Search

Rhizoctonia solani, the causative agent of sheath blight disease in rice, poses a significant threat to agricultural productivity. Traditional management approaches involving chemical fungicides have been effective but come with detrimental consequences for the ecosystem. This study aimed to investigate sustainable alternatives in the form of antifungal peptides derived from Solanaceous plant species as potential agents against R. solani. Peptide extracts were obtained using an optimized antimicrobial peptide (AMP) extraction method and desalted using the solid-phase extraction technique. The antifungal potential of peptide-rich extracts from Solanum tuberosum and Capsicum annum was assessed through in vitro tests employing the agar well diffusion method. Furthermore, peptide-protein docking analysis was performed on HPEPDOCK and HDOCK server; and molecular dynamics simulations (MDS) of 100 ns period were performed using the Gromacs 2020.4. The results demonstrated significant inhibition zones for both extracts at concentrations of 100 mg/mL. Additionally, the extracts of Solanum tuberosum and Capsicum annum had minimum inhibitory concentrations of 50 mg/mL and 25 mg/mL, respectively with minimum fungicidal concentrations of 25 mg/mL. Insights into the potential mechanisms of key peptides inhibiting R. solani targets were gleaned from in-silico studies. Notably, certain AMPs exhibited favorable free energy of binding against pathogenicity-related targets, including histone demethylase, sortin nexin, and squalene synthase, in protein-peptide docking simulations. Extended molecular dynamics simulations lasting 100 ns and MM-PBSA calculations were performed on select protein-peptide complexes. AMP10 displayed the most favorable binding free energy against all target proteins, with AMP3, AMP12b, AMP6, and AMP15 also exhibiting promising results against specific targets of R. solani. These findings underscore the potential of peptide extracts from S. tuberosum and C. annum as effective antifungal agents against rice sheath blight caused by R. solani. [ABSTRACT FROM AUTHOR]

Type 2 diabetes is a major health concern contributing to most of diabetic cases worldwide. Mangiferin and its congeners are known for their diverse pharmacological properties. This study sought to investigate the inhibitory property of naturally occurring mangiferin congeners on sodium-glucose co-transporter 2 protein (SGLT-2) using comprehensive computational methods. The naturally occurring mangiferin congeners were subjected to molecular docking, molecular dynamics (MDs) simulation (100 ns), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy, density functional theory calculations (B3LYP 6-31G basis set), and ADMET approaches to identify potential SGLT-2 inhibitor. The molecular docking studies revealed neomangiferin (−9.0 kcal/mol) as the hit molecule compared with dapagliflozin (−8.3 kcal/mol). Root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) plots from the MD simulations established that neomangiferin stabilizes SGLT-2 better than the dapagliflozin, a standard drug. The MM-PBSA binding free energy calculations showed that neomangiferin (−26.05 kcal/mol) elicited better binding affinity than dapagliflozin (−17.42 kcal/mol). The electronic studies showed that neomangiferin (3.48 eV) elicited high electrophilicity index compared with mangiferin (3.31 eV) and dapagliflozin (2.11 eV). Also, the ADMET properties showed that the hit molecule is safe when administered to diabetic subjects. The current in silico studies suggest that neomangiferin could emerge as a promising lead molecule as a SGLT-2 inhibitor. [ABSTRACT FROM AUTHOR]

Background and Objectives: PON1 is a multi-functional antioxidant protein that hydrolyzes a variety of endogenous and exogenous substrates in the human system. Growing evidence suggests that the Leu55Met and Gln192Arg substitutions alter PON1 activity and are linked with a variety of oxidative-stress-related diseases. Materials and Methods: We implemented structural modeling and molecular dynamics (MD) simulation along with essential dynamics of PON1 and molecular docking with their endogenous (n = 4) and exogenous (n = 6) substrates to gain insights into conformational changes and binding affinity in order to characterize the specific functional ramifications of PON1 variants. Results: The Leu55Met variation had a higher root mean square deviation (0.249 nm) than the wild type (0.216 nm) and Gln192Arg (0.202 nm), implying increased protein flexibility. Furthermore, the essential dynamics analysis confirms the structural change in PON1 with Leu55Met vs. Gln192Arg and wild type. Additionally, PON1 with Leu55Met causes local conformational alterations at the substrate binding site, leading to changes in binding affinity with their substrates. Conclusions: Our findings highlight the structural consequences of the variants, which would increase understanding of the role of PON1 in the pathogenesis of oxidative-stress-related diseases, as well as the management of endogenous and exogenous chemicals in the treatment of diseases. [ABSTRACT FROM AUTHOR]

The human ABCB1 (P-glycoprotein, Pgp) protein is an active exporter expressed in the plasma membrane of cells forming biological barriers. In accordance with its broad substrate spectrum and tissue expression pattern, it affects the pharmacokinetics of numerous chemotherapeutic drugs and it is involved in unwanted drug–drug interactions leading to side effects or toxicities. When expressed in tumor tissues, it contributes to the development of chemotherapy resistance in malignancies. Therefore, the understanding of the molecular details of the ligand–ABCB1 interactions is of crucial importance. In a previous study, we found that quercetin (QUR) hampers both the transport and ATPase activity of ABCB1, while cyandin-3O-sophroside (C3S) stimulates the ATPase activity and causes only a weak inhibition of substrate transport. In the current study, when QUR and C3S were applied together, both a stronger ATPase inhibition and a robust decrease in substrate transport were observed, supporting their synergistic ABCB1 inhibitory effect. Similar to cyclosporine A, a potent ABCB1 inhibitor, co-treatment with QUR and C3S shifted the conformational equilibrium to the "inward-facing" conformer of ABCB1, as it was detected by the conformation-selective UIC2 mAb. To gain deeper insight into the molecular details of ligand–ABCB1 interactions, molecular docking experiments and MD simulations were also carried out. Our in silico studies support that QUR and C3S can bind simultaneously to ABCB1. The most favourable ligand–ABCB1 interaction is obtained when C3S binds to the central substrate binding site and QUR occupies the "access tunnel". Our results also highlight that the strong ABCB1 inhibitory effect of the combined treatment with QUR and C3S may be exploited in chemotherapy protocols for the treatment of multidrug-resistant tumors or for improving drug delivery through pharmacological barriers. [ABSTRACT FROM AUTHOR]

Inflammatory bowel disease, comprising Crohn's disease (CD) and ulcerative colitis (UC), is often debilitating. The disease etiology is multifactorial, involving genetic susceptibility, microbial dysregulation, abnormal immune activation, and environmental factors. Currently, available drug therapies are associated with adverse effects when used long-term. Therefore, the search for new drug candidates to treat IBD is imperative. The peroxisome proliferator-activated receptor-γ (PPARγ) is highly expressed in the colon. PPARγ plays a vital role in regulating colonic inflammation. 1,8-cineole, also known as eucalyptol, is a monoterpene oxide present in various aromatic plants which possess potent anti-inflammatory activity. Molecular docking and dynamics studies revealed that 1,8-cineole binds to PPARγ and if it were an agonist, that would explain the anti-inflammatory effects of 1,8-cineole. Therefore, we investigated the role of 1,8-cineole in colonic inflammation, using both in vivo and in vitro experimental approaches. Dextran sodium sulfate (DSS)-induced colitis was used as the in vivo model, and tumor necrosis factor-α (TNFα)-stimulated HT-29 cells as the in vitro model. 1,8-cineole treatment significantly decreased the inflammatory response in DSS-induced colitis mice. 1,8-cineole treatment also increased nuclear factor erythroid 2-related factor 2 (Nrf2) translocation into the nucleus to induce potent antioxidant effects. 1,8-cineole also increased colonic PPARγ protein expression. Similarly, 1,8-cineole decreased proinflammatory chemokine production and increased PPARγ protein expression in TNFα-stimulated HT-29 cells. 1,8-cineole also increased PPARγ promoter activity time-dependently. Because of its potent anti-inflammatory effects, 1,8-cineole may be valuable in treating IBD. [ABSTRACT FROM AUTHOR]

NMDA receptors are considered as high profile therapeutic target in the treatment of pain and neurodegenerative diseases such as Alzheimer's, Huntington's and Parkinson's disease. NR2 subunit of NMDA receptor divided into four subunits i.e. NR2A, NR2B, NR2C and NR2D. Restricted distribution of NR2B subunit in the brain makes it potential target. In the present study, new structural insights into benzazepine derivatives as NR2B selective NMDA receptor antagonists have been reported using QSAR modelling. Total five QSAR models were developed using various statistical methods. 2D-QSAR models showed that chi3 and SsssNE-index descriptors are crucial for NMDA receptor antagonistic activity. Chi3 descriptor relates with non-hydrogen heteroatom connected with two or three bonds and SsssNE-index descriptor deals with Electrotopological state indices for number of nitrogen atom connected with three single bonds. Both the descriptors were negatively correlated with all the developed 2D-QSAR models. Significance of these descriptors is extensively studied in present work. In 3D-QSAR studies, steric and electrostatic fields were found to be important for antagonistic effect on NMDA receptors. 3D-QSAR studies clarify the substitution pattern of R group on nitrogen atom of benzazepine core. The substitutions with high electropositive with less or medium steric character are favourable for the activity. All developed models were critically validated to establish their reliability and accuracy for prediction of binding affinity of benzazepine derivatives towards NR2B subunit of NMDA receptor. The present study offered not only highly predictive and reliable QSAR models for benzazepine derivatives but also revealed some of the vital structural observations required for their higher binding affinity towards NR2B subunit of NMDA receptors. Image 1008 • A detailed QSAR studies offered new structural requirements for NMDA antagonistic activity. • Statistically robust and reliable 2D & 3D-QSAR models were developed. • Chi3 and SsssNE-index plays vital role for optimization of Benzazepine derivatives. [ABSTRACT FROM AUTHOR]

A library of 2,3‐dihydroquinazolin‐4(1H)‐one derivatives (5 a‐k) were synthesized in good yield by using 1‐Ethyl‐3‐Methylimidazolium hydrogen sulphate (10 mol %) as a catalyst and were evaluated for their anti‐biofilm, antimicrobial and cytotoxicity potential. Among the synthesized compounds, 2‐(4‐(1H‐1,2,4‐triazol‐1‐yl)phenyl)‐2,3‐dihydroquinazolin‐4(1H)‐one (5d) and 2,3‐dihydro‐2‐(2,4,6‐trimethoxyphenyl) quinazolin‐4(1H)‐one (5j) displayed better anti‐biofilm activity than fluconazole (IC50 = 40 μM) with IC50 values less than 30 μM. Compound 5d also appeared to be fungicidal against C. Albicans having MIC=33.5 μg/ml comparable with standard fluconazole (50 μg/ml). All the synthesized compounds were also evaluated for cytotoxic activity by using MTT assay against HeLa, A‐549 and MDA‐MB‐231 cell lines. The compound 5d was found to be more potent against MDA‐MB‐231 and A549 cell lines (IC50 = 11 ± 2 μM and 34±8 μM respectively) than 5‐fluorouracil (IC50 = 19 ± 3 μM and 51 ± 5 μM respectively). The compounds substituted with 6‐methyl‐4‐oxo‐4H‐chromen‐3‐yl (5a), biphenyl (5c) and 2‐hydroxy‐5‐bromophenyl (5e) were also found to be more potent against MDA‐MB‐231 cell lines (IC50 = 13 ± 3 – 14 ± 4 μM) than 5‐fluorouracil. Molecular docking simulations were also carried out using secreted aspartyl protease (SAP5), pepA enzyme of C. albicans for biofilm inhibition and EGFR tyrosine kinase for cyto‐toxicity studies. The study reveals that the compounds 5d and 5e can serve as an important lead moiety for biofilm inhibition and cyto‐toxicity against MDA‐MB‐231 and A549 cancer cell‐lines indicating their potential in the treatment of tougher fungal infections and breast and lung cancer. A library of 2,3‐dihydroquinazolin‐4(1H)‐one derivatives were synthesized and evaluated for the anti‐biofilm, antimicrobial and cyto‐toxicity potential. Molecular docking studies were also carried out using secreted aspartyl protease of C. albicans for biofilm inhibition and EGFR tyrosine kinase for cyto‐toxicity studies. The in‐vitro evaluation and docking studies revealed the potential of the compound 2‐(4‐(1H‐1,2,4‐triazol‐1‐yl)phenyl)‐2,3‐dihydroquinazolin‐4(1H)‐one (5d) as a lead moiety for biofilm inhibition and cyto‐toxicity against MDA‐MB‐231 and A549 cancer cell‐lines indicating its potential to treat breast and lung cancer. [ABSTRACT FROM AUTHOR]

• Synthesis of substituted ethyl-1,2,3,4-tetrahydro-4-phenylpyrimidine-5-carboxylates. • Characterization of synthesized compounds by IR, NMR and HRMS. • Anti-tubercular activity against Mycobacterium tuberculosis (Mtb) H37Rv strain. • In-silico molecular modeling studies against DHFR enzyme and MMGBSA analysis. • MD simulations, RMSD and RMSF suggest stable complex and potent inhibitory effect. A small library of substituted ethyl-1,2,3,4-tetrahydro-4-phenylpyrimidine-5-carboxylate was designed and synthesized. All the characterized molecules were screened for their anti-tubercular activity using the H37Rv strain of Mycobacterium tuberculosis (Mtb). The compounds 5c, 5d, 5f, 5h , and 5k showed equipotent activity (MIC 3.12 µg/mL), compounds 5b, 5e, 5g , 5i, and 5j were more potent (MIC 1.6 µg/mL), whereas, 5a and 5l shown moderate activity (MIC 6.25 µg/mL). The potent inhibitory activity of screened compounds was rationalized with in-silico molecular modeling studies against the Mtb- dihydrofolate reductase (DHFR) enzyme. Compound 5i displayed a good docking score of −8.56 Kcal/mole with H-bond and hydrophobic interactions. These interactions revealed the stability of the complex which in turn determined the potent inhibitory effect. To get in-depth mechanistic insight into the inhibitory effect and to assess the stability of the ligand–protein complex, a molecular dynamics (MD) simulation study was performed. The RMSD and RMSF values obtained by the MD simulation study were 2.39 Å and 0.92 Å, respectively. The obtained values suggested that the drug–ligand complex maintained the stability over entire 100 ns run and the molecule did not fluctuate. The H-bond and hydrophobic interactions displayed in molecular docking studies were found to be retained in the MD simulation run. The obtained MD simulation values indicate that the complex was stable and rationalize the potent inhibitory effect. The drug-likeliness properties of potent compounds were calculated and the values thus obtained suggested that the molecule 5i has drug-likeliness properties and complies with Lipinski's rule of five/Ro3. Hence, the identified compounds can be taken into further stages of drug discovery processes. [Display omitted] [ABSTRACT FROM AUTHOR]