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Nature Reviews. Drug Discovery Sep 2023The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly reveal... (Review)
Review
The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly reveal new ligands for a target of interest. Within the past 15 years, DNA-encoded library (DEL) technology has matured into a widely used platform for small-molecule discovery, yielding a wide variety of bioactive ligands for many therapeutically relevant targets. DELs offer many advantages compared with traditional screening methods, including efficiency of screening, easily multiplexed targets and library selections, minimized resources needed to evaluate an entire DEL and large library sizes. This Review provides accounts of recently described small molecules discovered from DELs, including their initial identification, optimization and validation of biological properties including suitability for clinical applications.
Topics: Humans; Small Molecule Libraries; Drug Discovery; DNA; Ligands; Gene Library
PubMed: 37328653
DOI: 10.1038/s41573-023-00713-6 -
Journal of Medicinal Chemistry Mar 2024RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery... (Review)
Review
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases. A deeper understanding of RNA biology reveals that RNA molecules can adopt a variety of structures, carrying defined binding pockets that can accommodate small-molecule drugs. Due to its functional diversity and structural complexity, RNA can be perceived as a prospective target for therapeutic intervention. This perspective highlights the proof of concept of RNA-small-molecule interactions, exemplified by targeting of various transcripts with functional modulators. The advent of RNA-oriented knowledge would help expedite drug discovery.
Topics: RNA; Drug Discovery; Proteins
PubMed: 38498010
DOI: 10.1021/acs.jmedchem.3c01354 -
Journal of Cheminformatics Oct 2023Ultra-large chemical libraries are reaching 10s to 100s of billions of molecules. A challenge for these libraries is to efficiently check if a proposed molecule is...
Ultra-large chemical libraries are reaching 10s to 100s of billions of molecules. A challenge for these libraries is to efficiently check if a proposed molecule is present. Here we propose and study Bloom filters for testing if a molecule is present in a set using either string or fingerprint representations. Bloom filters are small enough to hold billions of molecules in just a few GB of memory and check membership in sub milliseconds. We found string representations can have a false positive rate below 1% and require significantly less storage than using fingerprints. Canonical SMILES with Bloom filters with the simple FNV (Fowler-Noll-Voll) hashing function provide fast and accurate membership tests with small memory requirements. We provide a general implementation and specific filters for detecting if a molecule is purchasable, patented, or a natural product according to existing databases at https://github.com/whitead/molbloom .
PubMed: 37828615
DOI: 10.1186/s13321-023-00765-1 -
Small (Weinheim An Der Bergstrasse,... Sep 2023Chirality is a universal phenomenon in molecular and biological systems, denoting an asymmetric configurational property where an object cannot be superimposed onto its... (Review)
Review
Chirality is a universal phenomenon in molecular and biological systems, denoting an asymmetric configurational property where an object cannot be superimposed onto its mirror image by any kind of translation or rotation, which is ubiquitous on the scale from neutrinos to spiral galaxies. Chirality plays a very important role in the life system. Many biological molecules in the life body show chirality, such as the "codebook" of the earth's biological diversity-DNA, nucleic acid, etc. Intriguingly, living organisms hierarchically consist of homochiral building blocks, for example, l-amino acids and d-sugars with unknown reason. When molecules with chirality interact with these chiral factors, only one conformation favors the positive development of life, that is, the chiral host environment can only selectively interact with chiral molecules of one of the conformations. The differences in chiral interactions are often manifested by chiral recognition, mutual matching, and interactions with chiral molecules, which means that the stereoselectivity of chiral molecules can produce changes in pharmacodynamics and pathology. Here, the latest investigations are summarized including the construction and applications of chiral materials based on natural small molecules as chiral source, natural biomacromolecules as chiral sources, and the material synthesized by design as a chiral source.
PubMed: 37217989
DOI: 10.1002/smll.202303059 -
Journal of Biomolecular Structure &... Dec 2023CD1 immunoreceptors are a non-classical major histocompatibility complex (MHC) that present antigens to T cells to elucidate immune responses against disease. The...
CD1 immunoreceptors are a non-classical major histocompatibility complex (MHC) that present antigens to T cells to elucidate immune responses against disease. The antigen repertoire of CD1 has been composed primarily of lipids until recently when CD1d-restricted T cells were shown to be activated by non-lipidic small molecules, such as phenyl pentamethyl dihydrobenzofuran sulfonate (PPBF) and related benzofuran sulfonates. To date structural insights into PPBF/CD1d interactions are lacking, so it is unknown whether small molecule and lipid antigens are presented and recognized through similar mechanisms. Furthermore, it is unknown whether CD1d can bind to and present a broader range of small molecule metabolites to T cells, acting out functions analogous to the MHC class I related protein MR1. Here, we perform docking and molecular dynamics simulations to structurally characterize small molecule interactions with CD1d. PPBF was supported to be presented to T cell receptors through the CD1d F' pocket. Virtual screening of CD1d against more than 17,000 small molecules with diverse geometry and chemistry identified several novel scaffolds, including phytosterols, cholesterols, triterpenes, and carbazole alkaloids, that serve as candidate CD1d antigens. Protein-ligand interaction profiling revealed conserved residues in the CD1d F' pocket that similarly anchor small molecules and lipids. Our results suggest that CD1d could have the intrinsic ability to bind and present a broad range of small molecule metabolites to T cells to carry out its function beyond lipid antigen presentation.Communicated by Ramaswamy H. Sarma.
PubMed: 38109194
DOI: 10.1080/07391102.2023.2294388 -
Small (Weinheim An Der Bergstrasse,... Jun 2024Microneedles (MNs) have maintained their popularity in therapeutic and diagnostic medical applications throughout the past decade. MNs are originally designed to gently... (Review)
Review
Microneedles (MNs) have maintained their popularity in therapeutic and diagnostic medical applications throughout the past decade. MNs are originally designed to gently puncture the stratum corneum layer of the skin and have lately evolved into intelligent devices with functions including bodily fluid extraction, biosensing, and drug administration. MNs offer limited invasiveness, ease of application, and minimal discomfort. Initially manufactured solely from metals, MNs are now available in polymer-based varieties. MNs can be used to create systems that deliver drugs and chemicals uniformly, collect bodily fluids, and are stimulus-sensitive. Although these advancements are favorable in terms of biocompatibility and production costs, they are insufficient for the therapeutic use of MNs. This is the first comprehensive review that discusses individual MN functions toward the evolution and development of smart and multifunctional MNs for a variety of novel and impactful future applications. The study examines fabrication techniques, application purposes, and experimental details of MN constructs that perform multiple functions concurrently, including sensing, drug-molecule release, sampling, and remote communication capabilities. It is highly likely that in the near future, MN-based smart devices will be a useful and important component of standard medical practice for different applications.
Topics: Needles; Humans; Drug Delivery Systems; Animals; Theranostic Nanomedicine; Microinjections
PubMed: 38385813
DOI: 10.1002/smll.202308479 -
Small (Weinheim An Der Bergstrasse,... Dec 2023Patients with viral myocarditis are at risk of sudden death and may progress to dilated cardiomyopathy (DCM). Currently, no disease-specific therapies exist to treat...
Patients with viral myocarditis are at risk of sudden death and may progress to dilated cardiomyopathy (DCM). Currently, no disease-specific therapies exist to treat viral myocarditis. Here it is examined whether reconstituted, lyophilized extracellular vesicles (EVs) from platelets from healthy men and women reduce acute or chronic myocarditis in male mice. Human-platelet-derived EVs (PEV) do not cause toxicity, damage, or inflammation in naïve mice. PEV administered during the innate immune response significantly reduces myocarditis with fewer epidermal growth factor (EGF)-like module-containing mucin-like hormone receptor-like 1 (F4/80) macrophages, T cells (cluster of differentiation molecules 4 and 8, CD4 and CD8), and mast cells, and improved cardiac function. Innate immune mediators known to increase myocarditis are decreased by innate PEV treatment including Toll-like receptor (TLR)4 and complement. PEV also significantly reduces perivascular fibrosis and remodeling including interleukin 1 beta (IL-1β), transforming growth factor-beta 1, matrix metalloproteinase, collagen genes, and mast cell degranulation. PEV given at days 7-9 after infection reduces myocarditis and improves cardiac function. MicroRNA (miR) sequencing reveals that PEV contains miRs that decrease viral replication, TLR4 signaling, and T-cell activation. These data show that EVs from the platelets of healthy individuals can significantly reduce myocarditis and improve cardiac function.
Topics: Humans; Mice; Male; Female; Animals; Myocarditis; Myocardium; Cardiomyopathy, Dilated; Immunity, Innate; Macrophages
PubMed: 37612820
DOI: 10.1002/smll.202303317 -
Current Opinion in Plant Biology Aug 2023Biomolecular condensate (BMCs) formation facilitates the grouping of molecules, including proteins, nucleic acids, and small molecules, creating specific... (Review)
Review
Biomolecular condensate (BMCs) formation facilitates the grouping of molecules, including proteins, nucleic acids, and small molecules, creating specific microenvironments with particular functions. They are often assembled through liquid-liquid phase separation (LLPS), a phenomenon that arises when specific proteins, nucleic acids, and small molecules demix from the aqueous environment into another phase with different physiochemical properties. BMCs assemble and disassemble in response to external and internal stimuli such as temperature, molecule concentration, ionic strength, pH, and cellular redox state. Likewise, the nature of the regulatory stimuli may affect the lifespan, morphology, and content of BMCs. In humans, compelling evidence points to the critical role of BMCs in diseases. By contrast, the link between BMC formation, stress resistance, and cell survival has not been revealed in plants. Recent studies have pointed out the nascent roles of small molecules in the assembly and dynamics of BMCs; however, this is still an emerging field of study. This review briefly highlights the most significant efforts to identify the molecular mechanisms between small molecules and BMC formation and regulation in plants and other organisms. We then discuss (i) how small molecules exert control over the BMC assembly and dynamics in plants and (ii) how small molecules can influence the formation and material properties of plant BMCs. Finally, we propose novel alternatives that might help to understand the relationship between chemicals and condensation dynamics and their possible application to plant biotechnology.
Topics: Humans; Biomolecular Condensates; Nucleic Acids
PubMed: 37348448
DOI: 10.1016/j.pbi.2023.102385 -
Small (Weinheim An Der Bergstrasse,... Nov 2023Piezocatalysis is an emerging technique that holds great promise for the conversion of ubiquitous mechanical energy into electrochemical energy through piezoelectric... (Review)
Review
Piezocatalysis is an emerging technique that holds great promise for the conversion of ubiquitous mechanical energy into electrochemical energy through piezoelectric effect. However, mechanical energies in natural environment (such as wind energy, water flow energy, and noise) are typically tiny, scattered, and featured with low frequency and low power. Therefore, a high response to these tiny mechanical energies is critical to achieving high piezocatalytic performance. In comparison to nanoparticles or 1D piezoelectric materials, 2D piezoelectric materials possess characteristics such as high flexibility, easy deformation, large surface area, and rich active sites, showing more promise in future for practical applications. In this review, state-of-the-art research progresses on 2D piezoelectric materials and their applications in piezocatalysis are provided. First, a detailed description of 2D piezoelectric materials are offered. Then a comprehensive summary of the piezocatalysis technique is presented and examines the piezocatalysis applications of 2D piezoelectric materials in various fields, including environmental remediation, small-molecule catalysis, and biomedicine. Finally, the main challenges and prospects of 2D piezoelectric materials and their applications in piezocatalysis are discussed. It is expected that this review can fuel the practical application of 2D piezoelectric materials in piezocatalysis.
PubMed: 37386814
DOI: 10.1002/smll.202303586 -
Pharmaceuticals (Basel, Switzerland) Dec 2023In the rapidly evolving landscape of genetic engineering, the advent of CRISPR-Cas technologies has catalyzed a paradigm shift, empowering scientists to manipulate the... (Review)
Review
In the rapidly evolving landscape of genetic engineering, the advent of CRISPR-Cas technologies has catalyzed a paradigm shift, empowering scientists to manipulate the genetic code with unprecedented accuracy and efficiency. Despite the remarkable capabilities inherent to CRISPR-Cas systems, recent advancements have witnessed the integration of small molecules to augment their functionality, introducing new dimensions to the precision and versatility of gene editing applications. This review delves into the synergy between CRISPR-Cas technologies based specifically on Cas9 and small-molecule drugs, elucidating the pivotal role of chemicals in optimizing target specificity and editing efficiency. By examining a diverse array of applications, ranging from therapeutic interventions to agricultural advancements, we explore how the judicious use of chemicals enhances the precision of CRISPR-Cas9-mediated genetic modifications. In this review, we emphasize the significance of small-molecule drugs in fine-tuning the CRISPR-Cas9 machinery, which allows researchers to exert meticulous control over the editing process. We delve into the mechanisms through which these chemicals bolster target specificity, mitigate off-target effects, and contribute to the overall refinement of gene editing outcomes. Additionally, we discuss the potential of chemical integration in expanding the scope of CRISPR-Cas9 technologies, enabling tailored solutions for diverse genetic manipulation challenges. As CRISPR-Cas9 technologies continue to evolve, the integration of small-molecule drugs emerges as a crucial avenue for advancing the precision and applicability of gene editing techniques. This review not only synthesizes current knowledge but also highlights future prospects, paving the way for a deeper understanding of the synergistic interplay between CRISPR-Cas9 systems and chemical modulators in the pursuit of more controlled and efficient genetic modifications.
PubMed: 38256875
DOI: 10.3390/ph17010041