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González JEH, Salas-Sarduy E, Alvarez LH, Valiente PA, Arni RK, Pascutti PG. Three Decades of Targeting Falcipains to Develop Antiplasmodial Agents: What have we Learned and What can be Done Next? Curr Med Chem 2024; 31:2234-2263. [PMID: 37711130 DOI: 10.2174/0929867331666230913165219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/06/2023] [Accepted: 07/25/2023] [Indexed: 09/16/2023]
Abstract
Malaria is a devastating infectious disease that affects large swathes of human populations across the planet's tropical regions. It is caused by parasites of the genus Plasmodium, with Plasmodium falciparum being responsible for the most lethal form of the disease. During the intraerythrocytic stage in the human hosts, malaria parasites multiply and degrade hemoglobin (Hb) using a battery of proteases, which include two cysteine proteases, falcipains 2 and 3 (FP-2 and FP-3). Due to their role as major hemoglobinases, FP-2 and FP-3 have been targeted in studies aiming to discover new antimalarials and numerous inhibitors with activity against these enzymes, and parasites in culture have been identified. Nonetheless, cross-inhibition of human cysteine cathepsins remains a serious hurdle to overcome for these compounds to be used clinically. In this article, we have reviewed key functional and structural properties of FP-2/3 and described different compound series reported as inhibitors of these proteases during decades of active research in the field. Special attention is also paid to the wide range of computer-aided drug design (CADD) techniques successfully applied to discover new active compounds. Finally, we provide guidelines that, in our understanding, will help advance the rational discovery of new FP-2/3 inhibitors.
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Affiliation(s)
- Jorge Enrique Hernández González
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
- Department of Pharmaceutical Sciences, UZA II, University of Vienna, Vienna, 1090, Austria
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo Ugalde, Universidad Nacional de San Martín, CONICET, San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnología (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | | | - Pedro Alberto Valiente
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
| | | | - Pedro Geraldo Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, RJ, Brazil
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2
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Patel HN, Haines BE, Stauffacher CV, Helquist P, Wiest O. Computational Study of Base-Catalyzed Thiohemiacetal Decomposition in Pseudomonas mevalonii HMG-CoA Reductase. J Phys Chem B 2023. [PMID: 37219997 DOI: 10.1021/acs.jpcb.2c08969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Thiohemiacetals are key intermediates in the active sites of many enzymes catalyzing a variety of reactions. In the case of Pseudomonas mevalonii 3-hydroxy-3-methylglutaryl coenzyme A reductase (PmHMGR), this intermediate connects the two hydride transfer steps where a thiohemiacetal is the product of the first hydride transfer and its breakdown forms the substrate of the second one, serving as the intermediate during cofactor exchange. Despite the many examples of thiohemiacetals in a variety of enzymatic reactions, there are few studies that detail their reactivity. Here, we present computational studies on the decomposition of the thiohemiacetal intermediate in PmHMGR using both QM-cluster and QM/MM models. This reaction mechanism involves a proton transfer from the substrate hydroxyl to an anionic Glu83 followed by a C-S bond elongation stabilized by a cationic His381. The reaction provides insight into the varying roles of the residues in the active site that favor this multistep mechanism.
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Affiliation(s)
- Himani N Patel
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Brandon E Haines
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Cynthia V Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Paul Helquist
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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3
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Banerjee S. An insight into the interaction between α-ketoamide- based inhibitor and coronavirus main protease: A detailed in silico study. Biophys Chem 2021; 269:106510. [PMID: 33285430 PMCID: PMC7695570 DOI: 10.1016/j.bpc.2020.106510] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease (Mpro) is an attractive target for anti-coronavirus drug design. Further, α-ketoamide is proved to be very effective as a reversible covalent-inhibitor against cysteine proteases. Herein, we report on the non-covalent to the covalent adduct formation mechanism of α-ketoamide-based inhibitor with the enzyme active site amino acids by QM/SQM model (QM = quantum mechanical, SQM = semi-empirical QM). To uncover the mechanism, we focused on two approaches: a concerted and a stepwise fashion. The concerted pathway proceeds via deprotonation of the thiol of cysteine (here, Cys145 SγH) and simultaneous reversible nucleophilic attack of sulfur onto the α-ketoamide warhead. In this work, we propose three plausible concerted pathways. On the contrary, in a traditional two-stage pathway, the first step is proton transfer from Cys145 SγH to His41 Nδ forming an ion pair, and consecutively, in the second step, the thiolate ion attacks the α-keto group to form a thiohemiketal. In this reaction, we find that the stability of the tetrahedral intermediate oxyanion/hydroxyl group plays an important role. Moreover, as the α-keto group has two faces Si or Re for the nucleophilic attack, we considered both possibilities of attack leading to S- and R-thiohemiketal. We computed the structural, electronic, and energetic parameters of all stationary points including transition states via ONIOM and pure DFT method. Additionally, to characterize covalent, weak noncovalent interaction (NCI) and hydrogen-bonds, we applied NCI-reduced density gradient (NCI-RDG) methods along with Bader's Quantum Theory of Atoms-in-Molecules (QTAIM) and natural bonding orbital (NBO) analysis.
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Affiliation(s)
- Snehasis Banerjee
- Department of Chemistry, Government College of Engineering and Leather Technology, Salt Lake, Sector-3, Kolkata, PIN-700106, West Bengal, India.
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4
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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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Sivakumar D, Kumar V, Naumann M, Stein M. Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases. J Biol Chem 2020; 295:6972-6982. [PMID: 32265297 DOI: 10.1074/jbc.ra120.013073] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
The ovarian tumor domain (OTU) deubiquitinylating cysteine proteases OTUB1 and OTUB2 (OTU ubiquitin aldehyde binding 1 and 2) are representative members of the OTU subfamily of deubiquitinylases. Deubiquitinylation critically regulates a multitude of important cellular processes, such as apoptosis, cell signaling, and growth. Moreover, elevated OTUB expression has been observed in various cancers, including glioma, endometrial cancer, ovarian cancer, and breast cancer. Here, using molecular dynamics simulation approaches, we found that both OTUB1 and OTUB2 display a catalytic triad characteristic of proteases but differ in their configuration and protonation states. The OTUB1 protein had a prearranged catalytic site, with strong electrostatic interactions between the active-site residues His265 and Asp267 In OTUB2, however, the arrangement of the catalytic triad was different. In the absence of ubiquitin, the neutral states of the catalytic-site residues in OTUB2 were more stable, resulting in larger distances between these residues. Only upon ubiquitin binding did the catalytic triad in OTUB2 rearrange and bring the active site into a catalytically feasible state. An analysis of water access channels revealed only a few diffusion trajectories for the catalytically active form of OTUB1, whereas in OTUB2 the catalytic site was solvent-accessible, and a larger number of water molecules reached and left the binding pocket. Interestingly, in OTUB2, the catalytic residues His224 and Asn226 formed a stable hydrogen bond. We propose that the observed differences in activation kinetics, protonation states, water channels, and active-site accessibility between OTUB1 and OTUB2 may be relevant for the selective design of OTU inhibitors.
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Affiliation(s)
- Dakshinamurthy Sivakumar
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, 39106 Magdeburg, Germany
| | - Vikash Kumar
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, 39106 Magdeburg, Germany.,Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Matthias Stein
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, 39106 Magdeburg, Germany
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Elsässer B, Zauner FB, Messner J, Soh WT, Dall E, Brandstetter H. Distinct Roles of Catalytic Cysteine and Histidine in the Protease and Ligase Mechanisms of Human Legumain As Revealed by DFT-Based QM/MM Simulations. ACS Catal 2017; 7:5585-5593. [PMID: 28932620 PMCID: PMC5600538 DOI: 10.1021/acscatal.7b01505] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/10/2017] [Indexed: 11/30/2022]
Abstract
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The cysteine protease enzyme legumain hydrolyzes peptide bonds
with high specificity after asparagine and under more acidic conditions
after aspartic acid [BakerE. N.J. Mol. Biol.1980, 141, 441−4847003158; BakerE. N.; J. Mol. Biol.1977, 111, 207–210859183; DrenthJ.; Biochemistry1976, 15, 3731–3738952885; MenardR.; J. Cell. Biochem.1994, 137; PolgarL.Eur. J. Biochem.1978, 88, 513–521689035; StorerA. C.; Methods Enzymol.1994, 244, 486–5007845227. Remarkably,
legumain additionally exhibits ligase activity that prevails at pH
> 5.5. The atomic reaction mechanisms including their pH dependence
are only partly understood. Here we present a density functional theory
(DFT)-based quantum mechanics/molecular mechanics (QM/MM) study of
the detailed reaction mechanism of both activities for human legumain
in solution. Contrasting the situation in other papain-like proteases,
our calculations reveal that the active site Cys189 must be present
in the protonated state for a productive nucleophilic attack and simultaneous
rupture of the scissile peptide bond, consistent with the experimental
pH profile of legumain-catalyzed cleavages. The resulting thioester
intermediate (INT1) is converted by water attack on the thioester
into a second intermediate, a diol (INT2), which is released by proton
abstraction by Cys189. Surprisingly, we found that ligation is not
the exact reverse of the proteolysis but can proceed via two distinct
routes. Whereas the transpeptidation route involves aminolysis of
the thioester (INT1), at pH 6 a cysteine-independent, histidine-assisted
ligation route was found. Given legumain’s important roles
in immunity, cancer, and neurodegenerative diseases, our findings
open up possibilities for targeted drug design in these fields.
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Affiliation(s)
- Brigitta Elsässer
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
| | - Florian B. Zauner
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
| | - Johann Messner
- Information
Management, University of Linz, Alternberger Strasse 69, A-4040 Linz, Austria
| | - Wai Tuck Soh
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
| | - Elfriede Dall
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
| | - Hans Brandstetter
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
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Modeling covalent-modifier drugs. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1664-1675. [PMID: 28528876 DOI: 10.1016/j.bbapap.2017.05.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/10/2017] [Accepted: 05/12/2017] [Indexed: 11/21/2022]
Abstract
In this review, we present a summary of how computer modeling has been used in the development of covalent-modifier drugs. Covalent-modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly. Computer modeling is widely used in drug discovery, but different computational methods must be used to model covalent modifiers because of the chemical bonds formed. Structural and bioinformatic analysis has identified sites of modification that could yield selectivity for a chosen target. Docking methods, which are used to rank binding poses of large sets of inhibitors, have been augmented to support the formation of protein-ligand bonds and are now capable of predicting the binding pose of covalent modifiers accurately. The pKa's of amino acids can be calculated in order to assess their reactivity towards electrophiles. QM/MM methods have been used to model the reaction mechanisms of covalent modification. The continued development of these tools will allow computation to aid in the development of new covalent-modifier drugs. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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8
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Crystallographic, DFT and docking (cathepsin B) studies on an organotellurium(IV) compound. Z KRIST-CRYST MATER 2016. [DOI: 10.1515/zkri-2016-1931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Some biologically active organotellurium compounds exhibit inhibitory potency against cathepsin B. In this study, an alkyl derivative, viz. [CH3(CH2)2C(I)=C(H)](nBu)TeI2, 1, has been structurally characterised by X-ray crystallography and shown to be coordinated within a C2I2 donor set. When the stereochemically active lone pair of electrons is taken into account, a distorted trigonal bipyramidal geometry results with the iodide atoms in axial positions. Both intra- and inter-molecular Te···I interactions are also noted. If all interactions are considered, the coordination geometry is based on a Ψ-pentagonal bipyramidal geometry. An unusual feature of the structure is the curving of the functionalised C5 chain. This feature has been explored by DFT methods and shown to arise as a result of close C–H···I interactions. A docking study (cathepsin B) was performed to understand the inhibition mechanism and to compare the new results with previous observations. Notably, 1 has the same pose exhibited by analogous biologically active compounds with aryl groups. Thus, the present study suggests that (alkyl)2TeX2 compounds should also be evaluated for biological activity.
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9
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Uritsky N, Shokhen M, Albeck A. Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015; 55:1680-4. [DOI: 10.1002/anie.201507772] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Neta Uritsky
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
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Uritsky N, Shokhen M, Albeck A. Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Neta Uritsky
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
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11
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Löser R, Pietzsch J. Cysteine cathepsins: their role in tumor progression and recent trends in the development of imaging probes. Front Chem 2015; 3:37. [PMID: 26157794 PMCID: PMC4477214 DOI: 10.3389/fchem.2015.00037] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/29/2015] [Indexed: 12/16/2022] Open
Abstract
Papain-like cysteine proteases bear an enormous potential as drug discovery targets for both infectious and systemic human diseases. The considerable progress in this field over the last two decades has also raised interest in the visualization of these enzymes in their native context, especially with regard to tumor imaging. After a short introduction to structure and general functions of human cysteine cathepsins, we highlight their importance for drug discovery and development and provide a critical update on the current state of knowledge toward their involvement in tumor progression, with a special emphasis on their role in therapy response. In accordance with a radiopharmaceutical point of view, the main focus of this review article will be the discussion of recently developed fluorescence and radiotracer-based imaging agents together with related molecular probes.
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Affiliation(s)
- Reik Löser
- Department of Radiopharmaceutical and Chemical Biology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf Dresden, Germany ; Department of Chemistry and Food Chemistry, Technische Universität Dresden Dresden, Germany
| | - Jens Pietzsch
- Department of Radiopharmaceutical and Chemical Biology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf Dresden, Germany ; Department of Chemistry and Food Chemistry, Technische Universität Dresden Dresden, Germany
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12
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Sanz-Gaitero M, Keary R, Garcia-Doval C, Coffey A, van Raaij MJ. Crystal structure of the lytic CHAP(K) domain of the endolysin LysK from Staphylococcus aureus bacteriophage K. Virol J 2014; 11:133. [PMID: 25064136 PMCID: PMC4126393 DOI: 10.1186/1743-422x-11-133] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteriophages encode endolysins to lyse their host cell and allow escape of their progeny. Endolysins are also active against Gram-positive bacteria when applied from the outside and are thus attractive anti-bacterial agents. LysK, an endolysin from staphylococcal phage K, contains an N-terminal cysteine-histidine dependent amido-hydrolase/peptidase domain (CHAP(K)), a central amidase domain and a C-terminal SH3b cell wall-binding domain. CHAP(K) cleaves bacterial peptidoglycan between the tetra-peptide stem and the penta-glycine bridge. METHODS The CHAP(K) domain of LysK was crystallized and high-resolution diffraction data was collected both from a native protein crystal and a methylmercury chloride derivatized crystal. The anomalous signal contained in the derivative data allowed the location of heavy atom sites and phase determination. The resulting structures were completed, refined and analyzed. The presence of calcium and zinc ions in the structure was confirmed by X-ray fluorescence emission spectroscopy. Zymogram analysis was performed on the enzyme and selected site-directed mutants. RESULTS The structure of CHAP(K) revealed a papain-like topology with a hydrophobic cleft, where the catalytic triad is located. Ordered buffer molecules present in this groove may mimic the peptidoglycan substrate. When compared to previously solved CHAP domains, CHAP(K) contains an additional lobe in its N-terminal domain, with a structural calcium ion, coordinated by residues Asp45, Asp47, Tyr49, His51 and Asp56. The presence of a zinc ion in the active site was also apparent, coordinated by the catalytic residue Cys54 and a possible substrate analogue. Site-directed mutagenesis was used to demonstrate that residues involved in calcium binding and of the proposed active site were important for enzyme activity. CONCLUSIONS The high-resolution structure of the CHAP(K) domain of LysK was determined, suggesting the location of the active site, the substrate-binding groove and revealing the presence of a structurally important calcium ion. A zinc ion was found more loosely bound. Based on the structure, we propose a possible reaction mechanism. Future studies will be aimed at co-crystallizing CHAP(K) with substrate analogues and elucidating its role in the complete LysK protein. This, in turn, may lead to the design of site-directed mutants with altered activity or substrate specificity.
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Affiliation(s)
| | | | | | | | - Mark J van Raaij
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), Calle Darwin 3, E-28049 Madrid, Spain.
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13
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Shokhen M, Hirsch M, Khazanov N, Ozeri R, Perlman N, Traube T, Vijayakumar S, Albeck A. From Catalytic Mechanism to Rational Design of Reversible Covalent Inhibitors of Serine and Cysteine Hydrolases. Isr J Chem 2014. [DOI: 10.1002/ijch.201300144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Traube T, Shokhen M, Albeck A. A new method for filtering of reactive "warheads" of transition-state analog protease inhibitors. Eur J Med Chem 2014; 77:134-8. [PMID: 24631732 DOI: 10.1016/j.ejmech.2014.02.059] [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: 01/29/2014] [Accepted: 02/27/2014] [Indexed: 10/25/2022]
Abstract
In light of the major contribution of the reactive warhead to the binding energy trend in reversible covalent transition-state analog inhibitors of serine and cysteine hydrolases, would it be possible to rationally design and quickly filter such warheads, especially for large-scale screening? The previously defined W1 and W2 covalent descriptors quantitatively account for the energetic effect of the covalent bonds reorganization, accompanying enzyme-inhibitor covalent binding. The quantum mechanically calculated W1 and W2 reflect the warhead binding energy by modeling of the enzyme-inhibitor reaction core. Here, we demonstrate the use of these descriptors for warhead filtering, and examine its scope and limitations. The W1 and W2 descriptors provide a tool for rational design of various warheads as universal building blocks of real inhibitors without the requirement of 3D structural information about the target enzyme or QSAR studies. These warheads could then be used as hit structural templates in the subsequent optimization of inhibitors recognition sites.
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Affiliation(s)
- Tamar Traube
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
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Traube T, Shokhen M, Albeck A. Application of EMBM to Structure-Based Design of Warheads for Protease Inhibitors. Mol Inform 2014; 33:36-42. [PMID: 27485197 DOI: 10.1002/minf.201300099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/27/2013] [Indexed: 11/06/2022]
Abstract
Most CADD tools handle non-covalent enzyme inhibitors, despite the growing interest of the pharma industry in covalent inhibitors. We have recently introduced an enzyme mechanism-based method, EMBM, as a computational tool for binding trend analysis and prediction of chemical sites (CS) of reversible covalent enzyme inhibitors. In the current study we demonstrate the utility of EMBM to structure-based applications. In this mode, the energy of the enzyme-inhibitor covalent bond is accounted for by the W1 and W2 covalent descriptors we have developed, whereas the non-covalent interactions between the inhibitor CS and the enzyme active site can be estimated directly on the 3D structure of the enzyme-inhibitor complex.
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Affiliation(s)
- Tamar Traube
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel tel.: 972-3-5318862, fax: 972-3-7384053
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel tel.: 972-3-5318862, fax: 972-3-7384053.
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel tel.: 972-3-5318862, fax: 972-3-7384053.
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16
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Cohen M, Bretler U, Albeck A. Peptidyl cyclopropenones: reversible inhibitors, irreversible inhibitors, or substrates of cysteine proteases? Protein Sci 2013; 22:788-99. [PMID: 23553793 DOI: 10.1002/pro.2260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/25/2013] [Accepted: 03/25/2013] [Indexed: 11/11/2022]
Abstract
Peptidyl cyclopropenones were previously introduced as selective cysteine protease reversible inhibitors. In the present study we synthesized one such peptidyl cyclopropenone and investigated its interaction with papain, a prototype cysteine protease. A set of kinetics, biochemical, HPLC, MS, and (13)C-NMR experiments revealed that the peptidyl cyclopropenone was an irreversible inhibitor of the enzyme, alkylating the catalytic cysteine. In parallel, this cyclopropenone also behaved as an alternative substrate of the enzyme, providing a product that was tentatively suggested to be either a spiroepoxy cyclopropanone or a gamma-lactone. Thus, a single family of compounds exhibits an unusual variety of activities, being reversible inhibitors, irreversible inhibitors and alternative substrates towards enzymes of the same family.
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Affiliation(s)
- Meital Cohen
- Department of Chemistry, The Julius Spokojny Bioorganic Chemistry Laboratory, Bar Ilan University, Ramat Gan, Israel
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17
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Roca M, Aranda J, Moliner V, Tuñón I. Modeling methods for studying post-translational and transcriptional modifying enzymes. Curr Opin Chem Biol 2012; 16:465-71. [PMID: 23127358 DOI: 10.1016/j.cbpa.2012.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 09/20/2012] [Accepted: 10/11/2012] [Indexed: 10/27/2022]
Abstract
Biological catalysis is a complex chemical process that involves not only electronic reorganization in the substrate but also the reorganization of the catalyst. This complexity is even larger in the case of post-transcriptional and post-translational modifications which may involve the interaction between two biomacromolecules. However, the development over the past decades of new computational methods and strategies is offering a detailed molecular picture of the catalytic event and a deep understanding of the mechanisms of chemical reactions in biological environments. Here we review the efforts made in the last years to model catalysis in post-transcriptional and post-translational processes. We stress on the advantages and problems of the different computational strategies and their applicability in different cases.
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Affiliation(s)
- Maite Roca
- Departamento de Química Física, Universitat de València, 46100 Burjassot, Spain
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18
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Uritsky N, Shokhen M, Albeck A. The Catalytic Machinery of Rhomboid Proteases: Combined MD and QM Simulations. J Chem Theory Comput 2012; 8:4663-71. [DOI: 10.1021/ct3003767] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Neta Uritsky
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Michael Shokhen
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Amnon Albeck
- The Julius
Spokojny Bioorganic Chemistry Laboratory,
Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
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19
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Lecoq L, Bougault C, Hugonnet JE, Veckerlé C, Pessey O, Arthur M, Simorre JP. Dynamics induced by β-lactam antibiotics in the active site of Bacillus subtilis L,D-transpeptidase. Structure 2012; 20:850-61. [PMID: 22579252 DOI: 10.1016/j.str.2012.03.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/29/2012] [Accepted: 03/05/2012] [Indexed: 11/18/2022]
Abstract
β-lactams inhibit peptidoglycan polymerization by acting as suicide substrates of essential d,d-transpeptidases. Bypass of these enzymes by unrelated l,d-transpeptidases results in β-lactam resistance, although carbapenems remain unexpectedly active. To gain insight into carbapenem specificity of l,d-transpeptidases (Ldts), we solved the nuclear magnetic resonance (NMR) structures of apo and imipenem-acylated Bacillus subtilis Ldt and show that the cysteine nucleophile is present as a neutral imidazole-sulfhydryl pair in the substrate-free enzyme. NMR relaxation dispersion does not reveal any preexisting conformational exchange in the apoenzyme, and change in flexibility is not observed upon noncovalent binding of β-lactams (K(D) > 37.5 mM). In contrast, covalent modification of active cysteine by both carbapenems and 2-nitro-5-thiobenzoate induces backbone flexibility that does not result from disruption of the imidazole-sulfhydryl proton interaction or steric hindrance. The chemical step of the reaction determines enzyme specificity since no differences in drug affinity were observed.
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Affiliation(s)
- Lauriane Lecoq
- CEA, DSV, Institut de Biologie Structurale (IBS), Grenoble F-38027, France
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20
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Shokhen M, Traube T, Vijayakumar S, Hirsch M, Uritsky N, Albeck A. Differentiating serine and cysteine protease mechanisms by new covalent QSAR descriptors. Chembiochem 2011; 12:1023-6. [PMID: 21438106 PMCID: PMC3088911 DOI: 10.1002/cbic.201000459] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Indexed: 11/11/2022]
Affiliation(s)
- Michael Shokhen
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
| | - Tamar Traube
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
| | - Subramaniam Vijayakumar
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
| | - Michal Hirsch
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
| | - Neta Uritsky
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
| | - Amnon Albeck
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
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21
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Traube T, Vijayakumar S, Hirsch M, Uritsky N, Shokhen M, Albeck A. EMBM - a new enzyme mechanism-based method for rational design of chemical sites of covalent inhibitors. J Chem Inf Model 2010; 50:2256-65. [PMID: 21090595 DOI: 10.1021/ci100330y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We introduce an enzyme mechanism-based method (EMBM) aimed at rational design of chemical sites (CS) of reaction coordinate analog inhibitors. The energy of valence reorganization of CS, caused by the formation of the enzyme-inhibitor covalent complex, is accounted for by new covalent descriptors W1 and W2. We considered CS fragments with a carbonyl reactivity center, like in native protease substrates. The W1 and W2 descriptors are calculated quantum mechanically on small molecular clusters simulating the reaction core of the formed covalent tetrahedral complex, anionic TC(O-) or neutral TC(OH). The modeling on a reaction core allows generation of various CS and corresponding TC(O-) and TC(OH) as universal building blocks of real inhibitors and their covalent complexes with serine or cysteine hydrolases. Moreover, the approach avoids the need for 3D structure of the target enzyme, so EMBM may be used for ligand-based design. We have built a chemical site of inhibitors (CSI) databank with pairs of W1 and W2 descriptors precalculated for both CH₃O(-) and CH₃S(-) nucleophiles for every collected CS fragment. We demonstrated that contribution of a CS fragment to the binding affinity of an inhibitor depends on both its covalent reorganization during the chemical transformation and its noncovalent interactions in the enzyme active site. Consequently, prediction of inhibitors binding trend can be done only by accounting for all of these factors, using W1 and W2 in combination with noncovalent QSAR descriptors.
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Affiliation(s)
- Tamar Traube
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
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