Drug targets for cell cycle dysregulators in leukemogenesis: in silico docking studies

Target validation and structure-based virtual screening to Discover potential lead molecules against the oncogenic NSD1 histone methyltransferase

The aim of the study was to validate Nuclear receptor-binding SET Domain NSD1 as a cancer drug target followed by the design of lead molecules against NSD1. TCGA clinical data, molecular expression techniques were used to validate the target and structure-based virtual screening was performed to design hits against NSD1. Clinical data analysis suggests the role of NSD1 in metastasis, prognosis and influence on overall survival in various malignancies. Furthermore, the mRNA and protein expression profile of NSD1 was evaluated in various cell lines. NSD1 was exploited as a target protein for in silico design of inhibitors using two major databases including ZINC15 and ChemDiv by structure-based virtual screening approach. Virtual screening was performed using the pharmacophore hypothesis designed with a protein complex S-adenosyl-l-methionine (SAM) as an endogenous ligand. Subsequently, a combined score was used to distinguish the top 10 compounds from the docking screened compounds having high performance in all four scores (docking score, XP, Gscore, PhaseScreenScore, and MMGBSA delta G Bind). Finally, the top three Zinc compounds were subjected to molecular dynamic simulation. The binding MMGBSA data suggests that ZINC000257261703 and ZINC000012405780 can be taken for in vitro and in vivo studies as they have lesser MMGBSA energy towards the cofactor binding site of NSD1 than the sinefungin. Our data validates NSD1 as a cancer drug target and provides promising structures that can be utilized for further lead optimization and rational drug design to open new gateways in the field of cancer therapeutics.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-023-00158-0.

A Novel Compound Plumercine from Plumeria alba Exhibits Promising Anti-Leukemic Efficacies against B Cell Acute Lymphoblastic Leukemia

The current study was focused to evaluate the antioxidant and the anti-cancerous properties of Plumeria alba. Plumeria alba was chosen due to its existing medicinal values. Antioxidant assays like Superoxide radical scavenging assay, Nitrous Oxide radical scavenging assay, were performed, on the methanolic and ethyl acetate extracts of the plant, that depicts the pro-oxidant nature of the extract. Further, they were tested to check cell viability on B cell Acute Lymphoblastic Leukemia (ALL) Cell line (NALM 6), human lung cancer cell line (A549), T cell Acute Lymphoblastic Leukemia cell line (MOLT4), and PBMC isolated from normal donors utilizing MTT assay. Robust anti-proliferative activity was observed in the case of NALM 6 followed by A549, MOLT4, whereas negligible activity was observed in the case of PBMC. Intrigued by this finding, in silico docking was performed using three bioactive compounds namely Plumericine, Isoplumericine, and 13-O-p-Coumaroylplumieride, unique to Plumeria sp. They were docked against five different cyclins and Cdk proteins responsible for ALL. The compounds have shown satisfactory results and their druggability and ADMET properties were checked further. Plumercine turned out to be the most competent compound and hence can be considered as a potential leukemic drug candidate in the future.

E-pharmacophore hypothesis strategy to discover potent inhibitor for influenza treatment

The surface protein of Influenza virus, Neuraminidase (NA), is believed to play a critical role in the release of new viral particle and thus spreads infection. It has been recognized as a valid drug target for anti-influenza therapy. Despite the number of available approved drugs for the influenza infection treatment, the emergence of resistant variants with novel mutations are the foremost challenges for the currently used NA inhibitors. Thus, the current investigation was carried out to ascertain potent inhibitors using computational strategies such as e-pharmacophore based virtual screening and docking approach. A three-dimensional e-pharmacophore hypothesis was generated based on the chemical features of complexes of the drugs and NA protein using PHASE module of Schrödinger suite. The generated hypothesis consisted of one hydrogen bond acceptor (A), two hydrogen bond donors (D), one negatively charged group (N) and one aromatic ring (R), ADDNR. The hypothesis was further evaluated for its integrity using enrichment analysis and used to filter out molecules with similar pharmacophoric features from approved, investigational and experimental subsets of DrugBank and ZINC database. In addition, ligand filtration was performed to curb down the molecules to an efficient collection of hit molecules by using Lipinski “rule of five and ADME analysis by using Qikprop module. Overall, the results from our analysis suggest that compound lisinopril and formoterol could serve as potent antiviral compounds for the treatment of influenza A virus infection. It is worth mentioning that the results correlate well with literature evidences.

Engineered fusion protein-loaded gold nanocarriers for targeted co-delivery of doxorubicin and erbB2-siRNA in human epidermal growth factor receptor-2+ ovarian cancer

Gold nanoparticle based targeted drug delivery system (TDDS) for transporting DX and siRNA in HER2+ ovarian cancer.

Synthesis and Biological Evaluation of Novel Ursolic acid Derivatives as Potential Anticancer Prodrugs

Ursolic acid (UA) is a natural product which has been shown to possess a wide range of pharmacological activities, in particular those with anticancer activity. In this study, 13 novel ursolic acid derivatives were designed and synthesized in an attempt to further improve compound potency. The structures of the newly synthesized compounds were confirmed using mass spectrometry, infrared spectroscopy, and (1) H NMR. The ability of the UA derivatives to inhibit cell growth was assayed against both various tumor cell lines and a non-pathogenic cell line, HELF. Analysis of theoretical toxicity risks for all derivatives was performed using OSIRIS and indicated that the majority of compounds would present moderate to low risks. Pharmacological results indicated that the majority of the derivatives were more potent growth inhibitors than UA. In particular, 5b demonstrated IC50 values ranging from 4.09 ± 0.27 to 7.78 ± 0.43 μm against 12 different tumor cell lines. Flow cytometry analysis indicated that 5b induced G0/G1 arrest in three of these cell lines. These results were validated by structural docking studies, which confirmed that UA could bind to cyclins D1 (Cyc D1) and cyclin-dependent kinases (CDK6), the key regulators of G0/G1 transition in cell cycle, while the piperazine moiety of 5b could bind with glucokinase (GK), glucose transporter 1 (GLUT1), and ATPase, which are the main proteins involved in cancer cell metabolism. Acridine orange/ethidium bromide staining confirmed that 5b was capable of inducing apoptosis and decreasing cell viability in a dose-dependent manner.

Identifying new targets in leukemogenesis using computational approaches

There is a need to identify novel targets in Acute Lymphoblastic Leukemia (ALL), a hematopoietic cancer affecting children, to improve our understanding of disease biology and that can be used for developing new therapeutics. Hence, the aim of our study was to find new genes as targets using in silico studies; for this we retrieved the top 10% overexpressed genes from Oncomine public domain microarray expression database; 530 overexpressed genes were short-listed from Oncomine database. Then, using prioritization tools such as ENDEAVOUR, DIR and TOPPGene online tools, we found fifty-four genes common to the three prioritization tools which formed our candidate leukemogenic genes for this study. As per the protocol we selected thirty training genes from PubMed. The prioritized and training genes were then used to construct STRING functional association network, which was further analyzed using cytoHubba hub analysis tool to investigate new genes which could form drug targets in leukemia. Analysis of the STRING protein network built from these prioritized and training genes led to identification of two hub genes, SMAD2 and CDK9, which were not implicated in leukemogenesis earlier. Filtering out from several hundred genes in the network we also found MEN1, HDAC1 and LCK genes, which re-emphasized the important role of these genes in leukemogenesis. This is the first report on these five additional signature genes in leukemogenesis. We propose these as new targets for developing novel therapeutics and also as biomarkers in leukemogenesis, which could be important for prognosis and diagnosis.