Design, synthesis, and biological assessment of ABC transporter agonists for the development of novel Alzheimer’s disease therapeutics

• Applicant: Privatdozent Dr. Sven Marcel Stefan
• Subject Area: Pharmacy ; Molecular and Cellular Neurology and Neuropathology ; Organic Molecular Chemistry - Synthesis and Characterisation
• Term: from 2020 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 446812474

• Final Report Year: 2023

Final Report Abstract

As no curative treatment against Alzheimer’s disease (AD) is available to this date, the discovery and exploration of novel pharmacological targets necessitate to understand the molecular background of this disease and to develop new and effective drugs. ATP-binding cassette (ABC) transporters were linked to amyloid-β protein (Aβ) clearance from the brain, and their impaired function is a confounder of AD. Activation of these transport proteins was proposed as one strategy to oppose AD, however, activators of ABC transporters have barely been described in the literature, nor intentionally developed, and structure-activity relationships are unknown. The aim of the project was the systematic development of small-molecules that functionally activate the three most pronounced ABC transporters associated to AD, ABCB1, ABCC1, and ABCG2. This systematic development was based on three strategies: (i) development of a virtual screening protocol to predict structurally novel activators based on scarce literature data; (ii) identification of important scaffolds present in known activators of ABC transporters and design as well as development of monomer and dimer molecules by straight-forward synthesis approaches; and (iii) screening of collaborators’ physical compound libraries to serendipitously identify molecular-structurally novel activators. The first strategy provided a novel, chemical patterns-based computational prediction tool called ‘computer-aided pattern analysis’ (‘C@PA’). C@PA showed superiority compared to the classical computational approaches similarity search and pharmacophore modelling. C@PA identified dozens of structurally novel activators of ABCB1 and ABCC1, while none could be identified for ABCG2. Toward both ABCB1 and ABCC1, the compounds demonstrated activation of the energy-supplying unit, the ABCB1 / ABCC1 ATPase, which is a strong indication of real increase in pump activity of the transporters. Alternative assays could confirm the activating nature of certain representatives, also showing concentration dependency. The second strategy provided many scaffolds with activating properties against both ABCB1 and ABCC1, although phenothiazines demonstrated the strongest effect on ABCC1. Structureactivity relationship (SAR) studies showed that the sulfur is a critical part of the molecular structure of the activators. Unfortunately, by screening of a molecular-structurally diverse compound library consisting of 115 molecules of a collaborator, no hit molecule could be retrieved from the third strategy. In summary, two major achievements made within this project were (i) the development and establishment of C@PA as a reliable, robust, and novel prediction tool with great applicability; and (ii) the discovery of several molecular-structurally novel activators of which particularly the predicted phenothiazine-based ABCC1 activator is the most promising hit candidate as potential future therapeutic against AD.

Publications

• Superior Pyrimidine Derivatives as Selective ABCG2 Inhibitors and Broad-Spectrum ABCB1, ABCC1, and ABCG2 Antagonists. Journal of Medicinal Chemistry, 63(18), 10412-10432.
  Silbermann, Katja; Li, Jiyang; Namasivayam, Vigneshwaran; Baltes, Fabian; Bendas, Gerd; Stefan, Sven Marcel & Wiese, Michael
  
• Vesicular ATP-binding cassette transporters in human disease: relevant aspects of their organization for future drug development. Future Drug Discovery, 2(4).
  Stefan, Katja; Wen, Leck Lionel Yi; Namasivayam, Vigneshwaran; Bascuñana, Pablo; Huang, Michael Li-Hsuan; Riss, Patrick Johannes; Pahnke, Jens; Jansson, Patric Jan & Stefan, Sven Marcel
  
• Binding mode analysis of ABCA7 for the prediction of novel Alzheimer's disease therapeutics. Computational and Structural Biotechnology Journal, 19, 6490-6504.
  Namasivayam, Vigneshwaran; Stefan, Katja; Pahnke, Jens & Stefan, Sven Marcel
  
• Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1. Autophagy, 17(1), 1-382.
  Klionsky, Daniel J.; Abdel-Aziz, Amal Kamal; Abdelfatah, Sara; Abdellatif, Mahmoud; Abdoli, Asghar; Abel, Steffen; Abeliovich, Hagai; Abildgaard, Marie H.; Abudu, Yakubu Princely; Acevedo-Arozena, Abraham; Adamopoulos, Iannis E.; Adeli, Khosrow; Adolph, Timon E.; Adornetto, Annagrazia; Aflaki, Elma; Agam, Galila; Agarwal, Anupam; Aggarwal, Bharat B.; Agnello, Maria ... & Tong, Chun-Kit
  
• Rational drug design of 6-substituted 4-anilino-2-phenylpyrimidines for exploration of novel ABCG2 binding site. European Journal of Medicinal Chemistry, 212, 113045.
  Silbermann, Katja; Li, Jiyang; Namasivayam, Vigneshwaran; Stefan, Sven Marcel & Wiese, Michael
  
• Strategies to Gain Novel Alzheimer’s Disease Diagnostics and Therapeutics Using Modulators of ABCA Transporters. Free Neuropathol. 2021, 2, 33
  Pahnke, J.; Bascunana, P.; Brackhan, M.; Stefan, K.; Namasivayam, V.; Koldamova, R.; Möhle, L. & Stefan, S. M.
  
• A Novel Huntington’s Disease Assessment Platform to Support Future Drug Discovery and Development. International Journal of Molecular Sciences, 23(23), 14763.
  Wu, Jingyun; Möhle, Luisa; Brüning, Thomas; Eiriz, Iván; Rafehi, Muhammad; Stefan, Katja; Stefan, Sven Marcel & Pahnke, Jens
  
• ABC Transporter C1 Prevents Dimethyl Fumarate from Targeting Alzheimer’s Disease. Biology, 12(7), 932.
  Möhle, Luisa; Stefan, Katja; Bascuñana, Pablo; Brackhan, Mirjam; Brüning, Thomas; Eiriz, Ivan; El, Menuawy Ahmed El Menuawy; van Genderen, Sylvie; Santos-García, Irene; Górska, Anna Maria; Villa, María; Wu, Jingyun; Stefan, Sven Marcel & Pahnke, Jens