3D-QSAR Studies, Molecular Docking, Molecular Dynamic Simulation, and ADMET Proprieties of Novel Pteridinone Derivatives as PLK1 Inhibitors for the Treatment of Prostate Cancer

An in-silico investigation based on molecular simulations of novel and potential brain-penetrant GluN2B NMDA receptor antagonists as anti-stroke therapeutic agents

GluN2B-induced activation of NMDA receptors plays a key function in central nervous system (CNS) disorders, including Parkinson, Alzheimer, and stroke, as it is strongly involved in excitotoxicity, which makes selective NMDA receptor antagonists one of the potential therapeutic agents for the treatment of neurodegenerative diseases, especially stroke. The present study aims to examine a structural family of thirty brain-penetrating GluN2B N-methyl-D-aspartate (NMDA) receptor antagonists, using virtual computer-assisted drug design (CADD) to discover highly candidate drugs for ischemic strokes. Initially, the physicochemical and ADMET pharmacokinetic properties confirmed that C13 and C22 compounds were predicted as non-toxic inhibitors of CYP2D6 and CYP3A4 cytochromes, with human intestinal absorption (HIA) exceeding 90%, and designed to be as efficient central nervous system (CNS) agents due to the highest probability to cross the blood-brain barrier (BBB). Compared to ifenprodil, a co-crystallized ligand complexed with the transport protein encoded as 3QEL.pdb, we have noticed that C13 and C22 chemical compounds were defined by good ADME-Toxicity profiles, meeting Lipinski, Veber, Egan, Ghose, and Muegge rules. The molecular docking results indicated that C22 and C13 ligands react specifically with the amino acid residues of the NMDA receptor subunit GluN1 and GluN2B. These intermolecular interactions produced between the candidate drugs and the targeted protein in the B chain remain stable over 200 nanoseconds of molecular dynamics simulation time. In conclusion, C22 and C13 ligands are highly recommended as anti-stroke therapeutic drugs due to their safety and molecular stability towards NMDA receptors.Communicated by Ramaswamy H. Sarma.

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.

Investigating Potential Cancer Therapeutics: Insight into Histone Deacetylases (HDACs) Inhibitions

Histone deacetylases (HDACs) are enzymes that remove acetyl groups from ɛ-amino of histone, and their involvement in the development and progression of cancer disorders makes them an interesting therapeutic target. This study seeks to discover new inhibitors that selectively inhibit HDAC enzymes which are linked to deadly disorders like T-cell lymphoma, childhood neuroblastoma, and colon cancer. MOE was used to dock libraries of ZINC database molecules within the catalytic active pocket of target HDACs. The top three hits were submitted to MD simulations ranked on binding affinities and well-occupied interaction mechanisms determined from molecular docking studies. Inside the catalytic active site of HDACs, the two stable inhibitors LIG1 and LIG2 affect the protein flexibility, as evidenced by RMSD, RMSF, Rg, and PCA. MD simulations of HDACs complexes revealed an alteration from extended to bent motional changes within loop regions. The structural deviation following superimposition shows flexibility via a visual inspection of movable loops at different timeframes. According to PCA, the activity of HDACs inhibitors induces structural dynamics that might potentially be utilized to define the nature of protein inhibition. The findings suggest that this study offers solid proof to investigate LIG1 and LIG2 as potential HDAC inhibitors.

Phytochemical constituents, in-vitro anticancer activity and computational studies of Cymbopogon schoenanthus

The cytotoxic effects of Cymbopogon schoenanthus L. aerial part ethanol extract were examined against some cancer cell lines, and HUVEC normal cell lines using MTT assay. The ethanolic extract was prepared by ultrasonic-assisted extraction and analyzed by GC-MS and HPLC. The extract was found to be rich in terpene compounds. The extract proved to be highly selective and effective against breast and prostate cancer cell lines (MDA-MB-435, MCF-7, and DU 145) with IC50 as low as 0.7913 ± 0.14, 12.841 ± 0.21, and 30.51 ± 0.18 µg/ml, respectively. In silico modeling was performed to investigate the binding orientation and affinity of the major identified compounds against Polo-like kinase (PLK1 protein) a cancer molecular target using molecular docking and molecular dynamic whereas eudesm-5-en-11-ol, piperitone, and 2,3-dihydrobenzofuran displayed better binding affinity and stability against PLK1 compared to the reference drug. These findings encourage further in vivo studies to assess the anti-cancer effects of C. schoenanthus extract and its components.

3D-QSAR and ADMET studies of morpholino-pyrimidine inhibitors of DprE1 from Mycobacterium tuberculosis

DprE1 is involved in the synthesis of Mycobacterium tuberculosis cell wall and is a potent drug target for Tuberculosis (TB) treatment. The structure and dynamics of the loops L-I and L-II flanking the inhibitor binding site was studied using molecular dynamics (MD) simulation and MMPBSA in Amber v18. Docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) of 55 Morpholino-pyrimidine (MP) inhibitors was carried out using Autodock v1.2.0 and Forge v10. ADMET analysis was done using SwissADME and pkCSM. All MP inhibitors docked in the DprE1 binding pocket, making contacts with L-II residues. MD studies showed that L-I and L-II unfold in the absence of the inhibitor but fold stably structure with reduced protein motions in the presence of MP-38, the highest affinity inhibitor. This was confirmed by k-means clustering and secondary structure analysis. L-II residues, L317, F320 and R325 contributed most towards the MMPBSA binding free energy of MP-38. A robust field-based 3D-QSAR model showed values of r2train = 0.982, r2test = 0.702 and q2 = 0.516. The MP inhibitor field points were broadly divided into negative electrostatics near the A, B rings and hydrophobic electrostatics near the D, E rings. Addition of negative groups at methanone position and ring B as well as addition of hydrophobic and bulky groups at ring E will improve activity. Highly active compounds 47, 49 and 50 of MP series exhibited highly favourable drug-like properties. SAR and ADMET insights attained from this model will help in the development of active DprE1 inhibitors in future.Communicated by Ramaswamy H. Sarma.