IDENTIFICATION OF NOVEL INHIBITORS OF CDC25 PHOSPHATASES AS NEW ANTI-MELANOMA AGENTS BY LIGAND- AND STRUCTURE-BASED VIRTUAL SCREENING STUDIES

Cell division cycle 25 (CDC25) proteins are highly conserved dual specificity phosphatases that regulate the proper advancement of the cell cycle by activation of CDK/cyclin complexes. Overexpression of CDC25s, resulting in genomic instability and dysregulated cell growth, is frequently related to aggressiveness, high-grade tumors and poor prognosis. Thus, this family of enzymes represent an attractive target for drug discovery. Recently, compound 11, 3-(4,5,6-trihydroxy-3-oxo-3H-xanthen-9-yl)- propanoic acid, and compound 19, 4-(2-carboxybenzoyl)phthalic acid, were identified as novel inhibitors of CDC25s with a different inhibition profile, by using a structure-based virtual screening approach. Both compounds arrested cells at the G0/G1 and G2/M phases of the cell cycle, increased Cdk1 hyperphosphorylation in K562 leukemia cells, and significantly suppressed the growth of human MCF-7 breast, PC-3 prostate cancer lines as well as K562 leukemia cells, thus representing novel interesting leads. This thesis project focused on the computer-assisted lead optimization of the initial hits 11 and 19. Firstly, in order to expand our understanding of structure-activity relationships within the 6-xanthone class of CDC25 inhibitors, we identified a series of structural analogs of compound 11 by ligand-based chemoinformatic approach. We examined their activity against melanoma cancer cell lines, as well as the mechanism of action involved. Nine compounds (3, 5–9, 21, 24, and 25) were identified with Ki values for CDC25A, -B and -C ranging from 0.01 to 4.4 μM. One of these analogs, 7, showed a high antiproliferative effect on human melanoma cell lines, A2058 and SAN, associated with an arrest in G2/M phase of the cell cycle. Furthermore, 7 induced apoptosis through intrinsic pathway. Interestingly, compound 7 decreased the protein levels of phosphorylated Akt and increased those of p53, thus contributing to the regulation of chemosensitivity through the control of downstream Akt pathways in melanoma cells. Secondly, a series of novel derivatives of compound 19 was rationally designed by using a structure-based approach, guided by preliminary docking studies, with the aim to improve its binding affinity, pharmacokinetic properties as well as to investigate its anti-melanoma effect. A focused library of 24 derivatives was synthesized: a preliminary screening of the inhibitory activities toward CDC25B showed that ten molecules (compounds 2, 3d, 4, 4a, 4b, 5f, 6, 6a, 6b, 7) acted as powerful inhibitors with Ki values ranging between 2.8–20.1 μM. Among them, compounds 2 and 6a showed good antiproliferative effects on melanoma cell line A2058. Taken together, our data emphasize that CDC25 could be considered as a possible oncotarget in melanoma cells and that the designed compounds represent small molecule CDC25 inhibitors that merit to be further evaluated as chemotherapeutic agents for melanoma, likely in combination with other therapeutic compounds

Ligand-based chemoinformatic discovery of a novel small molecule inhibitor targeting CDC25 dual specificity phosphatases and displaying in vitro efficacy against melanoma cells

CDC25 phosphatases are important regulators of the cell cycle and represent promising targets for anticancer drug discovery. We recently identified NSC 119915 as a new quinonoid CDC25 inhibitor with potent anticancer activity. In order to discover more active analogs of NSC 119915, we performed a range of ligand-based chemoinformatic methods against the full ZINC drug-like subset and the NCI lead-like set. Nine compounds (3, 5?9, 21, 24, and 25) were identified with Ki values for CDC25A, -B and -C ranging from 0.01 to 4.4 ?M. One of these analogs, 7, showed a high antiproliferative effect on human melanoma cell lines, A2058 and SAN. Compound 7 arrested melanoma cells in G2/M, causing a reduction of the protein levels of CDC25A and, more consistently, of CDC25C. Furthermore, an intrinsic apoptotic pathway was induced, which was mediated by ROS, because it was reverted in the presence of antioxidant N-acetyl-cysteine (NAC). Finally, 7 decreased the protein levels of phosphorylated Akt and increased those of p53, thus contributing to the regulation of chemosensitivity through the control of downstream Akt pathways in melanoma cells. Taken together, our data emphasize that CDC25 could be considered as a possible oncotarget in melanoma cells and that compound 7 is a small molecule CDC25 inhibitor that merits to be further evaluated as a chemotherapeutic agent for melanoma, likely in combination with other therapeutic compounds

Structural basis for PPAR partial or full activation revealed by a novel ligand binding mode

The peroxisome proliferator-activated receptors (PPARs) are nuclear receptors involved in the regulation of the metabolic homeostasis and therefore represent valuable therapeutic targets for the treatment of metabolic diseases. The development of more balanced drugs interacting with PPARs, devoid of the side-effects showed by the currently marketed PPARλ 3 full agonists, is considered the major challenge for the pharmaceutical companies. Here we present a structure-based virtual screening approach that let us identify a novel PPAR pan-agonist with a very attractive activity profile and its crystal structure in the complex with PPARα and PPARλ 3, respectively. In PPARα this ligand occupies a new pocket whose filling is allowed by the ligand-induced switching of the F273 side chain from a closed to an open conformation. The comparison between this pocket and the corresponding cavity in PPARλ 3 provides a rationale for the different activation of the ligand towards PPARα and PPARλ 3, suggesting a novel basis for ligand design

Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination

Despite the approval of vaccines, monoclonal antibodies and restrictions during the pandemic, the demand for new efficacious and safe antivirals is compelling to boost the therapeutic arsenal against the COVID-19. The viral 3-chymotrypsin-like protease (3CLpro) is an essential enzyme for replication with high homology in the active site across CoVs and variants showing an almost unique specificity for Leu-Gln as P2–P1 residues, allowing the development of broad-spectrum inhibitors. The design, synthesis, biological activity, and cocrystal structural information of newly conceived peptidomimetic covalent reversible inhibitors are herein described. The inhibitors display an aldehyde warhead, a Gln mimetic at P1 and modified P2–P3 residues. Particularly, functionalized proline residues were inserted at P2 to stabilize the β-turn like bioactive conformation, modulating the affinity. The most potent compounds displayed low/sub-nM potency against the 3CLpro of SARS-CoV-2 and MERS-CoV and inhibited viral replication of three human CoVs, i.e. SARS-CoV-2, MERS-CoV, and HCoV 229 in different cell lines. Particularly, derivative 12 exhibited nM-low μM antiviral activity depending on the virus, and the highest selectivity index. Some compounds were co-crystallized with SARS-CoV-2 3CLpro validating our design. Altogether, these results foster future work toward broad-spectrum 3CLpro inhibitors to challenge CoVs related pandemics

New avenues in artificial-intelligence-assisted drug discovery

: Over the past decade, the amount of biomedical data available has grown at unprecedented rates. Increased automation technology and larger data volumes have encouraged the use of machine learning (ML) or artificial intelligence (AI) techniques for mining such data and extracting useful patterns. Because the identification of chemical entities with desired biological activity is a crucial task in drug discovery, AI technologies have the potential to accelerate this process and support decision making. In addition, the advent of deep learning (DL) has shown great promise in addressing diverse problems in drug discovery, such as de novo molecular design. Herein, we will appraise the current state-of-the-art in AI-assisted drug discovery, discussing the recent applications covering generative models for chemical structure generation, scoring functions to improve binding affinity and pose prediction, and molecular dynamics to assist in the parametrization, featurization and generalization tasks. Finally, we will discuss current hurdles and the strategies to overcome them, as well as potential future directions

In silico methods to address polypharmacology: Current status, applications and future perspectives

Polypharmacology, a new paradigm in drug discovery that focuses on multi-target drugs (MTDs), has potential application for drug repurposing, the process of finding new uses for existing approved drugs, prediction of off-target toxicities and rational design of MTDs. In this scenario, computational strategies have demonstrated great potential in predicting polypharmacology and in facilitating drug repurposing. Here, we provide a comprehensive overview of various computational approaches that enable the prediction and analysis of in vitro and in vivo drug-response phenotypes and outline their potential for drug discovery. We give an outlook on the latest advances in rational design of MTDs and discuss possible future directions of algorithm development in this field

Small Molecule Drugs And Targeted Therapy For Melanoma: Current Strategies And Future Directions

Malignant melanoma is the most aggressive and life-threatening skin cancer. Melanoma develops in melanocytes and is characterized by a very high tendency to spread to other parts of the body. Its pathogenesis depends on DNA mutations leading to the activation of oncogenes or to the inactivation of suppressor genes. The identification of misregulations in intracellular signal transduction pathways has provided an opportunity for development of mutation-specific inhibitors, which specifically target the mutated signaling cascades. Over the last few years, clinical trials with MAPK pathway inhibitors have shown significant clinical activity in melanoma; however, their efficacy is limited due to the onset of acquired resistance. This has prompted a large set of preclinical studies looking at new approaches of pathway- or target-specific inhibitors. This review gives an overview of the latest developments of small molecule targeting multiple molecular pathways in both preclinical and clinical melanoma settings, with particular emphasis on additional strategies to tackle the reduced responsiveness to inhibitor treatment as possible future directions

In Silico Drug Design and Discovery: Big Data for Small Molecule Design

Across life sciences, the steadily and rapidly increasing amount of data provide new opportunities for advancing knowledge and represent a key driver of emerging technological advancements [...

Novel inhibitors of signal transducer and activator of transcription 3 signaling pathway: an update on the recent patent literature

Introduction: The signal transducer and activator of transcription 3 (STAT3) is a transcription factor that plays a key role in normal cell growth and is constitutively activated in about 70% of solid and hematological cancers. Thus, the development of potent and selective inhibitors that target STAT3 is of interest especially in the cancer therapeutic area. Areas covered: This review updates new patents claiming STAT3 inhibitors and their uses published from 2011 to 2013. Pre-2011 patents have been extensively covered in previous reviews. Comments on the context of each chemical series are given where applicable to orientate the readers on the bewildering array of molecular designs now available. Expert opinion: The growing number of preclinical studies in numerous malignances as well as the first clinical trials of STAT3 inhibitors suggest that STAT3 remains a valid target for the treatment of human cancers as well as inflammatory diseases and/or autoimmune disorders. So, the future looks bright for patients because many new drugs are being developed and now combinations of STAT3 inhibitors with other targeted agents can diminish the resistance to traditional chemotherapy. These advances are expected to lead to further significant progress improving patient outcomes and quality of life