ABSTRACT
INTRODUCTION: Despite much progress in the field of oligonucleotide therapeutics, delivery in general remains an important aspect for innovation. Various lipids and lipophilic small molecules have long been conjugated to many oligonucleotides in hopes of creating better, drug-like substances. A few conjugates are beginning to enter clinical development as the understanding grows of how such conjugations change the pharmacology of the conjugate relative to the unmodified oligonucleotide. The delivery of different forms of oligonucleotides, such as antisense oligonucleotides and siRNA, is often a challenging, limiting aspect to this form of therapeutics. AREAS COVERED: Herein, the origins of covalent attachment of lipophilic moieties to oligonucleotides are described as well as listing a few of those lipids commonly used for lipidation. The author also describes the mechanism by which lipidation may enhance delivery and/or exposure of oligonucleotides in vitro and in vivo. EXPERT OPINION: The covalent attachment of lipophilic moieties is one means to enhance the delivery and exposure of oligonucleotides. Such methods may also be applicable to other oligonucleotide-based modalities as long as the lipidation does not interfere with some key interaction. Lipidation may also be useful to modulate the cell type-specific delivery within tissues. As the understanding of the effects of such covalent modification grows, more lipidated oligos are soon likely to enter clinical development.
Subject(s)
Oligonucleotides, Antisense , Oligonucleotides , Humans , Oligonucleotides/pharmacology , Oligonucleotides, Antisense/pharmacology , RNA, Small Interfering , LipidsABSTRACT
Stabilization of protein-protein interactions (PPIs) holds great potential for therapeutic agents, as illustrated by the successful drugs rapamycin and lenalidomide. However, how such interface-binding molecules can be created in a rational, bottom-up manner is a largely unanswered question. We report here how a fragment-based approach can be used to identify chemical starting points for the development of small-molecule stabilizers that differentiate between two different PPI interfaces of the adapter protein 14-3-3. The fragments discriminately bind to the interface of 14-3-3 with the recognition motif of either the tumor suppressor protein p53 or the oncogenic transcription factor TAZ. This X-ray crystallography driven study shows that the rim of the interface of individual 14-3-3 complexes can be targeted in a differential manner with fragments that represent promising starting points for the development of specific 14-3-3 PPI stabilizers.
Subject(s)
14-3-3 Proteins/metabolism , Small Molecule Libraries/pharmacology , 14-3-3 Proteins/chemistry , Drug Design , Models, Molecular , Protein Binding/drug effects , Protein ConformationABSTRACT
Artificial intelligence (AI) tools are increasingly being applied in drug discovery. While some protagonists point to vast opportunities potentially offered by such tools, others remain sceptical, waiting for a clear impact to be shown in drug discovery projects. The reality is probably somewhere in-between these extremes, yet it is clear that AI is providing new challenges not only for the scientists involved but also for the biopharma industry and its established processes for discovering and developing new medicines. This article presents the views of a diverse group of international experts on the 'grand challenges' in small-molecule drug discovery with AI and the approaches to address them.
Subject(s)
Artificial Intelligence , Drug Design , Drug Discovery/methods , HumansABSTRACT
Wnt signaling is critical for development, cell proliferation and differentiation, and mutations in this pathway resulting in constitutive signaling have been implicated in various cancers. A pathway screen using a Wnt-dependent reporter identified a chemical series based on a 1,2,3-thiadiazole-5-carboxamide (TDZ) core with sub-micromolar potency. Herein we report a comprehensive mechanism-of-action deconvolution study toward identifying the efficacy target(s) and biological implication of this chemical series involving bottom-up quantitative chemoproteomics, cell biology, and biochemical methods. Through observing the effects of our probes on metabolism and performing confirmatory cellular and biochemical assays, we found that this chemical series inhibits ATP synthesis by uncoupling the mitochondrial potential. Affinity chemoproteomics experiments identified sarco(endo)plasmic reticulum Ca2+ -dependent ATPase (SERCA2) as a binding partner of the TDZ series, and subsequent validation studies suggest that the TDZ series can act as ionophores through SERCA2 toward Wnt pathway inhibition.
Subject(s)
Oxidative Phosphorylation/drug effects , Sarcoplasmic Reticulum Calcium-Transporting ATPases/metabolism , Thiadiazoles/pharmacology , Wnt Signaling Pathway/drug effects , Dose-Response Relationship, Drug , Humans , Molecular Structure , Structure-Activity Relationship , Thiadiazoles/chemical synthesis , Thiadiazoles/chemistryABSTRACT
DNA-encoded chemical library technologies are increasingly being adopted in drug discovery for hit and lead generation. DNA-encoded chemistry enables the exploration of chemical spaces four to five orders of magnitude more deeply than is achievable by traditional high-throughput screening methods. Operation of this technology requires developing a range of capabilities including aqueous synthetic chemistry, building block acquisition, oligonucleotide conjugation, large-scale molecular biological transformations, selection methodologies, PCR, sequencing, sequence data analysis and the analysis of large chemistry spaces. This Review provides an overview of the development and applications of DNA-encoded chemistry, highlighting the challenges and future directions for the use of this technology.
Subject(s)
Chemistry/trends , DNA/genetics , Genomic Library , Animals , Drug Discovery/trends , High-Throughput Screening Assays , Humans , Small Molecule LibrariesABSTRACT
Modest success rates in fragment-based lead generation (FBLG) projects at AstraZeneca (AZ) prompted operational changes to improve performance. In this review, we summarize these changes, emphasizing the construction and composition of the AZ fragment library, screening practices and working model. We describe the profiles of the screening method for specific fragment subsets and statistically assess our ability to follow up on fragment hits through near-neighbor selection. Performance analysis of our second-generation fragment library (FL2) in screening campaigns illustrates the complementary nature of flat and 3D fragments in exploring protein-binding pockets and highlights our ability to deliver fragment hits using multiple screening techniques for various target classes. The new model has had profound impact on the successful delivery of lead series to drug discovery projects.
Subject(s)
Drug Discovery/methods , Drug Industry , Small Molecule LibrariesABSTRACT
Complex mixtures of DNA encoded small molecules may be readily interrogated via high-throughput sequencing. These DNA encoded libraries (DELs) are commonly used to discover molecules that interact with pharmaceutically relevant proteins. The chemical diversity displayed by the library is key to successful discovery of potent, novel, and drug-like chemical matter. The small molecule moieties of DELs are generally synthesized though a multistep process, and each chemical step is accomplished while it is simultaneously attached to an encoding DNA oligomer. Hence, library chemical diversity is often limited to DNA compatible synthetic reactions. Herein, protocols for 24 reactions are provided that have been optimized for high-throughput production of DELs. These protocols detail the multistep synthesis of benzimidazoles, imidazolidinones, quinazolinones, isoindolinones, thiazoles, and imidazopyridines. Additionally, protocols are provided for a diverse range of useful chemical reactions including BOC deprotection (under pH neutral conditions), carbamylation, and Sonogashira coupling. Last, step-by-step protocols for synthesizing functionalized DELs from trichloronitropyrimidine and trichloropyrimidine scaffolds are detailed.
Subject(s)
DNA/chemistry , Drug Discovery/methods , Small Molecule Libraries/chemical synthesis , HumansABSTRACT
Starting from screening hit, (4S,7R)-1,7,8,8-tetramethyl-2-phenyl-1,2,4,5,6,7-hexahydro-4,7-methano-indazol-3-one (7), we optimized the potency and pharmacokinetic properties. This led to the identification of compounds with good in vivo activity in a mouse pharmacodynamic model of inhibition of 11ßHSD1.
Subject(s)
11-beta-Hydroxysteroid Dehydrogenase Type 1/antagonists & inhibitors , Camphor/chemistry , Drug Discovery , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/pharmacology , Pyrazolones/chemical synthesis , Pyrazolones/pharmacology , 11-beta-Hydroxysteroid Dehydrogenase Type 1/metabolism , Animals , Enzyme Activation/drug effects , Female , Hydrocortisone/blood , Inhibitory Concentration 50 , Mice , Molecular Structure , RatsABSTRACT
We designed and synthesized a novel series of phenylamino- and phenoxy-substituted pyrazolo[3,4-d]pyrimidine derivatives as GPR119 agonists. SAR studies indicated that electron-withdrawing substituents on the phenyl ring are important for potency and full efficacy. Compound 26 combined good potency with a promising pharmacokinetic profile in mice, and lowered the glucose excursion in mice in an oral glucose-tolerance test.
Subject(s)
Drug Discovery , Pyrimidines/chemistry , Pyrimidines/pharmacology , Receptors, G-Protein-Coupled/agonists , Animals , Humans , Mice , Pyrazoles/chemical synthesis , Pyrazoles/chemistry , Pyrazoles/pharmacology , Pyrimidines/chemical synthesis , Structure-Activity RelationshipABSTRACT
The inhibition of LTB(4) binding to and activation of G-protein-coupled receptors BLT1 and BLT2 is the premise of a treatment for several inflammatory diseases. In a lead optimization effort starting with the leukotriene B(4) (LTB(4)) receptor antagonist (2), members of a series of 3,5-diarylphenyl ethers were found to be highly potent inhibitors of LTB(4) binding to BLT1 and BLT2 receptors, with varying levels of selectivity depending on the substitution. In addition, compounds 33 and 38 from this series have good in vitro ADME properties, good oral bioavailability, and efficacy after oral delivery in guinea pig LTB(4) and nonhuman primate allergen challenge models. Further profiling in a rat non-GLP toxicity experiment provided the rationale for differentiation and selection of one compound (33) for clinical development.
Subject(s)
Drug Discovery , Leukotriene Antagonists/chemistry , Phenyl Ethers/pharmacology , Receptors, Leukotriene B4/antagonists & inhibitors , Animals , Drug Evaluation, Preclinical , Guinea Pigs , HL-60 Cells , Humans , Leukotriene Antagonists/pharmacology , Phenyl Ethers/chemistry , Primates , Protein Binding , Rats , Receptors, G-Protein-Coupled/metabolism , Receptors, Leukotriene B4/metabolism , Structure-Activity RelationshipABSTRACT
Asthma, chronic obstructive pulmonary disease (COPD) and acute lung injury/acute respiratory distress syndrome (ALI/ARDS) are characterized by neutrophilic inflammation and elevated levels of leukotriene B4 (LTB4). However, the exact role of LTB4 pathways in mediating pulmonary neutrophilia and the potential therapeutic application of LTB4 receptor antagonists in these diseases remains controversial. Here we show that a novel dual BLT1 and BLT2 receptor antagonist, RO5101576, potently inhibited LTB4-evoked calcium mobilization in HL-60 cells and chemotaxis of human neutrophils. RO5101576 significantly attenuated LTB4-evoked pulmonary eosinophilia in guinea pigs. In non-human primates, RO5101576 inhibited allergen and ozone-evoked pulmonary neutrophilia, with comparable efficacy to budesonide (allergic responses). RO5101576 had no effects on LPS-evoked neutrophilia in guinea pigs and cigarette smoke-evoked neutrophilia in mice and rats. In toxicology studies RO5101576 was well-tolerated. Theses studies show differential effects of LTB4 receptor antagonism on neutrophil responses in vivo and suggest RO5101576 may represent a potential new treatment for pulmonary neutrophilia in asthma.
Subject(s)
Benzodioxoles/pharmacology , Phenylpropionates/pharmacology , Pneumonia/drug therapy , Primates , Receptors, Leukotriene B4/antagonists & inhibitors , Animals , Benzodioxoles/therapeutic use , Benzodioxoles/toxicity , Dogs , Drug-Related Side Effects and Adverse Reactions , Female , Guinea Pigs , HL-60 Cells , Humans , Hypersensitivity/complications , Lipopolysaccharides/pharmacology , Lung/drug effects , Male , Mice , Ozone/pharmacology , Phenylpropionates/therapeutic use , Phenylpropionates/toxicity , Pneumonia/chemically induced , Pneumonia/complications , Pneumonia/metabolism , Rats , Receptors, Leukotriene B4/metabolism , Smoking/adverse effects , Toxicity TestsABSTRACT
A straightforward and cost-effective synthesis of 5-aryl-3-alkylsulfonyl-phenols by a sequential scaffold derivatization strategy has been developed. The procedure is suitable for parallel synthesis of small libraries around the biphenyl privileged core having an unusual 1,3,5-substitution pattern. The synthesis is exemplified by a pilot library of 30 compounds.
Subject(s)
Combinatorial Chemistry Techniques/methods , Phenols/chemical synthesis , Small Molecule Libraries/chemical synthesis , Sulfones/chemical synthesis , Combinatorial Chemistry Techniques/economics , Phenols/chemistry , Small Molecule Libraries/chemistry , Sulfones/chemistryABSTRACT
Polymethoxyflavones (PMFs), which exist exclusively in the citrus genus, have biological activities including anti-inflammatory, anticarcinogenic, and antiatherogenic properties. A validated RPLC method was developed for quantitative analysis of six major PMFs, namely nobiletin, tangeretin, sinensetin, 5,6,7,4'-tetramethoxyflavone, 3,5,6,7,3',4'-hexamethoxyflavone, and 3,5,6,7,8,3',4'-heptamethoxyflavone. The polar embedded LC stationary phase was able to fully resolve the six analogues. The developed method was fully validated in terms of linearity, accuracy, precision, sensitivity, and system suitability. The LOD of the method was calculated as 0.15 microg/mL and the recovery rate was between 97.0 and 105.1%. This analytical method was successfully applied to quantify the individual PMFs in four commercially available citrus peel extracts (CPEs). Each extract shows significant difference in the PMF composition and concentration. This method may provide a simple, rapid, and reliable tool to help reveal the correlation between the bioactivity of the PMF extracts and the individual PMF content.
Subject(s)
Chromatography, Liquid/methods , Citrus/anatomy & histology , Citrus/chemistry , Flavones/analysis , Flavones/chemistry , Hydrophobic and Hydrophilic Interactions , Oxygen/chemistry , Methylation , Molecular Structure , Plant Extracts/chemistry , Sensitivity and SpecificityABSTRACT
BACKGROUND: Lead generation is a critical element in the successful discovery of new drugs. Scientists engaged in lead generation are faced with a huge array of strategies and technologies, and new approaches are constantly emerging. In part as a reaction to the large number of options, several guidelines have been developed over the last 10 - 20 years that enable scientists to focus on approaches which are likely to lead to the discovery and development of orally available drugs. Objective and conclusions: This paper examines some of these guidelines as they relate to specific examples of lead generation for drug discovery, and contends that in many cases valuable discoveries can be made at the margins or even outside areas considered mainstream.
ABSTRACT
Leukotriene B(4) (LTB(4)) is a lipid inflammatory mediator derived from membrane phospholipids by the sequential actions of cytosolic phospholipase A2 (PLA2), 5-lipoxygenase (5-LO) and leukotriene A(4) (LTA(4)) hydrolase. Several inflammatory diseases, including asthma, chronic obstructive pulmonary disease, arthritis and inflammatory bowel disease, have been associated with elevated levels of LTB(4). As a result, pharmacological strategies to modulate the synthesis of LTB(4) (inhibition of PLA2, 5-LO or LTA(4) hydrolase) or the effects of LTB(4) itself (antagonism of LTB(4) receptors) are being developed by several companies. Two G-protein-coupled receptors mediate the effects of LTB(4), namely BLT1 and BLT2. The pharmacology, expression and function of these two receptors were last reviewed by Tager and Luster in 2004. Since then, there has been an increased understanding of the function of these receptors, in particular for the lesser understood of the two receptors, BLT2. Furthermore, since last reviewed in 1996, there have been several clinical developments in the use of BLT receptor antagonists for inflammatory diseases. This review summarizes the latest preclinical and clinical developments in BLT antagonism for inflammatory diseases and discusses potential future developments.
Subject(s)
Drugs, Investigational/therapeutic use , Inflammation/drug therapy , Receptors, Leukotriene B4/antagonists & inhibitors , Animals , Clinical Trials as Topic/methods , Clinical Trials as Topic/trends , Drug Evaluation, Preclinical/methods , Drug Evaluation, Preclinical/trends , Drugs, Investigational/chemistry , Drugs, Investigational/pharmacology , Humans , Inflammation/metabolism , Receptors, Leukotriene B4/metabolism , Signal Transduction/drug effects , Signal Transduction/physiologyABSTRACT
Inhibition of the MDM2-p53 interaction can stabilize the p53 protein and offer a novel strategy for cancer therapy. The imidazoline compound (Nutlin-3) is a promising small molecule antagonist of the MDM2-p53 interaction. This compound was synthesized as a racemic mixture, and one enantiomer is 100-200-fold more active than the other enantiomer. In this study, various enantiomeric separation approaches were explored to resolve the Nutlin-3 enantiomers using chiral supercritical fluid chromatography (SFC) as well as chiral liquid chromatography (LC) under normal phase mode, reversed phase mode and polar organic phase mode. The chiral SFC method based on Chiralcel OD column showed superior separation in terms of selectivity and efficiency. Optimization of the chiral separation method enabled high throughput preparative scale purification. Ultimately, 5 g of racemic mixture were purified on Prep-SFC in 75 min with the recovery rate above 92%.
Subject(s)
Chromatography, Liquid , Chromatography, Supercritical Fluid/methods , Imidazoles/isolation & purification , Piperazines/isolation & purification , Proto-Oncogene Proteins c-mdm2/antagonists & inhibitors , Technology, Pharmaceutical/methods , Imidazoles/chemical synthesis , Imidazoles/chemistry , Molecular Structure , Piperazines/chemical synthesis , Piperazines/chemistry , Stereoisomerism , Time FactorsABSTRACT
Polymethoxyflavones (PMFs) from citrus genus are of particular interest because of their broad spectrum of biological activities, such as anti-inflammatory, anti-carcinogenic, and anti-atherogenic properties. Recently, the exploration into the beneficial health properties of PMFs in citrus fruits has dramatically increased. However, the supply of pure PMFs in the in vivo study is a limiting factor due to the difficulties in large-scale isolation of the interested PMFs. Therefore, the development of an efficient and a scalable separation method of PMFs is necessary and significant. In this paper, we report a newly developed method for efficient and relatively large-scale isolation of four PMFs from sweet orange (Citrus sinensis) peel by employing supercritical chromatography (SFC): nobiletin, tangeretin, 3,5,6,7,8,3',4'-heptamethoxyflavone and 5,6,7,4'-tetramethoxyflavone.