Do Chemformers Dream of Organic Matter? Evaluating a Transformer Model for Multistep Retrosynthesis.

Synthesis planning of new pharmaceutical compounds is a well-known bottleneck in modern drug design. Template-free methods, such as transformers, have recently been proposed as an alternative to template-based methods for single-step retrosynthetic predictions. Here, we trained and evaluated a transformer model, called the Chemformer, for retrosynthesis predictions within drug discovery. The proprietary data set used for training comprised ∼18 M reactions from literature, patents, and electronic lab notebooks. Chemformer was evaluated for the purpose of both single-step and multistep retrosynthesis. We found that the single-step performance of Chemformer was especially good on reaction classes common in drug discovery, with most reaction classes showing a top-10 round-trip accuracy above 0.97. Moreover, Chemformer reached a higher round-trip accuracy compared to that of a template-based model. By analyzing multistep retrosynthesis experiments, we observed that Chemformer found synthetic routes, leading to commercial starting materials for 95% of the target compounds, an increase of more than 20% compared to the template-based model on a proprietary compound data set. In addition to this, we discovered that Chemformer suggested novel disconnections corresponding to reaction templates, which are not included in the template-based model. These findings were further supported by a publicly available ChEMBL compound data set. The conclusions drawn from this work allow for the design of a synthesis planning tool where template-based and template-free models work in harmony to optimize retrosynthetic recommendations.

Carbon 14 synthesis of glycine transporter 1 inhibitor Iclepertin (BI 425809) and its major metabolites.

Carbon 14 labeled Iclepertin (BI 425809, 1) and its major metabolites were needed for ADME and several other studies necessary for the advancement of this drug candidate in clinical trials. Iclepertin is composed of two main chemical blocks, (R)-5-(methylsulfonyl)-2-([1,1,1-trifluoropropan-2-yl]oxy)benzoic acid (2), and 3-[(1R,5R)-3-azabicyclo[3.1.0]hexan-5-yl]-5-(trifluoromethyl)isoxazole (3) linked to each other via an amide bond. In the first synthesis of carbon 14 labeled 1, 2-fluorobenzoic acid, carboxyl-14 C was converted to [14 C]-2 in three steps and then coupled to 3 to provide [14 C]-1a in 45% overall yield. In the second synthesis, [14 C]-3 was prepared in six radioactive steps and coupled to the acid 2 to furnish [14 C]-1b in 20% overall yield. Both synthetic routes provided [14 C]-1a and [14 C]-1b with specific activities higher than 53 mCi/mmol and radiochemical, chemical, and enantiomeric purities above 98%. Two major metabolites of 1, BI 761036 and BI 758790, were also prepared labeled with carbon 14 using intermediates already available from the synthesis of [14 C]-1.

Red Pepper and Turmeric-Flavored Virgin Olive Oil Oleogels Prepared with Whale Spermaceti Wax.

This study aimed to prepare and evaluate ground red pepper and turmeric added virgin olive oil (VOO) oleogels with whale spermaceti wax (WSW) as organogelator. The concentration of WSW was 8 wt%, and each spice was added at 1 overall wt%. Prepared oleogels were analyzed for main physico-chemical, structural, thermal, rheological properties. Further, aromatics volatile compositions, sensory descriptive analysis and consumer tests were completed. Results indicated that the new oleogels were quite spreadable preparates with acceptable quality indices. The oleogels included ß type polymorphs, and showed up to 38℃ of peak melting temperatures. Rheological measurements proved true gel structure stable within applicable frequencies and above 38°C surrounding temperatures. The oleogels were thermo-reversible, and their gel state was recoverable after high shear. Around 25 different aromatic volatile compounds were identified in the two oleogels, most shown to be originating from the VOO, and the spices added. The panel defined and scored the samples with 12 sensory descriptive (hardness, spreadability, liquefaction, sandiness, olive fruit, grassy, waxy, rancid, bitter, hay, cooling and mouth coating) terms. Sensory scores were mostly similar to each other and also within the ranges given in the literature for similar spreadable fat products. Consumer test identified the samples with liked scores (above 4 in 5-max point scale) for appearance, aroma, flavour and overall acceptability. In conclusion, ground spices enriched VOO oleogels with WSW were developed successively to offer consumers spreadable olive oil products to extent consumption patterns with special flavors and health benefits of the spices.

l-Lysine-Based Gelators for the Formation of Oleogels in Four Vegetable Oils.

Supramolecular oleogel is a soft material with a three-dimensional structure, formed by the self-assembly of low-molecular-weight gelators in oils; it shows broad application prospects in the food industry, environmental protection, medicine, and other fields. Among all the gelators reported, amino-acid-based compounds have been widely used to form organogels and hydrogels because of their biocompatibility, biodegradation, and non-toxicity. In this study, four Nα, Nε-diacyl-l-lysine gelators (i.e., Nα, Nε-dioctanoyl-l-lysine; Nα, Nε-didecanoyl-l-lysine; Nα, Nε-dilauroyl-l-lysine; and Nα, Nε-dimyristoyl-l-lysine) were synthesized and applied to prepare oleogels in four kinds of vegetable oils. Gelation ability is affected not only by the structure of the gelators but also by the composition of the oils. The minimum gel concentration (MGC) increased with the increase in the acyl carbon-chain length of the gelators. The strongest gelation ability was displayed in olive oil for the same gelator. Rheological properties showed that the mechanical strength and thermal stability of the oleogels varied with the carbon-chain length of the gelators and the type of vegetable oil. The microstructure of oleogels is closely related to the carbon-chain length of gelators, regardless of oil type. The highest oil-binding capacity (OBC) was obtained in soybean oil for all four gelators, and Nα, Nε-dimyristoyl-l-lysine showed the best performance for entrapping oils.

Formation and Physical Analysis of Oleogels Composed of Edible Oils and High-Melting Fat Crystals.

This paper reports the preparation of oleogels composed of edible oils (olive oil, squalene, and caprylic/capric triglyceride) and high-melting fat crystals (tribehenoyl-glycerol (BBB)) to explore the potential use of BBB/edible oil mixtures as low-cost and stable gelators. These mixtures exhibited gel-like behaviors upon rapid cooling and subsequent heating. The mixtures of BBB in the liquid oils formed oleogels at BBB concentrations > 4.0 wt%. The thermal behaviors, crystal structures, and crystal morphologies of mixtures of BBB produced from 6.0 wt% BBB crystals in 94.0 wt% liquid oils were examined following the treatment of these systems according to different temperature regimes. In addition, rheological analysis was conducted to evaluate the physical properties and storage stabilities of the prepared oleogels. It was found that rapid cooling to the crystallization temperature (Tc) from 70°C and subsequent heating to the final temperature (Tf) were necessary to reveal the gel-like behavior. In addition, the crystals treated with rapid cooling were smaller and more uniform in size than those treated with a simple cooling procedure. The differential scanning calorimetry melting peaks were broad or split, and exhibited the eutectic mixing behavior of multi-component triacylglycerols. The X-ray diffraction spectra showed that the melt-mediated α to ß transformation of the mixtures was a prerequisite for revealing the gel-like behavior. Moreover, the tempering procedure was found to influence the physical properties of the oleogels, wherein no visible changes were observed for any of the oleogels after rapid cooling and storage for 6 months at 25°C.

Recyclable fluorous cinchona organocatalysts for asymmetric synthesis of biologically interesting compounds.

Organocatalysis has unique modes of activation, mild reaction conditions, and good catalyst structural amenability. The integration of green techniques such as catalyst recovery and one-pot reactions makes organocatalysis more efficient and attractive. Presented in this article are the recyclable cinchona alkaloid-catalyzed reactions including fluorination and Michael addition-initiated cascade reactions in asymmetric synthesis of functionalized compounds of biological interest.

Metagenome-Guided Analogue Synthesis Yields Improved Gram-Negative-Active Albicidin- and Cystobactamid-Type Antibiotics.

Natural products are a major source of new antibiotics. Here we utilize biosynthetic instructions contained within metagenome-derived congener biosynthetic gene clusters (BGCs) to guide the synthesis of improved antibiotic analogues. Albicidin and cystobactamid are the first members of a new class of broad-spectrum ρ-aminobenzoic acid (PABA)-based antibiotics. Our search for PABA-specific adenylation domain sequences in soil metagenomes revealed that BGCs in this family are common in nature. Twelve BGCs that were bio-informatically predicted to encode six new congeners were recovered from soil metagenomic libraries. Synthesis of these six predicted structures led to the identification of potent antibiotics with changes in their spectrum of activity and the ability to circumvent resistance conferred by endopeptidase cleavage enzymes.

Compounds targeting OSBPL7 increase ABCA1-dependent cholesterol efflux preserving kidney function in two models of kidney disease.

Impaired cellular cholesterol efflux is a key factor in the progression of renal, cardiovascular, and autoimmune diseases. Here we describe a class of 5-arylnicotinamide compounds, identified through phenotypic drug discovery, that upregulate ABCA1-dependent cholesterol efflux by targeting Oxysterol Binding Protein Like 7 (OSBPL7). OSBPL7 was identified as the molecular target of these compounds through a chemical biology approach, employing a photoactivatable 5-arylnicotinamide derivative in a cellular cross-linking/immunoprecipitation assay. Further evaluation of two compounds (Cpd A and Cpd G) showed that they induced ABCA1 and cholesterol efflux from podocytes in vitro and normalized proteinuria and prevented renal function decline in mouse models of proteinuric kidney disease: Adriamycin-induced nephropathy and Alport Syndrome. In conclusion, we show that small molecule drugs targeting OSBPL7 reveal an alternative mechanism to upregulate ABCA1, and may represent a promising new therapeutic strategy for the treatment of renal diseases and other disorders of cellular cholesterol homeostasis.

In vivo organic synthesis by metal catalysts.

The metal-catalyzed reactions have given various chemical modifications that could not be achieved through basic organic chemistry reactions. In the past decade, many metal-mediated catalytic systems have carried out different transformations in cellulo, such as decaging of fluorophores, drug release, and protein conjugation. However, translating abiotic metal catalysts for organic synthesis in vivo, including bacteria, zebrafish, or mice, could encounter numerous challenges regarding their biocompatibility, stability, and reactivity in the complicated biological environment. In this review, we categorize and summarize the relevant advances in this research field by emphasizing the system's framework, the design of each transformation, and the mode of action. These studies disclose the massive potential of the emerging field and the significant applications in synthetic biology.

Overcoming AlbD Protease Resistance and Improving Potency: Synthesis and Bioactivity of Antibacterial Albicidin Analogues with Amide Bond Isosteres.

Albicidin is a potent antibacterial oligoaromatic peptide that is susceptible to the protease AlbD, a resistance factor. This potentially restricts the use of albicidin as a drug. To overcome this obstacle, we synthesized and evaluated six analogues with isosteric replacement of the key amide link. Protease stability was established while maintaining the antibacterial activity, including three analogues with up to eight times higher activity compared with the natural albicidin.

Discovery of the first-in-class dual PPARδ/γ partial agonist for the treatment of metabolic syndrome.

The peroxisome proliferator-activated receptors (PPARs) exert vital function in the regulation of energy metabolism, which were considered as promising targets of metabolic syndrome. Until now, PPARδ/γ dual agonist is rarely reported, and thereby the pharmacologic action of PPARδ/γ dual agonist is still unclear. In this study, we identified a dual PPARδ/γ partial agonist 6 (ZLY06) based on the cyclization strategy of PPARα/δ dual agonist GFT505. ZLY06 revealed excellent pharmacokinetic profiles suitable for oral medication. Moreover, ZLY06 markedly improved glucolipid metabolism without weight gain, and alleviated fatty liver by promoting the ß-oxidation of fatty acid and inhibiting hepatic lipogenesis. In contrast, weight gain and hepatic steatosis were observed in Rosiglitazone, a widely used PPARγ full agonist. All of these results indicated that ZLY06 exhibits potential benefits on metabolic syndrome, while no adverse effects related to PPARγ full agonist.

Iodine containing porous organosilica nanoparticles trigger tumor spheroids destruction upon monochromatic X-ray irradiation: DNA breaks and K-edge energy X-ray.

X-ray irradiation of high Z elements causes photoelectric effects that include the release of Auger electrons that can induce localized DNA breaks. We have previously established a tumor spheroid-based assay that used gadolinium containing mesoporous silica nanoparticles and synchrotron-generated monochromatic X-rays. In this work, we focused on iodine and synthesized iodine-containing porous organosilica (IPO) nanoparticles. IPO were loaded onto tumor spheroids and the spheroids were irradiated with 33.2 keV monochromatic X-ray. After incubation in CO2 incubator, destruction of tumor spheroids was observed which was accompanied by apoptosis induction, as determined by the TUNEL assay. By employing the γH2AX assay, we detected double strand DNA cleavages immediately after the irradiation. These results suggest that IPO first generate double strand DNA breaks upon X-ray irradiation followed by apoptosis induction of cancer cells. Use of three different monochromatic X-rays having energy levels of 33.0, 33.2 and 33.4 keV as well as X-rays with 0.1 keV energy intervals showed that the optimum effect of all three events (spheroid destruction, apoptosis induction and generation of double strand DNA breaks) occurred with a 33.2 keV monochromatic X-ray. These results uncover the preferential effect of K-edge energy X-ray for tumor spheroid destruction mediated by iodine containing nanoparticles.

Fabrication and Evaluation of Celecoxib Oral Oleogel to Reduce the Inflammation of Ulcerative Colitis.

Oleogel consists of hydrophobic solvent and an oleogelator. In this study, attempts were made to study the influence of Celecoxib solubility, concentration and dispersability on its release, absorption, and biological performance. Oleogels were prepared to study the formulation variables on its stability and release. Castor oil was selected as the oil and the oleogelator concentration was 4.5% w/w. F3 revealed the highest release and stability compared to other formulae. The percent permeated across the rat intestine showed a 7.5-fold increase over free Celecoxib, and its lifetime was found to be greater than 18 months. The efficacy of free Celecoxib and oleogel formulae to treat rats with ulcerative colitis was done via the induction of ulcerative colitis (UC) through administration of 5% dextran sodium sulphate (DSS). Celecoxib besides its formulae significantly reduced the release of Leucine rich 2 glycoprotein (LRG), Myeloperoxidase (MPO), Tumor necrosis factor-α (TNF-α), proinflammatory cytokine expression, High mobility group box 1 (HMGB1), Nuclear factor kappa B (NF-ΚB), Trefoil Factor 3 (TFF3), Metalloproteinase-3 (MMP3), and miRNA31. Moreover, F3 significantly increased the colonic cAMP in DSS treated rats and reduced the intestinal inflammation beside healing of mucosa and restitution of the epithelium of the gastrointestinal tract.

Expanding the Rare-Earth Metal BINOLate Catalytic Multitool beyond Enantioselective Organic Synthesis.

Shibasaki's rare earth alkali metal BINOLate (REMB) framework has provided chemists with a general catalyst platform to access a range of enantioenriched small molecules from the single, commercially available pro-ligand (R)- or (S)-BINOL. A defining feature of these heterobimetallic frameworks is the high level of catalyst tunability, achieved through the simple modulation of the central rare-earth cation and peripheral alkali metal cations. While this family of multifunctional catalysts displays impressive generality and catalytic capability, detailed mechanistic understanding of these complex, multimetallic systems was lacking prior to our investigations. This backdrop served as initial inspiration for our investigations of this privileged class of complexes over the past decade, which have led to new and exciting advances in catalysis and beyond.In this Account, we describe our investigations using Shibasaki's framework focusing on the central metal-ion, the BINOLate ligands, and the secondary sphere cations. Our studies began with an investigation into the Lewis acidity of the complexes, where we demonstrated that Lewis bases readily coordinate to REMB frameworks when lithium occupies the secondary coordination sphere. This observation was contrasted by the complexes containing sodium or potassium in the secondary coordination sphere, as the rare earth cation is evidently less accessible for substrate binding. Our efforts in understanding the ligand exchange of the complexes enabled the discovery that associative processes dominate the mechanism of ligand exchange and LA/LA (Lewis acid/Lewis acid) and LA/BB (Lewis acid/Brønsted base) catalysis by the REMB frameworks. Replacing metal cations in the secondary coordination sphere with the N,N,N',N'-tetramethylguanidinium cation delivered an effective precatalyst that is air and water stable over the course of 6 months.To expand the reactivity of the REMB, we investigated the ability of UIV cations to occupy the primary coordination sphere and ZnEt+ and Cu(DBU)+ cations to occupy the secondary coordination sphere. Synthesizing the REMB complexes using the thiol congener monothioBINOL provided an unusual anionic REMB framework, driven by the oxophilicity of the lithium cations. Using the REMB as a platform for investigating the CeIII/CeIV redox couple, we demonstrated that, while oxidative cerium functionalization is observed in the case of lithium containing REMBs, salt elimination is observed in the sodium, potassium, and cesium containing REMBs. Furthermore, we found that while the rate of heterogeneous electron transfer for CeIII was ks(CsI) > ks(KI) > ks(NaI) > ks(LiI), the rates of reaction with the oxidant trityl chloride trended in the opposite order with kobs(LiI) ≫ kobs(NaI) > kobs(KI) > kobs(CsI). We attribute this to the ability to form inner-sphere complexes with the oxidant, rather than differences in redox potential or reorganization energies.Applying our knowledge in ligand exchange and redox behavior of Ce containing REMB complexes, we detailed the mechanism for oxidation of the heterochiral cerium REMB frameworks, reiterating the importance of the formation of inner-sphere complexes in the oxidation chemistry of cerium. There are many different avenues for both organic and inorganic investigation of Shibasaki's REMB framework, and our works have demonstrated the richness of the structural chemistry and properties of this framework that inform mechanism and properties of these privileged catalysts.

New Bioconjugated Technetium and Rhenium Folates Synthesized by Transmetallation Reaction with Zinc Derivatives.

The zinc dithiocarbamates functionalized with folic acid 2Zn and 3Zn were synthesized with a simple straightforward method, using an appropriated folic acid derivative and a functionalized zinc dithiocarbamate (1Zn). Zinc complexes 2Zn and 3Zn show very low solubilities in water, making them useful for preparing Tc-99m radiopharmaceuticals with a potentially high molar activity. Thus, the transmetallation reaction in water medium between the zinc complexes 2Zn or 3Zn and the cation fac-[99mTc(H2O)3(CO)3]+, in the presence of the monodentate ligand TPPTS, leads to the formation of the 2 + 1 complexes fac-[99mTc(CO)3(SS)(P)] bioconjugated to folic acid (2Tc and 3Tc). In spite of the low solubility of 2Zn and 3Zn in water, the reaction yield is higher than 95%, and the excess zinc reagent is easily removed by centrifugation. The Tc-99m complexes were characterized by comparing their HPLC with those of the homologous rhenium complexes (2Re and 3Re) previously synthesized and characterized by standard methods. Preliminary in vivo studies with 2Tc and 3Tc indicate low specific binding to folate receptors. In summary, Tc-99m folates 2Tc and 3Tc were prepared in high yields, using a one-pot transmetallation reaction with low soluble zinc dithiocarbamates (>1 ppm), at moderate temperature, without needing a subsequent purification step.

Reducing Challenges in Organic Synthesis with Stereoselective Hydrogenation and Tandem Catalysis.

Tandem catalysis enables the rapid construction of complex architectures from simple building blocks. This Perspective shares our interest in combining stereoselective hydrogenation with transformations such as isomerization, oxidation, and epimerization to solve diverse challenges. We highlight the use of tandem hydrogenation for preparing complex natural products from simple prochiral building blocks and present tandem catalysis involving transfer hydrogenation and dynamic kinetic resolution. Finally, we underline recent breakthroughs and opportunities for asymmetric hydrogenation.

Developing a variation of 3D-QSAR/MD method in drug design.

In continuation of the previous reports on a combination of 3D-quantitative structure-activity relationships (QSAR) with computational molecular dynamics (MD) studies, a new variation of 3D-QSAR/MD method has been employed for drug-design as an alternative or supplementary for the typical experimental methods. The presented method is more cost-effective and less time-consuming than the previous methods and avoids several restrictions of experimental methods, such as validity estimation, and predictability. For this purpose, seven inhibitors for bromodomain (BRD)-containing protein, as an important protein in the development of different types of cancer and responsible for oncogenic rearrangements, have been selected to study of their interactions by docking and MD simulations using molecular mechanics/generalized born surface area (MM/GBSA) method. To build the proposed model, a common variant of 3D-QSAR methods, comparative molecular field analysis has been employed using a dataset of 100 MD-extracted ligand conformations and their corresponding MM/GBSA BRD4-binding energies. The results showed excellent predictability of the generated model for both the training set and test groups. Finally, two new inhibitors were selected among total 4000 designed derivatives (generated through evolutionary techniques) using the proposed 3D-QSAR-MD model. The potentials of these inhibitors were assessed by MD simulations, which showed the higher inhibitory of these compounds than the previous inhibitors. Therefore, this method showed high potentials for acceleration of the procedure of drug design and a basis for joining researchers in computational biology and pharmaceutical sciences.

Synthetic Approaches to the New Drugs Approved during 2019.

New drugs introduced to the market are privileged structures having affinities for biological targets implicated in human diseases and conditions. These new chemical entities (NCEs), particularly small molecules and antibody-drug conjugates, provide insight into molecular recognition and simultaneously function as leads for the design of future medicines. This review is part of a continuing series presenting the most likely process-scale synthetic approaches to 40 NCEs approved for the first time anywhere in the world in 2019.

Installing the "magic methyl"- C-H methylation in synthesis.

The selective and efficient C-H methylation of sp2 and sp3 carbon centres has become a powerful transformation in the synthetic toolbox. Due to the potential for profound changes to physicochemical properties attributed to the installation of a "Magic Methyl" group at a strategic site in a lead compound, such techniques have become highly desirable in modern drug discovery and synthesis programmes. This review will cover the diverse techniques that have been employed to enable the selective installation of the C-Me bond in a wide range of chemical structures, from simple building blocks to complex drug-like architectures.

Mutual kinetic resolution: probing enantiorecognition phenomena and screening for kinetic resolution with racemic reagents.

Enantiorecognition between a racemic reagent and a racemic substrate can be a valuable process in organic synthesis. This review highlights representative examples of this phenomenon and the use of mutual kinetic resolution as a method for screening of kinetic and/or parallel kinetic resolutions.