1
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Potkule JB, Kahar SP, Kumar M, Annapure US. Impact of non-thermal techniques on enzyme modifications for their applications in food. Int J Biol Macromol 2024; 275:133566. [PMID: 38960264 DOI: 10.1016/j.ijbiomac.2024.133566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 06/28/2024] [Indexed: 07/05/2024]
Abstract
The present review elaborates on the details of the enzyme, its structure, specificity, and the mechanism of action of selected enzymes as well as structural changes and loss or gain of activity after non-thermal treatments for food-based applications. Enzymes are biological catalysts found in various systems such as plants, animals, and microorganisms. Most of the enzymes have their optimum pH, temperature, and substrate or group of substrates. The conformational modification of enzymes either increases or decreases the rate of reaction at different pH, and temperature conditions. Enzymes are modified by different techniques to enhance the activity of enzymes for their commercial applications mainly due to the high cost of enzymes, stability, and difficulties that occur during the use of enzymes in different conditions. On the opposite, enzyme inactivation provides its application to extend the shelf life of fruits and vegetables by denaturation and partial inactivation of enzymes. Hence, the activation and inactivation of enzymes are studied by non-thermal techniques in both the model and the food system. The highly reactive species generated during non-thermal techniques cause chemical and structural modification. The enzyme modifications depend on the type and source of the enzyme, type of technique, and the parameters used.
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Affiliation(s)
- Jayashree B Potkule
- Department of Food Engineering and Technology, Institute of Chemical Technology, Matunga, Mumbai, India
| | - Suraj P Kahar
- Department of Food Engineering and Technology, Institute of Chemical Technology, Matunga, Mumbai, India
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR - Central Institute for Research on Cotton Technology, Matunga, Mumbai, India
| | - Uday S Annapure
- Department of Food Engineering and Technology, Institute of Chemical Technology, Matunga, Mumbai, India; Institute of Chemical Technology, Marathwada Campus, Jalna, India.
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2
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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] [MESH Headings] [Grants] [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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3
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Tao Y, Zheng D, Zou W, Guo T, Liao G, Zhou W. Targeting the cysteine biosynthesis pathway in microorganisms: Mechanism, structure, and drug discovery. Eur J Med Chem 2024; 271:116461. [PMID: 38691891 DOI: 10.1016/j.ejmech.2024.116461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/16/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
Owing to the global health crisis of resistant pathogenic infections, researchers are emphasizing the importance of novel prevention and control strategies. Existing antimicrobial drugs predominantly target a few pathways, and their widespread use has pervasively increased drug resistance. Therefore, it is imperative to develop new antimicrobial drugs with novel targets and chemical structures. The de novo cysteine biosynthesis pathway, one of the microbial metabolic pathways, plays a crucial role in pathogenicity and drug resistance. This pathway notably differs from that in humans, thereby representing an unexplored target for developing antimicrobial drugs. Herein, we have presented an overview of cysteine biosynthesis pathways and their roles in the pathogenicity of various microorganisms. Additionally, we have investigated the structure and function of enzymes involved in these pathways as well as have discussed drug design strategies and structure-activity relationships of the enzyme inhibitors. This review provides valuable insights for developing novel antimicrobials and offers new avenues to combat drug resistance.
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Affiliation(s)
- Ying Tao
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Dandan Zheng
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Wei Zou
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Ting Guo
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Guojian Liao
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China.
| | - Wei Zhou
- State Key Laboratory of Resource Insects, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China.
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4
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Mori T, Abe I. Lincosamide Antibiotics: Structure, Activity, and Biosynthesis. Chembiochem 2024; 25:e202300840. [PMID: 38165257 DOI: 10.1002/cbic.202300840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/03/2024]
Abstract
Lincosamides are naturally occurring antibiotics isolated from Streptomyces sp. Currently, lincomycin A and its semisynthetic analogue clindamycin are used as clinical drugs. Due to their unique structures and remarkable biological activities, derivatizations of lincosamides via semi-synthesis and biosynthetic studies have been reported. This review summarizes the structures and biological activities of lincosamides, and the recent studies of lincosamide biosynthetic enzymes.
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Grants
- JP20H00490 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JP22H05126 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JP23H00393 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JP23H02641 Ministry of Education, Culture, Sports, Science and Technology, Japan
- JPNP20011 New Energy and Industrial Technology Development Organization
- JP21ak0101164 New Energy and Industrial Technology Development Organization
- JP23ama121027 New Energy and Industrial Technology Development Organization
- JPMJPR20DA Japan Science and Technology Agency
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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5
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Magoch M, McEwen AG, Napolitano V, Władyka B, Dubin G. Crystal Structure of Staphopain C from Staphylococcus aureus. Molecules 2023; 28:molecules28114407. [PMID: 37298883 DOI: 10.3390/molecules28114407] [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: 03/29/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Staphylococcus aureus is a common opportunistic pathogen of humans and livestock that causes a wide variety of infections. The success of S. aureus as a pathogen depends on the production of an array of virulence factors including cysteine proteases (staphopains)-major secreted proteases of certain strains of the bacterium. Here, we report the three-dimensional structure of staphopain C (ScpA2) of S. aureus, which shows the typical papain-like fold and uncovers a detailed molecular description of the active site. Because the protein is involved in the pathogenesis of a chicken disease, our work provides the foundation for inhibitor design and potential antimicrobial strategies against this pathogen.
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Affiliation(s)
- Malgorzata Magoch
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Alastair G McEwen
- CNRS, INSERM, Université de Strasbourg, IGBMC UMR 7104-UMR-S 1258, F-67400 Illkirch, France
| | - Valeria Napolitano
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Benedykt Władyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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6
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Kim H, Hauner D, Laureanti JA, Agustin K, Raugei S, Kumar N. Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors. Sci Rep 2022; 12:21037. [PMID: 36470873 PMCID: PMC9722715 DOI: 10.1038/s41598-022-23570-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
Targeted covalent inhibition represents one possible strategy to block the function of SARS-CoV-2 Main Protease (MPRO), an enzyme that plays a critical role in the replication of the novel SARS-CoV-2. Toward the design of covalent inhibitors, we built a covalent inhibitor dataset using deep learning models followed by high throughput virtual screening of these candidates against MPRO. Two top-ranking inhibitors were selected for mechanistic investigations-one with an activated ester warhead that has a piperazine core and the other with an acrylamide warhead. Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. Simulations show that both candidates form more stable enzyme-inhibitor (E-I) complexes than the chosen NSP. It was found that both the NSP fragment and the activated ester inhibitor react with CYS145 of MPRO in a concerted manner, whereas the acrylamide inhibitor follows a stepwise mechanism. Most importantly, the reversible reaction and the subsequent hydrolysis reaction from E-I complexes are less probable when compared to the reactions with an NSP fragment, showing promise for these candidates to be the base for efficient MPRO inhibitors.
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Affiliation(s)
- Hoshin Kim
- grid.451303.00000 0001 2218 3491Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Darin Hauner
- grid.451303.00000 0001 2218 3491Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Joseph A. Laureanti
- grid.451303.00000 0001 2218 3491Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Kruel Agustin
- grid.451303.00000 0001 2218 3491Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Simone Raugei
- grid.451303.00000 0001 2218 3491Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Neeraj Kumar
- grid.451303.00000 0001 2218 3491Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352 USA
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7
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Tripathy V, Mayhall NJ, Raghavachari K. ONIOM Method with Charge Transfer Corrections (ONIOM-CT): Analytic Gradients and Benchmarking. J Chem Theory Comput 2022; 18:6052-6064. [PMID: 36154125 DOI: 10.1021/acs.jctc.2c00584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hybrid methods such as ONIOM that treat different regions of a large molecule using different methods are widely used to investigate chemical reactions in a variety of materials and biological systems. However, there are inherent sources of significant errors due to the standard treatment of the boundary between the regions using hydrogen link atoms. In particular, an unbalanced charge distribution in the chemically important model region is a potential source of such problems. We have previously suggested ONIOM-CT (ONIOM with charge transfer corrections) which addresses this issue by applying a potential in the form of point charges to obtain a desired charge redistribution. The metric for charge redistribution relies on the type of population analysis used to obtain the charges. ONIOM-CT has been implemented using Mulliken and Löwdin population analyses and has been shown to improve computed reaction energies for illustrative chemical reactions. In this work, we derive and implement the analytic gradients for ONIOM-CT that requires solving two sets of coupled-perturbed self-consistent equations, one each for the model system and the full system. However, both are needed only at the low level of theory, allowing for an efficient formulation and implementation for both Mulliken and Löwdin population analyses. Benchmarking and illustrative geometry optimizations have been carried out for a previously studied set of reactions involving a single link atom between regions. Additionally, we have generalized our method for the treatment of model systems involving multiple link atoms to enable applications for a broader set of problems. The generalized methods are illustrated for both charge models. Furthermore, we have studied a set of three proton transfer reactions and demonstrate that significant improvement is achieved by ONIOM-CT over ONIOM using both Mulliken and Löwdin population analyses.
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Affiliation(s)
- Vikrant Tripathy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicholas J Mayhall
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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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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Gisdon FJ, Feiler CG, Kempf O, Foerster JM, Haiss J, Blankenfeldt W, Ullmann GM, Bombarda E. Structural and Biophysical Analysis of the Phytochelatin-Synthase-Like Enzyme from Nostoc sp. Shows That Its Protease Activity is Sensitive to the Redox State of the Substrate. ACS Chem Biol 2022; 17:883-897. [PMID: 35377603 DOI: 10.1021/acschembio.1c00941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phytochelatins (PCs) are nonribosomal thiol-rich oligopeptides synthetized from glutathione (GSH) in a γ-glutamylcysteinyl transpeptidation reaction catalyzed by PC synthases (PCSs). Ubiquitous in plant and present in some invertebrates, PCSs are involved in metal detoxification and homeostasis. The PCS-like enzyme from the cyanobacterium Nostoc sp. (NsPCS) is considered to be an evolutionary precursor enzyme of genuine PCSs because it shows sufficient sequence similarity for homology to the catalytic domain of the eukaryotic PCSs and shares the peptidase activity consisting in the deglycination of GSH. In this work, we investigate the catalytic mechanism of NsPCS by combining structural, spectroscopic, thermodynamic, and theoretical techniques. We report several crystal structures of NsPCS capturing different states of the catalyzed chemical reaction: (i) the structure of the wild-type enzyme (wt-NsPCS); (ii) the high-resolution structure of the γ-glutamyl-cysteine acyl-enzyme intermediate (acyl-NsPCS); and (iii) the structure of an inactive variant of NsPCS, with the catalytic cysteine mutated into serine (C70S-NsPCS). We characterize NsPCS as a relatively slow enzyme whose activity is sensitive to the redox state of the substrate. Namely, NsPCS is active with reduced glutathione (GSH), but is inhibited by oxidized glutathione (GSSG) because the cleavage product is not released from the enzyme. Our biophysical analysis led us to suggest that the biological function of NsPCS is being a part of a redox sensing system. In addition, we propose a mechanism how PCS-like enzymes may have evolved toward genuine PCS enzymes.
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Affiliation(s)
- Florian J. Gisdon
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
- Computational Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
| | - Christian G. Feiler
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Oxana Kempf
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
| | - Johannes M. Foerster
- Computational Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
| | - Jonathan Haiss
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - G. Matthias Ullmann
- Computational Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
| | - Elisa Bombarda
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
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10
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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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11
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Messner L, Antink MH, Guo T, Maas M, Beutel S. A versatile ceramic capillary membrane reactor system for continuous enzyme-catalyzed hydrolysis. Eng Life Sci 2021; 21:527-538. [PMID: 34584517 PMCID: PMC8456322 DOI: 10.1002/elsc.202100027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/14/2021] [Accepted: 06/24/2021] [Indexed: 01/06/2023] Open
Abstract
As an alternative to classical batch processes, enzyme-catalyzed hydrolysis can also be carried out continuously. To facilitate this, a continuous ceramic capillary membrane reactor system (CCCMRS) was developed which can be operated with various proteolytic enzymes immobilized on the porous ceramic capillary membranes. This system has several advantages over common batch processes regarding stability, reproducibility and controllability and can easily be adapted to optimal reaction conditions and individual preferences. Two exemplary applications utilizing the CCCMRS were carried out and investigated in long-term stability studies. In the first application the continuous enzymatic cleavage of human IgG into the antibody fragments Fab and Fc by immobilized papain was performed. A total volume of 22 mL of 1 mg mL-1 IgG-solution was enzymatically cleaved over a period of 33.3 h. The antibody cleavage products could be detected in an SEC-HPLC over the whole process time thus indicating long-term stability of the continuous hydrolysis process. The second application investigated the continuous digestion of pea and almond protein isolates by immobilized Alcalase resulting in the generation of a large variety of different peptides. This peptide fingerprint remains constant over a long period of time enabling fractionation and thus making the peptides accessible for further bioactivity studies in sufficient quantities. The constant peptide fingerprint could be shown in the RP-HPLC analysis for all 30 samples with a total volume of 29.7 mL collected over a period of 45 h.
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Affiliation(s)
- Lorn Messner
- Institute for Technical ChemistryLeibniz University HannoverHannoverGermany
| | | | - Tongwei Guo
- Advanced CeramicsUniversity of BremenBremenGermany
| | - Michael Maas
- Advanced CeramicsUniversity of BremenBremenGermany
- MAPEX Center for Materials and ProcessesUniversity of BremenBremenGermany
| | - Sascha Beutel
- Institute for Technical ChemistryLeibniz University HannoverHannoverGermany
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12
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Nano-organic supports for enzyme immobilization: Scopes and perspectives. Colloids Surf B Biointerfaces 2021; 204:111774. [PMID: 33932893 DOI: 10.1016/j.colsurfb.2021.111774] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/04/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022]
Abstract
A variety of organic nanomaterials and organic polymers are used for enzyme immobilization to increase enzymes stability and reusability. In this study, the effects of the immobilization of enzymes on organic and organic-inorganic hybrid nano-supports are compared. Immobilization of enzymes on organic support nanomaterials was reported to significantly improve thermal, pH and storage stability, acting also as a protection against metal ions inhibitory effects. In particular, the effects of enzyme immobilization on reusability, physical, kinetic and thermodynamic parameters were considered. Due to their biocompatibility with low health risks, organic support nanomaterials represent a good choice for the immobilization of enzymes. Organic nanomaterials, and especially organic-inorganic hybrids, can significantly improve the kinetic and thermodynamic parameters of immobilized enzymes compared to macroscopic supports. Moreover, organic nanomaterials are more environment friendly for medical applications, such as prodrug carriers and biosensors. Overall, organic hybrid nanomaterials are receiving increasing attention as novel nano-supports for enzyme immobilization and will be used extensively.
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13
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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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14
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Kaur P, Choudhury D. Functionality of receptor targeted zinc-insulin quantum clusters in skin tissue augmentation and bioimaging. J Drug Target 2020; 29:541-550. [PMID: 33307859 DOI: 10.1080/1061186x.2020.1864740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Quantum clusters with target specificity are suitable for tissue-specific imaging. In the present work, amorphous zinc insulin quantum clusters (IZnQCs) had been synthesised to promote and monitor wound recovery. Easy synthesis, biocompatibility, stability, enhanced quantum yield, and solubility made the cluster suitable for preclinical/clinical exploration. Zn2+ is known for its binding to insulin hexamer. Here we report the reformation of the structure in a quantum cluster form in the presence of Zn2+. The formation of IZnQCs was confirmed by the change in zeta potential from -25.6 mV to -17.9 mV and also the formation of protein metal interaction was confirmed in FTIR bands at 450, 480, and 613 cm-1 for Zn-O, Zn-N, and Zn-S, respectively. HRTEM-EDS and SAED data analysis showed an amorphous nature of the cluster. The binding of IZnQCs to the cells has been confirmed using confocal microscopy. IZnQCs showed a synergistic effect in wound recovery than insulin or Zn2+ alone. Further due to high fluorescence this recovery process can be monitored under an appropriate setup. Wound healing promotional activity, target specificity, and fluorescence properties make the IZnQCs ideal to use for bioimaging along with promoting and monitoring of wound recovery agent.
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Affiliation(s)
- Pawandeep Kaur
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| | - Diptiman Choudhury
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, India.,Thapar Institute of Engineering and Technology - Virginia Tech Centre for Excellence in Material Sciences, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
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15
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Erol K, Tatar D, Veyisoğlu A, Tokatlı A. Antimicrobial magnetic poly(GMA) microparticles: synthesis, characterization and lysozyme immobilization. JOURNAL OF POLYMER ENGINEERING 2020. [DOI: 10.1515/polyeng-2020-0191] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Abstract
Micron-sized magnetic particles currently find a wide range of applications in many areas including biotechnology, biochemistry, colloid sciences and medicine. In this study, magnetic poly(glycidyl methacrylate) microparticles were synthesized by providing a polymerization around Fe(II)-Ni(II) magnetic double salt. Adsorption of lysozyme protein from aqueous systems was studied with these particles. Adsorption studies were performed with changing pH values, variable amount of adsorbent, different interaction times and lysozyme amounts. The adsorption capacity of the particles was investigated, and a value of about 95.6 mg lysozyme/g microparticle was obtained. The enzyme activity of the immobilized lysozyme was examined and found to be more stable and reusable compared to the free enzyme. The immobilized enzyme still showed 80% activity after five runs and managed to maintain 78% of its initial activity at the end of 60 days. Besides, in the antimicrobial analysis study for six different microorganisms, the minimum inhibitory concentration value of lysozyme immobilized particles was calculated as 125 μg/mL like free lysozyme. Finally, the adsorption interaction was found to be compatible with the Langmuir isotherm model. Accordingly, it can be said that magnetic poly(GMA) microparticles are suitable materials for lysozyme immobilization and immobilized lysozyme can be used in biotechnological studies.
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Affiliation(s)
- Kadir Erol
- Department of Medical Services and Techniques , Vocational School of Health Services, Hitit University , Çorum , Turkey
| | - Demet Tatar
- Department of Medical Services and Techniques , Osmancık Ömer Derindere Vocational School, Hitit University , Çorum , Turkey
| | - Aysel Veyisoğlu
- Department of Medical Services and Techniques , Vocational School of Health Services, Sinop University , Sinop , Turkey
| | - Ali Tokatlı
- Department of Biology , Faculty of Art and Science, Ondokuz Mayıs University , Samsun , Turkey
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16
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Oanca G, Asadi M, Saha A, Ramachandran B, Warshel A. Exploring the Catalytic Reaction of Cysteine Proteases. J Phys Chem B 2020; 124:11349-11356. [PMID: 33264018 DOI: 10.1021/acs.jpcb.0c08192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cysteine proteases play a major role in many life processes and are the target of key drugs. The reaction mechanism of these enzymes is a complex process, which involves several steps that are divided into two main groups: acylation and deacylation. In this work, we studied the energy profile for the acylation and a part of the deacylation reaction of three different enzymes, cruzain, papain, and the Q19A-mutated papain with the benzyloxycarbonyl-phenylalanylarginine-4-methylcoumaryl-7-amide (CBZ-FR-AMC) substrate. The calculations were performed using the EVB and PDLD/S-LRA methods. The overall agreement between the calculated and observed results is encouraging and indicates that we captured the correct reaction mechanism. Finally, our finding indicates that the minimum of the reaction profile, between the acylation and deacylation steps, should provide an excellent state for the binding of covalent inhibitors.
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Affiliation(s)
- Gabriel Oanca
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Mojgan Asadi
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Arjun Saha
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Balajee Ramachandran
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States.,Structural Biology and Bio-computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630 004, India
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
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17
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Li J, Chen J, An L, Yuan X, Yao L. Polyol and sugar osmolytes can shorten protein hydrogen bonds to modulate function. Commun Biol 2020; 3:528. [PMID: 32968183 PMCID: PMC7511342 DOI: 10.1038/s42003-020-01260-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/28/2020] [Indexed: 12/19/2022] Open
Abstract
Polyol and sugar osmolytes are commonly used in therapeutic protein formulations. How they may affect protein structure and function is an important question. In this work, through NMR measurements, we show that glycerol and sorbitol (polyols), as well as glucose (sugar), can shorten protein backbone hydrogen bonds. The hydrogen bond shortening is also captured by molecular dynamics simulations, which suggest a hydrogen bond competition mechanism. Specifically, osmolytes weaken hydrogen bonds between the protein and solvent to strengthen those within the protein. Although the hydrogen bond change is small, with the average experimental cross hydrogen bond 3hJNC' coupling of two proteins GB3 and TTHA increased by ~ 0.01 Hz by the three osmolytes (160 g/L), its effect on protein function should not be overlooked. This is exemplified by the PDZ3-peptide binding where several intermolecular hydrogen bonds are formed and osmolytes shift the equilibrium towards the bound state.
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Affiliation(s)
- Jingwen Li
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Jingfei Chen
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Liaoyuan An
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiang Yuan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lishan Yao
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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18
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Jang DW, Ameer K, Oh JH, Park MK. Optimization and Pretreatment for Hot Water Extraction of Korean Deer ( Cervus canadensis Erxleben) Velvet Antlers. J Microbiol Biotechnol 2020; 30:1116-1123. [PMID: 32423187 PMCID: PMC9728161 DOI: 10.4014/jmb.2004.04009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/03/2020] [Indexed: 12/15/2022]
Abstract
Velvet antler (VA) is a historically traditional medicinal supplement and is well known in Asian countries for its pharmaceutical and health benefits. The objectives for this study were to optimize the hot water extraction (HWE) of VA for the Korean VA industry, and to determine the most effective pretreatment method among microwave (MW), ultrasonication (US), and enzymatic (EZ) techniques. Using response surface methodology, optimum extraction temperatures and times were determined by central composite design configuration based on extraction yield and sialic acid content. Various quality parameters of VA extract including yield, soluble solid, protein, and sialic acid contents were also compared with the conjunction of HWE and pretreatment. The yield and sialic acid content of VA extract were determined to be 40% and 0.73 mg/g, respectively, under an optimum temperature of 100°C at 24 h of extraction time. The yields from VA extracts pretreated with MW, US, and EZ were 17.42%, 19.73%, and 29.15%, respectively. Among the tested commercial enzymes, pepsin was the most effective proteolytic enzyme and led to the highest yield (47.65%), soluble solids (4.03 °brix), protein (1.12 mg/ml), and sialic acid (3.04 mg/ml) contents from VA extract.
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Affiliation(s)
- Dong Wook Jang
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kashif Ameer
- Department of Food Science and Technology and BK 21 Plus Program, Graduate School of Chonnam National University, Gwangju 61186, Republic of Korea,Institute of Food and Nutritional Sciences, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Jun-Hyun Oh
- Department of Plant and Food Sciences, Sangmyung University, Cheonan 31066, Republic of Korea
| | - Mi-Kyung Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea,Food and Bio-Industry Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea,Corresponding author Phone: +82-53-960-5776 Fax: +82-53-950-6772 E-mail:
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19
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Saranya V, Radhika R, Shankar R, Vijayakumar S. In silico studies of the inhibition mechanism of dengue with papain. J Biomol Struct Dyn 2020; 39:1912-1927. [PMID: 32249700 DOI: 10.1080/07391102.2020.1742205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Dengue virus is becoming a major global disease; the envelope protein is the major target for vaccine development against Dengue. Nowadays, the attention has focused on developing inhibitors based on Papain is a promising target for treating Dengue. In the present work, the theoretical studies of E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and His159) complexes are analysed by Density Functional Theory (M06-2X/cc-pVDZ) method. Among the E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and Hys159) complexes, E-protein(Glu76)…Papain(Cys25) complex has the highest interaction value of -352.22 kcal/mol. Moreover, the natural bond orbital analysis also supports the above results. The 100 ns Molecular Dynamics simulation reveals that, E-protein(Ala54-Ile129)…Papain(Cys25) complex had the lowest root mean square deviation value of 1 Å compared to the E-protein(Ala54-Ile129)… Papain(Asn175 & His159) complexes. The salt bridge formation between the Asp103 and Lys110 residues are the important stabilizing factor in E-protein(Ala54-Ile129)…Papain(Cys25) complex. This result can extend our knowledge of the functional behaviour of Papain and provides structural insight to target Envelope protein as forthcoming drug targets in Dengue.
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20
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Strategy for the Biosynthesis of Short Oligopeptides: Green and Sustainable Chemistry. Biomolecules 2019; 9:biom9110733. [PMID: 31766233 PMCID: PMC6920838 DOI: 10.3390/biom9110733] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 02/07/2023] Open
Abstract
Short oligopeptides are some of the most promising and functionally important amide bond-containing components, with widespread applications. Biosynthesis of these oligopeptides may potentially become the ultimate strategy because it has better cost efficiency and environmental-friendliness than conventional solid phase peptide synthesis and chemo-enzymatic synthesis. To successfully apply this strategy for the biosynthesis of structurally diverse amide bond-containing components, the identification and selection of specific biocatalysts is extremely important. Given that perspective, this review focuses on the current knowledge about the typical enzymes that might be potentially used for the synthesis of short oligopeptides. Moreover, novel enzymatic methods of producing desired peptides via metabolic engineering are highlighted. It is believed that this review will be helpful for technological innovation in the production of desired peptides.
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21
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Balogh G, Muszbek L, Komáromi I. First Step of the Transglutaminase Reaction Catalyzed by Activated Factor XIII Subunit A, Hybrid Quantum Chemistry/Molecular Mechanics Calculations. J Phys Chem B 2019; 123:3887-3897. [DOI: 10.1021/acs.jpcb.9b00542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Gábor Balogh
- Division of Clinical Laboratory Sciences, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - László Muszbek
- Division of Clinical Laboratory Sciences, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - István Komáromi
- Division of Clinical Laboratory Sciences, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
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22
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Wang X, Bakanina Kissanga GM, Li E, Li Q, Yao J. The catalytic mechanism of S-acyltransferases: acylation is triggered on by a loose transition state and deacylation is turned off by a tight transition state. Phys Chem Chem Phys 2019; 21:12163-12172. [DOI: 10.1039/c9cp02248a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction of S-acyltransferase is characterized by a loose transition state.
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Affiliation(s)
- Xia Wang
- School of Biological Science and Technology
- University of Jinan
- Jinan 250022
- China
| | | | - E. Li
- School of Biological Science and Technology
- University of Jinan
- Jinan 250022
- China
| | - Qiang Li
- School of Biological Science and Technology
- University of Jinan
- Jinan 250022
- China
| | - Jianzhuang Yao
- School of Biological Science and Technology
- University of Jinan
- Jinan 250022
- China
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23
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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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Bayazidi P, Almasi H, Asl AK. Immobilization of lysozyme on bacterial cellulose nanofibers: Characteristics, antimicrobial activity and morphological properties. Int J Biol Macromol 2017; 107:2544-2551. [PMID: 29079438 DOI: 10.1016/j.ijbiomac.2017.10.137] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/13/2017] [Accepted: 10/22/2017] [Indexed: 11/18/2022]
Abstract
The aim of this study was to immobilize of lysozyme onto bacterial cellulose nanofibers (BCNF) using physical absorption method. Antimicrobial activity and other properties of immobilized lysozyme and also morphological characteristics of BCNF were studied. Activity of lysozyme was decreased about 12% after immobilization. The lysozyme concentration of 1mg/ml was chosen for next studies on immobilized enzyme. The optimum pH and temperature were recorded as 7 and 45°C, respectively for immobilized enzyme. Storage stability was increased and immobilized lysozyme exhibited more than 70% of its initial activity after 9 cycles. Kinetic parameters of Km and Vmax were 31.18μg/ml and 112.35 ΔOD/min, respectively for immobilized enzyme. Antimicrobial activity of lysozyme against Staphylococcus aureus, Escherichia coli, Listeria monocytogenes, Yersinia entrocolitica, Aspergillus niger and Saccharomyces serviseae was increased after immobilization. The XRD analyses showed a decrease in diffraction intensities and crystallinity index of BCNF after immobilization of lysozyme. According to the results of scanning electron microscopy (SEM), the diameter of nanofibers was increased by lysozyme incorporation. This study demonstrates the potential for the use of BCNF as carrier for lysozyme immobilization.
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Affiliation(s)
- Pashew Bayazidi
- Department of Food Science and Technology, Faculty of Agriculture, Saba Higher Education Institute, Urmia, Iran
| | - Hadi Almasi
- Department of Food Science and Technology, Faculty of Agriculture, Urmia University, Urmia, Iran.
| | - Asghar Khosrowshahi Asl
- Department of Food Science and Technology, Faculty of Agriculture, Urmia University, Urmia, Iran
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Elsässer B, Zauner FB, Messner J, Soh WT, Dall E, Brandstetter H. Distinct Roles of Catalytic Cysteine and Histidine in the Protease and Ligase Mechanisms of Human Legumain As Revealed by DFT-Based QM/MM Simulations. ACS Catal 2017; 7:5585-5593. [PMID: 28932620 PMCID: PMC5600538 DOI: 10.1021/acscatal.7b01505] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/10/2017] [Indexed: 11/30/2022]
Abstract
![]()
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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26
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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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27
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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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28
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Mazmanian K, Sargsyan K, Grauffel C, Dudev T, Lim C. Preferred Hydrogen-Bonding Partners of Cysteine: Implications for Regulating Cys Functions. J Phys Chem B 2016; 120:10288-10296. [PMID: 27635780 DOI: 10.1021/acs.jpcb.6b08109] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hydrogen-bonding interactions of cysteine, which can serve as a hydrogen-bond donor and/or acceptor, play a central role in cysteine's diverse functional roles in proteins. They affect the balance between the neutral thiol (SH) or thiolate (S-) and the charge distribution in the rate-limiting transition state of a reaction. Despite their importance, no study has determined the preferred hydrogen-bonding partners of cysteine serving as a hydrogen-bond donor or acceptor. By computing the free energy for displacing a peptide backbone hydrogen-bonded to cysteine with amino acid side chains in various protein environments, we have evaluated how the strength of the hydrogen bond to the cysteine thiol/thiolate depends on its hydrogen-bonding partner and its local environment. The predicted hydrogen-bonding partners preferred by cysteine are consistent with the hydrogen-bonding interactions made by cysteines in 9138 nonredundant X-ray structures. Our results suggest a mechanism to regulate the reactivity of cysteines and a strategy to design drugs based on the hydrogen-bonding preference of cysteine.
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Affiliation(s)
- Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica , Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 10617, Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University , Sofia 1164, Bulgaria
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 300, Taiwan
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29
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Guo JT, Xiang Y, Guan Z, He YH. Papain-catalyzed aldol reaction for the synthesis of trifluoromethyl carbinol derivatives. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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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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31
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Njogu PM, Guantai EM, Pavadai E, Chibale K. Computer-Aided Drug Discovery Approaches against the Tropical Infectious Diseases Malaria, Tuberculosis, Trypanosomiasis, and Leishmaniasis. ACS Infect Dis 2016; 2:8-31. [PMID: 27622945 DOI: 10.1021/acsinfecdis.5b00093] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Despite the tremendous improvement in overall global health heralded by the adoption of the Millennium Declaration in the year 2000, tropical infections remain a major health problem in the developing world. Recent estimates indicate that the major tropical infectious diseases, namely, malaria, tuberculosis, trypanosomiasis, and leishmaniasis, account for more than 2.2 million deaths and a loss of approximately 85 million disability-adjusted life years annually. The crucial role of chemotherapy in curtailing the deleterious health and economic impacts of these infections has invigorated the search for new drugs against tropical infectious diseases. The research efforts have involved increased application of computational technologies in mainstream drug discovery programs at the hit identification, hit-to-lead, and lead optimization stages. This review highlights various computer-aided drug discovery approaches that have been utilized in efforts to identify novel antimalarial, antitubercular, antitrypanosomal, and antileishmanial agents. The focus is largely on developments over the past 5 years (2010-2014).
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Affiliation(s)
- Peter M. Njogu
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Eric M. Guantai
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Elumalai Pavadai
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
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32
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Takahashi T, Vo Ngo BC, Xiao L, Arya G, Heller MJ. Molecular mechanical properties of short-sequence peptide enzyme mimics. J Biomol Struct Dyn 2015; 34:463-74. [DOI: 10.1080/07391102.2015.1039586] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Takahashi T, Cheung M, Butterweck T, Schankweiler S, Heller MJ. Quest for a turnover mechanism in peptide-based enzyme mimics. CATAL COMMUN 2015. [DOI: 10.1016/j.catcom.2014.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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34
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Paasche A, Zipper A, Schäfer S, Ziebuhr J, Schirmeister T, Engels B. Evidence for substrate binding-induced zwitterion formation in the catalytic Cys-His dyad of the SARS-CoV main protease. Biochemistry 2014; 53:5930-46. [PMID: 25196915 DOI: 10.1021/bi400604t] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The coronavirus main protease (M(pro)) represents an attractive drug target for antiviral therapy of coronavirus (CoV) infections, including severe acute respiratory syndrome (SARS). The SARS-CoV M(pro) and related CoV proteases have several distinct features, such as an uncharged Cys-His catalytic dyad embedded in a chymotrypsin-like protease fold, that clearly separate these enzymes from archetypical cysteine proteases. To further characterize the catalytic system of CoV main proteases and to obtain information about improved inhibitors, we performed comprehensive simulations of the proton-transfer reactions in the SARS-CoV M(pro) active site that lead to the Cys(-)/His(+) zwitterionic state required for efficient proteolytic activity. Our simulations, comprising the free enzyme as well as substrate-enzyme and inhibitor-enzyme complexes, lead us to predict that zwitterion formation is fostered by substrate binding but not inhibitor binding. This indicates that M(pro) employs a substrate-induced catalytic mechanism that further enhances its substrate specificity. Our computational data are in line with available experimental results, such as X-ray geometries, measured pKa values, mutagenesis experiments, and the measured differences between the kinetic parameters of substrates and inhibitors. The data also provide an atomistic picture of the formerly postulated electrostatic trigger involved in SARS-CoV M(pro) activity. Finally, they provide information on how a specific microenvironment may finely tune the activity of M(pro) toward specific viral protein substrates, which is known to be required for efficient viral replication. Our simulations also indicate that the low inhibition potencies of known covalently interacting inhibitors may, at least in part, be attributed to insufficient fostering of the proton-transfer reaction. These findings suggest ways to achieve improved inhibitors.
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Affiliation(s)
- Alexander Paasche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg , Emil-Fischer-Straße 42, 97074 Würzburg, Germany
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35
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Silva JRA, Roitberg AE, Alves CN. Catalytic mechanism of L,D-transpeptidase 2 from Mycobacterium tuberculosis described by a computational approach: insights for the design of new antibiotics drugs. J Chem Inf Model 2014; 54:2402-10. [PMID: 25149147 DOI: 10.1021/ci5003069] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tuberculosis is perhaps the most persistent human disease caused by an infections bacterium, Mycobacterium tuberculosis. The L,D-transpeptidase enzyme catalyzes the formation of 3 → 3 peptidoglycan cross-links of the Mtb cell wall and facilitates resistance against classical β-lactams. Herein, the experimentally proposed mechanism for LdtMt2 was studied by performing QM/MM MD simulations. The whole mechanistic process includes two stages: acylation and deacylation. During the acylation step, two steps were observed: the first step is a thiolate/imidazole ion-pair in the zwitterionic form, and the second step is the nucleophilic attack on the carboxyl carbon of the natural substrate accompanied by the breaking of the peptide bond on substrate. In the deacylation step the acyl-enzyme suffers a nucleophilic attack on the carboxyl carbon by the amine group of the second substrate. Our free energy results obtained by PMF analysis reveal that the first step (acylation) is the rate-limiting step in the whole catalytic mechanism in accordance with the experimental proposal. Also, the residues responsible for binding of the substrate and transition state stabilization were identified by energy decomposition methods.
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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 , Belém, PA 66075-110, Brazil
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36
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Berteotti A, Vacondio F, Lodola A, Bassi M, Silva C, Mor M, Cavalli A. Predicting the reactivity of nitrile-carrying compounds with cysteine: a combined computational and experimental study. ACS Med Chem Lett 2014; 5:501-5. [PMID: 24900869 DOI: 10.1021/ml400489b] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/24/2014] [Indexed: 12/30/2022] Open
Abstract
Here, we report on a mechanistic investigation based on DFT calculations and kinetic measures aimed at determining the energetics related to the cysteine nucleophilic attack on nitrile-carrying compounds. Activation energies were found to correlate well with experimental kinetic measures of reactivity with cysteine in phosphate buffer. The agreement between computations and experiments points to this DFT-based approach as a tool for predicting both nitrile reactivity toward cysteines and the toxicity of nitriles as electrophile agents.
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Affiliation(s)
- Anna Berteotti
- Drug
Discovery and Development, Italian Institute of Technology, via Morego
30, 16163 Genova, Italy
| | - Federica Vacondio
- Dipartimento
di Farmacia, Università degli Studi di Parma, Parco Area
delle Scienze 27/A, 43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento
di Farmacia, Università degli Studi di Parma, Parco Area
delle Scienze 27/A, 43124 Parma, Italy
| | - Michele Bassi
- Dipartimento
di Farmacia, Università degli Studi di Parma, Parco Area
delle Scienze 27/A, 43124 Parma, Italy
| | - Claudia Silva
- Dipartimento
di Farmacia, Università degli Studi di Parma, Parco Area
delle Scienze 27/A, 43124 Parma, Italy
| | - Marco Mor
- Dipartimento
di Farmacia, Università degli Studi di Parma, Parco Area
delle Scienze 27/A, 43124 Parma, Italy
| | - Andrea Cavalli
- Drug
Discovery and Development, Italian Institute of Technology, via Morego
30, 16163 Genova, Italy
- Department
of Pharmacy and Biotechnology, University of Bologna, via Belmeloro
6, 40126 Bologna, Italy
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37
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Lodola A, Rivara S, Mor M. Insights in the Mechanism of Action and Inhibition of N-Acylethanolamine Acid Amidase by Means of Computational Methods. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:219-34. [DOI: 10.1016/bs.apcsb.2014.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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38
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Wei D, Huang X, Tang M, Zhan CG. Reaction pathway and free energy profile for papain-catalyzed hydrolysis of N-acetyl-Phe-Gly 4-nitroanilide. Biochemistry 2013; 52:5145-54. [PMID: 23862626 PMCID: PMC3770148 DOI: 10.1021/bi400629r] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Possible reaction pathways for papain-catalyzed hydrolysis of N-acetyl-Phe-Gly 4-nitroanilide (APGNA) have been studied by performing pseudobond first-principles quantum mechanical/molecular mechanical-free energy (QM/MM-FE) calculations. The whole hydrolysis process includes two stages: acylation and deacylation. For the acylation stage of the catalytic reaction, we have explored three possible paths (A, B, and C) and the corresponding free energy profiles along the reaction coordinates. It has been demonstrated that the most favorable reaction path in this stage is path B consisting of two reaction steps: the first step is a proton transfer to form a zwitterionic form (i.e., Cys-S⁻/His-H⁺ ion-pair), and the second step is the nucleophilic attack on the carboxyl carbon of the substrate accompanied by the dissociation of 4-nitroanilide. The deacylation stage includes the nucleophilic attack of a water molecule on the carboxyl carbon of the substrate and dissociation between the carboxyl carbon of the substrate and the sulfhydryl sulfur of Cys25 side chain. The free energy barriers calculated for the acylation and deacylation stages are 20.0 and 10.7 kcal/mol, respectively. Thus, the acylation is rate-limiting. The overall free energy barrier calculated for papain-catalyzed hydrolysis of APGNA is 20.0 kcal/mol, which is reasonably close to the experimentally derived activation free energy of 17.9 kcal/mol.
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Affiliation(s)
- Donghui Wei
- Department of Chemistry, Zhengzhou University, 75 Daxue Road, Zhengzhou, Henan, 450052, P. R. China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536
| | - Xiaoqin Huang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536
| | - Mingsheng Tang
- Department of Chemistry, Zhengzhou University, 75 Daxue Road, Zhengzhou, Henan, 450052, P. R. China
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536
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39
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Isegawa M, Wang B, Truhlar DG. Electrostatically Embedded Molecular Tailoring Approach and Validation for Peptides. J Chem Theory Comput 2013; 9:1381-93. [DOI: 10.1021/ct300845q] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Miho Isegawa
- Department of Chemistry, Chemical Theory Center, and
Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
55455-0431, United States
| | - Bo Wang
- Department of Chemistry, Chemical Theory Center, and
Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and
Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
55455-0431, United States
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40
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Paasche A, Schirmeister T, Engels B. Benchmark Study for the Cysteine-Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches. J Chem Theory Comput 2013; 9:1765-77. [PMID: 26587634 DOI: 10.1021/ct301082y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Proton transfer reactions are of crucial interest for the investigation of proteins. We have investigated the accuracy of commonly used quantum chemical methods for the description of proton transfer reactions in different environments (gas phase, COSMO, QM/MM) using the proton transfer between the catalytic dyad residues cysteine 145 and histidine 41 of SARS coronavirus main protease as a case study. The test includes thermodynamic, kinetic, and structural properties. The study comprises computationally demanding ab initio approaches (HF, CC2, MP2, SCS-CC2, SCS-MP2, CCSD(T)), popular density functional theories (BLYP, B3LYP, M06-2X), and semiempirical methods (MNDO/d, AM1, RM1, PM3, PM6). The approximated coupled cluster approach LCCSD(T) is taken as a reference method. We find that the robustness of the tested methods with respect to the environment correlates well with the level of theory. As an example HF, CC2, MP2, and their SCS variants show similar errors for gas phase, COSMO, or QM/MM computations. In contrast for semiempirical methods, the errors strongly diversify if one goes from gas phase to COSMO or QM/MM. Particular problems are observed for the recent semiempirical methods PM6 and RM1, which show the best performance for gas phase calculations but possess larger errors in conjunction with COSMO. Finally, a combination of SCS-MP2 and B3LYP or M06-2X allows reliable estimates about remaining errors.
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Affiliation(s)
- Alexander Paasche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Bernd Engels
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
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41
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Tsipis AC, Gkarmpounis DN, Kefalidis CE, Papamichael EM, Theodorou LG. Modeling the cysteamine catalyzed cysteine proteinases using DFT: mechanistic insights into the hydrolysis of acetyl-p-nitroanilide. NEW J CHEM 2013. [DOI: 10.1039/c3nj00769c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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42
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Méndez-Lucio O, Romo-Mancillas A, Medina-Franco JL, Castillo R. Computational study on the inhibition mechanism of cruzain by nitrile-containing molecules. J Mol Graph Model 2012; 35:28-35. [DOI: 10.1016/j.jmgm.2012.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 01/06/2012] [Accepted: 01/10/2012] [Indexed: 10/14/2022]
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43
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Hu W, Guan Z, Deng X, He YH. Enzyme catalytic promiscuity: The papain-catalyzed Knoevenagel reaction. Biochimie 2012; 94:656-61. [PMID: 21963435 DOI: 10.1016/j.biochi.2011.09.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 09/19/2011] [Indexed: 11/29/2022]
Affiliation(s)
- Wen Hu
- School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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44
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Lodola A, Branduardi D, De Vivo M, Capoferri L, Mor M, Piomelli D, Cavalli A. A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations. PLoS One 2012; 7:e32397. [PMID: 22389698 PMCID: PMC3289653 DOI: 10.1371/journal.pone.0032397] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 01/29/2012] [Indexed: 12/22/2022] Open
Abstract
The N-terminal nucleophile (Ntn) hydrolases are a superfamily of enzymes specialized in the hydrolytic cleavage of amide bonds. Even though several members of this family are emerging as innovative drug targets for cancer, inflammation, and pain, the processes through which they catalyze amide hydrolysis remains poorly understood. In particular, the catalytic reactions of cysteine Ntn-hydrolases have never been investigated from a mechanistic point of view. In the present study, we used free energy simulations in the quantum mechanics/molecular mechanics framework to determine the reaction mechanism of amide hydrolysis catalyzed by the prototypical cysteine Ntn-hydrolase, conjugated bile acid hydrolase (CBAH). The computational analyses, which were confirmed in water and using different CBAH mutants, revealed the existence of a chair-like transition state, which might be one of the specific features of the catalytic cycle of Ntn-hydrolases. Our results offer new insights on Ntn-mediated hydrolysis and suggest possible strategies for the creation of therapeutically useful inhibitors.
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Affiliation(s)
- Alessio Lodola
- Pharmaceutical Department, University of Parma, Parma, Italy
| | - Davide Branduardi
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
| | - Marco De Vivo
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
| | - Luigi Capoferri
- Pharmaceutical Department, University of Parma, Parma, Italy
| | - Marco Mor
- Pharmaceutical Department, University of Parma, Parma, Italy
| | - Daniele Piomelli
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
- Department of Pharmacology, University of California Irvine, Irvine, California, United States of America
| | - Andrea Cavalli
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
- Department of Pharmaceutical Sciences, University of Bologna, Bologna, Italy
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45
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He YH, Li HH, Chen YL, Xue Y, Yuan Y, Guan Z. Chymopapain-Catalyzed Direct Asymmetric Aldol Reaction. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201100555] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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46
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Yao JW, Xiao Y, Lin F. Effect of various pH values, ionic strength, and temperature on papain hydrolysis of salivary film. Eur J Oral Sci 2012; 120:140-6. [DOI: 10.1111/j.1600-0722.2012.00942.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Nandi TK, Bairagya HR, Mukhopadhyay BP, Mallik P, Sukul D, Bera AK. Conserved water-mediated H-bonding dynamics of catalytic His159 and Asp158: insight into a possible acid–base coupled mechanism in plant thiol protease. J Mol Model 2011; 18:2633-44. [DOI: 10.1007/s00894-011-1277-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 10/09/2011] [Indexed: 10/15/2022]
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48
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Wang M, Qi W, Yu Q, Su R, He Z. Kinetically controlled enzymatic synthesis of dipeptide precursor of l-alanyl-l-glutamine. Biotechnol Appl Biochem 2011; 58:449-55. [DOI: 10.1002/bab.55] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 08/26/2011] [Indexed: 11/07/2022]
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49
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Tian BX, Eriksson LA. Catalytic mechanism and roles of Arg197 and Thr183 in the Staphylococcus aureus sortase A enzyme. J Phys Chem B 2011; 115:13003-11. [PMID: 21950672 DOI: 10.1021/jp2058113] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The sortase A enzyme, which catalyzes the peptidoglycan cell wall anchoring reaction of LPXTG surface proteins, has been proposed to be a universal target for therapeutic agents against Gram-positive bacteria. The catalytic mechanism of the Staphylococcus aureus sortase A enzyme has been systematically studied using molecular dynamics simulations, ONIOM(DFT:MM) calculations, and QM/MM charge deletion analysis. The catalytic roles of Arg197 and Thr183 were analyzed. Our calculations show that Arg197 has several important roles in the mechanism. It is crucial for substrate binding, and is capable of reversible shift of its hydrogen bonds between the LP and TG carbonyls of the LPXTG substrate motif, depending on the protonation state of the catalytic Cys184-His120 dyad. Arg197 stabilizes the catalytic dyad in the active ion pair form but at the same time raises the barrier to acylation by approximately 8 kcal/mol. Thr183 is also essential for the catalytic reaction in that it correspondingly lowers the barrier by the same amount via electrostatic interactions. The catalytic mechanism proceeds via proton transfer from His120, followed by nucleophilic attack from the thiolate anion of Cys184. The data thus supports the proposed reverse protonation mechanism, and disproves the hypothesis of the Arg197 generating an oxyanion hole to stabilize the tetrahedral intermediate of the reaction.
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Affiliation(s)
- Bo-Xue Tian
- School of Chemistry, National University of Ireland-Galway, Galway, Ireland
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Rathore RS, Aparoy P, Reddanna P, Kondapi AK, Reddy MR. Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: case study of relative binding free energies of fructose-1,6-bisphosphatase inhibitors. J Comput Chem 2011; 32:2097-103. [PMID: 21503928 DOI: 10.1002/jcc.21791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/07/2011] [Accepted: 02/23/2011] [Indexed: 01/14/2023]
Abstract
In an attempt to establish the criteria for the length of simulation to achieve the desired convergence of free energy calculations, two studies were carried out on chosen complexes of FBPase-AMP mimics. Calculations were performed for varied length of simulations and for different starting configurations using both conventional- and QM/MM-FEP methods. The results demonstrate that for small perturbations, 1248 ps simulation time could be regarded a reasonable yardstick to achieve convergence of the results. As the simulation time is extended, the errors associated with free energy calculations also gradually tapers off. Moreover, when starting the simulation from different initial configurations of the systems, the results are not changed significantly, when performed for 1248 ps. This study carried on FBPase-AMP mimics corroborates well with our previous successful demonstration of requirement of simulation time for solvation studies, both by conventional and ab initio FEP. The establishment of aforementioned criteria of simulation length serves a useful benchmark in drug design efforts using FEP methodologies, to draw a meaningful and unequivocal conclusion.
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Affiliation(s)
- R S Rathore
- Bioinformatics Infrastructure Facility, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
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