Molecular docking, molecular dynamics simulation, and ADMET analysis of levamisole derivatives against the SARS-CoV-2 main protease (MPro)

Levamisole, as a viral vaccine adjuvant, induces robust host defense through the modulation of innate and adaptive immune responses

Introduction

An effective vaccination policy must be implemented to prevent foot-and-mouth disease (FMD). However, the currently used vaccines for FMD have several limitations, including induction of humoral rather than cellular immune responses.

Methods

To overcome these shortcomings, we assessed the efficacy of levamisole, a small-molecule immunomodulator, as an adjuvant for the FMD vaccine. We conducted in vitro studies using murine peritoneal exudate cells (PECs) and porcine peripheral blood mononuclear cells (PBMCs) and in vivo studies using mice (experimental animals) and pigs (target animals). We evaluated levamisole-mediated modulation of the innate and adaptive immune responses; early, mid-term, and long-term immune-inducing effects; modes of action; and host defense against viral infection.

Results

Levamisole treatment promoted IFNγ secretion in murine PECs and porcine PBMCs. Additionally, it induced robust and long-lasting immune responses by eliciting high antibody titers and high virus-neutralizing antibody titers. By activating downstream signaling pathways of various pattern-recognition receptors, levamisole stimulated the expression of multiple cytokines and costimulatory molecules. Owing to these immunostimulatory effects, levamisole elicited host defense against viral infections in pigs. Our findings demonstrate the potential of levamisole as an immunostimulatory agent.

Discussion

The results also indicate that levamisole, as an adjuvant for animal vaccines, can elicit robust innate and adaptive immune responses, thereby enhancing host defense against viral infections. This study provides a promising approach for the development of improved FMD vaccine strategies in the future.

Computational-driven discovery of AI-2 quorum sensing inhibitor targeting the 5'- methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) to combat drug-resistant Helicobacter pylori

MTAN is an attainable therapeutic target for H. pylori because it may minimize virulence production, limit resistance, and impair quorum sensing without affecting gut flora. Here, 457 compounds with anti-H. pylori activity were methodically analyzed, revealing a diverse array of chemical classes and unique compounds. Molecular docking studies identified three potential compounds with high binding affinities, Dehydrocostus lactone, keramamine B, and ZINC00013531409, each having binding affinity of -7.9, -9.2, and -8.3 kcal/mol, respectively. Molecular dynamics simulations of the ZINC00013531409-MTAN interactions in comparison with Apo-MTAN demonstrated stability and interactions of 300 ns, with key residues involved in protein-ligand binding illuminated. Analysis of hydrogen bonds (Ile52, Met174, and Arg194) and secondary structure variations further elucidated the binding interactions and conformational changes within the complex. Binding free energy calculations shed light on the energetics and interactions governing the complex formation of the ZINC00013531409-MTAN complex. PCA elucidated the dominant modes of motion, along with FEL revealed the energetically favorable states and then DCCM shed light on the correlated motions between residues. Overall, this study offers a detailed computational evaluation of ZINC00013531409 with anti-H. pylori activity, highlighting toxicity profile, conformational stability, and binding interactions, providing a foundation for further drug development efforts toward bacterial resistance.

Computational studies and structural insights for discovery of potential natural aromatase modulators for hormone-dependent breast cancer

Introduction

The aromatase enzyme plays an important role in the progress of hormone-dependent breast cancer, especially in estrogen receptor-positive (ER+) breast cancers. In case of postmenopausal women, the aromatization of androstenedione to estrone in adipose tissue is the most important source of estrogen. Generally 60%-75% of pre- and post-menopausal women suffer from estrogen-dependent breast cancer, and thus suppressing estrogen has been recognized to be a successful therapy. Hence, to limit the stimulation of estrogen, aromatase inhibitors (AIs) are used in the second-line treatment of breast cancer.

Methods

The present computational study employed an in silico approach in the identification of natural actives targeting the aromatase enzyme from a structurally diverse set of natural products. Molecular docking, QSAR studies and pharmacophore modeling were carried out using the VLife Molecular Design Suite (version 4.6). The stability of the compounds was confirmed by molecular dynamics.

Results

From molecular docking and analysis of interactions with the amino acid residues of the binding cavity, it was found that the amino acid residues interacting with the non-steroidal inhibitors exhibited π-stacking interactions with PHE134, PHE 221, and TRP 224, while the steroidal drug exemestane lacked π-stacking interactions. QSAR studies were performed using the flavonoid compounds, in order to identify the structural functionalities needed to improve the anti-breast cancer activity. Molecular dynamics of the screened hits confirmed the stability of compounds with the target in the binding cavity. Moreover, pharmacophore modelling presented the pharmacophoric features of the selected scaffolds for aromatase inhibitory activity.

Conclusion

The results presented 23 hit compounds that can be developed as anti-breast cancer modulating agents in the near future. Additionally, anthraquinone compounds with minor structural modification can also serve to be potential aromatase inhibitors. The in silico protocol utilised can be useful in the drug discovery process for development of new leads from structurally diverse set of natural products that are comparable to the drugs used clinically in breast cancer therapy.

The potential immunomodulatory effect of levamisole in humans and farm animals

This study conducted a literature review to investigate the immunomodulatory effect of levamisole in both humans and farm animals. The following procedure was followed for database searching: PubMed, Google Scholar, Web of Science, and Cochrane Library. All research works were updated to September 2022. The terms used in the literature search were included: ("levamisole" OR "immunity" OR "immune system") AND ("adjuvant" OR "fish" OR "poultry" OR "farm animal" OR "cattle" OR "sheep"). The current review enlightens the extensive potential of levamisole as an adjuvant immunotherapeutic agent and explains its divergent applications beyond its antiparasitic use as an adjuvant, dietary supplement, immunostimulant, antiviral, and anti-cancer drug in humans and farm animals. In the articles examined, various mechanisms have been proposed for levamisole immunoprotective effects, but hormonal alteration and stress hormone reduction are indicated as the main mechanisms in various animal species.

Identification of active compounds of traditional chinese medicine derived from maxing shigan decoction for COVID-19 treatment: a meta-analysis and in silico study

BACKGROUND

Coronavirus 2019 (COVID-19) poses a serious threat to human health. In China, traditional Chinese medicine (TCM), mainly based on the Maxing Shigan decoction (MXSGD), is used in conjunction with western medicine to treat COVID-19.

RESEARCH DESIGN AND METHODS

We conducted a network meta-analysis to investigate whether MXSGD-related TCM combined with western medicine is more effective in treating COVID-19 compared to western medicine alone. Additionally, using network pharmacology, cross-docking, and molecular dynamics (MD) simulation to explore the potential active compounds and possible targets underlying the therapeutic effects of MXSGD-related TCM.

RESULTS

MXSGD-related TCM combined with western medicine was better for treating COVID-19 compared to western medicine alone. Network pharmacological analysis identified 43 shared ingredients in the MXSGD-related TCM prescriptions and 599 common target genes. Cross-docking of the 43 compounds with 154 proteins that matched these genes led to the identification of 60 proteins. Pathway profiling revealed that the active ingredients participated in multiple signaling pathways that contribute to their efficacy. Molecular docking and MD simulation demonstrated that MOL007214, the most promising molecule, could stably bind to the active site of SARS-CoV-2 3CLpro.

CONCLUSION

This study demonstrates the important role of MXSGD-related TCM in the treatment of COVID-19.

Discover the Medication Potential of Algerian Medicinal Plants Against Sars-Cov-2 Main Protease (Mpro): Molecular Docking, Molecular Dynamic Simulation, and ADMET Analysis

At the end of 2019, the world faced a big challenge and crisis caused by the SARS-CoV-2 virus. It spreads rapidly and is contagious; no treatment has officially been found. Algeria has used medicinal plants native to the country to defend against this pandemic. The objective of this paper is based on a molecular docking study of the active compounds of five Algerian medicinal plants with their target Sars-2Cov-2 virus protease to assess their potential antiviral activity against COVID-19. Innovative software and computerized databases were introduced into the in-silico domain, mainly the Auto-Dock software version 1.5.6. Similar results were obtained for all ligands, with a better chemical affinity of − 5.600 kcal/mol for the protease target 6LU7 and − 5.700 kcal/mol for the protease target 6WTT, with an average of − 4.227 kcal/mol and − 4.221 kcal/mol, respectively. The protease targets 6LU7 and 6WTT. In the ADME-Tox study, the active compounds of Algerian medicinal plants also demonstrated an excellent pharmacokinetic and toxic profile. Best scores were noted for cedrol, camphor, and eucalyptol. A molecular dynamics simulation showed the stability of camphor-6LU7 and cedrol-6LU7 complexes, favoring the biological potential of white artemisia and cypress plants.

Computational approach investigation bioactive molecules from Saussurea Costus plant as SARS-CoV-2 main protease inhibitors using reverse docking, molecular dynamics simulation, and pharmacokinetic ADMET parameters

SARS-COV-2 virus causes (COVID-19) disease; it has become a global pandemic since 2019 and has negatively affected all aspects of human life. Scientists have made great efforts to find a reliable cure, vaccine, or treatment for this emerging disease. Efforts have been directed towards using medicinal plants as alternative medicines, as the active chemical compounds in them have been discovered as potential antiviral or anti-inflammatory agents. In this research, the potential of Saussurea costus (S. Costus) or QUST Al Hindi chemical consistent as potential antiviral agents was investigated by using computational methods such as Reverse Docking, ADMET, and Molecular Dynamics with different proteases COVID-19 such as PDB: 2GZ9; 6LU7; 7AOL, 6Y2E, 6Y84. The results of Reverse Docking the complex between 6LU7 proteases and Cynaropicrin compound being the best complex, as the same result, is achieved by molecular dynamics. Also, the toxicity testing result from ADMET method proved that the complex is the least toxic and the safest possible drug. In addition, 6LU7-Cynaropicrin complex obeyed Lipinski rule; it formed ≤5 H-bond donors and ≤10 H bond acceptors, MW < 500 Daltons, and octanol/water partition coefficient <5.

Molecular dynamics studies reveal structural and functional features of the SARS-CoV-2 spike protein

The SARS-CoV-2 virus is responsible for the COVID-19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new affliction. One of these methods, namely molecular dynamics (MD), has been used to characterize the function of the spike protein at the atomic level and unveil its structural features from a dynamic perspective. In this review, we focus on these main findings, including spike protein flexibility, rare S protein conformational changes, cryptic epitopes, the role of glycans, drug repurposing, and the effect of spike protein variants.