Probing Peptidoglycan Synthesis in the Gut Commensal Akkermansia muciniphila with Bioorthogonal Chemical Reporters
Chembiochem. 2024 Apr 30:e202400037. doi: 10.1002/cbic.202400037. Online ahead of print.ABSTRACTOur gut microbiota directly influences human physiology in health and disease. The myriad of surface glycoconjugates in both the bacterial cell envelope and our gut cells dominate the microbiota-host interface and play a critical role in host response and microbiota homeostasis. Among these, peptidoglycan is the basic glycan polymer offering the cell rigidity and a basis on which many other glycoconjugates are anchored. To directly study peptidoglycan in gut commensals and obtain the molecular insight required to understand thei...
Source: Chembiochem - April 30, 2024 Category: Biochemistry Authors: Tjerk Sminia Steven Aalvink Hanna de Jong Marcel Tempelaars Han Zuilhof Tjakko Abee Willem de Vos Hanne Tytgat Tom Wennekes Source Type: research
Task-similarity is a crucial factor for few-shot meta-learning of structure-activity relationships
In this study, we assessed the effectiveness of two different meta-learning methods, namely model-agnostic meta-learning (MAML) and adaptive deep kernel fitting (ADKF), specifically in the regression setting. We investigated how factors such as dataset size and the similarity of training tasks impact predictability. The results indicate that ADKF significantly outperformed both MAML and a single-task baseline model on the inhibition data. However, the performance of ADKF varied across different test tasks. Our findings suggest that considerable enhancements in performance can be anticipated primarily when the task of inter...
Source: Chembiochem - April 29, 2024 Category: Biochemistry Authors: Alexander K ötter Stephan Allenspach Christoph Grebner Hans Matter Jan Hiss Gisbert Schneider Gerhard Hessler Source Type: research
Binding and Stabilization of a Semiquinone Radical by an artificial Metalloenzyme containing a Binuclear copper (II) cofactor
Chembiochem. 2024 Apr 29:e202400139. doi: 10.1002/cbic.202400139. Online ahead of print.ABSTRACTA binuclear Cu(II) cofactor was covalently bound to a lauric acid anchor. The resulting conjugate was characterized then combined with beta-lactoglobulin (βLG) to generate a new biohybrid following the so-called "Trojan horse" strategy. This biohybrid was examined for its effectiveness in the oxidation of a catechol derivative to the corresponding quinone. The resulting biohybrid did not exhibit the sought after catecholase activity, likely due to its ability to bind and stabilize the semiquinone radical intermediate DTB-SQ. Th...
Source: Chembiochem - April 29, 2024 Category: Biochemistry Authors: R émy Gay Yannick Masson Wadih Ghattas Guillermo A Oliveira Udry Christian Herrero Agathe Urvoas Jean-Pierre Mahy R émy Ricoux Source Type: research
A Naphthalimide based "Turn-ON" probe for wash-free imaging of lipid-droplet in living cells with an excellent selectivity
Chembiochem. 2024 Apr 29:e202400270. doi: 10.1002/cbic.202400270. Online ahead of print.ABSTRACTThe impacts of dimethylation of 4-Amino-1,8- Naphthalimide (ANI) on its photophysical properties are reported. The resulting 4-DiMe-ANI displays completely different fluorescence properties, conferring it ability to selectively label lipid droplets in living cells. A comprehensive photophysical study revealed that this selectivity arises from an Internal Charge Transfer favored in lipophilic media to the detriment of a non-emissive TICT in more polar media. This results in a very high "LDs/Cytosol" signal ratio, enabling LDs to ...
Source: Chembiochem - April 29, 2024 Category: Biochemistry Authors: Laurane Michel Philippe Durand Arnaud Chevalier Source Type: research
Task-similarity is a crucial factor for few-shot meta-learning of structure-activity relationships
In this study, we assessed the effectiveness of two different meta-learning methods, namely model-agnostic meta-learning (MAML) and adaptive deep kernel fitting (ADKF), specifically in the regression setting. We investigated how factors such as dataset size and the similarity of training tasks impact predictability. The results indicate that ADKF significantly outperformed both MAML and a single-task baseline model on the inhibition data. However, the performance of ADKF varied across different test tasks. Our findings suggest that considerable enhancements in performance can be anticipated primarily when the task of inter...
Source: Chembiochem - April 29, 2024 Category: Biochemistry Authors: Alexander K ötter Stephan Allenspach Christoph Grebner Hans Matter Jan Hiss Gisbert Schneider Gerhard Hessler Source Type: research
Binding and Stabilization of a Semiquinone Radical by an artificial Metalloenzyme containing a Binuclear copper (II) cofactor
Chembiochem. 2024 Apr 29:e202400139. doi: 10.1002/cbic.202400139. Online ahead of print.ABSTRACTA binuclear Cu(II) cofactor was covalently bound to a lauric acid anchor. The resulting conjugate was characterized then combined with beta-lactoglobulin (βLG) to generate a new biohybrid following the so-called "Trojan horse" strategy. This biohybrid was examined for its effectiveness in the oxidation of a catechol derivative to the corresponding quinone. The resulting biohybrid did not exhibit the sought after catecholase activity, likely due to its ability to bind and stabilize the semiquinone radical intermediate DTB-SQ. Th...
Source: Chembiochem - April 29, 2024 Category: Biochemistry Authors: R émy Gay Yannick Masson Wadih Ghattas Guillermo A Oliveira Udry Christian Herrero Agathe Urvoas Jean-Pierre Mahy R émy Ricoux Source Type: research
A Naphthalimide based "Turn-ON" probe for wash-free imaging of lipid-droplet in living cells with an excellent selectivity
Chembiochem. 2024 Apr 29:e202400270. doi: 10.1002/cbic.202400270. Online ahead of print.ABSTRACTThe impacts of dimethylation of 4-Amino-1,8- Naphthalimide (ANI) on its photophysical properties are reported. The resulting 4-DiMe-ANI displays completely different fluorescence properties, conferring it ability to selectively label lipid droplets in living cells. A comprehensive photophysical study revealed that this selectivity arises from an Internal Charge Transfer favored in lipophilic media to the detriment of a non-emissive TICT in more polar media. This results in a very high "LDs/Cytosol" signal ratio, enabling LDs to ...
Source: Chembiochem - April 29, 2024 Category: Biochemistry Authors: Laurane Michel Philippe Durand Arnaud Chevalier Source Type: research
Role of Amyloidogenic and Non-Amyloidogenic Protein Spaces in Neurodegenerative Diseases and Their Mitigation Using Theranostic Agents
Chembiochem. 2024 Apr 26:e202400224. doi: 10.1002/cbic.202400224. Online ahead of print.ABSTRACTNeurodegenerative diseases (NDDs) refer to a complex heterogeneous group of diseases which are associated with the accumulation of amyloid fibrils or plaques in the brain leading to progressive loss of neuronal functions. Alzheimer's disease is one of the major NDD responsible for 60-80% of all dementia cases. Currently, there are no curative or disease-reversing/modifying molecules for NDDs except a few such as donepezil, rivastigmine, galantamine, carbidopa and levodopa which treat the disease-associated-symptoms. Similarly, t...
Source: Chembiochem - April 26, 2024 Category: Biochemistry Authors: Kapali Suri Madhu Ramesh Mansi Bhandari Vishakha Gupta Virendra Kumar Thimmaiah Govindaraju N Arul Murugan Source Type: research
Amodiaquine Nonspecifically Binds Double Stranded and Three-Way Junction DNA Structures
Chembiochem. 2024 Apr 26:e202400116. doi: 10.1002/cbic.202400116. Online ahead of print.ABSTRACTThe 4-aminoquinoline class of compounds includes the important antimalarial compounds amodiaquine and chloroquine. Despite their medicinal importance, the mode of action of these compounds is poorly understood. In a previous study we observed these compounds, as well as quinine and mefloquine, tightly bind the DNA cocaine-binding aptamer. Here, we further explore the range of nucleic acid structures bound by these compounds. To gauge a wide range of binding affinities, we used isothermal titration calorimetry to explore high aff...
Source: Chembiochem - April 26, 2024 Category: Biochemistry Authors: Sladjana Slavkovic Aron Shoara Yunus Kaiyum Zachary Churcher Tao Liu Lena Simine Philip Johnson Source Type: research
Protein engineering of lipase A from Candida antarctica to improve esterification of tertiary alcohols
Chembiochem. 2024 Apr 26:e202400082. doi: 10.1002/cbic.202400082. Online ahead of print.ABSTRACTChiral tertiary alcohols are important organic compounds in science as well as in industry. However, their preparation in enantiomerically pure form is still a challenge due to their complex structure and steric hindrances compared with primary and secondary alcohols, so kinetic resolution could be an attractive approach. Lipase A from Candida antarctica (CAL-A) has been shown to catalyze the enantioselective esterification of various tertiary alcohols with excellent enantioselectivity but low activity. Here we report a mutagene...
Source: Chembiochem - April 26, 2024 Category: Biochemistry Authors: Karla Wagner Anke Hummel Jianing Yang Satoshi Horino Kyohei Kanomata Shuji Akai Harald Gr öger Source Type: research
Role of Amyloidogenic and Non-Amyloidogenic Protein Spaces in Neurodegenerative Diseases and Their Mitigation Using Theranostic Agents
Chembiochem. 2024 Apr 26:e202400224. doi: 10.1002/cbic.202400224. Online ahead of print.ABSTRACTNeurodegenerative diseases (NDDs) refer to a complex heterogeneous group of diseases which are associated with the accumulation of amyloid fibrils or plaques in the brain leading to progressive loss of neuronal functions. Alzheimer's disease is one of the major NDD responsible for 60-80% of all dementia cases. Currently, there are no curative or disease-reversing/modifying molecules for NDDs except a few such as donepezil, rivastigmine, galantamine, carbidopa and levodopa which treat the disease-associated-symptoms. Similarly, t...
Source: Chembiochem - April 26, 2024 Category: Biochemistry Authors: Kapali Suri Madhu Ramesh Mansi Bhandari Vishakha Gupta Virendra Kumar Thimmaiah Govindaraju N Arul Murugan Source Type: research
Amodiaquine Nonspecifically Binds Double Stranded and Three-Way Junction DNA Structures
Chembiochem. 2024 Apr 26:e202400116. doi: 10.1002/cbic.202400116. Online ahead of print.ABSTRACTThe 4-aminoquinoline class of compounds includes the important antimalarial compounds amodiaquine and chloroquine. Despite their medicinal importance, the mode of action of these compounds is poorly understood. In a previous study we observed these compounds, as well as quinine and mefloquine, tightly bind the DNA cocaine-binding aptamer. Here, we further explore the range of nucleic acid structures bound by these compounds. To gauge a wide range of binding affinities, we used isothermal titration calorimetry to explore high aff...
Source: Chembiochem - April 26, 2024 Category: Biochemistry Authors: Sladjana Slavkovic Aron Shoara Yunus Kaiyum Zachary Churcher Tao Liu Lena Simine Philip Johnson Source Type: research
Protein engineering of lipase A from Candida antarctica to improve esterification of tertiary alcohols
Chembiochem. 2024 Apr 26:e202400082. doi: 10.1002/cbic.202400082. Online ahead of print.ABSTRACTChiral tertiary alcohols are important organic compounds in science as well as in industry. However, their preparation in enantiomerically pure form is still a challenge due to their complex structure and steric hindrances compared with primary and secondary alcohols, so kinetic resolution could be an attractive approach. Lipase A from Candida antarctica (CAL-A) has been shown to catalyze the enantioselective esterification of various tertiary alcohols with excellent enantioselectivity but low activity. Here we report a mutagene...
Source: Chembiochem - April 26, 2024 Category: Biochemistry Authors: Karla Wagner Anke Hummel Jianing Yang Satoshi Horino Kyohei Kanomata Shuji Akai Harald Gr öger Source Type: research
Role of Amyloidogenic and Non-Amyloidogenic Protein Spaces in Neurodegenerative Diseases and Their Mitigation Using Theranostic Agents
Chembiochem. 2024 Apr 26:e202400224. doi: 10.1002/cbic.202400224. Online ahead of print.ABSTRACTNeurodegenerative diseases (NDDs) refer to a complex heterogeneous group of diseases which are associated with the accumulation of amyloid fibrils or plaques in the brain leading to progressive loss of neuronal functions. Alzheimer's disease is one of the major NDD responsible for 60-80% of all dementia cases. Currently, there are no curative or disease-reversing/modifying molecules for NDDs except a few such as donepezil, rivastigmine, galantamine, carbidopa and levodopa which treat the disease-associated-symptoms. Similarly, t...
Source: Chembiochem - April 26, 2024 Category: Biochemistry Authors: Kapali Suri Madhu Ramesh Mansi Bhandari Vishakha Gupta Virendra Kumar Thimmaiah Govindaraju N Arul Murugan Source Type: research
Amodiaquine Nonspecifically Binds Double Stranded and Three-Way Junction DNA Structures
Chembiochem. 2024 Apr 26:e202400116. doi: 10.1002/cbic.202400116. Online ahead of print.ABSTRACTThe 4-aminoquinoline class of compounds includes the important antimalarial compounds amodiaquine and chloroquine. Despite their medicinal importance, the mode of action of these compounds is poorly understood. In a previous study we observed these compounds, as well as quinine and mefloquine, tightly bind the DNA cocaine-binding aptamer. Here, we further explore the range of nucleic acid structures bound by these compounds. To gauge a wide range of binding affinities, we used isothermal titration calorimetry to explore high aff...
Source: Chembiochem - April 26, 2024 Category: Biochemistry Authors: Sladjana Slavkovic Aron Shoara Yunus Kaiyum Zachary Churcher Tao Liu Lena Simine Philip Johnson Source Type: research
