Discovery of New Dual-Target Agents Against PPAR-γ and α-Glucosidase Enzymes with Molecular Modeling Methods: Molecular Docking, Molecular Dynamic Simulations, and MM/PBSA Analysis.

Type 2 diabetes mellitus (T2DM) has become a serious public health problem both in our country and worldwide, being the most prevalent type of diabetes. The combined use of drugs in the treatment of T2DM leads to serious side effects, including gastrointestinal problems, liver toxicity, hypoglycemia, and treatment costs. Hence, there has been a growing emphasis on drugs that demonstrate dual interactions. Several studies have suggested that dual-target agents for peroxisome proliferator-activated receptor-γ (PPAR-γ) and alpha-glucosidase (α-glucosidase) could be a potent approach for treating patients with diabetes. We aim to develop new antidiabetic agents that target PPAR-γ and α-glucosidase enzymes using molecular modeling techniques. These compounds show dual interactions, are more effective, and have fewer side effects. The molecular docking method was employed to investigate the enzyme-ligand interaction mechanisms of 159 newly designed compounds with target enzymes. Additionally, we evaluated the ADME properties and pharmacokinetic suitability of these compounds based on Lipinski and Veber's rules. Compound 70, which exhibited favorable ADME properties, demonstrated more effective binding energy with both PPAR-γ and α-glucosidase enzymes (-12,16 kcal/mol, -10.07 kcal/mol) compared to the reference compounds of Acetohexamide (-9.31 kcal/mol, -7.48 kcal/mol) and Glibenclamide (-11.12 kcal/mol, -8.66 kcal/mol). Further, analyses of MM/PBSA binding free energy and molecular dynamics (MD) simulations were conducted for target enzymes with compound 70, which exhibited the most favorable binding affinities with both enzymes. Based on this information, our study aims to contribute to the development of new dual-target antidiabetic agents with improved efficacy, reduced side effects, and enhanced reliability for diabetes treatment.

Synthesis, Antimicrobial Activities, and Molecular Modeling Studies of Agents for the Sortase A Enzyme.

Sortase A (SrtA) is an attractive target for developing new anti-infective drugs that aim to interfere with essential virulence mechanisms, such as adhesion to host cells and biofilm formation. Herein, twenty hydroxy, nitro, bromo, fluoro, and methoxy substituted chalcone compounds were synthesized, antimicrobial activities and molecular modeling strategies against the SrtA enzyme were investigated. The most active compounds were found to be T2, T4, and T19 against Streptococcus mutans (S. mutans) with MIC values of 1.93, 3.8, 3.94 µg/mL, and docking scores of -6.46, -6.63, -6.73 kcal/mol, respectively. Also, these three active compounds showed better activity than the chlorohexidine (CHX) (MIC value: 4.88 µg/mL, docking score: -6.29 kcal/mol) in both in vitro and in silico. Structural stability and binding free energy analysis of S.mutans SrtA with active compounds were measured by molecular dynamic (MD) simulations throughout 100 nanoseconds (ns) time. It was observed that the stability of the critical interactions between these compounds and the target enzyme was preserved. To prove further, in vivo biological evaluation studies could be conducted for the most promising precursor compounds T2, T4, and T19, and it might open new avenues to the discovery of more potent SrtA inhibitors.

Design, synthesis, and enzyme inhibition evaluation of some novel Mono- and Di-O-ß-D-Glycopyranosyl Chalcone analogues with molecular docking studies.

In this study, some novel mono- and di-O-ß-D-glycopyranosyl chalcone analogs were designed, synthesized, and characterized. The chalcone derivatives were synthesized with good yields by base-catalyzed Claisen-Schmidt condensation in EtOH solution. Then these chalcones were reacted with TAGBr (2,3,4,6-tetra-O-acetyl-α-D-glucopyranosylbromide) in dry acetone under the anhydrous condition at 0-5 °C. Deacylated was carried out by the Zemplen's method with NaOCH3 in dry methanol results in substituted chalcone-O-glycosides (mono- and di-O-ß-D-glycopyranosyl chalcone analogs). The chemical structures of all synthesized compounds were elucidated based on IR, NMR spectral data, and mass spectrometry. Further, the compounds (7a-c, 8a-c, 12a-c, 16a-c, and 17a-c) were tested for their enzyme inhibition activity against α-glycosidase, tyrosinase, and AChE with in vitro and in silico analysis. Amongst them, compounds 12a-c, 16a-c, and 17a-c displayed moderate or less enzyme inhibition activity against α-glycosidase while other compounds 7a-c and 8a-c) were not active. Remarkably interesting enzyme inhibition effects, with IC50 values below 30.59 ± 0.30 µM were recorded with 7c (IC50=11.07 ± 0.55 µM) against tyrosinase.

Investigation of α-glucosidase and α-amylase inhibitory effects of phenoxy chalcones and molecular modeling studies.

Diabetes mellitus is one of the most critical health problems affecting the quality of life of people worldwide, especially in developing countries. According to the World Health Organization reports, the number of patients with diabetes is approximately 420 million, and this number is estimated to be 642 million in 2040. There are 2 main types of diabetes: Type 1 (T1DM), where the body cannot produce enough insulin, and Type 2 (T2DM), where the body cannot use insulin properly. Patients with T1DM are treated with insulin injections while oral glucose-lowering drugs are used for patients with T2DM. Oral antihyperglycemic drugs used in the treatment of type 2 diabetes mellitus have different mechanisms. Among these, α-Glucosidase and α-amylase inhibitors are one of the most important inhibitors. The antidiabetic effect of the chalcones, which show rich activity, draws attention. This research aims to synthesize chalcone derivatives that could show potential antidiabetic activity. In this study, the inhibitory activity of the chalcone compounds (4a-4g, 5a-5g) was tested against α-glucosidase and α-amylase enzymes. Besides, molecular modeling was utilized to predict potential interactions of the synthesized compounds that exhibit inhibitory effects. In both in vitro and in silico studies, the analyses revealed that compound 5e exhibits strong inhibitory effects against α-glucosidase enzymes (Binding energy: -7.75 kcal/mol, IC50 : 28.88 µM). Additionally, compound 4f demonstrates encouraging inhibitory effects against α-Amylase (Binding energy: -11.08 kcal/mol, IC50 : 46. 21 µM).

Investigation of the antimicrobial activities of various antimicrobial agents on Streptococcus Mutans Sortase A through computer-aided drug design (CADD) approaches.

BACKGROUND AND OBJECTIVE: Tooth decay is a common chronic disease that causes pain, tooth loss, malnutrition, anxiety and significantly affects half of the world's population. Streptococcus mutans (S.mutans), is considered the main pathogen causing tooth decay. Sortase A (SrtA), one of the surface proteins of S. mutans, is a potential target in the development of antimicrobial and caries prevention agents for preventing infections associated with biofilm formation. Recently, various SrtA inhibitors, including small molecules and natural product, especially, trans-chalcone, chlorhexidine (CHX) and flavonoid compounds, which exhibit effective inhibition against SrtA, have been identified. However, due to the limited number of inhibitors, multi-drug resistance and side-effects the discovery of new inhibitors for SrtA is essential. METHODS: In this case, various compounds aimed at the target enzyme underwent high-throughput screening with small molecule libraries. For this screening of a total of 178 compounds, 163 were found to be pharmacokinetically suitable by performing an absorption, distribution, metabolism, and excretion (ADME) analysis. Molecular docking was then applied to investigate the interaction mechanism among these suitable compounds and the target enzyme structure at the molecular level. RESULTS: According to the results of the study, six compounds (CHEMBL243796 (kurarinone), CHEMBL2180472, CHEMBL3335591, CHEMBL373249, CHEMBL1395334, CHEMBL253467 (Isobavachalcone)) exhibited lower docking scores (-7.18, -6.59, -6.53, -6.47, -6.43, and -6.39 kcal/mol, respectively) against S. mutans SrtA than the positive control CHX (-6.29 kcal/mol). Finally, the 100 ns molecular dynamic simulations and binding free energy calculations were performed for the structure stability analysis of the enzyme with CHEMBL243796 (kurarinone), which showed the lowest docking score. As a result of these studies, the stability of the critical interactions between kurarinone and the target enzyme was preserved during the simulation time. CONCLUSIONS: These results indicate that flavonoid and chalcone scaffold compounds are clinically more reliable and potent than CHX as novel inhibitory agents for inhibiting oral biofilm formation. These finding can provide important contribution to the future clinical trials in the development of therapeutically useful inhibitors of SrtA by virtually screening several chemical compounds more rapidly to select suitable compounds for the prevention and treatment of dental caries.