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Jílková A, Horn M, Fanfrlík J, Küppers J, Pachl P, Řezáčová P, Lepšík M, Fajtová P, Rubešová P, Chanová M, Caffrey CR, Gütschow M, Mareš M. Azanitrile Inhibitors of the SmCB1 Protease Target Are Lethal to Schistosoma mansoni: Structural and Mechanistic Insights into Chemotype Reactivity. ACS Infect Dis 2021; 7:189-201. [PMID: 33301315 PMCID: PMC7802074 DOI: 10.1021/acsinfecdis.0c00644] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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Azapeptide
nitriles are postulated to reversibly covalently react
with the active-site cysteine residue of cysteine proteases and form
isothiosemicarbazide adducts. We investigated the interaction of azadipeptide
nitriles with the cathepsin B1 drug target (SmCB1) from Schistosoma
mansoni, a pathogen that causes the global neglected disease
schistosomiasis. Azadipeptide nitriles were superior inhibitors of
SmCB1 over their parent carba analogs. We determined the crystal structure
of SmCB1 in complex with an azadipeptide nitrile and analyzed the
reaction mechanism using quantum chemical calculations. The data demonstrate
that azadipeptide nitriles, in contrast to their carba counterparts,
undergo a change from E- to Z-configuration
upon binding, which gives rise to a highly favorable energy profile
of noncovalent and covalent complex formation. Finally, azadipeptide
nitriles were considerably more lethal than their carba analogs against
the schistosome pathogen in culture, supporting the further development
of this chemotype as a treatment for schistosomiasis.
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Affiliation(s)
- Adéla Jílková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Jim Küppers
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Pavla Fajtová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Petra Rubešová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Marta Chanová
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2028/7, 12800 Prague 2, Czech Republic
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases (CDIPD), Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
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Deng H, Lei Q, Wu Y, He Y, Li W. Activity-based protein profiling: Recent advances in medicinal chemistry. Eur J Med Chem 2020; 191:112151. [PMID: 32109778 DOI: 10.1016/j.ejmech.2020.112151] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 02/05/2023]
Abstract
Activity-based protein profiling (ABPP) has become an emerging chemical proteomic approach to illustrate the interaction mechanisms between compounds and proteins. This approach has combined organic synthesis, biochemistry, cell biology, biophysics and bioinformatics to accelerate the process of drug discovery in target identification and validation, as well as in the stage of lead discovery and optimization. This review will summarize new developments and applications of ABPP in medicinal chemistry. Here, we mainly described the design principles of activity-base probes (ABPs) and general workflows of ABPP approach. Moreover, we discussed various basic and advanced ABPP strategies and their applications in medicinal chemistry, including competitive and comparative ABPP, two-step ABPP, fluorescence polarization ABPP (FluoPol-ABPP) and ABPs for visualization. In conclusion, this review will give a general overview of the applications of ABPP as a powerful and efficient technique in medicinal chemistry.
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Affiliation(s)
- Hui Deng
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Qian Lei
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yangping Wu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yang He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
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