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Kulshreshtha A, Bhatnagar S. Structural effect of the H992D/H418D mutation of angiotensin-converting enzyme in the Indian population: implications for health and disease. J Biomol Struct Dyn 2024:1-18. [PMID: 38411559 DOI: 10.1080/07391102.2024.2321246] [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: 08/11/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
The Non synonymous SNPs (nsSNPs) of the renin-angiotensin-system (RAS) pathway, unique to the Indian population were investigated in view of its importance as an endocrine system. nsSNPs of the RAS pathway genes were mined from the IndiGenome database. Damaging nsSNPs were predicted using SIFT, PredictSNP, SNP and GO, Snap2 and Protein Variation Effect Analyzer. Loss of function was predicted based on protein stability change using I mutant, PremPS and CONSURF. The structural impact of the nsSNPs was predicted using HOPE and Missense3d followed by modeling, refinement, and energy minimization. Molecular Dynamics studies were carried out using Gromacsv2021.1. 23 Indian nsSNPs of the RAS pathway genes were selected for structural analysis and 8 were predicted to be damaging. Further sequence analysis showed that HEMGH zinc binding motif changes to HEMGD in somatic ACE-C domain (sACE-C) H992D and Testis ACE (tACE) H418D resulted in loss of zinc coordination, which is essential for enzymatic activity in this metalloprotease. There was a loss of internal interactions around the zinc coordination residues in the protein structural network. This was also confirmed by Principal Component Analysis, Free Energy Landscape and residue contact maps. Both mutations lead to broadening of the AngI binding cavity. The H992D mutation in sACE-C is likely to be favorable for cardiovascular health, but may lead to renal abnormalities with secondary impact on the heart. H418D in tACE is potentially associated with male infertility.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akanksha Kulshreshtha
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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2
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Sharma H, Raju B, Narendra G, Motiwale M, Sharma B, Verma H, Silakari O. QM/MM Studies on Enzyme Catalysis and Insight into Designing of New Inhibitors by ONIOM Approach: Recent Update. ChemistrySelect 2023. [DOI: 10.1002/slct.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Himani Sharma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Baddipadige Raju
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Gera Narendra
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Mohit Motiwale
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Bhavna Sharma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Himanshu Verma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Om Silakari
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
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3
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In Silico Prospecting for Novel Bioactive Peptides from Seafoods: A Case Study on Pacific Oyster ( Crassostrea gigas). Molecules 2023; 28:molecules28020651. [PMID: 36677709 PMCID: PMC9867001 DOI: 10.3390/molecules28020651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/28/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Pacific oyster (Crassostrea gigas), an abundant bivalve consumed across the Pacific, is known to possess a wide range of bioactivities. While there has been some work on its bioactive hydrolysates, the discovery of bioactive peptides (BAPs) remains limited due to the resource-intensive nature of the existing discovery pipeline. To overcome this constraint, in silico-based prospecting is employed to accelerate BAP discovery. Major oyster proteins were digested virtually under a simulated gastrointestinal condition to generate virtual peptide products that were screened against existing databases for peptide bioactivities, toxicity, bitterness, stability in the intestine and in the blood, and novelty. Five peptide candidates were shortlisted showing antidiabetic, anti-inflammatory, antihypertensive, antimicrobial, and anticancer potential. By employing this approach, oyster BAPs were identified at a faster rate, with a wider applicability reach. With the growing market for peptide-based nutraceuticals, this provides an efficient workflow for candidate scouting and end-use investigation for targeted functional product preparation.
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Impact of Gastrointestinal Digestion Simulation on the Formation of Angiotensin-I-Converting Enzyme Inhibitory (ACE-I) Peptides from Germinated Lamtoro Gung Flour. Foods 2022; 11:foods11233769. [PMID: 36496578 PMCID: PMC9737618 DOI: 10.3390/foods11233769] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022] Open
Abstract
The germination of lamtoro gung has been shown to increase the angiotensin-I-converting enzyme inhibitory (ACE-I) activity in previous studies. The 48 h germinated flour had the highest ACE-I activity. Administration of the gastrointestinal digestion (GID) simulation with commercial enzymes was expected to increase the ACE-I activity. However, the GID simulation to increase ACE-I in the germinated lamtoro gung flour has not been found. Therefore, this study aimed to evaluate the GID simulation of ACE-I peptides in sprouted lamtoro gung flour. This study also identified and characterised the peptide with the ACE-I activity. The GID simulation was performed using commercial pepsin (pH 2) and pancreatin (pH 7.5). Both simulations occurred at 37 °C for 240 min. The degree of hydrolysis, peptide concentration, and ACE-I activity was analysed. Samples with the highest ACE-I activity were then fractionated and identified, to determine the peptide responsible for the ACE-I activity. The 180 min GID simulation in the test sample showed the highest ACE-I activity (89.70%). This result was supported by an increased degree of hydrolysis (DH) and peptide concentrations throughout the GID simulation. The <1 kDa peptide fraction had the highest inhibitory activity and had the most elevated peptide portion (54.69%). Peptide sequences containing crucial amino acids were found in the <1 kDa peptide fraction. PRPPKPP, PPPPPGARAP, and PFPPSNPPP had proline in the C and N terminal residues. The peptides obtained also had other biological activities, such as a DPP IV inhibitor, an alpha-glucosidase inhibitor, and antioxidative activity. Based on the toxicity prediction, those peptides are non-toxic and safe to consume.
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5
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Lubbe L, Sewell BT, Woodward JD, Sturrock ED. Cryo-EM reveals mechanisms of angiotensin I-converting enzyme allostery and dimerization. EMBO J 2022; 41:e110550. [PMID: 35818993 PMCID: PMC9379546 DOI: 10.15252/embj.2021110550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/21/2022] [Accepted: 05/27/2022] [Indexed: 11/09/2022] Open
Abstract
Hypertension (high blood pressure) is a major risk factor for cardiovascular disease, which is the leading cause of death worldwide. The somatic isoform of angiotensin I‐converting enzyme (sACE) plays a critical role in blood pressure regulation, and ACE inhibitors are thus widely used to treat hypertension and cardiovascular disease. Our current understanding of sACE structure, dynamics, function, and inhibition has been limited because truncated, minimally glycosylated forms of sACE are typically used for X‐ray crystallography and molecular dynamics simulations. Here, we report the first cryo‐EM structures of full‐length, glycosylated, soluble sACE (sACES1211). Both monomeric and dimeric forms of the highly flexible apo enzyme were reconstructed from a single dataset. The N‐ and C‐terminal domains of monomeric sACES1211 were resolved at 3.7 and 4.1 Å, respectively, while the interacting N‐terminal domains responsible for dimer formation were resolved at 3.8 Å. Mechanisms are proposed for intradomain hinging, cooperativity, and homodimerization. Furthermore, the observation that both domains were in the open conformation has implications for the design of sACE modulators.
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Affiliation(s)
- Lizelle Lubbe
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Bryan Trevor Sewell
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - Jeremy D Woodward
- Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - Edward D Sturrock
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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6
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Zhou R, Yang C, Xie T, Zhang J, Wang C, Ma Z, Zhang L. Angiotensin-converting enzyme inhibitory activity of four Amadori compounds (ACs) and mechanism analysis of N-(1-Deoxy-D-fructos-1-yl)-glycine (Fru-Gly). Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Zhou R, Yang C, Xie T, Zhang J, Wang C, Ma Z, Zhang L. Angiotensin-Converting Enzyme (ACE) Inhibitory Activity and Mechanism Analysis of N-(1-Deoxy-d-fructos-1-yl)-histidine (Fru-His), a Food-Derived Amadori Compound. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2179-2186. [PMID: 35148100 DOI: 10.1021/acs.jafc.1c05583] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
N-(1-Deoxy-d-fructos-1-yl)-histidine (Fru-His), one of the Amadori compounds, widely presents in processed foods, and its potential functional activities have attracted extensive attention in recent years. In this work, the angiotensin-converting enzyme (ACE) inhibitory activity and mechanism of Fru-His were investigated. The IC50 value of Fru-His was 0.150 ± 0.019 mM, and there was no obvious degradation of Fru-His after digestion simulation, showing that Fru-His has good ACE inhibition and digestive stability. Fru-His was a competitive inhibitor according to the enzyme inhibition kinetic analysis. The interaction between ACE and Fru-His occurred spontaneously mainly through hydrogen bonding, and the process was accompanied by fluorescence quenching and the alteration of the secondary structure of ACE. The molecular docking data supported the above results. Fru-His was attached to ACE's S1 active pocket through hydrogen bonds and interacted with zinc ions in active sites. The present study demonstrates that food-derived Fru-His has the potential to relieve hypertension.
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Affiliation(s)
- Renjie Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Cheng Yang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Ting Xie
- Technical Center of Hefei Customs, Hefei 230041, Anhui, P. R. China
| | - Jian Zhang
- College of Food, Shihezi University, Beisi Road, Shihezi 832003, Xinjiang, P. R. China
| | - Chenqiang Wang
- Technology Center, Xinjiang Guannong Fruit & Antler Group Co., Ltd., Korla City 841000, Xinjiang, P. R. China
| | - Ziqiang Ma
- Technology Center, Xinjiang Guannong Fruit & Antler Group Co., Ltd., Korla City 841000, Xinjiang, P. R. China
| | - Lianfu Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
- College of Food, Shihezi University, Beisi Road, Shihezi 832003, Xinjiang, P. R. China
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8
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Borawska-Dziadkiewicz J, Darewicz M, Tarczyńska AS. Properties of peptides released from salmon and carp via simulated human-like gastrointestinal digestion described applying quantitative parameters. PLoS One 2021; 16:e0255969. [PMID: 34375367 PMCID: PMC8354434 DOI: 10.1371/journal.pone.0255969] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/27/2021] [Indexed: 01/17/2023] Open
Abstract
Apart from the classical (experimental) methods, biologically active peptides can be studied via bioinformatics approach, also known as in silico analysis. This study aimed to verify the following research hypothesis: ACE inhibitors and antioxidant peptides can be released from salmon and carp proteins during simulated in silico human-like gastrointestinal digestion. The potential to release biopeptides was evaluated using the BIOPEP-UWM quantitative criteria including the profile of biological activity, frequency of the occurrence (A)/release (AE) of fragments with an ACE inhibitory or antioxidant activity by selected enzymes, and relative frequency of release of bioactive fragments with a given activity by selected enzymes (W). Salmon collagen and myofibrillar proteins of carp turned out to be the best potential source of the searched peptides-ACE inhibitors and antioxidant peptides. Nonetheless, after digestion, the highest numbers of ACE inhibitors and antioxidant peptides were potentially released from the myofibrillar proteins of salmon and carp. Peptide Ranker Score, Pepsite2, and ADMETlab platform were applied to evaluate peptides' bioactivity potential, their safety and drug-like properties. Among the 63 sequences obtained after the simulated digestion of salmon and carp proteins, 30 were considered potential biopeptides. The amino acid sequences of ACE-inhibiting and antioxidant peptides were predominated by P, G, F, W, R, and L. The predicted high probability of absorption of most analyzed peptides and their low toxicity should be considered as their advantage.
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Affiliation(s)
- Justyna Borawska-Dziadkiewicz
- Faculty of Food Science, Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Małgorzata Darewicz
- Faculty of Food Science, Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anna Sylwia Tarczyńska
- Faculty of Food Science, Department of Dairy Science and Quality Management, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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9
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Robust analysis of angiotensin peptides in human plasma: Column switching-parallel LC/ESI-SRM/MS without adsorption or enzymatic decomposition. Anal Biochem 2021; 630:114327. [PMID: 34364857 DOI: 10.1016/j.ab.2021.114327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022]
Abstract
Angiotensin (Ang) peptides are the main effectors of the renin-angiotensin system (RAS) regulating diverse physiological conditions and are involved in renal and vascular diseases. Currently, quantitative analyses of Ang peptides in human plasma mainly rely on radioimmunoassay-based methods whose reported levels are quite divergent. Analyses are further complicated by the potential of Ang peptides to bind to solid surfaces, to be enzymatically decomposed during sample preparation, and to undergo post-translational modifications. A column switching-parallel LC/ESI-SRM/MS method has been developed for seven Ang peptides (Ang I, Ang II, Ang III, Ang IV, Ang 1-9, Ang 1-7, and Ang A) in human plasma. Aqueous acetonitrile (5%) containing 50 mM arginine (Arg) as a dissolving solution and a combination of protease inhibitors with formic acid were used to prevent adsorption and enzymatic degradation, respectively. Plasma samples were simply deproteinized with acetonitrile followed by clean-up with an on-line trap column via column-switching. Stable isotope dilution with [13C5,15N1-Val]-Ang peptides as internal standards was employed for quantitative analysis. The current methodology has been successfully applied to determine the plasma levels of Ang peptides in healthy participants, suggesting future applicability to studies of various diseases related to RAS.
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10
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Park J, Kim WJ, Kim W, Park C, Choi CY, Cho JH, Kim SJ, Cheong H. Antihypertensive Effects of Dehydroabietic and 4- Epi- Trans-Communic Acid Isolated from Pinus densiflora. J Med Food 2021; 24:50-58. [PMID: 33449861 DOI: 10.1089/jmf.2020.4797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Korean red pine needle (RPN) exhibits various biological and pharmacological activities. Among the various compounds of RPN, we isolated dehydroabietic and 4-epi-trans-communic acid. At first, we confirmed that two compounds inhibited angiotensin converting enzyme (ACE) and induced p-Akt in human umbilical vein endothelial cells (HUVEC). RPN extract powder significantly reduced systolic blood pressure in spontaneous hypertensive rats (SHRs) through the reduced expression of ACE and angiotensin type I receptors in the lungs of SHRs. The Lineweaver-Burk plots suggested that the two compounds were noncompetitive inhibitors of ACE. Using docking analysis, we found that two compounds showed the best returned pose at ACE active sites, and formed hydrogen and hydrophobic bonds with ACE residues. These results demonstrate that RPNs may be a source of compounds effective for preventing hypertension and may be useful in the development of antihypertensive drugs.
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Affiliation(s)
- Jaeyoung Park
- Department of Biomedical Science, Chosun University, Gwangju, Korea
| | - Won-Jin Kim
- Department of Biomedical Science, Chosun University, Gwangju, Korea
- Department of Integrative Biological Sciences & BK21 FOUR Educational Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju, Korea
| | - Woong Kim
- Department of Biomedical Science, Chosun University, Gwangju, Korea
| | | | - Chul Yung Choi
- Division of Food Science, Jeollanamdo Institute of Natural Resources Research, Jangheung-gun, Korea
| | | | - Seok-Jun Kim
- Department of Biomedical Science, Chosun University, Gwangju, Korea
- Department of Integrative Biological Sciences & BK21 FOUR Educational Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju, Korea
| | - Hyeonsook Cheong
- Department of Biomedical Science, Chosun University, Gwangju, Korea
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11
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Studies on molecular mechanism between ACE and inhibitory peptides in different bioactivities by 3D-QSAR and MD simulations. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112702] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Mu X, Xu D. QM/MM investigation of substrate binding of subclass B3 metallo-β-lactamase SMB-1 from Serratia marcescents: insights into catalytic mechanism. J Mol Model 2020; 26:71. [PMID: 32146530 DOI: 10.1007/s00894-020-4330-y] [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] [Received: 06/11/2019] [Accepted: 02/23/2020] [Indexed: 11/25/2022]
Abstract
Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel B3 subclass MβL, which could inactivate nearly all β-lactam-containing antibiotics, e.g., cephalosporins and carbapenems. It represents a new round of worrisome bacterial resistance. In this work, the Michaelis model of SMB-1 in complex with ampicillin was simulated using combined quantum mechanical and molecular mechanical method. Similar with other dizinc MβLs, a Zn-bridged hydroxide ion was simulated as the nucleophile for the hydrolysis reaction assisted by D120. The protonation of D120 could lead to the loss of Oδ2-Zn2 coordination bond, whereas the C3 carboxylate group moves down to become a new ligand to Zn2. The initial β-lactam ring-opening reaction leads to a conserved nitrogen anionic intermediate, which forms a new ligation between the resulted nitrogen anion and Zn2. The corresponding reaction free energy barrier for the first step of lactam ring-opening reaction was calculated to be 19.2 kcal/mol. During the reaction, Q157 serves as the putative "oxyanion hole" rather than Zn1 in L1 enzyme, which was confirmed via the site-directed mutagenesis simulation of Q157A. Our theoretical studies showed some insights into the substrate binding and catalytic mechanism of the SMB-1 metallo-β-lactamase.
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Affiliation(s)
- Xia Mu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China. .,Research Center for Material Genome Engineering, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
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13
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Mohd Salim MAS, Gan CY. Dual-function peptides derived from egg white ovalbumin: Bioinformatics identification with validation using in vitro assay. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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14
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Valdivieso ÁG, Santa‐Coloma TA. The chloride anion as a signalling effector. Biol Rev Camb Philos Soc 2019; 94:1839-1856. [DOI: 10.1111/brv.12536] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/20/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Ángel G. Valdivieso
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED), School of Medical SciencesPontifical Catholic University of Argentina Buenos Aires 1107 Argentina
- The National Scientific and Technical Research Council of Argentina (CONICET) Buenos Aires 1107 Argentina
| | - Tomás A. Santa‐Coloma
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research (BIOMED), School of Medical SciencesPontifical Catholic University of Argentina Buenos Aires 1107 Argentina
- The National Scientific and Technical Research Council of Argentina (CONICET) Buenos Aires 1107 Argentina
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15
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Global proteomic and functional analysis of Crotalus durissus collilineatus individual venom variation and its impact on envenoming. J Proteomics 2019; 191:153-165. [DOI: 10.1016/j.jprot.2018.02.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/29/2018] [Accepted: 02/10/2018] [Indexed: 11/17/2022]
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16
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Panyayai T, Sangsawad P, Pacharawongsakda E, Sawatdichaikul O, Tongsima S, Choowongkomon K. The potential peptides against angiotensin-I converting enzyme through a virtual tripeptide-constructing library. Comput Biol Chem 2018; 77:207-213. [PMID: 30347317 DOI: 10.1016/j.compbiolchem.2018.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/29/2018] [Accepted: 10/04/2018] [Indexed: 11/27/2022]
Abstract
Peptides derived from food proteins are promising bioactive source for inhibiting Angiotensin-I converting enzyme (ACE) activity. Bioactive peptides (BP) have received much attention, particularly from the pharmaceutical industry. As they not only own potent properties but also possess less side-effects than synthetic drugs. In this work, an 8000 possible tripeptides library was constructed to predict the potential ACE inhibitory peptides by using in silico tools. GOLD molecular docking was then applied to determine the binding mode of action between ACE and each of tripeptide from this in-house library. The first 662 high-ranking tripeptides by ChemScore were chosen to create association rules of tripeptides-ACE complexes. An orientation pattern of amino acid in the binding tunnel of ACE has been examined by frequency analysis. The association rules (confident values over 90%) illustrated that hydrophobic factor has been displayed as main components in the ACE tripeptides inhibitor from four factors in equation, hydrophobic, aromatic, polar, charged. According to in silico output, five tripeptides were chosen to test in vitro study of ACE-inhibitory activity. The half-maximal inhibitory concentration (IC50) of these selective five peptides, WCW, IWW, WWW, WWI and WLW for inhibiting ACE were 49.50 ± 3.88 μM, 489.14 ± 8.84 μM, 536.02 ± 38.57 μM, 752.91 ± 41.89 μM and 1783 ± 0.113 μM, respectively. Molecular dynamics simulations approach was applied to study the interaction of WCW (Trp-Cys-Trp) within ACE pocket site. This ligand was stabilized by strong hydrogen bonding interactions with ACE active site, Tyr523-Trp'1 (99.76%) and His353-Trp'1 (95.68%). Our computational protocol could be considered as a new tool for identifying active peptide against ACE from hydrolysated peptides of natural sources.
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Affiliation(s)
- Thitima Panyayai
- Genetic Engineering Interdisciplinary Program, Graduate School, Kasetsart University, 50 Ngam Wong Wan Rd, Bangkok, Chatuchak 10900, Thailand; Department of Research and Development, Betagro Science Center Co. Ltd., 136 Moo 9, Klong Nueng, Pathumthani 12120, Thailand
| | - Papungkorn Sangsawad
- Department of Research and Development, Betagro Science Center Co. Ltd., 136 Moo 9, Klong Nueng, Pathumthani 12120, Thailand
| | - Eakasit Pacharawongsakda
- Big Data Engineering Program, College of Innovative Technology and Engineering, Dhurakij Pundit University, 110/1-4 Prachachuen Road, Laksi, Bangkok 10210, Thailand
| | - Orathai Sawatdichaikul
- Functional Food Unit, Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Thailand
| | - Sissades Tongsima
- Biostatistic and Bioinformatics Laboratory, Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 121205, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam, Wong Wan Rd, Bangkok, Chatuchak 10900, Thailand; Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand.
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17
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Fan H, Liao W, Wu J. Molecular interactions, bioavailability, and cellular mechanisms of angiotensin-converting enzyme inhibitory peptides. J Food Biochem 2018; 43:e12572. [PMID: 31353484 DOI: 10.1111/jfbc.12572] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/16/2018] [Accepted: 03/22/2018] [Indexed: 12/31/2022]
Abstract
Food-derived angiotensin-converting enzyme inhibitory (ACEi) peptides have gained substantial interest as potential alternatives to synthetic drugs in the management of hypertension. Peptide size and sequence are two critical factors that determine their potency, bioavailability, and cellular mechanisms. Molecular interaction studies between ACE and ACEi peptides support that potent ACEi peptides are generally composed of hydrophobic, positively charged, and aromatic or cyclic amino acid residues at the third, second, and first position from the C-terminus, respectively. Small peptides containing N-terminal Tyr and/or C-terminal Pro could improve their stability against enterocyte peptidases, thus their bioavailability. Different ACEi peptides can reduce aberrant cellular proliferation, excessive inflammation, and oxidative stress but through different mechanisms. Further understanding the structure-activity-bioavailability relationships will help design novel potent ACEi peptides with improved bioavailability and in vivo efficacy. PRACTICAL APPLICATIONS: ACEi peptides have the potential for uses as functional food ingredients against hypertension.
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Affiliation(s)
- Hongbing Fan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Wang Liao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Jianping Wu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
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18
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Kugaevskaya EV, Veselovsky AV, Indeykina MI, Solovyeva NI, Zharkova MS, Popov IA, Nikolaev EN, Mantsyzov AB, Makarov AA, Kozin SA. N-domain of angiotensin-converting enzyme hydrolyzes human and rat amyloid-β(1-16) peptides as arginine specific endopeptidase potentially enhancing risk of Alzheimer's disease. Sci Rep 2018; 8:298. [PMID: 29321566 PMCID: PMC5762728 DOI: 10.1038/s41598-017-18567-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/13/2017] [Indexed: 01/28/2023] Open
Abstract
Alzheimer’s disease (AD) is a multifactorial neurodegenerative disorder. Amyloid-β (Aβ) aggregation is likely to be the major cause of AD. In contrast to humans and other mammals, that share the same Aβ sequence, rats and mice are invulnerable to AD-like neurodegenerative pathologies, and Aβ of these rodents (ratAβ) has three amino acid substitutions in the metal-binding domain 1-16 (MBD). Angiotensin-converting enzyme (ACE) cleaves Aβ-derived peptide substrates, however, there are contradictions concerning the localization of the cleavage sites within Aβ and the roles of each of the two ACE catalytically active domains in the hydrolysis. In the current study by using mass spectrometry and molecular modelling we have tested a set of peptides corresponding to MBDs of Aβ and ratAβ to get insights on the interactions between ACE and these Aβ species. It has been shown that the N-domain of ACE (N-ACE) acts as an arginine specific endopeptidase on the Aβ and ratAβ MBDs with C-amidated termini, thus assuming that full-length Aβ and ratAβ can be hydrolyzed by N-ACE in the same endopeptidase mode. Taken together with the recent data on the molecular mechanism of zinc-dependent oligomerization of Aβ, our results suggest a modulating role of N-ACE in AD pathogenesis.
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Affiliation(s)
| | | | - Maria I Indeykina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia.,Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia
| | | | | | - Igor A Popov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia.,Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia
| | - Eugene N Nikolaev
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia.,Skolkovo Institute of Science and technology, Moscow, Russia
| | - Alexey B Mantsyzov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia.
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19
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Yao S, Agyei D, Udenigwe CC. Structural Basis of Bioactivity of Food Peptides in Promoting Metabolic Health. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 84:145-181. [PMID: 29555068 DOI: 10.1016/bs.afnr.2017.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bioactive peptides have many structural features that enable them to become functional in controlling several biological processes in the body, especially those related to metabolic health. This chapter provides an overview of the multiple targets of food-derived peptides against metabolic health problems (e.g., hypertension, dyslipidemia, hyperglycemia, oxidative stress) and discusses the importance of structural chemistry in determining the bioactivities of peptides and protein hydrolysates.
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Affiliation(s)
- Shixiang Yao
- Southwest University, Chongqing, PR China; University of Ottawa, Ottawa, ON, Canada
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20
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Characterisation of novel angiotensin-I-converting enzyme inhibitory tripeptide, Gly-Val-Arg derived from mycelium of Pleurotus pulmonarius. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.07.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Dos Santos DMRC, de Souza CB, Pereira HJV. Angiotensin converting enzymes in fish venom. Toxicon 2017; 131:63-67. [PMID: 28284848 DOI: 10.1016/j.toxicon.2017.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 02/15/2017] [Accepted: 03/06/2017] [Indexed: 10/20/2022]
Abstract
Animal venoms are multifaceted mixtures, including proteins, peptides and enzymes produced by animals in defense, predation and digestion. These molecules have been investigated concerning their molecular mechanisms associated and possible pharmacological applications. Thalassophryne nattereri is a small venomous fish inhabiting the northern and northeastern coast of Brazil, and represents a relatively frequent cause of injuries. Its venom causes severe inflammatory response followed frequently by the necrosis of the affected area. Scorpaena plumieri is the most venomous fish in the Brazilian fauna and is responsible for relatively frequent accidents involving anglers and bathers. In humans, its venom causes edema, erythema, ecchymoses, nausea, vomiting, and syncope. Recently, the presence of a type of angiotensin converting enzyme (ACE) activity in the venom of Thalassophryne nattereri and Scorpaena plumieri, endemic fishes in northeastern coast of Brazil, has been described. The ACE converts angiotensin I (Ang I) into angiotensin II (Ang II) and inactivates bradykinin, there by regulating blood pressure and electrolyte homeostasis, however, their function in these venoms remains an unknown. This article provides an overview of the current knowledge on ACE in the venoms of Thalassophryne nattereri and Scorpaena plumier.
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22
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Xiong J, Xu D. Insights into the Catalytic Mechanism of Unsaturated Glucuronyl Hydrolase of Bacillus sp. GL1. J Phys Chem B 2017; 121:931-941. [DOI: 10.1021/acs.jpcb.6b10501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Xiong
- MOE Key Laboratory of Green Chemistry, College of Chemistry and ‡Geonome Research
Center for Biomaterials, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry, College of Chemistry and ‡Geonome Research
Center for Biomaterials, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
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23
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da Costa Marques ME, de Araújo Tenório H, dos Santos CWV, dos Santos DM, de Lima ME, Pereira HJV. Angiotensin converting enzyme of Thalassophryne nattereri venom. Int J Biol Macromol 2016; 91:980-6. [DOI: 10.1016/j.ijbiomac.2016.06.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 06/14/2016] [Accepted: 06/16/2016] [Indexed: 12/23/2022]
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24
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Mu X, Zhang C, Xu D. QM/MM investigation of the catalytic mechanism of angiotensin-converting enzyme. J Mol Model 2016; 22:132. [PMID: 27184002 DOI: 10.1007/s00894-016-3004-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
Abstract
Angiotensin-converting enzyme (ACE) converts angiotensin I to angiotensin II and degrades bradykinin and other vasoactive peptides. ACE inhibitors are used to treat diseases such as hypertension and heart failure. It is thus highly desirable to understand the catalytic mechanism of ACE, as this should facilitate the design of more powerful and selective ACE inhibitors. ACE exhibits two different active domains, the C-domain and the N-domain. In this work, we systematically investigated the inhibitor- and substrate-binding patterns in the N-domain of human ACE using a combined quantum mechanical and molecular mechanical approach. The hydrolysis of hippuryl-histidyl-leucine (HHL) as catalyzed by the N-domain of human somatic ACE was explored, and the effects of chloride ion on the overall reaction were also investigated. Two models, one with and one without a chloride ion at the first binding position, were then designed to examine the chloride dependence of inhibitor-substrate binding and the catalytic mechanism. Our calculations indicate that the hydrolysis reaction follows a stepwise general base/general acid catalysis path. The estimated mean free energy barrier height in the two models is about 15.6 kcal/mol, which agrees very well with the experimentally estimated value of 15.8 kcal/mol. Our simulations thus suggest that the N-domain is in a mixed form during ACE-catalyzed hydrolysis, with the single-chloride-ion and the double-chloride-ion forms existing simultaneously. Graphical Abstract Superposition of ACE C- and N- domains.
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Affiliation(s)
- Xia Mu
- MOE Key Laboratory of Green Chemistry, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China
| | - Chunchun Zhang
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China. .,Geonome Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China.
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25
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Ramírez C, Martí M, Roitberg A. Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics. Methods Enzymol 2016; 578:123-43. [DOI: 10.1016/bs.mie.2016.05.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Zhu W, Liu Y, Ling B. Quantum Mechanics and Molecular Mechanics Study of the Catalytic Mechanism of Human AMSH-LP Domain Deubiquitinating Enzymes. Biochemistry 2015; 54:5225-34. [PMID: 26256234 DOI: 10.1021/acs.biochem.5b00527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Deubiquitinating enzymes (DUBs) catalyze the cleavage of the isopeptide bond in polyubiquitin chains to control and regulate the deubiquitination process in all known eukaryotic cells. The human AMSH-LP DUB domain specifically cleaves the isopeptide bonds in the Lys63-linked polyubiquitin chains. In this article, the catalytic mechanism of AMSH-LP has been studied using a combined quantum mechanics and molecular mechanics method. Two possible hydrolysis processes (Path 1 and Path 2) have been considered. Our calculation results reveal that the activation of Zn(2+)-coordinated water molecule is the essential step for the hydrolysis of isopeptide bond. In Path 1, the generated hydroxyl first attacks the carbonyl group of Gly76, and then the amino group of Lys63 is protonated, which is calculated to be the rate limiting step with an energy barrier of 13.1 kcal/mol. The energy barrier of the rate limiting step and the structures of intermediate and product are in agreement with the experimental results. In Path 2, the protonation of amino group of Lys63 is prior to the nucleophilic attack of activated hydroxyl. The two proton transfer processes in Path 2 correspond to comparable overall barriers (33.4 and 36.1 kcal/mol), which are very high for an enzymatic reaction. Thus, Path 2 can be ruled out. During the reaction, Glu292 acts as a proton transfer mediator, and Ser357 mainly plays a role in stabilizing the negative charge of Gly76. Besides acting as a Lewis acid, Zn(2+) also influences the reaction by coordinating to the reaction substrates (W1 and Gly76).
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Affiliation(s)
- Wenyou Zhu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University , Jinan, Shandong 250100, China
| | - Yongjun Liu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University , Jinan, Shandong 250100, China
| | - Baoping Ling
- School of Chemistry and Chemical Engineering, Qufu Normal University , Qufu, Shandong 273165, China
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27
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Romero JM, Martin M, Ramirez CL, Dumas VG, Marti MA. Efficient Calculation of Enzyme Reaction Free Energy Profiles Using a Hybrid Differential Relaxation Algorithm: Application to Mycobacterial Zinc Hydrolases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 100:33-65. [PMID: 26415840 DOI: 10.1016/bs.apcsb.2015.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Determination of the free energy profile for an enzyme reaction mechanism is of primordial relevance, paving the way for our understanding of the enzyme's catalytic power at the molecular level. Although hybrid, mostly DFT-based, QM/MM methods have been extensively applied to this type of studies, achieving accurate and statistically converged results at a moderate computational cost is still an open challenge. Recently, we have shown that accurate results can be achieved in less computational time, combining Jarzynski's relationship with a hybrid differential relaxation algorithm (HyDRA), which allows partial relaxation of the solvent during the nonequilibrium steering of the reaction. In this work, we have applied this strategy to study two mycobacterial zinc hydrolases. Mycobacterium tuberculosis infections are still a worldwide problem and thus characterization and validation of new drug targets is an intense field of research. Among possible drug targets, recently two essential zinc hydrolases, MshB (Rv1170) and MA-amidase (Rv3717), have been proposed and structurally characterized. Although possible mechanisms have been proposed by analogy to the widely studied human Zn hydrolases, several key issues, particularly those related to Zn coordination sphere and its role in catalysis, remained unanswered. Our results show that mycobacterial Zn hydrolases share a basic two-step mechanism. First, the attacking water becomes deprotonated by the conserved base and establishes the new C-O bond leading to a tetrahedral intermediate. The intermediate requires moderate reorganization to allow for proton transfer to the amide N and C-N bond breaking to occur in the second step. Zn ion plays a key role in stabilizing the tetrahedral intermediate and balancing the negative charge of the substrate during hydroxide ion attack. Finally, comparative analysis of other Zn hydrolases points to a convergent mechanistic evolution.
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Affiliation(s)
- Juan Manuel Romero
- Instituto de Química Física de los Materiales Medio Ambiente y Energía (INQUIMAE), UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Mariano Martin
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Claudia Lilián Ramirez
- Instituto de Química Física de los Materiales Medio Ambiente y Energía (INQUIMAE), UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Victoria Gisel Dumas
- Instituto de Química Física de los Materiales Medio Ambiente y Energía (INQUIMAE), UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marcelo Adrián Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina.
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28
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Li F, Xu D. Functional role of R462 in the degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae. J Mol Model 2015; 21:196. [PMID: 26169310 DOI: 10.1007/s00894-015-2724-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/08/2015] [Indexed: 11/25/2022]
Abstract
Hyaluronan lyase from Streptococcus pneumoniae can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. Hyaluronan can regulate water balance, osmotic pressure, and act as an ion exchange resin. Followed by our recent work on the catalytic reaction mechanism and substrate binding mode, we in this work further investigate the functional role of active site arginine residue, R462, in the degradation of hyaluronan. The site directed mutagenesis simulation of R462A and R462Q were modeled using a combined quantum mechanical and molecular mechanical method. The overall substrate binding features upon mutations do not have significant changes. The energetic profiles for the reaction processes are essentially the same as that in wild type enzyme, but significant activation barrier height changes can be observed. Both mutants were shown to accelerate the overall enzymatic activity, e.g., R462A can reduce the barrier height by about 2.8 kcal mol(-1), while R462Q reduces the activation energy by about 2.9 kcal mol(-1). Consistent with the active site model calculated using density functional theory, our results can support that the positive charge on R462 guanidino side chain group plays a negative role in the catalysis. Finally, the functional role of R462 was proposed to facilitate the formation of initial enzyme-substrate complex, but not in the subsequent catalytic degradation reaction. Graphical Abstract Degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae.
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Affiliation(s)
- Fengxue Li
- MOE Key Laboratory of Green Chemistry, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China
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29
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Jalkute CB, Sonawane KD. Evaluation of a possible role of Stigmatella aurantiaca ACE in Aβ peptide degradation: a molecular modeling approach. J Mol Microbiol Biotechnol 2015; 25:26-36. [PMID: 25677850 DOI: 10.1159/000370114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Amyloid-β (Aβ)-degrading enzymes are known to degrade Aβ peptides, a causative agent of Alzheimer's disease. These enzymes are responsible for maintaining Aβ concentration. However, loss of such enzymes or their Aβ-degrading activity because of certain genetic as well as nongenetic reasons initiates the accumulation of Aβ peptides in the human brain. Considering the limitations of the human enzymes in clearing Aβ peptide, the search for microbial enzymes that could cleave Aβ is necessary. Hence, we built a three-dimensional model of angiotensin-converting enzyme (ACE) from Stigmatella aurantiaca using homology modeling technique. Molecular docking and molecular dynamics simulation techniques were used to outline the possible cleavage mechanism of Aβ peptide. These findings suggest that catalytic residue Glu 434 of the model could play a crucial role to degrade Aβ peptide between Asp 7 and Ser 8. Thus, ACE from S. aurantiaca might cleave Aβ peptides similar to human ACE and could be used to design new therapeutic strategies against Alzheimer's disease.
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30
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da Cruz CHB, Seabra GM. QM/MM simulations of amyloid-β 42 degradation by IDE in the presence and absence of ATP. J Chem Inf Model 2015; 55:72-83. [PMID: 25539133 DOI: 10.1021/ci500544c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ability of the insulin-degrading enzyme (IDE) to degrade amyloid-β 42 (Aβ42), a process regulated by ATP, has been studied as an alternative path in the development of drugs against Alzheimer's disease. In this study, we calculated the potential of mean force for the degradation of Aβ42 by IDE in the presence and absence of ATP by umbrella sampling with hybrid quantum mechanics and molecular mechanics (QM/MM) calculations, using the SCC-DFTB QM Hamiltonian and Amber ff99SB force field. Results indicate that the reaction occurs in two steps: The first step is characterized by the formation of the intermediate. The second step is characterized by breaking the peptide bond of the substrate, the latter being the rate-determining step. In our simulations, the activation energy barrier in the absence of ATP is 15 ± 2 kcal mol(-1), which is 7 kcal mol(-1) lower than in the presence of ATP, indicating that the presence of the nucleotide decreases the reaction rate by about 10(5) times.
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Affiliation(s)
- Carlos H B da Cruz
- Departamento de Química Fundamental, Universidade Federal de Pernambuco , Av. Jornalista Aníbal Fernandes, s/n, Cidade Universitária, Recife-PE, Brazil , 50.740-560
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31
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Li P, Qi M, Hu H, Liu Q, Yang Q, Wang D, Guo F, Bligh SWA, Wang Z, Yang L. Structure–inhibition relationship of phenylethanoid glycosides on angiotensin-converting enzyme using ultra-performance liquid chromatography-tandem quadrupole mass spectrometry. RSC Adv 2015. [DOI: 10.1039/c5ra05027h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The structure–inhibition relationship of phenylethanoid glycosides against ACE was investigated by an improved UPLC-MS/MS method. The number of hydroxyl groups and structural steric hindrance were critical for the ACEI of phenylethanoid glycosides.
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32
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Martı́nez-González JÁ, González M, Masgrau L, Martı́nez R. Theoretical Study of the Free Energy Surface and Kinetics of the Hepatitis C Virus NS3/NS4A Serine Protease Reaction with the NS5A/5B Substrate. Does the Generally Accepted Tetrahedral Intermediate Really Exist? ACS Catal 2014. [DOI: 10.1021/cs5011162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Miguel González
- Departament
de Quı́mica Fı́sica i IQTC, Universitat de Barcelona, C/Martı́ i Franquès, 1, 08028 Barcelona, Spain
| | - Laura Masgrau
- Institut
de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Rodrigo Martı́nez
- Departamento
de Quı́mica, Universidad de La Rioja, C/Madre de
Dios, 51, 26006 Logroño, Spain
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33
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Brás NF, Fernandes PA, Ramos MJ. QM/MM Study and MD Simulations on the Hypertension Regulator Angiotensin-Converting Enzyme. ACS Catal 2014. [DOI: 10.1021/cs500093h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Natércia F. Brás
- REQUIMTE,
Departamento de
Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE,
Departamento de
Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE,
Departamento de
Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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34
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35
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Syntheses and structural studies of hexa- and pentacoordinated Zn complexes derived from 2-(aminomethyl)benzimidazole and water. Struct Chem 2014. [DOI: 10.1007/s11224-014-0416-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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36
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Zheng M, Xu D. Catalytic Mechanism of Hyaluronate Lyase from Spectrococcus pneumonia: Quantum Mechanical/Molecular Mechanical and Density Functional Theory Studies. J Phys Chem B 2013; 117:10161-72. [DOI: 10.1021/jp406206s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Min Zheng
- MOE Key Laboratory of Green
Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Dingguo Xu
- MOE Key Laboratory of Green
Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
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