Proteopedia - User contributions [en]

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T17:24:27Z

Akash Bhadra:

== Introduction ==
<StructureSection load='1stp' size='340' side='right' caption='Notum crystallized with fragment 718' scene=''>
Wnt signalling is implicated in processes involved in animal embryonic development, adult tissue homeostasis, and regeneration. <ref>PMID: 35297539</ref> As the enzyme Notum can render Wnt inactive, it is a biologically and medically important target. In ''Structural Analysis and Development of Notum Fragment Screening Hits''<ref>DOI: 10.1021/acschemneuro.2c00325</ref>, the authors aim to discover small-molecule inhibitors of Notum, which suppresses Wnt signaling by removing a lipid modification from Wnt proteins.

== Biological role of the Wnt pathway ==

Signalling proteins are used by cells during development and adult homeostasis to facilitate communication and coordinate their activities. Wnt is a family of such signalling pathways, which are important as they represent links between normal development and tumorigenesis, and Wn proteins control a wide range of physiological functions, such as vertebrate axis specification, stem cell maintenance, and synaptogenesis. <ref> PMID: 33783220</ref>

Wnt ligands bind Frizzled receptors and co-receptors (such as LRP5/6) to stabilize β-catenin and direct context-dependent transcriptional programs that control proliferation, differentiation and morphogenesis. <ref> DOI: 10.1038/nature14259</ref>

Problems in Wnt signalling are associated with various diseases, including cancer, vascular disease, Alzheimer’s disease, and developmental defects.

== Notum significance in Wnt signalling ==

Notum is a negative regulator in both development and adult tissues. Notum is a secreted carboxylesterase that plays a key extracellular role in shaping Wnt signaling domains. It specifically removes the O-linked palmitoleate from Wnt ligands, a lipid modification required for receptor engagement. By deacylating Wnt proteins, Notum suppresses their signaling capacity, thereby modulating morphogen gradients and restraining Wnt-dependent proliferation. This enzymatic activity was structurally established in work showing how Notum accommodates the Wnt lipid within its catalytic pocket and catalyzes its hydrolysis.

As suppression or elevation in Wnt signalling is implicated in disease, Notum inhibition is investigated for therapeutic implementations. In osteoporosis and age-related bone loss, restoring Wnt activity through Notum inhibition has been shown to increase bone formation. In Alzheimer’s disease, where Wnt signaling is reduced, Notum inhibitors promote neurogenesis and progenitor activity. In colorectal cancer, Notum is often overexpressed in APC-mutant tumors, and inhibiting Notum can counteract tumor-driven Wnt dysregulation. Observed effects of Notum inhibition include enhanced bone density, improved neural progenitor responses, and rejuvenation of stem-cell compartments.

Notum is suitable for structure-guided drug design as it posses an enzymatic pocket that binds the palmitoleate group of Wnt proteins. This pocket presents multiple sub-regions that fragments or small molecules can occupy. Notum also readily forms high-quality crystals. These features make Notum a strong candidate for crystallographic fragment screening.

== Screening for Notum binding fragments ==

In the study ''Structural Analysis and Development of Notum Fragment Screening Hits'', the authors used an X-ray crystallographic fragment screen to identify chemical starting points for Notum inhibitor development. A total of 768 datasets were collected, leading to 61 initial candidates, with 59 confirmed fragment hits after filtering. 58 of these fragments bound within the Notum enzymatic pocket, while one fragment, bound at three distinct non-pocket sites.

Several fragments clustered in the central pocket region associated with stronger inhibition, including fragments 7, 15, 16, and 24. Fragment 7 (a 1-phenyl-1,2,3-triazole) became a lead and ultimately produced optimized analogues, including an inhibitor with an IC₅₀ of 0.0067 μM. 7BCE is an example from the structural dataset generated from this screen and represents Notum bound to a fragment hit. The results demonstrate the value of fragment-based screening for generating chemically tractable leads and provide a foundation for ongoing Notum inhibitor development.

</StructureSection>
== References ==
<references/>

Page made as part of the course BI3323-Aug2025.

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T17:23:33Z

Akash Bhadra:

== Introduction to BI3323-Aug2025 ==
<StructureSection load='1stp' size='340' side='right' caption='Notum crystallized with fragment 718' scene=''>
Wnt signalling is implicated in processes involved in animal embryonic development, adult tissue homeostasis, and regeneration. <ref>PMID: 35297539</ref> As the enzyme Notum can render Wnt inactive, it is a biologically and medically important target. In ''Structural Analysis and Development of Notum Fragment Screening Hits''<ref>DOI: 10.1021/acschemneuro.2c00325</ref>, the authors aim to discover small-molecule inhibitors of Notum, which suppresses Wnt signaling by removing a lipid modification from Wnt proteins.

== Biological role of the Wnt pathway ==

Signalling proteins are used by cells during development and adult homeostasis to facilitate communication and coordinate their activities. Wnt is a family of such signalling pathways, which are important as they represent links between normal development and tumorigenesis, and Wn proteins control a wide range of physiological functions, such as vertebrate axis specification, stem cell maintenance, and synaptogenesis. <ref> PMID: 33783220</ref>

Wnt ligands bind Frizzled receptors and co-receptors (such as LRP5/6) to stabilize β-catenin and direct context-dependent transcriptional programs that control proliferation, differentiation and morphogenesis. <ref> DOI: 10.1038/nature14259</ref>

Problems in Wnt signalling are associated with various diseases, including cancer, vascular disease, Alzheimer’s disease, and developmental defects.

== Notum significance in Wnt signalling ==

Notum is a negative regulator in both development and adult tissues. Notum is a secreted carboxylesterase that plays a key extracellular role in shaping Wnt signaling domains. It specifically removes the O-linked palmitoleate from Wnt ligands, a lipid modification required for receptor engagement. By deacylating Wnt proteins, Notum suppresses their signaling capacity, thereby modulating morphogen gradients and restraining Wnt-dependent proliferation. This enzymatic activity was structurally established in work showing how Notum accommodates the Wnt lipid within its catalytic pocket and catalyzes its hydrolysis.

As suppression or elevation in Wnt signalling is implicated in disease, Notum inhibition is investigated for therapeutic implementations. In osteoporosis and age-related bone loss, restoring Wnt activity through Notum inhibition has been shown to increase bone formation. In Alzheimer’s disease, where Wnt signaling is reduced, Notum inhibitors promote neurogenesis and progenitor activity. In colorectal cancer, Notum is often overexpressed in APC-mutant tumors, and inhibiting Notum can counteract tumor-driven Wnt dysregulation. Observed effects of Notum inhibition include enhanced bone density, improved neural progenitor responses, and rejuvenation of stem-cell compartments.

Notum is suitable for structure-guided drug design as it posses an enzymatic pocket that binds the palmitoleate group of Wnt proteins. This pocket presents multiple sub-regions that fragments or small molecules can occupy. Notum also readily forms high-quality crystals. These features make Notum a strong candidate for crystallographic fragment screening.

== Screening for Notum binding fragments ==

In the study ''Structural Analysis and Development of Notum Fragment Screening Hits'', the authors used an X-ray crystallographic fragment screen to identify chemical starting points for Notum inhibitor development. A total of 768 datasets were collected, leading to 61 initial candidates, with 59 confirmed fragment hits after filtering. 58 of these fragments bound within the Notum enzymatic pocket, while one fragment, bound at three distinct non-pocket sites.

Several fragments clustered in the central pocket region associated with stronger inhibition, including fragments 7, 15, 16, and 24. Fragment 7 (a 1-phenyl-1,2,3-triazole) became a lead and ultimately produced optimized analogues, including an inhibitor with an IC₅₀ of 0.0067 μM. 7BCE is an example from the structural dataset generated from this screen and represents Notum bound to a fragment hit. The results demonstrate the value of fragment-based screening for generating chemically tractable leads and provide a foundation for ongoing Notum inhibitor development.

</StructureSection>
== References ==
<references/>

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T17:16:09Z

Akash Bhadra:

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T17:14:22Z

Akash Bhadra:

== Introduction ==
<StructureSection load='1stp' size='340' side='right' caption='Notum crystallized with fragment 718' scene=''>
Wnt signalling is implicated in processes involved in animal embryonic development, adult tissue homeostasis, and regeneration. <ref>PMID: 35297539</ref> As the enzyme Notum can render Wnt inactive, it is a biologically and medically important target. In ''Structural Analysis and Development of Notum Fragment Screening Hits''<ref>DOI: 10.1021/acschemneuro.2c00325</ref>, the authors aim to discover small-molecule inhibitors of Notum, which suppresses Wnt signaling by removing a lipid modification from Wnt proteins.

== Biological role of the Wnt pathway ==

Signalling proteins are used by cells during development and adult homeostasis to facilitate communication and coordinate their activities. Wnt is a family of such signalling pathways, which are important as they represent links between normal development and tumorigenesis, and Wn proteins control a wide range of physiological functions, such as vertebrate axis specification, stem cell maintenance, and synaptogenesis. <ref> PMID: 33783220</ref>

Wnt ligands bind Frizzled receptors and co-receptors (such as LRP5/6) to stabilize β-catenin and direct context-dependent transcriptional programs that control proliferation, differentiation and morphogenesis. <ref> DOI: 10.1038/nature14259</ref>

Problems in Wnt signalling are associated with various diseases, including cancer, vascular disease, Alzheimer’s disease, and developmental defects.

== Notum significance in Wnt signalling ==

Notum is a negative regulator in both development and adult tissues. Notum is a secreted carboxylesterase that plays a key extracellular role in shaping Wnt signaling domains. It specifically removes the O-linked palmitoleate from Wnt ligands, a lipid modification required for receptor engagement. By deacylating Wnt proteins, Notum suppresses their signaling capacity, thereby modulating morphogen gradients and restraining Wnt-dependent proliferation. This enzymatic activity was structurally established in work showing how Notum accommodates the Wnt lipid within its catalytic pocket and catalyzes its hydrolysis.

As suppression or elevation in Wnt signalling is implicated in disease, Notum inhibition is investigated for therapeutic implementations. In osteoporosis and age-related bone loss, restoring Wnt activity through Notum inhibition has been shown to increase bone formation. In Alzheimer’s disease, where Wnt signaling is reduced, Notum inhibitors promote neurogenesis and progenitor activity. In colorectal cancer, Notum is often overexpressed in APC-mutant tumors, and inhibiting Notum can counteract tumor-driven Wnt dysregulation. Observed effects of Notum inhibition include enhanced bone density, improved neural progenitor responses, and rejuvenation of stem-cell compartments.

Notum is suitable for structure-guided drug design as it posses an enzymatic pocket that binds the palmitoleate group of Wnt proteins. This pocket presents multiple sub-regions that fragments or small molecules can occupy. Notum also readily forms high-quality crystals. These features make Notum a strong candidate for crystallographic fragment screening.

== Screening for Notum binding fragments ==

In the study ''Structural Analysis and Development of Notum Fragment Screening Hits'', the authors used an X-ray crystallographic fragment screen to identify chemical starting points for Notum inhibitor development. A total of 768 datasets were collected, leading to 61 initial candidates, with 59 confirmed fragment hits after filtering. 58 of these fragments bound within the Notum enzymatic pocket, while one fragment, bound at three distinct non-pocket sites. The screen revealed diverse binding modes that overlapped with the natural palmitoleate lipid site, and many hits showed measurable inhibitory activity. Several fragments clustered in the central pocket region associated with stronger inhibition, including fragments 7, 15, 16, and 24. Fragment 7 (a 1-phenyl-1,2,3-triazole) became a key lead and ultimately produced optimized analogues, including an inhibitor with an IC₅₀ of 0.0067 μM. The structural dataset generated from this screen is extensive, and one example structure is PDB entry 7BCE, which represents Notum bound to a fragment hit. Together, the results demonstrate the value of fragment-based screening for generating chemically tractable leads and provide a foundation for ongoing Notum inhibitor development.

</StructureSection>
== References ==
<references/>

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T17:05:12Z

Akash Bhadra:

== Introduction ==
<StructureSection load='1stp' size='340' side='right' caption='Notum crystallized with fragment 718' scene=''>
Wnt signalling is implicated in processes involved in animal embryonic development, adult tissue homeostasis, and regeneration. <ref>PMID: 35297539</ref> As the enzyme Notum can render Wnt inactive, it is a biologically and medically important target. ''In Structural Analysis and Development of Notum Fragment Screening Hits''<ref>DOI: 10.1021/acschemneuro.2c00325</ref>, the authors aim to discover small-molecule inhibitors of Notum, which suppresses Wnt signaling by removing a lipid modification from Wnt proteins.

== Biological role of the Wnt pathway ==

Signalling proteins are used by cells during development and adult homeostasis to facilitate communication and coordinate their activities. Wnt is a family of such signalling pathways, which are important as they represent links between normal development and tumorigenesis, and Wn proteins control a wide range of physiological functions, such as vertebrate axis specification, stem cell maintenance, and synaptogenesis. <ref> PMID: 33783220</ref>

Wnt ligands bind Frizzled receptors and co-receptors (such as LRP5/6) to stabilize β-catenin and direct context-dependent transcriptional programs that control proliferation, differentiation and morphogenesis. <ref> DOI: 10.1038/nature14259</ref>

Problems in Wnt signalling are associated with various diseases, including cancer, vascular disease, Alzheimer’s disease, and developmental defects.

== Notum significance in Wnt signalling ==

Notum is a negative regulator in both development and adult tissues. Notum is a secreted carboxylesterase that plays a key extracellular role in shaping Wnt signaling domains. It specifically removes the O-linked palmitoleate from Wnt ligands, a lipid modification required for receptor engagement. By deacylating Wnt proteins, Notum suppresses their signaling capacity, thereby modulating morphogen gradients and restraining Wnt-dependent proliferation. This enzymatic activity was structurally established in work showing how Notum accommodates the Wnt lipid within its catalytic pocket and catalyzes its hydrolysis.

As suppression or elevation in Wnt signalling is implicated in disease, Notum inhibition is investigated for therapeutic implementations. In osteoporosis and age-related bone loss, restoring Wnt activity through Notum inhibition has been shown to increase bone formation. In Alzheimer’s disease, where Wnt signaling is reduced, Notum inhibitors promote neurogenesis and progenitor activity. In colorectal cancer, Notum is often overexpressed in APC-mutant tumors, and inhibiting Notum can counteract tumor-driven Wnt dysregulation. Observed effects of Notum inhibition include enhanced bone density, improved neural progenitor responses, and rejuvenation of stem-cell compartments.

Notum is suitable for structure-guided drug design as it posses an enzymatic pocket that binds the palmitoleate group of Wnt proteins. This pocket presents multiple sub-regions that fragments or small molecules can occupy. Notum also readily forms high-quality crystals. These features make Notum a strong candidate for crystallographic fragment screening.

== Notum ==

== Structural highlights ==

</StructureSection>
== References ==
<references/>

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T16:32:11Z

Akash Bhadra:

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T16:28:26Z

Akash Bhadra:

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T15:59:38Z

Akash Bhadra:

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T15:24:58Z

Akash Bhadra:

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T14:54:05Z

Akash Bhadra:

== BI3323-Aug2025 Assignment ==
<StructureSection load='1stp' size='340' side='right' caption='Notum crystallized with fragment 718' scene=''>
Wnt signalling is implicated in processes involved in animal embryonic development, adult tissue homeostasis, and regeneration. <ref>PMID: 35297539</ref> As the enzyme Notum can render Wnt inactive, it is a biologically and medically important target. In Structural Analysis and Development of Notum Fragment Screening Hits<ref>DOI: 10.1021/acschemneuro.2c00325</ref>, the authors aim to discover small-molecule inhibitors of Notum, which suppresses Wnt signaling by removing a lipid modification from Wnt proteins.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

<scene name='10/1096867/7bce/1'>Notum fragment</scene>

</StructureSection>
== References ==
<references/>

User:Akash Bhadra

2025-11-30T13:52:13Z

Akash Bhadra:

* Full Real Name: Akash (Asmita) Bhadra

* Position: BS Student

* Institution (NO ABBREVIATIONS): Indian Institute of Science, Education and Research, Pune

* City, State/Province, Country: Pune, Maharashtra, India

* Field of Expertise or Study: Computational structural biology; molecular biophysics

* [[User:Akash_Bhadra/Structural_Analysis_and_Development_of_Notum_Fragment_Screening_Hits|BI3323_Aug2025: Structural Analysis and Development of Notum Fragment Screening Hits]]

User:Akash Bhadra

2025-11-30T13:50:38Z

Akash Bhadra:

* Full Real Name: Akash (Asmita) Bhadra

* Position: BS Student

* Institution (NO ABBREVIATIONS): Indian Institute of Science, Education and Research, Pune

* City, State/Province, Country: Pune, Maharashtra, India

* Field of Expertise or Study: Computational structural biology; molecular biophysics

* [[User:Akash_Bhadra/Structural_Analysis_and_Development_of_Notum_Fragment_Screening_Hits|Structural Analysis and Development of Notum Fragment Screening Hits]]

User:Akash Bhadra

2025-11-30T12:52:46Z

Akash Bhadra:

* Full Real Name: Akash (Asmita) Bhadra

* Position: BS Student

* Institution (NO ABBREVIATIONS): Indian Institute of Science, Education and Research, Pune

* City, State/Province, Country: Pune, Maharashtra, India

* Field of Expertise or Study: Computational structural biology; molecular biophysics

* [Structural Analysis and Development of Notum Fragment Screening Hits | https://proteopedia.org/wiki/index.php/User:Akash_Bhadra/Structural_Analysis_and_Development_of_Notum_Fragment_Screening_Hits]

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T12:51:30Z

Akash Bhadra:

== BI3323-Aug2025 Assignment ==
<StructureSection load='1stp' size='340' side='right' caption='Notum crystallized with fragment 718' scene=''>
Wnt signalling is implicated in processes involved in animal embryonic development, adult tissue homeostasis, and regeneration. <ref>PMID: 35297539</ref> As the enzyme Notum can render Wnt inactive, it is a biologically and medically important target. In Structural Analysis and Development of Notum Fragment Screening Hits, the authors aim to discover small-molecule inhibitors of Notum, which suppresses Wnt signaling by removing a lipid modification from Wnt proteins.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

<scene name='10/1096867/7bce/1'>Notum fragment</scene>

</StructureSection>
== References ==
<references/>

User:Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T09:17:50Z

Akash Bhadra: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Akash Bhadra/Structural Analysis and Development of Notum Fragment Screening Hits'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T09:14:10Z

Akash Bhadra: Removing all content from page

Structural Analysis and Development of Notum Fragment Screening Hits

2025-11-30T08:23:45Z

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Structural Analysis and Development of Notum Fragment Screening Hits'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Akash Bhadra

2025-11-30T08:15:28Z

Akash Bhadra: