Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase.

Calcium-dependent lectin I from Pseudomonas aeruginosa (PA-IL) binds specifically to oligosaccharides presenting an alpha-galactose residue at their nonreducing end, such as the disaccharides alphaGal1-2betaGalOMe, alphaGal1-3betaGalOMe, and alphaGal1-4betaGalOMe. This provides a unique model for studying the effect of the glycosidic linkage of the ligands on structure and thermodynamics of the complexes by means of experimental and theoretical tools. The structural features of PA-IL in complex with the three disaccharides were established by docking and molecular dynamics simulations and compared with those observed in available crystal structures, including PA-IL.alphaGal1-2betaGalOMe complex, which was solved at 2.4 A resolution and reported herein. The role of a structural bridge water molecule in the binding site of PA-IL was also elucidated through molecular dynamics simulations and free energy calculations. This water molecule establishes three very stable hydrogen bonds with O6 of nonreducing galactose, oxygen from Pro-51 main chain, and nitrogen from Gln-53 main chain of the lectin binding site. Binding free energies for PA-IL in complex with the three disaccharides were investigated, and the results were compared with the experimental data determined by titration microcalorimetry. When the bridge water molecule was included in the free energy calculations, the simulations predicted the correct binding affinity trends with the 1-2-linked disaccharide presenting three times stronger affinity ligand than the other two. These results highlight the role of the water molecule in the binding site of PA-IL and indicate that it should be taken into account when designing glycoderivatives active against P. aeruginosa adhesion.

Herbal plants are often used as alternative medicine because they contain active compounds for the treatment of diseases and disorders with minimal side effects, and are easily obtained from the surrounding environment. Some of them have antiviral activity. This study aimed to analyze the potential of phytochemical compounds in the leaf of “pangi” (Pangium edule Reinw) as antiSARS-CoV-2 using molecular docking study. The drug- and lead-likeness properties of the selected compounds were obtained from the Swiss ADME and admetSAR online server tools. Molecular dynamics (MD) simulation of the selected ligand was carried out to validate the stability of the interaction. The results suggested that pangi leaves contain three compounds with remarkable binding affinities with Mpro (main protease) and RBD (receptor binding domain) were (5.beta.) pregnane-3,20.beta.-diol, 14.alpha.,18.alpha.-[4-methyl-3-oxo-(1-oxa-4-azabutane-1,4-diyl)]-, diacetate (PD), ethyl cholate (EC), and bis(3,5,5-trimethylhexyl) phthalate. Because EC will be metabolized in the body into cholic acid (Cho), this compound was then docked and validated using MD simulation. The compound has the best free binding energy (ΔG) with SARS-CoV-2 (–7.1 kcal/ mol with Mpro and –6.0 kcal/mol with RBD). Moreover, the compound is bound strongly to the active cavity of Mpro on Thr24, Thr26, His41, and Cys145 residues. The MM-GBSA calculation showed that the interaction of Cho with Mpro was higher than with RBD. According to the RMSD (root mean square deviation), RMSF (root mean square fluctuation), the radius of gyration (Rg), and intermolecular hydrogen bond (H-bond) analysis obtained from 50 ns MD simulations, Cho formed stable interactions with Mpro and RBD. The finding of this study indicated that Cho showed good anti-SARS-CoV-2 activity. The potential of the compound to inhibit the virus can serve as a starting point in the process of developing COVID-19 therapeutic natural medicine.

The molecular dynamics (MD) simulation of two structures of human insulin hexamers (Zn-hexamer and Znfree-hexamer) in explicit solvent was performed and the role of the Zn2+ ions in the hexamer’s cavity as it may affect the propensities of the dissociation of insulin hexamer into dimers and monomers investigated. The starting structure of the Zn-hexamer contains two cavity water molecules and two Zn2+ ions in addition to the amino acids residues of the insulin hexamer while the starting structure Znfree-hexamer is made up of only the amino acids residues of the insulin hexamer. The MD simulation was performed for 1 µs under the isothermal-isobaric conditions (NPT) conditions using the GROMACS software, amber ff99-SB force field, TIP 3P water model with periodic boundary conditions imposed on x-, y- and z- directions. Structural analyses of the two experimental structures were carried out and root mean square deviations (RMSD) and root mean square fluctuations (RMSF) computed from the referenced initial structures. The average RMSD value of the backbone atoms for the Zn-hexamer is 0.293 nm and Znfree-hexamer is 0.785 nm. The structural analysis revealed that, there were dimer’s dissociation and pronounced fluctuations of the amino acids residues in the Znfree-hexamer compared to the Zn-hexamer during the MD simulation. This is evident in the higher inter-dimer distances of the six glutamate-13(β) residues in the Znfree-hexamer which confirmed the influence of the removal of the Zn2+ ions and cavity water molecules on dissociation of the insulin hexamer.

AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps. We show that PAE maps from AF2 are correlated with the distance variation (DV) matrices from molecular dynamics (MD) simulations, which reveals that the PAE maps can predict the dynamical nature of protein residues. Here, we introduce the AF2-scores, which are simply derived from pLDDT scores and are in the range of [0, 1]. We found that for most protein models, including large proteins and protein complexes, the AF2-scores are highly correlated with the root mean square fluctuations (RMSF) calculated from MD simulations. However, for an IDP and a randomized protein, the AF2-scores do not correlate with the RMSF from MD, especially for the IDP. Our results indicate that the protein structures predicted by AF2 also convey information of the residue flexibility, i.e., protein dynamics.

Insighting the inhibitory potential of novel modafinil drug derivatives against estrogen alpha (ERα) of breast cancer through a triple hybrid computational methodology

Cancer is a mechanistically complex and diverse disease with a plethora of fundamental genetic and epigenetic factors. Signal transducer and activator of transcription-3 (STAT3) is a transcription factor, and its constitutive activation executes promotion of cellular proliferation, cell cycle, angiogenesis, metastasis, immunosuppression, and chemo-resistance in cancer cells. Here, we aimed to design natural potential STAT3 inhibitors. For this purpose, we investigated 92 phytochemical compounds by molecular docking studies because they are diversified, multitargeted, affordable, easily available, and less- or non-toxic. We selected only 6 compounds such as sarsasapogenin (L3), peiminine (L9), solasodine (L10), tormentic acid (L23), obacunone (L29), and echinocystic acid (L34) due to their greater binding affinity than reference STAT3 inhibitor (S3I-201) with STAT3. The study was further continued by molecular dynamic (MD) simulations and ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis. The results of molecular docking showed that all selected ligands exhibited binding affinity range from -9.3 Kcal/mol to -7.9 Kcal/mol and predicted inhibition constant ([Formula: see text].) values range from 0.14 [Formula: see text]M to 1.5 [Formula: see text]M. These compounds showed effective hydrogen bonding and hydrophobic interactions with DNA binding domain as well as SH2-domain of STAT3. The MD simulations performed by nanoscale molecular dynamics (NAMD) calculated root mean square deviations (RMSD), root mean square fluctuations (RMSF), radius of gyration ([Formula: see text]), solvent accessible surface area (SASA) and number of hydrogen bond dynamics. All selected ligands with protein exhibited stability over 120 ns by MD simulation. Moreover, these ligands showed favorable ADMET profiling and drug likeness. So, our current computational investigations showed that these novel drug candidates can be potential STAT3 inhibitors and evoke the scientific interest for their further verification by in vitro and in vivo studies.

Objective:This research aims to study the target specificity of selective bioactive compounds in complexing with the human angiotensin-converting enzyme (hACE2) receptor to impede the severe acute respiratory syndrome coronavirus 2 influx mechanism resulting in cardiac injury and depending on the receptor’s active site properties and quantum tunneling.Materials and Methods:A library of 120 phytochemical ligands was prepared, from which 5 were selected considering their absorption, distribution, metabolism, and excretion (ADMET) and quantitative structure–activity relationship (QSAR) profiles. The protein active sites and belonging quantum tunnels were defined to conduct supramolecular docking of the aforementioned ligands. The hydrogen bond formation and hydrophobic interactions between the ligand–receptor complexes were studied following the molecular docking steps. A comprehensive molecular dynamic simulation (MDS) was conducted for each of the ligand–receptor complexes to figure out the values – root mean square deviation (RMSD) (Å), root mean square fluctuation (RMSF) (Å), H-bonds, Cα, solvent accessible surface area (SASA) (Å2), molecular surface area (MolSA) (Å2), Rg (nm), and polar surface area (PSA) (Å). Finally, computational programming and algorithms were used to interpret the dynamic simulation outputs into their graphical quantitative forms.Results:ADMET and QSAR profiles revealed that the most active candidates from the library to be used were apigenin, isovitexin, piperolactam A, and quercetin as test ligands, whereas serpentine as the control. Based on the binding affinities of supramolecular docking and the parameters of molecular dynamic simulation, the strength of the test ligands can be classified as isovitexin > quercetin > piperolactam A > apigenin when complexed with the hACE2 receptor. Surprisingly, serpentine showed lower affinity (−8.6 kcal/mol) than that of isovitexin (−9.9 kcal/mol) and quercetin (−8.9 kcal/mol). The MDS analysis revealed all ligands except isovitexin having a value lower than 2.5 Ǻ. All the test ligands exhibited acceptable fluctuation ranges of RMSD (Å), RMSF (Å), H-bonds, Cα, SASA (Å2), MolSA (Å2), Rg (nm), and PSA (Å) values.Conclusion:Considering each of the parameters of molecular optimization, docking, and dynamic simulation interventions, all of the test ligands can be suggested as potential targeted drugs in blocking the hACE2 receptor.

Crystal structures of the xenobiotic metabolizing cytochrome P450 2B4 have demonstrated markedly different conformations in the presence of imidazole inhibitors or in the absence of ligand. However, knowledge of the plasticity of the enzyme in solution has remained scant. Thus, hydrogen-deuterium exchange mass spectrometry (DXMS) was utilized to probe the conformations of ligand-free P450 2B4 and the complex with 4-(4-chlorophenyl)imidazole (4-CPI) or 1-biphenyl-4-methyl-1H-imidazole (1-PBI). The results of DXMS indicate that the binding of 4-CPI slowed the hydrogen-deuterium exchange rate over the B'- and C-helices and portions of the F-G-helix cassette compared with P450 2B4 in the absence of ligands. In contrast, there was little difference between the ligand-free and 1-PBI-bound exchange sets. In addition, DXMS suggests that the ligand-free P450 2B4 is predominantly open in solution. Interestingly, a new high resolution structure of ligand-free P450 2B4 was obtained in a closed conformation very similar to the 4-CPI complex. Molecular dynamics simulations performed with the closed ligand-free structure as the starting point were used to probe the energetically accessible conformations of P450 2B4. The simulations were found to equilibrate to a conformation resembling the 1-PBI-bound P450 2B4 crystal structure. The results indicate that conformational changes observed in available crystal structures of the promiscuous xenobiotic metabolizing cytochrome P450 2B4 are consistent with its solution structural behavior.

Minocycline, a repurposed approved medication, shows promise in treating neurodegeneration. However, the specific pathways targeted by minocycline remain unclear despite the identification of molecular targets. This study explores minocycline's potential protective effects against TNF-α-mediated neuronal death in PC12 cells, with a focus on unraveling its interactions with key molecular targets. The study begins by exploring minocycline's protective role against TNF-α-mediated neuronal death in PC12 cells, showcasing a substantial reduction in cleaved caspase-3 expression, DNA fragmentation, and intracellular ROS levels following minocycline pretreatment. Subsequently, a comprehensive analysis utilizing pull-down assays, computational docking, mutation analysis, molecular dynamics simulations, and free energy calculations is conducted to elucidate the direct interaction between minocycline and p47phox-the organizer subunit of NADPH oxidase-2 (NOX2) complex. Computational insights, including a literature survey and analysis of key amino acid residues, reveal a potential binding site for minocycline around Trp193 and Cys196. In silico substitutions of Trp193 and Cys196 further confirm their importance in binding with minocycline. These integrated findings underscore minocycline's protective mechanisms, linking its direct interaction with p47phox to the modulation of NOX2 activity and attenuation of NOX-derived ROS generation. Minocycline demonstrates protective effects against TNF-α-induced PC12 cell death, potentially linked to its direct interaction with p47phox. This interaction leads to a reduction in NOX2 complex assembly, ultimately attenuating NOX-derived ROS generation. These findings hold significance for researchers exploring neuroprotection and the development of p47phox inhibitors.

Quantum and dynamic investigations of Complex iron- alkaloid-extract Cytisine derivatives of Retama monosperma (L.) Boiss. Seeds as eco-friendly inhibitors for Mild steel corrosion in 1M HCl

Structure and dynamic studies of lunatic, manic and radical fringe

Although cancer continues to be one of the world’s major causes of death, current cancer drugs have many serious side effects. There remains a need for new anticancer agents to overcome these shortcomings. Alternaria is one of the most widespread fungal genera, many species of which produce several classes of metabolites with potential polypharmacological activities. A few quinones and pyrones from Alternaria spp. have proven to exert cytotoxic effects against certain cancer cell lines, but their molecular mode of action is not known. The current study aimed to investigate the potential mechanisms that underlie the anticancer activity of a few selected quinones and pyrones from Alternaria solani and Alternaria alternata by molecular docking and dynamic simulation approaches. The selected metabolites were screened for their binding affinity to Heat shock protein 90 (HSP90), which is a known anticancer drug target. Molecular docking studies have revealed that Macrosporin, Altersolanol B, Fonsecin, and Neoaltenuene have good binding affinities with the target protein and the stabilities of the formed complexes were evaluated through molecular dynamics simulations. By analyzing the Root Mean Square Distance (RMSD), Root Mean Square Fluctuation (RMSF), and Principal Component Analysis (PCA) plots obtained from molecular dynamics simulations, this study shows that the complexes of all 4 lead molecules with target protein are stable over a 100 ns period. Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations were used to compute the binding free energies. The lead molecules were studied using in-silico analysis to determine their drug-likeness based on their Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) and physicochemical properties. The results demonstrate that Macrosporin, Fonsecin, and Neoaltenuene could become promising anticancer molecules that target HSP90. Communicated by Ramaswamy H. Sarma

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a major respiratory disorder that is characterized by persistent airflow limitation and an abnormal inflammation response to noxious particles, such as cigarette smoke and environmental pollution. COPD is a leading cause of mortality, causing a significant economic and social burden in many countries worldwide. Umbelliferone, which is a coumarin derivative, has been shown to possess anti-inflammatory and antioxidant properties, which may be useful in alleviating COPD. METHODS: An integrative bioinformatics approach was adopted to analyze gene expression datasets from gene expression omnibus (GSE275503 for bulk RNA sequencing and GSE183974 for single-cell RNA sequencing). Differentially expressed genes (DEGs) were identified and overlapped with COPD-associated genes from GeneCards. Common genes were analyzed using the STRING database to construct a protein-protein interactions (PPI) network, and further processed in Cytoscape using the “cytoHubba” plug-in to identify the top 10 hub genes. Molecular docking of these genes, along with three key genes from single-cell analysis, was performed using AutoDock vina in SAMSON software. A molecular dynamic (MD) simulation study was carried out using Desmond and Schrodinger software. The MD simulations were performed to investigate the stability and dynamic behavior of the UMB with 6E3K and 1S9V over time 200 ns. RESULTS: From bulk and single-cell RNA sequencing analyses, 50 and 1053 DEGs were extracted, respectively, with the cut-off value of LogFC > 1 and [Formula: see text]-value < 0.05. A total number of 562 overlapping genes were identified between the DEGs and COPD-associated genes from GeneCards. The top 10 hub genes from the PPI network were ITGAM, CCL2, IFN-[Formula: see text], CCL5, FN1, IL-1B, BCL2, CDH1, IL-1A and CXCL8. Among these, molecular docking revealed the highest binding affinities for IFN-[Formula: see text] (PDB ID: 6E3K, −7.4 kcal/mol), ITGAM (PDB ID: 1NA5, −6.6 kcal/mol), IL-1B (PDB ID: 8C3U, −6.2 kcal/mol), FN1 (PDB ID: 3M7P, −6.1 kcal/mol) and BCL2 (PDB ID: 6YLD, −5.9 kcal/mol). Additionally, single-cell RNA analysis identified HLA-DQA2 (PDB ID: 1H15, −2.7 kcal/mol), HLA-DRB5 (PDB ID: 1S9V, −4.9 kcal/mol) and S100A9 (PDB ID: 6ZDY, −5.3 kcal/mol) as the top three genes. An MD simulation study evaluated protein-ligand stability, binding dynamics and conformational changes. Root mean square deviation (RMSD) and Root mean square fluctuation (RMSF) analyses identified key interacting residues involved in hydrogen bonding, hydrophobic interactions and water bridges. The 6E3K complex exhibited protein backbone RMSD of 5−7 Å, ligand RMSD of 2−5 Å and residue fluctuations <3 Å. The 1S9V complex showed protein RMSD of 2.85 Å, ligand RMSD of 1.95−2.30 Å and residue fluctuations around 1.25−3.25 Å. CONCLUSION: The top 10 Genes from the PPI network and the top 3 genes from the single-cell RNA analysis were associated with COPD-related pathways. Molecular docking with the UMB showed strong binding affinities, indicating its potential to inhibit these pathways and serve as a therapeutic option for COPD. The MD simulation confirmed stable binding, key interactions and structural flexibility.

EngA, a GTPase involved in the late steps of ribosome maturation, consists of two GTP binding domains (G-domains) [GD1, GD2] and a C-terminal domain. The combination of GTP/GDP in G-domains dictates its binding to the ribosomal subunits by altering its conformation. Studies and comparisons on the available structures of EngA enable us to understand the correlation between nucleotide bound states and its conformation. Using all-atom molecular dynamics (MD) simulations, we have explored the conformational behavior of EngA from Thermotoga maritima (TmDer) upon binding the various combinations of GTP and GDP. Analyses of Root Mean Square Deviation (RMSD), Radius of Gyration (Rg) and Root Mean Square Fluctuation (RMSF) emphasize the importance of the second G-domain nucleotide bound state. RMSD and Rg exhibit slightly lower values when GTP is embedded in GD2 compared to GDP. These lower values are due to Sw-II of GD2, which has been observed from RMSF plot. Further investigation on the effects of GD2 nucleotide bound state using Principal Component Analysis (PCA) and Free Energy Landscape (FEL) analysis manifests an allosteric connection between GD2 nucleotide bound state and the GD1–KH interface. This is further validated by extracting electrostatic interactions and H-bonds at the GD1–KH interface. In silico mutations at the GD1 interface of KH domain affect the Sw-II mobility of GD2 by showing inverted behavior. This suggests using the second G-domain as an antibacterial target and further simulation studies on different species of EngA are to be explored. Communicated by Ramaswamy H. Sarma

A series of novel 4-anilino quinazoline derivatives were taken based on the literature study and optimized with Autodock version 4.2 and molecular dynamics (MD) protocol to investigate the interaction between the target compounds and the amino acid residues of target protein epidermal growth factor receptor (EGFR) tyrosine kinase (PDB ID: 1M17). The free energies of binding and inhibition constants (Ki) of the docked ligands were calculated by the Lamarckian genetic algorithm (LGA). The docking results showed that the compounds SGQ4, DMUQ5, 6AUQ6, and PTQ8 had produced significant docking affinity for the protein tyrosine kinase with the binding energy of −7.46, −7.31, −6.85, and −6.74 kcal/mol, respectively, compared to the standard inhibitor Erlotinib (binding energy: −3.84 kcal/mol). Furthermore, molecular dynamics simulations (MDS) were performed using Gromacs to investigate the stability of a ligand-protein complex. The combined analysis of root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of 1M17 protein with docked ligands reveals that 1M17 protein has more stability when it interacts reacts with the inhibitor. Molecular descriptive properties and toxicity profile predicted by software. All the designed molecules passed Lipinski’s rule of five successfully and they were found to be safe.