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Molecular and in vivo studies of a glutamate-class prolyl-endopeptidase for coeliac disease therapy. Nat Commun 2022; 13:4446. [PMID: 35915115 PMCID: PMC9343461 DOI: 10.1038/s41467-022-32215-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/21/2022] [Indexed: 11/25/2022] Open
Abstract
The digestion of gluten generates toxic peptides, among which a highly immunogenic proline-rich 33-mer from wheat α-gliadin, that trigger coeliac disease. Neprosin from the pitcher plant is a reported prolyl endopeptidase. Here, we produce recombinant neprosin and its mutants, and find that full-length neprosin is a zymogen, which is self-activated at gastric pH by the release of an all-β pro-domain via a pH-switch mechanism featuring a lysine plug. The catalytic domain is an atypical 7+8-stranded β-sandwich with an extended active-site cleft containing an unprecedented pair of catalytic glutamates. Neprosin efficiently degrades both gliadin and the 33-mer in vitro under gastric conditions and is reversibly inactivated at pH > 5. Moreover, co-administration of gliadin and the neprosin zymogen at the ratio 500:1 reduces the abundance of the 33-mer in the small intestine of mice by up to 90%. Neprosin therefore founds a family of eukaryotic glutamate endopeptidases that fulfils requisites for a therapeutic glutenase. Celiac disease is characterized by intolerance to gluten, a cereal protein. Here, the authors show that neprosin, a glutamate peptidase from the pitcher plant, efficiently cleaves gluten components under physiological conditions in vitro and in the gut of mice.
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Ahsan M, Senapati S. Water Plays a Cocatalytic Role in Epoxide Ring Opening Reaction in Aspartate Proteases: A QM/MM Study. J Phys Chem B 2019; 123:7955-7964. [PMID: 31468966 DOI: 10.1021/acs.jpcb.9b04575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aspartate proteases are potential targets for various diseases, and many of their inhibitors are FDA-approved drugs. However, these peptidomimetic and reversibly bound drugs become ineffective upon prolonged use. Attempts have been made to design and synthesize various nonpeptidic epoxide-based irreversible inhibitors to combat the drug-resistance enigma. Here, we study the mechanism of epoxide ring opening in two widely studied aspartate proteases, HIV-1 protease and pepsin. Our results from QM/MM molecular dynamics show that the epoxide ring opening in aspartate proteases follow a two-step mechanism with the formation of an oxyanion intermediate, stabilized by a set of water molecules in the protein active site. These water molecules by virtue of "low-barrier hydrogen bonds" with the epoxide ring reduce the intrinsic reaction barrier while remaining structurally unperturbed, thus playing a cocatalytic role. We validated our results by reproducing the experimentally observed protease/pepsin-epoxide covalent complexes as end products. The observed stability of our oxyanion intermediate in a four-water-coordinated state is also consistent with the reported stable state of the hydroxide ion in water as OH-(H2O)4. Our study could pave the way for the design of new class "HIV protease irreversible inhibitors" from the acquired knowledge of the structures of intermediate and transition states traced during the explored reaction mechanism.
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Affiliation(s)
- Mohd Ahsan
- Department of Biotechnology and BJM School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Sanjib Senapati
- Department of Biotechnology and BJM School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
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Benedetti F, Berti F, Campaner P, Fanfoni L, Demitri N, Olajuyigbe FM, De March M, Geremia S. Impact of Stereochemistry on Ligand Binding: X-ray Crystallographic Analysis of an Epoxide-Based HIV Protease Inhibitor. ACS Med Chem Lett 2014; 5:968-72. [PMID: 25221650 DOI: 10.1021/ml500092e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 07/14/2014] [Indexed: 01/01/2023] Open
Abstract
A new pseudopeptide epoxide inhibitor, designed for irreversible binding to HIV protease (HIV-PR), has been synthesized and characterized in solution and in the solid state. However, the crystal structure of the complex obtained by inhibitor-enzyme cocrystallization revealed that a minor isomer, with inverted configuration of the epoxide carbons, has been selected by HIV-PR during crystallization. The structural characterization of the well-ordered pseudopeptide, inserted in the catalytic channel with its epoxide group intact, provides deeper insights into inhibitor binding and HIV-PR stereoselectivity, which aids development of future epoxide-based HIV inhibitors.
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Affiliation(s)
- Fabio Benedetti
- Department
of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Via Giorgeri 1, 34127 Trieste, Italy
| | - Federico Berti
- Department
of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Via Giorgeri 1, 34127 Trieste, Italy
| | - Pietro Campaner
- Department
of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Via Giorgeri 1, 34127 Trieste, Italy
| | - Lidia Fanfoni
- Department
of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Via Giorgeri 1, 34127 Trieste, Italy
| | - Nicola Demitri
- Department
of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Via Giorgeri 1, 34127 Trieste, Italy
| | - Folasade M. Olajuyigbe
- Department
of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Via Giorgeri 1, 34127 Trieste, Italy
- Department
of Biochemistry, Federal University of Technology, P.M.B. 704, Akure 340001, Ondo State, Nigeria
| | - Matteo De March
- Department
of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Via Giorgeri 1, 34127 Trieste, Italy
| | - Silvano Geremia
- Department
of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Via Giorgeri 1, 34127 Trieste, Italy
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Degel B, Staib P, Rohrer S, Scheiber J, Martina E, Büchold C, Baumann K, Morschhäuser J, Schirmeister T. Cis-Configured Aziridines Are New Pseudo-Irreversible Dual-Mode Inhibitors ofCandida albicans Secreted Aspartic Protease 2. ChemMedChem 2008; 3:302-15. [DOI: 10.1002/cmdc.200700101] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kóňa J. Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease. Org Biomol Chem 2008; 6:359-65. [DOI: 10.1039/b715828a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Zutshi R, Chmielewski J. Targeting the dimerization interface for irreversible inhibition of HIV-1 protease. Bioorg Med Chem Lett 2000; 10:1901-3. [PMID: 10987413 DOI: 10.1016/s0960-894x(00)00369-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel strategy was used to irreversibly inhibit HIV-1 protease. The inhibitor was designed to form a disulfide bond with Cys95, present at the dimerization interface of HIV-1 protease. The inhibitor was shown to be active against HIV-1 protease with K(inact) = 3.7 microM and V(inact) = 0.012 min(-1).
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Affiliation(s)
- R Zutshi
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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