Molecular Docking, Pharmacokinetic and Molecular Simulation Analysis of Novel Mono-Carbonyl Curcumin Analogs as L858R/T790M/C797S Mutant EGFR Inhibitors

INTRODUCTION

Curcumin, an anticancer natural compound with multiple pharmacological activities, has a weak pharmacokinetic and instability due to diketone moiety. Curcumin's stability challenges can be overcome by removing the diketone moiety and shortening the 7-carbon chain, resulting in mono-carbonyl analogs. Cancer proliferation is caused by the activation of Epidermal Growth Factor (EGFR) pathways. Current available EGFR inhibitors have an issue of resistance.

AIM

Thus, we aimed to design new mono-carbonyl curcumin derivatives and analyse their drug likeness properties. Further, to investigate them on three distinct crystal structures, namely two wild-type and L858R/T790M/C797S mutant generations for EGFR inhibitory activity.

METHOD

Ten New Molecular Entities (NME's) were designed using literature survey. These molecules were subjected to comparative molecular docking, on the EGFR crystal structures viz. wild-type (PDB: 1M17 and 4I23) and L858R/T790M/C797S mutant (PDB: 6LUD) using Schrodinger software. The molecules were also tested for Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties. The docked complex of the hit molecule was studied for molecular simulation.

RESULT AND DISCUSSION

In molecular docking studies, NMEs 1, 2, and 3 were found to have good binding affinity with 1st , 2nd , and 3rd generation EGFR crystal structures and a greater dock score than standard curcumin. All molecules have shown a good ADMET profile. Since L858R/T790M/C797S is currently being explored more, we decided to take the best molecule, NME 3, for molecular dynamics with 6LUD, and the results were compared with those of the co-crystallized ligand S4 (Osimertinib). It was found that the Relative mean square standard deviation (RMSD) (1.8 Å), Relative mean standard Fluctuation (RMSF) (1.45 Å) and radius of gyration (4.87 Å) values of NME 3 were much lower than those of reference S4. All these confirm that our designed NME 3 is more stable than reference S4.

CONCLUSION

NME 1 and NME 2 have shown better binding against wild type of EGFR. NME 3 have shown comparable binding and more stability as compared to Osimertinib against L858R/T790M/C797S mutated protein structure. The hit compound can be further explored for its Molecular mechanics with generalised Born and surface area solvation (MM-GBSA) and discrete Fourier transform (DFT) studies to find out the energy and atomic level study. In the future, this molecule could be taken for wet lab studies and can be tested for mutated EGFR inhibitory activity.

Explorations of novel pyridine-pyrimidine hybrid phosphonate derivatives as aurora kinase inhibitors

For developing novel therapeutic agents with good anticancer activities, a series of novel pyridine-pyrimidine hybrid phosphonate derivatives4(a-q) were synthesized by the Kabachnik-Fields method using CAN as catalyst. The compound 4o exhibited the most potent anticancer activity with an IC₅₀ value of 13.62 μM, 17.49 μM, 5.81 μM, 1.59 μM and 2.11 μM against selected cancer cell lines A549, Hep-G2, HeLa, MCF-7, and HL-60, respectively. Compound 4o displayed seven times more selectivity towards Hep-G2 cancer cell lines compared to the human normal hepatocyte cell line LO2 (IC₅₀ value 95.33 μM). Structure-Activity Relationship (SAR) studies were conducted on the variation in the aromatic ring (five-membered heterocyclic ring, six-membered heterocyclic ring) and the variation of substituents on the phenyl ring (electron donating groups, electron withdrawing groups). Furthermore, the mechanism of anticancer activity was clarified by further explorations in bioactivity by using in vitro aurora kinase inhibitory activity and molecular docking studies. The results showed that the compound 4o at IC₅₀concentrationdemonstrated distinctive morphological changes such as cell detachment, cell wall deformation, cell shrinkage and reduced number of viable cells in cancer cell lines. Compound 4o induced early apoptosis and late apoptosis of 27.7% and 6.1% respectively.

Optimization of pharmacophore of novel hybrid nucleus of 1,3,4-oxadiazole-chalcone using literature findings and in-silico approach as EGFR inhibitor

Introduction/Background:

Cancer is a leading cause of death worldwide. EGFR is one of the important targets considered for current chemotherapeutic agents. The problem of drug resistance can be overcome by the use of hybrid molecules. A hybrid of 1,3,4-oxadiazole and chalcone is proved to be an Anti-EGFR inhibitor.

Objective:

To carry out pharmacophore optimization of the hybrid nucleus of 1,3,4-oxadiazole and chalcone by using literature findings and in-silico approach. A series of 24 substituted hybrid molecules of 2-(5-phenyl-1,3,4-oxadiazol-2-ylthio)-N-(4-((Z)-3-phenylacryloyl)phenyl)acetamide derivatives were subjected to 2D and 3D QSAR studies.

Method:

The survey of literature was carried out for selected hybrid nucleus using different databases available. The 2D QSAR was performed by using the MLR, PLS, PCR methods 3D QSAR was performed using the KNN-MFA method.

Result:

Summary of literature findings was prepared. For 2D QSAR statistically significant model was obtained for the MLR method with r2=0.9128, q2=0.8065. For the 3D QSAR model I, is found to be significant with q2=0.834. The pharmacophoric requirements for inhibition of EGFR were optimized by use of the evidence attained after the generation of descriptors from QSAR studies and literature findings. This optimized pharmacophore will be useful in further drug design process.

A Rational Approach to Anticancer Drug Design: 2D and 3D- QSAR, Molecular Docking and Prediction of ADME Properties Using Silico Studies of Thymidine Phosphorylase Inhibitors

Background:

Cancer is the most prevalent disease seen nowadays. Thymidine phosphorylase (TP) is an angiogenic enzyme that is overexpressed in many solid tumors. Over the years, Thymidine phosphorylase has emerged as a novel target for anticancer drug development as an inhibitor.

Objective:

To design novel oxadiazole-isatin pharmacophore containing molecules and to explore their structural requirements related to the anticancer activity.

Methods:

Pharmacophore optimisation was carried out for oxadiazole-isatin hybrid molecules using molecular modeling studies (2D and 3D QSAR). Further, the new chemical entities were designed using combilib tool of V life software. To have a better understanding of the binding interactions, the newly designed molecules were docked. To achieve a drug-like pharmacokinetic profile, molecules were also tested for ADME prediction.

Results:

For Two-Dimensional Quantitative Structure-Activity Relationship (2D-QSAR) model was generated using the multiple regression method with r2 = 0.84 and q2 = 0.76. Three-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR) model was obtained by simulated annealing k nearest near (SA kNN) method with q2 = 0.8099. Molecular docking studies showed promising results. The compound with the best dock score and the best fit to the active site pocket of the thymidylate phosphorylase enzyme was found to be compound 5. The compounds have notable absorption, distribution, metabolism, and excretion (ADME) properties that can be predicted to assure a drug-like pharmacokinetic profile.

Conclusion:

One of the most successful and fast-increasing methodologies is molecular modeling. It not only aids in the prediction of specific target compounds but also aids in the cost reduction of valuable substances. The successful use of molecular modeling was done in this study, with caution taken to avoid any chance co-relation. Optimised pharmacophore was obtained and new chemical entities were designed. Docking studies revealed that Molecule 5 have shown better H-bond interaction with Lys 221 and Thr 151 with bond distances 2.0  and 1.8  which is the most active molecule. ADME tests discovered that the majority of the newly designed compounds were within a reasonable range as required in a drug like pharmacokinetic profile. Molecules 2, 4, 5, 6 can be considered as a lead for future synthesis and biological screening.

One pot synthesis, in silico study and evaluation of some novel flavonoids as potent topoisomerase II inhibitors

A library of novel flavonoid derivatives with diverse heterocyclic groups was designed and efficiently synthesized. Structures of the newly synthesized compounds 4a-i and 8a-l have been characterized by ¹H NMR, ¹³C NMR, MS and elemental analysis. Anticancer activities were evaluated against MCF-7, A549, HepG2 and MCF-10A by MTT based assay. Compared with the positive control Adriamycin, compounds 4a, 4b, 4c, 4d, 8d, 8e and 8j were found to be most active anti-proliferative compounds against human cancer cell line. We found that compounds 4a and 4c exhibited inhibition of enzyme topoisomerase II with IC₅₀ values 10.28 and 12.38 μM, respectively. In silico docking study of synthesized compounds showed that compounds 4a and 4c have good binding affinity toward topoisomerase IIα enzyme and have placed in between DNA base pair at active site of enzyme. In silico ADME prediction results that flavonoid coumarin analogues 4a-i could be exploited as an oral drug candidate.

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 nitric oxide donors containing 1,5-diarylpyrazolin-3-one as nontoxic NSAIDs

Various substituted 1,5-diarylpyrazol-3-one derivatives were synthesized and screened for analgesic, anti-inflammatory activities, ulcerogenic potential and for their ability to release nitric oxide. Most compounds exhibited significant analgesic and anti-inflammatory activities. It was interesting to note that out of ten compounds, 7j (59.64%) was found to have anti-inflammatory activity greater than the standard drug Indomethacin (57.89%), whereas compound 7b (57.89%) was found to be equipotent to that of standard, Indomethacin. The pharmacological studies suggested that the presence of 4-nitro and 2-methoxy on phenyl ring at C(5) of pyrazole has a significant anti-inflammatory activity and 4-chloro substitution on same phenyl ring was found to have decreased activity. However only a phenyl substituted derivative was found to have most potent activity. Compound 7j containing plane phenyl at C(5) of pyrazole was found to have significant analgesic activity (56.86%) in acetic acid induced writhing model. Compounds 7d and 7i having 4-chloro substituted phenyl ring showed least analgesic activity (10.78%) and (6.86%) respectively. The compounds also showed significantly reduced GI-ulcerogenicity and gastroprotective results in histopathological studies i.e. they were found to be causing no mucosal injury. All the synthesized compounds were found to exhibit significant nitric oxide releasing activity, in both in vitro and in vivo models. Molecular docking studies served to be an important tool for the study of binding of compounds with that of a COX-2 enzyme. The results of the docking studies were found to endorse the result of experimental work. Thus, the rationale used to design the NCEs was found to produce the promising results as anticipated. Therefore it can be said that the strategy employed can serve as an important tool in future for the design and development of novel therapeutic agents of various categories too.

Design, synthesis and evaluation of antiinflammatory, analgesic and ulcerogenicity studies of novel S-substituted phenacyl-1,3,4-oxadiazole-2-thiol and Schiff bases of diclofenac acid as nonulcerogenic derivatives

Diclofenac sodium is being used for its anti-inflammatory actions since 28 years, but as all the NSAIDs are suffering from the deadlier GI toxicities, diclofenac sodium is also not an exception to these toxicities. The free -COOH group is thought to be responsible for the GI toxicity associated with all traditional NSAIDs. In the present research work, the main motto was to develop new chemical entities as potential anti-inflammatory agents with no GI toxicities. In this paper, the results of synthesis and pharmacological screening of a series of S-substituted phenacyl 1,3,4-oxadiazoles and Schiff bases derived from 2-[(2,6-dichloroanilino) phenyl] acetic acid (diclofenac acid) are described. The 1,3,4-oxadiazoles and diclofenac moieties are important because of their versatile biological actions. In the present studies, the oxadiazole system has been functionalized onto the diclofenac acid moiety and 18 compounds in this series were synthesized. The structures of new compounds are characterized by TLC, FTIR, 1H NMR and Mass spectral data. These compounds were tested in vivo for their anti-inflammatory activity. The compounds, which showed significant activity (comparable to the standard drug diclofenac sodium), were screened for their analgesic activity and to check their ability to induce ulcers by ulcerogenicity and histopathology studies. Eight new compounds, out of 18, were found to have significant anti-inflammatory activity in the carrageenan induced rat paw oedema model, with significant analgesic activity in the acetic acid induced writhing model with no ulcerogenicity. The compounds, which showed negligible ulcerogenic action, also showed promising results in histopathology studies, that is, they were found to be causing no mucosal injury.