Tool For Drug Development Research Articles

Transforming Drug Development for Neurological Disorders: Proceedings from a Multidisease Area Workshop

Neurological disorders represent some of the most challenging therapeutic areas for successful drug approvals. The escalating global burden of death and disability for such diseases represents a significant worldwide public health challenge, and the rate of failure of new therapies for chronic progressive disorders of the nervous system is higher relative to other non-neurological conditions. However, progress is emerging rapidly in advancing the drug development landscape in both rare and common neurodegenerative diseases. In October 2022, the Critical Path Institute (C-Path) and the US Food and Drug Administration (FDA) organized a Neuroscience Annual Workshop convening representatives from the drug development industry, academia, the patient community, government agencies, and regulatory agencies regarding the future development of tools and therapies for neurological disorders. This workshop focused on five chronic progressive diseases: Alzheimer's disease, Parkinson's disease, Huntington's disease, Duchenne muscular dystrophy, and inherited ataxias. This special conference report reviews the key points discussed during the three-day dynamic workshop, including shared learnings, and recommendations that promise to catalyze future advancement of novel therapies and drug development tools.

A Human Neuron/Astrocyte Co-culture to Model Seeded and Spontaneous Intraneuronal Tau Aggregation.

Communication and contact between neurons and astrocytes is important for proper brain physiology. How neuron/astrocyte crosstalk is affected by intraneuronal tau aggregation in neurodegenerative tauopathies is largely elusive. Human induced pluripotent stem cell (iPSC)-derived neurons provide the opportunity to model tau pathology in a translationally relevant in vitro context. However, current iPSC models inefficiently develop tau aggregates, and co-culture models of tau pathology have thus far utilized rodent astrocytes. In this article, we describe the co-culture of human iPSC-derived neurons with primary human astrocytes in a 96-well format compatible with high-content microscopy. By lentiviral overexpression of different mutated tau variants, this protocol can be flexibly adapted for the efficient induction of seeded or spontaneous tau aggregation. We used this novel co-culture model to identify cell type-specific disease mechanisms and to provide proof of concept for intervention by antisense therapy. These results show that this human co-culture model provides a highly translational tool for target discovery and drug development for human tauopathies. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Human neuron/astrocyte co-culture for seeded and spontaneous intraneuronal tau aggregation Support Protocol 1: Human induced pluripotent stem cell culture Support Protocol 2: Human primary astrocyte culture.

Curing Classical Homocysteinuria with Pediatric in vitro engineered Liver Organoid Transplantation?

Organoids are groups of cells grown in the laboratory that have self- organized into cell structures resembling those of organs. The term "organoid" means "organ-like." In many cases, the cells and cell structures give organoids abilities similar to those of the organs they resemble. Brain organoids, for example, develop layers of nerve cells (neurons) with signaling activity and even "brain regions" that resemble areas of the human brain. Currently, organoids created by researchers may bear a strong resemblance to a fully mature organ in certain respects, but crucial differences still exist. Intestinal organoids have a variety of cellular structures that resemble parts of the intestinal mucosa, but are typically the size of a pea and thus not nearly as large or complex as our intestinal tract. But even though they are small, or do not correspond one hundred percent to entire organs, scientists can learn a lot from organoids. Experts believe that organoids represent the "next generation" of biological tools for research, drug development and medicine. Liver Organoid engineering could play an important role in treating and curing classic homocysteinuria in childhood by resetting the disturbed function of cystathion beta synthetase activity in the implanted organoid liver. This manuscript focus on liver organoid research to date with special attention to classic homocysteinuria in childhood.

Exploring the leishmanicidal potential of terpenoids: a comprehensive review on mechanisms of cell death.

Leishmaniasis is a neglected tropical disease with a wide spectrum of clinical manifestations, ranging from visceral to cutaneous, with millions of new cases and thousands of deaths reported each year. The species of Leishmania and the immune response of the host determine the severity of the disease. Leishmaniasis remains challenging to diagnose and treat, and there is no vaccine available. Several studies have been conducted on the use of herbal medicines for the treatment of leishmaniasis. Natural products can provide an inexhaustible source of chemical diversity with therapeutic potential. Terpenes are a class of natural products derived from a single isoprene unit, a five-carbon compound that forms the basic structure of isoprenoids. This review focuses on the most important and recent advances in the treatment of parasites of the genus Leishmania with different subclasses of terpenes. Several mechanisms have been proposed in the literature, including increased oxidative stress, immunomodulatory role, and induction of different types of parasite cell death. However, this information needs to be brought together to provide an overview of how these compounds can be used as therapeutic tools for drug development and as a successful adjuvant strategy against Leishmania sp.

Metabolomics in drug discovery: Restoring antibiotic pipeline

Metabolomics has emerged as a valuable tool in drug discovery and development, providing new insights into the mechanisms of action and toxicity of potential therapeutic agents. Metabolomics focuses on the comprehensive analysis of primary as well as secondary metabolites, within biological systems. Metabolomics provides a comprehensive understanding of the metabolic changes that occur within microbial pathogens when exposed to therapeutic agents, thus allowing for the identification of unique metabolic targets that can be exploited for therapeutic intervention. This approach can also uncover key metabolic pathways essential for survival, which can serve as potential targets for novel antibiotics. By analyzing the metabolites produced by diverse microbial communities, metabolomics can guide the discovery of previously unexplored sources of antibiotics. This review explores some examples that enable medicinal chemists to optimize drug structure, enhancing efficacy and minimizing toxicity via metabolomic approaches.

Measuring What Is Meaningful in Cancer Cachexia Clinical Trials: A Path Forward With Digital Measures of Real-World Physical Behavior.

The burden of cancer cachexia on patients' health-related quality of life, specifically their physical functioning, is well documented, but clinical trials thus far have failed to show meaningful improvement in physical functioning. The purpose of this review is to summarize existing methods of assessing physical function in cancer cachexia, outline a path forward for measuring what is meaningful to patients using digital measures derived from digital health technologies (DHTs), and discuss the current landscape of digital measures from the clinical and regulatory standpoint. For this narrative review, peer-reviewed articles were searched on PubMed, clinical trials records were searched on clinicaltrials.gov, and records of digital measures submitted for regulatory qualification were searched on the US Food and Drug Administration's Drug Development Tool Qualification Program database. There are gaps in assessing aspects of physical function that matter to patients. Existing assessment methods such as patient-reported outcomes and objective performance outcomes have limitations, including their episodic nature and burden to patients. DHTs such as wearable sensors can capture real-world physical behavior continuously, passively, and remotely, and may provide a more comprehensive picture of patients' everyday functioning. Recent regulatory submissions showcase potential clinical implementation of digital measures in various therapeutic areas. Digital measures of real-world physical behavior present an opportunity to detect and demonstrate improvements in physical functioning in cancer cachexia, but evidence-based development is critical. For their use in clinical and regulatory decision making, studies demonstrating meaningfulness to patients as well as feasibility and validation are necessary.

Transcriptome from Paired Samples Improves the Power of Comprehensive COVID-19 Host-Viral Characterization.

Previous transcriptome profiling studies showed significantly upregulated genes and altered biological pathways in acute COVID-19. However, changes in the transcriptional signatures during a defined time frame are not yet examined and described. The aims of this study included viral metagenomics and evaluation of the total expression in time-matched and tissue-matched paired COVID-19 samples with the analysis of the host splicing profile to reveal potential therapeutic targets. Prospective analysis of paired nasopharyngeal swabs (NPS) and blood (BL) samples from 18 COVID-19 patients with acute and resolved infection performed using Kallisto, Suppa2, Centrifuge, EdgeR, PantherDB, and L1000CDS2 tools. In NPS, we discovered 6 genes with changed splicing and 40 differentially expressed genes (DEG) that yielded 88 altered pathways. Blood samples yielded 15 alternatively spliced genes. Although the unpaired DEG analysis failed, pairing identified 78 genes and 242 altered pathways with meaningful clinical interpretation and new candidate drug combinations with up to 65% overlap. Metagenomics analyses showed SARS-CoV-2 dominance during and after the acute infection, with a significant reduction in NPS (0.008 vs. 0.002, p = 0.019). Even though both NPS and BL give meaningful insights into expression changes, this is the first demonstration of how the power of blood analysis is vastly maximized by pairing. The obtained results essentially showed that pairing is a determinant between a failed and a comprehensive study. Finally, the bioinformatics results prove to be a comprehensive tool for full-action insights, drug development, and infectious disease research when designed properly.

Molecular docking as a tool for the discovery of molecular targets of nutraceuticals in diseases management

Molecular docking is a computational technique that predicts the binding affinity of ligands to receptor proteins. Although it has potential uses in nutraceutical research, it has developed into a formidable tool for drug development. Bioactive substances called nutraceuticals are present in food sources and can be used in the management of diseases. Finding their molecular targets can help in the creation of disease-specific new therapies. The purpose of this review was to explore molecular docking's application to the study of dietary supplements and disease management. First, an overview of the fundamentals of molecular docking and the various software tools available for docking was presented. The limitations and difficulties of using molecular docking in nutraceutical research are also covered, including the reliability of scoring functions and the requirement for experimental validation. Additionally, there was a focus on the identification of molecular targets for nutraceuticals in numerous disease models, including those for sickle cell disease, cancer, cardiovascular, gut, reproductive, and neurodegenerative disorders. We further highlighted biochemistry pathways and models from recent studies that have revealed molecular mechanisms to pinpoint new nutraceuticals' effects on disease pathogenesis. It is convincingly true that molecular docking is a useful tool for identifying the molecular targets of nutraceuticals in the management of diseases. It may offer information about how nutraceuticals work and support the creation of new therapeutics. Therefore, molecular docking has a bright future in nutraceutical research and has a lot of potentials to lead to the creation of brand-new medicines for the treatment of disease.

Development and validation of qPCR methods for nucleic acid biomarkers as a drug development tool: points to consider.

Nucleic acid (NA) biomarkers play critical roles in drug development. However, the global regulatory guidelines for assessing quantification methods specific to NA biomarkers are limited. The validation of analytical methods is crucial for the use of biomarkers in clinical and post-marketing evaluations of drug efficacy and adverse reactions. Given that quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR) methods are the goldstandards for the quantification of NA biomarkers, the Biomarker Analytical Method Validation Study Group in Japan has discussed considerations and made recommendations for the development and validation of qPCR- and RT-qPCR-based analytical methods for endogenous NA biomarkers as drug development tools. This white paper aims to contribute to the global harmonization of NA biomarker assay validation.

Metabotropic Glutamate Receptor Subtype 5 Positron-Emission-Tomography Radioligands as a Tool for Central Nervous System Drug Development: Between Progress and Setbacks.

The metabotropic glutamate receptor subtype 5 (mGluR5) is a class C G-protein-coupled receptor (GPCR) that has been implicated in various neuronal processes and, consequently, in several neuropsychiatric or neurodevelopmental disorders. Over the past few decades, mGluR5 has become a major focus for pharmaceutical companies, as an attractive target for drug development, particularly through the therapeutic potential of its modulators. In particular, allosteric binding sites have been targeted for better specificity and efficacy. In this context, Positron Emission Tomography (PET) appears as a useful tool for making decisions along a drug candidate's development process, saving time and money. Thus, PET provides quantitative information about a potential drug candidate and its target at the molecular level. However, in this area, particular attention has to be given to the interpretation of the PET signal and its conclusions. Indeed, the complex pharmacology of both mGluR5 and radioligands, allosterism, the influence of endogenous glutamate and the choice of pharmacokinetic model are all factors that may influence the PET signal. This review focuses on mGluR5 PET radioligands used at several stages of central nervous system drug development, highlighting advances and setbacks related to the complex pharmacology of these radiotracers.

Cytochrome P450 1A2 and 2C enzymes autoinduced by omeprazole in dog hepatocytes and human HepaRG and HepaSH cells are involved in omeprazole 5-hydroxylation and sulfoxidation

The induction assay for the cytochromes P450 (P450s) is an important tool in drug discovery and development. The inductions of dog P450 1A2 and 3A12 by omeprazole and rifampicin were functionally characterised in dog hepatocytes and were compared with induction in human HepaRG and HepaSH cells. P450 1A2-dependent ethoxyresorufin O-deethylation was induced by R,S-omeprazole and P450 3 A-dependent midazolam 1′-hydroxylation was induced by rifampicin, and both reactions were significantly enhanced in cultured dog hepatocytes and human HepaRG and HepaSH cells. Recombinant dog P450 1A2 exhibited activities towards R- and S-omeprazole 5-hydroxylation with low K m values of 23–28 µM, whereas dog P450 2C21 and 3A12 efficiently mediated S-omeprazole 5-hydroxylation and sulfoxidation, respectively, with high V max values of 12–17 min−1. Although omeprazole 5-hydroxylation by human P450 2C19 (and sulfoxidation by P450 3A4) in human HepaSH cells were slightly (∼2-fold) induced by R,S-omeprazole, dog P450 1A2 was autoinduced by omeprazole in dog hepatocytes and showed enhanced R-omeprazole 5-hydroxylation activity (∼5-fold). These results indicate that omeprazole can be an autoinducer of P450 1A2 in hepatocytes, and this enzyme was found to be involved in omeprazole 5-hydroxylation and sulfoxidation in dog hepatocytes and human HepaRG and HepaSH cells.

Recommendations on the Selection, Development, and Modification of Performance Outcome Assessments: A Good Practices Report of an ISPOR Task Force

In evaluating the clinical benefit of new therapeutic interventions, it is critical that the treatment outcomes assessed reflect aspects of health that are clinically important and meaningful to patients. Performance outcome (PerfO) assessments are measurements based on standardized tasks actively undertaken by a patient that reflect physical, cognitive, sensory, and other functional skills that bring meaning to people’s lives. PerfO assessments can have substantial value as drug development tools when the concepts of interest being measured best suit task performance and in cases where patients may be limited in their capacity for self-report. In their development, selection, and modification, including the evaluation and documentation of validity, reliability, usability, and interpretability, the good practice recommendations established for other clinical outcome assessment types should continue to be followed, with concept elicitation as a critical foundation. In addition, the importance of standardization, and the need to ensure feasibility and safety, as well as their utility in patient groups, such as pediatric populations, or those with cognitive and psychiatric challenges, may enhance the need for structured pilot evaluations, additional cognitive interviewing, and evaluation of quantitative data, such as that which would support concept confirmation or provide ecological evidence and other forms of construct evidence within a unitary approach to validity. The opportunity for PerfO assessments to inform key areas of clinical benefit is substantial and establishing good practices in their selection or development, validation, and implementation, as well as how they reflect meaningful aspects of health is critical to ensuring high standards and in furthering patient-focused drug development.

How does the order of sample analysis influence the matrix effect during LC-MS bioanalysis?

Mass spectrometry coupled with liquid chromatography is a valuable tool for drug development and personalised drug therapy. The matrix effect is caused by enhancing or suppressing the analyte signal intensity by the interfering compounds of biological fluids. The matrix effect may influence the reliability of the quantitative results. Thus, its evaluation is a critical part of bioanalytical method validation. Identified factors affecting the matrix effect are the physicochemical properties of the analyte, type of biological material, analytical conditions, the ion source construction and calculation method. The order of analysis of test samples (pure solutions and post-extraction spiked samples) is another factor possibly affecting quantifying the matrix effect variability between sources. Our primary goal was to find which experimental design – interleaved or set of blocks – is more sensitive to detect matrix effect variability. Additionally, to better understand the reason of variability, we evaluated the influence of chromatographic elution and the type of plasma (normal, lipemic or hemolyzed), co-elution, and carry-over of phospholipids. We used chemometric methods: Principal Component Analysis and Partial Least-Squares Discriminant Analysis. Although a comparable (but statistically different) matrix effect (%RSDMF) is observed using the interleaved and block schemes, for some compounds, the order of the samples strongly influences the results. The interleaved scheme was generally more sensitive in detecting the matrix effect than the block scheme. Thus, reporting the order of samples is needed to ensure the repeatability of experiments. Chemometrics suggests that lipemic samples analyzed in isocratic conditions are most prone to the matrix effect. Different compositions of matrix lots of the same type – especially lipemic – may influence method reliability. Thus, evaluating more than one source of lipemic and hemolyzed plasma is recommended.

Applications of radiolabeled antibodies in neuroscience and neuro-oncology.

Positron emission tomography (PET) is a powerful tool in medicine and drug development, allowing for non-invasive imaging and quantitation of biological processes in live organisms. Targets are often probed with small molecules, but antibody-based PET is expanding because of many benefits, including ease of design of new antibodies toward targets, as well as the very strong affinities that can be expected. Application of antibodies to PET imaging of targets in the central nervous system (CNS) is a particularly nascent field, but one with tremendous potential. In this review, we discuss the growth of PET in imaging of CNS targets, present the promises and progress in antibody-based CNS PET, explore challenges faced by the field, and discuss questions that this promising approach will need to answer moving forward for imaging and perhaps even radiotherapy.

Improved structure-related prediction for insufficient homologous proteins using MSA enhancement and pre-trained language model.

guofei@csu.edu.cn, jj.tang@siat.ac.cn.

Genomic screening methodology not requiring barcoding: Single nucleotide polymorphism-based, mixed-cell screening (SMICS)

Although high-throughput, cancer cell-line screening is a time-honored, important tool for anti-cancer drug development, this process involves the testing of each, individual drug in each, individual cell-line. Despite the availability of robotic liquid handling systems, this process remains a time-consuming and costly investment. The Broad Institute developed a new method called Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) to screen a mixture of barcoded, tumor cell-lines. Although this methodology significantly improved the efficiency of screening large numbers of cell-lines, the barcoding process itself was tedious that requires gene transfection and subsequent selection of stable cell-lines. In this study, we developed a new, genomic approach for screening multiple cancer cell-lines using endogenous “tags” that did not require prior barcoding: single nucleotide polymorphism-based, mixed-cell screening (SMICS). The code for SMICS is available at https://github.com/MarkeyBBSRF/SMICS.

Comparing Cytology Brushes for Optimal Human Nasal Epithelial Cell Collection: Implications for Airway Disease Diagnosis and Research.

Primary nasal epithelial cells and culture models are used as important diagnostic, research and drug development tools for several airway diseases. Various instruments have been used for the collection of human nasal epithelial (HNE) cells but no global consensus yet exists regarding the optimal tool. This study compares the efficiency of two cytology brushes (Olympus (2 mm diameter) and Endoscan (8 mm diameter)) in collecting HNE cells. The study involved two phases, with phase one comparing the yield, morphology and cilia beat frequency (CBF) of cells collected from paediatric participants using each of the two brushes. Phase two compared nasal brushing under general anaesthetic and in the awake state, across a wide age range, via the retrospective audit of the use of the Endoscan brush in 145 participants. Results indicated no significant difference in CBF measurements between the two brushes, suggesting that the choice of brush does not compromise diagnostic accuracy. However, the Endoscan brush collected significantly more total and live cells than the Olympus brush, making it a more efficient option. Importantly, the Endoscan brush is more cost-effective, with a notable price difference between the two brushes.

Understanding the company landscape in AI-driven biopharma R&D

The potential of companies developing artificial intelligence (AI)-based tools for drug discovery and development has driven investment and deals with major biopharma companies, but challenges for AI biotechs and biopharma companies are emerging as the field moves beyond the hype towards impact. The potential of companies developing artificial intelligence (AI)-based tools for drug discovery and development has driven investment and deals with major biopharma companies, but challenges for AI biotechs and biopharma companies are emerging as the field moves beyond the hype towards impact.

Digital Tools-Regulatory Considerations for Application in Clinical Trials.

During the last few years, the pharmaceutical industry has adopted digital technologies/digital health technology (DHT) to improve the drug development process and the commercialization of new products. Technological advances are strongly supported by both the US-FDA and the EMA, but the regulatory landscape in the US seems to be more suitable to promote innovation in the digital health sector (e.g. Cures Act). In contrast, the new Medical Device Regulation sets high hurdles for Medical Device software to pass regulatory scrutiny.On both sides of the Atlantic, a digital tool must be fit-for-purpose for the intended use in the clinical drug trial. Irrespective of its status as a Medical Device, at least the basic safety and performance requirements according to local regulations should be met, quality system and surveillance requirements should be fulfilled, and the sponsor must ensure conformity with GxP and the local data privacy and cybersecurity legislations.There is an overlap in technical and clinical validation for drug development tool qualification in both regions to ensure that the digital tools deliver reliable data with tangible clinical benefits. Based on an analysis of the regulatory framework of the FDA and the EMA, this study proposes regulatory strategies for a global pharma company: It would be prudent for drug development companies to a) use approved solutions or b) consider qualification of drug development tools early and in parallel to clinical development. Early engagement with the FDA and the EMA/CA is recommended to define evidentiary standards and corresponding regulatory pathways for different contexts-of-use and to clarify regulator's expectations as to what extent data collected by digital tools are acceptable to support marketing authorization applications (MAA).Hence a harmonization of the partly disparate regulatory requirements in the US and the EU accompanied by further development of the regulatory landscape in the EU, could further foster the use of digital tools in drug clinical development. The outlook for the use of digital tools in clinical trials is hopeful.

In silico investigation and potential therapeutic approaches of isoquinoline alkaloids for neurodegenerative diseases: computer-aided drug design perspective

Microtubule affinity regulating kinase (MARK4) has been proposed as a potential therapeutic target for diabetes, cancer, and neurological diseases. We used a variety of computational studies techniques to examine the binding affinity and MARK4 inhibitory potential of several isoquinoline alkaloids. MARK4 has been associated with tau protein phosphorylation and, consequently, Alzheimer’s disease. The three molecules with the highest binding affinities inside the 5ES1 receptor, according to molecular docking experiments, are isoliensinine, liensinine, and methylcorypalline. Isoliensinine had the highest drug score and drug likeness, coming in at 1.17, while Liensinine and Methylcorypalline came in at 1.15 and 1.07, respectively. The thesis claims that three compounds have a better chance than the others of being identified as therapeutic leads. The bulk of the compounds under investigation didn’t break any of Lipinski’s five rules, especially methylcorypalline, which did and is probably orally active. The majority of the compounds under investigation, particularly Isoliensinine, Liensinine, and Methylcorypalline, show the potential to exhibit drug-like behaviour, which is strongly confirmed by ADMET characteristics estimates. The chemicals Isoliensinine, Liensinine, and Methylcorypalline, especially Methylcorypalline, form the most stable combination with the 5ES1, according to a 100 ns molecular dynamics simulation of these compounds docked inside 5ES1 complexes. Methylcorypalline has a higher binding affinity inside 5ES1, according to additional MM/GBSA experiments using MD trajectories. Overall, research supports the use of the drug development tool methylcolipalin for its ability to inhibit MARK4, which may have implications for the treatment of neurodegenerative diseases.Communicated by Ramaswamy H. Sarma