Medicinal Chemistry - Online First

In this research aiming at combating COVID-19, we employed advanced computer-based methods to identify potential inhibitors of SARS-CoV-2 helicase from a pool of 3009 clinical and FDA-approved drugs. Method: To narrow down the candidates, we focused on VXG, the helicase’s co-crystallized ligand, and sought compounds with chemical structures akin to VXG within the examined drugs. The initial phase of our study involved molecular fingerprinting in addition to structure similarity studies. Results: Once the compounds most closely resembling VXG (29 compounds) were identified, we conducted various studies to investigate and validate the binding potential of these selected compounds to the protein’s active site. The subsequent phase included molecular docking, molecular dynamic (MD) simulations, and MM-PBSA studies against the SARS-CoV-2 helicase (PDB ID: 5RMM).

Based on our analyses, we identified nine compounds with promising potential as SARS-CoV-2 helicase inhibitors, namely aniracetam, aspirin, chromocarb, cinnamic acid, lawsone, loxoprofen, phenylglyoxylic acid, and antineoplaston A10. The findings of this research help the scientific community to further investigate these compounds, both in vitro and in vivo.

Over the past ten years, a remarkable number of changes have occurred in the field of cancer drug research. Most anticancer drugs from the first generation work by breaking down DNA, preventing its production, interfering with cell division processes, or attaching to microtubules. The potential use of tryptanthrin as well as its analogues is well documented for anticancer properties.

To design a novel hybrid of tryptanthrin analogs with expected anticancer activity.

By changing the C-6 carbonyl position of the tryptanthrin molecule, a set of 72 derivatives of substituted-6-benzylidine-6H-indolo[2,1-b] quinazoline-12-one was developed. These ligands were screened in silico using Schrodinger Glide extra precision docking against DNA topoisomerase using doxorubicin and teniposide as references to identify their potential anticancer properties. Further, these ligands were subjected to an in silico ADMET study to identify their drug likeliness.

Combined results of molecular docking and in silico ADMET study suggest that out of the total 72 ligands, 6 ligands RC 51, RC 29, RC 42, RC 3, RC 54, and RC 63 were showing very better binding affinity than the natural ligand adenylyl-imidodiphosphate and the two standard reference drugs- doxorubicin and teniposide.

Our computational approach was successful in identifying ligands that are potentially potent topoisomerase inhibitors. These can be tested further using in vitro and in vivo analysis.

The aim is to halt the progression of liver cancer [Hepatocellular carcinoma] by suppressing the VEGF-R1 receptor using Myricetin and its de novo-designed analogues.

VEGF/VEGFR autocrine signalling promotes the growth, progression, and metastasis of Hepatocellular carcinoma, making the development of molecularly targeted therapies highly feasible. Invasive and metastatic behaviours in various cancers, including hepatocellular carcinoma [HCC], are closely monitored through the use of VEGF signalling pathway inhibitors. Specifically in HCC, VEGFR-1 facilitates the invasive capabilities of cancer cells primarily by triggering the epithelial-mesenchymal transition [EMT] process. VEGFR-1 significantly influences the activity of proteolytic enzymes that are critical for the invasive behaviour of HCC cells. Notably, a novel mechanism has been discovered where VEGFR-1 activation leads to the upregulation of MMP-9, thereby enhancing the invasiveness of HCC cells. The scientists, in their study, have elaborated on the various antiangiogenic agents developed for the treatment of HCC. They have highlighted clinical trials that explore the efficacy of these treatments, which include the application of monoclonal antibodies and small-molecule kinase inhibitors designed to target specific pathways involved in tumour angiogenesis and growth.

Creating a pharmaceutical chemistry table regarding ‘’Structure-Activity Relationship of New Compounds on anticancer”. To do so, Myricetin and its de novo designed structured variants were used in molecular docking, molecular dynamics, cluster analyses, and ¹H NMR estimation to specifically understand and enhance the mechanism of suppressing the VEGF-R1 receptor.

Proper ligand [Myricetin and its analogues] and receptor [VEGF-R1] preparations, and optimizations were done using the density functional theory [DFT]/B3LYP function along with the 6-31G[d,p] basis set principle in the latest software programs such as Gaussian 09, Gauss View 6.0 and Avogadro. Then using PyRx and Autodock Vina 1.1.2., many molecular docking trials were achieved with 100 posed simulations in each run. An extensive cluster analysis was performed to identify the most optimal docking poses with the highest accumulation and most favourable binding interactions, ensuring the accuracy of the study. The docking configurations that exhibited the most precise and advantageous binding energies were chosen as initial structured data for subsequent Molecular Dynamics [MD] simulations for each drug candidate. To verify the molecular docking results, MD runs were achieved in our supercomputers and the trajectory analyses were made. The data confirmed what was found in molecular docking results, verifying the high efficiency of the druggable molecules’ inhibition towards VEGF-R1.

Amine-derivatized Myricetin has a significantly high docking score [-10.56 kcal/mol] and great inhibition constant compared to pristine Myricetin [-4.77 kcal/mol] itself while Fluorine-derivatized Myricetin [-6.45 kcal/mol] has an affinity towards VEGF-R1 between the first two molecules. Thus, the structure-activity relationship concerning pharmaceutical chemistry aspects of all the molecules studied, yielded us a great insight into what Myricetin’s organic structure possesses towards inhibiting the progression of Liver Cancer. Also, ADME studies showed that both Amine and Fluorined-derivatized Myricetin molecules are good drug candidates.

This study highlighted the significant potential of Myricetin as an anti-cancer drug when modified with specific functional groups. Through comprehensive in silico computational analyses, our research group enhanced Myricetin's inhibitory capabilities by derivatizing its Hydroxyl group with Amine and Fluorine, resulting in improved docking scores and inhibition constants. The findings from molecular docking and molecular dynamics simulations provide a promising foundation for future in vitro and in vivo investigations of this molecule as a potential drug in cancer research.