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Molecular modeling techniques are widely used in medicinal chemistry for the study of biological targets, the rational design of new drugs, or the investigation of their mechanism of action.They are also applied in toxicology to identify chemical potential harmful effects.Molecular docking is a computational technique to predict the ligand binding mode and evaluate the interaction energy with a biological target.This chapter describes a computational workflow to predict possible endocrine disruptors on peroxisome proliferator-activated receptor alpha (PPARα), a nuclear receptor involved in glucose and lipid metabolism. The analyzed compounds are food contact chemicals, natural or synthetic substances intentionally added to food or released from the package or during production or technological processes.
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Simulação de Acoplamento Molecular , PPAR alfa , PPAR alfa/metabolismo , PPAR alfa/química , Ligantes , Disruptores Endócrinos/toxicidade , Disruptores Endócrinos/química , Disruptores Endócrinos/metabolismo , Humanos , Toxicologia/métodos , Ligação ProteicaRESUMO
The pharmacological space comprises all the dynamic events that determine the bioactivity (and/or the metabolism and toxicity) of a given ligand. The pharmacological space accounts for the structural flexibility and property variability of the two interacting molecules as well as for the mutual adaptability characterizing their molecular recognition process. The dynamic behavior of all these events can be described by a set of possible states (e.g., conformations, binding modes, isomeric forms) that the simulated systems can assume. For each monitored state, a set of state-dependent ligand- and structure-based descriptors can be calculated. Instead of considering only the most probable state (as routinely done), the pharmacological space proposes to consider all the monitored states. For each state-dependent descriptor, the corresponding space can be evaluated by calculating various dynamic parameters such as mean and range values.The reviewed examples emphasize that the pharmacological space can find fruitful applications in structure-based virtual screening as well as in toxicity prediction. In detail, in all reported examples, the inclusion of the pharmacological space parameters enhances the resulting performances. Beneficial effects are obtained by combining both different binding modes to account for ligand mobility and different target structures to account for protein flexibility/adaptability.The proposed computational workflow that combines docking simulations and rescoring analyses to enrich the arsenal of docking-based descriptors revealed a general applicability regardless of the considered target and utilized docking engine. Finally, the EFO approach that generates consensus models by linearly combining various descriptors yielded highly performing models in all discussed virtual screening campaigns.
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Simulação de Acoplamento Molecular , Ligantes , Humanos , Ligação Proteica , Proteínas/química , Proteínas/metabolismo , Descoberta de Drogas/métodos , Sítios de LigaçãoRESUMO
The Asclepios suite of KNIME nodes represents an innovative solution for conducting cheminformatics and computational chemistry tasks, specifically tailored for applications in drug discovery and computational toxicology. This suite has been developed using open-source and publicly accessible software. In this chapter, we introduce and explore the Asclepios suite through the lens of a case study. This case study revolves around investigating the interactions between per- and polyfluorinated alkyl substances (PFAS) and biomolecules, such as nuclear receptors. The objective is to characterize the potential toxicity of PFAS and gain insights into their chemical mode of action at the molecular level. The Asclepios KNIME nodes have been designed as versatile tools capable of addressing a wide range of computational toxicology challenges. Furthermore, they can be adapted and customized to accomodate the specific needs of individual users, spanning various domains such as nanoinformatics, biomedical research, and other related applications. This chapter provides an in-depth examination of the technical underpinnings and foundations of these tools. It is accompanied by a practical case study that demonstrates the utilization of Asclepios nodes in a computational toxicology investigation. This showcases the extendable functionalities that can be applied in diverse computational chemistry contexts. By the end of this chapter, we aim for readers to have a comprehensive understanding of the effectiveness of the Asclepios node functions. These functions hold significant potential for enhancing a wide spectrum of cheminformatics applications.
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Descoberta de Drogas , Software , Fluxo de Trabalho , Descoberta de Drogas/métodos , Humanos , Toxicologia/métodos , Quimioinformática/métodos , Biologia Computacional/métodos , Fluorocarbonos/química , Fluorocarbonos/toxicidadeRESUMO
The study examined the antihypertensive effect of peptides derived from pepsin-hydrolyzed corn gluten meal, namely KQLLGY and PPYPW, and their in silico gastrointestinal tract digested fragments, KQL and PPY, respectively. KQLLGY and PPYPW showed higher angiotensin I-converting enzyme (ACE)-inhibitory activity and lower ACE inhibition constant (Ki) values when compared to KQL and PPY. Only KQL showed a mild antihypertensive effect in spontaneously hypertensive rats with -7.83 and - 5.71 mmHg systolic and diastolic blood pressure values, respectively, after 8 h oral administration. During passage through Caco-2 cells, KQL was further degraded to QL, which had reduced ACE inhibitory activity. In addition, molecular dynamics revealed that the QL-ACE complex was less stable compared to the KQL-ACE. This study reveals that structural transformation during peptide permeation plays a vital role in attenuating antihypertensive effect of the ACE inhibitor peptide.
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Inibidores da Enzima Conversora de Angiotensina , Anti-Hipertensivos , Peptidil Dipeptidase A , Zea mays , Animais , Humanos , Masculino , Ratos , Inibidores da Enzima Conversora de Angiotensina/química , Inibidores da Enzima Conversora de Angiotensina/farmacologia , Inibidores da Enzima Conversora de Angiotensina/metabolismo , Anti-Hipertensivos/química , Anti-Hipertensivos/farmacologia , Pressão Sanguínea/efeitos dos fármacos , Células CACO-2 , Digestão/efeitos dos fármacos , Trato Gastrointestinal/metabolismo , Glutens/química , Glutens/metabolismo , Hidrólise , Hipertensão/metabolismo , Hipertensão/tratamento farmacológico , Hipertensão/fisiopatologia , Peptídeos/química , Peptídeos/farmacologia , Peptidil Dipeptidase A/química , Peptidil Dipeptidase A/metabolismo , Hidrolisados de Proteína/química , Hidrolisados de Proteína/farmacologia , Ratos Endogâmicos SHR , Zea mays/química , Zea mays/metabolismoRESUMO
ETHNOPHARMACOLOGICAL RELEVANCE: Thrombosis is a common cause of morbidity and mortality worldwide. Lagopsis supina (Stephan ex Willd.) Ikonn.-Gal. ex Knorring is an ancient Chinese herbal medicine used for treating thrombotic diseases. Nevertheless, the antithrombotic mechanisms and effective constituents of this plant have not been clarified. AIM OF THE STUDY: This work aimed to elucidate the pharmacodynamics and mechanism of L. supina against thrombosis. MATERIALS AND METHODS: Systematic network pharmacology was used to explore candidate effective constituents and hub targets of L. supina against thrombosis. Subsequently, the binding affinities of major constituents with core targets were verified by molecular docking analysis. Afterward, the therapeutic effect and mechanism were evaluated in an arteriovenous bypass thrombosis rat model. In addition, the serum metabolomics analysis was conducted using ultra-high performance liquid chromatography coupled with Q-Exactive mass spectrometry. RESULTS: A total of 124 intersected targets of L. supina against thrombosis were predicted. Among them, 24 hub targets were obtained and their mainly associated with inflammation, angiogenesis, and thrombosis approaches. Furthermore, 9 candidate effective constituents, including (22E,24R)-5α,8α-epidioxyergosta-6,22-dien-3ß-ol, aurantiamide, (22E,24R)-5α,8α-epidioxyergosta-6,9 (11),22-trien-3ß-ol, lagopsinA, lagopsin C, 15-epi-lagopsin C, lagopsin D, 15-epi-lagopsin D, and lagopsin G in L. supina and 6 potential core targets (TLR-4, TNF-α, HIF-1α, VEGF-A, VEGFR-2, and CLEC1B) were acquired. Then, these 9 constituents demonstrated strong binding affinities with the 6 targets, with their lowest binding energies were all less than -5.0 kcal/mol. The antithrombotic effect and potential mechanisms of L. supina were verified, showing a positively associated with the inhibition of inflammation (TNF-α, IL-1ß, IL-6, IL-8, and IL-10) and coagulation cascade (TT, APTT, PT, FIB, AT-III), promotion of angiogenesis (VEGF), suppression of platelet activation (TXB2, 6-keto-PGF1α, and TXB2/6-keto-PGF1α), and prevention of fibrinolysis (t-PA, u-PA, PAI-1, PAI-1/t-PA, PAI-1/u-PA, and PLG). Finally, 14 endogenous differential metabolites from serum samples of rats were intervened by L. supina based on untargeted metabolomics analysis, which were closely related to amino acid metabolism, inflammatory and angiogenic pathways. CONCLUSION: Our integrated strategy based on network pharmacology, molecular docking, metabolomics, and in vivo experiments revealed for the first time that L. supina exerts a significant antithrombotic effect through the inhibition of inflammation and coagulation cascade, promotion of angiogenesis, and suppression of platelet activation. This paper provides novel insight into the potential of L. supina as a candidate agent to treat thrombosis.
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Fibrinolíticos , Metabolômica , Simulação de Acoplamento Molecular , Farmacologia em Rede , Ratos Sprague-Dawley , Trombose , Animais , Fibrinolíticos/farmacologia , Fibrinolíticos/química , Fibrinolíticos/isolamento & purificação , Ratos , Masculino , Trombose/tratamento farmacológico , Medicamentos de Ervas Chinesas/farmacologia , Medicamentos de Ervas Chinesas/químicaRESUMO
ETHNOPHARMACOLOGICAL RELEVANCE: Pogostemonis Herba has long been used in traditional Chinese medicine to treat inflammatory disorders. Patchouli essential oil (PEO) is the primary component of Pogostemonis Herba, and it has been suggested to offer curative potential when applied to treat ulcerative colitis (UC). However, the pharmacological mechanisms of PEO for treating UC remain to be clarified. AIM OF THE STUDY: To elucidate the pharmacological mechanisms of PEO for treating UC. METHODS AND RESULTS: In the present study, transcriptomic and network pharmacology approaches were combined to clarify the mechanisms of PEO for treating UC. Our results reveal that rectal PEO administration in UC model mice significantly alleviated symptoms of UC. In addition, PEO effectively suppressed colonic inflammation and oxidative stress. Mechanistically, PEO can ameliorate UC mice by modulating gut microbiota, inhibiting inflammatory targets (OPTC, PTN, IFIT3, EGFR, and TLR4), and inhibiting the PI3K-AKT pathway. Next, the 11 potential bioactive components that play a role in PEO's anti-UC mechanism were identified, and the therapeutic efficacy of the pogostone (a bioactive component) in UC mice was partially validated. CONCLUSION: This study highlights the mechanisms through which PEO can treat UC, providing a rigorous scientific foundation for future efforts to develop and apply PEO for treating UC.
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Colite Ulcerativa , Óleos Voláteis , Animais , Colite Ulcerativa/tratamento farmacológico , Óleos Voláteis/farmacologia , Camundongos , Masculino , Microbioma Gastrointestinal/efeitos dos fármacos , Modelos Animais de Doenças , Camundongos Endogâmicos C57BL , Anti-Inflamatórios/farmacologia , Pogostemon/química , Estresse Oxidativo/efeitos dos fármacos , Farmacologia em Rede , Colo/efeitos dos fármacos , Colo/metabolismo , Colo/patologiaRESUMO
Mucormycosis is a concerning invasive fungal infection with difficult diagnosis, high mortality rates, and limited treatment options. Iron availability is crucial for fungal growth that causes this disease. This study aimed to computationally target iron uptake proteins in Rhizopus arrhizus, Lichtheimia corymbifera, and Mucor circinelloides to identify inhibitors, thereby halting fungal growth and intervening in mucormycosis pathogenesis. Seven important iron uptake proteins were identified, modeled, and validated using Ramachandran plots. An in-house antifungal library of ~ 15,401 compounds was screened in molecular docking studies with these proteins. The best small molecule-protein complexes were simulated at 100 ns using Maestro, Schrodinger. Toxicity predictions suggested all six molecules, identified as the best binding compounds to seven proteins, belonged to lower toxicity levels per GHS classification. A molecular mechanics GBSA study for all seven complexes indicated low standard deviations after calculating free binding energies every 10 ns of the 100 ns trajectory. Density functional theory via quantum mechanics approaches highlighted the HOMO, LUMO, and other properties of the six best-bound molecules, revealing their binding capabilities and behaviour. This study sheds light on the molecular mechanisms and protein-ligand interactions, providing a multi-dimensional view towards the use of FDBD01920, FDBD01923, and FDBD01848 as stable antifungal ligands. Supplementary Information: The online version contains supplementary material available at 10.1007/s40203-024-00264-7.
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Background: Safflower, phellodendron, scutellaria baicalensis, coptis, and gardenia (SPSCG) are medicinal plants with a wide range of anti-inflammatory and antioxidant effects. However, the related mechanism of SPSCG against hand-foot syndrome (HFS) has yet to be revealed. Objective: To investigate the mechanisms of SPSCG in the treatment of HFS using the Network Pharmacology. Methods: Active ingredients and targets of SPSCG for HFS were screened by the Chinese Medicine Systems Pharmacology (TCMSP) and Swiss Target Prediction databases. Potential therapeutic targets were collected from the GeneCards and OMIM databases. Subsequently, protein-protein interactions (PPI), Gene Ontology (GO) annotations, and pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to investigate the potential mechanism of the SPSCG in HFS. Then, molecular docking and molecular dynamics simulations were performed to predict the binding interactions between the active compound and the core target. Finally, vitro experiments were used to verify the repair effect of key ingredients of SPSCG on cell damage caused by 5-Fluorouracil. Results: Quercetin, kaempferol, ß-sitosterol, and stigmasterol were identified as the major active components of SPSCG. GO analysis showed a total of 1,127 biological processes, 42 terms cellular components, and 57 molecular functions. KEGG analysis showed that the MAPK, TNF, and IL-17 signaling pathways were significantly enriched. The PPI analysis discovered that EGFR, CASP3, AKT1, CCND1, and CTNNB1 shared the highest centrality among all target genes. The experimental results confirmed that these SPSCG active ingredients could treat HFS by reducing inflammation reaction and promoting cell damage repair. Conclusion: SPSCG may alleviate HFS by exerting antioxidative effects and suppressing inflammatory responses.
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Biomolecular interaction acts a pivotal part in understanding the mechanisms underlying the development of Alzheimer's disease (AD). Herein, we built a biosensing platform to explore the interaction between gelsolin (GSN) and different ß-amyloid protein 1-42 (Aß1-42) species, including Aß1-42 monomer (m-Aß), Aß1-42 oligomers with both low and high levels of aggregation (LLo-Aß and HLo-Aß) via dual polarization interferometry (DPI). Real-time molecular interaction process and kinetic analysis showed that m-Aß had the strongest affinity and specificity with GSN compared with LLo-Aß and HLo-Aß. The impact of GSN on inhibiting aggregation of Aß1-42 and solubilizing Aß1-42 aggregates was evaluated by circular dichroism (CD) spectroscopy. The maintenance of random coil structure of m-Aß and the reversal of ß-sheet structure in HLo-Aß were observed, demonstrating the beneficial effects of GSN on preventing Aß from aggregation. In addition, the structure of m-Aß/GSN complex was analyzed in detail by molecular dynamics (MD) simulation and molecular docking. The specific binding sites and crucial intermolecular forces were identified, which are believed to stabilize m-Aß in its soluble state and to inhibit the fibrilization of Aß1-42. Combined theoretical simulations and experiment results, we speculate that the success of GSN sequestration mechanism and the balance of GSN levels in cerebrospinal fluid and plasma of AD subjects may contribute to a delay in AD progression. This research not only unveils the molecular basis of the interaction between GSN and Aß1-42, but also provides clues to understanding the crucial functions of GSN in AD and drives the development of AD drugs and therapeutic approaches.
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Objective: Schizophrenia (SCZ) is a prevalent chronic mental disorder characterized by a high recurrence rate and significant disability. Currently, no satisfactory pharmacological treatments have been identified. Although Ningshen Wendan decoction (NSWDD) has shown promising results in improving cognitive function in patients with schizophrenia, its underlying mechanism of action remains unclear. Methods: This study systematically investigated the mechanisms of NSWDD in SCZ treatment using network pharmacology and molecular docking approaches. Results: Analysis of the interaction genes revealed 307 common targets of NSWDD and SCZ. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated the involvement of multiple signaling pathways including interleukin 17 signaling pathway, multiple virus infections, Advanced glycosylation end products (AGEs) - receptor of AGEs (AGEs-RAGE) signaling pathway, tumor necrosis factor signaling pathway, and Hypoxia-inducible factor-1 (HIF-1) signaling pathway as key pathways influenced by NSWDD in treating SCZ. These pathways are associated with various biological processes such as transcriptional regulation, apoptosis regulation, gene expression regulation, and external stimulus-response. Molecular docking simulations indicated favorable binding interactions between components of NSWDD and target proteins via intermolecular forces. Conclusion: The study provided initial insights into the internal molecular mechanisms underlying the beneficial effect of NSWDD on SCZ through multi-target modulation across multiple pathways.
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INTRODUCTION: Hyperpigmentation disorders are caused by excess production of the pigment melanin, catalyzed by the enzyme tyrosinase. Novel tyrosinase inhibitors are needed as therapeutic agents to treat these conditions. METHOD: To discover new inhibitors, we performed a virtual screening of the ZINC20 library containing 1.4 billion compounds. An initial filter for drug-likeness, ADMET properties, and synthetic accessibility reduced the library to 10,217 hits. Quantitative structure-activity relationship (QSAR) modeling of this subset predicted nanomolar inhibitory potency for several chemical scaffolds. Comparative molecular docking studies and rigorous binding energy calculations further prioritized four cysteine-containing dipeptide compounds based on predicted strong binding affinity and mode to tyrosinase. RESULTS: Microsecond-long molecular dynamics simulations provided additional atomistic insights into the stability of inhibitor-enzyme binding interactions. This integrated computational workflow effectively sampled an extremely large chemical space to discover four novel tyrosinase inhibitors with half-maximal inhibitory concentration values below 10 nM. CONCLUSION: Overall, this demonstrates the power of virtual screening and multi-faceted computational techniques to accelerate the discovery of potent bioactive ligands from massive compound libraries by efficiently sampling chemical space.
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Ovarian cancer stands as the foremost cause of mortality among gynaecological diseases globally, characterized by high morbidity and mortality. Pinocembrin, a flavonoid from natural plant sources, exhibits diverse pharmacological properties. Despite its known pharmacological activities, its specific role in ovarian cancer treatment remains scarcely reported, and its precise molecular mechanism remains elusive. This study integrates network pharmacology and molecular docking techniques to explore pinocembrin's potential mechanism in ovarian cancer treatment. The targets of pinocembrin were compiled from the several online databases. Ovarian cancer targets were identified using the GeneCards database, with common target genes determined by data aggregation. Protein-protein interactions were analysed using the STRING platform. Subsequent Gene Ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed. Molecular docking assessed the binding affinity between potential targets and active compounds. Finally, target validity was verified through in vitro experiments. We identified 163 potential pinocembrin targets for ovarian cancer treatment. GO and KEGG analyses revealed pinocembrin's involvement in protein kinase activity, protein phosphorylation, protein kinase complexes and cancer pathways in ovarian cancer treatment. Molecular docking demonstrated strong binding affinity between pinocembrin and most potential target active sites. In vitro experiments suggested pinocembrin's potential to induce apoptosis in ovarian cancer cells through the AKT1-mTOR signalling pathway. This study comprehensively elucidates pinocembrin's potential targets and mechanisms against ovarian cancer, aiming to provide promising candidates for developing novel and effective alternative and/or complementary nutritional supplements for the clinical treatment of ovarian cancer.
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BACKGROUND: Masticatory myofascial pain syndrome (MMPS) is a soft tissue inflammatory disorder that leads to acute or chronic localized pain and stiffness in the muscles. Catechol-O-methyltransferase (COMT) plays a crucial role in mediating pain perceptions in humans by transferring methyl groups to catecholamines. This process requires adequate S-adenosyl methionine (SAMe). A reduction in SAMe leads to COMT inhibition. Boswellia serrata possesses multiple therapeutic benefits and is used for treating chronic pain. AIM: The study aimed to evaluate the therapeutic potential of acetyl-11-keto-beta-boswellic acid (AKBA) by targeting COMT. Methodology: Molecular docking and dynamic simulations were conducted using Desmond software from Schrödinger LLC, USA, to evaluate the interaction between COMT protein and AKBA ligands. The COMT protein structure was sourced from the Protein Data Bank and preprocessed using optimized potentials for liquid simulations. Molecular docking identified potential binding sites between COMT and AKBA through hydrogen bonding, resulting in a docking score of -6.0 kcal/mol. RESULTS: The molecular docking revealed a docking score of -6.0 kcal/mol for the interaction between COMT and AKBA. The dynamic simulation demonstrated that the COMT-AKBA complex remained stable within a 3.0 Angstrom range over 60 nanoseconds. These findings indicate stable natural small molecular interactions between COMT and AKBA. CONCLUSION: AKBA exhibits potential as a therapeutic agent for MMPS, demonstrating stable interactions with COMT. These findings warrant further in vitro and in vivo analyses to confirm efficacy.
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We investigated the hypoglycemic activity and pharmacokinetic study of two synthesized benzoyl benzodioxol derivatives, compound I (methyl 2-(6-(2-bromobenzoyl)benzo[d][1,3]dioxol-5-yl)acetate), and compound II, 2-(6-benzoylbenzo[d][1,3]dioxol-5-yl)acetic acid, which showed very strong α-amylase inhibiting activity in our previous study. Then, diabetes was induced by the injection of streptozotocin to mice. The molecular docking simulations and analyses of density functional theory analyses were conducted to study the binding interactions with human pancreatic alpha-amylase, and their pharmacokinetic properties were further evaluated by ADMET profiling. Compound I showed the most important hypoglycemic effect, decreasing the blood glucose by 32.4%, higher than that of compound II by 14.8% and even the positive control acarbose by 22.9%. Histopathological examination revealed that diabetic livers showed portal inflammation with some apoptotic hepatocytes due to streptozotocin treatment, whereas controls without any treatment maintained normal liver architecture. Molecular docking studies gave results for the best binding affinity of the compound I, through its strong water bridges and π-π interactions, and also through analysis with density functional theory, was more stable and reactive when compared to compound II. Further ADMET analysis showed that both compounds shared a promising pharmacokinetic profile, and compound I had the potential for CNS penetration. Thus, compound I was selected as the best candidate for developing new hypoglycemic agents with potent efficacy, good binding interactions, and excellent pharmacokinetic properties.
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Farnesol is a natural acyclic sesquiterpene alcohol, found in various essential oils such as, lemon grass, citronella, tuberose, neroli, and musk. It has a molecular mass of 222.372 g/mol and chemical formula of C15H26O. The main objective of this study was to assess the effect of farnesol on mTOR and its two downstream effectors, p70S6K and eIF4E, which are implicated in the development of cancer, via molecular dynamic simulation, and docking analysis in an in silico study. A multilayer, primarily computer-based analysis was conducted to assess farnesol's anticancer potential, with a focus on primary cancer targets. From the calculations performed, farnesol showed a binding affinity of - 9.66 kcal/mol, followed by binding affinity of - 7.4 kcal/mol and - 7.8 kcal/mol for mTOR, p70S6K and eIF4E respectively. Rapamycin showed the binding affinity of - 10.45 kcal/mol for mTOR, for p70S6K and eIF4E the calculated binding affinity was - 10.65 kcal/mol and 8.16 kcal/mol respectively. The binding affinity of farnesol was comparable to the standard drug rapamycin indicating its potential as an mTOR inhibitor. Molecular dynamics simulations suggest that the ligands (farnesol and rapamycin) were well trapped within the active site of the protein over a time gap of 50 ns. It is clear that farnesol showed relatively stable MD simulation results, with minor fluctuations and maintains a consistent binding orientation, suggesting a strong and stable interaction with the target proteins when compared to simulation data of standard drug. This study explores the potential of farnesol as an anticancer agent through an in-silico approach, focusing on its interaction with mTOR and its downstream effectors. Inhibition of mTOR signaling pathway may be responsible for the anticancer effect of farnesol. As this pathway plays a crucial role in cell proliferation and survival, making it a significant target in cancer research.
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Background: Current treatments and prevention strategies for echinococcosis are inadequate. Recent advancements in molecular vaccine development show promise against Echinococcus granulosus; however, Echinococcus multilocularis remains a challenge. A Multi-epitope Vaccine could potentially induce specific B and T lymphocyte responses, thereby offering protection against Echinococcus multilocularis infection. Methods: This study aimed to develop a MEV against alveolar echinococcosis. Key epitopes from the Echinococcus multilocularis proteins EmTSP3 and EmTIP were identified using immunoinformatics analyses. These analyses were conducted to assess the MEV feasibility, structural characteristics, molecular docking, molecular dynamics simulations, and immune simulations. The immunogenicity and antigenicity of the vaccine were evaluated through in vitro and in vivo experiments, employing ELISA, Western blotting, FCM, challenge infection experiments, and ELISPOT. Results: The effective antigenicity and immunogenicity of MEV were demonstrated through immunoinformatics, as well as in vitro and in vivo experiments. In vitro experiments revealed that MEV increased the secretion of IFN-γ and IL-4 in PBMC and successfully bound to specific antibodies in patient serum. Furthermore, mice immunized with MEV developed a robust immune response, characterized by elevated levels of CD4+ and CD8+ T-cells, increased secretion of IFN-γ and IL-4 by specific Th1 and Th2 cells, and heightened serum antibody levels. Importantly, MEV reduced the weight of cysts by conferring resistance against echinococcosis. These findings suggest that MEV is a promising candidate for the prevention of Echinococcus multilocularis infection. Conclusion: A total of 7 CTL, 7 HTL, 5 linear B-cell, and 2 conformational B-cell epitopes were identified. The vaccine has demonstrated effective antigenicity and immunogenicity against AE through molecular docking, immune simulation, molecular dynamics studies, and both in vitro and in vivo experiments. It provides effective protection against Echinococcus multilocularis infection, thereby laying a foundation for further development.
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Antígenos de Helmintos , Equinococose , Echinococcus multilocularis , Animais , Echinococcus multilocularis/imunologia , Equinococose/prevenção & controle , Equinococose/imunologia , Camundongos , Antígenos de Helmintos/imunologia , Humanos , Vacinas/imunologia , Proteínas de Helminto/imunologia , Proteínas de Helminto/química , Feminino , Anticorpos Anti-Helmínticos/imunologia , Anticorpos Anti-Helmínticos/sangue , Camundongos Endogâmicos BALB C , Epitopos de Linfócito T/imunologia , Simulação de Acoplamento Molecular , Epitopos de Linfócito B/imunologiaRESUMO
BACKGROUND: Diabetic wound healing poses a significant challenge due to the intricate disruptions in cellular and molecular processes induced by hyperglycaemia, leading to delayed or impaired tissue repair. Computational techniques offer a promising avenue for unravelling the complexities of diabetic wound healing by elucidating the molecular mechanisms involved. METHODOLOGY: This study utilized in silico molecular docking and dynamics simulations to explore the potential therapeutic effectiveness of olivetol, a phenolic compound, in the context of diabetic wound healing. Furthermore, computational methodologies, encompassing pkCSM, Swiss ADME, OSIRIS® property explorer, PASS online web resource, and MOLINSPIRATION® software, were employed to forecast the pharmacokinetic properties, biological actions, and in vitro analyses, such as MTT and scratch assays, to evaluate the therapeutic effectiveness of olivetol in wound healing. RESULTS AND DISCUSSION: Our findings have revealed olivetol to be a promising candidate for targeting multiple pathways implicated in diabetic wound healing. Its ability to modulate inflammation, oxidative stress, extracellular matrix remodeling, angiogenesis, and cell signaling suggests a multifaceted approach to promoting effective wound repair. Moreover, olivetol has been found to demonstrate strong binding affinity with key MRSA target proteins, indicating its potential as an antimicrobial agent against MRSA infections in diabetic wounds. The in vitro MTT assay demonstrated cell viability with an IC50 value of 40.80 µM, highlighting its cytotoxicity potential. Additionally, the scratch assay confirmed promising wound healing activity, showcasing its effectiveness in promoting cell migration and closure. CONCLUSION: Olivetol emerges as a promising candidate for targeted interventions in non-healing diabetic wounds, particularly due to its ability to address prolonged inflammation, a common obstacle in diabetic wound healing.
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BACKGROUND: Nitric Oxide (NO) has recently gained recognition as a promising approach in the field of cancer therapy. The quinoline scaffold is pivotal in cancer drug research and is known for its versatility and diverse mechanisms of action. OBJECTIVE: This study presents the synthesis, characterization, and evaluation of novel quinoline nitrate derivatives as potential anticancer agents. METHODS: The compounds were synthesized through a multi-step process involving the preparation of substituted 1-(2-aminophenyl) ethan-1-one, followed by the synthesis of substituted 2- (chloromethyl)-3,4-dimethylquinolines, and finally, the formation of substituted (3,4- dimethylquinolin-2-yl) methyl nitrate derivatives. The synthesized compounds were characterized using various spectroscopic techniques. Molecular docking studies were conducted to assess the binding affinity of the compounds to the EGFR tyrosine kinase domain. RESULTS: The docking scores revealed varying degrees of binding affinity, with compound 6k exhibiting the highest score. The results suggested a correlation between molecular docking scores and anticancer activity. Further evaluations included MTT assays to determine the cytotoxicity of the compounds against Non-Small Cell Lung Cancer (A-549) and pancreatic cancer (PANC-1) cell lines. Compounds with electron-donating groups displayed notable anticancer potential, and there was a correlation between NO release and anticancer activity. The study also investigated nitric oxide release from the compounds, revealing compound 6g as the highest NO releaser. CONCLUSION: The synthesized quinoline nitrate derivatives showed promising anticancer activity, with compound 6g standing out as a potential lead compound. The correlation between molecular docking, NO release, and anticancer activity suggests the importance of specific structural features in the design of effective anticancer agents.
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Human Immunodeficiency Virus (HIV) has become an epidemic causing Acquired Immunodeficiency Syndrome (AIDS). Highly active antiretroviral therapy (HAART) consists of Nucleoside Reverse Transcriptase Inhibitors (NRTIS), Nucleotide Reverse Transcriptase Inhibitors (NtRTIS), and Non- Nucleoside Reverse Transcriptase Inhibitors (NNRTIS) with HIV Protease Inhibitors (HIV PIs). However, the emergence of resistant strains of NNRTIS necessitates the search for better HIV-1-RT inhibitors. METHODS: In this study, a series of novel imidazoles (SP01-SP30) was designed using molecular docking inside the non-nucleoside inhibitory binding pocket (NNIBP) of the HIV-1-RT (PDB ID-1RT2) using Glide v13.0.137, Autodock Vina, and FlexX v2.1.3. Prime MMGBSA was used to study the free energy of binding of the inhibitors with the target enzyme. Molecular dynamics simulation studies were carried out to discover the dynamic behavior of the protein as well as to unveil the role of the essential amino acids required for the better binding affinity of the inhibitor within the NNIBP of the enzyme. The QikProp software module of Schrodinger and online SwissADME were also used to evaluate the drug-likeliness of these compounds. RESULTS: The imidazole derivative SP08 is predicted to be the most promising design compound that can be considered for further synthetic exploitations to obtain a molecule with the highest therapeutic index against HIV-1-RT. CONCLUSION: The results of the current study demonstrate the robustness of our in-silico drug design strategy that can be used for the discovery of novel HIV-1-RT inhibitors.
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BACKGROUND: Recent epidemic survey data have revealed a globally increasing prevalence of autism spectrum disorders (ASDs). Currently, while Western medicine mostly uses a combination of comprehensive intervention and rehabilitative treatment, patient outcomes remain unsatisfactory. Polygala-Acorus, used as a pair drug, positively affects the brain and kidneys, and can improve intelligence, wisdom, and awareness; however, the underlying mechanism of action is unclear. OBJECTIVES: We performed network pharmacology analysis of the mechanism of Polygala-Acorus in treating ASD and its potential therapeutic effects to provide a scientific basis for the pharmaceutical's clinical application. METHODS: The chemical compositions and targets corresponding to Polygala-Acorus were obtained using the Traditional Chinese Medicine Systematic Pharmacology Database and Analysis Platform, Chemical Source Website, and PharmMapper database. Disease targets in ASD were screened using the DisGeNET, DrugBank, and GeneCards databases. Gene Ontology functional analysis and metabolic pathway analysis (Kyoto Encyclopedia of Genes and Genomes) were performed using the Metascape database and validated via molecular docking using AutoDock Vina and PyMOL software. RESULTS: Molecular docking analysis showed that the key active components of Polygala- Acorus interacted with the following key targets: EGFR, SRC, MAPK1, and ALB. Thus, the key active components of Polygala-Acorus (sibiricaxanthone A, sibiricaxanthone B tenuifolin, polygalic acid, cycloartenol, and 8-isopentenyl-kaempferol) have been found to bind to EGFR, SRC, MAPK1, and ALB. CONCLUSION: This study has preliminarily revealed the active ingredients and underlying mechanism of Polygala-Acorus in the treatment of ASD, and our predictions need to be proven by further experimentation.