Novel Chemical Entities Research Articles

Electrochemical Synthesis of the In Human S-oxide Metabolites of Phenothiazine-Containing Antipsychotic Medications.

The tractable preparation of Phase I drug metabolites is a critical step to understand the first-pass behaviour of novel chemical entities (NCEs) in drug discovery. In this study, we have developed a structure-electroactivity relationship (SeAR)-informed electrochemical reaction of the parent 2-chlorophenothiazine and the antipsychotic medication, chlorpromazine. With the ability to dial-in under current controlled conditions, the formation of S-oxide and novel S,S-dioxide metabolites has been achieved for the first time on a multi-milligram scale using a direct batch electrode platform. A potential rationale for the electrochemical formation of these metabolites in situ is proposed using molecular docking to a cytochrome P450 enzyme.

Abstract LB071: A phenomics platform combining imaging and artificial intelligence for rapid validation and advancement of novel oncology targets

Abstract The emergence of technological innovations has created the opportunity to envision new approaches to discover therapeutics at scale. We combined advances in high content microscopy with arrayed CRISPR genome editing techniques and machine learning (ML) to build a rigorously controlled dataset enabling exploration of biology and chemistry at scale. Phenotypes from millions of perturbations in multiple cell types were embedded in a unified representation space and leveraged to accelerate discovery and reverse translation, ultimately yielding novel biological insights, and optimizing the advancement of lead molecular series through structure-activity relationships (SAR). Here, we demonstrate the capability of our platform to discover potential cancer therapies with distinct mechanisms of action. First, we describe the identification of a novel compound series that potentiates the effects of immunotherapy in syngeneic mouse models, producing complete responses and immunological memory, while also limiting peripheral inflammation. Specific novel chemical entities (NCEs) caused robust CD45+ cell influx into the tumor microenvironment and significantly attenuated exhausted T cells and immunosuppressive macrophages, thereby enhancing anti-tumor immunity. Strikingly, the same NCEs suppressed peripheral inflammation while sustaining elevated levels of intra-tumoral proinflammatory cytokines. Second, we highlight a novel and differentiated strategy to potentiate PARP inhibitor response in homologous repair deficient (HRD) - negative or HR-proficient ovarian cancers. NCEs altered the expression of genes within the DNA damage repair (DDR) network and cell cycle checkpoints to synergize with PARP inhibition in vivo and re-sensitized a PARP-resistant patient-derived xenograft (PDX) model. Collectively, we believe future efforts on the industrialization and integration of various technological innovations across biology, chemistry, automation, data science, and engineering will ultimately modernize drug discovery and radically improve patient lives. Citation Format: Jenny Rudnick, Kiran Nadella, Chase Neumann, Shane Rowley, Ethan Gardner, Shadi Swaidani, Aimee Iberg, Lu Chen, Daria Beshnova, Aurora Blucher, Rebecca Sarto Basso, Malini Rajan, Kevin Fales, Ashraf Saeed, Christopher Bailey, Weston Judd, Chrissy Egbert, Joel Ellis, John Ansede, Pouya Hadipour, Kevin Jessing, Janet Paulsen, Paul Rearden, Vamshi Manda, Sashi Kasimsetty, Sashi Kasimsetty, Michael Hancock, Harish Shankaran, Bryan Ellis, Meenakshy Iyer, Carl Brooks, Ashish Bhandari, Chris Gibson, Irit Rappley, Laura Schaevitz, Imran Haque, Hayley Donnella, Michael Cuccarese, Marie Evangelista. A phenomics platform combining imaging and artificial intelligence for rapid validation and advancement of novel oncology targets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB071.

A Brief Review on Solubility Enhancement Techniques with Drug and Polymer

The process of a solid dissolving in a liquid phase to create a homogenous mixture is known as solubility. A crucial factor in getting the right quantity of drug into the bloodstream to show a pharmacological effect is solubility. The main issue in developing formulations for new chemical entities as well as for the creation of generics is low water solubility. More than 40% of novel chemical entities (NCEs) created in the pharmaceutical sector are essentially water insoluble. For formulation scientists, solubility is a significant challenge. Any medicine that is to be absorbed at the absorption site must be there in solution form. The solubility of pharmaceuticals that are poorly soluble can be improved using a variety of approaches, such as complexation, salt formation, particle size reduction, crystal engineering, salt formation, solid dispersion, and the like. The choice of a solubility-improving technology is influenced by pharmacological properties, absorption sites, and the requirements for the dosage form. This review article’s goal is to improve bioavailability and promote effective absorption.

Identification and validation of potent inhibitor of Escherichia coli DHFR from MMV pathogen box

The present study is conducted to find the solution of rising antimicrobial resistance (AMR) in Escherichia coli which is a pathogen responsible for fatal systemic infections in human and animals. The enzyme dihydrofolate reductase (DHFR) is found in all organisms. In this study DHFR of E. coli (ec-DHFR) and human DHFR (h-DHFR) is targeted by novel chemical entities (NCE) from the Pathogen box of Medicines for Malaria Venture, Switzerland (MMV) using molecular modelling. The in-silico studies were further validated by in-vitro assays. The virtual screening of 400 MMV compounds was conducted using PyRx standard tool followed by manual docking of selected compounds by Autodock vina and Ligplot program. The in-silico studies showed good binding energy and strong hydrogen bond in docking of MMV675968 with ec-DHFR and no hydrogen bond with h-DHFR. This was further validated by the Molecular dynamic studies that revealed high binding free energy in ec-DHFR and in-vitro assays that produced good synergy in combination study of MMV675968 with last line (meropenem) and last resort (colistin) antibiotics. The extensive MD simulation and energetic analysis thus concludes that MMV675968 targets ec-DHFR. The combination studies were conducted with MMV675968 and FDA approved drugs against a panel of multidrug resistant Escherichia coli isolates. The synergistic results obtained in combination studies concluded that in-vitro data is consistent with in-silico data and that MMV675968 is a potential lead for future process of antimicrobial drug development against the multidrug resistance E. coli. Communicated by Ramaswamy H. Sarma

Molecular docking-based interactions in QSAR studies on Mycobacterium tuberculosis ATP synthase inhibitors

ABSTRACT Tuberculosis (TB) is a global threat with a large burden across the continents in terms of mortality, morbidity, and financial losses. The disease has evolved into multi-drug-resistant (MDR-TB) and extensively drug-resistant (XDR-TB) tuberculosis owing to numerous factors ranging from patients’ non-compliance to demographical implications. There have been very few new drugs for resistant TB. Resistance has already been reported even for the newly introduced drug bedaquiline. An attempt has been made to integrate both structure-based and QSAR drug design techniques (QSAR-SBDD) for the identification of novel leads. The docking scores normally do not correlate with the activity. Hence, the docking results have been analysed in terms of the number of interactions rather than docking scores. The parameters derived from interactions have been used in developing the QSAR models. The best model shows a good correlation (r = 0.908) between the activity and interaction parameter ‘C’ describing the sum of all the interactions with each amino acid residue. This model also predicts external dataset with a good correlation (r ext = 0.851) and can be used for the identification of novel chemical entities (NCEs) and repurposed drugs for TB therapeutics.

Reappraisal of FDA approved drugs against Alzheimer’s disease based on differential gene expression and protein interaction network analysis: an in silico approach

Alzheimer’s disease (AD), a most prevailing neurodegenerative disorder with turbulence in cognitive and behavioural abilities, epitomizes one of the highest unmet medical requirements. The current AD treatment focuses merely on symptomatic relief, this explains a dearth in drug research oriented towards unwinding of disease specific druggable targets. On the other hand, toxicity and poor bioavailability hamper the evolution of novel chemical entities (NCE) in clinical trials. Drug repurposing offers a gateway to rejuvenate new therapeutic applications for existing approved drugs. This study concentrates on the identification of potential druggable AD targets and screening of FDA approved drugs with a concept of drug repurposing. differentially expressed genes (DEGs) were identified in frontal cortex, temporal cortex and hippocampus in AD patients from Gene Expression Omnibus (GEO) dataset GSE36980. Protein-protein interaction (PPI) analysis revealed SERPINA3 and BDNF to possess high node degree interaction with literature derived candidate genes (LDGs) in AD males and females, respectively, thus were selected as potential AD targets. Subsequently, FDA approved drugs were screened through the above shortlisted targets and were ranked based on molecular docking and MM-GBSA energy calculations using Glide and Prime tools, respectively. Drugs possessing best docking score and maximum binding energy were further evaluated through molecular dynamics simulation studies, which revealed the affinity of Tiludronic acid and Olsalazine towards SERPINA3 and BDNF, respectively.

Secondary Metabolites from Plants: The Thin Border Between Beneficent and Harmful

The main family of phytochemical compounds derived from naturally synthesised secondary metabolites are alkaloids, terpenoids and phenolics. Recently, these compounds known also as novel chemical entities (NCE) have been used as drug precursors or templates for synthetic moieties. Also, their potential for pharmacological applications has been as well extensively investigated. However, in recent years, a serious problem worldwide has become the use of illegal drugs, where to potential of some secondary metabolites to act as bio- or a psychoactive component is often refined. Considering that, forensic analysis of secondary metabolites from plants is of the utmost importance. Moreover, great effort has been given to developing testing strategies capable of identifying and quantifying secondary metabolites from various precursors over the past few years. Chromatography is a powerful instrumental technique in the analyses of selected NCE and seems entirely to fulfill the requirements of various laboratories all over the world.

A multicenter assessment of single-cell models aligned to standard measures of cell health for prediction of acute hepatotoxicity

Assessing the potential of a new drug to cause drug-induced liver injury (DILI) is a challenge for the pharmaceutical industry. We therefore determined whether cell models currently used in safety assessment (HepG2, HepaRG, Upcyte and primary human hepatocytes in conjunction with basic but commonly used endpoints) are actually able to distinguish between novel chemical entities (NCEs) with respect to their potential to cause DILI. A panel of thirteen compounds (nine DILI implicated and four non-DILI implicated in man) were selected for our study, which was conducted, for the first time, across multiple laboratories. None of the cell models could distinguish faithfully between DILI and non-DILI compounds. Only when nominal in vitro concentrations were adjusted for in vivo exposure levels were primary human hepatocytes (PHH) found to be the most accurate cell model, closely followed by HepG2. From a practical perspective, this study revealed significant inter-laboratory variation in the response of PHH, HepG2 and Upcyte cells, but not HepaRG cells. This variation was also observed to be compound dependent. Interestingly, differences between donors (hepatocytes), clones (HepG2) and the effect of cryopreservation (HepaRG and hepatocytes) were less important than differences between the cell models per se. In summary, these results demonstrate that basic cell health endpoints will not predict hepatotoxic risk in simple hepatic cells in the absence of pharmacokinetic data and that a multicenter assessment of more sophisticated signals of molecular initiating events is required to determine whether these cells can be incorporated in early safety assessment.

New lumefantrine self nanoemulsifying delivery system – will it by-pass lymphatic transport mechanisms?

Dear editor-in-chief The recently published article in the esteemed journal entitled “Design and evaluation of Lumefantrine – Oleic acid self nanoemulsifying ionic complex for enhanced dissolution” [1], describes an in-depth research pertaining to the formulation attributes of lumefantrine, an important ani-malarial drug, to enhance its in vitro dissolution and thereby improving its bioavailability upon oral administration. As discussed by authors’ poor solubility of novel chemical entities (NCEs) leads to lack of in vivo translation of the promising in vitro attributes of NCEs because they fail to achieve adequate exposure needed to modulate the target or receptors under in vivo conditions [1]. Since lumefantrine has a low and variable bioavailability dependent on the food intake, it is extremely challenging to maintain the threshold levels of the drug needed to combat malarial infections [2]. While the dosing recommendation of lumefantrine takes into consideration food intake especially milk consumption to improve its solubility and bioavailability, it may be difficult to maintain the same food intake conditions within the same individual or across individuals who are suffering from malaria. Therefore, the need of a formulation strategy to overcome this barrier and maximize the delivery of lumefantrine was warranted. In this context, the development and complete characterization of a self nanoemulsifying delivery system is the step in the right direction as it potentially eliminates the influence of food on the bioavailability of lumefantrine [1]. In this interesting work, a complete optimization of the nanoemulsifying delivery system has been achieved – consideration has been given to the various excipients and the composition needed to maximize the dissolution of lumefantrine [1]. Interestingly, comparative dissolution profiles of the current marketed formulation vs the newly developed lumefantrine nanoemulsifying delivery system,

Investigating the Effect of Emetic Compounds on Chemotaxis in Dictyostelium Identifies a Non-Sentient Model for Bitter and Hot Tastant Research

Novel chemical entities (NCEs) may be investigated for emetic liability in a range of unpleasant experiments involving retching, vomiting or conditioned taste aversion/food avoidance in sentient animals. We have used a range of compounds with known emetic /aversive properties to examine the possibility of using the social amoeba, Dictyostelium discoideum, for research into identifying and understanding emetic liability, and hence reduce adverse animal experimentation in this area. Twenty eight emetic or taste aversive compounds were employed to investigate the acute (10 min) effect of compounds on Dictyostelium cell behaviour (shape, speed and direction of movement) in a shallow chemotaxic gradient (Dunn chamber). Compound concentrations were chosen based on those previously reported to be emetic or aversive in in vivo studies and results were recorded and quantified by automated image analysis. Dictyostelium cell motility was rapidly and strongly inhibited by four structurally distinct tastants (three bitter tasting compounds - denatonium benzoate, quinine hydrochloride, phenylthiourea, and the pungent constituent of chilli peppers - capsaicin). In addition, stomach irritants (copper chloride and copper sulphate), and a phosphodiesterase IV inhibitor also rapidly blocked movement. A concentration-dependant relationship was established for five of these compounds, showing potency of inhibition as capsaicin (IC50 = 11.9±4.0 µM) > quinine hydrochloride (IC50 = 44.3±6.8 µM) > denatonium benzoate (IC50 = 129±4 µM) > phenylthiourea (IC50 = 366±5 µM) > copper sulphate (IC50 = 1433±3 µM). In contrast, 21 compounds within the cytotoxic and receptor agonist/antagonist classes did not affect cell behaviour. Further analysis of bitter and pungent compounds showed that the effect on cell behaviour was reversible and not cytotoxic, suggesting an uncharacterised molecular mechanism of action for these compounds. These results therefore demonstrate that Dictyostelium has potential as a non-sentient model in the analysis of the molecular effects of tastants, although it has limited utility in identification of emetic agents in general.

ChemInform Abstract: Chemical Biology of Histone Acetyltransferase Natural Compounds Modulators

AbstractReview: 130 refs.

Chemical biology of Histone acetyltransferase natural compounds modulators

Histone acetyltransferases (HATs) are a class of epigenetic enzymes crucial for chromatin restructuring and transcriptional regulation in eukaryotic cells, thus being a promising target for therapeutic development. Nonetheless, differently from histone deacetylases (HDACs) inhibitors, there is still paucity of small-molecule modulators of HAT activity. After a decline during past decade, natural products and their derivatives could be once again a valuable tool in the lead discovery process and meet such need of Novel Chemical Entities (NCEs). In this review, we will provide a comprehensive summary on the discovery of small-molecule HAT modulators from naturally occurring molecular scaffolds.

First-in-Human Assays: Excitement and Introspection

First-in-Human Assays: Excitement and Introspection

Assessing the issue of instability due to Michael adduct formation in novel chemical entities possessing a carbon–carbon double bond during early drug development— applicability of common laboratory analytical protocols

The discovery of small-molecule novel chemical entities (NCEs) is often a complex play between appropriate structural requirements and optimization of the desired efficacy, safety and pharmacokinetic properties. One of the typical structural variants such as having an active carbon-carbon double bond (alpha, beta-unsaturated carbonyl group) in xenobiotics may lead to stability issues. Such functionalities are extremely reactive, paving way to nucleophilic attack by endogenously occurring and ubiquitous nucleophiles like thiols. While it is easy to make a unilateral decision to not pursue the development of xenobiotics with such functionalities, we question the wisdom of such a decision. In this report, we present in vitro methodologies with appropriate examples to illustrate the ease of assessing the reactivity of the xenobiotics containing double bonds with a known nucleophile. The protocols involve simple reaction procedures followed by measurements using standard laboratory equipments (UV spectrophotometer, HPLC and LC-MS). Our data suggests that not all xenobiotics with carbon-carbon double bonds readily form a Michael's adduct product with glutathione. Hence, the criterion for dropping discovery compounds because of alpha,beta-unsaturated double bonds needs to be reconsidered.

The Preclinical Testing Strategy for the Development of Novel Chemical Entities for the Treatment of Asthma

Identifying and developing novel chemical entities (NCE) for the treatment of asthma is a time-consuming process and liabilities that endanger the successful progression of a compound from research into the patient are found throughout all phases of drug discovery. In particular the failure of advanced compounds in clinical studies due to lack of efficacy and/or safety concerns is tremendously costly. Therefore, in order to try and reduce the failure rate in clinical trials various in vitro and in vivo tests are performed during preclinical development, to rapidly identify liabilities, eliminate high risk compounds and promote promising potential drug candidates. To achieve this objective, numerous prerequisites have to be met regarding the physico-chemical properties of the compound, and bioactivity or model systems are needed to rate the therapeutic potential of new compounds. Drug liabilities such as target and species specificity, formulation issues, pharmacokinetics as well as pharmacodynamics and the toxic potential of the compound have to be analyzed in great detail before a compound can enter a clinical trial. A particularly challenging aspect of developing novel NCEs for the treatment of asthma is choosing and setting up in vivo models believed to be predictive for human disease. Numerous companies have in the past and are currently developing NCEs targeting many different pathways and cells with the aim to treat asthma. However, currently the only NCE having a significant market share are long-acting beta-agonists (LABA), inhaled and orally active steroids and leukotriene receptor antagonists. In the past many novel NCE for the treatment of asthma were effective in animal models but failed in the clinic. In this review we outline the prerequisites of novel NCE needed for clinical development.

A novel workflow for the inverse QSPR problem using multiobjective optimization

A workflow for the inverse quantitative structure-property relationship (QSPR) problem is reported in this paper for the de novo design of novel chemical entities (NCE) in silico through the application of existing QSPR models to calculate multiple objectives, including prediction confidence measures, to be optimized during the de novo design process. Two physical property datasets are applied as case studies of the inverse QSPR workflow (IQW): mean molecular polarizability and aqueous solubility. The case studies demonstrate the optimization of molecular structures to within a property range of interest; the optimized structures are then validated against QSPR models that are generated from sets of alternative descriptors to those used in the IQW. The paper concludes with a discussion of the results from the case studies.

Recent clinical failures in Parkinson's disease with apoptosis inhibitors underline the need for a paradigm shift in drug discovery for neurodegenerative diseases

Understanding the mechanisms of neuronal death in concert with the identification of drugable molecular targets key to this process has held great promise for the development of novel chemical entities (NCEs) to halt neurodegenerative disease progression. Two key targets involved in the apoptotic process identified over the past decade include the mixed lineage kinase (MLK) family and glyceraldehyde phosphate dehydrogenase (GAPDH). Two NCEs, CEP-1347 and TCH346, directed against these respective targets have progressed to the clinic. For each, robust neuroprotective activity was demonstrated in multiple in vitro and in vivo models of neuronal cell death, but neither NCE proved effective Parkinson's disease (PD) patients. These recent clinical failures require a reassessment of both the relevance of apoptosis to neurodegenerative disease etiology and the available animal models used to prioritize NCEs for advancement to the clinic in this area.

Drug disposition of chiral and achiral drug substrates metabolized by cytochrome P450 2D6 isozyme: case studies, analytical perspectives and developmental implications

The concepts of drug development have evolved over the last few decades. Although number of novel chemical entitities belonging to varied classes have made it to the market, the process of drug development is challenging, intertwined as it is with complexities and uncertainities. The intention of this article is to provide a comprehensive review of novel chemical entities (NCEs) that are substrates to cytochrome P450 (CYP) 2D6 isozyme. Topics covered in this review aim: (1) to provide a framework of the importance of CYP2D6 isozyme in the biotransformation of NCEs as stand-alones and/or in conjunction with other CYP isozymes; (2) to provide several case studies of drug disposition of important drug substrates, (3) to cover key analytical perspectives and key assay considerations to assess the role and involvement of CYP2D6, and (4) to elaborate some important considerations from the development point of view. Additionally, wherever applicable, special emphasis is provided on chiral drug substrates in the various subsections of the review.