Molecular dynamics simulation approach for discovering potential inhibitors against SARS-CoV-2: A structural review

Phytochemical Analysis, Computational Study, and in vitro Assay of Etlingera elatior Inflorescence Extract Towards Inducible Nitric Oxide Synthase

Background

Overproduction of nitric oxide (NO), catalyzed by inducible nitric oxide synthase (iNOS), in the gastric mucosa, contributes to the inflammatory process caused by oxidative stress. Current medications for gastric ulcers, such as proton pump inhibitors and histamine-2 receptor antagonists, have been reported to generate adverse reactions.

Purpose

To obtain the phytochemical profile of Etlingera elatior inflorescence extract, computational studies, and in vitro assay of the extract towards iNOS.

Methods

Fresh E. elatior inflorescence petals collected from West Java, Indonesia, were extracted using ethanol, and their nutritional composition, anthocyanin content, and levels of vitamin C, C3G, and quercetin in the extract were determined. Drug-likeness and ADMET properties were predicted, and the binding affinity and stability of the phytoconstituents towards iNOS were studied using molecular docking and molecular dynamic simulation, and in vitro assay of the extract towards human iNOS.

Results

The extract contains protein 21.81%, fat 0.99%, carbohydrate 38.27%, water 24.56%, and ash 14.37%. The total anthocyanin and vitamin C levels were 47.535 mg/100 g and 985.250 mg/100 g, respectively. The levels of C3G and quercetin were 0.0007% w/w, 0.004% w/w, and 0.0005% w/w, respectively. Drug-likeness and ADMET properties of the constituents showed that most followed Lipinski Rules of Five (Ro5), with few violations. All phytoconstituents occupied the catalytic site by binding to Glu377, and Trp372, similar to S-ethylisothiourea (SEITU) and quinazoline, the iNOS inhibitors. Among these, the flavylium cation of cyanidin, demethoxycurcumin, C3G, cyanidin, and quercetin showed the best binding affinities. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (Rg) graphs confirmed the stability of the complexes. E. elatior inflorescence extract inhibited human iNOS with an IC50 value of 24.718 µg/mL.

Conclusion

Etlingera elatior inflorescence may inhibit iNOS activity due to its anthocyanin and flavonoid content. The flavylium cation of cyanidin, demethoxycurcumin, C3G, cyanidin, and quercetin play leading roles in the interaction with iNOS.

Combination of citrus peel-derived essential oils with acarbose to inhibit amylolytic enzymes - A potential type II diabetes treatment approach

Type 2 diabetes (T2D) can be managed by inhibiting amylolytic enzymes, α-amylase and α-glucosidase, reducing the impact of dietary carbohydrates on blood glucose elevation. Acarbose, a current α-glucose inhibitor (AGI), has excessive α-amylase inhibition, resulting in side effects associated with large amounts of undigested starch being fermented in the colon. This study evaluated the AGI efficacy of citrus peel-derived essential oils, where they were first tested in silico against the target amylolytic enzymes, and then their AGI activity was tested in vitro. The synergistic effects of the essential oils with acarbose against amylolytic enzymes were also determined. In silico and in vitro data of the efficacy of the essential oils as AGIs correlated positively; lower Ki values correlated with more negative binding affinity. Furthermore, molecular dynamic simulations of the most potent compounds were evaluated and indicated relative flexibility and stability induced upon ligand interactions with the protein. The standard AGI drug, acarbose, had the lowest Ki (0.10 ± 0.01 mg/mL) and more negative binding affinity (-7.5 kcal/mol) than the essential oils for α-glucosidase; however, the essential oils only showed potent inhibition against α-glucosidase, with the most potent essential oils being valencene (Ki = 0.33 ± 0.04 mg/mL), carveol (Ki = 0.53 ± 0.02 mg/mL) and geraniol (Ki = 0.56 ± 0.02 mg/mL). The essential oils and acarbose displayed competitive inhibition of α-glucosidase. Furthermore, a combination of acarbose with carveol or geraniol at a ratio of 12.5 μg/mL: 2 mg/mL exhibited antagonistic (CI > 10) and synergistic (CI < 0.7) effects on α-amylase and α-glucosidase inhibition, respectively. Carveol or geraniol can be considered as potentially therapeutic in managing T2D, as it may display lowered AGI-associated side effects.

Comprehensive bioinformatics analysis of selected germline variants of uncertain significance identified in a cohort of Sri Lankan hereditary breast cancer patients

BACKGROUND

Next-generation sequencing (NGS)-based testing is a cost-effective method for identifying pathogenic germline genetic variations in cancer-predisposing genes in hereditary breast cancer. However, many of the variants detected through NGS are classified as variants of uncertain significance (VUS), where the impact of the variants on protein function remains unclear. Bioinformatics analysis using multiple computational tools is postulated to aid in generating new knowledge regarding the functional relevance of these VUS. This study aimed to gain new insights into the potential pathogenicity of a selected set of VUS identified in a cohort of Sri Lankan hereditary breast cancer patients using advanced bioinformatics tools.

METHODS

The cancer database at the Centre for Genetics and Genomics contains genomic and clinical data from patients who had undergone germline genetic testing between 2015 and 2023. Five germline VUS detected in breast cancer affected patients were identified from the existing database and selected for further bioinformatics analysis using a combination of in-silico pathogenicity prediction tools, 3D protein modeling with structural analysis, and protein structural stability assessment with molecular dynamic simulation (MDS). The VUS included: BRCA1:(NM_007294.4):c.3392A > G;p.Asp1131Gly, (rs1555587813); BRIP1:(NM_032043.3):c.3103C > T;p.Arg1035Cys, (rs45437094); CHEK2:(NM_007194.4):c.60G > T;p.Gln20His, (rs375507194); MET:(NM_000245.4):c.840G > T;p.Arg280Ser, (rs1207381066); and STK11:(NM_000455.5):c.355A > G;p.Asn119Asp, (rs545015076).

RESULTS

Two variants MET:(NM_000245.4):c.840G > T;p.Arg280Ser and BRCA1:(NM_007294.4):c.3392A > G; p.Asp1131Gly are predicted to have high-risk potential for causing significant impacts on the protein structure and function. Align GVGD results and the MDS data for the BRIP1:(NM_032043.3):c.3103C > T;p.Arg1035Cys variant suggested some alterations that require further confirmation. The CHEK2:(NM_007194.4):c.60G > T;p.Gln20His variant suggested an intermediate impact, whereas STK11:(NM_000455.5):c.355A > G;p.Asn119Asp suggested no significant structural or functional impact on the protein.

CONCLUSIONS

This study contributes valuable insights into the potential structural and functional implications of five VUS in cancer predisposition genes. Our results suggest a high-risk potential for variants in MET, BRCA1 and BRIP1, warranting further investigation to delineate their exact biological effects and to better understand their role in breast cancer risk.

Assessing the molecular interaction between a COVID-19 drug, nirmatrelvir, and human serum albumin: calorimetric, spectroscopic, and microscopic investigations

The research examined the molecular interaction between nirmatrelvir (NIR), a drug used to treat COVID-19, and human serum albumin (HSA) using various techniques, viz., isothermal titration calorimetry (ITC), absorption, fluorescence, CD spectroscopy, and atomic force microscopy (AFM). ITC analysis showed that the NIR-HSA system possessed a moderate binding affinity, with a K a value of 6.53 ± 0.23 × 104 M-1 at a temperature of 300 K. The thermodynamic values demonstrated that the NIR-HSA complex was stabilized by hydrophobic contacts, hydrogen bonds, and van der Waals forces. The research also discovered modifications in the UV-Vis absorption spectrum of the protein as well as swelling of the HSA molecule when exposed to NIR, based on AFM results. The three-dimensional fluorescence spectral data indicated changes in the microenvironment around HSA's Trp and Tyr residues. Alterations in the protein structure (both secondary and tertiary structures) of HSA after NIR binding were verified using CD spectral studies in the far-UV and near-UV regions. The identification of the NIR binding site in subdomain IB (Site III) of HSA was predicted through competitive displacement experiments.

Molecular modelling and experimental validation of mangiferin and its related compounds as quorum sensing modulators of Pseudomonas aeruginosa

The LasR quorum sensing system regulates the virulence factors of Pseudomonas aeruginosa, a multi-drug resistant pathogen. Mangiferin and related compounds have been found to modulate this system as determined by in silico and in vitro experimental procedures. ZINCPharmer was used to compile a library of over 1000 metabolites that were screened to the top five based on shared pharmacophores and drug-like properties with mangiferin. Molecular docking and molecular dynamics simulation (140 ns) showed that ZINC E (- 55.64 ± 2.93 kcal/mol) and ZINC D (- 54.51 ± 2.82 kcal/mol) had significantly lower binding free energy compared to mangiferin-LasR (- 42.24 ± 3.94 kcal/mol) and the reference standard (azithromycin-LasR (- 40.01 ± 6.15 kcal/mol). ZINC D (95.16%) competed favorably with mangiferin (95.77%) as potential QS modulators at sub-minimum inhibitory concentrations relative to ZINC E (85.07%) and azithromycin (85.79%). These observations suggest mangiferin and related lead compounds as potential drug candidates for P. aeruginosa infection management.

Virtual Screening, Toxicity Evaluation and Pharmacokinetics of Erythrina Alkaloids as Acetylcholinesterase Inhibitor Candidates from Natural Products

Purpose

Alzheimer's disease (AD) is a progressive neurodegenerative disorder with limited treatment options, necessitating the development of safer and more effective therapies. The potential of alkaloids derived from the genus Erythrina as acetylcholinesterase (AChE) inhibitors is being investigated to enhance acetylcholine levels in the brain, which is crucial for the treatment of AD. The objective of this study is to identify Erythrina alkaloids with strong inhibitory capacity against AChE and favorable pharmacokinetic profiles.

Materials and Methods

A multi-step computational approach was employed, beginning with the virtual screening of 143 Erythrina alkaloid structures using molecular docking against the human AChE crystal structure. The binding affinities were compared with the known AChE inhibitor, galantamine. The top alkaloid, 8-oxoerymelanthine (128), was subjected to further analysis through molecular dynamics simulations, with the objective of evaluating its stability and interactions. In silico ADMET predictions were conducted to assess the pharmacokinetic properties. The applicability of Lipinski's Rule of Five was applied to evaluate oral drug-likeness.

Results

8-Oxoerymelanthine (128) exhibited the highest binding affinity and remarkable stability in molecular dynamics simulations. The toxicity predictions indicated a low risk of mutagenicity, hepatotoxicity, and cardiotoxicity. Pharmacokinetic assessments indicated good absorption, moderate blood-brain barrier penetration, and favorable metabolic and excretion profiles, supporting its potential as an orally active drug candidate.

Conclusion

8-Oxoerythmelanthine (128) exhibits strong potential as an AChE inhibitor with a favorable balance of efficacy, safety, and pharmacokinetic properties. These results warrant further investigation in preclinical and clinical studies to validate its therapeutic potential and safety for Alzheimer's disease treatment.

Idiopathic Pulmonary Fibrosis: In Silico Therapeutic Potential of Doxycycline, Pirfenidone, and Nintedanib, and the Role of Next-Generation Phenomics in Drug Discovery

Innovation in drug discovery for human diseases stands to benefit from systems science and next-generation phenomics approaches. An example is idiopathic pulmonary fibrosis (IPF) that is a chronic pulmonary disorder leading to respiratory failure and for which preventive and therapeutic medicines are sorely needed. Matrix metalloproteinases (MMPs), particularly MMP1 and MMP7, have been associated with IPF pathogenesis and are thus relevant to IPF drug discovery. This study evaluates the comparative therapeutic potentials of doxycycline, pirfenidone, and nintedanib in relation to MMP1 and MMP7 using molecular docking, molecular dynamics simulations, and a next-generation phenomics approach. Adsorption, distribution, metabolism, excretion, and toxicity analysis revealed that doxycycline and nintedanib adhered to Lipinski's rule of five, while pirfenidone exhibited no violations. The toxicity analysis revealed favorable safety profiles, with lethal dose 50 values of doxycycline, pirfenidone, and nintedanib being 2240kg, 580, and 500 mg/kg, respectively. Homology modeling validated the accuracy of the structures of the target proteins, that is, MMP1 and MMP7. The Protein Contacts Atlas tool, a next-generation phenomics platform that broadens the scope of phenomics research, was employed to visualize protein contacts at atomic levels, revealing interaction surfaces in MMP1 and MMP7. Docking studies revealed that nintedanib exhibited superior binding affinities with the candidate proteins (-6.9 kcal/mol for MMP1 and -7.9 kcal/mol for MMP7) compared with doxycycline and pirfenidone. Molecular dynamics simulations further demonstrated the stability of protein-ligand complexes. These findings highlight the notable potential of nintedanib in relation to future IPF therapeutics innovation. By integrating in silico and a next-generation phenomics approach, this study opens up new avenues for drug discovery and development for IPF and possibly, for precision/personalized medicines that consider the molecular signatures of therapeutic candidates for each patient.

Physico-chemical, nutritional, and anti-inflammatory properties of processed Garcinia pedunculata fruit: A combined in vitro and in silico approach

This study aimed to evaluate the physico-chemical, nutritional, antioxidant, and anti-inflammatory properties of Garcinia pedunculata fruit powders obtained from different drying methods to explore their potential use in health-promoting functional foods. The fruits were processed at mature and ripe stages. Molecular modeling studies were also performed to find effective inhibitors from G. pedunculata fruit against inflammatory targets. Among the drying methods, the hot-air oven drying method was found to be most effective in reducing moisture content and water activity, while freeze-drying resulted in better color retention and the highest antioxidant and anti-inflammatory properties. The mature fruit powders showed better results than the ripe fruit powders in most of the analyzed parameters, such as lowest moisture content (13.87 %) and water activity (0.477 aw) indicating better shelf life, highest TPC (9.58 mg GAE/g), TFC (5.05 mg QE/g), antioxidant (IC50: 300.02 µg/mL), and anti-inflammatory (IC50:163.46 µg/mL) activities. The processed fruit powders had high levels of crude fiber (5.95-10.18 %) and good amounts of minerals (Na, Ca, K, Mg, Fe, Mn, Zn, Cu). The molecular modeling studies revealed that the compounds garcinol and isogarcinol exhibited the highest binding affinities (-9.6 kcal/mol and -8.8 kcal/mol, respectively) and stability against the target Cyclooxygenase-2 (COX-2) responsible for inflammation compared to other compounds. Moreover, these compounds exhibited better pharmacokinetic qualities and may serve as promising bioactive components for preventing inflammation-related diseases. The findings underscored the promising potential of G. pedunculata powders as a viable active ingredient in functional foods with anti-inflammatory properties.

In silico study of selected alkaloids as dual inhibitors of β- and γ-secretases for Alzheimer's disease

BACKGROUND

Alzheimer's disease (AD) has become common as the number of aged people increases making it as a socioeconomic problem lately. To date, no success is recorded for disease-modifying therapies for AD but only drugs for symptomatic relief exist. Research has been centered on the role of amyloid-β on the pathogenesis of AD, which has led to the development of drugs that target Aβ (β- and γ-secretase inhibitors) to reduce the amount of Aβ formed. However, the existing β and γ-secretase inhibitors were associated with harmful side effects, low efficacy, and inability to cross the blood-brain barrier.

OBJECTIVE

This study therefore used in silico approach to predict the inhibitory properties of alkaloids as potential drug targets against AD.

METHODS

Thus, in this current study, 54 alkaloids from the PhytoHub server (phytohub.eu), and two approved drugs were docked against β-secretases. Additionally, galantamine and 5 alkaloids with the utmost binding potential with β-secretase were subjected to pharmacokinetics evaluation and docked against γ-secretase.

RESULTS

From the result, 5 compounds displayed for both docking periods, with demissidine, solasodine, tomatidine, and solanidine having better BE than the control drugs. Based on the pharmacokinetics evaluation, 4 compounds possessed good pharmacokinetic evaluation and biological activities than galantamine.

CONCLUSIONS

This study suggests that demissidine, solasodine, tomatidine, and solanidine are promising dual inhibitors against β- and γ-secretase proteins in silico. However, there is an urgent need to carry out in vitro and in vivo experiments on these new leads to validate the findings of this study.

An insight for the inhibition of anxiolytic and anti-convulsant effects in zebrafish using the curcumins via exploring molecular docking and molecular dynamics simulations

In the contemporary landscape, anxiety and seizures stand as major areas of concern, prompting researchers to explore potential drugs against them. While numerous drugs have shown the potential to treat these two neurological conditions, certain adverse effects emphasize the need for development of safer alternatives. This study seeks to employ an in silico approach to evaluate natural compounds, particularly curcumins, as potential inhibitors of GABA-AT to mitigate anxiety and seizures. The proposed methodology includes generating a compound library, minimizing energy, conducting molecular docking using AutoDock, molecular dynamics simulations using Amber, and MM-GBSA calculations. Remarkably, CMPD50 and CMPD88 exhibited promising binding affinities of - 9.0 kcal/mol and - 9.1 kcal/mol with chains A and C of GABA-AT, respectively. Further, MM-GBSA calculations revealed binding free energies of - 10.88 kcal/mol and - 10.72 kcal/mol in CMPD50 and CMPD88, respectively. ADME analysis showed that these compounds contain drug-likeness properties and might be considered as potential drug candidates. The findings from this study will have practical applications in the field of drug discovery for the development of safer and effective drugs for treatment of anxiety and seizures. Overall, this study will lay the groundwork for providing valuable insights into the potential therapeutic effects of curcumins in alleviating anxiety and seizures, establishing a computational framework for future experimental validation.

Investigating the binding of fluorescent probes to a trypanosomal-tRNA synthetase: A fluorescence spectroscopic and molecular dynamics study

Given the high prevalence of Chagas disease in the Americas, we targeted the unique arginyl-tRNA synthetase of its causative agent Trypanosoma cruzi. Among their many possible uses, naphthalene-derived fluorescent ligands, such as ANS and bis-ANS, may be employed in pharmacokinetic research. Although ANS and bis-ANS have become prominent fluorescent probes for protein characterization, the structural and spectroscopic characteristics of protein-ANS/bis-ANS complexes remain largely unknown. Both fluorescent dyes bind to either the folded or partially folded hydrophobic regions of proteins. Additionally, they serve to identify molten globule-like intermediates. These probes have been used to study the folding problems of protein structures and the mechanisms of protein-protein interactions. ANS and bis-ANS exhibited significant enhancement and blue shift in their emission spectra upon binding to TcArgRS, the primary enzyme responsible for attaching l-arginine to its corresponding tRNA. Through fluorescence spectroscopy and computational studies, we concluded that bis-ANS binds more tightly to TcArgRS and that ATP affects bis-ANS fluorescence signal. Thus, these probes are useful resources for studying the intricate intermolecular relationships between proteins in terms of their structure, function, and mechanism. Our study provides a framework for identifying the hydrophobic regions present in TcArgRS. The utilization of hydrophobic patches on proteins for drug targeting is noteworthy because they can assist in identifying regions on the surface of proteins that are likely to interact with ligands. These patches help identify hotspot residues that play a vital role in determining binding affinity. Drugs are mainly small and hydrophobic in nature, and they target protein surfaces which have complementary properties. In this study, we elucidated the potential of TcArgRS as a target for combating trypanosomal diseases and extending life expectancy.

Structure-guided identification of mitogen-activated protein kinase-1 inhibitors towards anticancer therapeutics

Mitogen-activated protein kinase 1 (MAPK1) is a serine/threonine kinase that plays a crucial role in the MAP kinase signaling transduction pathway. This pathway plays a crucial role in various cellular processes, including cell proliferation, differentiation, adhesion, migration, and survival. Besides, many chemotherapeutic drugs targeting the MAPK pathway are used in clinical practice, and novel inhibitors of MAPK1 with improved specificity and efficacy are required. Hence, targeting MAPK1 can be crucial to control metastasis in cancer therapeutics. In this study, we utilized a structure-guided virtual screening approach to screen a library of thousands of natural compounds from the ZINC database. The Lipinski rule of five (RO5) was used as a criterion for the primary selection of natural compounds. The screened compounds were prioritized based on their binding affinity, docking scores, and specificity towards the kinase domain of MAPK1 during the molecular docking process. Subsequently, the selected hits underwent rigorous screening that included the identification of potential pan-assay interference compounds (PAINS), ADMET evaluation, and prediction of pharmacological activities using PASS analysis. Afterwards, we performed a comprehensive interaction analysis to explore the binding prototypes of the screened molecules with the key residues within the MAPK1 kinase domain. Finally, selected molecules underwent extensive all-atom molecular dynamics (MD) simulations for a time duration of 200 nanoseconds. The study pinpointed three natural compounds with ZINC database IDs ZINC0209285, ZINC02130647, and ZINC02133691 as potential inhibitors of MAPK1. The study highlights that these compounds could be explored further in preclinical and clinical investigations to develop anticancer therapeutics.

Moroccan natural products for multitarget-based treatment of Alzheimer's disease: A computational study

Alzheimer's disease is a neurodegenerative disorder that impairs neurocognitive functions. Acetylcholinesterase, Butyrylcholinesterase, Monoamine Oxidase B, Beta-Secretase, and Glycogen Synthase Kinase Beta play central roles in its pathogenesis. Current medications primarily inhibit AChE but fail to halt or reverse disease progression due to the multifactorial nature of Alzheimer's. This underscores the necessity of developing multi-target ligands for effective treatment. This study investigates the potential of phytochemical compounds from Moroccan medicinal plants as multi-target agents against Alzheimer's disease, employing computational approaches. A virtual screening of 386 phytochemical compounds, followed by an assessment of pharmacokinetic properties and ADMET profiles, led to the identification of two promising compounds, naringenin (C23) and hesperetin (C24), derived from Anabasis aretioides. These compounds exhibit favourable pharmacokinetic profiles and strong binding affinities for the five key targets associated with the disease. Density functional theory, molecular dynamics simulations, and MM-GBSA calculations further confirmed their structural stability, with a slight preference for C24, exhibiting superior intermolecular interactions and overall stability. These findings provide a strong basis for further experimental research, including in vitro and in vivo studies, to substantiate their potential efficacy in Alzheimer's disease.

Deoxygenated hydroxyapatite inhibits macrophage inflammation through fibronectin restricted adsorption

Macrophages can determine the ultimate outcome of the foreign body reaction (FBR). Although researchers confirmed that differences in the elemental composition of the implant interface can lead to varying levels of biological function, the mechanism underlying the polarization directions of macrophages induced by varying oxygen proportions remains unclear. This research presented the fabrication of a deoxygenated hydroxyapatite (dHAP) surface to investigate the impact of oxygen content on macrophage activation. The dHAP surface exhibited a pronounced inhibitory effect on the inflammatory activation of macrophages when compared to the HAP surface. Results from total internal reflection microscopy (TIRFM) and molecular dynamic (MD) simulation have revealed that the significant extracellular matrix adhesion protein, Fibronectin (Fn), showed a lower level of adsorption on dHAP surfaces. The Arg-Gly-Asp (RGD) structural domain showed a reduction in the exposure. The diminished adhesion capacity and impaired active site recognition ability of Fn resulted in lower activation of the integrin-focal adhesion kinase (FAK) pathway of macrophages on the dHAP surface, thereby suppressing the inflammation. In summary, this work explains the mechanism of the FBR impacted by the proportion of oxygen at the protein level. It also introduces a new approach to enhance the compatibility of biomaterials. STATEMENT OF SIGNIFICANCE: Macrophages are key in the foreign body response (FBR). Researches indicate that implant material's elemental interface content can regulate the functionality of biomaterials, but the mechanism of this regulation is unclear. To study the relationship between the elemental content at the interface and macrophages in the FBR, we prepared a deoxygenated hydroxyapatite (dHAP). Our results showed that the dHAP surface inhibited the adsorption behavior and changed the orientation of an ECM protein-fibronectin (Fn)-as well as the exposure of fewer active sites of the Arg-Gly-Asp (RGD) sequence, leading to less integrin activation. And then, the activation of the integrin- focal adhesion kinase (FAK) signaling pathway was reduced, leading to a greater activation of macrophages towards a pro-regenerative direction.

High-Throughput Screening for Enhanced Thermal Stability of Inherently Salt-Tolerant l-Glutaminase and Its Efficient Expression in Bacillus licheniformis

In addressing the challenges posed by extended fermentation cycles and high-salt conditions in high-salt liquid-state fermentation soy sauce (HLFSS) production, a high-throughput screening method was devised to identify thermally stable l-glutaminase mutants. This study yielded mutants A146D and A51D, exhibiting enhanced thermal stability. Computer-aided analysis revealed that these mutations introduced additional forces, compacting the protein structure and lowering the Gibbs free energy, thereby improving thermostability. Furthermore, the incorporation of aspartic acid augmented the negative surface charge, contributing to superior salt tolerance compared to the wild type (WT). Notably, in a 25% NaCl buffer, A146D and A51D demonstrated half-lives of 72.57 and 71.31 day, respectively, surpassing the WT's 59.08 day. In a 5 L bioreactor, the optimal mutant A146D achieved a remarkable enzymatic activity of 2800.78 ± 98.1 U/mL in recombinant Bacillus licheniformis fermentation broth, setting a new benchmark. This research offers valuable insights and a foundation for the modification and application of l-glutaminase in the food industry, particularly in HLFSS brewing.

Fuentes L, Pimenta A, Nagem RAP, Chávez-Olórtegui C, Schneider FS, Molina F, Sanchez EF, Suárez D, Ferreira RS. Assessing the Interactions between Snake Venom Metalloproteinases and Hydroxamate Inhibitors Using Kinetic and ITC Assays, Molecular Dynamics Simulations and MM/PBSA-Based Scoring Functions

Bothrops species are the main cause of snake bites in rural communities of tropical developing countries of Central and South America. Envenomation by Bothrops snakes is characterized by prominent local inflammation, hemorrhage and necrosis as well as systemic hemostatic disturbances. These pathological effects are mainly caused by the major toxins of the viperidae venoms, the snake venom metalloproteinases (SVMPs). Despite the antivenom therapy efficiency to block the main toxic effects on bite victims, this treatment shows limited efficacy to prevent tissue necrosis. Thus, drug-like inhibitors of these toxins have the potential to aid serum therapy of accidents inflicted by viper snakes. Broad-spectrum metalloprotease inhibitors bearing a hydroxamate zinc-binding group are potential candidates to improve snake bites therapy and could also be used to study toxin-ligand interactions. Therefore, in this work, we used both docking calculations and molecular dynamics simulations to assess the interactions between six hydroxamate inhibitors and two P-I SVMPs selected as models: Atroxlysin-I (hemorrhagic) from Bothrops atrox, and Leucurolysin-a (nonhemorrhagic) from Bothrops leucurus. We also employed a large variety of end-point free energy methods in combination with entropic terms to produce scoring functions of the relative affinities of the inhibitors for the toxins. Then we identified the scoring functions that best correlated with experimental data obtained from kinetic activity assays. In addition, to the characterization of these six molecules as inhibitors of the toxins, this study sheds light on the main enzyme-inhibitor interactions, explaining the broad-spectrum behavior of the inhibitors, and identifies the energetic and entropic terms that improve the performance of the scoring functions.

Molecular dynamic studies of gold nanoparticles in a dental material TEGDMA

CONTEXT

In the context of biomaterials, triethylene glycol dimethacrylate (TEGDMA) is a widely used monomer in dental resins due to its favorable mechanical properties and ease of polymerization. However, improving its structural stability and enhancing its performance in biological applications remain crucial goals. This study examines the impact of incorporating gold (Au) nanoparticles into the TEGDMA matrix, focusing on their potential to improve mechanical, thermal, and optical properties for biomedical applications. Gold is known for its bio-compatibility, antimicrobial properties, and ability to improve material conductivity, making it an attractive addition for dental and tissue engineering composites. By introducing Au nanoparticles at varying concentrations (0%, 3%, 4%, and 5%), this research aims to optimize TEGDMA's performance in medical grade materials, particularly in dental composites where enhanced strength and durability are vital.

METHODS

Molecular dynamics (MD) simulations were employed to investigate the structural, thermal, and mechanical properties of TEGDMA with varying concentrations of Au nanoparticles. LAMMPS software was used to compute cohesive energy, surface tension, viscosity, and mechanical moduli. Quantum chemical calculations were conducted using Gaussian and RDKit to optimize the molecular structure and obtain electronic properties, including UV-Vis and IR spectra. Phonon spectra and lattice energy were analyzed to evaluate the vibrational properties and thermal stability of the Au-doped TEGDMA matrix. The results were benchmarked against experimental data, offering a comprehensive computational analysis of the impact of Au nanoparticles on the material's performance. Functional data analysis techniques were applied to correlate nanoparticle concentration with the computed properties.

Identification of Bioactive Compounds from the Roots of Rehmannia glutinosa and Their In Silico and In Vitro AMPK Activation Potential

Rehmannia glutinosa Libosch., which belongs to the Orobanchaceae family, is a perennial herb found in China, Japan, and Korea. In traditional medicine, it is used to cool the body, improve water metabolism in the kidney, and provide protection from metabolic diseases such as type 2 diabetes mellitus (T2DM) and obesity. In this study, three new compounds were isolated from the roots of R. glutinosa, along with eighteen known compounds. Structure elucidation was performed with spectroscopic analyses including nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. As the AMP-activated protein kinase (AMPK) signaling pathway is reportedly related to metabolic diseases, AMPK activation studies were conducted using in silico simulations and in vitro assays. Among the isolated compounds, 1 showed a potential as an AMPK activator in both in silico simulations and in vitro experiments. Our findings expand the chemical profiles of the plant R. glutinosa and suggest that one newly found compound (1) activates AMPK.

Assessment of binding affinity of major bioactive compounds from Momordica charantia, Azadirachta indica, Nelumbo nucifera, Caesalpinia crista, Martynia annua and Erythrina variegate to COX-2 receptor: an in silico study

In traditional medicine, potential anti-inflammatory and pain-relieving activity of Momordica charantia, Azadirachta indica, Nelumbo nucifera, Caesalpinia crista, Martynia annua and Erythrina variegate has been emphasized. In this study, we explored binding affinity of 36 bioactive compounds from these plants to cyclooxygenase-2 (COX-2) receptor using docking method. Six compounds namely, beta carotene, lycopene, lutein, momordicoside, rutin and azadirachtin showed excellent binding affinities (-10.29, -10.22, -10.03, -7.9, -8.81 and -7.88 kcal/mol, respectively) and stable interactions with COX-2 (greater than those of aspirin and diclofenac) and they were chosen for the molecular dynamics (MD) assessments done throughout a 100-ns time period. Based on the computed RMSD, RMSF, Rg, SASA and PCA, all ligands were found to form stable and adequate interactions with COX-2 protein; these findings were comparable to those of aspirin and diclofenac, indicating the potential inhibitory properties of these ligands on COX-2 protein. In addition, the toxicity of compounds was evaluated using Pred-hERG, Pred-Skin and ProTox-II. Since COX-2 inhibitors have been reported to activate the Nrf2 pathway, it is hypothesized that they may confer other health-promoting effects through triggering Nrf2 signaling.

Potential candidates from a functional food Zanthoxyli Pericarpium (Sichuan pepper) for the management of hyperuricemia: high-through virtual screening, network pharmacology and dynamics simulations

Introduction

Hyperuricemia (HUA) is a metabolic syndrome caused by purine metabolism disorders. Zanthoxyli Pericarpium (ZP) is a medicinal and food homologous plant, and its ripe peel is used to treat diseases and as a spice for cooking. Some studies have shown that ZP can inhibit the formation of xanthine oxidase and reduce the production of uric acid.

Methods

Through network pharmacology, ZP's potential targets and mechanisms for HUA treatment were identified. Databases like TCMSP, UniProt, and Swiss Target Prediction were utilized for ZP's active ingredients and targets. HUA-related targets were filtered using GeneCards, Drugbank, and Open Targets. Core targets for ZP's HUA treatment were mapped in a PPI network and analyzed with Cytoscape. GO and KEGG pathway enrichments were conducted on intersected targets via DAVID. Molecular docking and virtual screening were performed to find optimal binding pockets, and ADMET screening assessed compound safety. Molecular dynamics simulations confirmed compound stability in binding sites.

Results

We identified 81 ZP active ingredient targets, 140 HUA-related targets, and 6 drug targets, with xanthine dehydrogenase (XDH) as the top core target. Molecular docking revealed ZP's active ingredients had strong binding to XDH. Virtual screening via Protein plus identified 48 compounds near the optimal binding pocket, with 2'-methylacetophenone, ledol, beta-sitosterol, and ethyl geranate as the most promising. Molecular dynamics simulations confirmed binding stability, suggesting ZP's potential in HUA prevention and the need for further experimental validation.

Conclusion

Our study provides foundations for exploring the mechanism of the lowering of uric acid by ZP and developing new products of ZP. The role of ZP in the diet may provide a new dietary strategy for the prevention of HUA, and more experimental studies are needed to confirm our results in the future.

Synthesis and Structure-Activity Relationship (SAR) Studies on New 4-Aminoquinoline-Hydrazones and Isatin Hybrids as Promising Antibacterial Agents

In response to the escalating crisis of antimicrobial resistance (AMR), there is an urgent need to research and develop novel antibiotics. This study presents the synthesis and assessment of innovative 4-aminoquinoline-benzohydrazide-based molecular hybrids bearing aryl aldehydes (HD1-23) and substituted isatin warheads (HS1-12), characterized using multispectroscopic techniques with high purity confirmed by HRMS. The compounds were evaluated against a panel of clinically relevant antibacterial strains including the Gram-positive Enterococcus faecium, Bacillus subtilis, and Staphylococcus aureus and a Gram-negative Pseudomonas aeruginosa bacterial strain. Preliminary screenings revealed that several test compounds had significant antimicrobial effects, with HD6 standing out as a promising compound. Additionally, HD6 demonstrated impressively low minimum inhibitory concentrations (MICs) in the range of (8-128 μg/mL) against the strains B. subtilis, S. aureus and P. aeruginosa. Upon further confirmation, HD6 not only showed bactericidal properties with low minimum bactericidal concentrations (MBCs) such as (8 μg/mL against B. subtilis) but also displayed a synergistic effect when combined with the standard drug ciprofloxacin (CIP), highlighted by its FICI value of (0.375) against P. aeruginosa, while posing low toxicity risk. Remarkably, HD6 also inhibited a multidrug-resistant (MDR) bacterial strain, marking it as a critical addition to our antimicrobial arsenal. Computation studies were performed to investigate the possible mechanism of action of the most potent hybrid HD6 on biofilm-causing protein (PDB ID: 7C7U). The findings suggested that HD6 exhibits favorable binding free energy, which is supported by the MD simulation studies, presumably responsible for the bacterial growth inhibition. Overall, this study provides a suitable core for further synthetic alterations for their optimization as an antibacterial agent.

Developing a universal multi-epitope protein vaccine candidate for enhanced borna virus pandemic preparedness

Introduction

Borna disease virus 1 (BoDV-1) is an emerging zoonotic RNA virus that can cause severe acute encephalitis with high mortality. Currently, there are no effective countermeasures, and the potential risk of a future outbreak requires urgent attention. To address this challenge, the complete genome sequence of BoDV-1 was utilized, and immunoinformatics was applied to identify antigenic peptides suitable for vaccine development.

Methods

Immunoinformatics and antigenicity-focused protein screening were employed to predict B-cell linear epitopes, B-cell conformational epitopes, and cytotoxic T lymphocyte (CTL) epitopes. Only overlapping epitopes with antigenicity greater than 1 and non-toxic, non-allergenic properties were selected for subsequent vaccine construction. The epitopes were linked using GPGPG linkers, incorporating β-defensins at the N-terminus to enhance immune response, and incorporating Hit-6 at the C-terminus to improve protein solubility and aid in protein purification. Computational tools were used to predict the immunogenicity, physicochemical properties, and structural stability of the vaccine. Molecular docking was performed to predict the stability and dynamics of the vaccine in complex with Toll-like receptor 4 (TLR-4) and major histocompatibility complex I (MHC I) receptors. The vaccine construct was cloned through in silico restriction to create a plasmid for expression in a suitable host.

Results

Among the six BoDV-1 proteins analyzed, five exhibited high antigenicity scores. From these, eight non-toxic, non-allergenic overlapping epitopes with antigenicity scores greater than 1 were selected for vaccine development. Computational predictions indicated favorable immunogenicity, physicochemical properties, and structural stability. Molecular docking analysis showed that the vaccine remained stable in complex with TLR-4 and MHC I receptors, suggesting strong potential for immune recognition. A plasmid construct was successfully generated, providing a foundation for the experimental validation of vaccines in future pandemic scenarios.

Discussion

These findings demonstrate the potential of the immunoinformatics-designed multi-epitope vaccines for the prevention and treatment of BoDV-1. Relevant preparations were made in advance for possible future outbreaks and could be quickly utilized for experimental verification.

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.

Computational exploration of palmitoyl-protein thioesterase 1 inhibition by Juniperus phoenicea L. for anti-dementia treatment

Objectives

Dementia, a growing concern globally, affects more than 55 million people-a number projected to rise to 152 million by 2050. Current medications target Alzheimer's disease, the most prevalent form of dementia. This study investigated Juniperus phoenicea L., a plant used in traditional Chinese medicine, as a potential inhibitor of palmitoyl-protein thioesterase 1 (PPT1), an enzyme associated with dementia.

Methods

J. phoenicea phytochemicals were subjected to in silico docking against PPT1 (PDB ID: 1EH5). Docking simulations were performed in YASARA Structure with VINA scoring. Top-ranked ligands were subjected to ADMET analysis (admetlab 2.0, Protox 3.0) and PASS bioactivity prediction. Stability and reactivity were analyzed with DFT calculations (Gaussian 09), and 500 ns MD simulations (YASARA Structure, AMBER 14 force field) to assess protein-ligand complex stability. MM-PBSA was used to calculate binding free energies.

Results

The docking simulations identified amentoflavone (-9.6 kcal/mol) as the top hit, followed by ferruginol and quercetin 3-O-pentoside. Amentoflavone formed the most interactions (19) with PPT1. In silico toxicity analysis predicted amentoflavone and quercetin 3-O-pentoside to be safe, whereas ferruginol violated the Pfizer rule. The PASS server indicated a higher probability of activity for quercetin 3-O-pentoside (0.423) than amentoflavone (0.287) for dementia treatment. DFT calculations revealed similar electronic properties for both ligands, although amentoflavone showed slightly more favorable values. MD simulations demonstrated that amentoflavone, compared with to galantamine, had superior binding stability in the PPT1 binding pocket.

Conclusion

This in silico study was aimed at identifying potential inhibitors of PPT1 from J. phoenicea phytochemicals, given that PPT1 is a target for developing new dementia medications. Our findings identified amentoflavone as a promising candidate for further investigation. These findings warrant further research to validate this compound's potential as a PPT1 inhibitor for dementia treatment.

Exploring the Potential of Biomimetic Peptides in Targeting Fibrillar and Filamentous Alpha-Synuclein-An In Silico and Experimental Approach to Parkinson's Disease

Alpha-synuclein (ASyn) is a protein that is known to play a critical role in Parkinson's disease (PD) due to its propensity for misfolding and aggregation. Furthermore, this process leads to oxidative stress and the formation of free radicals that cause neuronal damage. In this study, we have utilized a biomimetic approach to design new peptides derived from marine natural resources. The peptides were designed using a peptide scrambling approach where antioxidant moieties were combined with fibrillary inhibition motifs in order to design peptides that would have a dual targeting effect on ASyn misfolding. Of the 20 designed peptides, 12 were selected for examining binding interactions through molecular docking and molecular dynamics approaches, which revealed that the peptides were binding to the pre-NAC and NAC (non-amyloid component) domain residues such as Tyr39, Asn65, Gly86, and Ala85, among others. Because ASyn filaments derived from Lewy body dementia (LBD) have a different secondary structure compared to pathogenic ASyn fibrils, both forms were tested computationally. Five of those peptides were utilized for laboratory validation based on those results. The binding interactions with fibrils were confirmed using surface plasmon resonance studies, where EQALMPWIWYWKDPNGS, PYYYWKDPNGS, and PYYYWKELAQM showed higher binding. Secondary structural analyses revealed their ability to induce conformational changes in ASyn fibrils. Additionally, PYYYWKDPNGS and PYYYWKELAQM also demonstrated antioxidant properties. This study provides insight into the binding interactions of varying forms of ASyn implicated in PD. The peptides may be further investigated for mitigating fibrillation at the cellular level and may have the potential to target ASyn.

Network pharmacology and bioinformatic integrative analysis reveals candidate gene targets and potential therapeutic of East Kalimantan propolis against hepatocellular carcinoma

Introduction

Hepatocellular Carcinoma (HCC) is commonly treated with surgery, liver transplantation, and chemotherapy, but recurrence and metastasis remain challenges. Natural complementary therapies like propolis, known for its hepatoprotective properties, are gaining interest due to limited efficacy and toxicity of conventional chemotherapy. This study aims to identify core targets for HCC, assess the therapeutic potential of East Kalimantan propolis (EKP) from stingless bees, and analyze the molecular interactions.

Methods

EKP compounds were analyzed using target prediction tools related to HCC, alongside clinical data from the Gene Expression Omnibus (GEO) database, to identify overlapping genes with clinical relevance. The selected genes were then subjected to protein-protein interaction (PPI), GO and KEGG enrichment, immunohistochemical comparison and survival analysis to identify potential core targets and related pathways for HCC therapy. Furthermore, molecular docking and dynamics were conducted to verify the molecular interactions and stability of EKP compounds with targets.

Results

108 genes have been selected as HCC potential targets, which mostly associated with MicroRNAs in cancer, chemical carcinogenesis, and viral carcinogenesis pathways. These targets were obtained by overlapping genes from GEO clinical databases and target predictors. PPI network analysis revealed 4 main targets of propolis in HCC. Furthermore, differential expression genes, survival analysis, and Immunohistochemical analysis from databases suggested that AKR1C3 and MAPK1 promote HCC progression and shorten survival rate of HCC patients. Molecular docking and dynamic studies confirmed strong binding affinity and stability of Baicalein, Chrysin, Quercetin, and Myricetin with receptor targets within simulation time.

Conclusions

This study provides insight into the mechanism of action of EKP on HCC and identifies AKR1C3 and MAPK1 as candidate target treatments for future drug development.

Robust superhydrophobic self-cleaning coating prepared by silane modified multi-walled carbon nanotubes: A combined experimental and molecular dynamics study

As a functional material, superhydrophobic coating has been widely studied in the field of self-cleaning. However, obtaining superhydrophobic coatings with robustness through simple preparation processes remains a challenge. In this paper, a robust superhydrophobic coating is prepared based on multi-walled carbon nanotubes modified by octyltrimethoxysilane, and its performance and hydrophobic mechanism are studied by experiments and molecular dynamics simulation. The superhydrophobic coating is prepared by one-step spraying method. The coating is characterized and analyzed by scanning electron microscopy and Fourier transform infrared spectroscopy, and the properties of the coating are tested by experiments. Molecular dynamics simulation is used in the study to construct a molecular model system, and the molecular modification mechanism and coating wettability are simulated under the COMPASSII force field. The results show that octyltrimethoxysilane successfully modified carbon nanotubes, and the hydroxyl groups at the head of the molecular chain are bound to the surface of the carbon nanotubes in the form of hydrogen bonds, while the tail of the molecular chain is far away from the surface. After modification, the surface of carbon nanotubes changed from hydrophilic to hydrophobic. The prepared superhydrophobic coating not only has excellent self-cleaning properties, but also exhibits corrosion resistance to acid and alkali solutions. The coating still has superhydrophobic when the wear length is in the range of 400 cm. It can be seen that a robust superhydrophobic self-cleaning coating is successfully prepared by a simple one-step spraying method. The modification mechanism and the hydrophobic mechanism of the coating were obtained by the combination of experiment and molecular dynamics simulation, which provided theoretical support for the superhydrophobic of the coating at the micro level.

Investigating the Potency of Erythrina‒Derived Flavonoids as Cholinesterase Inhibitors and Free Radical Scavengers Through in silico Approach: Implications for Alzheimer's Disease Therapy

Purpose

This study aimed to evaluate the potency of 471 flavonoids from the genus Erythrina as potential acetylcholinesterase (AChE) inhibitors and free radical scavengers through computational studies to develop Alzheimer's disease (AD) therapies from natural products.

Methods

A total of 471 flavonoids from the genus Erythrina were subjected to molecular docking against AChE, followed by toxicity screening. The potential AChE inhibitors with the least toxic profile were subjected to further investigation through molecular dynamics (MD) simulations, density functional theory (DFT) study, and in silico pharmacokinetic predictions.

Results

A combination of molecular docking and in silico toxicity screening led to the identification of 2(S)‒5,7‒dihydroxy‒5'‒methoxy‒[2'',2''‒(3''‒hydroxy)‒dimethylpyrano]‒(5'',6'':3',4') flavanone (89) and Abyssinoflavanone IV (83) as potential AChE inhibitors. These compounds had stable binding to AchE and exhibited lower Root Mean Square Deviation (RMSD) values compared to the apo state of AChE. In addition, Molecular Mechanics Generalized Born Surface Area (MMGBSA) analysis revealed that the binding energies of 89 and 83 were significantly lower compared to acetylcholine, the natural substrate of AChE. Based on DFT study, these compounds exhibited a higher energy in the highest occupied molecular orbital (EHOMO) and lower electron affinity (EA) than Quercetin. This indicated that 89 and 83 could be potential radical scavengers through their electron-donating activity.

Conclusion

Although this study primarily relied on computational methods, the results showed the dual functionality of compounds 89 and 83 as both potential AChE inhibitors and free radical scavengers. Further investigation in wet laboratory experiments is required to validate their therapeutic potential for AD.

Widely-targeted in silico and in vitro evaluation of veratrum alkaloid analogs as FAK inhibitors and dual targeting of FAK and Hh/SMO pathways for cancer therapy: A critical analysis

Focal Adhesive Kinase (FAK), a key player in aggressive cancers, mediates signals crucial for progression, invasion, and metastasis. Despite advances in targeted therapies, drug resistance is still a challenge, and survival rates remain low, particularly for late-stage patients, emphasizing the need for innovative cancer therapeutics. Cyclopamine, a veratrum alkaloid, has shown promising anti-tumor properties, but the search for more potent analogs with enhanced affinity for the biological target continues. This study employs a hybrid virtual screening approach combining pharmacophore model-based virtual screening (PB-VS) and docking-based virtual screening (DB-VS) to identify potential inhibitors of the FAK catalytic domain. PB-VS on the PubChem database yielded a set of hits, which were then docked with the FAK catalytic domain in two stages (1st and 2nd DB-VS). Hits were ranked based on docking scores and interactions with the active site. The top three compounds underwent molecular dynamics simulations, alongside two control compounds (SMO inhibitor(s) and FAK inhibitor(s)), to assess stability through RMSD, RMSF, Rg, and SASA analyses. ADMET properties were evaluated, and compounds were filtered based on drug-likeness criteria. Molecular dynamics simulations demonstrated the stability of compounds when complexed with the FAK catalytic domain. Compounds 16 (-25 kcal/mol), 87 (-27.47 kcal/mol), and 88 (-18.94 kcal/mol) exhibited comparable docking scores, interaction profiles, stability, and binding energies, indicating their potential as lead candidates. However, further validation and optimization through quantitative structure-activity relationship (QSAR) studies are essential to refine their efficacy and therapeutic potential. The in vitro cell-based assay demonstrated that compound 101PF, a FAK inhibitor, significantly inhibited the proliferation and migration of A549 cells. However, the results regarding the combined effects of FAK and SMO inhibitors were inconclusive, highlighting the need for further investigation. This study contributes to developing more effective anti-cancer drugs by improving the understanding of potential cyclopamine-based veratrum alkaloid analogs with enhanced interactions with the FAK catalytic domain.

Identification of acetylcholinesterase inhibitors from traditional medicinal plants for Alzheimer's disease using in silico and machine learning approaches

Acetylcholinesterase (AChE) holds significance in Alzheimer's disease (AD), where cognitive impairment correlates with insufficient acetylcholine levels. AChE's role involves the breakdown of acetylcholine, moderating cholinergic neuron activity to prevent overstimulation and signal termination. Hence, inhibiting AChE emerges as a potential treatment avenue for AD. A library of 2500 compounds, derived from 25 traditionally used medicinal plants, was constructed using the IMPAAT database of traditional medicinal plants. The canonical SMILES of these compounds were collected and underwent virtual screening based on physicochemical properties, with subsequent determination of IC50 values for the screened compounds followed by analysis using machine learning (ML). Subsequently, a molecular docking study elucidated both binding affinity and interactions between these compounds and AChE. The top three compounds, exhibiting robust binding affinities, underwent MM-GBSA analysis for molecular docking validation, succeeded by pharmacokinetics and toxicity evaluations to gauge safety and efficacy. These three compounds underwent MD simulation studies to assess protein-ligand complex conformational stability. Additionally, Density Functional Theory (DFT) was employed to ascertain HOMO, LUMO, energy gap, and molecular electrostatic potential. Among 2500 compounds, physicochemical properties-based virtual screening identified 80 with good properties, of which 32 showed promising IC50 values. Molecular docking studies of these 32 compounds revealed various binding energies with AChE, with the best three compounds (CID 102267534, CID 15161648, CID 12441) selected for further analysis. MM-GBSA studies confirmed the promising binding energies of these three compounds, validating the molecular docking study. Further, the MD simulation studies have confirmed the structural and conformational stability of these three protein-ligand complexes. Finally, DFT calculations revealed favorable chemical features of these compounds. Thus, we can conclude that these three compounds (CID 102267534, CID 15161648, CID 12441) may inhibit the activity of AChE and can be useful as a treatment for Alzheimer's disease.

Antimicrobial potential of Hippocratea Indica Willd. Acetone Leaf fractions against Salmonella Typhi: an in vitro and in silico study

Salmonella Typhi is a major global concern in many low- and middle-income countries. In addition, the emergence and persistence of drug resistant strains has increased the impact of this disease. Plant metabolites have been explored traditionally and scientifically as antimicrobial agents. Thus, this study was designed to investigate the antimicrobial potential of acetone leaf fractions of H. indica against S. Typhi. Dried pulverized leaves of H. indica were extracted using cold maceration with acetone after defatting with n-hexane. The leaf extract was concentrated and subjected to column chromatography and eight bioactive fractions were identified. The fractions were characterized using gas chromatography-mass spectrometry. The fractions were evaluated for antibacterial activity against Salmonella Typhi in-vitro and in-silico. The lowest MIC was observed in fractions 20 and 21 (0.375 mg/mL) while the lowest MBC was observed in all fractions except 7, 17 and 18 (0.375 mg/mL). A ligand from fraction 8 had the highest binding affinity to Type I dehydroquinase (-3.4) and a ligand from fraction 7 had the highest binding affinity to Gyrase B (-11.2). This study concludes that the overall antimicrobial activity of the acetone leaf extract of H. indica provided evidence that it contains drug-like compounds that can be further explored as a drug candidate against S. Typhi.

Phytoconstituents of Withania somnifera (L.) Dunal (Ashwagandha) unveiled potential cerebroside sulfotransferase inhibitors: insight through virtual screening, molecular dynamics, toxicity, and reverse pharmacophore analysis

Cerebroside sulfotransferase (CST) is considered as therapeutic target for substrate reduction therapy (SRT) for metachromatic leukodystrophy (MLD). The present study evaluates the therapeutic potential of 57 phytoconstituents of Withania somnifera against CST. Using binding score cutoff ≤-7.0 kcal/mol, top 10 compounds were screened and after ADME and toxicity-based screening, Withasomidienone, 2,4-methylene-cholesterol, and 2,3-Didehydrosomnifericin were identified as safe and potent drug candidates for CST inhibition. Key substrate binding site residues involved in interaction were LYS82, LYS85, SER89, TYR176, PHE170, PHE177. Four steroidal Lactone-based withanolide backbone of these compounds played a critical role in stabilizing their position in the active site pocket. 100 ns molecular dynamics simulation and subsequent trajectory analysis through structural deviation and compactness, principal components, free energy landscape and correlation matrix confirmed the stability of CST-2,3-Didehydrosomnifericin complex throughout the simulation and therefore is considered as the most potent drug candidate for CST inhibition and Withasomidienone as the second most potent drug candidate. The reverse pharmacophore analysis further confirmed the specificity of these two compounds towards CST as no major cross targets were identified. Thus, identified compounds in this study strongly present their candidature for oral drug and provide route for further development of more specific CST inhibitors.

Identification of novel drug targets for Helicobacter pylori: structure-based virtual screening of potential inhibitors against DAH7PS protein involved in the shikimate pathway

Background

Helicobacter pylori, a bacterium associated with severe gastrointestinal diseases and malignancies, poses a significant challenge because of its increasing antibiotic resistance rates. This study aimed to identify potential drug targets and inhibitors against H. pylori using a structure-based virtual screening (SBVS) approach.

Methods

Core-proteome analysis of 132 H. pylori genomes was performed using the EDGAR database. Essential genes were identified and human and gut microbiota homolog proteins were excluded. The DAH7PS protein involved in the shikimate pathway was selected for the structure-based virtual screening (SBVS) approach. The tertiary structure of the protein was predicted through homology modeling (based on PDB ID: 5UXM). Molecular docking was performed to identify potential inhibitors of DAH7PS among StreptomeDB compounds using the AutoDock Vina tool. Molecular dynamics (MD) simulations assessed the stability of DAH7PS-ligand complexes. The complexes were further evaluated in terms of their binding affinity, Lipinski's Rule of Five, and ADMET properties.

Results

A total of 54 novel drug targets with desirable properties were identified. DAH7PS was selected for further investigation, and virtual screening of StreptomeDB compounds yielded 36 high-affinity binding of the ligands. Two small molecules, 6,8-Dihydroxyisocoumarin-3-carboxylic acid and Epicatechin, also showed favorable RO5 and ADMET properties. MD simulations confirmed the stability and reliability of DAH7PS-ligand complexes, indicating their potential as inhibitors.

Conclusion

This study identified 54 novel drug targets against H. pylori. The DAH7PS protein as a promising drug target was evaluated using a computer-aided drug design. 6,8-Dihydroxyisocoumarin-3-carboxylic acid and Epicatechin demonstrated desirable properties and stable interactions, highlighting their potential to inhibit DAH7PS as an essential protein. Undoubtedly, more experimental validations are needed to advance these findings into practical therapies for treating drug-resistant H. pylori.

Ligand modelling of Trachyspermum ammi phytocompounds for Aeromonas hydrophila cell wall synthesis enzyme in Labeo rohita

Aquaculture faces challenges from Aeromonas hydrophila, causing Motile Aeromonas Septicaemia, particularly affecting Labeo rohita (Rohu) in Pakistan. This study explores potential herbal antibacterials targeting A. hydrophila, molecular docking of Trachyspermum ammi (ajwain) phytocompounds against pathogen. The cell wall synthesis ligase, D-alanine-D-alanine ligase (PDB ID 6ll9) was processed in BIOVIA Discovery Studio and docked with 13 antibacterial phytocompounds found after QSAR analysis of T. ammi. Binding energies were calculated using PyRx to assess complex stability. ADME-TOX assessment for selected phytocompounds and parameterisation in CHARMM-GUI were performed. Docking the two best ligands with highest binding energies and ADME-TOX compliance, we found carvacrol and limonene formed most stable protein-ligand complexes, with raw and processed protein. Our findings suggest these herbal compounds can inhibit D-alanine-D-alanine ligase. These in-silico results support the potential of 'ajwain' in managing A. hydrophila, further in-vivo experiments are necessary to validate these inhibitory properties.

Unveiling the Anticancer Potential: Computational Exploration of Nitrogenated Derivatives of (+)-Pancratistatin as Topoisomerase I Inhibitors

Cancer poses a substantial global health challenge, driving the need for innovative therapeutic solutions that offer improved effectiveness and fewer side effects. Topoisomerase I (Topo I) has emerged as a validated molecular target in the pursuit of developing anticancer drugs due to its critical role in DNA replication and transcription. (+)-Pancratistatin (PST), a naturally occurring compound found in various Amaryllidaceae plants, exhibits promising anticancer properties by inhibiting Topo I activity. However, its clinical utility is hindered by issues related to limited chemical availability and aqueous solubility. To address these challenges, molecular modelling techniques, including virtual screening, molecular docking, molecular mechanics with generalised born and surface area solvation (MM-GBSA) calculations, and molecular dynamics simulations were utilised to evaluate the binding interactions and energetics of PST analogues with Topo I, comparing them with the well-known Topo I inhibitor, Camptothecin. Among the compounds screened for this study, nitrogenated analogues emerged as the most encouraging drug candidates, exhibiting improved binding affinities, favourable interactions with the active site of Topo I, and stability of the protein-ligand complex. Structural analysis pinpointed key molecular determinants responsible for the heightened potency of nitrogenated analogues, shedding light on essential structural modifications for increased activity. Moreover, in silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) predictions highlighted favourable drug-like properties and reduced toxicity profiles for the most prominent nitrogenated analogues, further supporting their potential as effective anticancer agents. In summary, this screening study underscores the significance of nitrogenation in augmenting the anticancer efficacy of PST analogues targeting Topo I. The identified lead compounds exhibit significant potential for subsequent experimental validation and optimisation, thus facilitating the development of novel and efficacious anticancer therapeutics with enhanced pharmacological profiles.

Exploring Marine-Derived Compounds: In Silico Discovery of Selective Ketohexokinase (KHK) Inhibitors for Metabolic Disease Therapy

The increasing prevalence of metabolic diseases, including nonalcoholic fatty liver disease (NAFLD), obesity, and type 2 diabetes, poses significant global health challenges. Ketohexokinase (KHK), an enzyme crucial in fructose metabolism, is a potential therapeutic target due to its role in these conditions. This study focused on the discovery of selective KHK inhibitors using in silico methods. We employed structure-based drug design (SBDD) and ligand-based drug design (LBDD) approaches, beginning with molecular docking to identify promising compounds, followed by induced-fit docking (IFD), molecular mechanics generalized Born and surface area continuum solvation (MM-GBSA), and molecular dynamics (MD) simulations to validate binding affinities. Additionally, shape-based screening was conducted to assess structural similarities. The findings highlight several potential inhibitors with favorable ADMET profiles, offering promising candidates for further development in the treatment of fructose-related metabolic disorders.

Exploring the potential of Scabiosa columbaria in Alzheimer's disease treatment: An in silico approach

Objectives

Alzheimer's disease (AD) is posing an increasing global threat and currently lacks effective treatments. Therefore, this study was aimed at exploring phytochemicals in Scabiosa columbaria (S. columbaria) as inhibitors of acetylcholinesterase (AChE), β-site APP cleavage enzyme 1 (BACE1), and TNF-α converting enzyme (TACE) in AD. S. columbaria contains various bioactive compounds, such as chlorogenic acid, linalool, and catechins, which are known for their detoxification properties, capacity to resist and manage harmful moisture buildup, and therapeutic roles in COVID-19. Several studies have also shown that S. columbaria extract has strong antioxidant activity, and may potentially decrease neuroinflammation in AD. Therefore, this study investigated the interactions between S. columbaria phytochemicals and key enzymes associated with AD, thus providing opportunities for the development of new therapeutic candidates.

Methods

A total of 27 phytochemicals were evaluated for their inhibitory activity against AChE, BACE1, and TACE with YASARA Structure. ADMET profiles and toxicity were assessed. The top candidate compounds underwent 100 ns MD simulations.

Results

All ligands met Lipinski's rule and showed low toxicity. Catechins, compared with the known drug galantamine, showed higher inhibitory activity and interacted with additional active sites on AChE, thus suggesting potentially higher efficacy. Moreover, chlorogenic acid showed stronger inhibitory activity against TACE than the control drug (aryl-sulfonamide), thereby suggesting a different mechanism of action. MD simulation revealed that the formed complexes had good stability. However, further exploration is necessary.

Conclusion

S. columbaria derivative compounds are promising drug candidates because of their properties, including the affinity of chlorogenic acid toward TACE and hydrogen bond enhancing ligand-receptor interactions. MD simulation indicated stable ligand-protein complexes, and the radius of gyration and MM-PBSA calculations revealed favorable binding and interaction energies. Our findings demonstrate the identified compounds' potential for further drug development.

Exploring the anti-protozoal mechanisms of Syzygium aromaticum phytochemicals targeting Cryptosporidium parvum lactate dehydrogenase through molecular dynamics simulations

Cryptosporidium parvum (C. parvum), a protozoan parasite, is known to induce significant gastrointestinal disease in humans. Lactate dehydrogenase (LDH), a protein of C. parvum, has been identified as a potential therapeutic target for developing effective drugs against infection. This study utilized a computational drug discovery approach to identify potential drug molecules against the LDH protein of C. parvum. In the present investigation, we conducted a structure-based virtual screening of 55 phytochemicals from the Syzygium aromaticum (S. aromaticum). This process identified four phytochemicals, including Gallotannin 23, Eugeniin, Strictinin, and Ellagitannin, that demonstrated significant binding affinity and dynamic stability with LDH protein. Interestingly, these four compounds have been documented to possess antibacterial, antiviral, anti-inflammatory, and antioxidant properties. The docked complexes were simulated for 100 ns using Desmond to check the dynamic stability. Finally, the free binding energy was computed from the last 10ns MD trajectories. Gallotannin 23 and Ellagitannin exhibited considerable binding affinity and stability with the target protein among all four phytochemicals. These findings suggest that these predicted phytochemicals from S. aromaticum could be further explored as potential hit candidates for developing effective drugs against C. parvum infection. The in vitro and in vivo experimental validation is still required to confirm their efficacy and safety as LDH inhibitors.

Structure based exploration of potential lead molecules against the extracellular cysteine protease (EcpA) of Staphylococcus epidermidis: a therapeutic halt

Nosocomial infection caused by Staphylococcus epidermidis is one of the most widely spread diseases affecting the world's population. No strategies have been developed to overcome this infection and inhibit its spread in immunocompromised patients or patients with indwelling medical devices. EcpA is an extracellular cysteine protease protein involved in biofilm formation on medical devices. Thus, blocking this mechanism may be viable for developing a drug against S. epidermidis. The current research aimed to find new, potent inhibitors that could stop the S. epidermidis EcpA protein from functioning. This study attempted to identify the most promising drug candidates using structure-based virtual screening (SBVS) from libraries of natural ligands. The top-scored molecules were shortlisted based on their IC50 values and pharmacophore properties and further validated through density functional theory (DFT) studies. We found five inhibitors using virtual screening, and the results indicate that these drugs had the highest energy binding potential towards the EcpA targets when compared to the reference molecule E-64, a known cysteine protease inhibitor. In order to evaluate the binding conformational stability of protein-ligand complexes, molecular dynamics (MD) simulations were performed in triplicate for 100 ns, revealing the significant stability of anticipated molecules at the docked site. Furthermore, principal component analysis and binding free energy calculations were performed to understand the dynamics and stability of the complexes. The current study indicated that these compounds looked to be suitable novel inhibitors of the EcpA protein and pave the path for further discovery of novel inhibitors of EcpA.Communicated by Ramaswamy H. Sarma.

Alisol C 23-acetate might be a lead compound of potential lipase inhibitor from Alismatis Rhizoma: Screening, identification and molecular dynamics simulation

Alismatis Rhizoma (AR), a traditional Chinese medicine for treating obesity in traditional Chinese medicine clinic, is recognized as a promising source of lead compounds of lipase inhibitors. Ultrafiltration centrifugal combined with liquid chromatography-mass spectrometry (UF-LC-MS) was used for screening potential lipase inhibitors from AR, and the result indicated the binding capacity between compound 7 and lipase (92.3 ± 1.28 %) was significantly higher than other triterpenoids, and was identified as alisol C 23-acetate. It exhibited a mixed-type inhibitory behavior with an IC50 value of 84.88 ± 1.03 μM. Subsequently, the binding pockets of alisol C 23-acetate to lipase were predicted, and their binding mechanism was explored with molecular simulation. Pocket 1 (active center) and pocket 4 might be the orthosteric and allosteric binding sites of alisol C 23-acetate to lipase, respectively. The interaction between alisol C 23-acetate and lipase was identified to involve key amino acid residues such as GLY-77, PHE-78, TYR-115, LEU-154, PRO-181, PHE-216, LEU-264, ASP-278, GLN-306, ARG-313, and VAL-426. Meanwhile, alisol C 23-acetate remained stable during the intestinal digestive but degraded in the gastric digestion. Overall, alisol C 23-acetate is expected to be the lead compound of lipase inhibitors for treating obesity.

Identifying Potential Human Monoacylglycerol Lipase Inhibitors from the Phytoconstituents of Morinda Citrifolia L. Fruits by in silico Pharmacology and in vitro Study

Background

Human monoacylglycerol lipase (MGL) is accountable for the hydrolysis of 2-arachidonoylglycerol (2-AG), thus contributing pivotally to neuroprotection because 2-AG is the main source of arachidonic acid, the precursor of prostaglandins production. Inhibiting MGL reduces inflammatory damage in the ischemic brain and enhances cerebral blood flow. Plants have been reported for their neuroprotective effect, such as Morinda citrifolia on pentylenetetrazol (PTZ)-induced kindling seizures in mice, by reducing the seizures and restoring behavioral and biochemical changes, although the mechanism is not described.

Purpose

To evaluate the binding affinity and stability of phytoconstituents in M. citrifolia fruits toward human MGL (PDB ID 3PE6), compared to the known MGL inhibitors (JZL195 and ZYH). The in silico pharmacology study was validated by an in vitro study of the phytosterols and the ethanol extract of M. citrifolia fruits (EEMC) towards MGL.

Methods

Initially, nine phytoconstituents of M. citrifolia fruits were docked to the catalytic pocket of human MGL (PDB ID: 3PE6), and compounds with the best affinity were subjected to a molecular dynamic (MD) simulation. The in vitro study was performed using the MGL inhibitor screening assay kit.

Results

The best binding affinity and stability toward human MGL were shown by stigmasterol and beta-sitosterol, and the MM-PBSA total binding energy of stigmasterol and beta-sitosterol to MGL is stronger than that of JZL195 and ZYH. Moreover, beta-sitosterol and EEMC inhibit MGL with an IC50 value of, respectively, 8.10 μg/mL and 196.20 μg/mL, while JZL195 shows an IC50 of 0.028 μg/mL.

Conclusion

Beta-sitosterol of Morinda citrifolia fruits may have the potential to protect human neurons by occupying the catalytic site of human MGL, thus competitively inhibiting the substrate of the enzyme. However, the inhibitory activity towards human MGL is lower than JZL195.

Triazole fungicides disrupt embryonic stem cell differentiation: Potential modulatory role of the retinoic acid signaling pathway

The developmental toxicity and human health risks of triazole fungicides (TFs) have attracted worldwide attention due to the ability to enter the human body in a variety of ways. Nevertheless, the specific mechanism by which TFs exert remains incompletely understood. Given that retinoic acid (RA) signaling pathway are closely related to development, this study aimed to screen and identify developmentally disabled chemicals in commonly used TFs and to reveal the potential effects of TFs on developmental retardation through the RA signaling pathway in mouse embryonic stem cells (mESCs). Specifically, six typical TFs (myclobutanil, tebuconazole, hexaconazole, propiconazole, difenoconazole, and flusilazole) were exposed through the construction of an embryoid bodies (EBs)-based in vitro global differentiation models. Our results clarified that various TFs disturbed lineage commitment during early embryonic development. Crucially, the activation of RA signaling pathway, which alters the expression of key genes and interferes the transport and metabolism of retinol, may be responsible for this effect. Furthermore, molecular docking, molecular dynamics simulations, and experiments using a retinoic acid receptor α inhibitor provide evidence supporting the potential modulatory role of the retinoic acid signaling pathway in developmental injury. The current study offers new insights into the TFs involved in the RA signaling pathway that interfere with the differentiation process of mESCs, which is crucial for understanding the impact of TFs on pregnancy and early development.

Co-localization and co-expression of Olfml3 with Iba1 in brain of mice

Olfml3 is a microglia-specific protein whose role in neuroinflammation is elusive. In silico analysis was conducted to characterize the Olfml3 protein, followed by molecular docking and MD simulation to check possible interaction with Iba1. Further, expression and co-localization analysis was performed in the LPS-induced neuroinflammatory mice brains. Results suggest that Olfml3 physically interacts with Iba1. Olfml3 and Iba1 expression increases during neuroinflammation in mice brains. Olfml3 was observed to co-localize with Iba1, and the number of Olfml3 and Iba1 dual-positive cells increased in the brain of the neuroinflammatory mice model. Thus, Olfml3 could potentially participate in microglia functions by interacting with Iba1.

Molecular dynamics simulation and purification of chimeric L1/L2 protein from human papillomavirus type 52 expressed in Escherichia coli BL21 (DE3)

The available prophylactic vaccines for human papillomavirus (HPV) in the market are only effective against specific types of HPV, rendering them ineffective for other types of HPV infections. The objective of this research is to investigate the stability of the recombinant protein constructed, namely chimeric L1/L2 protein from HPV type 52, with improved cross-neutralization ability. The 3D model, predicted using Alphafold, Robetta, I-Tasser, and refined with Galaxy Refinement, is validated using Ramachandran plot analysis. The stability is verified through molecular dynamics simulations, considering parameters such as RMSD, RMSF, Rg, and SASA, where stable conditions are observed. The chimeric L1/L2 protein from HPV type 52 is purified using affinity chromatography, and the His-tag is cleaved using SUMO protease to obtain pure chimeric protein with the size of ~ 55 kDa. Western blot analysis confirms binding to anti-L1 HPV type 52 polyclonal antibody. The obtained vaccine candidate can be utilized as an effective prophylactic vaccine against HPV.

In silico study on antidiabetic and antioxidant activity of bioactive compounds in Ficus carica L

Hyperglycemia is one of the diagnostic issues in diabetes mellitus and is considered as a complex metabolic condition. It has been one of the most prevalent illnesses of the twenty-first century and still rising at an alarming rate across the globe and expected to impact 693 million individuals by 2045. Therefore, it is mandatory to develop more effective and safer treatments to manage diabetes. One of the ways to manage hyperglycemia is through inhibiting carbohydrate digestion and thereby lowering the glucose formation in the human body. The enzyme salivary amylase and pancreatic amylase is responsible for cleaving α-1,4-glucoside bond. Amylase inhibitors can lower blood glucose in diabetics by slowing digestion. Ficus carica is commonly known for its medicinal properties due to its various phytochemicals. In the present study, 10 phytochemicals present in F. carica compounds named, β-carotene, lutein, cyanidin-3-glucoside, gallic acid, luteolin, catechin, kaempferol, vanillic acid, peonidin-3-glucoside, and quercetin hydrate were taken to study their inhibition potential against pancreatic amylase and salivary amylase through molecular docking and molecular dynamics simulations. Further, density functional theory calculations are used to investigate the delocalization of electron density on the molecule as well as study ADME properties of the molecules take. A QSAR model has been developed using the binding energy obtained using molecular docking and thermodynamic parameters from DFT calculations.Communicated by Ramaswamy H. Sarma.

Exploring the Synergistic Mechanism of AP2A2 Transcription Factor Inhibition via Molecular Modeling and Simulations as a Novel Computational Approach for Combating Breast Cancer: In Silico Interpretations

Studies have shown that transcription factor AP2A2 (activator protein-2 alpha-2) is involved in the expression of DLEC1, a tumor suppressor gene, which, when mutated, will cause breast cancer and is thus an excellent target for breast cancer studies. Therefore, in the present research, a synergistic approach toward combating breast cancer is proposed by blocking AP2A2 factor, and allowing the cancer cells to be sensitive to anti-cancer drugs. The effect of AP2A2 on breast cancer was first understood via gene analysis from cBioPortal. AP2A2 was then modeled using RaptorX and its structure was validated from Ramachandran plots. Using all ligands from MolPort database, molecular docking was performed against AP2A2, from which the top three best docked ligands were studied for toxicity in humans using Protox-II. Once the ligands passed these tests, the best complexes were simulated at 200ns in Desmond Maestro, to comprehend their stabilities, followed by the computations of free energies of binding via Molecular mechanics- Generalized Born Solvent Accessibility method (MM-GBSA). The results showed that molecules MolPort-005-945-556 (sachharolipids), MolPort-001-741-124 (flavonoids), and MolPort-005-944-667 (lignan glycosides) with AP2A2 passed toxicity evaluation and belonged to toxicity classes 6, 5, and 5, respectively, with good docking energies. 200 ns simulations revealed stable complexes with slight conformational changes. Stability of ligands was confirmed via snapshots at every 20 ns of the trajectory. Radial distribution of these molecules against the protein revealed very slight deviation from binding pocket. Additionally, the free binding energies for these complexes were found to be - 54.93 ± 12.982 kcal/mol, - 44.39 ± 14.393 kcal/mol, and - 66.51 ± 13.522 kcal/mol, respectively. A preliminary computational validation of the inability of AP2A2 to bind to DLEC1 in the presence of ligands offers beneficial insights into the potential of these ligands. Therefore, this study sheds light on the potential natural molecules that could stably block AP2A2 with least deviation and act in synergy to aid anti-cancer drugs work on breast cancer cells.

A novel robust inhibitor of papain-like protease (PLpro) as a COVID-19 drug

Regarding the significance of SARS-CoV-2, scientists have shown considerable interest in developing effective drugs. Inhibitors for PLpro are the primary strategies for locating suitable COVID-19 drugs. Natural compounds comprise the majority of COVID-19 drugs. Due to limitations on the safety of clinical trials in cases of COVID, computational methods are typically utilized for inhibition studies. Whereas papain is highly similar to PLpro and is entirely safe, the current study aimed to examine several plant secondary metabolites to identify the most effective papain inhibitor and validate the results using molecular dynamics and docking. This simulation was conducted identically for PLpro and the optimal inhibitor. The results indicated that the experimental results are comparable to those obtained In-Silico, and the inhibition effects of Chlorogenic acid (CGA) on papain attained in the experiment were validated (IC50=0.54 mM). CGA as an inhibitor was located in the active site of PLpro and papain (total energy -2009410 and -456069 kJ/mol, respectively) at the desired location and distance. The study revealed that CGA and its derivatives are effective PLpro inhibitors against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Deciphering structural variation upon biotinylation of biotin carboxyl carrier protein domain in Streptococcus pneumoniae

Streptococcus pneumoniae is a leading cause of community-acquired pneumonia and is responsible for acute invasive and non-invasive infections. Fight against pneumococcus is currently hampered by insufficient vaccine coverage and rising antimicrobial resistance, making the research necessary on novel drug targets. High-throughput mutagenesis has shown that acetyl-CoA carboxylase (ACC) is an essential enzyme in S. pneumoniae which converts acetyl-CoA to malonyl-CoA, a key step in fatty acid biosynthesis. ACC has four subunits; Biotin carboxyl carrier protein (BCCP), Biotin carboxylase (BC), Carboxyl transferase subunit α and β. Biotinylation of S. pneumoniae BCCP (SpBCCP) is required for the activation of ACC complex. In this study, we have biophysically characterized the apo- and holo- biotinylating domain SpBCCP80. We have performed 2D and 3D NMR experiments to analyze the changes in amino acid residues upon biotinylation of SpBCCP80. Further, we used NMR backbone chemical shift assignment data for bioinformatical analyses to determine the secondary and tertiary structure of proteins. We observed major changes in AMKVM motif and thumb region of SpBCCP80 upon biotinylation. Overall, this work provides structural insight into the apo- to holo- conversion of SpBCCP80 which can be further used as a drug target against S. pneumoniae.

Examining sialic acid derivatives as potential inhibitors of SARS-CoV-2 spike protein receptor binding domain

Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) has been the primary reason behind the COVID-19 global pandemic which has affected millions of lives worldwide. The fundamental cause of the infection is the molecular binding of the viral spike protein receptor binding domain (SP-RBD) with the human cell angiotensin-converting enzyme 2 (ACE2) receptor. The infection can be prevented if the binding of RBD-ACE2 is resisted by utilizing certain inhibitors or drugs that demonstrate strong binding affinity towards the SP RBD. Sialic acid based glycans found widely in human cells and tissues have notable propensity of binding to viral proteins of the coronaviridae family. Recent experimental literature have used N-acetyl neuraminic acid (Sialic acid) to create diagnostic sensors for SARS-CoV-2, but a detailed interrogation of the underlying molecular mechanisms is warranted. Here, we perform all atom molecular dynamics (MD) simulations for the complexes of certain Sialic acid-based molecules with that of SP RBD of SARS CoV-2. Our results indicate that Sialic acid not only reproduces a binding affinity comparable to the RBD-ACE2 interactions, it also assumes the longest time to dissociate completely from the protein binding pocket of SP RBD. Our predictions corroborate that a combination of electrostatic and van der Waals energies as well the polar hydrogen bond interactions between the RBD residues and the inhibitors influence free energy of binding.Communicated by Ramaswamy H. Sarma.

3D-QSAR, Scaffold Hopping, Virtual Screening, and Molecular Dynamics Simulations of Pyridin-2-one as mIDH1 Inhibitors

Isocitrate dehydrogenase 1 (IDH1) is a necessary enzyme for cellular respiration in the tricarboxylic acid cycle. Mutant isocitrate dehydrogenase 1 (mIDH1) has been detected overexpressed in a variety of cancers. mIDH1 inhibitor ivosidenib (AG-120) was only approved by the Food and Drug Administration (FDA) for marketing, nevertheless, a range of resistance has been frequently reported. In this study, several mIDH1 inhibitors with the common backbone pyridin-2-one were explored using the three-dimensional structure-activity relationship (3D-QSAR), scaffold hopping, absorption, distribution, metabolism, excretion (ADME) prediction, and molecular dynamics (MD) simulations. Comparative molecular field analysis (CoMFA, R2 = 0.980, Q2 = 0.765) and comparative molecular similarity index analysis (CoMSIA, R2 = 0.997, Q2 = 0.770) were used to build 3D-QSAR models, which yielded notably decent predictive ability. A series of novel structures was designed through scaffold hopping. The predicted pIC50 values of C3, C6, and C9 were higher in the model of 3D-QSAR. Additionally, MD simulations culminated in the identification of potent mIDH1 inhibitors, exhibiting strong binding interactions, while the analyzed parameters were free energy landscape (FEL), radius of gyration (Rg), solvent accessible surface area (SASA), and polar surface area (PSA). Binding free energy demonstrated that C2 exhibited the highest binding free energy with IDH1, which was -93.25 ± 5.20 kcal/mol. This research offers theoretical guidance for the rational design of novel mIDH1 inhibitors.