Utilizing the growing wealth of chemical reaction data can boost synthesis planning and increase ... more Utilizing the growing wealth of chemical reaction data can boost synthesis planning and increase success rates. Yet, the effectiveness of machine learning tools for retrosynthesis planning and forward reaction prediction relies on accessible, well-curated data presented in a structured format. Although some public and licensed reaction databases exist, they often lack essential information about reaction conditions. To address this issue and promote the principles of findable, accessible, interoperable, and reusable (FAIR) data reporting and sharing, we introduce the Simple User-Friendly Reaction Format (SURF). SURF standardizes the documentation of reaction data through a structured tabular format, requiring only a basic understanding of spreadsheets. This format enables chemists to record the synthesis of molecules in a format that is understandable by both humans and machines, which facilitates seamless sharing and integration directly into machine learning pipelines. SURF files are designed to be interoperable, easily imported into relational databases, and convertible into other formats. This complements existing initiatives like the Open Reaction Database (ORD) and Unified Data Model (UDM). At Roche, SURF plays a crucial role in democratizing FAIR reaction data sharing and expediting the chemical synthesis process.
The diversity of physiological roles of the endocannabinoid system has turned it into an attracti... more The diversity of physiological roles of the endocannabinoid system has turned it into an attractive yet elusive therapeutic target. However, chemical probes with various functionalities could pave the way for a better understanding of the endocannabinoid system at the cellular level. Notably, inverse agonists of CB2R-a key receptor of the endocannabinoid system-lagged behind despite the evidence regarding the therapeutic potential of its antagonism. Herein, we report a matched fluorescent probe pair based on a common chemotype to address and visualize both the active and inactive states of CB2R, selectively. Alongside with extensive cross-validation by flow cytometry and confocal microscopy, we successfully visualize the intracellular localization of CB2R pools in live cells. The synthetic simplicity together with the high CB2R-selectivity and specificity of our probes, turn them into valuable tools in chemical biology and drug development that can benefit the clinical translatability of CB2R-based drug.
CB₂R ligands to treat inflammatory diabetes openaccessgovernment.org/article/cb₂r-ligands-to-trea... more CB₂R ligands to treat inflammatory diabetes openaccessgovernment.org/article/cb₂r-ligands-to-treat-inflammatory-diabetes/168275 Figure 1: Scientific innovations in ECS research and drug discovery that will strongly impact the future discovery of improved and tailor-made CB2R medicines.
We report the structure-based design of cannabinoid receptor type 2 (CB 2 R)selective inverse ago... more We report the structure-based design of cannabinoid receptor type 2 (CB 2 R)selective inverse agonists (S)-1 and (R)-1, which were derived from privileged agonist HU-308 by introduction of a phenyl group at the gem-dimethylheptyl sidechain. Epimer (R)-1 exhibits high affinity for CB 2 R with K d = 39 nM and serves as a platform for the synthesis of a wide variety of probes. Notably, the fluorescent probes, for the first time, retain their inverse agonist functionality, high affinity, and selectivity for CB 2 R independent of linker and fluorophore substitution. Ligands (S)-1, (R)-1, and their derivatives act as inverse agonists in CB 2 R-mediated cAMP as well as G protein recruitment assays, and do not trigger β-arrestin-receptor association. Furthermore, no receptor activation was detected in live cell ERK 1/2 phosphorylation and Ca 2+-release assays. Confocal fluorescence imaging experiments with (R)-7 (Alexa488) and (R)-9 (Alexa647) probes employing BV-2 microglial cells visualized CB 2 R expressed at endogenous levels. Finally, molecular dynamics simulations corroborate the initial docking data in which inverse agonists restrict movement of toggle switch, Trp258 6.48 , and thereby stabilize CB 2 R in its inactive state. The present study
Enhancing the properties of advanced drug candidates is aided by the direct incorporation of spec... more Enhancing the properties of advanced drug candidates is aided by the direct incorporation of specific chemical groups, avoiding the need to construct the entire compound from the ground up. Nevertheless, their chemical intricacy often poses challenges in predicting reactivity for C-H activation reactions and planning their synthesis. We adopted a reaction screening approach that combines high-throughput experimentation (HTE) at a nanomolar scale with computational graph neural networks (GNNs). This approach aims to identify suitable substrates for late-stage C-H alkylation using Minisci-type chemistry. GNNs were trained using experimentally generated reactions derived from in-house HTE and literature data. These trained models were then used to predict, in a forward-looking manner, the coupling of 3180 advanced heterocyclic building blocks with a diverse set of sp 3-rich carboxylic acids. This predictive approach aimed to explore the substrate landscape for Miniscitype alkylations. Promising candidates were chosen, their production was scaled up, and they were subsequently isolated and characterized. This process led to the creation of 30 novel, functionally modified molecules that hold potential for further refinement. These results positively advocate the application of HTE-based machine learning to virtual reaction screening.
The utilization of an activatable, substrate-based probe design in combination with a cellular ta... more The utilization of an activatable, substrate-based probe design in combination with a cellular targeting approach has been rarely explored for cancer imaging on a small-molecule basis, although such probes could benefit from advantages of both concepts. Cysteine proteases like cathepsin S are known to be involved in fundamental processes associated with tumor development and progression and thus are valuable cancer markers. We report the development of a combined dual functional DOTAM-based, RGD-targeted internally quenched fluorescent probe that is activated by cathepsin S. The probe exhibits excellent in vitro activation kinetics which can be fully translated to human cancer cell lines. We demonstrate that the targeted, activatable probe is superior to its nontargeted analog, exhibiting improved uptake into ανβ3-integrin expressing human sarcoma cells (HT1080) and significantly higher resultant fluorescence staining. However, profound activation was also found in cancer cells with a lower integrin expression level, whereas in healthy cells almost no probe activation could be observed, highlighting the high selectivity of our probe toward cancer cells. These auspicious results show the outstanding potential of the dual functionality concept combining a substrate-based probe design with a targeting approach, which could form the basis for highly sensitive and selective in vivo imaging probes.
European journal of medicinal chemistry, Dec 1, 2022
Monoacylglycerol lipase (MAGL) is a gatekeeper in regulating endocannabinoid signaling and has ga... more Monoacylglycerol lipase (MAGL) is a gatekeeper in regulating endocannabinoid signaling and has gained substantial attention as a therapeutic target for neurological disorders. We recently discovered a morpholin-3-one derivative as a novel scaffold for imaging MAGL via positron emission tomography (PET). However, its slow kinetics in vivo hampered the application. In this study, structural optimization was conducted and eleven novel MAGL inhibitors were designed and synthesized. Based on the results from MAGL inhibitory potency, in vitro metabolic stability and surface plasmon resonance assays, we identified compound 7 as a potential MAGL PET tracer candidate. [ 11 C]7 was synthesized via direct 11 CO 2 fixation method and successfully mapped MAGL distribution patterns on rodent brains in in vitro autoradiography. PET studies in mice using [ 11 C]7 demonstrated its improved kinetic profile compared to the lead structure. Its high specificity in vivo was proved by using MAGL KO mice. Although further studies confirmed that [ 11 C]7 is a P-glycoprotein (P-gp) substrate in mice, its low P-gp efflux ratio on cells transfected with human protein suggests that it should not be an issue for the clinical translation of [ 11 C]7 as a novel reversible MAGL PET tracer in human subjects. Overall, [ 11 C]7 ([ 11 C] RO7284390) showed promising results warranting further clinical evaluation.
Leveraging the increasing volume of chemical reaction data can enhance synthesis planning and imp... more Leveraging the increasing volume of chemical reaction data can enhance synthesis planning and improve suc- cess rates. However, machine learning applications for retrosynthesis planning and forward reaction prediction tools depend on having readily available, high-quality data in a structured format. While some public and licensed reaction databases are available, they frequently lack essential information about reaction condi- tions. To address this issue and promote the principles of findable, accessible, interoperable, and reusable (FAIR) data reporting and sharing, we introduce the Simple User-Friendly Reaction Format (SURF). SURF standardizes the documentation of reaction data through a structured tabular format, requiring only a basic understanding of spreadsheets. This format enables chemists to record the synthesis of molecules in a format that is both human- and machine-readable, making it easier to share and integrate directly into machine- learning pipelines. SURF files a...
Monoacylglycerol lipase (MAGL) is one of the key enzymes in the endocannabinoid system. Inhibitio... more Monoacylglycerol lipase (MAGL) is one of the key enzymes in the endocannabinoid system. Inhibition of MAGL has been proposed as an attractive approach for the treatment of various diseases. In this study, we designed and successfully synthesized two series of piperazinyl pyrrolidin-2-one derivatives as novel reversible MAGL inhibitors. (R)-[18F]13 was identified through the preliminary evaluation of two carbon-11-labeled racemic structures [11C]11 and [11C]16. In dynamic positron-emission tomography (PET) scans, (R)-[18F]13 showed a heterogeneous distribution and matched the MAGL expression pattern in the mouse brain. High brain uptake and brain-to-blood ratio were achieved by (R)-[18F]13 in comparison with previously reported reversible MAGL PET radiotracers. Target occupancy studies with a therapeutic MAGL inhibitor revealed a dose-dependent reduction of (R)-[18F]13 accumulation in the mouse brain. These findings indicate that (R)-[18F]13 ([18F]YH149) is a highly promising PET probe for visualizing MAGL non-invasively in vivo and holds great potential to support drug development.
Previous high throughput screening studies led to the discovery of two novel, non-lipid-like chem... more Previous high throughput screening studies led to the discovery of two novel, non-lipid-like chemotypes as Toll-like receptor 4 (TLR4) agonists. One of these chemotypes, the pyrimido[5,4b]indoles, was explored for structure-activity relationship trends relative to production of TLR4 dependent cytokines/chemokines resulting in a semi-optimized lead (compound 1) that provided a starting point for further optimization studies. In this report, compounds belonging to three areas of structural modification were evaluated for biological activity using murine and human TLR4 reporter cells, primary murine bone marrow derived dendritic cells, and human peripheral blood mononuclear cells. The compounds bearing certain aryl groups at the C8 position, such as phenyl (36) and β-naphthyl (39), had potencies significantly greater than compound 1. Compound 36 displayed human TLR4 agonist activity at submicromolar concentrations. The computational analysis suggests that the improved potency of these C8-aryl derivatives may be the result of additional binding interactions at the interface of the TLR4/ myeloid differentiation protein-2 (MD-2) complex.
Her research focuses on epigenetic regulation and its targeting with chemical molecules. She prev... more Her research focuses on epigenetic regulation and its targeting with chemical molecules. She previously directed the Epigenetic Targeting of Cancer (ETaC) unit, a joint public-private laboratory between the
The endocannabinoid (eCB) system is implied in various human diseases ranging from central nervou... more The endocannabinoid (eCB) system is implied in various human diseases ranging from central nervous system to autoimmune disorders. Cannabinoid receptor 2 (CB2R) is an integral component of the eCB system. Yet, the downstream effects elicited by this G protein-coupled receptor upon binding of endogenous or synthetic ligands are insufficiently understood-likely due to the limited arsenal of reliable biological and chemical tools. Herein, we report the design and synthesis of CB2R-selective cannabinoids along with their in vitro pharmacological characterization (binding and functional studies). They combine structural features of HU-308 and AM841 to give chimeric ligands that emerge as potent CB2R agonists with high selectivity over the closely related cannabinoid receptor 1 (CB1R). The synthesis work includes convenient preparation of substituted resorcinols often found in cannabinoids. The utility of the synthetic cannabinoids in this study is showcased by preparation of the most selective high-affinity fluorescent probe for CB2R to date.
Visualizing the anti-inflammatory cannabinoid Type-2 receptor Medicinal chemists describe how sma... more Visualizing the anti-inflammatory cannabinoid Type-2 receptor Medicinal chemists describe how small molecule probes allow for the detection of CB2R, and thereby enable the discovery of novel anti-inflammatory treatments. The G-protein-coupled receptor (GPCR) CB2R (1) is an essential constituent of the endocannabinoid system (ECS), a central lipid signalling system in all vertebrates (2). Preclinical studies have shown that CB2R activation is a general and robust principle to attenuate inflammation and associated tissue injury in a wide variety of pathological conditions. Strong accumulating evidence suggests that diseases such as heart disorders, gastrointestinal, liver, kidney, lung, neurodegenerative or neuroinflammatory diseases, pain, skin pathologies, rheumatoid arthritis, endometriosis and eye diseases might be therapeutically addressable by CB2R (3).
Utilizing the growing wealth of chemical reaction data can boost synthesis planning and increase ... more Utilizing the growing wealth of chemical reaction data can boost synthesis planning and increase success rates. Yet, the effectiveness of machine learning tools for retrosynthesis planning and forward reaction prediction relies on accessible, well-curated data presented in a structured format. Although some public and licensed reaction databases exist, they often lack essential information about reaction conditions. To address this issue and promote the principles of findable, accessible, interoperable, and reusable (FAIR) data reporting and sharing, we introduce the Simple User-Friendly Reaction Format (SURF). SURF standardizes the documentation of reaction data through a structured tabular format, requiring only a basic understanding of spreadsheets. This format enables chemists to record the synthesis of molecules in a format that is understandable by both humans and machines, which facilitates seamless sharing and integration directly into machine learning pipelines. SURF files are designed to be interoperable, easily imported into relational databases, and convertible into other formats. This complements existing initiatives like the Open Reaction Database (ORD) and Unified Data Model (UDM). At Roche, SURF plays a crucial role in democratizing FAIR reaction data sharing and expediting the chemical synthesis process.
The diversity of physiological roles of the endocannabinoid system has turned it into an attracti... more The diversity of physiological roles of the endocannabinoid system has turned it into an attractive yet elusive therapeutic target. However, chemical probes with various functionalities could pave the way for a better understanding of the endocannabinoid system at the cellular level. Notably, inverse agonists of CB2R-a key receptor of the endocannabinoid system-lagged behind despite the evidence regarding the therapeutic potential of its antagonism. Herein, we report a matched fluorescent probe pair based on a common chemotype to address and visualize both the active and inactive states of CB2R, selectively. Alongside with extensive cross-validation by flow cytometry and confocal microscopy, we successfully visualize the intracellular localization of CB2R pools in live cells. The synthetic simplicity together with the high CB2R-selectivity and specificity of our probes, turn them into valuable tools in chemical biology and drug development that can benefit the clinical translatability of CB2R-based drug.
CB₂R ligands to treat inflammatory diabetes openaccessgovernment.org/article/cb₂r-ligands-to-trea... more CB₂R ligands to treat inflammatory diabetes openaccessgovernment.org/article/cb₂r-ligands-to-treat-inflammatory-diabetes/168275 Figure 1: Scientific innovations in ECS research and drug discovery that will strongly impact the future discovery of improved and tailor-made CB2R medicines.
We report the structure-based design of cannabinoid receptor type 2 (CB 2 R)selective inverse ago... more We report the structure-based design of cannabinoid receptor type 2 (CB 2 R)selective inverse agonists (S)-1 and (R)-1, which were derived from privileged agonist HU-308 by introduction of a phenyl group at the gem-dimethylheptyl sidechain. Epimer (R)-1 exhibits high affinity for CB 2 R with K d = 39 nM and serves as a platform for the synthesis of a wide variety of probes. Notably, the fluorescent probes, for the first time, retain their inverse agonist functionality, high affinity, and selectivity for CB 2 R independent of linker and fluorophore substitution. Ligands (S)-1, (R)-1, and their derivatives act as inverse agonists in CB 2 R-mediated cAMP as well as G protein recruitment assays, and do not trigger β-arrestin-receptor association. Furthermore, no receptor activation was detected in live cell ERK 1/2 phosphorylation and Ca 2+-release assays. Confocal fluorescence imaging experiments with (R)-7 (Alexa488) and (R)-9 (Alexa647) probes employing BV-2 microglial cells visualized CB 2 R expressed at endogenous levels. Finally, molecular dynamics simulations corroborate the initial docking data in which inverse agonists restrict movement of toggle switch, Trp258 6.48 , and thereby stabilize CB 2 R in its inactive state. The present study
Enhancing the properties of advanced drug candidates is aided by the direct incorporation of spec... more Enhancing the properties of advanced drug candidates is aided by the direct incorporation of specific chemical groups, avoiding the need to construct the entire compound from the ground up. Nevertheless, their chemical intricacy often poses challenges in predicting reactivity for C-H activation reactions and planning their synthesis. We adopted a reaction screening approach that combines high-throughput experimentation (HTE) at a nanomolar scale with computational graph neural networks (GNNs). This approach aims to identify suitable substrates for late-stage C-H alkylation using Minisci-type chemistry. GNNs were trained using experimentally generated reactions derived from in-house HTE and literature data. These trained models were then used to predict, in a forward-looking manner, the coupling of 3180 advanced heterocyclic building blocks with a diverse set of sp 3-rich carboxylic acids. This predictive approach aimed to explore the substrate landscape for Miniscitype alkylations. Promising candidates were chosen, their production was scaled up, and they were subsequently isolated and characterized. This process led to the creation of 30 novel, functionally modified molecules that hold potential for further refinement. These results positively advocate the application of HTE-based machine learning to virtual reaction screening.
The utilization of an activatable, substrate-based probe design in combination with a cellular ta... more The utilization of an activatable, substrate-based probe design in combination with a cellular targeting approach has been rarely explored for cancer imaging on a small-molecule basis, although such probes could benefit from advantages of both concepts. Cysteine proteases like cathepsin S are known to be involved in fundamental processes associated with tumor development and progression and thus are valuable cancer markers. We report the development of a combined dual functional DOTAM-based, RGD-targeted internally quenched fluorescent probe that is activated by cathepsin S. The probe exhibits excellent in vitro activation kinetics which can be fully translated to human cancer cell lines. We demonstrate that the targeted, activatable probe is superior to its nontargeted analog, exhibiting improved uptake into ανβ3-integrin expressing human sarcoma cells (HT1080) and significantly higher resultant fluorescence staining. However, profound activation was also found in cancer cells with a lower integrin expression level, whereas in healthy cells almost no probe activation could be observed, highlighting the high selectivity of our probe toward cancer cells. These auspicious results show the outstanding potential of the dual functionality concept combining a substrate-based probe design with a targeting approach, which could form the basis for highly sensitive and selective in vivo imaging probes.
European journal of medicinal chemistry, Dec 1, 2022
Monoacylglycerol lipase (MAGL) is a gatekeeper in regulating endocannabinoid signaling and has ga... more Monoacylglycerol lipase (MAGL) is a gatekeeper in regulating endocannabinoid signaling and has gained substantial attention as a therapeutic target for neurological disorders. We recently discovered a morpholin-3-one derivative as a novel scaffold for imaging MAGL via positron emission tomography (PET). However, its slow kinetics in vivo hampered the application. In this study, structural optimization was conducted and eleven novel MAGL inhibitors were designed and synthesized. Based on the results from MAGL inhibitory potency, in vitro metabolic stability and surface plasmon resonance assays, we identified compound 7 as a potential MAGL PET tracer candidate. [ 11 C]7 was synthesized via direct 11 CO 2 fixation method and successfully mapped MAGL distribution patterns on rodent brains in in vitro autoradiography. PET studies in mice using [ 11 C]7 demonstrated its improved kinetic profile compared to the lead structure. Its high specificity in vivo was proved by using MAGL KO mice. Although further studies confirmed that [ 11 C]7 is a P-glycoprotein (P-gp) substrate in mice, its low P-gp efflux ratio on cells transfected with human protein suggests that it should not be an issue for the clinical translation of [ 11 C]7 as a novel reversible MAGL PET tracer in human subjects. Overall, [ 11 C]7 ([ 11 C] RO7284390) showed promising results warranting further clinical evaluation.
Leveraging the increasing volume of chemical reaction data can enhance synthesis planning and imp... more Leveraging the increasing volume of chemical reaction data can enhance synthesis planning and improve suc- cess rates. However, machine learning applications for retrosynthesis planning and forward reaction prediction tools depend on having readily available, high-quality data in a structured format. While some public and licensed reaction databases are available, they frequently lack essential information about reaction condi- tions. To address this issue and promote the principles of findable, accessible, interoperable, and reusable (FAIR) data reporting and sharing, we introduce the Simple User-Friendly Reaction Format (SURF). SURF standardizes the documentation of reaction data through a structured tabular format, requiring only a basic understanding of spreadsheets. This format enables chemists to record the synthesis of molecules in a format that is both human- and machine-readable, making it easier to share and integrate directly into machine- learning pipelines. SURF files a...
Monoacylglycerol lipase (MAGL) is one of the key enzymes in the endocannabinoid system. Inhibitio... more Monoacylglycerol lipase (MAGL) is one of the key enzymes in the endocannabinoid system. Inhibition of MAGL has been proposed as an attractive approach for the treatment of various diseases. In this study, we designed and successfully synthesized two series of piperazinyl pyrrolidin-2-one derivatives as novel reversible MAGL inhibitors. (R)-[18F]13 was identified through the preliminary evaluation of two carbon-11-labeled racemic structures [11C]11 and [11C]16. In dynamic positron-emission tomography (PET) scans, (R)-[18F]13 showed a heterogeneous distribution and matched the MAGL expression pattern in the mouse brain. High brain uptake and brain-to-blood ratio were achieved by (R)-[18F]13 in comparison with previously reported reversible MAGL PET radiotracers. Target occupancy studies with a therapeutic MAGL inhibitor revealed a dose-dependent reduction of (R)-[18F]13 accumulation in the mouse brain. These findings indicate that (R)-[18F]13 ([18F]YH149) is a highly promising PET probe for visualizing MAGL non-invasively in vivo and holds great potential to support drug development.
Previous high throughput screening studies led to the discovery of two novel, non-lipid-like chem... more Previous high throughput screening studies led to the discovery of two novel, non-lipid-like chemotypes as Toll-like receptor 4 (TLR4) agonists. One of these chemotypes, the pyrimido[5,4b]indoles, was explored for structure-activity relationship trends relative to production of TLR4 dependent cytokines/chemokines resulting in a semi-optimized lead (compound 1) that provided a starting point for further optimization studies. In this report, compounds belonging to three areas of structural modification were evaluated for biological activity using murine and human TLR4 reporter cells, primary murine bone marrow derived dendritic cells, and human peripheral blood mononuclear cells. The compounds bearing certain aryl groups at the C8 position, such as phenyl (36) and β-naphthyl (39), had potencies significantly greater than compound 1. Compound 36 displayed human TLR4 agonist activity at submicromolar concentrations. The computational analysis suggests that the improved potency of these C8-aryl derivatives may be the result of additional binding interactions at the interface of the TLR4/ myeloid differentiation protein-2 (MD-2) complex.
Her research focuses on epigenetic regulation and its targeting with chemical molecules. She prev... more Her research focuses on epigenetic regulation and its targeting with chemical molecules. She previously directed the Epigenetic Targeting of Cancer (ETaC) unit, a joint public-private laboratory between the
The endocannabinoid (eCB) system is implied in various human diseases ranging from central nervou... more The endocannabinoid (eCB) system is implied in various human diseases ranging from central nervous system to autoimmune disorders. Cannabinoid receptor 2 (CB2R) is an integral component of the eCB system. Yet, the downstream effects elicited by this G protein-coupled receptor upon binding of endogenous or synthetic ligands are insufficiently understood-likely due to the limited arsenal of reliable biological and chemical tools. Herein, we report the design and synthesis of CB2R-selective cannabinoids along with their in vitro pharmacological characterization (binding and functional studies). They combine structural features of HU-308 and AM841 to give chimeric ligands that emerge as potent CB2R agonists with high selectivity over the closely related cannabinoid receptor 1 (CB1R). The synthesis work includes convenient preparation of substituted resorcinols often found in cannabinoids. The utility of the synthetic cannabinoids in this study is showcased by preparation of the most selective high-affinity fluorescent probe for CB2R to date.
Visualizing the anti-inflammatory cannabinoid Type-2 receptor Medicinal chemists describe how sma... more Visualizing the anti-inflammatory cannabinoid Type-2 receptor Medicinal chemists describe how small molecule probes allow for the detection of CB2R, and thereby enable the discovery of novel anti-inflammatory treatments. The G-protein-coupled receptor (GPCR) CB2R (1) is an essential constituent of the endocannabinoid system (ECS), a central lipid signalling system in all vertebrates (2). Preclinical studies have shown that CB2R activation is a general and robust principle to attenuate inflammation and associated tissue injury in a wide variety of pathological conditions. Strong accumulating evidence suggests that diseases such as heart disorders, gastrointestinal, liver, kidney, lung, neurodegenerative or neuroinflammatory diseases, pain, skin pathologies, rheumatoid arthritis, endometriosis and eye diseases might be therapeutically addressable by CB2R (3).
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Papers by Uwe Grether