ATPase Screening Libraries

ATPases are enzymes that convert ATP to ADP through the hydrolysis of a phosphate bond. There are four different types of ATPases (P, V, F, and ABC types) that operate within biological membranes to ensure moving many different types of ions or molecules across these membranes (Fig. 1) [1]. The energy released during this process is utilized for the catalysis of other cellular reactions. Thus, ATPases are crucial enzymes engaged in energy homeostasis and signal transduction [2]. Also, mutations in these proteins account for numerous diseases, ranging from cancer to those that affect bones (osteoporosis), ears (hearing), eyes (macromolecular degeneration), the heart (hypercholesterolemia/cardiac arrest), immune system (immune deficiency disease), kidney (nephrotoxicity), lungs (cystic fibrosis), pancreas (diabetes and cystic fibrosis), skin (Darier disease), and stomach (ulcers) [1, 3].

Life Chemicals has designed two ATPase Screening Libraries of over 18,200 drug-like screening compounds to boost high-throughput screening (HTS) programs focused on ATPase drug discovery:

• ATPase Focused Library (13,500 compounds)
• ATPase Targeted Library (4,700 compounds)

The compound selection can be customized based on your requirements, cherry picking is available.

Please, contact us at orders@lifechemicals.com for any additional information and price quotations.

For a pre-plated set based on this Screening Library, please explore our Pre-plated Focused Libraries.

Figure 1. Classification of ATPase and its inhibitors [4]

ATPase Focused Library

Life Chemicals has designed its proprietary ATPase Focused Library of over 13,500 drug-like screening compounds with a 2D fingerprint similarity search against two different reference databases, applying the MDL public keys (75-85 % Tanimoto similarity cut-off).

First, the Life Chemicals HTS Compound Collection was screened against 30,000 reference compounds with reported activity values lower than 11 uM by similarity search (85 % Tanimoto similarity cut-off) to provide a set of over 5,000 structurally diverse screening compounds with potential ATPase inhibitory activity against different target types.

The following ATPases were selected as drug targets:

• 26S proteasome non-ATPase regulatory subunit 14
• ATPase family AAA domain-containing protein type 2 and 5
• Cystic fibrosis transmembrane conductance regulator ATPase Activity
• Katanin p60 ATPase-containing subunit A1
• Multidrug resistance-associated protein 1 ATPase Activity
• Potassium-transporting ATPase
• Sodium/potassium-transporting ATPase
• Transitional endoplasmic reticulum ATPase
• V-type proton ATPase subunit c'

Additionally, the HTS Compound Collection was filtered against a reference set of 13,000 biologically active compounds from 127 ATPase-related assays, referring to the data available from patents, scientific publications and other sources (according to the PubChem and ChEMBL databases). As a result, around 8,500 potential ATPase inhibitors were additionally selected, using the 75 % Tanimoto similarity. All data could be traced back to the targets or assays indicated in the column “Target type” or “Description” within the corresponding SD file.

The list of selected targets from this reference set is represented below:

Representative compounds from the ATPase-focused Screening Set

F0543-0207

F0016-0594

F0007-1055

F0012-0499

F0016-0518

F0361-0018

F0570-0041

F0665-0138

F0327-0341

F0381-4714

F0393-0247

F0039-0201

ATPase Targeted Library

• The Life Chemicals team has developed a library of drug-like compounds based on the SP ligand-receptor docking and structure-based virtual screening, taking advantage of Phase (receptor-ligand complex) methods and our proprietary HTS Compound Collection. The results were filtered by binding affinity parameters to check docking (docking score) and also by similarity parameters in terms of the pharmacophore hypothesis related to structure-based virtual screening (PhaseScreenScore). After that, the obtained compounds were filtered according to physicochemical parameters, biological activity, metabolism and/or toxicity, depending on the expediency. These filtering parameters are listed in "Filters used".

  This Set contains 4,700 structurally-diverse molecules picked out by SP ligand-receptor docking and structure-based virtual screening against ATPase-related drug target, using Phase (receptor-ligand complex) methods, with the targets shown below:

  • ATPase p97
  • Vacuolar protein sorting-associated protein 4
    

ATPase p97

ATPase p97 (also known as valosin-containing protein (VCP) in mammals or Cdc48p in S.cerevisiae) is a protein that belongs to the AAA+ ATPase superfamily. It is a highly evolutionarily conserved ATPase in all eukaryotes and archaebacteria. This ATPase is found to be essential in many cellular processes [5]. ATPase p97 comprises six identical subunits (hexamers) arranged in a barrel-like structure. These subunits consist of four domains: N-terminal and C-terminal, which mediate protein-protein interaction and substrate recognition; and two ATPase domains, D1 and D2, which are responsible for binding and hydrolysis of ATP [6-8].

ATPase p97 plays a great role in the quality control of newly synthesized proteins and regulates their degradation in case of detection of "errors" [9]. The action of this protein is characteristic of molecular chaperones [10]. In the ER-associated protein degradation (ERAD) pathway, p97 ATPase is indispensable in ensuring the clearance of misfolded proteins, thereby preventing ER stress and activation of the unfolded protein response (UPR) [11-12]. In addition, p97 ATPase is involved in many other cellular processes, including membrane fusion, vesicle trafficking, DNA repair, cell cycle progression regulation, mitosis, embryogenesis, and organogenesis. Also, it is included in sperm maturation and motility. To perform its diverse functions, the ATPase under discussion interacts with a wide range of adaptor proteins and cofactors [13-18].

ATPase p97 is ubiquitously expressed in various tissues and cell types, reflecting its importance in cellular physiology. It is especially abundant in tissues with high secretory activity, such as the liver and pancreas, and in neural tissues [19]. Dysregulation of p97 ATPase function is associated with several human health problems, including neurodegenerative disorders, cancer, and certain genetic diseases characterized by protein aggregation [20-22].

The functional importance of this target triggered the interest of our cheminformatics team which has resulted in the design of a docking library of more than 1,000 drug-like compounds targeting p97 ATPase.

Key features:

• Method: SP (standard precision) ligand-receptor docking
• X-Ray data used: 5FTJ
• Constraints: no
• Filters used: QikProp properties and descriptors
• Number of compounds selected: 1,063

Figure. 2. Compound F5655-0309 in the ATPase p97 binding site. The complex has been obtained with molecular docking.

Vacuolar protein sorting-associated protein 4

VPS4 proteins are ATPases that mediate the final steps of membrane fission and protein sorting. They disassemble ESCRT-III filaments, which are vital for the formation of multivesicular bodies (MVBs) and the release of intraluminal vesicles (ILVs). This results in the sorting and degradation of various cellular proteins. Some of these proteins are involved in the development and progression of cancer. Thus, VPS4 ATPases are promising targets in the therapy of multiple types of cancer [23-25]. Focusing on the functions of the above targets, the Life Chemicals cheminformatics team has prepared a dedicated docking-based Screening Library comprising over 2,500 drug-like compounds designed to target VPS4A.

Vacuolar protein sorting-associated protein 4A (VPS4A)

Key features:

• Method: SP (standard precision) ligand-receptor docking
• X-Ray data used: Homology Modeling with Prime (2ZAN)
• Constraints: no
• Filters used: metabolism
• Number of compounds selected: 1,172

Figure 3. Compound F6525-5683 in the VPS4A binding site (docking score = -9.6052).

Vacuolar protein sorting-associated protein 4B (VPS4B)

Key features:

• Method: SP (standard precision) ligand-receptor docking
• X-Ray data used: Homology Modeling with Prime (7L9X)
• Constraints: no
• Filters used: metabolism
• Number of compounds selected: 1,392

Figure 4. Compound F5955-0065 in the VPS4B binding site (docking score = -10.3482).

Vacuolar protein sorting-associated protein 4B (VPS4B)

Key features:

• Method: structure-based virtual screening using Phase (receptor-ligand complex)
• X-Ray data used: 7L9X
• Filters used: metabolism
• Number of compounds selected: 1,125

Fig. 5. Compound F3264-0013 (pink) in the binding site of VPS4B with inhibitor (green) complex (PhaseScreenScore = 2.0148).

Reference:

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3. Ghosh S., Sen P.C. Role of ATPases in Disease Processes. In: Chakraborti S., Dhalla N. (eds) Regulation of Ca2+-ATPases, V-ATPases and F-ATPases. Advances in Biochemistry in Health and Disease. 2016;14. Springer, Cham. 10.1007/978-3-319-24780-9_24.
4. https://www.selleck.co.jp/ATPase.html
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8. Bodnar N, Rapoport T. Toward an understanding of the Cdc48/p97 ATPase. F1000Res. 2017;6:1318. Published 2017 Aug 3. doi:10.12688/f1000research.11683.1
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15. Fielden J, Popović M, Ramadan K. TEX264 at the intersection of autophagy and DNA repair. Autophagy. 2022;18(1):40-49. doi:10.1080/15548627.2021.1894059
16. Shearer RF, Typas D, Coscia F, et al. K27-linked ubiquitylation promotes p97 substrate processing and is essential for cell proliferation. EMBO J. 2022;41(9):e110145. doi:10.15252/embj.2021110145
17. Kaneko Y, Shimoda K, Ayala R, et al. p97 and p47 function in membrane tethering in cooperation with FTCD during mitotic Golgi reassembly. EMBO J. 2021;40(9):e105853. doi:10.15252/embj.2020105853
18. Kondoh E, Konno A, Inaba K, Oishi T, Murata M, Yoshida M. Valosin-containing protein/p97 interacts with sperm-activating and sperm-attracting factor (SAAF) in the ascidian egg and modulates sperm-attracting activity. Dev Growth Differ. 2008;50(8):665-673. doi:10.1111/j.1440-169X.2008.01064.x
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