Oxaprozin Analogues as Selective RXR Agonists with Superior Properties and Pharmacokinetics

We are MedChem: The Frontiers in Medicinal Chemistry 2024

The Frontiers in Medicinal Chemistry (FiMC) is the largest international Medicinal Chemistry conference in Germany and took place from March 17th to 20th 2024 in Munich. Co-organized by the Division of Medicinal Chemistry of the German Chemical Society (Gesellschaft Deutscher Chemiker; GDCh) and the Division of Pharmaceutical and Medicinal Chemistry of the German Pharmaceutical Society (Deutsche Pharmazeutische Gesellschaft; DPhG), and supported by a local organizing committee from the Ludwigs-Maximilians-University Munich headed by Daniel Merk, the meeting brought together approximately 225 participants from 20 countries. The outstanding program of the four-day conference included 40 lectures by leading scientists from industry and academia as well as early career investigators. Moreover, 100 posters were presented in two highly interactive poster sessions.

Synthesis of deoxybenzoins from β-alkoxy styrenes and arylboronic acids via palladium-catalyzed regioselective Heck-arylation reactions

Palladium-catalyzed synthesis of deoxybenzoin derivatives from styryl ethers and arylboronic acids is reported. The reaction proceeds under mild conditions in the presence of TEMPO and provides the desired products in good to excellent yields. Simple operation, broad substrate scope, and functional group tolerance are the salient features of the developed methodology.

1,1-Oxycarbonation of Terminal Alkynes via Sequential Borylation, 1,2-Migration, and Oxidation with Oxone

Alkynes are readily available and multifunctional synthetic intermediates, but their 1,1-oxofunctionalization remains challenging. Herein, we report a 1,1-oxycarbonation of terminal alkynes to construct ketones through sequential borylation, 1,2-carbon migration, and oxidation with Oxone as the proton source and oxidant. The synthetic potential of this transformation is showcased by the broad functional groups, scale-up synthesis, and diverse product transformations.

Development of an oxazole-based cleavable linker for peptides

We report the development of a new oxazole-based cleavable linker to release peptides from attached cargo. Oxazoles are stable to most reaction conditions, yet they can be rapidly cleaved in the presence of single-electron oxidants like cerium ammonium nitrate (CAN). An oxazole linker could be synthesized and attached to peptides through standard solid-phase peptide coupling reactions. Cleavage of these peptide-oxazole conjugates is demonstrated on a broad scope of peptides containing various natural and unnatural amino acids. These results represent the first example of a peptide-based linker that is cleaved through single-electron oxidation. The oxazole is also demonstrated to be a suitable linker for both the release of a peptide from a conjugated small molecule and the orthogonal release of cargo from a peptide containing multiple cleavable linkers. Oxazole linkers could serve as a promising tool for peptide screening platforms such as peptide-encoded libraries.

Sample efficient reinforcement learning with active learning for molecular design

Reinforcement learning (RL) is a powerful and flexible paradigm for searching for solutions in high-dimensional action spaces. However, bridging the gap between playing computer games with thousands of simulated episodes and solving real scientific problems with complex and involved environments (up to actual laboratory experiments) requires improvements in terms of sample efficiency to make the most of expensive information. The discovery of new drugs is a major commercial application of RL, motivated by the very large nature of the chemical space and the need to perform multiparameter optimization (MPO) across different properties. In silico methods, such as virtual library screening (VS) and de novo molecular generation with RL, show great promise in accelerating this search. However, incorporation of increasingly complex computational models in these workflows requires increasing sample efficiency. Here, we introduce an active learning system linked with an RL model (RL-AL) for molecular design, which aims to improve the sample-efficiency of the optimization process. We identity and characterize unique challenges combining RL and AL, investigate the interplay between the systems, and develop a novel AL approach to solve the MPO problem. Our approach greatly expedites the search for novel solutions relative to baseline-RL for simple ligand- and structure-based oracle functions, with a 5-66-fold increase in hits generated for a fixed oracle budget and a 4-64-fold reduction in computational time to find a specific number of hits. Furthermore, compounds discovered through RL-AL display substantial enrichment of a multi-parameter scoring objective, indicating superior efficacy in curating high-scoring compounds, without a reduction in output diversity. This significant acceleration improves the feasibility of oracle functions that have largely been overlooked in RL due to high computational costs, for example free energy perturbation methods, and in principle is applicable to any RL domain.

Rational design and virtual screening identify mimetics of the RXR agonist valerenic acid

The ligand-sensing transcription factor retinoid X receptor (RXR) is the universal heterodimer partner of nuclear receptors and involved in multiple physiological processes. Its pharmacological modulation holds therapeutic potential in cancer and neurodegeneration but many available RXR ligands lack specificity. The sesquiterpenoid valerenic acid has been identified as RXR agonist with unprecedented subtype and homodimer preference. Here, we identified simplified mimetics of the complex natural product by rational design and virtual screening that exhibited similar activity profiles on RXR and informed about structural elements contributing to the favorable activity.

Discovery of small molecules from natural compound databases as potent retinoid X alpha receptor agonists to treat Alzheimer's disease

Alzheimer's is characterized as a progressive neurodegenerative disease due to beta-amyloid accumulation in the brain. Some previous studies reported that RXR agonists could be effective in the treatment of Alzheimer's disease. There are currently numerous attempts being made to discover a natural RXR agonist that is more potent than 9-cis-retinoic acid (9CR). One of the most efficient resources for finding high-potential compounds is natural databases. In this study, 81215 compounds from the IB screen library as natural databases were docked against the RXR-alpha binding site. The best compounds discovered interact with the RXR-alpha binding site with a lower binding energy (-11 to -13 kcal/mol) than the binding energy of -10.94 kcal/mol for 9-cis, which means that these compounds could interact stronger with RXR-alpha than 9CR. All selected compounds could pass the blood-brain barrier. Physiochemical properties assessment indicated that all compounds passed Lipinski's rule and had the potential to be oral drug candidates. The stability of protein-ligand complexes during a timescale of 100 ns by Molecular Dynamics simulation demonstrated that all compounds could effectively interact with the RXR binding site. The molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) represented that all selected hit compounds had a better binding affinity to the alpha RXR binding site compared to 9CR, which means these hit compounds had potential drug candidates for the treatment of Alzheimer's disease. However, experimental assessment is needed to validate this result.Communicated by Ramaswamy H. Sarma.

Structure-Guided Design of a Highly Potent Partial RXR Agonist with Superior Physicochemical Properties

Retinoid X receptors (RXRs, NR2B1-3) hold therapeutic potential in oncology, neurodegeneration, and metabolic diseases, but traditional RXR agonists mimicking the natural ligand 9-cis retinoic acid exhibit poor physicochemical properties, pharmacokinetics, and safety profiles. Improved RXR ligands are needed to exploit RXR modulation as a promising therapeutic concept in various indications beyond its current role in second-line cancer treatment. Here, we report the co-crystal structure of RXR in complex with a novel pyrimidine-based ligand and the structure-informed optimization of this scaffold to highly potent and highly soluble RXR agonists. Focused structure-activity relationship elucidation and rigidization resulted in a substantially optimized partial RXR agonist with low nanomolar potency, no cytotoxic activity, and very favorable physicochemical properties highlighting this promising scaffold for the development of next-generation RXR targeting drugs.

Structural Fusion of Natural and Synthetic Ligand Features Boosts RXR Agonist Potency

The retinoid X receptors (RXRs) are ligand-activated transcription factors involved in, for example, differentiation and apoptosis regulation. Currently used reference RXR agonists suffer from insufficient specificity and poor physicochemical properties, and improved tools are needed to capture the unexplored therapeutic potential of RXR. Endogenous vitamin A-derived RXR ligands and the natural product RXR agonist valerenic acid comprise acrylic acid residues with varying substitution patterns to engage the critical ionic contact with the binding site arginine. To mimic and exploit this natural ligand motif, we probed its structural fusion with synthetic RXR modulator scaffolds, which had profound effects on agonist activity and remarkably boosted potency of an oxaprozin-derived RXR agonist chemotype. Bioisosteric replacement of the acrylic acid to overcome its pan-assay interference compounds (PAINS) character enabled the development of a highly optimized RXR agonist chemical probe.

Antitumor activity against human promyelocytic leukemia and in silico studies of some benzoxazines

Cancer is one of the deadliest diseases in the world today, and the incidence of cancer is increasing. Leukemia is a type of blood cancer defined as the uncontrolled proliferation of abnormal leukocytes in the blood and bone marrow. The HL-60 (human promyelocytic leukemia) cell line, derived from a single patient with acute promyelocytic leukemia, provides a unique in vitro model system for studying the cellular and molecular events involved in the proliferation and differentiation of leukemic cells. In this study, antitumor activities on the HL-60 of some of the resynthesized benzoxazine derivatives (BXN-01 and BXN-02) were investigated. The results of in vitro studies obtained were compared a standard drug, etoposide. In vitro results showed that BXN-01 and BXN-02 were found to be extremely effective compared to etoposide (IC50 value: 10 µM) with IC50 values of 5 nM and 25 nM, respectively. Furthermore, molecular docking studies were carried out for preliminary prediction of possible interaction modes between compounds and the active site of the target macromolecules, hTopo IIα, HDAC2, and RXRA. Then, in silico ADME/Tox studies were performed to predict drug-likeness and pharmacokinetic properties of BXN-01 and BXN-02.Communicated by Ramaswamy H. Sarma.

Rational Design of a New RXR Agonist Scaffold Enabling Single-Subtype Preference for RXRα, RXRβ, and RXRγ

The three retinoid X receptor subtypes (RXRα, RXRβ, RXRγ) exhibit critical regulatory roles in cell proliferation and differentiation, metabolism, and inflammation. Due to their importance in nuclear receptor signaling, RXRs are widely distributed and pan-RXR agonists cause adverse effects, but the three highly conserved RXR ligand binding sites render the development of subtype-selective ligands a major challenge. We have fused elements of known RXR ligands to obtain a new RXR agonist chemotype on which minor structural modifications enabled the development of tools with single-subtype preference for RXRα, RXRβ, and RXRγ. Molecular modeling indicated different binding conformations and interaction patterns with the RXR LBDs as factors of preferential binding. In a phenotypic adipocyte differentiation experiment, only the RXRα preferential tool enhanced the adipogenic effects of pioglitazone, suggesting this subtype as particularly relevant in adipogenesis and highlighting the set of subtype-preferential RXR agonist tools as suitable for functional cellular studies.

Development of β,β-Dibrominated Secondary Enamides and Their Application to the Synthesis of 5-Br Oxazoles

Herein, we report a base promoted dibromination of enamides using CBr₄ as a bromine source to provide expedient access to β,β-dibrominated secondary enamides. Preliminary synthetic application study shows that these novel products can be readily transformed to 5-Br oxazoles via Cu(I) catalyzed intramolecular cyclization in good yields.

Teratogenicity and Fetal-Transfer Assessment of the Retinoid X Receptor Agonist Bexarotene

Bexarotene, a retinoid X receptor (RXR) agonist, is used to treat cutaneous T-cell lymphoma, and drug repositioning research has also been reported, despite warnings of teratogenicity. However, fetal transfer of bexarotene and its effect on rat fetal bone formation have not been examined. In this study, we conducted a detailed teratogenicity and fetal transferability assessment of bexarotene in rats. Repeated administration of bexarotene during pregnancy caused marked fetal atrophy and bone dysplasia. Although fetal transfer was not detectable by dynamic imaging of [11C]bexarotene by means of positron emission tomography, transfer to the fetus was confirmed by using a gamma counter. Similar levels were found in mother and fetus. In addition, we found that bexarotene was accumulated in the placenta. These findings will be useful for the toxicity assessment of bexarotene as well as for drug discovery research targeting RXR agonists, which are expected to have therapeutic effects in various diseases.

Activity Screening of Fatty Acid Mimetic Drugs Identified Nuclear Receptor Agonists

Fatty acid mimetics (FAM) are bioactive molecules acting through the binding sites of endogenous fatty acid metabolites on enzymes, transporters, and receptors. Due to the special characteristics of these binding sites, FAMs share common chemical features. Pharmacological modulation of fatty acid signaling has therapeutic potential in multiple pathologies, and several FAMs have been developed as drugs. We aimed to elucidate the promiscuity of FAM drugs on lipid-activated transcription factors and tested 64 approved compounds for activation of RAR, PPARs, VDR, LXR, FXR, and RXR. The activity screening revealed nuclear receptor agonism of several FAM drugs and considerable promiscuity of NSAIDs, while other compound classes evolved as selective. These screening results were not anticipated by three well-established target prediction tools, suggesting that FAMs are underrepresented in bioactivity data for model development. The screening dataset may therefore valuably contribute to such tools. Oxaprozin (RXR), tianeptine (PPARδ), mycophenolic acid (RAR), and bortezomib (RAR) exhibited selective agonism on one nuclear receptor and emerged as attractive leads for the selective optimization of side activities. Additionally, their nuclear receptor agonism may contribute relevant and valuable polypharmacology.

Medicinal Chemistry and Chemical Biology of Nurr1 Modulators: An Emerging Strategy in Neurodegeneration

Nuclear receptor related 1 (Nurr1) is a transcription factor with neuroprotective and antineuroinflammatory properties. Observations from genetic studies and human patients support potential of Nurr1 as a therapeutic target in neurodegeneration, but due to a lack of high-quality chemical tools for pharmacological control of Nurr1, its target validation is pending. Nevertheless, considerable progress has recently been made in elucidating structural and functional characteristics of Nurr1, and several ligand scaffolds have been discovered. Here, we analyze Nurr1's structure and mechanisms compared to other nuclear receptors, summarize the known small molecule Nurr1 ligands, and discuss the available evidence for the therapeutic potential of Nurr1 in neurodegeneration.

Development and Profiling of Inverse Agonist Tools for the Neuroprotective Transcription Factor Nurr1

The ligand-sensing transcription factor nuclear receptor related 1 (Nurr1) evolves as an appealing target to treat neurodegenerative diseases. Despite its therapeutic potential observed in various rodent models, potent modulators for Nurr1 are lacking as pharmacological tools. Here, we report the structure-activity relationship and systematic optimization of indole-based inverse Nurr1 agonists. Optimized analogues decreased the receptor's intrinsic transcriptional activity by up to more than 90% and revealed preference for inhibiting Nurr1 monomer activity. In orthogonal cell-free settings, we detected displacement of NCoRs and disruption of the Nurr1 homodimer as molecular modes of action. The inverse Nurr1 agonists reduced the expression of Nurr1-regulated genes in T98G cells, and treatment with an inverse Nurr1 agonist mimicked the effect of Nurr1 silencing on interleukin-6 release from LPS-stimulated human astrocytes. The indole-based inverse Nurr1 agonists valuably extend the toolbox of Nurr1 modulators to further probe the role of Nurr1 in neuroinflammation, cancer, and beyond.