Structural-based virtual screening and identification of novel potent antimicrobial compounds against YsxC of Staphylococcus aureus

Design, synthesis, and mechanism study of novel tetrahydroisoquinoline derivatives as antifungal agents

In screening for natural-derived fungicides, a series of 32 novel tetrahydroisoquinoline derivatives were designed and synthesized based on tetrahydroisoquinoline alkaloids. Their structures were verified by 1H NMR, 13C NMR, HRMS, and single X-ray crystal diffraction analysis. Most of the target products exhibited medium to excellent antifungal activity against 6 phytopathogenic fungi in vitro at a concentration of 50 mg/L. Interestingly, compounds A13 and A25 with EC50 values of 2.375 and 2.251 mg/L against A. alternate were similar to boscalid (EC50 = 1.195 mg/L). The in vivo experiments revealed that A13 presented 51.61 and 70.97% protection activities against A. alternate at the dosage of 50 and 100 mg/L, respectively, which were equal to that of boscalid (64.52 and 77.42%). SDH enzyme assays and molecular docking studies indicated that compound A13 may act on SDH. In addition, the SEM analysis showed that compound A13 could strongly damage the mycelium morphology. These results revealed that A13 may be a promising lead compound for the development of natural-derived fungicides.

Computational investigation of natural compounds as inhibitors against macrolide-resistant protein using virtual screening, molecular docking and MD simulations

Macrolide resistance is the ability of bacteria to survive the effects of macrolide antibiotics, which include drugs such as erythromycin, clarithromycin, and azithromycin. Efforts to combat resistance mechanisms like this frequently involve the discovery and development of new antibiotics or therapeutic strategies capable of overcoming these modifications and restoring the efficacy of current antibiotics. In this study, we explored natural products against enzymes of macrolide resistance Macrolide 2'-phosphotransferase type I (mphA or ErmE), Macrolide 2'-phosphotransferase type II (mphB), Tripartite macrolide-specific efflux pump, Erythromycin esterase EreC, and rRNA methyltransferase (ErmAM) by molecular modelling techniques. The standard precision protocol of the Glide tool was utilized to dock a library of 1,400 natural product compounds from the LOTUS database against various enzymes associated with macrolide resistance. The docking results were assessed using the glide score, and the top ten compounds that were docked to each receptor were selected. Additionally, these selected compounds underwent ADMET analysis, suggesting their potential for therapeutic development. Among the selected compounds, LTS0271681 showed the highest binding affinity against ErmAM, LTS0263188 showed highest binding affinity against Tripartite macrolide-specific efflux pump, LTS0024216 showed the highest binding affinity against mphA, LTS0110759 showed the highest binding affinity against mphB, and LTS0100971 showed the highest binding affinity against EreC. The study incorporated molecular dynamic simulations and MM-GBSA binding free energy calculations to enhance the docking experiments. The results indicate that these compounds could potentially serve as inhibitors of macrolide resistance. However, while computational validations were part of this research, additional in-vitro studies are necessary to develop these potential inhibitors into therapeutic drugs.

Discovery of novel DdlA inhibitors in multidrug-resistant Pseudomonas aeruginosa using virtual screening, molecular docking, and dynamics simulations

Pseudomonas aeruginosa is a gram-negative, opportunistic pathogen that represents a serious risk factor in healthcare services due to its natural resistance mechanisms and the increasing prevalence of multi-drug resistant strains. This study utilized in silico computational approaches to identify the novel inhibitors for D-alanine-D-alanine ligase A (DdlA), an essential enzyme for the bacterial peptidoglycan biosynthesis pathway necessary for cell wall integrity. A structure-based virtual screening of The Medicinal Fungi Secondary Metabolites and Therapeutics (MeFSAT) chemical library was conducted, followed by molecular docking to evaluate the binding affinity of small molecules to the DdlA active site. MSID000191, MSID000200, and MSID000102 were recognized as the leading candidates in the preliminary docking data due to their low binding energy values. These compounds exhibited binding energies markedly superior to the control drug (D-cycloserine), suggesting a substantial potential for inhibiting the DdlA enzyme. Detailed interaction analyses revealed significant salt bridges and hydrogen bonds with active site residues, which enhance the stability of the complex. Density Functional Theory (DFT) analysis and MMPBSA calculations also provided insights into electronic properties and binding free energy, respectively. These findings highlight the potential of these inhibitors as therapeutic candidates and showcase the effectiveness of computational methods in accelerating drug discovery against multidrug-resistant P. aeruginosa. Future research should incorporate more in-silico techniques and experimental validations to confirm these results.

Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models

Vigna sesquipedalis is traditionally used for the treatment of various disorders including diabetes but without scientific rational. Therefore, the current study was designed to evaluate its anti-diabetic potential. Antioxidant activity was assessed through DPPH and ABTS radical scavenging assays, while α-glucosidase and α-amylase inhibitory activities for anti-diabetic potential. Based on in vitro results, acute toxicity tests were performed, followed by in vivo studies using streptozotocin-induced diabetic model in mice. The ethyl acetate fraction exhibited the highest antioxidant potential, followed by crude extract. The methanolic crude extract showed the strongest in vitro antidiabetic activity. It was also found to be non-toxic up to 2000 mg/kg body weight. In vivo, the crude extract significantly (P < 0.05) improved body weight and displayed significant anti-diabetic effects. Further analysis of liver glycogen, serum insulin, glycosylated hemoglobin, and histopathology supported the extract overall performance. The virtual screening results showed highest binding energy of the Cyanidin-3-0-G (Cyanidin) with the amylase, Daucosterol with the GLP1, and Psoralidin with the Glucosidase. Similarly, MD simulation of the top hits was performed to investigate the dynamic stability and results showed that the ligand-protein system remains stable for during the simulation. The thermodynamic stability of the system was assessed by performing the binding free energy calculation using MM-PBSA/GBSA. The results of the binding free energy calculations showed favorable binding energies ligand-protein system. In short, the results illustrated potential as a pharmaceutical drug for insulin-dependent diabetes mellitus.

Inhibition of acyl-homoserine-lactone synthase in Pseudomonas aeruginosa biofilms by 7-O-methyl-aromadendrin by using molecular docking and molecular dynamics simulation

This study investigates the potential of 7-O-methyl aromadendrin (7-OMA), a naturally occurring flavonoid-glycoside, as an inhibitor of acyl-homoserine-lactone (AHL) synthase in Pseudomonas aeruginosa, a key enzyme in quorum sensing and biofilm formation. Using molecular docking and molecular dynamics simulations, we evaluated the binding interactions and inhibitory effects of 7-OMA on AHL synthase. Molecular docking revealed a suitable binding affinity (-6.66 kcal/mol) between 7-OMA and the enzyme, with interactions at critical active site residues. Molecular dynamics simulations demonstrated that 7-OMA stabilizes the enzyme through hydrogen bonds and van der Waals interactions while enhancing its structural flexibility. The average RMSD of AHL synthase increased slightly in the presence of 7-OMA, indicating partial instability of the enzyme. Additionally, the average Rg value increased, suggesting that 7-OMA may expand the enzyme structure or reduce its compactness. MM-PBSA analysis confirmed the strength of these interactions, with favorable van der Waals and electrostatic contributions to the binding energy. These results suggest that 7-OMA disrupts the structural dynamics of AHL synthase, potentially inhibiting biofilm formation and reducing the virulence of Pseudomonas aeruginosa. The findings highlight the therapeutic potential of 7-OMA as a novel inhibitor of AHL synthase, offering a promising strategy to combat biofilm-associated infections. Future studies should focus on evaluating the bioavailability, in vivo efficacy, and clinical applicability of 7-OMA, as well as its broader activity against other multidrug-resistant pathogens.

Graphical abstract

Drug repositioning and experimental validation for targeting ZZ domain of p62 as a cancer treatment

Cancer treatment is often confounded by development of resistance to chemotherapy. This research explores the complex relationship between p62 (also known as SQSTM1), a multifunctional protein central in cancer signaling pathways - especially the NF-κB pathway - and chemoresistance. Our data indicate that disruption of the interaction between p62 and the serine/threonine protein kinase RIP1 is a viable strategy to counteract NF-κB activation and overcome chemoresistance. Employing a comprehensive drug repositioning approach, we utilized bioinformatics tools to perform docking, virtual screening, absorption, distribution, metabolism, and excretion analyses, toxicity analysis, and molecular dynamics simulations to identify FDA-approved drugs that prevent the binding of p62 to RIP1. Notable candidates, particularly montelukast and asunaprevir, blocked the p62-RIP1 interaction, establishing a basis for potential therapeutic interventions against chemoresistant cancers. This study highlights the critical role of the ZZ domain of p62 protein in chemotherapy resistance and sheds light on the possibility of repurposing existing drugs for novel applications in cancer treatment. Our findings provide a solid groundwork for preclinical studies.

Molecular dynamics simulation reveals structural insights into isozyme selectivity of carbonic anhydrase XII inhibitors in hypoxic tumor microenvironment

Human carbonic anhydrase (CA) isoenzymes IX and XII are overexpressed in cancer cells, contributing to tumor microenvironment acidification and representing important targets for cancer therapy. In this study, we identified compound V35 (ZINC09419065) as a selective inhibitor of CA IX and CA XII with enhanced binding stability and selectivity compared to standard inhibitors. We analyzed conserved regions in CA I, CA II, CA IX, and CA XII to investigate their isozyme selectivity, revealing critical selectivity determinants at positions 95, 141, and 203. Molecular docking results indicated that V35 interacts robustly with CA XII, forming a metal ion coordination complex with Zn via HIS94, HIS96, HIS119, and THR199, similar to the interaction pattern of standard inhibitor SLC-0111. Molecular dynamics (MD) simulations conducted over 500 ns under hypoxic conditions showed that V35 has high binding stability, with root mean square deviation (RMSD) and fluctuation (RMSF) values comparable to SLC-0111, demonstrating its conformational stability in CA XII. Binding free energy calculations using the MMGBSA method showed that V35 achieves binding free energy of -44.17 kcal/mol with CA XII, closely matching SLC-0111 (-49.41 kcal/mol). Density functional theory (DFT) calculations further highlighted V35's electrostatic potential distribution, supporting its isozyme selectivity. Post-dynamics analysis indicated that the ester functional groups and the inward movement of HIS64 stabilize V35's interactions in CA XII, a feature absent in CA I.

Computational insights into the targeted inhibition of lipoxygenase in Pseudomonas aeruginosa: hints for drug design

Pseudomonas aeruginosa is regarded as the most opportunistic pathogen. It can induce ferroptosis in humans. It secretes a unique lipoxygenase (LOX) isoform, pLoxA that can oxidize polyenoic fatty acids. Unlike other lipoxygenases, pLoxA can oxygenate membrane phospholipids like phosphatidylethanolamine, leading to hemolysis of red blood cells (RBC). This functional overlap with human 15-LOX that uses the same substrate has provided a bottleneck to the discovery of pLoxA-specific inhibitors and there is an immediate need to find pLoxA specific drugs. The active site of pLoxA is much larger than LOX enzymes, reflecting its ability to accommodate bulky substrates, such as phospholipids. The molecular docking of two experimentally established inhibitors and the further molecular dynamics simulations provided possible key residues in the active site of pLoxA. Our study found that this region is essentially hydrophobic including His 377 and His 382 that are placed to the non-heme iron atom and help to stabilize the inhibitors in the binding site along with hydrophobic residues contribute well toward ligand interactions that involve Phe 415, Ile 416 and Leu 424. MD simulations showed that interactions with those residues were dynamic in nature. Main contribution to binding stability arose via π-π stacking, π-cation, and alkyl interactions.

Exploring the Anticancer Potential of Furanpydone A: A Computational Study on its Inhibition of MTHFD2 Across Diverse Cancer Cell Lines

Cancer poses a significant global health challenge due to its high mortality rate and complex treatment strategies. Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2), which is notably overexpressed in various malignancies, represents a promising target for anticancer drug development. Furanpydone A, a new 4-hydroxy-2-pyridone alkaloid isolated from the endophytic fungus Arthrinium sp. GZWMJZ-606, has shown potent inhibitory activity against several cancer cell lines. This study provides the first computational evaluation of furanpydone A, focusing on its potential inhibition of MTHFD2 through molecular docking and 200 ns molecular dynamics (MD) simulations. Molecular docking revealed a binding free energy of -8.08 kcal/mol for furanpydone A, comparable to the control compound DS44960156 (-8.13 kcal/mol), indicating stable interactions with the MTHFD2 active site. MD simulations confirmed the structural stability of the furanpydone A-MTHFD2 complex, with RMSD values ranging from 1.5 to 2.9 Å, RMSF values below 4 Å, and a radius of gyration (Rg) of 26.7 Å. Furanpydone A maintained approximately four consistent hydrogen bonds throughout the simulation. Analysis of furanpydone A binding pose orientations and interactions with the MTHFD2 enzyme at 0 ns, 40 ns, 80 ns, 120 ns, 160 ns, and 200 ns revealed consistent and stable binding. MM-PBSA analysis showed a binding free energy (ΔGbind) of -23.57 ± 0.13 kcal/mol, with electrostatic and van der Waals interactions contributing significantly, suggesting competitive binding affinity to the control compound (-25.32 ± 0.11 kcal/mol). The contribution of individual amino acid residues, including key residues such as ARG43, TYR84, ASN87, LYS88, GLN132, and PRO314, indicated strong interactions that support the stability of the furanpydone A-MTHFD2 complex. ADMET predictions indicated that furanpydone A met key drug-likeness criteria and demonstrated good oral bioavailability, suitable distribution profile, minimal risk of drug-drug interactions, efficient elimination, and low toxicity potential. These findings suggest that furanpydone A is a promising candidate for cancer treatment, warranting further in vitro and in vivo validation, and highlighting its potential impact on the development of new anticancer therapies.

Unveiling the properties of ascorbic acid against M. tb through in silico approach: A comparative drug-based study

CONTEXT

Tuberculosis (TB) is a highly contagious and potentially life-threatening disease caused by Mycobacterium tuberculosis (M. tb). According to the World Health Organization (WHO), 7.5 million people were diagnosed with TB in 2022. Combating this disease requires ongoing efforts in TB drug discovery and the development of new treatment regimens. Identifying novel drug targets and inhibitory molecules is crucial in the fight against latent TB, particularly due to the rising issue of M. tb drug resistance. In modern drug discovery, the focus has shifted towards identifying new, safe natural compounds with enhanced biological activity against TB. One promising compound is ascorbic acid (Vitamin C), which possesses pro-oxidant properties that generate free radicals along with the first and second-line anti-TB drugs, aiding in the eradication of M. tb during latent infections.

METHODS

In the current research, extensive in silico studies have been conducted to investigate the potential of ascorbic acid as an inhibitor of various M. tb pathways, especially those involving protein folding (chaperone-mediated) and detoxification pathways. The proteins were analysed by various physicochemical and pharmacological parameters. Molecular docking of the selected proteins with existing first-line, second-line drugs and ascorbic acid was performed. Furthermore, the top-scoring molecular docking of ascorbic acid was subjected to Molecular Dynamics Simulation. The 500 ns Molecular Dynamics Simulation studies were carried out by GROMACS v2024.1 using CHARMM27 force field, TIP3P water model and using triclinic box for solvation. The obtained trajectories were analysed through XMGRACE tool.

Synthesis, molecular dynamics simulation and antimicrobial activity of novel s-triazine clubbed with three different hybrid pharmacophores

To address microbial infections and combat drug resistance, we designed, synthesized, and evaluated three novel s-triazine clubbed pharmacophores: 1-acetylpyrazoline (5a-e), 2-aminopyrimidine (6a-e), and 1,5-benzodiazepine (7a-e). These were derived from chalcone (4a-e), showing improved pharmacological profiles. The compounds underwent characterization by FTIR, NMR, and Mass Spectroscopy, and their antimicrobial activities, along with structure-activity relationships (SAR), were assessed using in silico and in vitro methods. Among the tested compounds, 5c, 5e, 6d, 7a, 7d, and 7e demonstrated significant antibacterial activities with MIC values between 50 and 62.5 μg/mL against Staphylococcus aureus, Streptococcus pyogenes, Escherichia coli, and Pseudomonas aeruginosa, which indicates their therapeutic potential. Similarly, 5b, 6a, 6c, 7b, and 7c exhibited vigorous antifungal activities against Candida albicans, Aspergillus niger, and Aspergillus clavatus, indicating their broad-spectrum antifungal efficacy. Moreover, the antitubercular potential of the compounds was evaluated against the Mycobacterium tuberculosis H37Rv strain, identifying 5c, 6a, 6d, 7a, and 7d as promising antimycobacterial agents. Molecular docking and molecular dynamics simulation analyses indicated excellent binding energies and stable complexes for 6c, 6e, 7a, and 7e against selected proteins from E. coli, Mycobacterium tuberculosis, and Candida albicans after 40 ns MD simulation. Compound 7a shows the best antimycobacterial activity, while 6c possessed significant antifungal properties in both in silico and in vitro analyses. Moreover, 7a and 7e exhibited desirable antibacterial activities in both experiment, indicating the synthesized compounds' broad-spectrum efficacy against various bacterial and fungal species.

Identification of novel 3-dehydroquinate dehydratase (DHQD) inhibitors for anti-tuberculosis activity: insights from virtual screening, molecular docking, and dynamics simulations

Tuberculosis (TB) remains a pressing global health concern, causing substantial mortality and morbidity despite existing drugs and vaccines. The escalating challenge of drug-resistant TB underscores the critical need for novel medications. This study focuses on the enzyme 3-hydroquinate dehydratase (DHQD) in the shikimate pathway of Mycobacterium tuberculosis (Mtb), essential for Mtb growth. Using an in silico approach, the crystal structure of DHQD complexed with 1,3,4-trihydroxy-5-(3-phenoxypropyl)-cyclohexane-1-carboxylic acid (CA) was obtained from the Protein Data Bank. After meticulous preparation, a diverse library of 9699 compounds from Zinc and PubChem databases was subjected to virtual screening, complying with Lipinski's rule of five and compounds capable of binding to DHQD with less binding energy. Molecular docking analysis identified eight compounds with highly favorable binding energies, ranging from -8.99 to -8.39 kcal/mol, surpassing CA's -4.93 kcal/mol. To assess their potential as inhibitors, these eight compounds were subjected to scrutiny for pharmacokinetic properties, encompassing Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET). Five compounds (ZINC14981770, ZINC14741224, ZINC14743698, ZINC13165465, and ZINC8442077) demonstrated desirable pharmacokinetic attributes and were selected for further investigation. Subsequent molecular dynamics (MD) simulations and molecular generalized born surface area (MM-GBSA) analyses were conducted. Molecular dynamics (MD) simulations showed that these five compounds formed stable complexes with DHQD over 50 ns, with root mean square deviation (RMSD) values ranging from 1.57 Å to 2.34 Å, indicating high structural stability. In addition, the MM-GBSA binding energy calculations showed that these compounds had favourable binding affinities, with ZINC14981770 exhibiting the lowest free binding energy of -32.70 kcal/mol, followed by ZINC14741224 at -29.67 kcal/mol and ZINC14743698 at -28.79 kcal/mol. These binding energies significantly outperformed the reference compound CA, which had a binding energy of -10.62 kcal/mol. Based on these findings; these five compounds hold promise as potent inhibitors of Mtb DHQD, pending validation through in vitro and in vivo experiments.

Integrated computational biophysics approach for drug discovery against Nipah virus

The Nipah virus (NiV) poses a pressing global threat to public health due to its high mortality rate, multiple modes of transmission, and lack of effective treatments. NiV glycoprotein G (NiV-G) emerges as a promising target for the discovery of NiV drugs because of its essential role in viral entry and membrane fusion. Therefore, in this study, we applied an integrated computational and biophysics approach to identify potential inhibitors of NiV-G within a curated dataset of Peruvian phytochemicals. The virtual screening results indicated that these compounds could represent a natural source of potential NiV-G inhibitors with ΔG values ranging from -8 to -11 kcal/mol. Among them, procyanidin B2, B3, B7, and C1 exhibited the highest binding affinities and formed the most molecular interactions with NiV-G. Molecular dynamics simulations revealed the induced-fit mechanism of NiV-G pocket interaction with these procyanidins, primarily driven by its hydrophobic nature. Non-equilibrium free energy calculations were used to determine binding affinities, highlighting Procyanidin B3 and B2 as the ligands with the most substantial interactions. In general, this work underscores the potential of Peruvian phytochemicals, particularly procyanidins B2, B3, B7, and C1, as lead compounds for developing anti-NiV drugs through an integrated computational biophysics approach.

Antilipase and antioxidant activities of topiramate-phenolic acid conjugates: Computational modelling, synthesis, and in-vitro investigations

A series of ten topiramate-phenolic acid conjugates (T1-T10) were synthesized, and evaluated for their pancreatic lipase inhibitory and antioxidant potentials. The design of the compounds reflected the structural attributes extracted from robust QSAR models developed for predicting the pancreatic lipase inhibition potency. Conjugate T4 competitively inhibited pancreatic lipase with IC50 value of 8.96 μM, comparable to the standard drug, orlistat (IC50 = 11.68 μM). Molecular docking of T4 into the active site of human PL (PDB ID: 1LPB) revealed strong binding score of -11.54 kcal/mol. Molecular dynamics simulation of T4 complexed with pancreatic lipase, confirmed the role of phenolic acid core in stabilizing the ligand through hydrophobic interactions (maximum observed RMSD = 3.77 Å). Additionally, T4 with its LUMO (-0.20254) and HOMO (0.30502) values, abstracted from DFT studies, depicts considerable promise in the pursuit of selecting an effective enzyme inhibitor binding to the enzyme's active site and disrupting its catalytic function. The conjugation of topiramate with phenolic acids has imparted potential antioxidant properties to the synthesized conjugates especially T3, T4 and T5. Conclusively, with good safety profile as predicted from in silico ADMET studies, potent pancreatic lipase inhibition and free radical quenching, T4 stands taller as promising anti-obesity drug candidate.

Network Pharmacology and In silico Elucidation of Phytochemicals Extracted from Ajwa Dates (Phoenix dactylifera L.) to Inhibit Akt and PI3K Causing Triple Negative Breast Cancer (TNBC)

BACKGROUND

About 10-15% of all breast cancers comprise triple-negative breast cancer (TNBC), defined as cancer cells that lack ER, PR, and HER2 protein receptors. Due to the absence of these receptors, treating TNBC using conventional chemotherapy is challenging and, therefore, requires the discovery of novel chemotherapeutic agents derived from natural sources.

OBJECTIVE

The current work was intended to study the potential phytochemicals of Ajwa dates (Phoenix dactylifera L.) with the predicted potential targets (namely, Akt and PI3K) to determine possible TNBC inhibitors.

METHODS

We harnessed network pharmacology, molecular docking, drug-likeness studies, Molecular Dynamics (MD) simulation, and binding free energy (MM-GBSA) calculation to get phytochemicals with potential effects against TNBC. Firstly, molecular docking was performed on 125 phytochemicals against the Akt and PI3K proteins utilizing PyRx. Then, the phytochemicals with the highest binding affinity (≤ -8.1 kcal/mol) were examined for in silico drug-likeness and toxicity profiles. Finally, phytochemicals with optimal druglikeness and toxicity profiles were studied by Molecular Dynamics (MD) simulation and binding free energy (MM-GBSA) to identify compounds that can form stable complexes.

RESULTS

The results of the network pharmacology revealed that the Akt and PI3K proteins are potential targets of TNBC for the phytochemicals of Phoenix dactylifera L. used in this study. The outcomes of molecular docking displayed that among 125 phytochemicals, 42 of them (with a binding affinity ≤ -8.1 kcal/mol) have potentially inhibiting effects on both proteins PI3K and Akt expressed in TNBC. Then, the results of in silico drug-likeness identified seven phytochemicals with optimal pharmacokinetic profiles. Furthermore, toxicity studies showed that three phytochemicals (namely, Chrysoeriol, Daidzein, and Glycitein) did not cause any toxicities. Finally, the Molecular Dynamics (MD) simulation studies and binding free energy (MM-GBSA) verified that Daidzein stayed within the binding cavities of both proteins (Akt and PI3K) by establishing a stable protein-ligand complex during simulation.

CONCLUSION

Taken together, the current work emphasizes the potential effects of Daidzein from Phoenix dactylifera L. against TNBC, and it can be further studied to establish it as a standard chemotherapy for TNBC.

Elucidating the potential of bioactive of Trichoderma sp.. in combating pathogenesis by Fusarium sp.. by targeting pectin lyases: a bioinformatics approach

Pectin lyase is an industrially important enzyme, predominately used in fruit juice clarification and retting of fibers. It also promotes pathogenesis via the degradation of the pectin. The phytopathogen, Fusarium infects various crops and causes several diseases. Trichoderma sp. is a promising biocontrol agent that is vital in maintaining plant health and disease prevention. In the current study, a computational approach utilizing structure prediction, molecular docking, molecular dynamics, and MM-PBSA analysis was used to analyze the potential role of bioactive compounds secreted by Trichoderma sp. in inhibiting the pectin lyase enzyme from Fusarium proliferatum, F. fujikuroi, F. graminearum, F. oxysporum and F. verticillioides. Molecular docking with secondary metabolites revealed that Viridiofungin A secreted by Trichoderma harzianum and Virone secreted by T. virens are bioactive compounds with immense potential to inhibit PNLs of Fusarium species. Further, the rigidity of the structure and stability of the docked complex were confirmed via Molecular dynamic simulations assessed through multiple parameters from the simulation trajectory data. Dual culture assay of T. harzianum and T. virens with F. proliferatum, F. fujikuroi, F. graminearum, F. oxysporum, and F. verticillioides showed variable mycelial inhibition. The research provides insight into the potential of the bioactive compounds secreted by Trichoderma species as an effective agent for the inhibition of pectin lyases produced by phytopathogens, especially Fusarium species. The proposed research can be used to develop bioformulations that function as biopesticides, offering a sustainable replacement for chemical products.

Modeling of FAK-PROTAC candidates from GSK2256098 analogs for targeted protein degradation

Protein inhibition via the traditional drug-designing approach has been shown to be an effective method for developing numerous small-molecule-based therapeutics. In the last decade, small inhibitors-guided protein degradation has arisen as an alternative method with the potential to fulfill the drug requirement for undruggable targets. Focal adhesion kinase (FAK) is a crucial modulator of the growth and spread of tumors, apart from it also acts as a scaffold for signaling of other proteins. FAK inhibitors have thus far had unsatisfactory results in clinical trials for cancer applications. Unlike prior attempts to control FAK expression, which were restricted to kinase domain inhibition with limited success in clinical research, protein degradation has the potential to concurrently disrupt FAK's kinase and scaffolding function. Recently, several FAK degraders were reported based on FAK Type I inhibitors using complex chemical synthesis approaches. Interestingly, recently a ternary complex was published revealing the binding mode of the FAK-PROTAC-E3 complex. This complex opens an avenue for the development of rational PROTAC design against FAK protein. Therefore, in the present study, we selected the most active Type I FAK inhibitor GSK2256098. The binding mode of the inhibitor prompted us to identify the most suitable analog for PROTAC design. We have identified a high-affinity analog that is suitable for PTOTAC design through the application of molecular docking (MD) and molecular dynamics simulations (MDS). Further based on the ternary FAK-PROTAC-E3 complex we build a binary complex FAK-Hit-E3-VHL between both proteins. Using the structure-based approach ten different potential FAK PROTACs candidates were designed. The stability of the complexes was analyzed using MDS and binding free energies were used to predict the binding affinity. Finally, based on desirable intermolecular interactions with the target and E3 ligase ProTAC4 was selected as the best candidate when compared with known FAK PROTAC GSK215.

A comprehensive computer-based assessment of Deacetylnomilin as an inhibitor for antibiotic-resistant genes identified from the whole genome sequence of the multidrug-resistant Enterobacter cloacae isolate 1382

The twenty-first century presents a serious threat to public health due to the growth in antibiotic resistance among opportunistic bacteria, particularly within the ESKAPE group, which includes Enterobacter species with high morbidity, mortality, virulence, and nosocomial dissemination rates. Enterobacter species, especially Enterobacter cloacae, bacteria have developed resistance to multiple antibiotics through mechanisms, such as continuous production of AmpC beta-lactamase. In this study, a comprehensive bioinformatics approach was employed to analyze the genome of Enterobacter cloacae, utilizing sequence data from GenBank (ID: OW968328.1). The AbritAMR and ResFinder tools were utilized to identify antibiotic-resistant genes, which included the presence of blaOXA-48, blaCMH, FosA, OqxA, and OqxB each conferring resistance to specific antibiotics such as β-lactams and fluoroquinolones. These proteins were analyzed using bioinformatics tools such as ProtParam, SOPMA, Robetta, I-TASSER, AlphaFold, and PROCHECK to investigate different structural models and their properties. The models from AlphaFold had the best quality in terms of structural accuracy, providing valuable insights into the 3D conformations of these resistant proteins. Based on the Molecular docking studies, these constructed targets were docked with 20 natural compounds known for their activity against Gram-negative bacteria. Among them, Deacetylnomilin showed the highest docking score and passed their ADMET properties. Molecular dynamic (MD) simulation was conducted for 100 ns for Deacetylnomilin with different resistant proteins. Deacetylnomilin exhibited more favorable binding free energies compared to the reference compounds across all five proteins, indicating higher stability and affinity. These results suggest that Deacetylnomilin could be an effective inhibitor against the resistant proteins of Enterobacter cloacae, making it a promising candidate for further drug development.

Gaining molecular insights towards inhibition of foodborne fungi Aspergillus fumigatus by a food colourant violacein via computational approach

Filamentous Fungal Human Pathogens (FFHPs) such as Aspergillus fumigatus, are growing resistant to currently available antifungal drugs. One possible target, the Nucleoside diphosphate kinase (Ndk) is significant for nucleotide biosynthesis and crucial for fungal metabolism. Violacein, a natural food colorant, was examined for its antifungal effects against Aspergillus fumigatus via computational approach against the Ndk protein. Known and predicted interactions of Ndk with proteins was performed using the STRING application. Molecular docking was performed using Schrodinger Maestro software (V.14.1) under enhanced precision docking, with OPLS4 forcefield. MDS was performed for 500ns under OPLS4 forcefield and the TIP3P solvent system. The geometry optimization for DFT was performed using the Becke 3-parameter exchange functional (B3LYP) method. The Molecular Docking Studies revealed significant interactions with good binding energy between Violacein and Ndk. Subsequent MD Simulations confirmed the stability of Violacein-Ndk complex, compared to the reference ligand-complex, indicating a stable interaction between the protein and violacein. The energy band gap of violacein was found to be 0.072567 eV suggesting its softness with lower kinetic stability and higher chemical reactivity. The results suggest Violacein could potentially disrupt nucleotide metabolism by targeting Ndk, thus demonstrating antifungal activity. However, further experimental validation is required to confirm these computational findings and explore the practical use of Violacein in antifungal treatments.

Unraveling the mechanism of carbonic anhydrase IX inhibition by alkaloids from Ruta chalepensis: A synergistic analysis of in vitro and in silico data

Due to the pivotal role of carbonic anhydrase IX (CA IX) in pathological conditions, there's a pressing need for novel inhibitors to improve patient outcomes and clinical management. Herein, we investigated the inhibitory efficacy of six alkaloids from Ruta chalepensis against CA IX through in vitro inhibition assay and computational modeling. Skimmianine and maculosidine displayed significant inhibitory activity in vitro, with low IC50 values of 105.2 ± 3.2 and 295.7 ± 14.1 nM, respectively. Enzyme kinetics analyses revealed that skimmianine exhibited a mixed inhibition mode, contrasting with the noncompetitive inhibition mechanism observed for the reference drug (acetazolamide), as indicated by intersecting lines in the Lineweaver-Burk plots. The findings of docking calculations revealed that skimmianine and maculosidine exhibited extensive polar interactions with the enzyme. These alkaloids demonstrate substantial binding interactions and occupy identical binding site as acetazolamide, thereby enhancing their efficacy as inhibitors of CA IX. Utilizing a 100 ns molecular dynamics (MD) simulation, the dynamic interactions between isolated alkaloids and CA IX were intensively assessed. Analysis of diverse MD parameters revealed that skimmianine and maculosidine displayed consistent trajectories and notable energy stabilization during their interaction with CA IX. The findings of MM/PBSA analysis depicted the minimum binding free energy for skimmianine and maculosidine. In addition, the Potential Energy Landscape (PEL) analysis revealed distinct and stable conformational states for the CA IX-ligand complexes, with Skimmianine showing the most stable and lowest energy configuration. These computational findings align with experimental results, emphasizing the potential efficacy of skimmianine and maculosidine as inhibitors of CA IX.

Discovery of potential natural therapeutics targeting cell wall biosynthesis in multidrug-resistant Enterococcus faecalis: a computational perspective

BACKGROUND

Identifying therapeutic inhibitors of crucial enzymes involved in the peptidoglycan biosynthesis pathway is pivotal for developing new treatments against multidrug-resistant Enterococcus faecalis V583. MurM, an essential enzyme in this pathway, plays a significant role in the bacterium's cell wall synthesis, making it an attractive druggable target for novel antimicrobial strategies. This study explored the potential of natural compounds as inhibitors of MurM, aiming to discover promising drug candidates that could serve as the foundation for future therapeutic development.

METHODS

The three-dimensional structure of MurM was predicted, optimized, and its binding pocket was analyzed by comparing it with related structures. Over 4,70,000 natural compounds from the COCONUT database were subjected to virtual high-throughput screening (vHTS). The top lead candidates were selected based on their Lipinski's profile, ADME profile, toxicity profile, estimated binding free energy (ΔG) and estimated inhibition constant (Ki). Interaction pattern analysis was used to evaluate the non-covalent interactions between the inhibitors and key residues in MurM's binding pocket. Molecular dynamics simulations were performed over 300 ns to assess the structural stability and impact of these inhibitors on MurM's enzyme.

RESULTS

Three lead compounds-CNP0056520, CNP0126952, and CNP0248480-were identified and prioritized with estimated ΔG ranging from - 9.35 to -7.9 kcal/mol. Molecular dynamics simulations revealed minimal impact on MurM's overall structure and dynamics, with the candidate inhibitors forming stable protein-ligand complexes. These interactions were supported by several non-covalent interactions between the candidate inhibitors and key residues within MurM's binding pocket.

CONCLUSION

These findings suggest that the identified natural product candidates could serve as promising inhibitors of MurM, potentially leading to novel therapeutics targeting cell wall biosynthesis in multidrug-resistant E. faecalis.

Targeting Matrix Metalloproteinase-3 for Dental Caries Prevention Using Herbal Isolates: MMP3 Inhibition by Cinnamic Acids

Objectives: Dental caries, a prevalent infectious disease affecting teeth, ranks highest among 328 diseases, according to a 2017 Lancet study. In demineralized human dentin, matrix metalloproteinase-3 (MMP3) functions as a proteoglycanase, contributing to the degradation of proteoglycan components. This process exposes collagen fibrils, thereby facilitating the demineralization of the dentin matrix. Inhibiting MMP3 shows potential for preventing dental caries. Methods: The binding affinity of 20 cinnamic acid derivatives, namely cynarin, chlorogenic acid, rosmarinic acid, cinnamyl caffeate, phenethyl caffeate, N-p-coumaroyltyramine, caffeic acid 3-glucoside, caffeic acid phenethyl ester, roscovitine, benzyl caffeate, o-coumaric acid, artepillin C, caffeic acid, methyl caffeate, 2-methylcinnamic acid, ferulic acid, drupanin, p-coumaric acid, cinnamic acid, and sinapinic acid, to the MMP3 catalytic cleft, was assessed utilizing AutoDock 4.0. Molecular dynamics simulation was then employed to analyze the stability of backbone atoms in free MMP3, MMP3-positive control inhibitor, and MMP3 complexed with the top-ranked cinnamic acid over a 100 ns computer simulation. Results: Four cinnamic acids demonstrated ΔG binding scores below -10 kcal/mol, with cynarin emerging as the most potent MMP3 inhibitor, featuring a ΔG binding score and inhibition constant value of -15.57 kcal/mol and 3.83 pM, respectively. The MMP3-cynarin complex exhibited stability after a 50 ns computer simulation, showing a root-mean-square deviation of 8 Å. Conclusions: The inhibition of MMP3 by cynarin, chlorogenic acid, rosmarinic acid, and cinnamyl caffeate holds promise as a potential preventive strategy for dental caries.

Computational targeting of iron uptake proteins in Covid-19 induced mucormycosis to identify inhibitors via molecular dynamics, molecular mechanics and density function theory studies

Mucormycosis is a concerning invasive fungal infection with difficult diagnosis, high mortality rates, and limited treatment options. Iron availability is crucial for fungal growth that causes this disease. This study aimed to computationally target iron uptake proteins in Rhizopus arrhizus, Lichtheimia corymbifera, and Mucor circinelloides to identify inhibitors, thereby halting fungal growth and intervening in mucormycosis pathogenesis. Seven important iron uptake proteins were identified, modeled, and validated using Ramachandran plots. An in-house antifungal library of ~ 15,401 compounds was screened in molecular docking studies with these proteins. The best small molecule-protein complexes were simulated at 100 ns using Maestro, Schrodinger. Toxicity predictions suggested all six molecules, identified as the best binding compounds to seven proteins, belonged to lower toxicity levels per GHS classification. A molecular mechanics GBSA study for all seven complexes indicated low standard deviations after calculating free binding energies every 10 ns of the 100 ns trajectory. Density functional theory via quantum mechanics approaches highlighted the HOMO, LUMO, and other properties of the six best-bound molecules, revealing their binding capabilities and behaviour. This study sheds light on the molecular mechanisms and protein-ligand interactions, providing a multi-dimensional view towards the use of FDBD01920, FDBD01923, and FDBD01848 as stable antifungal ligands.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00264-7.

Microbiological Characteristics of Clinically Isolated Staphylococcus aureus with Different Hemolytic Phenotypes in China

Purpose

This study aimed to investigate the microbiological characteristics of clinically isolated Staphylococcus aureus with different hemolytic phenotypes in China.

Materials and Methods

Using the three-point inoculation method, the hemolytic phenotypes of 1295 clinically isolated S. aureus strains were detected and categorized. Antimicrobial susceptibility testing of all strains was performed using a VITEK 2 Compact System. After sample size matching, plasma coagulase activity, catalase activity, mRNA expression of hemolysin genes (hla, hlb, hlc, and hld), biofilm formation, growth kinetics, inflammatory response of macrophages and cytotoxicity of S. aureus with different hemolytic phenotypes using the rabbit plasma kit, the catalase test on slides, qRT-PCR, crystal violet staining, the microcultivation assay, the ELISA kits, and the CCK-8 assay, respectively.

Results

Seven categories of hemolytic phenotypes were identified. Accordingly, strains were categorized into seven different groups, including S. aureus with complete hemolytic phenotype (SCHP), S. aureus with weak hemolytic phenotype (SWHP), S. aureus with incomplete hemolytic phenotype 1 (SIHP-1), SIHP-2, SIHP-3, SIHP-4 and SIHP-5, the last three of which were reported for the first time. Except for the hemolytic phenotype, all seven groups differed in clinical isolation rates, antibiotic resistance profile, plasma coagulase activity, mRNA expression of hemolysin genes, biofilm formation, growth kinetics, inflammatory response of macrophages, and cytotoxicity.

Conclusion

S. aureus with different hemolytic phenotypes have distinctive microbiological characteristics. Clinical microbiologists need to be vigilant about the hemolytic phenotypes when culturing S. aureus strains, and actively enhance communication with clinicians to optimize the treatment of infection.

Human UDP-glucuronosyltransferase 1As catalyze aristolochic acid D O-glucuronidation to form a lesser nephrotoxic glucuronide

ETHNOPHARMACOLOGICAL RELEVANCE

Aristolochic acids (AAs) are naturally occurring nitro phenanthrene carboxylic acids primarily found in plants of the Aristolochiaceae family. Aristolochic acid D (AAD) is a major constituent in the roots and rhizomes of the Chinese herb Xixin (the roots and rhizomes of Asarum heterotropoides F. Schmidt), which is a key material for preparing a suite of marketed Chinese medicines. Structurally, AAD is nearly identical to the nephrotoxic aristolochic acid I (AAI), with an additional phenolic group at the C-6 site. Although the nephrotoxicity and metabolic pathways of AAI have been well-investigated, the metabolic pathway(s) of AAD in humans and the influence of AAD metabolism on its nephrotoxicity has not been investigated yet.

AIM OF THE STUDY

To identify the major metabolites of AAD in human tissues and to characterize AAD O-glucuronidation kinetics in different enzyme sources, as well as to explore the influence of AAD O-glucuronidation on its nephrotoxicity.

MATERIALS AND METHODS

The O-glucuronide of AAD was biosynthesized and its chemical structure was fully characterized by both 1H-NMR and 13C-NMR. Reaction phenotyping assays, chemical inhibition assays, and enzyme kinetics analyses were conducted to assess the crucial enzymes involved in AAD O-glucuronidation in humans. Docking simulations were performed to mimic the catalytic conformations of AAD in human UDP-glucuronosyltransferases (UGTs), while the predicted binding energies and distances between the deprotonated C-6 phenolic group of AAD and the glucuronyl moiety of UDPGA in each tested human UGT isoenzyme were measured. The mitochondrial membrane potentials (MMP) and reactive oxygen species (ROS) levels in HK-2 cells treated with either AAI, or AAD, or AAD O-glucuronide were tested, to elucidate the impact of O-glucuronidation on the nephrotoxicity of AAD.

RESULTS

AAD could be rapidly metabolized in human liver and intestinal microsomes (HLM and HIM, respectively) to form a mono-glucuronide, which was purified and fully characterized as AAD-6-O-β-D-glucuronide (AADG) by NMR. UGT1A1 was the predominant enzyme responsible for AAD-6-O-glucuronidation, while UGT1A9 contributed to a lesser extent. AAD-6-O-glucuronidation in HLM, HIM, UGT1A1 and UGT1A9 followed Michaelis-Menten kinetics, with the Km values of 4.27 μM, 9.05 μM, 3.87 μM, and 7.00 μM, respectively. Docking simulations suggested that AAD was accessible to the catalytic cavity of UGT1A1 or UGT1A9 and formed catalytic conformations. Further investigations showed that both AAI and AAD could trigger the elevated intracellular ROS levels and induce mitochondrial dysfunction and in HK-2 cells, but AADG was hardly to trigger ROS accumulation and mitochondrial dysfunction.

CONCLUSION

Collectively, UGT1A-catalyzed AAD 6-O-glucuronidation represents a crucial detoxification pathway of this naturally occurring AAI analogs in humans, which is very different from that of AAI.

Identification of novel CA IX inhibitor: Pharmacophore modeling, docking, DFT, and dynamic simulation

Human Carbonic anhydrase IX (hCA IX) is found to be an essential biomarker for the treatment of hypoxic tumors in both the early and metastatic stages of cancer. Due to its active function in maintaining pH levels and overexpression in hypoxic conditions, hCA IX inhibitors can be a potential candidate specifically designed to target cancer development at various stages. In search of selective hCA IX inhibitors, we developed a pharmacophore model from the existing natural product inhibitors with IC50 values less than 50 nm. The identified hit molecules were then investigated on protein-ligand interactions using molecular docking experiments followed by molecular dynamics simulations. Among the zinc database 186 hits with an RMSD value less than 1 were obtained, indicating good contact with key residues HIS94, HIS96, HIS119, THR199, and ZN301 required for optimum activity. The top three compounds were subjected to molecular dynamics simulations for 100 ns to know the protein-ligand complex stability. Based on the obtained MD simulation results, binding free energies are calculated. Density Functional Theory (DFT) studies confirmed the energy variation between the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO). The current study has led to the discovery of lead compounds that show considerable promise as hCA IX inhibitors and suggests that three compounds with special molecular features are more likely to be better-inhibiting hCA IX. Compound S35, characterized by a higher stability margin and a smaller energy gap in quantum studies, is an ideal candidate for selective inhibition of CA IX.

Structural insight into the binding mode of cefotaxime and meropenem to TEM-1, SHV-1, KPC-2, and Amp-C type beta-lactamases

Antimicrobial resistance is an emerging threat to public health around the world. The study employs computational and biophysical methods to investigate the properties of cefotaxime and meropenem's binding to various beta-lactamases like TEM-1, SHV-1, KPC-2, and Amp-C. The enzyme kinetics of purified proteins revealed an increase in Michaelis constant (Km) value in the presence of meropenem and cefotaxime, indicating a decrease in enzyme affinity for nitrocefin. Proteins interact with meropenem/cefotaxime, causing quenching through complex formation. All proteins have one binding site, and binding constant (Kb) values are 104, indicating strong interaction. The study found that meropenem and cefotaxime had high fitness scores for Amp-C, KPC-2,TEM-1 and SHV-1, with binding energy ranging from -7.4 to -7.8, and hydrogen bonds between them. Molecular Dynamic simulation of protein-ligand complexes revealed cefotaxime-binding proteins have slightly lower Root Mean Square Deviation(RMSD) than meropenem-binding proteins, indicating stable association antibiotics with these proteins.

3D computer modeling of inhibitors targeting the MCF-7 breast cancer cell line

This study focused on developing new inhibitors for the MCF-7 cell line to contribute to our understanding of breast cancer biology and various experimental techniques. 3D QSAR modeling was used to design new tetrahydrobenzo[4, 5]thieno[2, 3-d]pyrimidine derivatives with good characteristics. Two robust 3D-QSAR models were developed, and their predictive capacities were confirmed through high correlations [CoMFA (Q2 = 0.62, R 2 = 0.90) and CoMSIA (Q2 = 0.71, R 2 = 0.88)] via external validations (R2 ext = 0.90 and R2 ext = 0.91, respectively). These successful evaluations confirm the potential of the models to provide reliable predictions. Six candidate inhibitors were discovered, and two new inhibitors were developed in silico using computational methods. The ADME-Tox properties and pharmacokinetic characteristics of the new derivatives were evaluated carefully. The interactions between the new tetrahydrobenzo[4, 5]thieno[2, 3-d]pyrimidine derivatives and the protein ERα (PDB code: 4XO6) were highlighted by molecular docking. Additionally, MM/GBSA calculations and molecular dynamics simulations provided interesting information on the binding stabilities between the complexes. The pharmaceutical characteristics, interactions with protein, and stabilities of the inhibitors were examined using various methods, including molecular docking and molecular dynamics simulations over 100 ns, binding free energy calculations, and ADME-Tox predictions, and compared with the FDA-approved drug capivasertib. The findings indicate that the inhibitors exhibit significant binding affinities, robust stabilities, and desirable pharmaceutical characteristics. These newly developed compounds, which act as inhibitors to mitigate breast cancer, therefore possess considerable potential as prospective drug candidates.

Molecular modeling and simulation approaches to characterize potential molecular targets for burdock inulin to instigate protection against autoimmune diseases

In the current study, we utilized molecular modeling and simulation approaches to define putative potential molecular targets for Burdock Inulin, including inflammatory proteins such as iNOS, COX-2, TNF-alpha, IL-6, and IL-1β. Molecular docking results revealed potential interactions and good binding affinity for these targets; however, IL-1β, COX-2, and iNOS were identified as the best targets for Inulin. Molecular simulation-based stability assessment demonstrated that inulin could primarily target iNOS and may also supplementarily target COX-2 and IL-1β during DSS-induced colitis to reduce the role of these inflammatory mechanisms. Furthermore, residual flexibility, hydrogen bonding, and structural packing were reported with uniform trajectories, showing no significant perturbation throughout the simulation. The protein motions within the simulation trajectories were clustered using principal component analysis (PCA). The IL-1β-Inulin complex, approximately 70% of the total motion was attributed to the first three eigenvectors, while the remaining motion was contributed by the remaining eigenvectors. In contrast, for the COX2-Inulin complex, 75% of the total motion was attributed to the eigenvectors. Furthermore, in the iNOS-Inulin complex, the first three eigenvectors contributed to 60% of the total motion. Furthermore, the iNOS-Inulin complex contributed 60% to the total motion through the first three eigenvectors. To explore thermodynamically favorable changes upon mutation, motion mode analysis was carried out. The Free Energy Landscape (FEL) results demonstrated that the IL-1β-Inulin achieved a single conformation with the lowest energy, while COX2-Inulin and iNOS-Inulin exhibited two lowest-energy conformations each. IL-1β-Inulin and COX2-Inulin displayed total binding free energies of - 27.76 kcal/mol and - 37.78 kcal/mol, respectively, while iNOS-Inulin demonstrated the best binding free energy results at - 45.89 kcal/mol. This indicates a stronger pharmacological potential of iNOS than the other two complexes. Thus, further experiments are needed to use inulin to target iNOS and reduce DSS-induced colitis and other autoimmune diseases.

Anticholinesterase activities of novel isoindolin-1,3-dione-based acetohydrazide derivatives: design, synthesis, biological evaluation, molecular dynamic study

In pursuit of developing novel cholinesterase (ChE) inhibitors through molecular hybridization theory, a novel series of isoindolin-1,3-dione-based acetohydrazides (compounds 8a-h) was designed, synthesized, and evaluated as possible acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitors. In vitro results revealed IC50 values ranging from 0.11 ± 0.05 to 0.86 ± 0.02 µM against AChE and 5.7 ± 0.2 to 30.2 ± 2.8 µM against BChE. A kinetic study was conducted on the most potent compound, 8a, to ascertain its mode of inhibition, revealing its competitive mode against AChE. Furthermore, the binding interaction modes of the most active compound within the AChE active site was elucidated. Molecular dynamics simulations of compound 8a were performed to assess the stability of the 8a-AChE complex. In silico pharmacokinetic predictions for the most potent compounds indicated their potential as promising lead structure for the development of new anti-Alzheimer's disease (anti-AD) agents.

Iso-mukaadial acetate and ursolic acid acetate bind to Plasmodium Falciparum heat shock protein 70: towards targeting parasite protein folding pathway

Plasmodium falciparum is the most lethal malaria parasite. P. falciparum Hsp70 (PfHsp70) is an essential molecular chaperone (facilitates protein folding) and is deemed a prospective antimalarial drug target. The present study investigates the binding capabilities of select plant derivatives, iso-mukaadial acetate (IMA) and ursolic acid acetate (UAA), against P. falciparum using an in silico docking approach. The interaction between the ligands and PfHsp70 was evaluated using plasmon resonance (SPR) analysis. Molecular docking, binding free energy analysis and molecular dynamics simulations were conducted towards understanding the mechanisms by which the compounds bind to PfHsp70. The molecular docking results revealed ligand flexibilities, conformations and positions of key amino acid residues and protein-ligand interactions as crucial factors accounting for selective inhibition of Hsp70. The simulation results also suggest protein-ligand van der Waals forces as the driving force guiding the interaction of these compounds with PfHsp70. Of the two compounds, UAA and IMA bound to PfHsp70 within the micromolar range based on surface plasmon resonance (SPR) based binding assay. Our findings pave way for future rational design of new selective compounds targeting PfHsp70.

In silico investigation of cholesterol-lowering drugs to find potential inhibitors of dehydrosqualene synthase in Staphylococcus aureus

Staphylococcus aureus is a lethal pathogen that can cause various bacterial infections. This study targets the CrtM enzyme of S. aureus, which is crucial for synthesizing golden carotenoid pigment: staphyloxanthin, which provides anti-oxidant activity to this bacterium for combating antimicrobial resistance inside the host cell. The present investigation quests for human SQS inhibitors against the CrtM enzyme by employing structure-based drug design approaches including induced fit docking (IFD), molecular dynamic (MD) simulations, and binding free energy calculations. Depending upon the docking scores, two compounds, lapaquistat acetate and squalestatin analog 20, were identified as the lead molecules exhibit higher affinity toward the CrtM enzyme. These docked complexes were further subjected to 100 ns MD simulation and several thermodynamics parameters were analyzed. Further, the binding free energies (ΔG) were calculated for each simulated protein-ligand complex to study the stability of molecular contacts using the MM-GBSA approach. Pre-ADMET analysis was conducted for systematic evaluation of physicochemical and medicinal chemistry properties of these compounds. The above study suggested that lapaquistat acetate and squalestatin analog 20 can be selected as potential lead candidates with promising binding affinity for the S. aureus CrtM enzyme. This study might provide insights into the discovery of potential drug candidates for S. aureus with a high therapeutic index.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03862-y.

Mechanisms Involved in Therapeutic Effects of Scutellaria baicalensis Georgi in Oral Squamous Cell Carcinoma Based on Systems Biology and Structural Bioinformatics Approaches

Objective

Oral squamous cell carcinoma (OSCC) is the most frequent oral cancer, constituting more than 90% of all oral carcinomas. The 5-year survival rate of OSCC patients is not satisfactory, and therefore, there is an urgent need for new practical therapeutic approaches besides the current therapies to overcome OSCC. Scutellaria baicalensis Georgi (SBG) is a plant of the family Lamiaceae with several pharmaceutical properties such as antioxidant, anti-inflammatory, and anticancer effects. Previous studies have demonstrated the curative effects of SBG in OSCC.

Methods

A systems biology approach was conducted to identify differentially expressed miRNAs (DEMs) in OSCC patients with a dismal prognosis compared to OSCC patients with a favorable prognosis. A protein interaction map (PIM) was built based on DEMs targets, and the hub genes within the PIM were indicated. Subsequently, the prognostic role of the hubs was studied using Kaplan-Meier curves. Next, the binding affinity of SBG's main components, including baicalein, wogonin, oroxylin-A, salvigenin, and norwogonin, to the prognostic markers in OSCC was evaluated using molecular docking analysis.

Results

Survival analysis showed that overexpression of CAV1, SERPINE1, ACTB, SMAD3, HMGA2, MYC, EIF2S1, HSPA4, HSPA5, and IL6 was significantly related to a poor prognosis in OSCC. Besides, molecular docking analysis demonstrated the ΔGbinding and inhibition constant values between SBG's main components and SERPINE1, ACTB, HMGA2, EIF2S1, HSPA4, and HSPA5 were as <-8.00 kcal/mol and nanomolar concentration, respectively. The most salient binding affinity was observed between wogonin and SERPINE1 with a criterion of ΔGbinding < -10.02 kcal/mol.

Conclusion

The present results unraveled potential mechanisms involved in therapeutic effects of SBG in OSCC based on systems biology and structural bioinformatics analyses.

Structural Insights into the Catalytic Activity of Cyclobacterium marinum N-Acetylglucosamine Deacetylase

N-Acetylglucosamine deacetylase from Cyclobacterium marinum (CmCBDA) is a highly effective and selective biocatalyst for the production of d-glucosamine (GlcN) from N-acetylglucosamine (GlcNAc). However, the underlying catalytic mechanism remains elusive. Here, we show that CmCBDA is a metalloenzyme with a preference for Ni2+ over Mn2+. Crystal structures of CmCBDA in complex with Ni2+ and Mn2+ revealed slight remodeling of the CmCBDA active site by the metal ions. We also demonstrate that CmCBDA exists as a mixture of homodimers and monomers in solution, and dimerization is indispensable for catalytic activity. A mutagenesis analysis also indicated that the active site residues Asp22, His72, and His143 as well as the residues involved in dimerization, Pro52, Trp53, and Tyr55, are essential for catalytic activity. Furthermore, a mutation on the protein surface, Lys219Glu, resulted in a 2.3-fold improvement in the deacetylation activity toward GlcNAc. Mechanistic insights obtained here may facilitate the development of CmCBDA variants with higher activities.

Ginkgolide B attenuates cerebral ischemia-reperfusion injury via inhibition of ferroptosis through disrupting NCOA4-FTH1 interaction

ETHNOPHARMACOLOGICAL RELEVANCE

Cerebral ischemia/reperfusion (I/R) injury is a major cause of neuronal damage and death. Ginkgolide B (GB) has been shown to exhibit neuroprotective effects in various brain injury models.

AIM OF STUDY

The aim of study was to investigate the potential role of GB in protecting against cerebral I/R injury and explore the underlying mechanisms.

MATERIALS AND METHODS

Adult male Sprague-Dawley rats were exposed to transient middle cerebral artery occlusion (tMCAO) followed by reperfusion in order to trigger cerebral I/R injury. The rats were treated with different doses of GB, vehicle control or positive drug. Neurological function, infarct volume, and levels of ferroptosis markers were evaluated. In vitro experiments were performed using OGD/R-induced PC12 cells to further investigate the effects of GB on ferroptosis and its mechanisms. In addition, molecular docking, and microscale thermophoresis (MST) assay were conducted to explore the combination of GB and NCOA4.

RESULTS

Reduced infarct volume and enhanced neurological function were signs of dose-dependent protection from cerebral I/R injury by GB therapy. Additionally, GB treatment had an impact on the levels of oxidative stress and ferroptosis markers, including reactive oxygen species (ROS), malondialdehyde (MDA), superoxide dismutase (SOD), and Fe2+ in the cerebral environment during IR injury. Moreover, relevant ferroptosis key factors such as ACSL4, GPX4, FTH1, and NCOA4 can be regulated by GB. In OGD/R-induced PC12 cells, GB protected against ferroptosis by inhibiting autophagy and disrupting the interaction of NCOA4-FTH1.

CONCLUSION

Our findings suggest that GB may protect against cerebral I/R injury by inhibiting ferroptosis through disrupting NCOA4-FTH1 interaction. GB has potential therapeutic applications for cerebral I/R injury, and further investigation of the underlying mechanisms and clinical trials are warranted.

Molecular Modelling of Resveratrol Derivatives with SIRT1 for the Stimulation of Deacetylase Activity

BACKGROUND

Resveratrol is a polyphenol that is found in plants and has been proposed to have a potential therapeutic effect through the activation of SIRT1, which is a crucial member of the mammalian NAD+ -dependent deacetylases. However, how its activity is enhanced toward specific substrates by resveratrol derivatives has not been studied. This study aimed to evaluate the types of interaction of resveratrol and its derivatives with SIRT1 as the target protein, as well as to find out the best ligand with the strangest interaction with SIRT1.

MATERIALS AND METHODS

In this study, we employed the extensive molecular docking analysis using AutoDock Vina to comparatively evaluate the interactions of resveratrol derivatives (22 molecules from the ZINC database) as ligands with SIRT1 (PDB ID: 5BTR) as a receptor. The ChemDraw and Chem3D tools were used to prepare 3D structures of all ligands and energetically minimize them by the MM2 force field.

RESULTS

The molecular docking and visualizations showed that conformational change in resveratrol derivatives significantly influenced the parameter for docking results. Several types of interactions, including conventional hydrogen bonds, carbon-hydrogen bonds, Pi-donor hydrogen bonds, and Pi-Alkyl, were found via docking analysis of resveratrol derivatives and SIRT1 receptors. The possible activation effect of resveratrol 4'-(6-galloylglucoside) with ZINC ID: ZINC230079516 with higher binding energy score (-46.8608 kJ/mol) to the catalytic domain (CD) of SIRT1 was achieved at the maximum value for SIRT1, as compared to resveratrol and its other derivatives.

CONCLUSION

Finally, resveratrol 4'-(6-galloylglucoside), as a derivative for resveratrol, has stably interacted with the CD of SIRT1 and might be a potential effective activator for SIRT1.

The Potential Roles of Ficus carica Extract in the Management of COVID-19 Viral Infections: A Computer-aided Drug Design Study

INTRODUCTION

The conventional processes of drug discovery are too expensive, timeconsuming and the success rate is limited. Searching for alternatives that have evident safety and potential efficacy could save money, time and improve the current therapeutic regimen outcomes.

METHODS

Clinical phytotherapy implies the use of extracts of natural origin for prophylaxis, treatment, or management of human disorders. In this work, the potential role of common Fig (Ficus carica) in the management of COVID-19 infections has been explored. The antiviral effects of Cyanidin 3-rhamnoglucoside which is abundant in common Figs have been illustrated on COVID-19 targets. The immunomodulatory effect and the ability to ameliorate the cytokine storm associated with coronavirus infections have also been highlighted. This work involves various computational studies to investigate the potential roles of common figs in the management of COVID-19 viral infections.

RESULTS

Two molecular docking studies of all active ingredients in common Figs were conducted starting with MOE to provide initial insights, followed by Autodock Vina for further confirmation of the results of the top five compounds with the best docking score.

CONCLUSION

Finally, Molecular dynamic simulation alongside MMPBSA calculations were conducted using GROMACS to endorse and validate the entire work.

Induction of apoptotic cell death of cholangiocarcinoma cells by tiliacorinine from Tiliacora triandra: A mechanistic insight

BACKGROUND

Cholangiocarcinoma (CCA) exhibits poor response to the present chemotherapeutic agents and frequently develops drug resistance. Finding novel anticancer drugs might enhance patient outcomes. Tiliacorinine, a bisbenzylisoquinoline alkaloid from the Thai medicinal plant Tiliacora triandra, effectively induced apoptosis of human CCA cell lines and inhibited tumor growth in mice. Here, we elucidate further the molecular mechanisms underlining the cytotoxicity of tiliacorinine and its implication in overcoming gemcitabine-resistance of CCA cells.

METHODS

Cytotoxicity of tiliacorinine against CCA cell lines was assessed using MTT assay. The molecular signaling was determined using Western blot analysis. Molecular docking simulations were applied to predict the binding affinity and orientation of tiliacorinine to the possible binding site(s) of the target proteins.

RESULTS

Tiliacorinine induced apoptotic cell death of CCA cells in a dose- and time-dependent manner. Tiliacorinine significantly suppressed the expression of anti-apoptotic proteins, Bcl-xL and XIAP; activated apoptotic machinery proteins, caspase-3, caspase-9, and PARP; and decreased the levels of pAkt and pSTAT3. EGF/EGFR activation model and molecular docking simulations revealed EGFR, Akt, and STAT3 as potent targets of tiliacorinine. Molecular docking simulations indicated a strong binding affinity of tiliacorinine to the ATP-binding pockets of EGFR, PI3K, Akt, JAK2, and SH2 domain of STAT3. Tiliacorinine could synergize with gemcitabine and restore the cytotoxicity of gemcitabine against gemcitabine-resistant CCA cells.

CONCLUSION

Tiliacorinine effectively induced apoptosis via binding and blocking the actions of EGFR, Akt, and STAT3.

GENERAL SIGNIFICANCE

Tiliacorinine is a novel multi-kinase inhibitor and possibly a potent anti-cancer agent, in cancers with high activation of EGFR.

Lignin-ultrasound method: Enhancement of antimicrobial capacity of MoS2-containing films

To improve the antimicrobial ability of MoS2-containing films, we used lignin and triple-frequency ultrasound for liquid-phase exfoliation (LPE) to obtain MoS2 nanosheets. Photoresponsive antimicrobial films with MoS2 nanosheets, lignin, polyvinyl alcohol and deep eutectic solvents were subsequently prepared. Lignin functionalized the MoS2 nanosheets by chemically linking with S in MoS2 and significantly improved the exfoliation efficiency. Tri-frequency ultrasound produces beneficial effects on the LPE process by creating a more homogeneous sound field and a stronger degree of cavitation. The concentration of MoS2 nanosheets in the exfoliating solution could reach 1.713 mg/mL under the effect of lignin-ultrasound. The antimicrobial ability of the films was analyzed, and the colony-forming units of E. coli and S. aureus could be reduced from 7 × 106 to 1 × 106 cfu/mL under the irradiation of infrared. The lignin in the film undergoes depolymerization and demethoxylation under the irradiation of infrared to have a more phenolic hydroxyl structure, which confers the growth inhibition ability of the films for bacteria that cannot be in close contact with the film. The method we used has some significance for the preparation of MoS2 nanosheets, and composite films prepared from MoS2, and lignin can be used in food packaging, wound antimicrobials, and other fields.

Ab initio and comparative 3D modeling of FAM222A-encoded protein and target-driven-based virtual screening for the identification of novel therapeutics against Alzheimer's disease

The complex nature of Alzheimer's disease (AD) makes it difficult to understand the exact molecular processes leading to neuron death. However, two molecular factors - the production of amyloid-beta plaques and tau tangles - are considered to be linked to AD. A genetic marker for brain atrophy, FAM222A, has been identified by the unique cross-phenotype meta-analysis of genetics imaging and the molecular features show an interaction between the protein aggregatin encoded by FAM222A and amyloid beta (Aβ)-peptide (1-42) via its N-terminal Aβ binding domain, thus increasing Aβ aggregation. Function of Aggregatin protein is unclear, and its 3D structure has not been investigated in experimental analysis, so far. Hence, in the present study, first time in literature, 3D models of FAM222A-encoded Aggregatin were systematically constructed by applying diverse homology modeling approaches and they were used as target structures at the virtual screening of FDA-approved drugs and drugs currently under research in clinical trials. Then, the identified hit molecules were chosen for further molecular dynamics (MD) simulations and post-MD analyses. Our integrated ligand-based and protein-driven-based virtual screening results show that Cefpiramide, Diniprofylline, Fostriecin, and Droperidol may target Aggregatin.

Potential inhibitors of FemC to combat Staphylococcus aureus: virtual screening, molecular docking, dynamics simulation, and MM-PBSA analysis

FemC is a methicillin resistance factor involved in the alterations of peptidoglycan and glutamine synthesis in Staphylococcus aureus. To identify the potent antibacterial agents, antibacterial molecules were screened against the predicted and validated FemC model. Based on docking scores, presence of essential interactions with active site residues of FemC, pharmacokinetic, and ADMET properties, six candidates were shortlisted and subjected to molecular dynamics to evaluate the stability of FemC-ligand complexes. Further, per residue decomposition analysis and Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA) analysis confirmed that S15, M16, S17, R31, R43, Q47, K48 and R49 of FemC played a vital role in the formation of lower energy stable FemC-inhibitor(s) complexes. Therefore, in the present study, the reported six molecules (Z317461228, Z92241701, Z30923155, Z30202349, Z2609517102 and Z92470167) may pave the path to design the scaffold of novel potent antimicrobials against S. aureus.Communicated by Ramaswamy H. Sarma.

Structure-Based In Silico Screening of Marine Phlorotannins for Potential Walrus Calicivirus Inhibitor

A new calicivirus isolated from a walrus was reported in 2004. Since unknown marine mammalian zoonotic viruses could pose great risks to human health, this study aimed to develop therapeutic countermeasures to quell any potential outbreak of a pandemic caused by this virus. We first generated a 3D model of the walrus calicivirus capsid protein and identified compounds from marine natural products, especially phlorotannins, as potential walrus calicivirus inhibitors. A 3D model of the target protein was generated using homology modeling based on two publicly available template sequences. The sequence of the capsid protein exhibited 31.3% identity and 42.7% similarity with the reference templates. The accuracy and reliability of the predicted residues were validated via Ramachandran plotting. Molecular docking simulations were performed between the capsid protein 3D model and 17 phlorotannins. Among them, five phlorotannins demonstrated markedly stable docking profiles; in particular, 2,7-phloroglucinol-6,6-bieckol showed favorable structural integrity and stability during molecular dynamics simulations. The results indicate that the phlorotannins are promising walrus calicivirus inhibitors. Overall, the study findings showcase the rapid turnaround of in silico-based drug discovery approaches, providing useful insights for developing potential therapies against novel pathogenic viruses, especially when the 3D structures of the viruses remain experimentally unknown.

Compound effect and mechanism of oxidative damage induced by nanoplastics and benzo [a] pyrene

Nanoplastics and polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in soil environments. In order to objectively evaluate the toxic interaction between polystyrene nanoplastics (PS NPs) and benzo [a] pyrene (BaP), oxidative damage at the level of earthworm cells and biomacromolecules was investigated by experiments combined with molecular dynamics simulation. Studies on cells reveal that PS NPs and BaP had synergistic toxicity when it came to causing oxidative stress. Cellular reactive oxygen species (ROS) levels under combined pollutant exposure were 24% and 19% higher, respectively than when PS NPs and BaP were exposed alone (compared to the blank group). In addition, BaP and PS NPs inhibited the ability of CAT to decompose H2O2 by affecting the structure of the proximal amino acid Tyr 357 in the active center of CAT, which exacerbated oxidative stress to a certain extent. Therefore, the synergistic toxic effect of BaP and PS NPs is due to the mutual complement of the two to the induction of protein structural looseness, and the strengthening of the stability of the conjugate (CAT-BaP-PS) under the weak interaction. This work provides a new perspective and approach on how to talk about the toxicity of combined pollutants.

Preparation and characterization of porous membranes of glucomannan and silver decorated cellulose nanocrystals for application as biomaterial

Bacterial infection usually represents a threat in medical wound care, due to the increase in treatment complexity and the risk of antibiotic resistance. For presenting interesting characteristics for the use as biomaterial, natural polymers have been explored for this application. Among them, a promising candidate is the konjac glucomannan (KGM) with outstanding biocompatibility and biodegradability but lack of antibacterial activity. In this study, KGM was combined with silver decorated cellulose nanocrystals (CNC-Ag) to prepare membranes by using a recent reported casting-freezing method. The results highlight the potential anti-adhesive activity of the new materials against Staphylococcus aureus upon contact, without the burst release of silver nanoparticles. Furthermore, the incorporation of CNC enhanced the thermal stability of these membranes while preserving the favorable mechanical properties of the KGM-based material. These findings highlight a straightforward approach to enhance the antibacterial properties of natural polymers, which can be effectively useful in medical devices like wound dressings that typically lack such properties.

The inhibitory mechanism of echinacoside against Staphylococcus aureus Ser/Thr phosphatase Stp1 by virtual screening and molecular modeling

CONTEXT

Stp1 is a new potential target closely related to the pathogenicity of Staphylococcus aureus (S. aureus). In this study, effective Stp1 inhibitors were screened via virtual screening and enzyme activity experiments, and the inhibition mechanism was analyzed using molecular dynamics simulation.

METHODS

AutoDock Vina 4.0 software was used for virtual screening. The molecular structures of Stp1 and ligands were obtained from the RCSB Protein Data Bank and Zinc database, respectively. The molecular dynamics simulation used the Gromacs 4.5.5 software package with the Amberff99sb force field and TIP3P water model. AutoDock Tools was used to add polar hydrogen atoms to Stp1 and distribute part of the charge generated by Kollman's combined atoms. The binding free energies were calculated using the Amber 10 package.

RESULTS

The theoretical calculation results are consistent with the experimental results. We found that echinacoside (ECH) substantially inhibits the hydrolytic activity of Stp1. ECH competes with the substrate by binding to the active center of Stp1, resulting in a decrease in Stp1 activity. In addition, Met39, Gly41, Asp120, Asn162, and Ile163 were identified to play key roles in the binding of Stp1 to ECH. The benzene ring of ECH also plays an important role in complex binding. These findings provide a robust foundation for the development of innovative anti-infection drugs.

Promising antibacterials for LLM of Staphylococcus aureus using virtual screening, molecular docking, dynamics, and MMPBSA

In S. aureus, lipophilic membrane (LLM) protein is a methicillin resistance factor and is an essential role in peptidoglycan metabolism. The virtual screening of antibacterial molecules against the model of LLM was performed to identify the potent antibacterial molecules. Molecular docking results of pharmacokinetic filtered molecules illustrated that five molecules had higher binding affinities than tunicamycin (TUM) and were stabled via non-covalent interactions (hydrogen bond and hydrophobic interactions) at the active site of LLM. Further, molecular dynamics results revealed that binding of identified antibacterial molecules with LLM resulted in stable LLM-inhibitor(s) complexes. Molecular Mechanics/Position-Boltzmann Surface Area (MMPBSA) analysis showed that LLM-inhibitor(s) complexes had high binding affinities in the range of -213.49 ± 2.24 to -227.42 ± 3.05 kJ/mol. The amino acid residues decomposition analysis confirmed that identified antibacterial molecules bound at the active site (Asn148, Leu149, Asp151, Asp208, His269, His271, and His272) of LLM. Noticeably, the current study found five antibacterial molecules (BDE 27575101, BDE 33638168, BDE 33672484, LAS 51502073, and BDE 25098678) were highly potent than TUM and even than earlier reported molecules. Therefore, here reported antibacterial molecules may be used directly or developed to inhibit LLM of S. aureus.Communicated by Ramaswamy H. Sarma.

Application of CRISPR-Cas system in the diagnosis and therapy of ESKAPE infections

Antimicrobial-resistant ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. ESKAPE pathogens are the most common opportunistic pathogens in nosocomial infections, and a considerable number of their clinical isolates are not susceptible to conventional antimicrobial therapy. Therefore, innovative therapeutic strategies that can effectively deal with ESKAPE pathogens will bring huge social and economic benefits and ease the suffering of tens of thousands of patients. Among these strategies, CRISPR (clustered regularly interspaced short palindromic repeats) system has received extra attention due to its high specificity. Regrettably, there is currently no direct CRISPR-system-based anti-infective treatment. This paper reviews the applications of CRISPR-Cas system in the study of ESKAPE pathogens, aiming to provide directions for the research of ideal new drugs and provide a reference for solving a series of problems caused by multidrug-resistant bacteria (MDR) in the post-antibiotic era. However, most research is still far from clinical application.

Exploring and targeting potential druggable antimicrobial resistance targets ArgS, SecY, and MurA in Staphylococcus sciuri with TCM inhibitors through a subtractive genomics strategy

Staphylococcus sciuri (also currently Mammaliicoccus sciuri) are anaerobic facultative and non-motile bacteria that cause significant human pathogenesis such as endocarditis, wound infections, peritonitis, UTI, and septic shock. Methicillin-resistant S. sciuri (MRSS) strains also infects animals that include healthy broilers, cattle, dogs, and pigs. The emergence of MRSS strains thereby poses a serious health threat and thrives the scientific community towards novel treatment options. Herein, we investigated the druggable genome of S. sciuri by employing subtractive genomics that resulted in seven genes/proteins where only three of them were predicted as final targets. Further mining the literature showed that the ArgS (WP_058610923), SecY (WP_058611897), and MurA (WP_058612677) are involved in the multi-drug resistance phenomenon. After constructing and verifying the 3D protein homology models, a screening process was carried out using a library of Traditional Chinese Medicine compounds (consisting of 36,043 compounds). The molecular docking and simulation studies revealed the physicochemical stability parameters of the docked TCM inhibitors in the druggable cavities of each protein target by identifying their druggability potential and maximum hydrogen bonding interactions. The simulated receptor-ligand complexes showed the conformational changes and stability index of the secondary structure elements. The root mean square deviation (RMSD) graph showed fluctuations due to structural changes in the helix-coil-helix and beta-turn-beta changes at specific points where the pattern of the RMSD and root mean square fluctuation (RMSF) (< 1.0 Å) support any major domain shifts within the structural framework of the protein-ligand complex and placement of ligand was well complemented within the binding site. The β-factor values demonstrated instability at few points while the radius of gyration for structural compactness as a time function for the 100-ns simulation of protein-ligand complexes showed favorable average values and denoted the stability of all complexes. It is assumed that such findings might facilitate researchers to robustly discover and develop effective therapeutics against S. sciuri alongside other enteric infections.

An integrated computational approach towards novel drugs discovery against polyketide synthase 13 thioesterase domain of Mycobacterium tuberculosis

The acquired drug resistance by Mycobacterium tuberculosis (M. tuberculosis) to antibiotics urges the need for developing novel anti-M. tuberculosis drugs that possess novel mechanism of action. Since traditional drug discovery is a labor-intensive and costly process, computer aided drug design is highly appreciated tool as it speeds up and lower the cost of drug development process. Herein, Asinex antibacterial compounds were virtually screened against thioesterase domain of Polyketide synthase 13, a unique enzyme that forms α-alkyl β-ketoesters as a direct precursor of mycolic acids which are essential components of the lipid-rich cell wall of M. tuberculosis. The study identified three drug-like compounds as the most promising leads; BBB_26582140, BBD_30878599 and BBC_29956160 with binding energy value of - 11.25 kcal/mol, - 9.87 kcal/mol and - 9.33 kcal/mol, respectively. The control molecule binding energy score is -9.25 kcal/mol. Also, the docked complexes were dynamically stable with maximum root mean square deviation (RMSD) value of 3 Å. Similarly, the MM-GB\PBSA method revealed highly stable complexes with mean energy values < - 75 kcal/mol for all three systems. The net binding energy scores are validated by WaterSwap and entropy energy analysis. Furthermore, The in silico druglike and pharmacokinetic investigation revealed that the compounds could be suitable candidates for additional experimentations. In summary, the study findings are significant, and the compounds may be used in experimental validation pipeline to develop potential drugs against drug-resistant tuberculosis.