Diversity-oriented synthesis (DOS) aims to efficiently generate collections of small molecules with diverse appendages, functional groups, stereochemistry and skeletons, thus yielding diverse biological activities capable of modulating a wide variety of biological processes. In this review, we discussed the common strategies employed in DOS with specific examples from recent literature, including reagent-based approach, substrate-based approach, build-couple-pair strategy and privileged substructure-based DOS. The application of some DOS libraries in drug discovery is also presented.
Drug Design ; Drug Discovery ; Small Molecule Libraries

Primary cilia have critical roles in coordinating multiple cellular signaling pathways. Dysregulation of primary cilia is implicated in various ciliopathies. To identify specific regulators of autophagy, we screened chemical libraries and identified mefloquine, an anti-malaria medicine, as a potent regulator of primary cilia in human retinal pigmented epithelial (RPE) cells. Not only ciliated cells but also primary cilium length was increased in mefloquine-treated RPE cells. Treatment with mefloquine strongly induced the elongation of primary cilia by blocking disassembly of primary cilium. In addition, we found that autophagy was increased in mefloquine-treated cells by enhancing autophagic flux. Both chemical and genetic inhibition of autophagy suppressed ciliogenesis in mefloquine-treated RPE cells. Taken together, these results suggest that autophagy induced by mefloquine positively regulates the elongation of primary cilia in RPE cells.
Autophagy* ; Cilia* ; Humans ; Mefloquine ; Retinaldehyde ; Small Molecule Libraries

Coculture Techniques ; Hematopoietic Stem Cells ; cytology ; Humans ; Small Molecule Libraries

Chemical genetics is the science which takes the small molecular compounds as tools to solve the genetics problems or to disturb/adjust normal biological process so as to find out protein functions. Because the small molecules have the diverse chemical characters and the ability to identify the target proteins, they also can be filtrated on the basis of phenotype. So the methods of chemical genetics have been applied in almost all of the researches on biology and medicine. In this paper, the methods to acquire small molecular compounds are introduced. The enormous progress achieved in the field of combinatorial chemistry, which has allowed the rapid production of a large number of chemically diverse molecules, is an important prerequisite to make chemical libraries available to academic researchers. And the applications of the compounds in early embryo development, cell differentiation, on-set and course of disease are discussed, too. The application of small molecules has an enormous impact on our understanding of cell biology. There are many examples where small molecules, in combination with genetic screens, have facilitated the dissection of complex cellular processes.
Combinatorial Chemistry Techniques ; Genetic Techniques ; Genetics ; trends ; Humans ; Molecular Probe Techniques ; Small Molecule Libraries ; chemistry

Computational virtual screening has become an essential platform of drug discovery for the efficient identification of active candidates. Moleculardocking, a key technology of receptor-centric virtual screening, is commonly used to predict the binding affinities of chemical compounds on target receptors. Despite the advancement and extensive application of these methods, substantial improvement is still required to increase their accuracy and time-efficiency. Here, we evaluate several advanced structure-based virtual screening approaches for elucidating the rank-order activity of chemical libraries, and the quantitative structureactivity relationship (QSAR). Our results show that the ensemble-average free energy estimation, including implicit solvation energy terms, significantly improves the hit enrichment of the virtual screening. We also demonstrate that the assignment of quantum mechanical-polarized (QM-polarized) partial charges to docked ligands contributes to the reproduction of the crystal pose of ligands in the docking and scoring procedure.
Drug Discovery* ; Ligands ; Mass Screening* ; Quantitative Structure-Activity Relationship ; Reproduction ; Small Molecule Libraries

PURPOSE: Proprotein convertase subtilisin/kexin type 9 (PCSK9) binds to the low density lipoprotein receptor (LDLR) and promotes degradation of the LDLR. Inhibition of PCSK9 either by reducing its expression or by blocking its activity results in the upregulation of the LDLR and subsequently lowers the plasma concentration of LDL-cholesterol. As a modality to inhibit PCSK9 action, we searched the chemical library for small molecules that block the binding of PCSK9 to the LDLR. MATERIALS AND METHODS: We selected 100 chemicals that bind to PCSK9 where the EGF-AB fragment of the LDLR binds via in silico screening of the ChemBridge chemical library, using the computational GOLD algorithm analysis. Effects of chemicals were evaluated using the PCSK9-LDLR binding assay, immunoblot analysis, and the LDL-cholesterol uptake assay in vitro, as well as the fast performance liquid chromatography assay for plasma lipoproteins in vivo. RESULTS: A set of chemicals were found that decreased the binding of PCSK9 to the EGF-AB fragment of the LDLR in a dose-dependent manner. They also increased the amount of the LDLR significantly and subsequently increased the uptake of fluorescence-labeled LDL in HepG2 cells. Additionally, one particular molecule lowered the plasma concentration of total cholesterol and LDL-cholesterol significantly in wild-type mice, while such an effect was not observed in Pcsk9 knockout mice. CONCLUSION: Our findings strongly suggest that in silico screening of small molecules that inhibit the protein-protein interaction between PCSK9 and the LDLR is a potential modality for developing hypercholesterolemia therapeutics.
Animals ; Cholesterol/*blood ; Cholesterol, LDL/blood ; Hep G2 Cells ; Humans ; Mice ; Mice, Knockout ; Proprotein Convertases/*metabolism ; Receptors, LDL/*metabolism ; Serine Endopeptidases/*metabolism ; *Small Molecule Libraries

As an extension of the structure-based drug discovery, fragment-based drug discovery is matured increasingly, and plays an important role in drug development. Fragments in a small library, with lower molecular mass and high "ligand efficiency", are detected by SPR, MS, NMR, X-ray crystallography technologies and other biophysical methods. Then they are considered as starting points for chemical optimization with the guidance of structural biology methods to get good "drug-like" lead and candidate compounds. In this article, we reviewed the current progress of fragment-based drug discovery and detailed a number of examples to illustrate the novel strategies.
Computer-Aided Design ; Crystallography, X-Ray ; Drug Discovery ; methods ; Ligands ; Magnetic Resonance Spectroscopy ; Peptide Fragments ; chemical synthesis ; chemistry ; Protein Conformation ; Small Molecule Libraries ; Surface Plasmon Resonance

Medical community and pharmaceutical companies are currently facing a dire need for discovery and identification of new druggable targets. However, the discovery of small-molecule target is an important and arduous task for the biological and medical scientists. To overcome the bottlenecks for target validation, many new approaches are being developed, such as chemical proteomics. As a part of proteomics approaches, chemical proteomics employs small-molecule compounds that can specifically interact with the target protein to interfere with and detect proteomics. Therefore, new target identification, drug discovery and research on multi-target-directed drugs will all be benefited from the further advances in chemical proteomics approaches. Chemical proteomics has the potential to greatly enhance the efficiency of the drug discovery process.
Animals ; Drug Delivery Systems ; methods ; Drug Design ; Drug Discovery ; Drugs, Chinese Herbal ; chemistry ; Humans ; Protein Array Analysis ; Proteomics ; methods ; Small Molecule Libraries ; chemistry

Circular dichroism (CD) is an useful technique for monitoring DNA conformation changes resulting from changes in environmental conditions, such as temperature, ionic strength, and pH, and also for the study of the interaction between DNA and ligands (including small molecules and proteins). CD spectroscopy of DNA arises from the asymmetric backbone sugars and by the helical structures often adopted by nucleic acids. By the interpretation of induced circular dichroism (ICD) of ligand signals resulting from the coupling of electric transition moments of the ligand, DNA bases within the asymmetric DNA environment, ligand-DNA interactions, as well as the DNA-binding mode can be assessed. A number of important conclusions have been reported that related to the observed ICD signals resulting from the interactions between intercalators and groove binders with DNA. If short oligonucleotide sequences are used in the study, sequences-specific of binding also can be deduced. CD determination requires smaller amounts of sample, and not limited by the molecular weight or size and can be performed rapidly; though CD is of low resolution, but it's a complement to NMR and X-ray diffraction methods. This review will introduce the characters of the CD spectra of DNA, and its application to the studies of DNA with small molecules; some progress of the studies in our laboratory will also be discussed. CD is expected to be used as a screening method in seeking more DNA-targeted drugs, such as, antineoplastic, antimicrobial and antiviral drugs.
Animals ; Antineoplastic Agents ; chemistry ; Base Sequence ; Circular Dichroism ; methods ; DNA ; chemistry ; metabolism ; Humans ; Intercalating Agents ; chemistry ; Ligands ; Protein Binding ; Small Molecule Libraries ; pharmacology

The growing demand for new therapeutic strategies in the medical and pharmaceutic fields has resulted in a pressing need for novel druggable targets. Paradoxically, however, the targets of certain drugs that are already widely used in clinical practice have largely not been annotated. Because the pharmacologic effects of a drug can only be appreciated when its interactions with cellular components are clearly delineated, an integrated deconvolution of drug-target interactions for each drug is necessary. The emerging field of chemical proteomics represents a powerful mass spectrometry (MS)-based affinity chromatography approach for identifying proteome-wide small molecule-protein interactions and mapping these interactions to signaling and metabolic pathways. This technique could comprehensively characterize drug targets, profile the toxicity of known drugs, and identify possible off-target activities. With the use of this technique, candidate drug molecules could be optimized, and predictable side effects might consequently be avoided. Herein, we provide a holistic overview of the major chemical proteomic approaches and highlight recent advances in this area as well as its potential applications in drug discovery.
Chromatography, Affinity ; Drug Delivery Systems ; methods ; Drug Design ; Drug Discovery ; methods ; Humans ; Mass Spectrometry ; Proteome ; chemistry ; Proteomics ; methods ; Small Molecule Libraries ; chemistry