Discovery of a Potent and Selective DGAT1 Inhibitor with a Piperidinyl-oxy-cyclohexanecarboxylic Acid Moiety

Drug Targeting of Acyltransferases in the Triacylglyceride and 1-O-AcylCeramide Biosynthetic Pathways

Acyltransferase enzymes (EC 2.3.) are a large group of enzymes that transfer acyl groups to a variety of substrates. This review focuses on fatty acyltransferases involved in the biosynthetic pathways of glycerolipids and sphingolipids and how these enzymes have been pharmacologically targeted in their biologic context. Glycerolipids and sphingolipids, commonly treated independently in their regulation and biologic functions, are put together to emphasize the parallelism in their metabolism and bioactive roles. Furthermore, a newly considered signaling molecule, 1-O-acylceramide, resulting from the acylation of ceramide by DGAT2 enzyme, is discussed. Finally, the implications of DGAT2 as a putative ceramide acyltransferase (CAT) enzyme, with a putative dual role in TAG and 1-O-acylceramide generation, are explored. SIGNIFICANCE STATEMENT: This manuscript reviews the current status of drug development in lipid acyltransferases. These are current targets in metabolic syndrome and other diseases, including cancer. A novel function for a member in this group of lipids has been recently reported in cancer cells. The responsible enzyme and biological implications of this added member are discussed.

The role of triacylglycerols and repurposing DGAT1 inhibitors for the treatment of Mycobacterium tuberculosis

Latent tuberculosis poses a significant threat to global health through the incubation of undiagnosed infections within the community, and through its tolerance to antibiotics. This Special Features article explores the mechanisms by which the dormant Mycobacterium tuberculosis pathogen can store energy in the form of lipid inclusion bodies and triacylglycerols, which may be key in the development of novel therapeutics to treat TB.

Structure-Based Ligand Design Targeting Pseudomonas aeruginosa LpxA in Lipid A Biosynthesis

Enzymes involved in lipid A biosynthesis are promising antibacterial drug targets in Gram-negative bacteria. In this study, we use a structure-based design approach to develop a series of novel tetrazole ligands with low μM affinity for LpxA, the first enzyme in the lipid A pathway. Aided by previous structural data, X-ray crystallography, and surface plasmon resonance bioanalysis, we identify 17 hit compounds. Two of these hits were subsequently modified to optimize interactions with three regions of the LpxA active site. This strategy ultimately led to the discovery of ligand L13, which had a K_D of 3.0 μM. The results reveal new chemical scaffolds as potential LpxA inhibitors, important binding features for ligand optimization, and protein conformational changes in response to ligand binding. Specifically, they show that a tetrazole ring is well-accommodated in a small cleft formed between Met169, the "hydrophobic-ruler" and His156, both of which demonstrate significant conformational flexibility. Furthermore, we find that the acyl-chain binding pocket is the most tractable region of the active site for realizing affinity gains and, along with a neighboring patch of hydrophobic residues, preferentially binds aliphatic and aromatic groups. The results presented herein provide valuable chemical and structural information for future inhibitor discovery against this important antibacterial drug target.

In Search of Small Molecules That Selectively Inhibit MBOAT4

Ghrelin is a 28-residue peptide hormone produced by stomach P/D1 cells located in oxyntic glands of the fundus mucosa. Post-translational octanoylation of its Ser-3 residue, catalyzed by MBOAT4 (aka ghrelin O-acyl transferase (GOAT)), is essential for the binding of the hormone to its receptor in target tissues. Physiological roles of acyl ghrelin include the regulation of food intake, growth hormone secretion from the pituitary, and inhibition of insulin secretion from the pancreas. Here, we describe a medicinal chemistry campaign that led to the identification of small lipopeptidomimetics that inhibit GOAT in vitro. These molecules compete directly for substrate binding. We further describe the synthesis of heterocyclic inhibitors that compete at the acyl coenzyme A binding site.

Ultrahigh-Throughput Experimentation for Information-Rich Chemical Synthesis

The incorporation of data science is revolutionizing organic chemistry. It is becoming increasingly possible to predict reaction outcomes with accuracy, computationally plan new retrosynthetic routes to complex molecules, and design molecules with sophisticated functions. Critical to these developments has been statistical analysis of reaction data, for instance with machine learning, yet there is very little reaction data available upon which to build models. Reaction data can be mined from the literature, but experimental data tends to be reported in a text format that is difficult for computers to read. Compounding the issue, literature data are heavily biased toward "productive" reactions, and few "negative" reaction data points are reported even though they are critical for training of statistical models. High-throughput experimentation (HTE) has evolved over the past few decades as a tool for experimental reaction development. The beauty of HTE is that reactions are run in a systematic format, so data points are internally consistent, the reaction data are reported whether the desired product is observed or not, and automation may reduce the occurrence of false positive or negative data points. Additionally, experimental workflows for HTE lead to datasets with reaction metadata that are captured in a machine-readable format. We believe that HTE will play an increasingly important role in the data revolution of chemical synthesis. This Account details the miniaturization of synthetic chemistry culminating in ultrahigh-throughput experimentation (ultraHTE), wherein reactions are run in ∼1 μL droplets inside of 1536-well microtiter plates to minimize the use of starting materials while maximizing the output of experimental information. The performance of ultraHTE in 1536-well microtiter plates has led to an explosion of available reaction data, which have been used to identify specific substrate-catalyst pairs for maximal efficiency in novel cross-coupling reactions. The first iteration of ultraHTE focused on the use of dimethyl sulfoxide (DMSO) as a high-boiling solvent that is compatible with the plastics most commonly used in consumable well plates, which generated homogeneous reaction mixtures that are perfect for use with nanoliter-dosing liquid handling robotics. In this way, DMSO enabled diverse reagents to be arrayed in ∼1 μL droplets. Reactions were run at room temperature with no agitation and could be scaled up from the ∼0.05 mg reaction scale to the 1 g scale. Engineering enhancements enabled the use of ultraHTE with diverse and semivolatile solvents, photoredox catalysis, heating, and acoustic agitation. A main driver in the development of ultraHTE was the recognition of the opportunity for a direct merger between miniaturized reactions and biochemical assays. Indeed, a strategy was developed to feed ultraHTE reaction mixtures directly to a mass-spectrometry-based affinity selection bioassay. Thus, micrograms of starting materials could be used in the synthesis and direct biochemical testing of drug-like molecules. Reactions were performed at a reactant concentration of ∼0.1 M in an inert atmosphere, enabling even challenging transition-metal-catalyzed reactions to be used. Software to enable the workflow was developed. We recently initiated the mapping of reaction space, dreaming of a future where transformations, reaction conditions, structure, properties and function are studied in a systems chemistry approach.

ONO-8430506: A Novel Autotaxin Inhibitor That Enhances the Antitumor Effect of Paclitaxel in a Breast Cancer Model

Lysophosphatidic acid (LPA) is a bioactive lipid mediator that elicits a number of biological functions, including smooth muscle contraction, cell motility, proliferation, and morphological change. LPA is endogenously produced by autotaxin (ATX) from extracellular lysophosphatidylcholine (LPC) in plasma. Herein, we report our medicinal chemistry effort to identify a novel and highly potent ATX inhibitor, ONO-8430506 (20), with good oral availability. To enhance the enzymatic ATX inhibitory activity, we designed several compounds by structurally comparing our hit compound with the endogenous ligand LPC. Further optimization to improve the pharmacokinetic profile and enhance the ATX inhibitory activity in human plasma resulted in the identification of ONO-8430506 (20), which enhanced the antitumor effect of paclitaxel in a breast cancer model.

Structure and catalytic mechanism of a human triacylglycerol-synthesis enzyme

Triglycerides (triacylglycerols, TGs) store metabolic energy in organisms and have industrial uses for foods and fuels. Excessive accumulation of TGs in humans causes obesity and is associated with metabolic diseases¹. TG synthesis is catalyzed by acyl-CoA:diacylglycerol acyltransferase (DGAT) enzymes^2–4 whose structures and catalytic mechanisms are unknown. Here we determined the structure of dimeric human DGAT1, a member of the membrane-bound O-acyltransferase (MBOAT) family, by cryo-electron microscopy at 3.0-Å resolution. DGAT1 forms a homodimer through N-terminal segments and a hydrophobic interface, with putative active sites within the membrane region. A structure obtained with oleoyl-CoA substrate resolved at 3.2-Å shows that the CoA moiety binds DGAT1 on the cytosolic side and the acyl group lies deep within a hydrophobic channel, positioning the acyl-CoA thioester bond near an invariant catalytic histidine residue. The reaction center is located inside a large cavity, which opens laterally to the membrane bilayer, providing lipid access to the active site. A lipid-like density, possibly an acyl-acceptor molecule, is located within the reaction center, orthogonal to acyl-CoA. Insights provided by the DGAT1 structures, together with mutagenesis and functional studies, give rise to a model of catalysis for DGAT’s generation of TGs.

Design and Synthesis of Benzimidazole-Chalcone Derivatives as Potential Anticancer Agents

Numerous reports have shown that conjugated benzimidazole derivatives possess various kinds of biological activities, including anticancer properties. In this report, we designed and synthesized 24 new molecules comprising a benzimidazole ring, arene, and alkyl chain-bearing cyclic moieties. The results showed that the N-substituted benzimidazole derivatives bearing an alkyl chain and a nitrogen-containing 5- or 6-membered ring enhanced the cytotoxic effects on human breast adenocarcinoma (MCF-7) and human ovarian carcinoma (OVCAR-3) cell lines. Among the 24 synthesized compounds, (2E)-1-(1-(3-morpholinopropyl)-1H-benzimidazol-2 -yl)-3-phenyl-2-propen-1-one) (23a) reduced the proliferation of MCF-7 and OVCAR-3 cell lines demonstrating superior outcomes to those of cisplatin.

In silico design of diacylglycerol acyltransferase-1 (DGAT1) inhibitors based on SMILES descriptors using Monte-Carlo method

Diabetes, obesity and other diseases related to metabolism are worldwide health problems. These syndromes can be well treated when a particular enzyme-based therapy is developed. Diacylglycerol acyltransferase (DGAT; EC 2.3.1.20) is a microsomal enzyme which is responsible for the synthesis of triglycerides from 1,2-diacylglycerol by catalyzing the acyl-CoA-dependent acylation. The obesity and type-II diabetes can be checked by the inhibition of DGAT1 enzyme. Quantitative structure-activity relationship (QSAR) modelling is an essential technique in drug design and development. To study the aspect of DGAT1 inhibitors, Monte-Carlo method-based QSAR was developed for 197 DGAT1 inhibitors. QSAR models were derived by using the optimal descriptor based on SMILES notation. Different statistical parameters including the novel index of ideality of correlation were applied to validate the generated QSAR models. Four random splits were prepared from the data set. The statistical criteria r² = 0.8129, CCC = 0.8979 and Q² = 0.7962 of the validation set of split 1 were the best; therefore, the developed QSAR model of split 1 was decided to be the leading model. The molecular fragments, which were promoter of endpoint increase or decrease were also determined. Thirteen new DGAT1 inhibitors were designed from the lead compound DGAT011.

mRNA Levels of Imprinted Genes in Bovine In Vivo Oocytes, Embryos and Cross Species Comparisons with Humans, Mice and Pigs

Twenty-six imprinted genes were quantified in bovine in vivo produced oocytes and embryos using RNA-seq. Eighteen were detectable and their transcriptional patterns were: largely decreased (MEST and PLAGL1); first decreased and then increased (CDKN1C and IGF2R); peaked at a specific stage (PHLDA2, SGCE, PEG10, PEG3, GNAS, MEG3, DGAT1, ASCL2, NNAT, and NAP1L5); or constantly low (DIRAS3, IGF2, H19 and RTL1). These patterns reflect mRNAs that are primarily degraded, important at a specific stage, or only required at low quantities. The mRNAs for several genes were surprisingly abundant. For instance, transcripts for the maternally imprinted MEST and PLAGL1, were high in oocytes and could only be expressed from the maternal allele suggesting that their genomic imprints were not yet established/recognized. Although the mRNAs detected here were likely biallelically transcribed before the establishment of imprinted expression, the levels of mRNA during these critical stages of development have important functional consequences. Lastly, we compared these genes to their counterparts in mice, humans and pigs. Apart from previously known differences in the imprinting status, the mRNA levels were different among these four species. The data presented here provide a solid reference for expression profiles of imprinted genes in embryos produced using assisted reproductive biotechnologies.