Current Computer - Aided Drug Design - Volume 18, Issue 3, 2022

Background and Objective: Phthalimide, as the rigid form of ameltolide, exhibits a phenytoin-like profile of drug-receptor interaction and is active in the MES model and inactive in the PTZ model as an anti-epileptic agent. In this research, based on the isosteric replacement, we reported the design, preparation, and antiepileptic activity of 13 new analogs of pyrrolopyridine and isoindole. Methods: The designed compounds were prepared by condensing 3, 4-pyridine dicarboxylic anhydride, or 4-fluorophthalic anhydride with different aryl amines. MES and PTZ-induced seizure models were utilized to evaluate the antiepileptic effect of the prepared ligands. Results: It was found that the prepared ligands have significantly affected both tonic and clonic seizures. In tonic seizures, the prepared compounds decreased mortality to a significant extent, and in clonic seizures, they significantly showed better frequency and latency. Compounds 9, 12, and 13 were the most potent ligands than phenytoin. Conclusion: It is concluded that the best distance between two aryl parts is two bonds, and the substitution of the nitro group at the meta position of the phenyl ring is better than the para position. Our research group has investigated this concept for designing newer compounds with better anticonvulsant activity.

Introduction: Annona muricata is a member of the Annonaceae family. This plant has a high concentration of acetogenin, which gives it excellent therapeutic property. Researchers have tested this miraculous herb in breast cancer cells treatment and observed that it could be a source of anti-cancer agents. The proposed study focused on screening the anticancer biological activity of Annona muricata plant by using the in vitro, in vivo, and in silico methods. Methods: In in vitro analysis, the IC50 was determined on two-dimensional and three-dimensional breast cancer cells. 2D cells were cultured on flat dishes typically made of plastic, while 3D cells were cultured using the hanging drop method. In in vivo analysis, Drosophila melanogaster was preferred, and the LC50 was determined. In in silico analysis, molecular docking studies have been carried out on the different classes of Annona muricata acetogenins against the target proteins. Nearly, five acetogenins were selected from the literature, and docking was performed against human Bcl-2, Bad and Akt-1 proteins. Results: In vitro and in vivo results revealed the IC50 value of 2D MDA-MB-231 cells as 330 μg.m132;“-1, of 2D MCF-7 cells as290 μg.m132;“-1, and of 3D MCF-7 and MDA-MB-231 cells about 0.005 g.m132;“-1; the LC50 value of Drosophila melanogaster was determined as 0.1 g.m132;“-1. In silico results revealed that the docked complex formed by Isoquercetin showed better binding affinity towards target proteins. Conclusion: As a result of the analysis, the Annona muricata plant has been observed to be effective against cancer and likely to be a potential drug.

Background: Circular RNAs (circRNAs) act as competing endogenous RNAs (ceRNAs) that indirectly regulate gene expression and function by binding microRNAs (miRNAs). A growing body of evidence indicates that the ceRNA networks can be used as an effective method to investigate cancer; however, the construction and analysis of ceRNA networks, especially circRNA-miRNA-mRNA regulatory network, in different subtypes of breast cancer have not been previously performed. Objectives: In the present study, we generated a ceRNA network to explore their roles in two BC subtypes, namely Luminal A and triple negative breast cancer (TNBC). Methods: First, the expression profiles of circRNA, miRNA, and mRNA were downloaded from the GEO database, differentially expressed genes were obtained using GEO2R, and a ceRNA network was constructed based on circRNA-miRNA pairs and miRNA-mRNA pairs, consisted of 10 circRNAs, 25 miRNAs and 39 mRNAs. Further studies of BC subtypes based on TCGA datasets were also performed to validate the effect of a novel ceRNA network. Results and Discussion: Then, the related genes in the regulatory network were analyzed by GO functional annotation and KEGG pathway enrichment. The analysis showed that targeted genes were enriched in 97 GO terms and 25 KEGG pathways, involved in the molecular typing of breast cancer. Meanwhile, Kaplan-Meier analysis revealed that three key genes (MKI67, DEF8, and GFRA1) were significantly associated with BC tumor differentiation and prognosis. Conclusion: The current study provides a potential application of the ceRNA network within BC subtypes and may offer new targets for their diagnosis, therapy and prognosis.

Background: Breast cancer is one of the greatest global dilemmas, and the current treatment option is to target hormone receptors with partial agonists/antagonists. Estrogen and aromatase enzymes play important roles in breast cancer. Excessive estrogen activity or inadequate estrogen production leads to various hormonal issues, including breast cancer. Potent breast cancer drugs are Tamoxifen, Paclitaxel, Cyclophosphamide, Trastuzumab, etc., and aromatase inhibitors, include Anastrozole, Letrozole, and Exemestane, etc. In general, breast cancer drugs cause numerous adverse effects in humans. Objectives: This study has attempted to identify alternative drug candidates from Carica papaya for treating breast cancer with fewer side effects. Methods: To achieve this, we have utilized computational methods to predict the characteristics of bioactive compounds from Carica papaya and determine the target binding affinities using the Schrödinger suite (Maestro 9.5). The target protein and ligands were obtained from the well-known database. Carica papaya has 35 identified bioactive compounds that were drawn using ChemDraw software and performed Ligand preparation wizard. Absorption, Distribution, Metabolism, and Excretion (ADME) analysis is performed with QikProp. Results: From the docking studies, the phytocompounds such as Chlorogenic acid, Myricetin, Quercetin, Isorhamnetin, and Catechin showed the highest Glide scores (G Score). Among the five bioactive phytocompounds, Chlorogenic acid has a higher G Score with good binding energy than Tamoxifen, Anastrozole, and Letrozole standards. The pharmacokinetic properties and drug-likeness of phytocompounds were determined using ADME profiling. Conclusion: Carica papaya phytocompounds serve as an antiestrogen or aromatase inhibitor that regulates estrogen levels to reduce the risk of breast cancer in postmenopausal women. As a result, we recommend that these top five bioactive phytocompounds be investigated further in in vitro and in vivo studies.

Aims: The present study aimed to search for novel potent inhibitor(s) against the recently discovered maltosyltransferase (GlgE) target of M.tb. Background: GlgE belongs to an α-amylase family and catalyzes the elongation of cytosolic branched α-glucan. Inactivation of M.tb. GlgE results in DNA damage and rapid death of M.tb. due to the accumulation of a toxic altosyl donor, maltose-1-phosphate (M1P), suggesting that GlgE is an intriguing target for inhibitor design. Methods: 1000 natural compounds were compiled from public databases and literature through virtual screening, of which 25 compounds were found to satisfy all drug-likeness properties and ADME/ toxicity criteria, followed by molecular docking with GlgE. Compound(s) showing the lowest binding energy was further subjected to molecular dynamics simulation (MDS) and in vitro analysis. Results: Molecular docking analysis allowed the selection of 5 compounds withsignificant binding affinity to GlgE targets. Amongst these compounds, asiatic acid exhibited the lowest binding energy (-12.61 kcal/mol). The results of 20-ns MDS showed that asiatic acid formed a stable complex with GlgE. Additionally, asiatic acid exhibited in vitro anti-mycobacterial activity against M.tb. H37Ra, M. bovis BCG, and M. smegmatis strains. Conclusion: The study reveals asiatic acid as a promising anti-mycobacterial agent that might emerge as a novel natural anti-TB lead molecule in the future.

Background: The compound Sophora flavescenes (Kushen) decoction was found to reduce the inflammatory symptom of Ulcerative Colitis (UC). However, there exists a very limited understanding of the molecular pharmacological mechanisms. Objective: This study aimed to explore the mechanism of compound Sophora flavescens (Kushen) decoction in treating ulcerative colitis from the perspective of network pharmacology. Methods: Active components and potential targets of compound Sophora flavescens (Kushen) decoction were obtained through the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database. GeneCards and other databases were used to predict and screen ulcerative colitis-related genes. Cytoscape software was applied to construct the “drugactive component-disease-target” network. GO function and KEGG pathway enrichment analyses revealed the potential pathway of the compound Sophora flavescenes (Kushen) decoction for UC. Results: After the screening, a total of 124 active ingredients and 163 potential therapeutic targets for UC were obtained from the compound Sophora flavescens (Kushen) decoction. Protein interaction network analysis showed that 15 key targets could be identified for the possible treatment of UC. GO and KEGG analyses showed that the active ingredients in the compound Sophora flavescens (Kushen) decoction were mainly enriched in 2556 biological processes and 172 signaling pathways. Conclusion: The study showed that the compound Sophora flavescens (Kushen) decoction has therapeutic effects on UC through multi-component, multi-target, and multi-pathway.

Aim: This study aimed at screening and development of Pim-1 inhibitors as anticancer agent. Background: Pim-1, a member of the Ser/Thr kinase family, plays a crucial role in cell proliferation and is being regarded as a promising target for cancer therapeutics. Objective: The present work focused on screening more potent Pim-1 inhibitors by in-silico method and biological evaluation. Materials and Methods: To identify more potent Pim-1 inhibitors, a GALAHAD pharmacophore model was constructed based on nine known Pim-1 inhibitors and followed by in silico screening including pharmacophore and molecular docking-based virtual screening. The hit compounds were further assessed the Pim-1, 2, and 3 kinase activities and the anticancer inhibition property against human myeloma RPMI-8226 and U266 cells using cytotoxicity studies. Results: Based on Qfit value (from pharmacophore), docking score and clustering analysis, six compounds including C445_0268, C470_0769, 4456_0744, 0806_0325, G395_1510 and V023_3227 were hit. Binding mode analysis showed that hydrogen bond, hydrophobic and π-π stacking interactions dominated the bindings of these compounds to Pim-1. The further biological evaluation indicated that compounds C445_0268 and C470_0769 possessed excellent pan-Pim kinase activities and inhibited the growths of RPMI-8226 and U266 cell lines with IC50 values lower than 3.75 μM. Conclusion: We reported a series of Pim-1 small molecule inhibitors that could serve as the lead compounds to develop new targeted anticancer therapeutics.