Fossils constitute the principal repository of data that allow for independent tests of hypotheses of biological evolution derived from observations of the extant biota. Traditionally, transformational series of structure, consisting of sequences of fossils of the same lineage through time, have been employed to reconstruct and interpret morphological evolution. More recently, a move toward an updated paradigm was fueled by the deliberate integration of developmental thinking in the inclusion of fossils in reconstruction of morphological evolution. The vehicle for this is provided by structural fingerprints – recognizable morphological and anatomical structures generated by (and reflective of) the deployment of specific genes and regulatory pathways during development. Furthermore, because the regulation of plant development is both modular and hierarchical in nature, combining structural fingerprints recognized in the fossil record with our understanding of the developmental regulation of those structures produces a powerful tool for understanding plant evolution. This is particularly true when the systematic distribution of specific developmental regulatory mechanisms and modules is viewed within an evolutionary (paleo-evo-devo) framework. Here, we discuss several advances in understanding the processes and patterns of evolution, achieved by tracking structural fingerprints with their underlying regulatory modules across lineages, living and fossil: the role of polar auxin regulation in the cellular patterning of secondary xylem and the parallel evolution of arborescence in lycophytes and seed plants; the morphology and life history of early polysporangiophytes and tracheophytes; the role of modularity in the parallel evolution of leaves in euphyllophytes; leaf meristematic activity and the parallel evolution of venation patterns among euphyllophytes; mosaic deployment of regulatory modules and the diverse modes of secondary growth of euphyllophytes; modularity and hierarchy in developmental regulation and the evolution of equisetophyte reproductive morphology. More generally, inclusion of plant fossils in the evo-devo paradigm has informed discussions on the evolution of growth patterns and growth responses, sporophyte body plans and their homology, sequences of character evolution, and the evolution of reproductive systems.

BackgroundThe present review summarizes the state-of-the-art of in silico methods and techniques that are the most useful in drug discovery, their relationship with data science, as well as the successful application of data science, machine learning (ML) and artificial intelligence (AI) applications. A meta-analysis of the various technologies available is furthermore proposed as a guideline for the non-expert, reader relative to the several subject areas is also discussed in this article. The scope of this meta-analysis is to rank the enlisted technologies by their field of applications and to depict the latter according to knowledge accessibility, from students to experts.Method The search strategy utilized for this review first produced a general collection of 900 papers without duplications, which were subsequently streamlined and divided into two independent collections: the top 300 most-cited papers of all time (since 2000) and the papers with the highest interest for a systematic review analysis (high-impact exciting papers). Results In Part 1, we discuss the most cited and quality 97 articles in these top 300 papers most relevant to the field of in silico drug discovery. The different disciplines are listed according to their industrial and economic incurred to society, independently from the “metric” results of how many new drug approvals (NDAs) each discipline has generated to date.ConclusionBig data, the ensemble of known items stored in publicly available databases, has improved our understanding of the many fates of a potential drug candidate during its development and even after its commercialization. Moreover, the combination of new screening techniques and “omics” with old drugs has led to a new paradigm in which the unknown knowledge of any biological molecule and its cellular structure, now plays an important role as a target for a series of yet-to-be-developed drugs: the chemical space. Furthermore, leveraging big data, data science, ML, and AI can revolutionize drug discovery by swiftly analyzing massive datasets, predicting efficacy and safety profiles, streamlining development, cutting costs, and boosting success rates for new drugs. AI also speeds up the search for promising drug candidates, advancing innovative therapies.

The regulatory approvals of tumor agnostic therapies have led to reevaluation of the drug development process. Conventional models of drug development are histology-based. On the other hand, tumor agnostic drug development of a new drug (or combination) focuses on targeting a common genomic biomarker in multiple cancers, regardless of histology. Basket-like clinical trials with multiple cohorts allow clinicians to evaluate pan-cancer efficacy and toxicity. There are currently 8 tumor agnostic approvals granted by the Food and Drug Administration (FDA). This includes two immune checkpoint inhibitors, and 5 targeted therapy agents. Pembrolizumab is an anti-PD-1 antibody that was the first FDA approved tumor agnostic treatment for unresectable or metastatic microsatellite instability-high (MSI-H) or deficient mismatch repair (dMMR) solid tumors in 2017. It was later approved for tumor mutational burden-high (TMB-H) solid tumors, although the TMB cut-off used is still debated. Subsequently, in 2021, another anti-PD-1 antibody, Dostarlimab was also approved for dMMR solid tumors in the refractory setting. Patients with fusion-positive cancers are typically difficult to treat due to their rare prevalence and distribution. Gene rearrangements or fusions are present in a variety of tumors. neurotrophic tyrosine kinase (NTRK) fusions are present in a range of pediatric and adult solid tumors in varying frequency. Larotrectinib and entrectinib were approved for neurotrophic tyrosine kinase (NTRK) fusion-positive cancers. Similarly, selpercatinib was approved for Rearranged During Transfection (RET) fusion-positive solid tumors. FDA approved the first combination therapy of dabrafenib, a B-Raf Proto-Oncogene Serine/Threonine Kinase (BRAF) inhibitor, plus trametinib, a mitogen-activated protein kinase (MEK) inhibitor for patients 6 months or older with unresectable or metastatic tumors (except colorectal cancer) carrying BRAFV600E mutation. The most recent FDA tumor agnostic approval is of fam-trastuzumab deruxtecan-nxki (T-Dxd) for HER2-positive solid tumors. It is important to identify and expeditiously develop drugs that have the potential to provide clinical benefit across tumor types.