Virtual Docking Research Articles

Exploring the Molecular Mechanisms of Acorus tatarinowii and Ginseng in the Treatment of Autism Spectrum Disorder Based on Network Pharmacology and Molecular Docking

Background: Acorus tatarinowii and Ginseng (AT-G) are traditional Chinese herbal medicines extensively utilized in neurological disorders treatment. However, due to the complex components of AT-G and the pathological mechanism of ASD, the mechanisms involved in the treatment of ASD with AT-G remain elusive. Objective: We explored AT-G potential mechanisms in ASD treatment. Methods: We used the network pharmacology approach to evaluate the beneficial effects of AT-G for ASD, including obtaining the active components of AT-G by the Traditional Chinese Medicine Systems Pharmacology (TCMSP) platform, detecting the potential targets genes associated with ASD of Genecards and DisGenet databases, network analysis, and virtual docking. Results: A total of 26 AT-G components, 130 AT-G targets, and 806 ASD-related genes were identified using the bioinformatics analysis tool, including TCMSP, Genecards, and DisGenet. In the intersection of potential pharmacodynamic targets of AT-G and genes associated with ASD, we identified 41 potential common targets. Then, GO enrichment analysis revealed that the common targets were mainly associated with biological processes (i.e., positive regulation of nitric oxide biosynthetic process, response to xenobiotic stimulus), cellular components (i.e., the presynaptic membrane and postsynaptic membrane), and molecular functions (i.e., RNA polymerase II transcription factor activity, identical protein binding). KEGG pathway analysis found that the common targets were enriched in chemical carcinogenesis - receptor activation, fluid shear stress and atherosclerosis, lipid and atherosclerosis, and IL-17 signaling pathways. In addition, 10 core targets were screened from the PPI network (e.g., TNF, AKT1, PTGS2, MMP, PPARG, IFNG, NOS2, TGFB1, and CASP1). Molecular docking revealed that the common component kaempferol has a high affinity for the four primary disease targets. Conclusion: Our results facilitated the in-depth development of AT-G and their individual components and provided a reference for clinical practice

Development of Anti-Inflammatory Drug from Crataeva Nurvala: In Silico and In Vitro Approach

ABSTRACT Background: Crataeva nurvala, a medicinal plant with potential therapeutic properties, offers a promising avenue for the development of novel anti-inflammatory drugs. This study adopted a combined in silico and in vitro approach to investigate the anti-inflammatory potential of compounds derived from Crataeva nurvala. Materials and Methods: In the in silico phase, virtual screening and molecular docking analyses were conducted to identify bioactive compounds from Crataeva nurvala that could interact with key inflammatory targets. Subsequently, selected compounds were synthesized and subjected to in vitro experimentation. Cellular models were employed to assess the anti-inflammatory effects of Crataeva nurvala-derived compounds, focusing on the modulation of pro-inflammatory cytokine levels and the underlying signaling pathways. Results: Virtual screening and molecular docking led to the identification of several bioactive compounds with favorable interactions with inflammatory targets. In the in vitro experiments, treatment with Crataeva nurvala-derived compounds resulted in a significant reduction in pro-inflammatory cytokine production. Moreover, the compounds exhibited the ability to modulate inflammatory signaling pathways, further substantiating their anti-inflammatory potential. Conclusions: This study not only contributes to the development of effective anti-inflammatory drugs but also underscores the value of harnessing natural sources such as Crataeva nurvala for therapeutic interventions in inflammatory disorders. The dual-phase strategy presented here provides a robust framework for anti-inflammatory drug discovery and validation.

Integrative computational approaches for designing novel alpha-glucosidase inhibitors based on curculigoside A derivatives: Virtual screening, molecular docking, and molecular dynamics

Introduction: Over 422 million people worldwide suffer from diabetes, causing 1.5 million fatalities annually. The existing medications have shortcomings, including poor glucose control and adverse effects. The present study aimed to create possible alpha-glucosidase inhibitors utilizing a curculigoside A derivative ligand-based model. Methods: A pharmacophore model was constructed utilizing the structure information of curculigoside A derivatives and PharmaGist. Subsequently, virtual screening, molecular docking, and molecular dynamics were employed to simulate the hits. Results: From six training sets, eleven pharmacophore models were developed; the model with the highest score (18.0435) was chosen for further analysis. Using the verified pharmacophore model, 270 547 chemicals from the ZINC natural product database were subjected to virtual screening. Subsequently, molecular docking was performed on the top 1000 hits with AutoDock Wizard from PyRx. This analysis unveiled 434 hits with better binding energies than acarbose, the native ligand. Subsequently, second optimal docking configurations were evaluated with AutoDock 2.4; this process yielded the discovery of three prospective inhibitors (ZINC000150350051, ZINC000008382292, and ZINC000085595291) characterized by the most advantageous binding energies. To evaluate the stability and dynamics of these ligand-receptor complexes, Gromacs 2022 molecular dynamics simulations were executed for one hundred nanoseconds. Out of the three hits, ZINC000085595291 (Hit03) exhibited good energy components and interaction stability constantly during the simulation. Conclusion: The integrated computational strategy identified promising alpha-glucosidase inhibitors in curculigoside A compounds, highlighting the potential of ZINC000085595291 (Hit03) as a potential diabetes therapeutic agent.

In silico Identification of HDAC Inhibitors for Multiple Myeloma: A Structure-based Virtual Screening, Drug Likeness, ADMET Profiling, Molecular Docking, and Molecular Dynamics Simulation Study

Background: Multiple myeloma (MM) is a hematological malignancy of plasma cells that produce a monoclonal immunoglobulin protein. Despite significant advances in the treatment of MM, currently available therapies are associated with toxicity and resistance. As a result, there is an increasing demand for novel, effective therapeutics. Inhibition of histone deacetylases (HDACs) is emerging as a potential method for treating cancer. HDAC6 is one of 18 different HDAC isoforms that regulate tubulin lysine 40 and function in the microtubule network. HDAC6 participates in tumorigenesis and metastasis through protein ubiquitination, tubulin, and Hsp90. Several studies have found that inhibiting HDAC6 causes AKT and ERK dephosphorylation, which leads to decreased cell proliferation and promotes cancer cell death via the PI3K/AKT and MAPK/ERK signaling pathways. Objective: The objective of this study is to target HDAC6 and identify potent inhibitors for the treatment of multiple myeloma by employing computer-aided drug design. Materials and Methods: A total of 199,611,439 molecules from five different chemical databases, such as CHEMBL25, ChemSpace, Mcule, MolPort, and ZINC, have been screened against HDAC6 by structure- based virtual screening, followed by filtering for various drug-likeness, ADME, toxicity, consensus molecular docking, and 100 ns MD simulation. Results: Our research work resulted in three molecules that have shown strong binding affinity (CHEMBL2425964 -9.99 kcal/mol, CHEMBL2425966 -9.89 kcal/mol, and CSC067477144 -9.86 kcal/mol) at the active site HDAC6, along with effective ADME properties, low toxicity, and high stability. Inhibiting HDAC6 with these identified molecules will induce AKT and ERK dephosphorylation linked to reduced cell proliferation and promote cancer cell death. Conclusion: CHEMBL2425964, CHEMBL2425966, and CSC067477144 could be effective against multiple myeloma.

Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations

The kinesin spindle protein (Eg5) is a mitotic protein that plays an essential role in the formation of the bipolar spindles during the mitotic phase. Eg5 protein controls the segregation of the chromosomes in mitosis which renders it a vital target for cancer treatment. In this study our approach to identifying novel scaffold for Eg5 inhibitors is based on targeting the novel allosteric pocket (α4/α6/L11). Extensive computational techniques were applied using ligand-based virtual screening and molecular docking by two approaches, MOE and AutoDock, to screen a library of commercial compounds. We identified compound 8-(3-(1H-imidazol-1-ylpropylamino)-3-methyl-7-((naphthalen-3-yl)methyl)-1H-purine-2, 6 (3H,7H)-dione (compound 5) as a novel scaffold for Eg5 inhibitors. This compound inhibited cancer cell Eg5 ATPase at 2.37 ± 0.15 µM. The molecular dynamics simulations revealed that the identified compound formed stable interactions in the allosteric pocket (α4/α6/L11) of the receptor, indicating its potential as a novel Eg5 inhibitor.Graphical

IN SILICO APPROACHES ON PHENYLALANINE HYDROXYLASE INHIBITOR-RELATED COMPOUNDS USED IN PARKINSON’S DISEASE TREATMENT

Objective: In Parkinson’s disease, Levodopa with Carbidopa addresses dopamine deficiency. Phenylalanine hydroxylase catalyzes phenylalanine to tyrosine conversion crucial for dopamine synthesis. Inhibiting phenylalanine hydroxylase may enhance Carbidopa's effects, preventing peripheral dopamine synthesis. The study used virtual scanning, molecular docking, and dynamics simulation to explore phenylalanine hydroxylase interactions with Carbidopa and similar ligands. ADME/T assessments and drug similarity tests were conducted to evaluate therapeutic potential in biological systems. Material and Method: A molecular docking study was performed on the structures obtained from the PubChem database and human PAH (PDB ID: 6PAH) using Autodock Vina within Chimera 1.16. Furthermore, the ligands underwent ADME/T assays, which are crucial aspects in drug development. Result and Discussion: The study suggests that 2-(2-Aminohydrazinyl)-3-(3,4-dihydroxyphenyl)-2-methylpropanoic acid shows promise as a phenylalanine hydroxylase inhibitor for Parkinson's disease treatment, but further research is needed to assess its safety, efficacy, and specificity, particularly in extracerebral regions, while also exploring its potential to improve the effectiveness of Levadopa/Carbidopa combination therapy.

Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations.

We have assembled a computational pipeline based on virtual screening, docking techniques, and nonequilibrium molecular dynamics simulations, with the goal of identifying possible inhibitors of the SARS-CoV-2 NSP13 helicase, catalyzing by ATP hydrolysis the unwinding of double or single-stranded RNA in the viral replication process inside the host cell. The druggable sites for broad-spectrum inhibitors are represented by the RNA binding sites at the 5' entrance and 3' exit of the central channel, a structural motif that is highly conserved across coronaviruses. Potential binders were first generated using structure-based ligand techniques. Their potency was estimated by using four popular docking scoring functions. Common docking hits for NSP13 were finally tested using advanced nonequilibrium alchemical techniques for binding free energy calculations on a high-performing parallel cluster. Four potential NSP13 inhibitors with potency from submicrimolar to nanomolar were finally identified.

Targeting MurB from Helicobacter pylori: insights from virtual screening, molecular docking and molecular dynamics simulation

ABSTRACT Helicobacter pylori is a gram-negative, helical-shaped bacteria found in the mucus lining of the stomach of humans responsible for causing sores or an ulcer. H. pylori is becoming a multi-drug resistant bacterium, which in turn demands the need for development of alternative treatment strategies for the proper management of diseases. The peptidoglycan biosynthesis pathway is critical for the synthesis of cell walls and for the survival of H. pylori. There are several crucial enzymes in this biosynthesis pathway which can act as significant drug targets against H. pylori. One of these important enzymes is UDP-N-acetylenolpyruvoylglucosamine reductase (MurB), which catalyses an important committed step of cell wall biosynthesis. In the present study, we performed a high throughput virtual screening using the Enamine HTSC library against the MurB enzyme. The molecules were also screened for druglike properties by ADME screening, toxicity, and tumorigenic nature, followed by MD simulations. We found that Z102621114_1 and Z228235240_1 ligand molecules can act as potential inhibitors of MurB protein. Our results suggest, these molecules may be able to meet the demand for novel antimicrobials to treat H. pylori medication resistance. The subsequent experimental investigations can increase their potential as a novel agents against H. pylori infections. Research highlights Helicobacter pylori infects 50% of the Global population. Helicobacter pylori infection is associated with gastric cancer. MurB is a key drug target protein as it is responsible for cell wall synthesis. Z102621114_1 and Z228235240_1 were identified as potential inhibitors of MurB of Helicobacter pylori.

Identification of novel potential cathepsin-B inhibitors through pharmacophore-based virtual screening, molecular docking, and dynamics simulation studies for the treatment of Alzheimer's disease.

Cathepsin B is a cysteine protease lysosomal enzyme involved in several physiological functions. Overexpression of the enzyme enhances its proteolytic activity and causes the breakdown of amyloid precursor protein (APP) into neurotoxic amyloid β (Aβ), a characteristic hallmark of Alzheimer's disease (AD). Therefore, inhibition of the enzyme is a crucial therapeutic aspect for treating the disease. Combined structure and ligand-based drug design strategies were employed in the current study to identify the novel potential cathepsin B inhibitors. Five different pharmacophore models were developed and used for the screening of the ZINC-15 database. The obtained hits were analyzed for the presence of duplicates, interfering PAINS moieties, and structural similarities based on Tanimoto's coefficient. The molecular docking study was performed to screen hits with better target binding affinity. The top seven hits were selected and were further evaluated based on their predicted ADME properties. The resulting best hits, ZINC827855702, ZINC123282431, and ZINC95386847, were finally subjected to molecular dynamics simulation studies to determine the stability of the protein-ligand complex during the run. ZINC123282431 was obtained as the virtual lead compound for cathepsin B inhibition and may be a promising novel anti-Alzheimer agent.

Unraveling umami complexity: From exploring umami peptides in fermented soybean curd to molecular elucidation of taste mechanisms

Sufu is a traditional umami fermented soybean curd (FSC). We isolated and identified 25 potential umami peptides using ethanol precipitation, dialysis desalination, resin adsorption recovery, nano-HPLC-MS/MS and virtual docking prediction. The results of sensory experiments showed that 23 of the synthetic peptides presented a lower umami threshold than that of MSG (0.50 mg/mL), and 10 peptides had obvious effects of increasing umami and saltiness. Seven peptides were quantified in FSC by UPLC-QQQ-MS, and the content of one novel umami tripeptide ADL (0.51 ± 0.03 mg/mL) was four times its umami threshold (0.125 mg/mL). Taste reconstitution experiments revealed that the umami peptides enhanced the umami and saltiness of the simulated system by 24.53% and 24.00%, respectively. Molecular dynamics proved that hydrogen bonding is the main interaction between peptide and receptors. This study is important for understanding and improving the taste quality of FSC.

Cr(VI) induces ferroptosis in DF-1 cells by simultaneously perturbing iron homeostasis of ferritinophagy and mitophagy

Hexavalent chromium [Cr(VI)] is an environmental pollutant known for its strong oxidizing and carcinogenic effects. However, its potential to induce ferroptosis in poultry remains poorly understood. This study aims to investigate the induction of ferroptosis by Cr(VI) in DF-1 cells and elucidate the underlying mechanisms. DF-1 cells exposed to Cr(VI) showed increased lipid reactive oxygen species and changes in ferroptosis marker genes (decreased expression of GPX4 and increased expression of COX2). Notably, the addition of the ferroptosis-specific inhibitor ferrostatin-1 (Fer-1) can reverse this effect. During the cell death process, Cr(VI) induced ferritinophagy, disrupting iron homeostasis and releasing labile iron ions. We predicted by docking that these iron ions would bind to mitochondrial membrane proteins through virtual docking. This binding was validated through colocalization analysis. In addition, Cr(VI) caused mitophagy, which releases additional ferrous ions. Therefore, Cr(VI) can induce the simultaneous release of ferrous ions through these pathways, thereby exacerbating lipid peroxidation and ultimately triggering ferroptosis in DF-1 cells. This study demonstrates that Cr(VI) can induce ferroptosis in DF-1 cells by disrupting intracellular iron homeostasis and providing valuable insights into the toxic effects of Cr(VI) in poultry and potentially other organisms.

Identification of flavor peptides based on virtual screening and molecular docking from Hypsizygus marmoreuss

Hypsizygus marmoreuss is an under-explored source of flavor peptides that can enhance the flavor of NaCl or MSG, allowing products to be reformulated in line with reduction policies. This study utilized advanced techniques, including UPLC-Q-TOF MS/MS and molecular docking, to identify H. marmoreuss peptides. Sensory evaluations revealed 10 peptides with pronounced umami flavors and seven with dominantly salty tastes. VLPVPQK scored highest for umami intensity (5.2), and EGNPAHQK for salty intensity (6.2). Further investigation influenced by 0.35 % MSG or 0.35 % NaCl exposed peptides with elevated umami and salty thresholds. LDSPATPEK, VVEGEPSLK, and QKLPEKPER had umami-enhancing thresholds of 0.18, 0.18, and 0.35 mM, while LDSPATPEK and VVEGEPSLK had similar thresholds for salt (0.09 mM). Molecular docking revealed that taste receptor proteins interacted with umami peptides through hydrogen, carbon-hydrogen, alkyl, and van der Waals forces. Specific amino acids in the umami receptor T1R1 had roles in bonding with umami peptides through hydrogen and carbon-hydrogen interactions. In conclusion, molecular docking proved to be an effective and efficient method for flavor peptide screening. Further, this study demonstrated that flavor peptides from H. marmoreuss had the capacity to enhance NaCl and MSG flavours and might be useful tools for reformulation, reducing salt and MSG contents.

Picroside Ⅱ Inhibits Glycolysis and Migration in HepG2 Cells

Objectives: The objective of this study was to investigate the impacts and mechanisms of Picroside II on hepatocellular carcinoma (HCC). Materials and Methods: The GeneCards database was mined for HCC-related targets. The targets of Picroside Ⅱ were predicted using PharmMapper and SwissTarget Prediction. The molecular complex detection (MCODE) plugin in Cytoscape was used to screen core genes. The DAVID database was subsequently used to enrich the core targets by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), which was used to determine the possible mode of action of Picroside II on HCC. Gene Expression Profiling Interactive Analysis 2 (GEPIA2) examined core targets and patient mortality. Auto Dock 4.2.6 was used to simulate the docking of potential targets with Picroside II. Then, surface plasmon resonance (SPR) was used to validate the targets’ docking ability. Finally, Western blotting and in vitro experiments were used to evaluate the effect of Picroside II on HepG2 cells. Results: The result of network pharmacology showed that 94 genes may be possible targets for Picroside II treating of HCC, with GPI, LGALS3, SRC, HRAS, HSP90AA1, MMP9, PPARG, SERPINE1, and VEGFA being the most promising. GPI and Picroside II have strong virtual docking capabilities, and SPR tests verified their binding ability. In vitro studies revealed that Picroside II could suppress HepG2 cell migration. It has been demonstrated that Picroside II can stop tumors from migrating by attaching to the glycolytic proteins GPI and suppressing the downstream glycolytic pathway proteins ALDOA and GAPDH. Picroside II’s potential new target for treating tumors is GPI. Conclusion: The results of this study suggest that Picroside Ⅱ can affect glucose metabolism by binding to glycolytic protein GPI and that this protein is a potential new target for Picroside Ⅱ in the treatment of tumors.

Salidroside directly activates HSC70, revealing a new role for HSC70 in BDNF signalling and neurogenesis after cerebral ischemia.

Salidroside, a principal bioactive component of Rhodiola crenulata, is neuroprotective across a wide time window in stroke models. We investigated whether salidroside induced neurogenesis after cerebral ischemia and aimed to identify its primary molecular targets. Rats, subjected to transient 2 h of middle cerebral artery occlusion (MCAO), received intraperitoneal vehicle or salidroside ± intracerebroventricular HSC70 inhibitor VER155008 or TrkB inhibitor ANA-12 for up to 7 days. MRI, behavioural tests, immunofluorescent staining and western blotting measured effects of salidroside. Reverse virtual docking and enzymatic assays assessed interaction of salidroside with purified recombinant HSC70. Salidroside dose-dependently decreased cerebral infarct volumes and neurological deficits, with maximal effects by 50 mg/kg/day. This dose also improved performance in beam balance and Morris water maze tests. Salidroside significantly increased BrdU+/nestin+, BrdU+/DCX+, BrdU+/NeuN+, BrdU-/NeuN+ and BDNF+ cells in the peri-infarct cortex, with less effect in striatum and no significant effect in the subventricular zone. Salidroside was predicted to bind with HSC70. Salidroside dose-dependently increased HSC70 ATPase and HSC70-dependent luciferase activities, but it did not activate HSP70. HSC70 immunoreactivity concentrated in the peri-infarct cortex and was unchanged by salidroside. However, VER155008 prevented salidroside-dependent increases of neurogenesis, BrdU-/NeuN+ cells and BDNF+ cells in peri-infarct cortex. Salidroside also increased BDNF protein and p-TrkB/TrkB ratio in ischemic brain, changes prevented by VER155008 and ANA-12, respectively. Additionally, ANA-12 blocked salidroside-dependent neurogenesis and increased BrdU-/NeuN+ cells in the peri-infarct cortex. Salidroside directly activates HSC70, thereby stimulating neurogenesis and neuroprotection via BDNF/TrkB signalling after MCAO. Salidroside and similar activators of HSC70 might provide clinical therapies for ischemic stroke.

A Combination of Pharmacophore Generation, Ligand-based Virtual Screening, Atom-based 3D-QSAR, and Molecular Docking Studies on Febuxostat-based Amides Analogues as Anti-inflammatory Agents.

A defence mechanism of the body includes inflammation. It is a process through which the immune system identifies, rejects, and starts to repair foreign and damaging stimuli. In the world, chronic inflammatory disorders are the leading cause of death. To obtain optimized pharmacophore, previously reported febuxostat- based anti-inflammatory amide derivatives series were subjected to pharmacophore hypothesis, ligand-based virtual screening, and 3D-QSAR studies in the present work using Schrodinger suite 2022-4. QuikProp module of Schrodinger was used for ADMET prediction, and HTVS, SP, and XP protocols of GLIDE modules were used for molecular docking on target protein (PDB ID:3LN1). Utilising 29 compounds, a five-point model of common pharmacophore hypotheses was created, having pIC50 ranging between 5.34 and 4.871. The top pharmacophore hypothesis AHHRR_ 1 model consists of one hydrogen bond acceptor, two hydrophobic groups and two ring substitution features. The hypothesis model AHHRR_1 underwent ligand-based virtual screening using the molecules from Asinex. Additionally, a 3D-QSAR study based on individual atoms was performed to assess their contributions to model development. The top QSAR model was chosen based on the values of R2 (0.9531) and Q2 (0.9424). Finally, four potential hits were obtained by molecular docking based on virtual screening. The virtual screen compounds have shown similar docking interaction with amino acid residues as shown by standard diclofenac sodium drugs. Therefore, the findings in the present study can be explored in the development of potent anti-inflammatory agents.

In Silico and In Vitro Screening of Some Pregnane Glycosides Isolated from Certain Caralluma Species as SARS-COV-2 Main Protease Inhibitors.

SARS-CoV-2 caused pandemic represented a major risk for the worldwide human health, animal health and economy, forcing extraordinary efforts to discover drugs for its prevention and cure. Considering the extensive interest in the pregnane glycosides because of their diverse structures and excellent biological activities, we investigated them as antiviral agents against SARS-COV-2. We selected 21 pregnane glycosides previously isolated from the genus Caralluma from Asclepiadaceae family to be tested through virtual screening molecular docking simulations for their potential inhibition of SARS-CoV-2 Mpro. Almost all target compounds showed a more or equally negative docking energy score relative to the co-crystallized inhibitor X77 (S=-12.53 kcal/mol) with docking score range of (-12.55 to -19.76 kcal/mol) and so with a potent predicted binding affinity to the target enzyme. The activity of the most promising candidates was validated by in vitro testing. Arabincoside C showed the highest activity (IC50=35.42 μg/ml) and the highest selectivity index (SI=9.9) followed by Russelioside B (IC50=50.80 μg/ml), and Arabincoside B (IC50=53.31 μg/ml).

Identification of Potent Acetylcholinesterase Inhibitors as New Candidates for Alzheimer Disease via Virtual Screening, Molecular Docking, Dynamic Simulation, and Molecular Mechanics-Poisson-Boltzmann Surface Area Calculations.

Huperzine A (HUP) plays a crucial role in Alzheimer's therapy by enhancing cognitive function through increased cholinergic activity as a reversible acetylcholinesterase (AChE) inhibitor. Despite some limitations being seen in AChE inhibitors, ongoing research remains dedicated to finding innovative and more effective treatments for Alzheimer's disease. To achieve the goal of the discovery of potential HUP analogues with improved physicochemical properties, less toxic properties, and high biological activity, many in silico methods were applied. Based on the acetylcholinesterase-ligand complex, an e-pharmacophore model was developed. Subsequently, a virtual screening involving a collection of 1762 natural compounds, sourced from the PubChem database, was performed. This screening yielded 131 compounds that exhibited compatibility with the established pharmacophoric hypothesis. These selected ligands were then subjected to molecular docking within the active site of the 4EY5 receptor. As a result, we identified four compounds that displayed remarkable docking scores and exhibited low free binding energy to the target. These top four compounds, CID_162895946, CID_44461278, CID_44285285, and CID_81108419, were submitted to ADMET prediction and molecular dynamic simulations, yielding encouraging findings in terms of their pharmacokinetic characteristics and stability. Finally, the molecular dynamic simulation, cross-dynamic correlation matrix, free energy landscape, and MM-PBSA calculations demonstrated that two ligands from the selected ligands formed very resilient complexes with the enzyme acetylcholinesterase, with significant binding affinity. Therefore, these two compounds are recommended for further experimental research as possible (AChE) inhibitors.

Identification of a Novel Peptide with Alcohol Dehydrogenase Activating Ability from Ethanol-Induced Lactococcus lactis: A Combined In Silico Prediction and In Vivo Validation.

Alcohol dehydrogenase (ADH) is a crucial rate-limiting enzyme in alcohol metabolism. Our previous research found that ethanol-induced intracellular extracts of Lactococcus lactis (L. lactis) could enhance alcohol metabolism in mice, but the responsible compounds remain unidentified. The study aimed to screen potential ADH-activating peptides from ethanol-induced L. lactis using virtual screening and molecular docking calculation. Among them, the pentapeptide FAPEG might bind to ADH through hydrophobic interaction and hydrogen bonds, then enhancing ADH activity. Spectroscopy analysis further investigated the peptide-enzyme interaction between FAPEG and ADH, including changes in the amino acid residue microenvironment and secondary structural alterations. Furthermore, FAPEG could protect against alcoholic liver injury (ALI) in mice by reducing blood alcohol concentration, enhancing the activity of antioxidant and alcohol metabolism enzymes, and attenuating alcohol-induced hepatotoxicity, which was related to the activation of the Nrf2/keap1/HO-1 signaling pathway. The study provided preliminary evidence that the generation of ADH-activating peptides in ethanol-induced L. lactis has the potential in preventing ALI in mice using in silico prediction and in vivo validation approaches.

Potent, selective and reversible hMAO-B inhibition by benzalphthalides: Synthesis, enzymatic and cellular evaluations and virtual docking and predictive studies

Monoaminooxidases (MAOs) are important targets for drugs used in the treatment of neurological and psychiatric disorders and particularly on Parkinson's Disease (PD). Compounds containing a trans-stilbenoid skeleton have demonstrated good selective and reversible MAO-B inhibition. Here, twenty-two (Z)-3-benzylidenephthalides (benzalphthalides, BPHs) displaying a trans-stilbenoid skeleton have been synthesised and evaluated as inhibitors of the MAO-A and MAO-B isoforms. Some BPHs have selectively inhibited MAO-B, with IC50 values ranging from sub-nM to μM. The most potent compound with IC50 = 0.6 nM was the 3′,4′-dichloro-BPH 16, which showed highly selective and reversible MAO-B inhibitory activity. Furthermore, the most selective BPHs displayed a significant protection against the apoptosis, and mitochondrial toxic effects induced by 6-hydroxydopamine (6OHDA) on SH-SY5Y cells, used as a cellular model of PD. The results of virtual binding studies on the most potent compounds docked in MAO-B and MAO-A were in agreement with the potencies and selectivity indexes found experimentally. Additionally, related to toxicity risks, drug-likeness and ADME properties, the predictions found for the most relevant BPHs in this research were within those ranges established for drug candidates.

High-throughput virtual search of small molecules for controlling the mechanical stability of human CD4

Protein mechanical stability determines the function of a myriad of proteins, especially proteins from the extracellular matrix. Failure to maintain protein mechanical stability may result in diseases and disorders such as cancer, cardiomyopathies, or muscular dystrophy. Thus, developing mutation-free approaches to enhance and control the mechanical stability of proteins using pharmacology-based methods, may have important implications in drug development and discovery. Here, we present the first approach that employs computational High-Throughput Virtual Screening (HTVS) and Molecular Docking to search for small-molecules in chemical libraries that function as mechano-regulators of the stability of human CD4, receptor of HIV-1. Using single-molecule force spectroscopy we prove that these small-molecules can increase the mechanical stability of CD4D1D2 domains over 4-fold in addition to modifying the mechanical unfolding pathways. Our experiments demonstrate that chemical libraries are a source of mechanoactive molecules and that drug discovery approaches provide the foundation of a new type of molecular function, i.e., mechano-regulation, paving the way towards mechanopharmacology.