and its ability to cause fatal infections in human has raised serious concerns about a pending global flu pandemic. Neuraminidase (NA) inhibitors are currently the only option for treatment or prophylaxis in humans infected with this strain. However, drugs currently on the market often meet with rapidly emerging resistant mutants and only have limited application as inadequate supply of synthetic material. To dig out helpful information for designing potent inhibitors with novel structures against the NA, we used automated docking, CoMFA, CoMSIA, and HQSAR methods to investigate the quantitative structure-activity relationship for 126 NA inhibitors (NIs) with great structural diversities and wide range of bioactivities against influenza A virus. Based on the binding conformations discovered via molecular docking into the crystal structure of NA, CoMFA and CoMSIA models were successfully built with the cross-validated q (2) of 0.813 and 0.771, respectively. HQSAR was also carried out as a complementary study in that HQSAR technique does not require 3D information of these compounds and could provide a detailed molecular fragment contribution to the inhibitory activity. These models also show clearly how steric, electrostatic, hydrophobicity, and individual fragments affect the potency of NA inhibitors. In addition, CoMFA and CoMSIA field distributions are found to be in well agreement with the structural characteristics of the corresponding binding sites. Therefore, the final 3D-QSAR models and the information of the inhibitor-enzyme interaction should be useful in developing novel potent NA inhibitors.

Amino Acid Sequence↗

Docking and database screening reveal new classes of Plasmodium falciparum dihydrofolate reductase inhibitors.

Plasmodium falciparum dihydrofolate reductase (PfDHFR) is an important target for antimalarial chemotherapy. Unfortunately, the emergence of resistant parasites has significantly reduced the efficiency of classical antifolate drugs such as cycloguanil and pyrimethamine. In this study, an approach toward molecular docking of the structures contained in the Available Chemicals Directory (ACD) database to search for novel inhibitors of PfDHFR is described. Instead of docking the whole ACD database, specific 3D pharmacophores were used to reduce the number of molecules in the database by excluding a priori molecules lacking essential requisites for the interaction with the enzyme and potentially unable to bind to resistant mutant PfDHFRs. The molecules in the resulting "focused" database were then evaluated with regard to their fit into the PfDHFR active site. Twelve new compounds whose structures are completely unrelated to known antifolates were identified and found to inhibit, at the micromolar level, the wild-type and resistant mutant PfDHFRs harboring A16V, S108T, A16V + S108T, C59R + S108N + I164L, and N51I + C59R + S108N + I164L mutations. Depending on the functional groups interacting with key active site residues of the enzyme, these inhibitors were classified as N-hydroxyamidine, hydrazine, urea, and thiourea derivatives. The structures of the complexes of the most active inhibitors, as refined by molecular mechanics and molecular dynamics, provided insight into how these inhibitors bind to the enzyme and suggested prospects for these novel derivatives as potential leads for antimalarial development.

Animals↗

Conformational analysis and automated receptor docking of selective arylacetamide-based kappa-opioid agonists.

The three-dimensional structure, dynamics, and binding modes of representative kappa-opioid agonists of the arylacetamide class (U50, 488; U69,593; U62,066; CI-977; ICI199,441; ICI197,067; BRL52,537; and BRL52,656) have been investigated using molecular modeling techniques. Systematic exploration of the conformational space of the ligand combined with molecular dynamics (MD) simulations in water revealed consistent conformational preferences for all the kappa-agonists in this series. The results were further compared with available X-ray and 1D- and 2D-NMR data to identify potential "lead" conformers for molecular docking. Ligand binding modes were initially determined using automated docking of two of the ligands (U50,488 and BRL52,537) to the kappa-opioid receptor. Extrapolation of the predicted binding mode to other members in this ligand series revealed similar docking preferences, with each ligand docked along the receptor helical axis. The binding modes were further refined using MD simulations of the receptor-ligand complexes. The results show a that salt bridge is formed between the amino proton of the ligands and the carboxylate group of Asp138 in TM3. This interaction most likely serves as a key anchoring point for the agonist association. Additional ligand contacts were noted with kappa-specific residues Ile294, Leu295, and Ala298, which may, in part, explain the kappa-selectivity in this series. In comparing the arylacetamides with opiate-based ligands, no evidence was found to link these classes through a common binding motif (except for the ion pair). The binding site model was also applied to explain the enantiomeric preference of U50,488 and to provide insight to the mu/kappa-selectivity of representative ligands in this series. Overall, the results provide a structure-based rationale for ligand recognition that is consistent both with site-directed mutagenesis experiments and structure-function relationship data.

Acetamides↗