3D-QSAR Studies of 1,2,4-Oxadiazole Derivatives as Sortase A Inhibitors

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

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

Structure-based virtual screening and molecular dynamics approaches to identify new inhibitors of Staphylococcus aureus sortase A

Staphylococcus aureus is a prevalent Gram-positive bacteria leading cause of a wide range of human pathologies. Moreover, antibiotic résistance of pathogenesis bacteria is one of the worldwide health problems. In Gram-positive bacteria, the enzyme of SrtA, is responsible for the anchoring of surface-exposed proteins to the cell wall peptidoglycan. Because of its critical role in Gram-positive bacterial pathogenesis, SrtA is an attractive target for anti-virulence during drug development. To date, some SrtA inhibitors have been discovered most of them being derived from flavonoid compounds, like Myricetin. In order to provide potential hit molecules against SrtA for clinical use, we obtained a total of 293 compounds by performing in silico shape-based screening of compound libraries against Myristin as a reference structure. Employing molecular docking and scoring functions, the top 3 compounds Apigenin, Efloxate, and Compound 8261032 were screened by comparing their docking scores with Myricetin. Furthermore, MD simulations and MM-PBSA binding energy calculation studies revealed that only Compound 8261032 strongly binds to the catalytic core of the SrtA enzyme than Myricetin, and stable behavior was consistently observed in the docking complex. Compound 8261032 showed a good number of hydrogen bonds with SrtA and higher MM-PBSA binding energy when compared to all three molecules. Also, it makes strength interactions with Arg139 and His62, which are critical for SrtA biological activity. This study showed that the development of this inhibitor could be a fundamental strategy against resistant bacteria, but further studies in vitro are needed to confirm this claim.Communicated by Ramaswamy H. Sarma.

Discovery of non-peptide GLP-1r natural agonists for enhancing coronary safety in type 2 diabetes patients

This study explores the computational discovery of non-peptide agonists targeting the Glucagon-Like Peptide-1 Receptor (GLP-1R) to enhance the safety of major coronary outcomes in individuals affected by Type 2 Diabetes. The objective is to identify novel compounds that can activate the GLP-1R pathway without the limitations associated with peptide agonists. Type 2 diabetes mellitus (T2DM) is associated with an increased risk of cardiovascular disease (CVD) and mortality, which is attributed to the accumulation of fat in organs, including the heart. Glucagon-like peptide-1 receptor agonists (GLP-1RAs) are frequently used to manage T2DM and could potentially offer cardiovascular benefits. Therefore, this study examines non-peptide agonists of GLP-1R to improve coronary safety in type 2 diabetes patients. After rigorous assessments, two standout candidates were identified, with natural compound 12 emerging as the most promising. This study represents a notable advancement in enhancing the management of coronary outcomes among individuals with type 2 diabetes. The computational methodology employed successfully pinpointed potential GLP-1R natural agonists, providing optimism for the development of safer and more effective therapeutic interventions. Although computational methodologies have provided crucial insights, realizing the full potential of these compounds requires extensive experimental investigations, crucial in advancing therapeutic strategies for this critical patient population.Communicated by Ramaswamy H. Sarma.

Evaluating the Antivirulence Effects of New Thiazolidinedione Compounds Against Pseudomonas aeruginosa PAO1

Pseudomonas aeruginosa is an opportunistic pathogen that causes several serious health problems and numerous forms of virulence. During the treatment of P. aeruginosa infections, the development of multidrug-resistant isolates creates significant clinical problems. Using antivirulence compounds to disrupt pathogenicity rather than killing the bacterium may be an interesting strategy to overcome this problem, because less harsh conditions will exist for the development of resistance. To reduce pathogenicity and biofilm formation, newly synthesized analogs of imidazolyl (8n) and previously synthesized analogs (8a-8m) with a similar backbone [the 5-(imidazolyl-methyl) thiazolidinediones] were tested against pyoverdine and pyocyanin production, protease activity, and biofilm formation. Compared to the positive control group, the best compounds reduced the production of pyoverdine (8n) by 89.57% and pyocyanin (8i) by 22.68%, and protease activity (8n) by 2.80% for PAO1 strain, at a concentration of 10 μM. Moreover, the biofilm formation assay showed a reduction of 87.94% (8i) for PAO1, as well as 30.53% (8d) and 44.65% (8m) for 1074 and 1707 strains, respectively. The compounds used in this study did not show any toxicity in the human dermal fibroblasts and 4T1 cells (viability higher than 90%). The in silico study of these compounds revealed that their antivirulence activity could be due to their interaction with the PqsR, PqsE, and LasR receptors.

In-silico modelling studies of 5-benzyl-4-thiazolinone derivatives as influenza neuraminidase inhibitors via 2D-QSAR, 3D-QSAR, molecular docking, and ADMET predictions

Influenza virus disease is one of the most infectious diseases responsible for many human deaths, and the high mutability of the virus causes drug resistance effects in recent times. As such, it became necessary to explore more inhibitors that could avert future influenza pandemics. The present research utilized some in-silico modelling concepts such as 2D-QSAR, 3D-QSAR, molecular docking simulation, and ADMET predictions on some 5-benzyl-4-thiazolinone derivatives as influenza neuraminidase (NA) inhibitors. The 2D-QSAR modelling results revealed GFA-MLR (R train 2 =0.8414, Q2 = 0.7680) and GFA-ANN (R train ​ 2 =0.8754, Q2 = 0.8753) models with the most relevant descriptors (MATS3i, SpMax5_Bhe, minsOH and VE3_D) for predicting the inhibitory activities of the molecules which has passed the global criteria of accepting QSAR models. The results of the 3D-QSAR modelling results showed that CoMFA_ES (R train ​ 2 =0.9030, Q2 = 0.5390) and CoMSIA_EA (R train 2 =0.880, Q2 = 0.547) models are having good predicting ability among other developed models. The molecules were virtually screened via molecular docking simulation with the active site of NA protein receptor (pH1N1) which confirms their resilient potency when compared with zanamivir standard drug. Molecule 11 as the most potent molecule formed more H-bond interactions with the key residues such as TRP178, ARG152, ARG292, ARG371, and TYR406 that triggered the catalytic reactions for NA inhibition. Furthermore, six (6) molecules (9, 10, 11, 17, 22, and 31) with relatively high inhibitory activities and docking scores were identified as the possible leads for in-silico exploration of novel NA inhibitors. The drug-likeness and ADMET predictions of the lead molecules revealed non-violation of Lipinski's rule and good pharmacokinetic profiles respectively, which are important guidelines for rational drug design. Hence, the outcome of this study overlaid a solid foundation for the in-silico design and exploration of novel NA inhibitors with improved potency.