Molecular Docking and Molecular Dynamics Simulation Studies of Triterpenes from Vernonia patula with the Cannabinoid Type 1 Receptor

Gastrodin Ameliorates Post-Stroke Depressive-Like Behaviors Through Cannabinoid-1 Receptor-Dependent PKA/RhoA Signaling Pathway

Post-stroke depression (PSD) is a significant complication in stroke patients, increases long-term mortality, and exaggerates ischemia-induced brain injury. However, the underlying molecular mechanisms and effective therapeutic targets related to PSD have remained elusive. Here, we employed an animal behavioral model of PSD by combining the use of middle cerebral artery occlusion (MCAO) followed by spatial restraint stress to study the molecular underpinnings and potential therapies of PSD. Interestingly, we found that sub-chronic application of gastrodin (Gas), a traditional Chinese medicinal herb Gastrodia elata extraction, relieved depression-related behavioral deficits, increased the impaired expression of synaptic transmission-associated proteins, and restored the altered spine density in hippocampal CA1 of PSD animals. Furthermore, our results indicated that the anti-PSD effect of Gas was dependent on membrane cannabinoid-1 receptor (CB1R) expression. The contents of phosphorated protein kinase A (p-PKA) and phosphorated Ras homolog gene family member A (p(ser188)-RhoA) were decreased in the hippocampus of PSD-mice, which was reversed by Gas treatment, and CB1R depletion caused a diminished efficacy of Gas on p-PKA and p-RhoA expression. In addition, the anti-PSD effect of Gas was partially blocked by PKA inhibition or RhoA activation, indicating that the anti-PSD effect of Gas is associated with the CB1R-mediated PKA/RhoA signaling pathway. Together, our findings revealed that Gas treatment possesses protective effects against the post-stroke depressive-like state; the CB1R-involved PKA/RhoA signaling pathway is critical in mediating Gas's anti-PSD potency, suggesting that Gas application may be beneficial in the prevention and adjunctive treatment of PSD.

In silico studies on the anti-acne potential of Garcinia mangostana xanthones and benzophenones

Garcinia mangostana fruits are used traditionally for inflammatory skin conditions, including acne. In this study, an in silico approach was employed to predict the interactions of G. mangostana xanthones and benzophenones with three proteins involved in the pathogenicity of acne, namely the human JNK1, Cutibacterium acnes KAS III and exo-β-1,4-mannosidase. Molecular docking analysis was performed using Autodock Vina. The highest docking scores and size-independent ligand efficiency values towards JNK1, C. acnes KAS III and exo-β-1,4-mannosidase were obtained for garcinoxanthone T, gentisein/2,4,6,3',5'-pentahydroxybenzophenone and mangostanaxanthone VI, respectively. To the best of our knowledge, this is the first report of the potential of xanthones and benzophenones to interact with C. acnes KAS III. Molecular dynamics simulations using GROMACS indicated that the JNK1-garcinoxanthone T complex had the highest stability of all ligand-protein complexes, with a high number of hydrogen bonds predicted to form between this ligand and its target. Petra/Osiris/Molinspiration (POM) analysis was also conducted to determine pharmacophore sites and predict the molecular properties of ligands influencing ADMET. All ligands, except for mangostanaxanthone VI, showed good membrane permeability. Garcinoxanthone T, gentisein and 2,4,6,3',5'-pentahydroxybenzophenone were identified as the most promising compounds to explore further, including in experimental studies, for their anti-acne potential.

Influence of structural characteristics on the binding of synthetic cannabinoids from the JWH family to the CB1 receptor: A computational study

Synthetic cannabinoids, including some from the John W. Huffman (JWH) family, emerged on the drug scene around 2004 as "alternative marijuana," despite being considerably more potent than marijuana. Like Δ9-tetrahydrocannabinol (THC), the principal psychoactive ingredient in marijuana, synthetic cannabinoids have also been found to interact with cannabinoid receptors CB1 and CB2, found in the brain, immune system, and peripheral organs. The JWH compounds and other synthetic cannabinoids have become important subjects of research in the forensic science community due to their drug-abuse potential, undetectability under routine drug screening, and unpredictable toxicity. In this study, an active-state CB1 receptor model was used to assess the receptor-ligand interactions between the CB1 receptor and ligands from the JWH synthetic cannabinoid family, as well as some newly designed JWH-like virtual compounds, labeled as MGCS compounds, using docking, binding free-energy calculations (ΔG), and molecular dynamics simulations (MDs). The calculated ΔG revealed that the carbonyl group between the naphthalene and the indole, characteristic of the JWH family, and the length of the N-linked alkyl chain were two important structural characteristics that influenced the predicted CB1 binding affinity, especially as increasing the length of the alkyl chain led to better predicted binding affinity. MDs and per-residue-breakdown results showed that the designed MGCS compounds with a pentyl chain attached to the naphthalene moiety and selected JWH compounds formed stable and strong hydrophobic interactions with the key residues Phe170, Phe174, Phe177, Phe200, Phe268, and Trp279 of the CB1 receptor. Comprehension of these critical interactions can help forensic chemists predict the structure of undiscovered families of synthetic cannabinoids.

Poria cocos compounds targeting neuropeptide Y1 receptor (Y1R) for weight management: A computational ligand- and structure-based study with molecular dynamics simulations identified beta-amyrin acetate as a putative Y1R inhibitor

Poria cocos (PC) is a medicinal herb frequently used in weight-loss clinical trials, however the mechanisms by which its compounds target orexigenic receptors including the neuropeptide Y1 receptor (Y1R) remain largely unknown. This study aimed to screen PC compounds for favourable pharmacokinetics profiles and examine their molecular mechanisms targeting Y1R. Forty-three PC compounds were systematically sought from pharmacological databases and docked with Y1R (PDB: 5ZBQ). By comparing the relative binding affinities, pharmacokinetics and toxicity profiles, we hypothesised that compounds designated PC1 3,4-Dihydroxybenzoic acid, PC8 Vanillic acid, PC40 1-(alpha-L-Ribofuranosyl)uracil, could be potential antagonists as they contact major residues Asn283 and Asp287, similar to various potent Y1R antagonists. In addition, PC21 Poricoic acid B, PC22 Poricoic acid G and PC43 16alpha,25-Dihydroxy-24-methylene-3,4-secolanosta-4(28),7,9(11)-triene-3,21-dioic acid, contacting Asn299, Asp104 and Asp200 proximal to the extracellular surface could also interfere with agonist binding by stabilising the extracellular loop (ECL) 2 of Y1R in a closed position. Owing to their selective interaction with Phe302, an important residue in binding of selective Y1R antagonists, PC12 beta-Amyrin acetate, PC26 3-Epidehydrotumulosic acid and PC27 Cerevisterol were proposed as putative antagonists. Following the consensus approach, PC12 beta-Amyrin acetate, PC26 3-Epidehydrotumulosic acid and PC27 Cerevisterol were identified as candidate compounds due to their high affinities (-12.2, -11.0 and -10.8 kcal, respectively), high drug-likeness and low toxicity profiles. Trajectory analyses and energy contributions of PC12-Y1R complex further confirmed their structural stability and favourable binding free energies, highlighting the feasibility and possible development of PC12 beta-Amyrin acetate as a future Y1R inhibitor.

New mechanistic insights into PAHs transport across wheat root cell membrane: Evidence for ABC transporter mediation

Polycyclic aromatic hydrocarbons (PAHs) are a class of highly carcinogenic organic pollutants. Our previous results revealed that the active uptake of PAHs by plant roots is performed through H⁺/PAHs co-transport. However, the proteins and mechanisms of co-transport of PAHs remain unknown. We hypothesized that ABC transporters are involved in PAHs co-transport via the roots. We found a total of 47 ABC transporters with alkalinity and hydrophobicity which were up-regulated or newly expressed in the wheat roots after phenanthrene exposure. And the concentration of ABC transporters rose. There was a positive relationship between the concentration of phenanthrene and ABC transporter expression in the wheat roots. Additionally, the trend observed in the ABC transporters expression was also found in the gene expression. With energies below -6 kcal mol^-1, a stable docking conformation formed between ABC transporters and PAHs. π-π stacking and van der Waals force bound PAHs to ABCB or ABCG. The binding strength of ABCB subfamily proteins with homodimers is stronger than that of ABCG subfamily proteins with single molecules. ABC transporters may transport PAHs by forming a dimer-shaped pocket, translocating it into cells, then opening it within the cells, to release the bound PAHs. These results contributed to our understanding of how ABC transporters aid plant root uptake of PAHs.

Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach

During the second phase of SARS-CoV-2, an unknown fungal infection, identified as black fungus, was transmitted to numerous people among the hospitalized COVID-19 patients and increased the death rate. The black fungus is associated with the Mycolicibacterium smegmatis, Mucor lusitanicus, and Rhizomucor miehei microorganisms. At the same time, other pathogenic diseases, such as the Monkeypox virus and Marburg virus, impacted global health. Policymakers are concerned about these pathogens due to their severe pathogenic capabilities and rapid spread. However, no standard therapies are available to manage and treat those conditions. Since the coptisine has significant antimicrobial, antiviral, and antifungal properties; therefore, the current investigation has been designed by modifying coptisine to identify an effective drug molecule against Black fungus, Monkeypox, and Marburg virus. After designing the derivatives of coptisine, they have been optimized to get a stable molecular structure. These ligands were then subjected to molecular docking study against two vital proteins obtained from black fungal pathogens: Rhizomucor miehei (PDB ID: 4WTP) and Mycolicibacterium smegmatis (PDB ID 7D6X), and proteins found in Monkeypox virus (PDB ID: 4QWO) and Marburg virus (PDB ID 4OR8). Following molecular docking, other computational investigations, such as ADMET, QSAR, drug-likeness, quantum calculation and molecular dynamics, were also performed to determine their potentiality as antifungal and antiviral inhibitors. The docking score reported that they have strong affinities against Black fungus, Monkeypox virus, and Marburg virus. Then, the molecular dynamic simulation was conducted to determine their stability and durability in the physiological system with water at 100 ns, which documented that the mentioned drugs were stable over the simulated time. Thus, our in silico investigation provides a preliminary report that coptisine derivatives are safe and potentially effective against Black fungus, Monkeypox virus, and Marburg virus. Hence, coptisine derivatives may be a prospective candidate for developing drugs against Black fungus, Monkeypox and Marburg viruses.

Anti-Inflammatory and Anti-Rheumatic Potential of Selective Plant Compounds by Targeting TLR-4/AP-1 Signaling: A Comprehensive Molecular Docking and Simulation Approaches

Plants are an important source of drug development and numerous plant derived molecules have been used in clinical practice for the ailment of various diseases. The Toll-like receptor-4 (TLR-4) signaling pathway plays a crucial role in inflammation including rheumatoid arthritis. The TLR-4 binds with pro-inflammatory ligands such as lipopolysaccharide (LPS) to induce the downstream signaling mechanism such as nuclear factor κappa B (NF-κB) and mitogen activated protein kinases (MAPKs). This signaling activation leads to the onset of various diseases including inflammation. In the present study, 22 natural compounds were studied against TLR-4/AP-1 signaling, which is implicated in the inflammatory process using a computational approach. These compounds belong to various classes such as methylxanthine, sesquiterpene lactone, alkaloid, flavone glycosides, lignan, phenolic acid, etc. The compounds exhibited different binding affinities with the TLR-4, JNK, NF-κB, and AP-1 protein due to the formation of multiple hydrophilic and hydrophobic interactions. With TLR-4, rutin had the highest binding energy (−10.4 kcal/mol), poncirin had the highest binding energy (−9.4 kcal/mol) with NF-κB and JNK (−9.5 kcal/mol), respectively, and icariin had the highest binding affinity (−9.1 kcal/mol) with the AP-1 protein. The root means square deviation (RMSD), root mean square fraction (RMSF), and radius of gyration (RoG) for 150 ns were calculated using molecular dynamic simulation (MD simulation) based on rutin’s greatest binding energy with TLR-4. The RMSD, RMSF, and RoG were all within acceptable limits in the MD simulation, and the complex remained stable for 150 ns. Furthermore, these compounds were assessed for the potential toxic effect on various organs such as the liver, heart, genotoxicity, and oral maximum toxic dose. Moreover, the blood–brain barrier permeability and intestinal absorption were also predicted using SwissADME software (Lausanne, Switzerland). These compounds exhibited promising physico-chemical as well as drug-likeness properties. Consequently, these selected compounds portray promising anti-inflammatory and drug-likeness properties.

Molecular docking studies of natural immunomodulators indicate their interactions with the CD40L of CD40/CD40L pathway and CSF1R kinase domain of microglia

Natural products have proved beneficial in reducing neuroinflammation in neurological diseases. Their impacts have also been associated with the activities of microglia, responsible for brain-specific immunity. Recent studies have shown the involvement of the number of microglia-specific proteins in the regulation of brain-specific immunity. However, molecular targets of natural products and their mechanism of interaction with microglia-specific proteins are elusive. Since the genetic signature of microglia offers many potential targets for drug discovery, molecular docking followed by molecular dynamics (MD) simulations of cluster of differentiation 40 ligand (CD40L) and colony-stimulating factor 1 receptor (CSF1R) kinase domain protein with some known neuro-immunomodulators (Curcumin, Cannabidiol, Ginsenoside Rg1, Resveratrol, and Sulforaphane) has been evaluated. Curcumin and cannabidiol were observed likely to modulate CD40L and expression of cytokines and entry of inflammatory cells. Resveratrol and cannabidiol may affect the CSF1R kinase domain and activation of microglia. Our finding suggests that curcumin, cannabidiol, and resveratrol may serve specific drug ligands in regulating microglia-mediated brain immunity.

The Physical Chemistry and Chemical Physics (PCCP) Section of the International Journal of Molecular Sciences in Its Publications: The First 300 Thematic Articles in the First 3 Years

The Physical Chemistry and Chemical Physics Section (PCCP Section) is one of the youngest among the sections of the International Journal of Molecular Sciences (IJMS)-the year 2021 will only mark three years since its inception [...].