1
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Radisky ES. Extracellular proteolysis in cancer: Proteases, substrates, and mechanisms in tumor progression and metastasis. J Biol Chem 2024; 300:107347. [PMID: 38718867 PMCID: PMC11170211 DOI: 10.1016/j.jbc.2024.107347] [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: 02/09/2024] [Revised: 04/08/2024] [Accepted: 04/25/2024] [Indexed: 06/02/2024] Open
Abstract
A vast ensemble of extracellular proteins influences the development and progression of cancer, shaped and reshaped by a complex network of extracellular proteases. These proteases, belonging to the distinct classes of metalloproteases, serine proteases, cysteine proteases, and aspartic proteases, play a critical role in cancer. They often become dysregulated in cancer, with increases in pathological protease activity frequently driven by the loss of normal latency controls, diminished regulation by endogenous protease inhibitors, and changes in localization. Dysregulated proteases accelerate tumor progression and metastasis by degrading protein barriers within the extracellular matrix (ECM), stimulating tumor growth, reactivating dormant tumor cells, facilitating tumor cell escape from immune surveillance, and shifting stromal cells toward cancer-promoting behaviors through the precise proteolysis of specific substrates to alter their functions. These crucial substrates include ECM proteins and proteoglycans, soluble proteins secreted by tumor and stromal cells, and extracellular domains of cell surface proteins, including membrane receptors and adhesion proteins. The complexity of the extracellular protease web presents a significant challenge to untangle. Nevertheless, technological strides in proteomics, chemical biology, and the development of new probes and reagents are enabling progress and advancing our understanding of the pivotal importance of extracellular proteolysis in cancer.
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Affiliation(s)
- Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA.
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2
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Grigorenko BL, Polyakov IV, Khrenova MG, Giudetti G, Faraji S, Krylov AI, Nemukhin AV. Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms. J Am Chem Soc 2023; 145:13204-13214. [PMID: 37294056 DOI: 10.1021/jacs.3c02229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work. They were derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of reacting with the catalytic cysteine residue in the MPro active site. The reaction mechanisms of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) simulations. The results show that all four compounds form covalent adducts with the catalytic cysteine Cys 145 of MPro. From the chemical perspective, the reactions of these four molecules with MPro follow three distinct mechanisms. The reactions are initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand is accompanied by the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir (which has a reactive nitrile group) leads to the formation of a covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site. Our results contribute to the ongoing search for efficient inhibitors of the SARS-CoV-2 enzymes.
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Affiliation(s)
- Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia
| | - Goran Giudetti
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
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3
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Shao Q, Xiong M, Li J, Hu H, Su H, Xu Y. Unraveling the catalytic mechanism of SARS-CoV-2 papain-like protease with allosteric modulation of C270 mutation using multiscale computational approaches. Chem Sci 2023; 14:4681-4696. [PMID: 37181765 PMCID: PMC10171076 DOI: 10.1039/d3sc00166k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Papain-like protease (PLpro) is a promising therapeutic target against SARS-CoV-2, but its restricted S1/S2 subsites pose an obstacle in developing active site-directed inhibitors. We have recently identified C270 as a novel covalent allosteric site for SARS-CoV-2 PLpro inhibitors. Here we present a theoretical investigation of the proteolysis reaction catalyzed by the wild-type SARS-CoV-2 PLpro as well as the C270R mutant. Enhanced sampling MD simulations were first performed to explore the influence of C270R mutation on the protease dynamics, and sampled thermodynamically favorable conformations were then submitted to MM/PBSA and QM/MM MD simulations for thorough characterization of the protease-substrate binding and covalent reactions. The disclosed proteolysis mechanism of PLpro, as characterized by the occurrence of proton transfer from the catalytic C111 to H272 prior to the substrate binding and with deacylation being the rate-determining step of the whole proteolysis process, is not completely identical to that of the 3C-like protease, another key cysteine protease of coronaviruses. The C270R mutation alters the structural dynamics of the BL2 loop that indirectly impairs the catalytic function of H272 and reduces the binding of the substrate with the protease, ultimately showing an inhibitory effect on PLpro. Together, these results provide a comprehensive understanding at the atomic level of the key aspects of SARS-CoV-2 PLpro proteolysis, including the catalytic activity allosterically regulated by C270 modification, which is crucial to the follow-up inhibitor design and development.
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Affiliation(s)
- Qiang Shao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jiameng Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Hangchen Hu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
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4
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Movilla S, Martí S, Roca M, Moliner V. Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer's Disease. J Chem Inf Model 2023; 63:950-958. [PMID: 36648276 PMCID: PMC10882967 DOI: 10.1021/acs.jcim.2c01198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Alzheimer's disease represents one of the most ambitious challenges for biomedical sciences due to the growing number of cases worldwide in the elderly population and the lack of efficient treatments. One of the recent attempts to develop a treatment points to the cysteine protease RgpB as a promising drug target. In this attempt, several small-molecule covalent inhibitors of this enzyme have been proposed. Here, we report a computational study at the atomic level of the inhibition mechanism of the most promising reported compounds. Molecular dynamics simulations were performed on six of them, and their binding energies in the active site of the protein were computed. Contact maps and interaction energies were decomposed by residues to disclose those key interactions with the enzyme. Finally, quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations were performed to evaluate the reaction mechanism by which these drug candidates lead to covalently bound complexes, inhibiting the RgpB protease. The results provide a guide for future re-design of prospective and efficient inhibitors for the treatment of Alzheimer's disease.
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Affiliation(s)
- Santiago Movilla
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Sergio Martí
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Maite Roca
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
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5
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A New Pharmacological Vitreolysis through the Supplement of Mixed Fruit Enzymes for Patients with Ocular Floaters or Vitreous Hemorrhage-Induced Floaters. J Clin Med 2022; 11:jcm11226710. [PMID: 36431188 PMCID: PMC9695351 DOI: 10.3390/jcm11226710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Purpose: Ocular floaters caused by vitreous degeneration or blood clots may interfere with various visual functions. Our study investigated the pharmacologic effects of oral supplementation of mixed fruit enzymes (MFEs) for treating spontaneous symptomatic vitreous opacities (SVOs) and those secondary to vitreous hemorrhage (VH). Methods: 224 patients with monocular symptomatic vitreous opacities (SVOs) were recruited between September and December 2017 and received oral supplementation of MFEs (190 mg bromelain, 95 mg papain, and 95 mg ficin) for 3 months in a double-blind clinical trial. Participants were divided according to the etiology of the SVOs, spontaneous (experiment 1) versus VH (experiment 2), and then randomly assigned into four treatments groups: one group received oral vitamin C, as a placebo; and the other 3 groups received 1 capsule per day (low dose), 2 capsules per day (middle dose), or 3 capsules per day (high dose) of MFEs. The number of SVOs was determined at baseline and then 1, 2, and 3 months after initiating treatment. Further, in cases secondary to VH, the changes in corrected distance visual acuity (CDVA) were assessed after 3 months. Second, we compared the free radical scavenging capabilities of each substance: vitamin C, bromelain, papain, ficin, and MFEs (combination of bromelain, papain, and ficin) by DDPH assay. Finally, SVOs-related symptoms and satisfaction with the treatments were evaluated at the last follow-up visit Results: In experiment 1, the disappearance rate of SVOs was 55%, 62.5%, and 70% after taking 1, 2, and 3 capsules daily, respectively (total p < 0.001), in a dose-dependent manner. In experiment 2, the disappearance rate of VH-induced SVOs was 18%, 25%, and 56% (p < 0.001) after 1, 2, and 3 capsules of the supplement daily, respectively. Additionally, the patients’ vision elevated from 0.63LogMAR to 0.19LogMAR (p = 0.008). Conclusions: A pharmacological approach using a high dose of oral supplementation with MFEs (bromelain, papain, and ficin) was effective in reducing vitreous opacities, even after intraocular hemorrhage. Furthermore, pharmacologic vitreolysis with MFEs supplementation showed high patient satisfaction, and also improved CDVA in patients with vitreous hemorrhage-induced floaters
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6
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Zlobin A, Golovin A. Between Protein Fold and Nucleophile Identity: Multiscale Modeling of the TEV Protease Enzyme-Substrate Complex. ACS OMEGA 2022; 7:40279-40292. [PMID: 36385818 PMCID: PMC9647873 DOI: 10.1021/acsomega.2c05201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
The cysteine protease from the tobacco etch virus (TEVp) is a well-known and widely utilized enzyme. TEVp's chymotrypsin-like fold is generally associated with serine catalytic triads that differ in terms of a reaction mechanism from the most well-studied papain-like cysteine proteases. The question of what dominates the TEVp mechanism, nucleophile identity, or structural composition has never been previously addressed. Here, we use enhanced sampling multiscale modeling to uncover that TEVp combines the features of two worlds in such a way that potentially hampers its activity. We show that TEVp cysteine is strictly in the anionic form in a free enzyme similar to papain. Peptide binding shifts the equilibrium toward the nucleophile's protonated form, characteristic of chymotrypsin-like proteases, although the cysteinyl anion form is still present and interconversion is rapid. This way cysteine protonation generates enzyme states that are a diversion from the most effective course of action, with only 13.2% of Michaelis complex sub-states able to initiate the reaction. As a result, we propose an updated view on the reaction mechanism catalyzed by TEVp. We also demonstrate that AlphaFold is able to construct protease-substrate complexes with high accuracy. We propose that our findings open a way for its industrious use in enzymological tasks. Unique features of TEVp discovered in this work open a discussion on the evolutionary history and trade-offs of optimizing serine triad-associated folds to cysteine as a nucleophile.
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Affiliation(s)
- Alexander Zlobin
- Belozersky
Institute of Physico-Chemical Biology, Lomonosov
Moscow State University, 119991 Moscow, Russia
- Shemyakin
and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Andrey Golovin
- Belozersky
Institute of Physico-Chemical Biology, Lomonosov
Moscow State University, 119991 Moscow, Russia
- Shemyakin
and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Sirius
University of Science and Technology, 354340 Sochi, Russia
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7
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Dos Santos AM, Oliveira ARS, da Costa CHS, Kenny PW, Montanari CA, Varela JDJG, Lameira J. Assessment of Reversibility for Covalent Cysteine Protease Inhibitors Using Quantum Mechanics/Molecular Mechanics Free Energy Surfaces. J Chem Inf Model 2022; 62:4083-4094. [PMID: 36044342 DOI: 10.1021/acs.jcim.2c00466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have used molecular dynamics (MD) simulations with hybrid quantum mechanics/molecular mechanics (QM/MM) potentials to investigate the reaction mechanism for covalent inhibition of cathepsin K and assess the reversibility of inhibition. The computed free energy profiles suggest that a nucleophilic attack by the catalytic cysteine on the inhibitor warhead and proton transfer from the catalytic histidine occur in a concerted manner. The results indicate that the reaction is more strongly exergonic for the alkyne-based inhibitors, which bind irreversibly to cathepsin K, than for the nitrile-based inhibitor odanacatib, which binds reversibly. Gas-phase energies were also calculated for the addition of methanethiol to structural prototypes for a number of warheads of interest in cysteine protease inhibitor design in order to assess electrophilicity. The approaches presented in this study are particularly applicable to assessment of novel warheads, and computed transition state geometries can be incorporated into molecular models for covalent docking.
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Affiliation(s)
- Alberto M Dos Santos
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, 66075-110 Belém, PA, Brazil.,Laboratório de Química Quântica Computacional, Universidade Federal do Maranhão, 65080 401 São Luis, MA, Brazil
| | - Amanda Ruslana Santana Oliveira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, 66075-110 Belém, PA, Brazil
| | - Clauber H S da Costa
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, 66075-110 Belém, PA, Brazil
| | - Peter W Kenny
- Medicinal and Biological Chemistry Group, Institute of Chemistry of Sao Carlos, University of Sao Paulo, Avenue Trabalhador Sancarlense 400, 13566-590 São Carlos, SP, Brazil
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group, Institute of Chemistry of Sao Carlos, University of Sao Paulo, Avenue Trabalhador Sancarlense 400, 13566-590 São Carlos, SP, Brazil
| | - Jaldyr de Jesus G Varela
- Laboratório de Química Quântica Computacional, Universidade Federal do Maranhão, 65080 401 São Luis, MA, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, 66075-110 Belém, PA, Brazil
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8
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Gisdon FJ, Bombarda E, Ullmann GM. Serine and Cysteine Peptidases: So Similar, Yet Different. How the Active-Site Electrostatics Facilitates Different Reaction Mechanisms. J Phys Chem B 2022; 126:4035-4048. [PMID: 35609250 DOI: 10.1021/acs.jpcb.2c01484] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The catalytic mechanisms of serine and cysteine peptidases are similar: the proton of the nucleophile (serine or cysteine) is transferred to the catalytic histidine, and the nucleophile attacks the substrate for cleavage. However, they differ in an important aspect: cysteine peptidases form a stable ion-pair intermediate in a stepwise mechanism, while serine peptidases follow a concerted mechanism. While it is known that a positive electrostatic potential at the active site of cysteine peptidases stabilizes the cysteine anion in the ion-pair state, the physical basis of the concerted mechanism of serine peptidases is poorly understood. In this work, we use continuum electrostatic analysis and quantum mechanical/molecular mechanical (QM/MM) simulations to demonstrate that a destabilization of an anionic serine by a negative electrostatic potential in combination with a compact active site geometry facilitates a concerted mechanism in serine peptidases. Moreover, we show that an anionic serine would destabilize the protein significantly compared to an anionic cysteine in cysteine peptidases, which underlines the necessity of a concerted mechanism for serine peptidases. On the basis of our calculations on an inactive serine mutant of a natural cysteine peptidase, we show that the energy barrier for the catalytic mechanism can be substantially decreased by introducing a negative electrostatic potential and by reducing the relevant distances indicating that these parameters are essential for the activity of serine peptidases. Our work demonstrates that the concerted mechanism of serine peptidases represents an evolutionary innovative way to perform catalysis without the energetically expensive need to stabilize the anionic serine. In contrast in cysteine peptidases, the anionic cysteine is energetically easily accessible and it is a very efficient nucleophile, making these peptidases mechanistically simple. However, a cysteine is highly oxygen sensitive, which is problematic in an aerobic environment. On the basis of the analysis in this work, we suggest that serine peptidases represent an oxygen-insensitive alternative to cysteine peptidases.
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Affiliation(s)
- Florian J Gisdon
- Biochemistry, University of Bayreuth, Universitätsstraße 30, BGI, 95447 Bayreuth, Germany.,Computational Biochemistry, University of Bayreuth, Universitätsstraße 30, BGI, 95447 Bayreuth, Germany
| | - Elisa Bombarda
- Computational Biochemistry, University of Bayreuth, Universitätsstraße 30, BGI, 95447 Bayreuth, Germany
| | - G Matthias Ullmann
- Computational Biochemistry, University of Bayreuth, Universitätsstraße 30, BGI, 95447 Bayreuth, Germany
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9
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Movilla S, Martí S, Roca M, Moliner V. Unrevealing the Proteolytic Activity of RgpB Gingipain from Computational Simulations. J Chem Inf Model 2021; 61:4582-4593. [PMID: 34472342 DOI: 10.1021/acs.jcim.1c00666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease represents one of the greatest medical concerns for today's population and health services. Its multifactorial inherent nature represents a challenge for its treatment and requires the development of a broad spectrum of drugs. Recently, the cysteine protease gingipain RgpB has been related to neurodegenerative diseases, including Alzheimer's disease, and its inhibition appears to be a promising neuroprotective strategy. Given these features, a computational study that integrates molecular dynamics (MD) simulations with classical and hybrid quantum mechanics/molecular mechanics (QM/MM) potentials was carried out to unravel the atomistic details of RgpB activity. First, a preliminary study based on principal component analysis (PCA), determined the protonation state of the Cys/His catalytic dyad, as well as the crucial role of a flexible loop that favors reactive interactions of the catalytic residues and the peptide in the precatalytic state in its closed conformation. Then, different mechanisms were explored by means of QM/MM MD simulations. The most favorable mechanism consists of two stages. First is an acylation stage that takes place in two steps where, initially, the sulfur atom of the C244 residue attacks the carbonylic carbon of the peptide and the proton of the C244 residue is transferred to the amino group of the peptide in a concerted manner. Subsequently, the peptide bond is broken, and a fragment of the peptide is released. After that, the deacylation stage takes place in a single step where a water molecule attacks the carbonylic carbon of the peptide and a proton of the water is transferred to the C244 residue. The free energy barrier of the rate limiting step is in very good agreement with available experimental data. The mechanism exhibits an unusual role of H211 residue compared with other cysteine proteases but a crucial role of the peptide in triggering the catalysis. Notably, the atomic and energetic particularities found represent a significant contribution to the comprehension of the reaction mechanism and a great opportunity for the design of efficient inhibitors of gingipain RgpB.
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Affiliation(s)
- Santiago Movilla
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
| | - Sergio Martí
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
| | - Maite Roca
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
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10
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Arafet K, González FV, Moliner V. Elucidating the Dual Mode of Action of Dipeptidyl Enoates in the Inhibition of Rhodesain Cysteine Proteases. Chemistry 2021; 27:10142-10150. [PMID: 33852187 DOI: 10.1002/chem.202100892] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/06/2023]
Abstract
A computational study of the two possible inhibition mechanisms of rhodesain cysteine protease by the dipeptidyl enoate Cbz-Phe-Leu-CH=CH-CO2 C2 H5 has been carried out by means of molecular dynamics simulations with hybrid QM/MM potentials. The low free energy barriers confirm that the Cys25 residue can attack both Cβ and C1 atoms of the inhibitor, confirming a dual mode of action in the inhibition of the rhodesain by enoates. According to the results, the inhibition process through the Cys25 attack on the Cβ atom of the inhibitor is an exergonic and irreversible process, while the inhibition process when Cys25 attacks on the C1 atom of the inhibitor is and exergonic but reversible process. The interactions between the inhibitor and rhodesain suggest that P2 is the most important fragment to consider in the design of new efficient inhibitors of rhodesain. These results may be useful for the design of new inhibitors of rhodesain and other related cysteine proteases based on dipeptidyl enoates scaffolds.
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Affiliation(s)
- Kemel Arafet
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castelló, Spain
| | - Florenci V González
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain
| | - Vicent Moliner
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castelló, Spain
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11
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Elsässer B, Goettig P. Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies. Int J Mol Sci 2021; 22:3232. [PMID: 33810118 PMCID: PMC8004986 DOI: 10.3390/ijms22063232] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/11/2022] Open
Abstract
Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.
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Affiliation(s)
| | - Peter Goettig
- Structural Biology Group, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria;
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12
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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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13
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Qian Y, Wei J, Wang Y, You D, Lin F, Yue W, Bi Y. Thermal and enzymatic dual‐stimuli responsive linear‐dendritic block copolymers based on poly(
N
‐vinylcaprolactam). POLYM ADVAN TECHNOL 2020. [DOI: 10.1002/pat.5006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yangyang Qian
- College of Chemistry and Chemical Engineering Yunnan Normal University Kunming China
| | - Junwu Wei
- College of Chemistry and Chemical Engineering Yunnan Normal University Kunming China
| | - Yujia Wang
- College of Chemistry and Chemical Engineering Yunnan Normal University Kunming China
| | - Dan You
- College of Chemistry and Chemical Engineering Yunnan Normal University Kunming China
| | - Feng Lin
- College of Chemistry and Chemical Engineering Yunnan Normal University Kunming China
| | - Wenzhe Yue
- College of Chemistry and Chemical Engineering Yunnan Normal University Kunming China
| | - Yunmei Bi
- College of Chemistry and Chemical Engineering Yunnan Normal University Kunming China
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14
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Prejanò M, Romeo I, Russo N, Marino T. On the Catalytic Activity of the Engineered Coiled-Coil Heptamer Mimicking the Hydrolase Enzymes: Insights from a Computational Study. Int J Mol Sci 2020; 21:E4551. [PMID: 32604744 PMCID: PMC7352413 DOI: 10.3390/ijms21124551] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 01/22/2023] Open
Abstract
Recently major advances were gained on the designed proteins aimed to generate biomolecular mimics of proteases. Although such enzyme-like catalysts must still suffer refinements for improving the catalytic activity, at the moment, they represent a good example of artificial enzymes to be tested in different fields. Herein, a de novo designed homo-heptameric peptide assembly (CC-Hept) where the esterase activity towards p-nitro-phenylacetate was obtained for introduction of the catalytic triad (Cys-His-Glu) into the hydrophobic matrix, is the object of the present combined molecular dynamics and quantum mechanics/molecular mechanics investigation. Constant pH Molecular Dynamics simulations on the apoform of CC-Hept suggested that the Cys residues are present in the protonated form. Molecular dynamics (MD) simulations of the enzyme-substrate complex evidenced the attitude of the enzyme-like system to retain water molecules, necessary in the hydrolytic reaction, in correspondence of the active site, represented by the Cys-His-Glu triad on each of the seven chains, without significant structural perturbations. A detailed reaction mechanism of esterase activity of CC-Hept-Cys-His-Glu was investigated on the basis of the quantum mechanics/molecular mechanics calculations employing a large quantum mechanical (QM) region of the active site. The proposed mechanism is consistent with available esterases kinetics and structural data. The roles of the active site residues were also evaluated. The deacylation phase emerged as the rate-determining step, in agreement with esterase activity of other natural proteases.
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Affiliation(s)
| | | | - Nino Russo
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy; (M.P.); (I.R.)
| | - Tiziana Marino
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy; (M.P.); (I.R.)
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15
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Świderek K, Moliner V. Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 M pro by QM/MM computational methods. Chem Sci 2020; 11:10626-10630. [PMID: 34094317 PMCID: PMC8162313 DOI: 10.1039/d0sc02823a] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
SARS-CoV-2 Mpro is one of the enzymes essential for the replication process of the virus responsible for the COVID-19 pandemic. This work is focused on exploring its proteolysis reaction by means of QM/MM methods. The resulting free energy landscape of the process provides valuable information on the species appearing along the reaction path and suggests that the mechanism of action of this enzyme, taking place in four steps, slightly differs from that of other cysteine proteases. Our predictions, which are in agreement with some recently published experimental data, can be used to guide the design of COVID-19 antiviral compounds with clinical potential. The molecular mechanism of the proteolysis reaction catalyzed by SARS-CoV-2 Mpro, one of the enzymes essential for the replication process of the virus responsible for the COVID-19 pandemic, is described using computational QM/MM methods.![]()
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Affiliation(s)
- Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I 12071 Castelló Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I 12071 Castelló Spain
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16
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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: 14] [Impact Index Per Article: 3.5] [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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17
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Yang F, Totsingan F, Dolan E, Khare SD, Gross RA. Protease-Catalyzed l-Aspartate Oligomerization: Substrate Selectivity and Computational Modeling. ACS OMEGA 2020; 5:4403-4414. [PMID: 32175488 PMCID: PMC7066554 DOI: 10.1021/acsomega.9b03290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/11/2019] [Indexed: 05/20/2023]
Abstract
Poly(aspartic acid) (PAA) is a biodegradable water-soluble anionic polymer that can potentially replace poly(acrylic acid) for industrial applications and has shown promise for regenerative medicine and drug delivery. This paper describes an efficient and sustainable route that uses protease catalysis to convert l-aspartate diethyl ester (Et2-Asp) to oligo(β-ethyl-α-aspartate), oligo(β-Et-α-Asp). Comparative studies of protease activity for oligo(β-Et-α-Asp) synthesis revealed α-chymotrypsin to be the most efficient. Papain, which is highly active for l-glutamic acid diethyl ester (Et2-Glu) oligomerization, is inactive for Et2-Asp oligomerization. The assignment of α-linkages between aspartate repeat units formed by α-chymotrypsin catalysis is based on nuclear magnetic resonance (NMR) trifluoacetic acid titration, circular dichroism, and NMR structural analysis. The influence of reaction conditions (pH, temperature, reaction time, and buffer/monomer/α-chymotrypsin concentrations) on oligopeptide yield and average degree of polymerization (DPavg) was determined. Under preferred reaction conditions (pH 8.5, 40 °C, 0.5 M Et2-Asp, 3 mg/mL α-chymotrypsin), Et2-Asp oligomerizations reached maximum oligo(β-Et-α-Asp) yields of ∼60% with a DPavg of ∼12 (M n 1762) in just 5 min. Computational modeling using Rosetta software gave relative energies of substrate docking to papain and α-chymotrypsin active sites. The substrate preference calculated by Rosetta modeling of α-chymotrypsin and papain for Et2-Asp and Et2-Glu oligomerizations, respectively, is consistent with experimental results.
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Affiliation(s)
- Fan Yang
- Center for Biotechnology
and Interdisciplinary Studies (CBIS), Rensselaer
Polytechnic Institute, 1623 15th Street, Troy, New York 12180, United
States
| | - Filbert Totsingan
- Center for Biotechnology
and Interdisciplinary Studies (CBIS), Rensselaer
Polytechnic Institute, 1623 15th Street, Troy, New York 12180, United
States
| | - Elliott Dolan
- Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Sagar D. Khare
- Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Richard A. Gross
- Center for Biotechnology
and Interdisciplinary Studies (CBIS), Rensselaer
Polytechnic Institute, 1623 15th Street, Troy, New York 12180, United
States
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18
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Silva JRA, Cianni L, Araujo D, Batista PHJ, de Vita D, Rosini F, Leitão A, Lameira J, Montanari CA. Assessment of the Cruzain Cysteine Protease Reversible and Irreversible Covalent Inhibition Mechanism. J Chem Inf Model 2020; 60:1666-1677. [PMID: 32126170 DOI: 10.1021/acs.jcim.9b01138] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Reversible and irreversible covalent ligands are advanced cysteine protease inhibitors in the drug development pipeline. K777 is an irreversible inhibitor of cruzain, a necessary enzyme for the survival of the Trypanosoma cruzi (T. cruzi) parasite, the causative agent of Chagas disease. Despite their importance, irreversible covalent inhibitors are still often avoided due to the risk of adverse effects. Herein, we replaced the K777 vinyl sulfone group with a nitrile moiety to obtain a reversible covalent inhibitor (Neq0682) of cysteine protease. Then, we used advanced experimental and computational techniques to explore details of the inhibition mechanism of cruzain by reversible and irreversible inhibitors. The isothermal titration calorimetry (ITC) analysis shows that inhibition of cruzain by an irreversible inhibitor is thermodynamically more favorable than by a reversible one. The hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) and Molecular Dynamics (MD) simulations were used to explore the mechanism of the reaction inhibition of cruzain by K777 and Neq0682. The calculated free energy profiles show that the Cys25 nucleophilic attack and His162 proton transfer occur in a single step for a reversible inhibitor and two steps for an irreversible covalent inhibitor. The hybrid QM/MM calculated free energies for the inhibition reaction correspond to -26.7 and -5.9 kcal mol-1 for K777 and Neq0682 at the MP2/MM level, respectively. These results indicate that the ΔG of the reaction is very negative for the process involving K777, consequently, the covalent adduct cannot revert to a noncovalent protein-ligand complex, and its binding tends to be irreversible. Overall, the present study provides insights into a covalent inhibition mechanism of cysteine proteases.
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Affiliation(s)
- José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos. Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, CEP 66075-110, Belém, Pará, Brazil
| | - Lorenzo Cianni
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Deborah Araujo
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Pedro Henrique Jatai Batista
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Daniela de Vita
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Fabiana Rosini
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Andrei Leitão
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos. Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, CEP 66075-110, Belém, Pará, Brazil
| | - Carlos A Montanari
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
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19
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da Costa CHS, Bonatto V, Dos Santos AM, Lameira J, Leitão A, Montanari CA. Evaluating QM/MM Free Energy Surfaces for Ranking Cysteine Protease Covalent Inhibitors. J Chem Inf Model 2020; 60:880-889. [PMID: 31944110 DOI: 10.1021/acs.jcim.9b00847] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
One tactic for cysteine protease inhibition is to form a covalent bond between an electrophilic atom of the inhibitor and the thiol of the catalytic cysteine. In this study, we evaluate the reaction free energy obtained from a hybrid quantum mechanical/molecular mechanical (QM/MM) free energy profile as a predictor of affinity for reversible, covalent inhibitors of rhodesain. We demonstrate that the reaction free energy calculated with the PM6/MM potential is in agreement with the experimental data and suggest that the free energy profile for covalent bond formation in a protein environment may be a useful tool for the inhibitor design.
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Affiliation(s)
- Clauber H S da Costa
- Laboratório de Planejamento e Desenvolvimento de Fármacos , Universidade Federal do Pará , Rua Augusto Correa S/N , 66075-110 Belém , PA , Brazil
| | - Vinícius Bonatto
- Grupo de Quı́mica Medicinal do Instituto de Quı́mica de São Carlos da , Universidade de São Paulo, NEQUIMED/IQSC/USP , 13566-590 São Carlos , SP , Brazil
| | - Alberto M Dos Santos
- Laboratório de Planejamento e Desenvolvimento de Fármacos , Universidade Federal do Pará , Rua Augusto Correa S/N , 66075-110 Belém , PA , Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos , Universidade Federal do Pará , Rua Augusto Correa S/N , 66075-110 Belém , PA , Brazil.,Grupo de Quı́mica Medicinal do Instituto de Quı́mica de São Carlos da , Universidade de São Paulo, NEQUIMED/IQSC/USP , 13566-590 São Carlos , SP , Brazil
| | - Andrei Leitão
- Grupo de Quı́mica Medicinal do Instituto de Quı́mica de São Carlos da , Universidade de São Paulo, NEQUIMED/IQSC/USP , 13566-590 São Carlos , SP , Brazil
| | - Carlos A Montanari
- Grupo de Quı́mica Medicinal do Instituto de Quı́mica de São Carlos da , Universidade de São Paulo, NEQUIMED/IQSC/USP , 13566-590 São Carlos , SP , Brazil
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20
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Deng Q, Li SJ, Wei D, Lan Y. Insights into Lewis base-catalyzed chemoselective [3 + 2] and [3 + 4] annulation reactions of MBH carbonates. Org Chem Front 2020. [DOI: 10.1039/d0qo00457j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chemoselectivity of Lewis base-catalyzed [3 + 2] and [3 + 4] annulation reactions of MBH carbonates can be predicted using FMO overlap analysis.
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Affiliation(s)
- Qianqian Deng
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Shi-Jun Li
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Donghui Wei
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Yu Lan
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
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21
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Deng Q, Wang Y, Li SJ, Qu LB, Lan Y, Wei D. Origin and stabilization of axial chirality in the construction of naphthyl-C2-indoles: a DFT study. Org Chem Front 2020. [DOI: 10.1039/d0qo00936a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A novel method for predicting the stabilization of axial chirality in the construction of naphthyl-C2-indoles has been suggested for the first time.
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Affiliation(s)
- Qianqian Deng
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Yang Wang
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 450002
- P.R. China
| | - Shi-Jun Li
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Ling-Bo Qu
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Yu Lan
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Donghui Wei
- College of Chemistry
- and Institute of Green Catalysis
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
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22
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Lameira J, Bonatto V, Cianni L, Dos Reis Rocho F, Leitão A, Montanari CA. Predicting the affinity of halogenated reversible covalent inhibitors through relative binding free energy. Phys Chem Chem Phys 2019; 21:24723-24730. [PMID: 31680132 DOI: 10.1039/c9cp04820k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Nitrile reversible covalent inhibitors of human cathepsin L (hCatL) bind covalently to the side chain of the catalytic Cys25 residue in the S1 pocket to form thioimidates. Predicting the binding of reversible covalent inhibitors is essential for their practical application in drug design. In this report, five nitrile-based inhibitors coded Neq0570, Neq0710, Neq0802, Neq0803 and Neq0804 had their hCatL inhibition constants, Ki, determined. These analogs of the prototypical Neq0570 are halogenated reversible covalent inhibitors of hCatL, which bear a halogen atom in the meta position of the P3 benzyl ring that can form a halogen bond with the Gly61 of the hCatL. To describe halogen bonding interaction in an inhibitor-hCatL complex, we applied an extra point (EP) of charge to represent the anisotropic distribution of charge on the iodine, bromine and chlorine atoms. Besides, we have used alchemical free energy calculations for evaluating the overall relative binding free energies of these inhibitors using a two-state binding model: noncovalent and covalent bond states. Our results show that free energy perturbation (FEP) can predict the hCatL binding affinities of halogenated reversible covalent inhibitors in close agreement with experiments.
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Affiliation(s)
- Jerônimo Lameira
- On leave from Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, 66075-110, Belém, PA, Brazil.
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23
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Artificial cysteine-lipases with high activity and altered catalytic mechanism created by laboratory evolution. Nat Commun 2019; 10:3198. [PMID: 31324776 PMCID: PMC6642262 DOI: 10.1038/s41467-019-11155-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/24/2019] [Indexed: 11/13/2022] Open
Abstract
Engineering artificial enzymes with high activity and catalytic mechanism different from naturally occurring enzymes is a challenge in protein design. For example, many attempts have been made to obtain active hydrolases by introducing a Ser → Cys exchange at the respective catalytic triads, but this generally induced a breakdown of activity. We now report that this long-standing dogma no longer pertains, provided additional mutations are introduced by directed evolution. By employing Candida antarctica lipase B (CALB) as the model enzyme with the Ser-His-Asp catalytic triad, a highly active cysteine-lipase having a Cys-His-Asp catalytic triad and additional mutations W104V/A281Y/A282Y/V149G can be evolved, showing a 40-fold higher catalytic efficiency than wild-type CALB in the hydrolysis of 4-nitrophenyl benzoate, and tolerating bulky substrates. Crystal structures, kinetics, MD simulations and QM/MM calculations reveal dynamic features and explain all results, including the preference of a two-step mechanism involving the zwitterionic pair Cys105−/His224+ rather than a concerted process. Candida antarctica lipase B (CALB) is a serine lipase. Here, the authors use directed evolution to exchange serine with cysteine in the catalytic triad of the enzyme, thereby obtaining a highly active CALB variant that — unlike the wild type — accommodates bulky substrates.
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24
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Gimenez-Dejoz J, Tsuchiya K, Numata K. Insights into the Stereospecificity in Papain-Mediated Chemoenzymatic Polymerization from Quantum Mechanics/Molecular Mechanics Simulations. ACS Chem Biol 2019; 14:1280-1292. [PMID: 31063345 DOI: 10.1021/acschembio.9b00259] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemoenzymatic peptide synthesis is an efficient and clean method to generate polypeptides for new applications in the fields of biomedical and functional materials. However, this enzyme-mediated synthesis is dependent on the reaction rate of the protease biocatalyst, which is essentially determined by the natural substrate specificity of the enzyme. Papain, one of the most studied cysteine proteases, is extensively used for the chemoenzymatic synthesis of new polypeptides. Similar to most proteases, papain displays high stereospecificity toward l-amino acids, with limited reactivity for the d-stereoisomer counterparts. However, the incorporation of d-amino acids into peptides is a promising approach to increase their biostability by conferring intrinsic resistance to proteolysis. Herein, we determined the stereospecific-limiting step of the papain-mediated polymerization reaction with the chiral substrates l/d-alanine ethyl ester (Ala-OEt). Afterward, we used Quantum Mechanics/Molecular Mechanics (QM/MM) simulations to study the catalytic mechanism at atomic level of detail and investigate the origin of its stereospecificity. The experimental and computational results show that papain is able to attack both l- and d-stereoisomers of Ala-OEt, forming an enzyme-substrate intermediate, and that the two reactions display a similar activation barrier. Moreover, we found that the reduced catalytic activity of papain in the polymerization of d-amino acids arises from the aminolysis step of the reaction, in which l-Ala-OEt displays a significantly lower free-energy barrier (12 kcal/mol) than d-Ala-OEt (30 kcal/mol). Further simulations suggest that the main factor affecting the polymerization of d-amino acids is the configuration of the d-acyl-intermediate enzyme, and in particular the orientation of its methyl group, which hinders the nucleophilic attack by other monomers and thus the formation of polypeptides.
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Affiliation(s)
- Joan Gimenez-Dejoz
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Kousuke Tsuchiya
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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25
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Dos Santos AM, Cianni L, De Vita D, Rosini F, Leitão A, Laughton CA, Lameira J, Montanari CA. Experimental study and computational modelling of cruzain cysteine protease inhibition by dipeptidyl nitriles. Phys Chem Chem Phys 2019; 20:24317-24328. [PMID: 30211406 DOI: 10.1039/c8cp03320j] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chagas disease affects millions of people in Latin America. This disease is caused by the protozoan parasite Trypanossoma cruzi. The cysteine protease cruzain is a key enzyme for the survival and propagation of this parasite lifecycle. Nitrile-based inhibitors are efficient inhibitors of cruzain that bind by forming a covalent bond with this enzyme. Here, three nitrile-based inhibitors dubbed Neq0409, Neq0410 and Neq0570 were synthesized, and the thermodynamic profile of the bimolecular interaction with cruzain was determined using isothermal titration calorimetry (ITC). The result suggests the inhibition process is enthalpy driven, with a detrimental contribution of entropy. In addition, we have used hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) and Molecular Dynamics (MD) simulations to investigate the reaction mechanism of reversible covalent modification of cruzain by Neq0409, Neq0410 and Neq0570. The computed free energy profile shows that the nucleophilic attack of Cys25 on the carbon C1 of inhibitiors and the proton transfer from His162 to N1 of the dipeptidyl nitrile inhibitor take place in a single step. The calculated free energy of the inhibiton reaction is in agreement with covalent experimental binding. Altogether, the results reported here suggests that nitrile-based inhibitors are good candidates for the development of reversible covalent inhibitors of cruzain and other cysteine proteases.
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Affiliation(s)
- Alberto Monteiro Dos Santos
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Cidade Universitária Prof. José da Silveira Netto, Rua Augusto Correa S/N, Belém-PA, Brazil.
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26
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Li X, Li SJ, Wang Y, Wang Y, Qu LB, Li Z, Wei D. Insights into NHC-catalyzed oxidative α-C(sp3)–H activation of aliphatic aldehydes and cascade [2 + 3] cycloaddition with azomethine imines. Catal Sci Technol 2019. [DOI: 10.1039/c9cy00526a] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The NHC catalyst is identified to promote [2 + 3] cycloaddition by avoiding the poor FMO overlap mode in theory.
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Affiliation(s)
- Xue Li
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Shi-Jun Li
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Yanyan Wang
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Yang Wang
- Department of Material and Chemical Engineering
- Zhengzhou University of Light Industry
- Zhengzhou
- P.R. China
| | - Ling-Bo Qu
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Zhongjun Li
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
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Liu Q, Li SJ, Li. X, Qu LB, Wei D. A Computational Study on the 4-Dimethylaminopyridine (DMAP)-Catalyzed Regioselective [2+4] Cyclization of Allenic Ester with Cyclic Ketimine. ChemistrySelect 2018. [DOI: 10.1002/slct.201802267] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qiuli Liu
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P. R. China
| | - Shi-Jun Li
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P. R. China
| | - Xue Li.
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P. R. China
| | - Ling-Bo Qu
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P. R. China
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28
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Li X, Wang Y, Wang Y, Tang M, Qu LB, Li Z, Wei D. Insights into the N-Heterocyclic Carbene (NHC)-Catalyzed Oxidative γ-C(sp 3)-H Deprotonation of Alkylenals and Cascade [4 + 2] Cycloaddition with Alkenylisoxazoles. J Org Chem 2018; 83:8543-8555. [PMID: 29927597 DOI: 10.1021/acs.joc.8b01112] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The N-heterocyclic carbene (NHC)-catalyzed oxidative C-H deprotonations have attracted increasing attention; however, the general mechanism regarding this kind of oxidative organocatalysis remains unclear. In this paper, the competing mechanisms and origin of the stereoselectivity of the NHC-catalyzed oxidative γ-C(sp3)-H deprotonation of alkylenals and cascade [4 + 2] cycloaddition with alkenylisoxazoles were systematically investigated for the first time using density functional theory (DFT). The computed results indicate that the oxidation of the Breslow intermediate by 3,3',5,5'-tetra- tert-butyl diphenoquinone (DQ) via a hydride transfer to oxygen (HTO) pathway is the most favorable among the four competing pathways. In addition, the analyses demonstrate that oxidant DQ plays a double role, i.e., strengthening the acidity of the hydrogen of the γ-carbon of alkylenal and forming π···π interactions with conjugated C═C bonds to promote the γ-C(sp3)-H deprotonation. The NHC catalyst acts as a Lewis base, and the hydrogen-bond network between the NHC and the substrate formed in the key Michael addition step is responsible for the origin of the stereoselectivity. Further DFT calculations reveal that the nonpolar solvent can stabilize the nonpolar R isomer but destabilize the polar S isomer for the stereoselectivity-determining transition states, thus improving the stereoselectivity.
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29
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Fekete A, Komáromi I. Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain. Phys Chem Chem Phys 2018; 18:32847-32861. [PMID: 27883128 DOI: 10.1039/c6cp06869c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to be a single elementary step process in all the methods we applied.
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Affiliation(s)
- Attila Fekete
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Nagyerdei krt. 98., Debrecen, Hungary.
| | - István Komáromi
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Nagyerdei krt. 98., Debrecen, Hungary.
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30
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Yu J, Chen X, Jiang M, Wang A, Yang L, Pei X, Zhang P, Wu SG. Efficient promiscuous Knoevenagel condensation catalyzed by papain confined in Cu3(PO4)2 nanoflowers. RSC Adv 2018; 8:2357-2364. [PMID: 35541490 PMCID: PMC9077389 DOI: 10.1039/c7ra12940h] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 12/29/2017] [Indexed: 11/21/2022] Open
Abstract
To develop an efficient and green immobilized biocatalyst for promiscuous catalysis which has a broad scope of applications, hybrid nanoflower (hNF) confined papain as a biocatalyst has been proposed and characterized in this study. hNFs were firstly prepared through mixing CuSO4 aqueous solution with papain in phosphate saline (PBS) at room temperature. The resulting hNFs were characterized by SEM and verified through a hydrolysis reaction with N-benzoyl-dl-arginine amide as substrate. Under optimal conditions, this nano-biocatalyst demonstrated a 15-fold hydrolytic activity compared with papain of free form, along with better thermal stability. A series of reaction factors (reaction temperature, time, and solvent) have been investigated for Knoevenagel condensation reactions with hNFs as catalyst. At optimal conditions, product yield of the hNFs catalyzed reaction was 1.3 fold higher than that of the free enzyme with benzaldehyde and acetylacetone as substrates. A few aldehydes and methylene compounds have also been used to test the generality and scope of this new enzymatic promiscuity. To sum up, the obtained hNFs demonstrate better catalytic properties than free papain and the inorganic metal-salt crystal can function as both support and promotor in biocatalysis. Knoevenagel condensation was catalyzed and enhanced by Cu2+ and papain on hybrid nanoflowers (hNFs) in the promiscuous catalysis.![]()
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Affiliation(s)
- Jianyun Yu
- College of Materials, Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310014
- P. R. China
| | - Xinxin Chen
- College of Materials, Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310014
- P. R. China
| | - Min Jiang
- College of Materials, Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310014
- P. R. China
| | - Anming Wang
- College of Materials, Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310014
- P. R. China
| | - Linlin Yang
- College of Materials, Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310014
- P. R. China
| | - Xiaolin Pei
- College of Materials, Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310014
- P. R. China
| | - Pengfei Zhang
- College of Materials, Chemistry and Chemical Engineering
- Hangzhou Normal University
- Hangzhou 310014
- P. R. China
| | - Stephen Gang Wu
- Department of Energy, Environmental and Chemical Engineering
- Washington University
- St. Louis
- USA
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31
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Liu C, Han P, Xie Z, Xu Z, Wei D. Insights into Ag(i)-catalyzed addition reactions of amino alcohols to electron-deficient olefins: competing mechanisms, role of catalyst, and origin of chemoselectivity. RSC Adv 2018; 8:40338-40346. [PMID: 35558202 PMCID: PMC9091461 DOI: 10.1039/c8ra09065c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/28/2018] [Indexed: 12/29/2022] Open
Abstract
The competing mechanisms of Ag(i)-catalyzed chemoselective addition reactions of amino alcohols and electron-deficient olefins leading to the O-adduct or N-adduct products were systematically studied with density functional theory methods. Calculations indicate that the AgHMDS/dppe versus AgOAc/dppe catalytic systems can play different roles and thereby generate two different products. The AgHMDS/dppe system works as a Brønsted base to deprotonate the amino alcohol OH to form the Ag–O bond, which leads to formation of the O-adduct. In contrast, the AgOAc/dppe system mainly acts as a Lewis acid to coordinate with O and N atoms of the amino alcohol, but it cannot act as the Brønsted base to further activate the OH group because of its weaker basicity. Therefore, the AgOAc/dppe catalyzed reaction has a mechanism that is similar to the non-catalyzed reaction, and generates the same N-adduct. The obtained insights will be important for rational design of the various kinds of cooperatively catalyzed chemoselective addition reactions, including the use of the less nucleophilic hydroxyl groups of unprotected amino alcohols. The origin of the chemoselectivities of Ag(i)-catalyzed addition reactions of amino alcohols to olefin has been predicted for the first time.![]()
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Affiliation(s)
- Chunhui Liu
- School of Chemistry and Chemical Engineering
- Xuchang University of China
- Xuchang
- P. R. China
| | - Peilin Han
- School of Chemistry and Chemical Engineering
- Xuchang University of China
- Xuchang
- P. R. China
| | - Zhizhong Xie
- Department of Chemistry
- School of Chemistry, Chemical Engineering and Life Sciences
- Wuhan University of Technology
- Wuhan
- P. R. China
| | - Zhihong Xu
- School of Chemistry and Chemical Engineering
- Xuchang University of China
- Xuchang
- P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University of China
- Zhengzhou
- P. R. China
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32
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Li X, Wei D, Li Z. Theoretical Study on DBU-Catalyzed Insertion of Isatins into Aryl Difluoronitromethyl Ketones: A Case for Predicting Chemoselectivity Using Electrophilic Parr Function. ACS OMEGA 2017; 2:7029-7038. [PMID: 31457285 PMCID: PMC6645149 DOI: 10.1021/acsomega.7b00907] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 10/05/2017] [Indexed: 06/10/2023]
Abstract
The possible mechanisms of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU)-catalyzed chemoselective insertion of N-methyl isatin into aryl difluoronitromethyl ketone to synthesize 3,3-disubstituted and 2,2-disubstituted oxindoles have been studied in this work. As revealed by calculated results, the reaction occurs via two competing paths, including α and β carbonyl paths, and each path contains five steps, that is, nucleophilic addition of DBU to ketone, C-C bond cleavage affording difluoromethylnitrate anion and phenylcarbonyl-DBU cation, nucleophilic addition of difluoromethylnitrate anion to carbonyl carbon of N-methyl isatin, acyl transfer process, and dissociation of DBU and product. The computational results suggest that nucleophilic additions on different carbonyl carbons of N-methyl isatin via α and β carbonyl paths would lead to different products in the third step, and β carbonyl path associated with the main product 3,3-disubstituted oxindole is more energetically favorable, which is consistent with the experimental observations. Noteworthy, electrophilic Parr function can be successfully applied for exactly predicting the activity of reaction site and reasonably explaining the chemoselectivity. In addition, the distortion/interaction and noncovalent interaction analyses show that much more hydrogen bond interactions should be responsible for the lower energy of the transition state associated with β carbonyl path. The obtained insights would be valuable for the rational design of efficient organocatalysts for this kind of reactions with high selectivities.
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33
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Wang W, Wei D. A DFT Study of N-Heterocyclic Carbene Catalyzed [4+2] Annulation between Saturated Carboxylate withortho-Quinone Methide: Possible Mechanisms and Origin of Enantioselectivity. ChemistrySelect 2017. [DOI: 10.1002/slct.201701679] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wei Wang
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering; Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
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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: 30] [Impact Index Per Article: 4.3] [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
![]()
The cysteine protease enzyme legumain hydrolyzes peptide bonds
with high specificity after asparagine and under more acidic conditions
after aspartic acid [BakerE. N.1980, 141, 441−4847003158; BakerE. N.; 1977, 111, 207–210859183; DrenthJ.; 1976, 15, 3731–3738952885; MenardR.; 1994, 137; PolgarL.1978, 88, 513–521689035; StorerA. C.; 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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35
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Wei D, Huang X, Qiao Y, Rao J, Wang L, Liao F, Zhan CG. Catalytic Mechanisms for Cofactor-Free Oxidase-Catalyzed Reactions: Reaction Pathways of Uricase-Catalyzed Oxidation and Hydration of Uric Acid. ACS Catal 2017; 7:4623-4636. [PMID: 28890842 DOI: 10.1021/acscatal.7b00901] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
First-principles quantum mechanical/molecular mechanical (QM/MM)-free energy calculations have been performed to uncover how uricase catalyzes metabolic reactions of uric acid (UA), demonstrating that the entire reaction process of UA in uricase consists of two stages-oxidation followed by hydration. The oxidation consists of four steps: (1) chemical transformation from 8-hydroxyxythine to an anionic radical via a proton transfer along with an electron transfer, which is different from the previously proposed electron-transfer mechanism that involves a dianion intermediate (UA2-) during the catalytic reaction process; (2) proton transfer to the O2- anion (radical); (3) diradical recombination to form a peroxo intermediate; (4) dissociation of H2O2 to generate the dehydrourate. Hydration, for the most favorable pathway, is initiated by the nucleophilic attack of a water molecule on dehydrourate, along with a concerted proton transfer through residue Thr69 in the catalytic site. According to the calculated free energy profile, the hydration is the rate-determining step, and the corresponding free energy barrier of 16.2 kcal/mol is consistent with that derived from experimental kinetic data, suggesting that the computational insights into the catalytic mechanisms are reasonable. The mechanistic insights not only provide a mechanistic base for future rational design of uricase mutants with improved catalytic activity against uric acid as an improved enzyme therapy, but also are valuable for understanding a variety of other cofactor-free oxidase-catalyzed reactions involving an oxygen molecule.
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Affiliation(s)
- Donghui Wei
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Xiaoqin Huang
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Center
for Theoretical Biological Physics, and Center for Research Computing, Rice University, Houston, Texas 77030, United States,
| | - Yan Qiao
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Jingjing Rao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Lu Wang
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Fei Liao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Chang-Guo Zhan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Molecular
Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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Wang W, Wang Y, Zheng L, Qiao Y, Wei D. A DFT Study on Mechanisms and Origin of Selectivity of Phosphine-Catalyzed Vicinal Acylcyanation of Alkynoates. ChemistrySelect 2017. [DOI: 10.1002/slct.201700996] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Wei Wang
- The College of Chemistry and Molecular Engineering, Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
| | - Yang Wang
- The College of Chemistry and Molecular Engineering, Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
| | - Linjie Zheng
- The College of Chemistry and Molecular Engineering, Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
| | - Yan Qiao
- Department of Pathophysiology, School of Basic Medical Sciences; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering, Center of Computational Chemistry; Zhengzhou University; Zhengzhou, Henan Province 450001 P. R. China
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37
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Purification, catalytic, kinetic and thermodynamic characteristics of a novel ficin from Ficus johannis. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.04.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Arafet K, Ferrer S, Moliner V. Computational Study of the Catalytic Mechanism of the Cruzain Cysteine Protease. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03096] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kemel Arafet
- Departament de Química
Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Silvia Ferrer
- Departament de Química
Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Departament de Química
Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
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Brás NF, Ferreira P, Calixto AR, Jaspars M, Houssen W, Naismith JH, Fernandes PA, Ramos MJ. The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac. Chemistry 2016; 22:13089-97. [PMID: 27389424 DOI: 10.1002/chem.201601670] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Indexed: 11/11/2022]
Abstract
Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including antitumor and antiviral (including anti-HIV). Despite their desirability, efficient design and production of these compounds has not been achieved to date. The catalytic mechanism of patellamide macrocyclization by the PatG macrocyclase domain has been computationally investigated by using quantum mechanics/molecular mechanics methodology, specifically ONIOM(M06/6-311++G(2d,2p):ff94//B3LYP/6-31G(d):ff94). The mechanism proposed herein begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 on the substrate leads to the formation of an acyl-enzyme covalent complex. The leaving group Ala-Tyr-Asp-Gly (AYDG) of the substrate is protonated by the substrate's N terminus, leading to the breakage of the P1-P1' bond. Finally, the substrate's N terminus attacks the P1 residue, decomposing the acyl-enzyme complex forming the macrocycle. The formation and decomposition of the acyl-enzyme complex have the highest activation free energies (21.1 kcal mol(-1) and 19.8 kcal mol(-1) respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.
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Affiliation(s)
- Natércia F Brás
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Pedro Ferreira
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Ana R Calixto
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, AB24 3UE, Scotland, UK
| | - Wael Houssen
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, Scotland, UK.,Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
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40
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Bhattacharjee N, Field MJ, Simorre JP, Arthur M, Bougault CM. Hybrid Potential Simulation of the Acylation of Enterococcus faecium l,d-Transpeptidase by Carbapenems. J Phys Chem B 2016; 120:4767-81. [DOI: 10.1021/acs.jpcb.6b02836] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicholus Bhattacharjee
- DYNAMO/DYNAMOP,
UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie
Structurale, 71 Avenue des Martyrs,
CS 10090, 38044 Grenoble Cedex 9, France
| | - Martin J. Field
- DYNAMO/DYNAMOP,
UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie
Structurale, 71 Avenue des Martyrs,
CS 10090, 38044 Grenoble Cedex 9, France
| | - Jean-Pierre Simorre
- RMN, UMR 5075,
Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
| | - Michel Arthur
- Centre de Recherche
des Cordeliers, Equipe 12, UMR S 872, Université Pierre et
Marie Curie-Paris 6, INSERM, Université Paris Descartes, Sorbonne
Paris Cité, 15 rue de l’Ecole
de Médecine, 75006 Paris, France
| | - Catherine M. Bougault
- RMN, UMR 5075,
Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
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41
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Activation of Bacteroides fragilis toxin by a novel bacterial protease contributes to anaerobic sepsis in mice. Nat Med 2016; 22:563-7. [PMID: 27089515 PMCID: PMC4860040 DOI: 10.1038/nm.4077] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 03/07/2016] [Indexed: 12/19/2022]
Abstract
Bacteroides fragilis is the leading cause of anaerobic bacteremia and sepsis 1. Enterotoxigenic strains producing B. fragilis toxin (BFT, fragilysin) contribute to colitis 2 and intestinal malignancy 3, yet are also isolated in bloodstream infection 4,5. It is not known whether these strains harbor unique genetic determinants that confer virulence in extra-intestinal disease. We demonstrate that BFT contributes to sepsis and identify a B. fragilis protease, fragipain (Fpn), which is required for endogenous activation of BFT through removal of its auto-inhibitory prodomain. Structural analysis of Fpn reveals a His-Cys catalytic dyad characteristic of C11 family cysteine proteases that are conserved in multiple pathogenic Bacteroides spp and Clostridium spp. Fpn-deficient enterotoxigenic B. fragilis is attenuated in its ability to induce sepsis, however Fpn is dispensable in B. fragilis colitis wherein host proteases mediate BFT activation. Our findings define a role for B. fragilis enterotoxin and its activating protease in the pathogenesis of bloodstream infection, indicating a greater complexity of cellular targeting and action of BFT than previously appreciated. The expression of fpn by both toxigenic and non-toxigenic strains suggests this protease may contribute to anaerobic sepsis beyond its role in toxin activation, potentially serving as a target for disease modification.
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Wei D, Tang M, Zhan CG. Fundamental reaction pathway and free energy profile of proteasome inhibition by syringolin A (SylA). Org Biomol Chem 2016; 13:6857-65. [PMID: 26018983 DOI: 10.1039/c5ob00737b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, molecular dynamics (MD) simulations and first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations have been performed to uncover the fundamental reaction pathway of proteasome with a representative inhibitor syringolin A (SylA). The calculated results reveal that the reaction process consists of three steps. The first step is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is a nucleophilic attack on the olefin carbon of SylA by the negatively charged Thr1-O(γ) atom. The last step is a proton transfer from Thr1-N(z) to another olefin carbon of SylA to complete the inhibition reaction process. The calculated free energy profile demonstrates that the second step should be the rate-determining step and has the highest free energy barrier of 24.6 kcal mol(-1), which is reasonably close to the activation free energy (∼22.4-23.0 kcal mol(-1)) derived from the available experimental kinetic data. In addition, our computational results indicate that no water molecule can assist the rate-determining step, since the second step is not involved in a proton transfer process. The obtained mechanistic insights should be valuable for understanding the inhibition process of proteasome by SylA and structurally related inhibitors at a molecular level, and thus provide a solid mechanistic base and valuable clues for future rational design of novel, more potent inhibitors of proteasome.
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Affiliation(s)
- Donghui Wei
- Department of Chemistry, Zhengzhou University, Daxue Road, Zhengzhou, Henan 450052, China
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43
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Zheng L, Tang M, Wang Y, Guo X, Wei D, Qiao Y. A DFT study on PBu3-catalyzed intramolecular cyclizations of N-allylic substituted α-amino nitriles for the formation of functionalized pyrrolidines: mechanisms, selectivities, and the role of catalysts. Org Biomol Chem 2016; 14:3130-41. [DOI: 10.1039/c6ob00150e] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The detailed mechanisms and stereoselectivities of PBu3-catalyzed intramolecular cyclizations for the formation of functionalized pyrrolidines have been investigated using a DFT method.
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Affiliation(s)
- Linjie Zheng
- School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou
- P.R. China
- The College of Chemistry and Molecular Engineering
| | - Mingsheng Tang
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Yang Wang
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Xiaokang Guo
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Yan Qiao
- School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou
- P.R. China
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Yao Y, Liu J, Zheng F, Zhan CG. Reaction Pathway for Cocaine Hydrolase-Catalyzed Hydrolysis of (+)-Cocaine. Theor Chem Acc 2016; 135. [PMID: 28250715 DOI: 10.1007/s00214-015-1788-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recently designed and discovered cocaine hydrolase (CocH), engineered from human butyrylcholinesterase (BChE), has been proven promising as a novel enzyme therapy for treatment of cocaine overdose and addiction because it is highly efficient in catalyzing hydrolysis of naturally occurring (-)-cocaine. It has been known that the CocH also has a high catalytic efficiency against (+)-cocaine, a synthetic enantiomer of cocaine. Reaction pathway and the corresponding free energy profile for the CocH-catalyzed hydrolysis of (+)-cocaine have been determined, in the present study, by performing first-principles pseudobond quantum mechanical/molecular mechanical (QM/MM)-free energy (FE) calculations. Acordingt to the QM/MM-FE results, the catalytic hydrolysis process is initiated by the nucleophilic attack on carbonyl carbon of (-)-cocaine benzoyl ester via hydroxyl oxygen of S198 side chain, and the second reaction step (i.e. dissociation of benzoyl ester) is rate-determining. This finding for CocH-catalyzed hydrolysis of (+)-cocaine is remarkably different from that for the (+)-cocaine hydrolysis catalyzed by bacterial cocaine esterase in which the first reaction step of the deacylation is associated with the highest free energy barrier (~17.9 kcal/mol). The overall free energy barrier (~16.0 kcal/mol) calculated for the acylation stage of CocH-catalyzed hydrolysis of (+)-cocaine is in good agreement with the experimental free energy barrier of ~14.5 kcal/mol derivated from the experimental kinetic data.
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Affiliation(s)
- Yuan Yao
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536; The Academy of Fundamental and Interdisciplinary Sciences, Harbin Institute of Technology, Harbin 150080, P.R. China
| | - Junjun Liu
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536; Tongji School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, P.R. China
| | - Fang Zheng
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536
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Azad CS, Khan IA, Narula AK. Organocatalyzed asymmetric Michael addition by an efficient bifunctional carbohydrate–thiourea hybrid with mechanistic DFT analysis. Org Biomol Chem 2016; 14:11454-11461. [DOI: 10.1039/c6ob02158a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of thiourea based bifunctional organocatalysts having d-glucose as a core scaffold were synthesized and examined as catalysts for the asymmetric Michael addition reaction of aryl/alkyl trans-β-nitrostyrenes over cyclohexanone and other Michael donors having active methylene.
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Affiliation(s)
- Chandra S. Azad
- “Hygeia” Centre of Excellence in Pharmaceutical Sciences (CEPS)
- GGS Indraprastha University
- New Delhi
- India
| | - Imran A. Khan
- Department of Chemistry
- Guru Nanak Dev University
- Amritsar
- India
| | - Anudeep K. Narula
- “Hygeia” Centre of Excellence in Pharmaceutical Sciences (CEPS)
- GGS Indraprastha University
- New Delhi
- India
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Zhang M, Wei D, Wang Y, Li S, Liu J, Zhu Y, Tang M. DFT study on the reaction mechanisms and stereoselectivities of NHC-catalyzed [2 + 2] cycloaddition between arylalkylketenes and electron-deficient benzaldehydes. Org Biomol Chem 2015; 12:6374-83. [PMID: 24940721 DOI: 10.1039/c4ob00606b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, two possible mechanisms (mechanisms A and B) on the stereoselective [2 + 2] cycloaddition of aryl(alkyl)ketenes and electron-deficient benzaldehydes catalyzed by N-heterocyclic carbenes (NHCs) have been investigated using density functional theory (DFT). Our calculated results indicate that the favorable mechanism (mechanism A) includes three processes: the first step is the nucleophilic attack on the arylalkylketene by the NHC catalyst to form an intermediate, the second step is the [2 + 2] cycloaddition of the intermediate and benzaldehyde for the formation of a β-lactone, and the last step is the dissociation of the NHC catalyst and the β-lactone. Notably, the [2 + 2] cycloaddition, in which two chiral centers associated with four configurations (SS, RR, SR and RS) are formed, is demonstrated to be both the rate- and stereoselectivity-determining step. Moreover, the reaction pathway associated with the SR configuration is the most favorable pathway and leads to the main product, which is in good agreement with the experimental results. Furthermore, the analysis of global and local reactivity indexes has been performed to explain the role of the NHC catalyst in the [2 + 2] cycloaddition reaction. Therefore, this study will be of great use for the rational design of more efficient catalysts for this kind of cycloaddition.
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Affiliation(s)
- Mengmeng Zhang
- The College of Chemistry and Molecular Engineering, Center of Computational Chemistry, Zhengzhou University, Zhengzhou, Henan Province 450001, P.R. China.
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Arafet K, Ferrer S, Moliner V. First quantum mechanics/molecular mechanics studies of the inhibition mechanism of cruzain by peptidyl halomethyl ketones. Biochemistry 2015; 54:3381-91. [PMID: 25965914 DOI: 10.1021/bi501551g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cruzain is a primary cysteine protease expressed by the protozoan parasite Trypanosoma cruzi during Chagas disease infection, and thus, the development of inhibitors of this protein is a promising target for designing an effective therapy against the disease. In this paper, the mechanism of inhibition of cruzain by two different irreversible peptidyl halomethyl ketones (PHK) inhibitors has been studied by means of hybrid quantum mechanics/molecular mechanics-molecular dynamics (MD) simulations to obtain a complete representation of the possible free energy reaction paths. These have been traced on free energy surfaces in terms of the potential of mean force computed at AM1d/MM and DFT/MM levels of theory. An analysis of the possible reaction mechanisms of the inhibition process has been performed showing that the nucleophilic attack of an active site cysteine, Cys25, on a carbon atom of the inhibitor and the cleavage of the halogen-carbon bond take place in a single step. PClK appears to be much more favorable than PFK from a kinetic point of view. This result would be in agreement with experimental studies in other papain-like enzymes. A deeper analysis of the results suggests that the origin of the differences between PClK and PFK can be the different stabilizing interactions established between the inhibitors and the residues of the active site of the protein. Any attempt to explore the viability of the inhibition process through a stepwise mechanism involving the formation of a thiohemiketal intermediate and a three-membered sulfonium intermediate has been unsuccessful. Nevertheless, a mechanism through a protonated thiohemiketal, with participation of His159 as a proton donor, appears to be feasible despite showing higher free energy barriers. Our results suggest that PClK can be used as a starting point to develop a proper inhibitor of cruzain.
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Affiliation(s)
- Kemel Arafet
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Silvia Ferrer
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
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Wang Y, Guo X, Wu B, Wei D, Tang M. Mechanistic and stereoselectivity study for the reaction of trifluoropyruvates with arylpropenes catalyzed by a cationic Lewis acid rhodium complex. RSC Adv 2015. [DOI: 10.1039/c5ra21074g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The mechanism and stereoselectivity of a Lewis acid catalyzed carbonyl–ene reaction of trifluoropyruvates with arylpropenes have been investigated using a DFT method.
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Affiliation(s)
- Yang Wang
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Xiaokang Guo
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Bohua Wu
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Mingsheng Tang
- The College of Chemistry and Molecular Engineering
- Center of Computational Chemistry
- Zhengzhou University
- Zhengzhou
- P. R. China
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49
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Mechanistic insights into the stereoselective C2-functionalization of 1-substituted imidazoles with cyanophenylacetylene and aldehydes. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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50
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Qiao Y, Han K, Zhan CG. Reaction pathways and free energy profiles for cholinesterase-catalyzed hydrolysis of 6-monoacetylmorphine. Org Biomol Chem 2014; 12:2214-27. [PMID: 24595354 DOI: 10.1039/c3ob42464b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As the most active metabolite of heroin, 6-monoacetylmorphine (6-MAM) can penetrate into the brain for the rapid onset of heroin effects. The primary enzymes responsible for the metabolism of 6-MAM to the less potent morphine in humans are acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The detailed reaction pathways for AChE- and BChE-catalyzed hydrolysis of 6-MAM to morphine have been explored, for the first time, in the present study by performing first-principles quantum mechanical/molecular mechanical free energy calculations. It has been demonstrated that the two enzymatic reaction processes follow similar catalytic reaction mechanisms, and the whole catalytic reaction pathway for each enzyme consists of four reaction steps. According to the calculated results, the second reaction step associated with the transition state TS2(a)/TS2(b) should be rate-determining for the AChE/BChE-catalyzed hydrolysis, and the free energy barrier calculated for the AChE-catalyzed hydrolysis (18.3 kcal mol(-1)) is 2.5 kcal mol(-1) lower than that for the BChE-catalyzed hydrolysis (20.8 kcal mol(-1)). The free energy barriers calculated for the AChE- and BChE-catalyzed reactions are in good agreement with the experimentally derived activation free energies (17.5 and 20.7 kcal mol(-1) for the AChE- and BChE-catalyzed reactions, respectively). Further structural analysis reveals that the aromatic residues Phe295 and Phe297 in the acyl pocket of AChE (corresponding to Leu286 and Val288 in BChE) contribute to the lower energy of TS2(a) relative to TS2(b). The obtained structural and mechanistic insights could be valuable for use in future rational design of a novel therapeutic treatment of heroin abuse.
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Affiliation(s)
- Yan Qiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, P. R. China
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