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.

In Search of HIV Entry Inhibitors Using Molecular Docking, ADME, and Toxicity Studies of Some Thiazolidinone-Pyrazine Derivatives Against CXCR4 Co-receptor.

BACKGROUND: Entry inhibitors prevent the binding of human immunodeficiency virus protein to the chemokine receptor CXCR4 and are used along with conventional anti-HIV therapy. They aid in restoring immunity and can prevent the development of HIV-TB co-infection. AIMS: In the present study, various thiazolidinone-pyrazine derivatives earlier studied for NNRT inhibition activity were gauged for their entry inhibitor potential. OBJECTIVE: The objective of the study is to perform molecular docking, ADME, toxicity studies of some thiazolidinone-pyrazine derivatives as entry inhibitors targeting CXCR4 co-receptors. METHODS: In-silico docking studies were performed using AutoDock Vina software and compounds were further studied for ADME and toxicity using SwissADME and pkCSM software, respectively. RESULTS: Taking into consideration the docking results, pharmacokinetic behaviour and toxicity profile, four molecules (compounds 1, 9, 11, and 16) have shown potential as entry inhibitors. CONCLUSION: These compounds have shown potential as both NNRTI and entry inhibitors and hence can be used in management of immune compromised diseases like TB-HIV coinfection.

In silico Studies, Synthesis and Antitubercular Activity of Some Novel Quinoline - Azitidinone Derivatives.

BACKGROUND: Diarylquinolines like Bedaquiline have shown promising antitubercular activity by their action of Mycobacterial ATPase. OBJECTIVE: The structural features necessary for a good antitubercular activity for a series of quinoline derivatives were explored through computational chemistry tools like QSAR and combinatorial library generation. In the current study, 3-Chloro-4-(2-mercaptoquinoline-3-yl)-1- substitutedphenylazitidin-2-one derivatives have been designed and synthesized based on molecular modeling studies as anti-tubercular agents. METHODS: 2D and 3D QSAR analyses were used to designed compounds having a quinoline scaffold. The synthesized compounds were evaluated against active and dormant strains of Mycobacterium tuberculosis (MTB) H37 Ra and Mycobacterium bovis BCG. The compounds were also tested for cytotoxicity against MCF-7, A549 and Panc-1 cell lines using MTT assay. The binding affinity of designed compounds was gauged by molecular docking studies. RESULTS: Statistically significant QSAR models generated by the SA-MLR method for 2D QSAR exhibited r2 = 0.852, q2 = 0.811, whereas 3D QSAR with SA-kNN showed q2 = 0.77. The synthesized compounds exhibited MIC in the range of 1.38-14.59(µg/ml). These compounds showed some crucial interaction with MTB ATPase. CONCLUSION: The present study has shown some promising results which can be further explored for lead generation.

Non Nucleoside Reverse Transcriptase Inhibitors, Molecular Docking Studies and Antitubercular Activity of Thiazolidin-4-one Derivatives.

BACKGROUND: Management of Co-existence of Acquired immunodeficiency syndrome and Tuberculosis has become a global challenge due to the emergence of resistant strains and pill burden. OBJECTIVE: Hence the aim of the present work was to design and evaluate compounds for their dual activity on HIV-1 and Tuberculosis (TB). METHODS: A series of seven, novel Thiazolidin-4-one derivatives were synthesized and evaluated for their anti-HIV and anti-tubercular activity along with Molecular docking studies. All the seven compounds displayed promising activity against the replication of HIV-1 in cell-based assays. The four most active compounds were further evaluated against X4 tropic HIV-1UG070 and R5 tropic HIV-1VB59 primary isolates. The binding affinity of all the designed compounds for HIV-RT and Mycobacterium tuberculosis Enol Reductase (MTB InhA) was gauged by molecular docking studies which revealed crucial thermodynamic interactions governing their binding. RESULTS: The CC50 values for the test compounds were in the range of, 15.08-34.9 µg/ml, while the IC50 values were in the range of 16.1-27.13(UG070; X4) and 12.03-23.64 (VB59; R5) µg/ml. The control drug Nevirapine (NVP) exhibited CC50 value of 77.13 µg/ml and IC50 value of 0.03 µg/ml. Amongst all these compounds, compound number 3 showed significant activity with a TI value of 2.167 and 2.678 against the HIV-1 X4 and the R5 tropic virus respectively. In anti-mycobacterial screening, the compounds proved effective in inhibiting the growth of both log phase and starved MTB cultures. CONCLUSION: Compound 3 has been found to be active against HIV-1 as well as MTB.

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.

Pharmacophore optimization and design of competitive inhibitors of thymidine monophosphate kinase through molecular modeling studies.

A series of N(1) -(4-substituted-benzyl)-pyrimidines were subjected to 2D and 3D quantitative structure-activity relationship analyses. Statistically significant models were generated, and the most robust model for 2D quantitative structure-activity relationship was obtained using simulated annealing-multiple linear regression. The physicochemical descriptors, viz., slogp, estate descriptors like SaaCHE index and SdsCHE index contribute significantly to the biological activity. The pharmacophore requirements for selective inhibition of Mycobacterium tuberculosis thymidine monophosphate kinase were optimized using the information derived from 2D and 3D quantitative structure-activity relationship studies. With the results from the studies, we have designed new chemical entities using the CombiLib Tool of V-Life Molecular Design Suite. In addition, using structure-based drug design, the distances between interacting groups of ligands and amino acid residues of the protein Mycobacterium tuberculosis thymidine monophosphate kinase (PDB ID:1W2H) were thoroughly analyzed. Thus, we have successfully replaced the sugar moiety with substituted aromatic ring on N1 of thymidine. Thorough studies on substitution pattern around pyrimidine ring were carried out.

Design, synthesis, and evaluation of anti-inflammatory, analgesic, ulcerogenicity, and nitric oxide releasing studies of novel indomethacin analogs as non-ulcerogenic derivatives.

Most non-steroidal anti-inflammatory drugs (NSAIDs) suffer from the deadlier gastrointestinal (GI) toxicities. The free -COOH group is responsible for the GI toxicity associated with all traditional NSAIDs. In the present research work, the main objective was to develop new chemical entities as potential anti-inflammatory agents with no GI toxicities. The results of synthesis and pharmacological screening of a series of hybrid molecules having general formula 2-(5-(5-(substituted phenyl)-2-oxo-ethylthio)-1,3,4-oxadiazole-2-yl)-2-phenyl-1H-indol-1-yl)-2-oxoethyl nitrate are described. These compounds were tested in vivo for their anti-inflammatory, analgesic, and ulcerogenic properties, and subjected to histopathological studies. Compound 7c, 2-(5-(5-(3-hydroxyphenyl)-2-oxo-ethylthio)-1,3,4-oxadiazole-2-yl)-2-phenyl-1H-indol-1-yl)-2-oxoethyl nitrate, was the most potent in this series. The compounds that showed significantly reduced GI ulcerogenicity also showed promising results in histopathological studies, and they were found to cause no mucosal injury. All the synthesized compounds were found to exhibit significant nitric oxide releasing activity in an in vitro method. In conclusion, the designed hybrid molecules were found to be significantly promising.

Design, synthesis and pharmacological screening of novel antihypertensive agents using hybrid approach.

Eight derivatives of general formula 2-(2-(4-(3-((5-substituted methylene)-4-oxo-2-(phenylimino)thiazolidin-3-yl)-2-hydroxypropylamino)benzoyl)hydrazinyl)-2-oxoethyl nitrate were synthesized and tested for electrocardiographic, antiarrhythmic, vasorelaxing and antihypertensive activity as well as for in-vitro nitric oxide (NO) releasing ability. Compound 8b 2-(2-(4-(3-(5-benzyliden-4-oxo-2-(phenylimino)thiazolidin-3-yl)-2-hydroxypropylamino)benzoyl)hydrazinyl)-2-oxoethyl nitrate, was the most potent in this series. The pharmacological results suggested that the antiarrhythmic effects of these compounds were related to their adrenolytic properties which are believed to be due to the presence of the 5-(substituted)methylen-2-(phenylimino)thiazolidin-4-one moiety with less bulky, electron donating substituent on the phenyl ring at 5th position of the thiazolidin-4-one. In conclusion, most of the synthesized compounds were significantly potent as antiarrhythmic and antihypertensive; this might be due to the presence of different pharmacopores which might act at different locations with different mode of action. Further insights of the same can be obtained by doing investigation at receptor level. The potency of compounds 8a-8h were promising enough to continue further experiments.