Mixture-Based Screening of Focused Combinatorial Libraries by NMR: Application to the Antiapoptotic Protein HMcl-1

Overview

Journal J Med Chem

Publisher American Chemical Society

Specialty Chemistry

Date 2023 Jul 19

PMID 37464766

Authors

Giulia Alboreggia

Parima Udompholkul

Carlo Baggio

Maurizio Pellecchia

Affiliations

Soon will be listed here.

Abstract

We report on an innovative ligand discovery strategy based on protein NMR-based screening of a combinatorial library of ∼125,000 compounds that was arranged in 96 distinct mixtures. Using sensitive solution protein NMR spectroscopy and chemical perturbation-based screening followed by an iterative synthesis, deconvolutions, and optimization strategy, we demonstrate that the approach could be useful in the identification of initial binding molecules for difficult drug targets, such as those involved in protein-protein interactions. As an application, we will report novel agents targeting the Bcl-2 family protein hMcl-1. The approach is of general applicability and could be deployed as an effective screening strategy for de novo identification of ligands, particularly when tackling targets involved in protein-protein interactions.

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References

Eichler J, Appel J, Blondelle S, Dooley C, Dorner B, Ostresh J . Peptide, peptidomimetic, and organic synthetic combinatorial libraries. Med Res Rev. 1995; 15(6):481-96. DOI: 10.1002/med.2610150603. View

Pellecchia M, Meininger D, Dong Q, Chang E, Jack R, Sem D . NMR-based structural characterization of large protein-ligand interactions. J Biomol NMR. 2002; 22(2):165-73. DOI: 10.1023/a:1014256707875. View

Barile E, Pellecchia M . NMR-based approaches for the identification and optimization of inhibitors of protein-protein interactions. Chem Rev. 2014; 114(9):4749-63. PMC: 4027952. DOI: 10.1021/cr500043b. View

Souers A, Leverson J, Boghaert E, Ackler S, Catron N, Chen J . ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets. Nat Med. 2013; 19(2):202-8. DOI: 10.1038/nm.3048. View

Pervushin K, Wider G, Wuthrich K . Single Transition-to-single Transition Polarization Transfer (ST2-PT) in [15N,1H]-TROSY. J Biomol NMR. 2010; 12(2):345-8. DOI: 10.1023/A:1008268930690. View

Hewitt W, Leung S, Pye C, Ponkey A, Bednarek M, Jacobson M . Cell-permeable cyclic peptides from synthetic libraries inspired by natural products. J Am Chem Soc. 2014; 137(2):715-21. DOI: 10.1021/ja508766b. View

Naylor M, Bockus A, Blanco M, Lokey R . Cyclic peptide natural products chart the frontier of oral bioavailability in the pursuit of undruggable targets. Curr Opin Chem Biol. 2017; 38:141-147. DOI: 10.1016/j.cbpa.2017.04.012. View

Leone M, Crowell K, Chen J, Jung D, Chiang G, Sareth S . The FRB domain of mTOR: NMR solution structure and inhibitor design. Biochemistry. 2006; 45(34):10294-302. DOI: 10.1021/bi060976+. View

Udompholkul P, Baggio C, Gambini L, Alboreggia G, Pellecchia M . Lysine Covalent Antagonists of Melanoma Inhibitors of Apoptosis Protein. J Med Chem. 2021; 64(21):16147-16158. DOI: 10.1021/acs.jmedchem.1c01459. View

10.

Gambini L, Udompholkul P, Baggio C, Muralidharan A, Kenjic N, Assar Z . Design, Synthesis, and Structural Characterization of Lysine Covalent BH3 Peptides Targeting Mcl-1. J Med Chem. 2021; 64(8):4903-4912. PMC: 8550878. DOI: 10.1021/acs.jmedchem.1c00005. View

11.

Du J, Liu L, Liu B, Yang J, Hou X, Yu J . Structure-based virtual screening, biological evaluation and biophysical study of novel Mcl-1 inhibitors. Future Med Chem. 2020; 12(14):1293-1304. DOI: 10.4155/fmc-2020-0114. View

12.

Pinilla C, Appel J, Borras E, Houghten R . Advances in the use of synthetic combinatorial chemistry: mixture-based libraries. Nat Med. 2003; 9(1):118-22. DOI: 10.1038/nm0103-118. View

13.

Zhu J, Wang Z, Guo Z, Zhang X, Song T, Guo Y . Structure-based design, synthesis, and evaluation of Bcl-2/Mcl-1 dual inhibitors. Arch Pharm (Weinheim). 2020; 353(5):e2000005. DOI: 10.1002/ardp.202000005. View

14.

Furukawa A, Townsend C, Schwochert J, Pye C, Bednarek M, Lokey R . Passive Membrane Permeability in Cyclic Peptomer Scaffolds Is Robust to Extensive Variation in Side Chain Functionality and Backbone Geometry. J Med Chem. 2016; 59(20):9503-9512. DOI: 10.1021/acs.jmedchem.6b01246. View

15.

Bottini A, Wu B, Barile E, K DE S, Leone M, Pellecchia M . High-Throughput Screening (HTS) by NMR Guided Identification of Novel Agents Targeting the Protein Docking Domain of YopH. ChemMedChem. 2015; 11(8):919-27. PMC: 4838521. DOI: 10.1002/cmdc.201500441. View

16.

Chia L, Kumar P, Maki M, Ravichandran G, Thilagar S . A Review: The Antiviral Activity of Cyclic Peptides. Int J Pept Res Ther. 2022; 29(1):7. PMC: 9713128. DOI: 10.1007/s10989-022-10478-y. View

17.

Zhang Z, Su P, Li X, Song T, Chai G, Yu X . Novel Mcl-1/Bcl-2 dual inhibitors created by the structure-based hybridization of drug-divided building blocks and a fragment deconstructed from a known two-face BH3 mimetic. Arch Pharm (Weinheim). 2015; 348(2):89-99. DOI: 10.1002/ardp.201400296. View

18.

Wu B, Barile E, K DE S, Wei J, Purves A, Pellecchia M . High-Throughput Screening by Nuclear Magnetic Resonance (HTS by NMR) for the Identification of PPIs Antagonists. Curr Top Med Chem. 2015; 15(20):2032-42. PMC: 4545611. DOI: 10.2174/1568026615666150519102459. View

19.

Pinilla C, Buencamino J, Appel J, Hopp T, Houghten R . Mapping the detailed specificity of a calcium-dependent monoclonal antibody through the use of soluble positional scanning combinatorial libraries: identification of potent calcium-independent antigens. Mol Divers. 1995; 1(1):21-8. DOI: 10.1007/BF01715806. View

20.

Ramadhani D, Maharani R, Gazzali A, Muchtaridi M . Cyclic Peptides for the Treatment of Cancers: A Review. Molecules. 2022; 27(14). PMC: 9317348. DOI: 10.3390/molecules27144428. View