In Silico Studies on Psilocybin Drug Derivatives Against SARS-CoV-2 and Cytokine Storm of Human Interleukin-6 Receptor

Alterations in brain network connectivity and subjective experience induced by psychedelics: a scoping review

Intense interest surrounds current research on psychedelics, particularly regarding their potential in treating mental health disorders. Various studies suggest a link between the subjective effects produced by psychedelics and their therapeutic efficacy. Neuroimaging evidence indicates an association of changes in brain functional connectivity with the subjective effects of psychedelics. We conducted a review focusing on psychedelics and brain functional connectivity. The review focused on four psychedelic drugs: ayahuasca, psilocybin and LSD, and the entactogen MDMA. We conducted searches in databases of MEDLINE, Embase, APA PsycInfo and Scopus from inception to Jun 2023 by keywords related to functional connectivity and psychedelics. Using the PRISMA framework, we selected 24 articles from an initial pool of 492 for analysis. This scoping review and analysis investigated the effects of psychedelics on subjective experiences and brain functional connectivity in healthy individuals. The studies quantified subjective effects through psychometric scales, revealing significant experiences of altered consciousness, mood elevation, and mystical experiences induced by psychedelics. Neuroimaging results indicated alterations in the functional connectivity of psychedelics, with consistent findings across substances of decreased connectivity within the default mode network and increased sensory and thalamocortical connectivity. Correlations between these neurophysiological changes and subjective experiences were noted, suggesting a brain network basis of the psychedelics' neuropsychological impact. While the result of the review provides a potential neural mechanism of the subjective effects of psychedelics, direct clinical evidence is needed to advance their clinical outcomes. Our research serves as a foundation for further exploration of the therapeutic potential of psychedelics.

A computational quest for identifying potential vaccine candidates against Moraxella lacunata: a multi-pronged approach

Moraxella lacunata is an emerging gram-negative bacterium that is responsible for multiple nosocomial infections. The bacterium is evolving resistance to several antibiotics, and currently, no effective licensed vaccines are available, which warrants the search for new therapeutics. A multi-epitope-based vaccine has been designed for M. lacunata. The complete proteome of M. lacunata contains 10,110 core proteins. Subcellular localization analysis revealed the presence of five proteins in the extracellular matrix, while 19 proteins were predicted to be located in the outer membrane, and 21 proteins were predicted to be located in the periplasmic region. Only two proteins, the type VI secretion system tube protein (Hcp) and the transporter substrate-binding domain-containing protein, were selected for epitope prediction as they fulfilled all the criteria for being potential vaccine candidates. Shortlisted epitopes from the selected proteins were fused together using "GPGPG" linkers to overcome the limitations of single-epitope vaccines. Next, the cholera toxin-B adjuvant was attached to the peptide epitope using an EAAAK linker. Docking analysis was performed to examine the interaction between the vaccine and immune cell receptors, revealing robust intermolecular interactions and a stable binding conformation. Molecular dynamics simulation findings revealed no drastic changes in the binding conformation of complexes during the simulation period. The net binding free energy of vaccine-receptor complexes was estimated using the molecular mechanics energies combined with the Poisson-Boltzmann and surface area continuum solvation (MM-PBSA) method. The reported values were -586.38 kcal/mol, -283.74 kcal/mol, and -296.88 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. Furthermore, the molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM-GBSA) analysis predicted binding free energies of -596.69 kcal/mol, -287.39 kcal/mol, and -298.28 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. The theoretical vaccine design proposed in the study could potentially serve as a powerful therapeutic against targeted pathogens, subject to validation through experimental studies.Communicated by Ramaswamy H. Sarma.

Deciphering psilocybin: Cytotoxicity, anti-inflammatory effects, and mechanistic insights

A decade of clinical research has indicated psilocybin's effectiveness in treating various neuropsychiatric disorders, such as depression and substance abuse. The correlation between increased pro-inflammatory cytokines and the severity of neuropsychiatric symptoms, along with the known anti-inflammatory potential of some psychedelics, suggests an immunomodulatory role for psilocybin. This study aims to understand the mechanism of action of psilocybin by investigating the cytotoxic and immunomodulatory effects of psilocybin and psilocin on both resting and LPS-activated RAW 264.7 murine macrophages. The study evaluated the cytotoxicity of psilocybin and psilocin using an LDH assay across various doses and assessed their impact on cytokine production in RAW 264.7 cells, measuring cytokine expression via ELISA. Different doses, including those above and below the LC50, were used in both pre-treatment and post-treatment approaches. The LDH assay revealed that psilocybin is almost twice as cytotoxic as psilocin, with an LC50 of 12 ng/ml and 28 ng/ml, respectively. In resting macrophages, both psilocybin and psilocin triggered significant release of TNF- α after 4 h, with the lowest doses inducing higher levels of the cytokine than the highest doses. IL-10 expression in resting cells was only triggered by the highest dose of psilocin in the 4-hour incubation group. In LPS-stimulated cells, psilocin reduced TNF- α levels more than psilocybin in pre-treatment and post-treatment, with no significant effects on IL-10 in pre-treatment. Psilocin, but not psilocybin, induced a significant increase of IL-10 in post-treatment, leading to the conclusion that psilocin, but not psilocybin, exerts anti-inflammatory effects on classically activated macrophages.

Unveiling MurE ligase potential inhibitors for treating multi-drug resistant Acinetobacter baumannii

Acinetobacter baumannii is an opportunistic pathogen with ability to cause serious infection such as bacteremia, ventilator associated pneumonia, and wound infections. As strains of A. baumannii are resistant to almost all clinically used antibiotics and with the emergence of carbapenems resistant phenotypes warrants the search for novel antibiotics. Considering this, herein, a series of computer aided drug designing approach was utilized to search novel chemical scaffolds that bind stronger to MurE ligase enzyme of A. baumannii, which is involved peptidoglycan synthesis. The work identified LAS_22461675, LAS_34000090 and LAS_51177972 compounds as promising binding molecules with MurE enzyme having binding energy score of -10.5 kcal/mol, -9.3 kcal/mol and -8.6 kcal/mol, respectively. The compounds were found to achieve docked inside the MurE substrate binding pocket and established close distance chemical interactions. The interaction energies were dominated by van der Waals and less contributions were seen from hydrogen bonding energy. The dynamic simulation assay predicted the complexes stable with no major global and local changes noticed. The docked stability was also validated by MM/PBSA and MM/GBSA binding free energy methods. The net MM/GBSA binding free energy of LAS_22461675 complex, LAS_34000090 complex and LAS_51177972 complex is -26.25 kcal/mol, -27.23 kcal/mol and -29.64 kcal/mol, respectively. Similarly in case of MM-PBSA, the net energy value was in following order; LAS_22461675 complex (-27.67 kcal/mol), LAS_34000090 complex (-29.94 kcal/mol) and LAS_51177972 complex (-27.32 kcal/mol). The AMBER entropy and WaterSwap methods also confirmed stable complexes formation. Further, molecular features of the compounds were determined that predicted compounds to have good druglike properties and pharmacokinetic favorable. The study concluded the compounds to good candidates to be tested by in vivo and in vitro experimental assays.Communicated by Ramaswamy H. Sarma.

Identifying repurposed drugs as potential inhibitors of Apolipoprotein E: A bioinformatics approach to target complex diseases associated with lipid metabolism and neurodegeneration

Apolipoprotein E (ApoE), a pivotal contributor to lipid metabolism and neurodegenerative disorders, emerges as an attractive target for therapeutic intervention. Within this study, we deployed an integrated in-silico strategy, harnessing structure-based virtual screening, to identify potential compounds from DrugBank database. Employing molecular docking, we unveil initial hits by evaluating their binding efficiency with ApoE. This first tier of screening narrows our focus to compounds that exhibit a strong propensity to bind with ApoE. Further, a detailed interaction analysis was carried out to explore the binding patterns of the selected hits towards the ApoE binding site. The selected compounds were then evaluated for the biological properties in PASS analysis, which showed anti-neurodegenerative properties. Building upon this foundation, we delve deeper, employing all-atom molecular dynamics (MD) simulations extending over an extensive 500 ns. In particular, Ergotamine and Dihydroergocristine emerge as noteworthy candidates, binding to ApoE in a competitive mode. This intriguing binding behavior positions these compounds as potential candidates warranting further analysis in the pursuit of novel therapeutics targeting complex diseases associated with lipid metabolism and neurodegeneration. This approach holds the promise of catalyzing advancements in therapeutic intervention for complex disorders, thereby reporting a meaningful pace towards improved healthcare outcomes.

Expanding the therapeutic arsenal against cancer: a computational investigation of hybrid xanthone derivatives as selective Topoisomerase 2α ATPase inhibitors

The DNA topoisomerase II (topo II) enzyme plays an important role in the replication, recombination, and repair of DNA. Despite their widespread applications in cancer therapy, new, selective, and potent topo II inhibitors with better pharmaceutical profiles are needed to handle drug resistance and severe adverse effects. In this respect, an array of 36 new anticancer compounds was designed based on a Xanthone core tethered to multifunctional Pyridine-amines and Imidazole scaffold via alkyl chain linkers. An integrated in silico approach was used to understand the structural basis and mechanism of inhibition of the hybrid xanthone derivatives. In this study, we established an initial virtual screening workflow based on pharmacophore mapping, docking, and cancer target association to validate the target selection process. Next, a simulation-based docking was conducted along with pharmacokinetic analysis to filter out the five best compounds (7, 10, 25, 27, and 30) having binding energies within the range of -60.45 to -40.97 kcal/mol. The screened compounds were further subjected to molecular dynamics simulation for 200 ns followed by MM-GBSA and ligand properties analysis to assess the stability and binding affinity to hTOP2α. The top-ranking hits 3,7-bis(3-(2-aminopyridin-3-ylhydroxy)propoxy)-1-hydroxy-9H-xanthen-9-one (ligand 7) and 3,8-bis(3-(2-aminopyridin-3-ylhydroxy)propoxy)-1-hydroxy-9H-xanthen-9-one (ligand 25) were found to have no toxicity, optimum pharmacokinetic and, DFT properties and stable intermolecular interactions with the active site of hTopo IIα protein. In conclusion, further in vitro and in vivo experimental validation of the identified lead molecules is warranted for the discovery of new human Topoisomerase 2 alpha inhibitors.Communicated by Ramaswamy H. Sarma.

Exploring EGFR inhibitors with the aid of virtual screening, docking, and dynamics simulation studies

In humans, Epidermal Growth Factor Receptor (EGFR) is linked to small-cell lung cancer, breast cancer, and glioblastoma. Receptor kinase inhibitors against EGFR have become a standard treatment option for non-small cell lung cancer (NSCLC), breast cancer patients, and even for those with EGFR mutations or resistance. About 2734 FDA-approved medication compounds were subjected to virtual screening for EGFR kinase inhibitory activity. The top 30 molecules were chosen based on the binding affinity scores and subjected to extra-precision docking and binding free energy analysis. The ADMET profile of the top three hit molecules was verified to confirm their druggability nature. Top three hits- compound 1047 (ZINC000001550477), 1302 (ZINC00003781952), and 2332 (ZINC000019632618) were identified on account of their MMGBSA binding affinity values. The top three hit compounds were subjected to molecular dynamics (MD) simulation for 100 ns. The dynamic nature of the ligand-protein complex was analyzed which corroborated the results of molecular docking and MMGBSA analysis studies. All the top three hits were further subjected to steered MD studies for testing the strength of these ligand-receptor binding in the presence of an external force. Compound 2332 (ZINC000019632618) was identified as the best hit molecule that can be used as a lead to develop newer derivatives of EGFR kinase inhibitors.Communicated by Ramaswamy H. Sarma.

Indole-Based Compounds as Potential Drug Candidates for SARS-CoV-2

The COVID-19 pandemic has posed a significant threat to society in recent times, endangering human health, life, and economic well-being. The disease quickly spreads due to the highly infectious SARS-CoV-2 virus, which has undergone numerous mutations. Despite intense research efforts by the scientific community since its emergence in 2019, no effective therapeutics have been discovered yet. While some repurposed drugs have been used to control the global outbreak and save lives, none have proven universally effective, particularly for severely infected patients. Although the spread of the disease is generally under control, anti-SARS-CoV-2 agents are still needed to combat current and future infections. This study reviews some of the most promising repurposed drugs containing indolyl heterocycle, which is an essential scaffold of many alkaloids with diverse bio-properties in various biological fields. The study also discusses natural and synthetic indole-containing compounds with anti-SARS-CoV-2 properties and computer-aided drug design (in silico studies) for optimizing anti-SARS-CoV-2 hits/leads.

Carvacrol instigates intrinsic and extrinsic apoptosis with abrogation of cell cycle progression in cervical cancer cells: Inhibition of Hedgehog/GLI signaling cascade

Recent times have seen a strong surge in therapeutically targeting the hedgehog (HH)/GLI signaling pathway in cervical cancer. HH signaling pathway is reported to be a crucial modulator of carcinogenesis in cervical cancer and is also associated with recurrence and development of chemoresistance. Moreover, our previous reports have established that carvacrol (CAR) inhibited the proliferation of prostate cancer cells via inhibiting the Notch signaling pathway and thus, it was rational to explore its antiproliferative effects in cervical cancer cell lines. Herein, the present study aimed to investigate the anticancer and apoptotic potential of CAR on C33A cervical cancer cells and further explore the underlying mechanisms. We found that CAR significantly suppressed the growth of C33A cells, induced cell cycle arrest, and enhanced programmed cell death along with augmentation in the level of ROS, dissipated mitochondrial membrane potential, activation of caspase cascade, and eventually inhibited the HH signaling cascade. In addition, CAR treatment increased the expression of pro-apoptotic proteins (Bax, Bad, Fas-L, TRAIL, FADDR, cytochrome c) and concomitantly reduced the expression of anti-apoptotic proteins (Bcl-2 and Bcl-xL) in C33A cells. CAR mediates the activation of caspase-9 and -3 (intrinsic pathway) and caspase-8 (extrinsic pathway) accompanied by the cleavage of PARP in cervical cancer cells. Thus, CAR induced apoptosis by both the intrinsic and extrinsic apoptotic pathways. CAR efficiently inhibited the growth of cervical cancer cells via arresting the cell cycle at G0/G1 phase and modulated the gene expression of related proteins (p21, p27, cyclin D1 and CDK4). Moreover, CAR inhibited the HH/GLI signaling pathway by down regulating the expression of SMO, PTCH and GLI1 proteins in cervical carcinoma cells. With evidence of the above results, our data revealed that CAR treatment suppressed the growth of HPV^-C33A cervical cancer cells and further elucidated the mechanistic insights into the functioning of CAR.

Structures and Biological Activities of Alkaloids Produced by Mushrooms, a Fungal Subgroup

Alkaloids are a wide family of basic N-containing natural products, whose research has revealed bioactive compounds of pharmacological interest. Studies on these compounds have focused more attention on those produced by plants, although other types of organisms have also been proven to synthesize bioactive alkaloids, such as animals, marine organisms, bacteria, and fungi. This review covers the findings of the last 20 years (2002–2022) related to the isolation, structures, and biological activities of the alkaloids produced by mushrooms, a fungal subgroup, and their potential to develop drugs and agrochemicals. In some cases, the synthesis of the reviewed compounds and structure−activity relationship studies have been described.