Pharmacophore Optimization and Design of Competitive Inhibitors of Thymidine Monophosphate Kinase Through Molecular Modeling Studies

2,4,6-Trimethoxy chalcone derivatives: an integrated study for redesigning novel chemical entities as anticancer agents through QSAR, molecular docking, ADMET prediction, and computational simulation

QSAR, an efficient and successful approach for optimizing lead compounds in drug design, was employed to study a reported series of compounds derived from 2,4,6-trimethoxy chalcone derivatives. The ability of these compounds to inhibit CDK1 was examined, with the help of QSARINS software for model development. The generated QSAR model revealed three significant descriptors, exhibiting strong correlations with impressive statistical values: cross-validation leave-one-out correlation coefficient (Q2LOO) = 0.6663, coefficient of determination (R2) = 0.7863, external validation coefficient (R2ext) = 0.7854, cross-validation leave-many-out correlation coefficient (Q2LMO) = 0.6256, Concordance Correlation Coefficient for cross-validation (CCCcv) = 0.8150, CCCtr = 0.8804, and CCCext = 0.8750. From the key structural findings and the insights gained from the descriptors, ETA_dPsi_A, WTPT-5, and GATS7s, new lead molecules were designed. The designed molecules were then evaluated for their CDK1 inhibitory activity using the three-descriptor model developed in this study. To evaluate their drug likeliness, in-silico ADMET predictions were made using Schrodinger's Software. Molecular docking was carried out to determine the interactions of designed compounds with the target protein. The designed compounds having excellent binding pocket molecular stability and anticancer effectiveness was substantiated by the findings of the molecular dynamics simulation. The results of this work point out important properties and crucial interactions necessary for efficient protein inhibition, suggesting lead candidates for further development as novel anticancer agents.Communicated by Ramaswamy H. Sarma.

In-silico studies of 2-aminothiazole derivatives as anticancer agents by QSAR, molecular docking, MD simulation and MM-GBSA approaches

Targeting Hec1/Nek2 is considered as crucial target for cancer treatment due to its significant role in cell proliferation. In pursuit of this, a series of twenty-five 2-aminothiazoles derivatives, along with their Hec1/Nek2 inhibitory activities were subjected to QSAR studies utilizing QSARINS software. The significant three descriptor QSAR model was generated, showing noteworthy statistical parameters: a correlation coefficient of cross validation leave one out (Q2LOO) = 0.7965, coefficient of determination (R2) = 0.8436, (R2ext) = 0.6308, cross validation leave many out (Q2LMO) = 0.7656, Concordance Correlation Coefficient (CCCCV = 0.8875), CCCtr = 0.9151, and CCCext = 0.0.7241. The descriptors integral to generated QSAR model include Moreau-Broto autocorrelation, which represents the spatial autocorrelation of a property along the molecular graph's topological structure (ATSC1i), Moran autocorrelation at lag 8, which is weighted by charges (MATS8c) and RPSA representing the total molecular surface area. It was noted that these descriptors significantly influence Hec1/Nek2 inhibitory activity of 2-aminothiazoles derivatives. New lead molecules were designed and predicted for their Hec1/Nek2 inhibitory activity based on the developed three descriptor model. Further, the ADMET and Molecular docking studies were carried out for these designed molecules. The three molecules were selected based on their docking score and further subjected for MD simulation studies. Post-MD MM-GBSA analysis were also performed to predicted the free binding energies of molecules. The study helped us to understand the key interactions between 2-aminothiazoles derivatives and Hec1/Nek2 protein that may be necessary to develop new lead molecules against cancer.Communicated by Ramaswamy H. Sarma.

Design, synthesis and anti-Tb evaluation of chalcone derivatives as novel inhibitors of InhA

A series of halogenated chalcone derivatives were designed and developed for anti-tubercular activity. Novel molecules were designed and in-silico screening were performed using admetSAR, SwissADME, and Osiris Property Explorer. From the initial filter the top 10 compounds were docked using the Autodock tool 1.5.6. and the binding energies of the docked compounds were higher than the standard drugs Isoniazid.and Ethionamide. Based on the in-silico and docking results, the top halogenated chalcones were synthesized and characterized using FT-IR, mass spectrometry, 1H, and 13C NMR spectroscopy. The chalcones were further evaluated for anti-tubercular activity using MABA against the H37Rv strain. Among the series of compounds, DK12 and DK14 showed potent in-vitro activity, with MICs of 0.8 µg/ml, in comparison with 1.6 µg/ml of the first-line drug Isoniazid. Further molecular dynamics simulations studies for 100 ns revealed that the key interaction with TYR 158 were observed in both DK12 and DK14 in the InhA active site. The compound DK12 further showed significant interactions with PHE 149 and ARG 153 residues and is a hit molecule among the series. Further DK12 and DK14 does not show any significance toxicity. The compounds DK12 needs to be optimized and further investigation to be carried out against InhA.Communicated by Ramaswamy H. Sarma.

Lead optimization of 4-(thio)-chromenone 6-O-sulfamate analogs using QSAR, molecular docking and DFT - a combined approach as steroidal sulfatase inhibitors

Aromatase and steroidal sulfatase (STS) are steroidogenic enzyme that increases the concentration of estrogens in circulation, a primary factor leading to breast cancer. At molecular level, 87% of STS is expressed and an inhibitor targeting STS could decrease the level of estrogens. In an attempt to identify the chemical structural requirement targeting placental STS inhibition, 26 compounds with pIC₅₀ ranging from 4.61 to 9.46 were subjected to computational studies including Quantitative Structural-Activity Relationship (QSAR), MolecularDocking followed by Density Functional Theory (DFT) studies. A robust and predictable model were developed with good R² (0.834) and cross-validated correlation coefficient value Q² _LOO (0.786) explaining the relationship quantitatively. The regression graphs suggests that the STS inhibition was greatly dependent on the electro topological state of an atom, sum of the atom type E-state (SdssC), maximum E-states for strong hydrogen bond acceptors (maxHBa) and basic group count descriptor (BCUTp-1h). Furthermore, docking results showed favorable interactions of sulfamate analogs with catalytically important amino acid residues such as LEU74, VAL101, and VAL486. The interactions of the best active compound 3j when compared with standard Irosustat show similar binding energies. DFT studies further confirm the presence of HOMO orbital centered on chromenone ring further highlighting its importance for receptor ligand hydrophobic interaction. The study reveals that substitution of thio in chromenone nucleus and introduction of adamantyl substitution at second position are favorable in inhibiting the enzyme STS.

Computational Overview of Mycobacterial Thymidine Monophosphate Kinase

Tuberculosis (TB) ranks among the diseases with the highest morbidity rate with significantly high prevalence in developing countries. Globally, tuberculosis poses the most substantial burden of mortality. Further, a partially treated tuberculosis patient is worse than untreated; they may lead to standing out as a critical obstacle to global tuberculosis control. The emergence of multi-drug resistant (MDR) and extremely drug-resistant (XDR) strains, and co-infection of HIV further worsen the situation. The present review article discusses validated targets of the bacterial enzyme thymidine monophosphate kinase (TMPK). TMPKMTB enzyme belongs to the nucleoside monophosphate kinases (NMPKs) family. It is involved in phosphorylation of TMP to TDP, and TDP is phosphorylated to TTP. This review highlights structure elucidation of TMP enzymes and their inhibitors study on TMP scaffold, and it also discusses different techniques; including molecular docking, virtual screening, 3DPharmacophore, QSAR for finding anti-tubercular agents.

Insights into structures of imidazo oxazines as potent polyketide synthase XIII inhibitors using molecular modeling techniques

Tuberculosis, a major global health concern, and its drug development toward the disease are too devastating to meet the clinical demands. The present work emphasizes a detailed QSAR study using QSARINS which developed descriptors favoring an excellent model equation. The best model equation generated has four variables namely AlogP, ATSc4, mindssC, and MDEC23 with statistical values R² = 0.7406, LOF = 0.1858, CCC_tr = 0.8510, Q₂LOO = 0.6569, Q₂LMO = 0.6286, CCC_cv = 0.8037, R²_ext = 0.8600, and CCC_ext = 0.9252. The developed QSAR model justifies that the key structural fragments highly correlate with activity. Docking the designed compounds with PKS XIII, a novel target catalyzes the formation of mycolic acids and its results distinctly improve expected antitubercular activity showing all probable interactions. Compounds were further screened for ADME analysis and toxicity.

QSAR, docking studies of 1,3-thiazinan-3-yl isonicotinamide derivatives for antitubercular activity

The enzyme - enoyl acyl carrier protein reductase (enoyl ACP reductase) is a validated target for antitubercular activity. Inhibition of this enzyme interferes with mycolic acid synthesis which is crucial for Mycobacterium tuberculosis cell growth. In the present work 2D and 3D quantitative structure activity relationship (QSAR) studies were carried out on a series of thiazinan-Isoniazid pharmacophore to design newer analogues. For 2D QSAR, the best statistical model was generated using SA-MLR method (r²=0.958, q²=0.922) while 3D QSAR model was derived using the SA KNN method (q²=0.8498). These studies could guide the topological, electrostatic, steric, hydrophobic substitutions around the nucleus based on which the NCEs were designed. Furthermore, molecular docking was performed to gauze the binding affinity of the designed analogues for enoyl ACP reductase enzyme. Amongst all the designed analogues the binding energies of SKS 01 and SKS 05 were found to be -5.267kcal/mol and -5.237kcal/mol respectively which was comparable with the binding energy of the standard Isoniazid (-6.254kcal/mol).

QSAR and Molecular Docking Studies of Oxadiazole-Ligated Pyrrole Derivatives as Enoyl-ACP (CoA) Reductase Inhibitors

A quantitative structure-activity relationship model was developed on a series of compounds containing oxadiazole-ligated pyrrole pharmacophore to identify key structural fragments required for anti-tubercular activity. Two-dimensional (2D) and three-dimensional (3D) QSAR studies were performed using multiple linear regression (MLR) analysis and k-nearest neighbour molecular field analysis (kNN-MFA), respectively. The developed QSAR models were found to be statistically significant with respect to training, cross-validation, and external validation. New chemical entities (NCEs) were designed based on the results of the 2D- and 3D-QSAR. NCEs were subjected to Lipinski’s screen to ensure the drug-like pharmacokinetic profile of the designed compounds in order to improve their bioavailability. Also, the binding ability of the NCEs with enoyl-ACP (CoA) reductase was assessed by docking.