When Quality Beats Quantity: Decision Theory, Drug Discovery, and the Reproducibility Crisis

Screening out irrelevant cell-based models of disease

The common and persistent failures to translate promising preclinical drug candidates into clinical success highlight the limited effectiveness of disease models currently used in drug discovery. An apparent reluctance to explore and adopt alternative cell- and tissue-based model systems, coupled with a detachment from clinical practice during assay validation, contributes to ineffective translational research. To help address these issues and stimulate debate, here we propose a set of principles to facilitate the definition and development of disease-relevant assays, and we discuss new opportunities for exploiting the latest advances in cell-based assay technologies in drug discovery, including induced pluripotent stem cells, three-dimensional (3D) co-culture and organ-on-a-chip systems, complemented by advances in single-cell imaging and gene editing technologies. Funding to support precompetitive, multidisciplinary collaborations to develop novel preclinical models and cell-based screening technologies could have a key role in improving their clinical relevance, and ultimately increase clinical success rates.

A Framework for Improving the Quality of Research in the Biological Sciences

The American Academy of Microbiology convened a colloquium to discuss problems in the biological sciences, with emphasis on identifying mechanisms to improve the quality of research. Participants from various disciplines made six recommendations: (i) design rigorous and comprehensive evaluation criteria to recognize and reward high-quality scientific research; (ii) require universal training in good scientific practices, appropriate statistical usage, and responsible research practices for scientists at all levels, with training content regularly updated and presented by qualified scientists; (iii) establish open data at the timing of publication as the standard operating procedure throughout the scientific enterprise; (iv) encourage scientific journals to publish negative data that meet methodologic standards of quality; (v) agree upon common criteria among scientific journals for retraction of published papers, to provide consistency and transparency; and (vi) strengthen research integrity oversight and training. These recommendations constitute an actionable framework that, in combination, could improve the quality of biological research.

Transcriptome Profiling of Patient-Specific Human iPSC-Cardiomyocytes Predicts Individual Drug Safety and Efficacy Responses In Vitro

Understanding individual susceptibility to drug-induced cardiotoxicity is key to improving patient safety and preventing drug attrition. Human induced pluripotent stem cells (hiPSCs) enable the study of pharmacological and toxicological responses in patient-specific cardiomyocytes (CMs) and may serve as preclinical platforms for precision medicine. Transcriptome profiling in hiPSC-CMs from seven individuals lacking known cardiovascular disease-associated mutations and in three isogenic human heart tissue and hiPSC-CM pairs showed greater inter-patient variation than intra-patient variation, verifying that reprogramming and differentiation preserve patient-specific gene expression, particularly in metabolic and stress-response genes. Transcriptome-based toxicology analysis predicted and risk-stratified patient-specific susceptibility to cardiotoxicity, and functional assays in hiPSC-CMs using tacrolimus and rosiglitazone, drugs targeting pathways predicted to produce cardiotoxicity, validated inter-patient differential responses. CRISPR/Cas9-mediated pathway correction prevented drug-induced cardiotoxicity. Our data suggest that hiPSC-CMs can be used in vitro to predict and validate patient-specific drug safety and efficacy, potentially enabling future clinical approaches to precision medicine.

The reproducibility issue and preclinical academic drug discovery: educational and institutional initiatives fostering translation success

INTRODUCTION

Drug discovery depends critically upon published results from the academy. The reproducibility of preclinical research findings reported by academia in the peer-reviewed literature has been called into question, seriously jeopardizing the value of academic science for inventing therapeutics.

AREAS COVERED

The corrosive effects of the reproducibility issue on drug discovery are considered. Purported correctives imposed upon academia from the outside deal mainly with expunging fraudulent literature and imposing punitive sanctions on the responsible authors. The salutary influence of such post facto actions on the reproducibility of discovery-relevant preclinical research data from academia appears limited. Rather, intentional doctoral-scientist education focused on data replicability and translationally-meaningful science and active participation of university entities charged with research innovation and asset commercialization toward ensuring data quality are advocated as key academic initiatives for addressing the reproducibility issue.

EXPERT OPINION

A mindset shift on the part of both senior university faculty and the academy to take responsibility for the data reproducibility crisis and commit proactively to positive educational, incentivization, and risk- and reward-sharing practices will be fundamental for improving the value of published preclinical academic research to drug discovery.

Accelerating Drug Development: Antiviral Therapies for Emerging Viruses as a Model

Drug discovery and development is a lengthy and expensive process. Although no one, simple, single solution can significantly accelerate this process, steps can be taken to avoid unnecessary delays. Using the development of antiviral therapies as a model, we describe options for acceleration that cover target selection, assay development and high-throughput screening, hit confirmation, lead identification and development, animal model evaluations, toxicity studies, regulatory issues, and the general drug discovery and development infrastructure. Together, these steps could result in accelerated timelines for bringing antiviral therapies to market so they can treat emerging infections and reduce human suffering.

SD, Verho O, Dandapani S, Wagner BK, Clemons PA, Booker-Milburn K, Boskovic ZV, Schreiber SL. Real-Time Biological Annotation of Synthetic Compounds

Organic chemists are able to synthesize molecules in greater number and chemical complexity than ever before. Yet, a majority of these compounds go untested in biological systems, and those that do are often tested long after the chemist can incorporate the results into synthetic planning. We propose the use of high-dimensional "multiplex" assays, which are capable of measuring thousands of cellular features in one experiment, to annotate rapidly and inexpensively the biological activities of newly synthesized compounds. This readily accessible and inexpensive "real-time" profiling method can be used in a prospective manner to facilitate, for example, the efficient construction of performance-diverse small-molecule libraries that are enriched in bioactives. Here, we demonstrate this concept by synthesizing ten triads of constitutionally isomeric compounds via complexity-generating photochemical and thermal rearrangements and measuring compound-induced changes in cellular morphology via an imaging-based "cell painting" assay. Our results indicate that real-time biological annotation can inform optimization efforts and library syntheses by illuminating trends relating to biological activity that would be difficult to predict if only chemical structure were considered. We anticipate that probe and drug discovery will benefit from the use of optimization efforts and libraries that implement this approach.

Centenary of the death of Elie Metchnikoff: a visionary and an outstanding team leader

Elie Metchnikoff passed away on July 15th, 1916. He is considered to be the father of phagocytes, cellular innate immunity, probiotics, and gerontology. In all of these fields, he was a visionary. To achieve such a notability and produce so many masterpieces, Metchnikoff used more than 30 animal species to support his findings, and his pasteurian laboratory published more than 200 papers in the Annales de l'Institut Pasteur. As a wonderful team leader and a great mentor, during his 28 years at Institut Pasteur, he welcomed and supervised more than 100 young trainees. Trained as an embryologist, he contributed to the birth of immunology and to the understanding of physiology and pathology. Indeed, Metchnikoff and his team investigated inflammation in guinea pigs, rats, frogs; studied infectious diseases in monkeys, caimans, geese; investigated aging in parrots, dogs, humans; proposed hypotheses to understand age-associated senility using rabbits and humans; developed germ free tadpoles, flies, chicks; studied the gut flora in bats, horses, birds, humans; and popularized the use of probiotics as a tool to delay the deleterious effects of toxic compounds derived from putrefactive gut bacteria. He was also a philosopher and penned essays on human disharmony and on pessimism and optimism.

Ionic liquids as a potential tool for drug delivery systems

The pharmaceutical industries face a series of challenges in the delivery of many newly developed drug molecules because of their low solubility, bioavailability, stability and polymorphic conversion.