1
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Ding Y, Wu Y, Chen J, Zhou Z, Zhao B, Zhao R, Cui Y, Li Q, Cong Y. Protective effect of
Eucommia ulmoides
Oliver male flowers on ethanol‐induced DNA damage in mouse cerebellum and cerebral cortex. FOOD SCIENCE & NUTRITION 2022; 10:2794-2803. [PMID: 35959248 PMCID: PMC9361448 DOI: 10.1002/fsn3.2882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 11/17/2022]
Abstract
Ethanol is a principal ingredient of alcoholic beverages with potential neurotoxicity and genotoxicity, and the ethanol‐associated oxidative DNA damage in the central nervous system is well documented. Natural product may offer new options to protect the brain against ethanol‐induced neurotoxicity. The male flower of Eucommia ulmoides (EUF) Oliver has been extensively utilized as the tea, the healthy hot drink on the market. In this study, 19 constituents in the effective fraction of EUF were identified by ultra‐performance liquid chromatography–tandem mass spectrometry (UPLC–MS/MS). In the single‐cell gel electrophoresis assay, EUF was observed to ameliorate DNA damage in mouse cerebellum and cerebral cortex caused by acute ethanol administration, which was further confirmed by the morphological observation. The protective effects of EUF were associated with increasing total superoxide dismutase (T‐SOD) and glutathione peroxidase (GSH‐PX) activities, and a decrease in nitric oxide (NO), malondialdehyde (MDA), 8‐hydroxy‐2′‐deoxyguanosine (8‐OHdG), and kelch‐like ECH‐associated protein‐1 (Keap1) levels. Molecular docking results demonstrated that compounds 4, 7, 9, and 16 from EUF have a strong affinity to the Keap1 Kelch domain to hinder the interaction of nuclear factor‐erythroid 2‐related factor 2 (Nrf2) with Keap1. These findings suggest that EUF is a potent inhibitor of ethanol‐induced brain injury possibly via the inhibition of oxidative stress.
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Affiliation(s)
- Yanxia Ding
- Institute of Pharmacy Engineering Center of Henan Province Eucommia ulmoides Cultivation and Utilization School of Pharmacy Henan University Kaifeng China
| | - Yantong Wu
- Institute of Pharmacy Engineering Center of Henan Province Eucommia ulmoides Cultivation and Utilization School of Pharmacy Henan University Kaifeng China
| | - Juan Chen
- Institute of Pharmacy Engineering Center of Henan Province Eucommia ulmoides Cultivation and Utilization School of Pharmacy Henan University Kaifeng China
| | - Zhaoli Zhou
- Institute of Pharmacy Engineering Center of Henan Province Eucommia ulmoides Cultivation and Utilization School of Pharmacy Henan University Kaifeng China
| | - Bing Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement Henan Joint International Laboratory for Crop Multi‐Omics Research School of Life Sciences Henan University Kaifeng China
| | - Rihong Zhao
- Institute of Pharmacy Engineering Center of Henan Province Eucommia ulmoides Cultivation and Utilization School of Pharmacy Henan University Kaifeng China
| | - Yuzi Cui
- Institute of Pharmacy Engineering Center of Henan Province Eucommia ulmoides Cultivation and Utilization School of Pharmacy Henan University Kaifeng China
| | - Qin Li
- Institute of Pharmacy Engineering Center of Henan Province Eucommia ulmoides Cultivation and Utilization School of Pharmacy Henan University Kaifeng China
| | - Yue Cong
- Institute of Pharmacy Engineering Center of Henan Province Eucommia ulmoides Cultivation and Utilization School of Pharmacy Henan University Kaifeng China
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2
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Fu Y, Zhang Y, Fan F, Wang B, Cao Z. Degradation of pesticides diazinon and diazoxon by phosphotriesterase: insight into divergent mechanisms from QM/MM and MD simulations. Phys Chem Chem Phys 2022; 24:687-696. [PMID: 34927643 DOI: 10.1039/d1cp05034f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymatic hydrolysis by phosphotriesterase (PTE) is one of the most effective ways of degrading organophosphorus pesticides, but the catalytic efficiency depends on the structural features of substrates. Here the enzymatic degradation of diazinon (DIN) and diazoxon (DON), characterized by PS and PO, respectively, have been investigated by QM/MM calculations and MM MD simulations. Our calculations demonstrate that the hydrolysis of DON (with PO) is inevitably initiated by the nucleophilic attack of the bridging-OH- on the phosphorus center, while for DIN (with PS), we proposed a new degradation mechanism, initiated by the nucleophilic attack of the Znα-bound water molecule, for its low-energy pathway. For both DIN and DON, the hydrolytic reaction is predicted to be the rate-limiting step, with energy barriers of 18.5 and 17.7 kcal mol-1, respectively. The transportation of substrates to the active site, the release of the leaving group and the degraded product are generally verified to be favorable by MD simulations via umbrella sampling, both thermodynamically and dynamically. The side-chain residues Phe132, Leu271 and Tyr309 play the gate-switching role to manipulate substrate delivery and product release. In comparison with the DON-enzyme system, the degraded product of DIN is more easily released from the active site. These new findings will contribute to the comprehensive understanding of the enzymatic degradation of toxic organophosphorus compounds by PTE.
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Affiliation(s)
- Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Yuwei Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Fangfang Fan
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, 310023, China.
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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3
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Fan F, Zheng YC, Fu Y, Zhang Y, Zheng H, Lyu C, Chen L, Huang J, Cao Z. QM/MM and MM MD simulations on decontamination of the V-type nerve agent VX by phosphotriesterase: Toward a comprehensive understanding of steroselectivity and activity. Phys Chem Chem Phys 2022; 24:10933-10943. [DOI: 10.1039/d2cp00773h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to deadly toxicity and high environmental stability of the nerve agent VX, an efficient decontamination approach is desperately needed in tackling its severe threat to human secu-rity. The enzymatic...
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4
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Wu L, Qin L, Nie Y, Xu Y, Zhao YL. Computer-aided understanding and engineering of enzymatic selectivity. Biotechnol Adv 2021; 54:107793. [PMID: 34217814 DOI: 10.1016/j.biotechadv.2021.107793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
Abstract
Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally occurring enzymes are often inefficient or have undesired selectivity toward non-native substrates hinders the broadening of biocatalytic applications. To match the demands of specific selectivity in asymmetric synthesis, biochemists have implemented various computer-aided strategies in understanding and engineering enzymatic selectivity, diversifying the available repository of artificial enzymes. Here, given that the entire asymmetric catalytic cycle, involving precise interactions within the active pocket and substrate transport in the enzyme channel, could affect the enzymatic efficiency and selectivity, we presented a comprehensive overview of the computer-aided workflow for enzymatic selectivity. This review includes a mechanistic understanding of enzymatic selectivity based on quantum mechanical calculations, rational design of enzymatic selectivity guided by enzyme-substrate interactions, and enzymatic selectivity regulation via enzyme channel engineering. Finally, we discussed the computational paradigm for designing enzyme selectivity in silico to facilitate the advancement of asymmetric biosynthesis.
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Affiliation(s)
- Lunjie Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lei Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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5
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Zhang X, Zhang Z, Guo J, Ma J, Xie S, Zhao Y, Wang C. Combination of multiple computational methods revealing specific sub-sectional recognition and hydrogen-bond dependent transportation of CKII peptide fragment in O-GlcNAc transferase. Comput Struct Biotechnol J 2021; 19:2045-2056. [PMID: 33995901 PMCID: PMC8085782 DOI: 10.1016/j.csbj.2021.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 11/17/2022] Open
Abstract
Mechanism of CKII peptide recognition, transportation and binding in OGT is obtained. Peptide delivery is strong exothermic, highly dependent on hydrogen bond network. Typical ‘spread’ & ‘V’ conformation change noticed for peptide accompanies stable OGT. Specific subsection of peptide has diverse performance in its recognition and delivery. Multiple methods combination may be used in other bio-system with flexible substrate.
O-linked β-N-acetyl-D-glucosamine (O-GlcNAc) transferase (OGT) is an essential enzyme in many cellular physiological catalytic reactions that regulates protein O-GlcNAcylation. Aberrant O-GlcNAcylation is related to insulin resistance, diabetic complications, cancer and neurodegenerative diseases. Understanding the peptide delivery in OGT is significant in comprehending enzymatic catalytic process, target-protein recognition and pathogenic mechanism. Herein extensive molecular dynamics (MD) simulations combined with various techniques are utilized to study the recognizing and binding mechanism of peptide fragment extracted from casein kinase II by OGT from atomic level. The residues of His496, His558, Thr633, Lys634, and Pro897 are demonstrated to play a dominant role in the peptide stabilization via hydrogen bonds and σ-π interaction, whose van der Waals and non-polar solvent effects provide the main driving force. In addition, two channels are identified. The delivery mode, mechanism together with thermodynamic and dynamic characterizations for the most favorable channel are determined. The peptide is more inclined to be recognized by OGT through the cavity comprised of residues 799–812, 893–899, and 865–871, and Tyr13-terminal is prior recognized to Met26-terminal. The transportation process is accompanied with conformation changes between the “spread” and “V” shapes. The whole process is strong exothermic that is highly dependent on the variation of hydrogen bond interactions between peptide and OGT as well as the performance of different subsections of peptide. Besides that, multiple computational methods combinations may contribute meaningfully to calculation of similar bio-systems with long and flexible substrate.
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Affiliation(s)
- Xiao Zhang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, People's Republic of China
| | - Zhiyang Zhang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, People's Republic of China
| | - Jia Guo
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, People's Republic of China
| | - Jing Ma
- School of Pharmacy, Henan University, Kaifeng 475004, People's Republic of China
| | - Songqiang Xie
- School of Pharmacy, Henan University, Kaifeng 475004, People's Republic of China
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, People's Republic of China
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, People's Republic of China
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6
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Guo J, Shen S, Zhang X, Wang G, Lu Y, Liu X, Wang S, Li Q, Cong Y, Shi B. Chemical compounds with a neuroprotective effect from the seeds of Celosia argentea L. Food Funct 2021; 12:83-96. [PMID: 33191416 DOI: 10.1039/d0fo02033h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Oxidative stress plays a central role in the common pathophysiology of neurodegenerative diseases such as Alzheimer's disease, amyotrophic lateral sclerosis, and Parkinson's disease. Antioxidant therapy has been suggested for the prevention and treatment of neurodegenerative diseases. Compounds derived from natural sources may offer the potential for new treatment options. Semen Celosiae is a traditional Chinese edible herbal medicine with a long history in China and exhibits wide-reaching biological activities such as hepatoprotective, anti-tumor, anti-diarrheal, anti-diabetic, anti-oxidant, etc. In this study, nine saponins and two phenylacetonitrile glycosides were isolated from Semen Celosiae and their structures were identified using ESI-MS and NMR techniques. Among them, compounds 1 and 2 have not been previously reported. The total concentrations of the five triterpenoid saponins and the two phenylacetonitrile glycosides were 3.348 mg g-1 and 0.187 mg g-1, respectively, suggesting that Semen Celosiae is a novel viable source of the two kinds of compounds. These compounds were observed to significantly attenuate t-BHP-induced neuronal damage by effectively enhancing cell viability and decreasing reactive oxygen species generation and cell apoptosis rate in NSC-34 cells. Furthermore, compounds 1 and 7 reduced the ratios of cleaved caspase-3: caspase-3 and cleaved caspase-7: caspase-7 and the level of cytochrome C, while they increased the levels of SOD1 and Beclin 1. These findings suggest that compounds 1-11 are potent inhibitors of neuron injury elicited by t-BHP, possibly via inhibition of oxidative stress and apoptosis, and activation of autophagy; therefore they may be valuable leads for future therapeutic development.
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Affiliation(s)
- Jinggong Guo
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Shan Shen
- Institute of Pharmacy, School of Pharmacy, Henan University, Kaifeng, China. and Ludong Hospital, Yantai, China
| | - Xiao Zhang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China
| | - Guoying Wang
- Faculty of Medicine & Health Sciences, Macquarie University, Sydney, NSW, Australia.
| | - Yiqing Lu
- Centre for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW, Australia
| | - Xiping Liu
- Institute of Pharmacy, School of Pharmacy, Henan University, Kaifeng, China.
| | - Shuyun Wang
- Institute of Pharmacy, School of Pharmacy, Henan University, Kaifeng, China.
| | - Qin Li
- Institute of Pharmacy, School of Pharmacy, Henan University, Kaifeng, China.
| | - Yue Cong
- Institute of Pharmacy, School of Pharmacy, Henan University, Kaifeng, China.
| | - Bingyang Shi
- Faculty of Medicine & Health Sciences, Macquarie University, Sydney, NSW, Australia. and International Joint Center for Biomedical Innovation, College of Life Sciences, Henan University, Kaifeng, China
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7
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Zhang Z, Fan F, Luo W, Zhao Y, Wang C. Molecular Dynamics Revealing a Detour-Forward Release Mechanism of Tacrine: Implication for the Specific Binding Characteristics in Butyrylcholinesterase. Front Chem 2020; 8:730. [PMID: 33195011 PMCID: PMC7477934 DOI: 10.3389/fchem.2020.00730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/14/2020] [Indexed: 01/29/2023] Open
Abstract
Butyrylcholinesterase (BChE) is a non-specific enzyme with clinical pharmacological and toxicological significance, which was a renewed interest as therapeutic target in Alzheimer's disease (AD) nowadays. Here, all-atom molecular dynamics simulations of butyrylcholinesterase with tacrine complex were designed to characterize inhibitor binding modes, strengths, and the hydrogen-bond dependent non-covalent release mechanism. Four possible release channels were identified, and the most favorable channel was determined by random acceleration molecular dynamics molecular dynamics (RAMD MD) simulations. The thermodynamic and dynamic properties as well as the corresponding Detour-forward delivery mechanism were determined according to the classical molecular dynamics (MD) simulations accompanied with umbrella sampling. The free energy barrier of the tacrine release process for the most beneficial pathway is about 10.95 kcal/mol, which is related to the non-covalent interactions from the surrounding residues, revealing the specific binding characteristics in the active site. The residues including Asp70, Ser79, Trp82, Gly116, Thr120, Tyr332, and His438 were identified to play major roles in the stabilization of tacrine in the pocket of BChE, where hydrogen bonding and π-π interactions are significant factors. Tyr332 and Asp70, which act as gate keepers, play crucial roles in the substrate delivery. The present results provide a basic understanding for the ligand transport mechanism depending on the BChE enzymatic environment, which is useful for the design of BChE inhibitors in the future.
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Affiliation(s)
- Zhiyang Zhang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China
| | - Fangfang Fan
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Wen Luo
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, China
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8
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Biggers L, Elhabashy H, Ackad E, Yousef MS. Molecular dynamics simulations of an engineered T4 lysozyme exclude helix to sheet transition, and provide insights into long distance, intra-protein switchable motion. Protein Sci 2020; 29:542-554. [PMID: 31702853 PMCID: PMC6954740 DOI: 10.1002/pro.3780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/23/2019] [Accepted: 11/05/2019] [Indexed: 01/05/2023]
Abstract
An engineered variant of T4 lysozyme serves as a model for studying induced remote conformational changes in a full protein context. The design involves a duplicated surface helix, flanked by two loops, that switches between two different conformations spanning about 20 Å. Molecular dynamics simulations of the engineered protein, up to 1 μs, rule out α-helix to β-sheet transitions within the duplicated helix as suggested by others. These simulations highlight how the use of different force fields can lead to radical differences in the structure of the protein. In addition, Markov state modeling and transition path theory were employed to map a 6.6 μs simulation for possible early intermediate states and to provide insights into the onset of the switching motion. The putative intermediates involve the folding of one helical turn in the C-terminal loop through energy driven, sequential rearrangement of nearby salt bridges around the key residue Arg63. These results provide a first step towards understanding the energetics and dynamics of a rather complicated intra-protein motion.
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Affiliation(s)
- Laurence Biggers
- Department of Internal MedicineUniversity of Texas Southwestern Medical CenterDallasTexas
| | - Hadeer Elhabashy
- Biomolecular Interactions, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Edward Ackad
- Department of PhysicsCollege of Arts and Sciences, Southern Illinois University EdwardsvilleEdwardsvilleIllinois
| | - Mohammad S. Yousef
- Premedical Unit, Weill Cornell Medicine‐QatarCornell UniversityDohaQatar
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9
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Fan F, Zheng Y, Zhang Y, Zheng H, Zhong J, Cao Z. A Comprehensive Understanding of Enzymatic Degradation of the G-Type Nerve Agent by Phosphotriesterase: Revised Role of Water Molecules and Rate-Limiting Product Release. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01877] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Fangfang Fan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of China
| | - Yongchao Zheng
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, People’s Republic of China
| | - Yuwei Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of China
| | - He Zheng
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, People’s Republic of China
| | - Jinyi Zhong
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, People’s Republic of China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of China
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10
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Wei W, Ma J, Xie D, Zhou Y. Linking inhibitor motions to proteolytic stability of sunflower trypsin inhibitor-1. RSC Adv 2019; 9:13776-13786. [PMID: 35519558 PMCID: PMC9063939 DOI: 10.1039/c9ra02114k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/25/2019] [Indexed: 12/20/2022] Open
Abstract
The remarkable capability of an enzyme isn't only determined by its active site but also controlled by the environment. To unravel the environment role in catalysis, the dynamic motions as well as the static mechanism need to be studied. In this work, QM/MM MD simulations were employed to study the proteolysis process of SFTI-1 and BiKF, which revealed that a combination of static non-bonded interactions and dynamic motions along the reaction coordinate can account for the different hydrolysis rates between them. A comparison among SFTI-1 and three analogs with similar non-bonded interactions further revealed a positive correlation between the mobility of inhibitors and the hydrolysis rates. Apart from the cyclic backbone and disulfide bond, intramolecular hydrogen bonds also increase the rigidity of the backbone of inhibitors, and therefore hinder inhibitor motions to resist proteolysis. These new detailed mechanistic insights suggest the need to consider inhibitor motions in the rational design of peptide inhibitors. Besides the non-bonded interactions, inhibitor motions especially rotation of the scissile bond also influence proteolytic stability.![]()
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Affiliation(s)
- Wanqing Wei
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Daiqian Xie
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Yanzi Zhou
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
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Fan F, Zhao Y, Cao Z. Insight into the delivery channel and selectivity of multiple binding sites in bovine serum albumin towards naphthalimide-polyamine derivatives. Phys Chem Chem Phys 2019; 21:7429-7439. [PMID: 30892331 DOI: 10.1039/c9cp00527g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naphthalimide derivatives are types of small-molecule anticancer drug candidates; however, their negative factors and potential side effects make their application limited. The pharmacophores select a direct access into the tumor cells as the first choice; this can reduce the side effect of the anti-cancer drugs on the normal cells. Herein, the delivery and binding of the naphthalimide-polyamine complex assisted by the bovine serum albumin (BSA) protein have been studied by combining several molecular dynamic simulations. The plausible transportation channels and the most favorable pathways for the delivery of the naphthalimide-polyamine complex to two drug sites (DSI and DSII), their thermodynamic and dynamic properties and the mechanisms have been discussed in detail. The residues His287 and Phe394 acted as guards in the DSI and DSII, respectively, which played a gating-switch role by flipping the ring from open to close during the compound delivery. The binding mode, binding energy and substituent effects have been also identified. The two drug sites have different preferences towards the compound with the electron-withdrawing and electron-donating substituents, and their strong interactions are more sensitive to the number of the substituent groups. The naphthalimide-polyamine complexes are more likely to choose DSI, both thermodynamically and dynamically, as compared to DSII. This selective specificity of these two drug sites manipulated by the electron-withdrawing and electron-donating substituents is quite promising for the design of new naphthalimide drugs.
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Affiliation(s)
- Fangfang Fan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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12
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Wei W, Chen Y, Xie D, Zhou Y. Molecular insight into chymotrypsin inhibitor 2 resisting proteolytic degradation. Phys Chem Chem Phys 2019; 21:5049-5058. [PMID: 30762035 DOI: 10.1039/c8cp07784c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chymotrypsin inhibitor 2 (CI2) is a special serine protease inhibitor which can resist hydrolysis for several days with a rapid equilibrium between the Michaelis complex and acyl-enzyme intermediate. The energies and conformational changes for subtilisin-catalyzed proteolysis of CI2 were examined in this paper for the first time by employing pseudo bond ab initio QM/MM MD simulations. In the acylation reaction, a low-barrier hydrogen bond between His64 and Asp32 in the transition state together with the lack of covalent backbone constraints makes the peptide bonds of CI2 break more easily than in other serine protease inhibitors. After acyl-enzyme formation, molecular dynamics simulations showed that the access of hydrolytic water to the active site requires partial dissociation of the leaving group. However, retention of the leaving group mainly by the intra- and inter-molecular H-bonding networks hinders the access of water and retards the deacylation reaction. Instead of the dissociation constant of inhibitors, we suggest employing the free energy at the acyl-enzyme state to predict the relative hydrolysis rates of CI2 mutants, which are testified by the experimental relative hydrolysis rates.
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Affiliation(s)
- Wanqing Wei
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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13
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She N, Zhao Y, Hao J, Xie S, Wang C. Uridine diphosphate release mechanism in O-N-acetylglucosamine (O-GlcNAc) transferase catalysis. Biochim Biophys Acta Gen Subj 2018; 1863:609-622. [PMID: 30550897 DOI: 10.1016/j.bbagen.2018.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 01/17/2023]
Abstract
O-linked N-acetylglucosamine transferase (OGT) is an essential enzyme that catalyzes the covalent bonding of N-acetylglucosamine (GlcNAc) to the hydroxyl group of a serine or threonine in the target protein. It plays an important role in many important cellular physiological catalytic reactions. Here, we determine the binding mode and the binding free energy of the OGT product (uridine diphosphate, UDP) as well as the hydrogen-bond-dependent release mechanism using extensive molecular dynamic simulations. The Lys634, Asn838, Gln839, Lys842, His901, and Asp925 residues were identified to play a major role in the UDP stabilization in the active site of OGT, where hydrogen bonding and π-π interactions mainly occur. The calculations on the mutant forms support our results. Sixteen possible release channels were identified while the two most favorable channels were determined using random acceleration molecular dynamics (RAMD) simulations combined with the constant velocity pulling (PCV) method. The thermodynamic and dynamic properties as along with the corresponding mechanism were determined and discussed according to the umbrella sampling technique. For the most optimal channel, the main free energy barrier is 13 kcal/mol, which probably originates from the hydrogen bonds between UDP and the Ala896 and Asp925 residues. Moreover, the unstable hydrogen bonds and the rollback of the ligand likely cause the other two small obstacles. This work clarifies the ligand transport mechanism in the OGT enzymatic process and is a great resource for designing inhibitors based on UDP or UDP-GlcNAc.
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Affiliation(s)
- Nai She
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China.
| | - Jingjing Hao
- People's Hospital of Kaifeng, Kaifeng 475004, China
| | - Songqiang Xie
- Pharmaceutical College, Henan University, Kaifeng 475004, China
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China.
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14
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Zhao Y, She N, Ma Y, Wang C, Cao Z. A Description of Enzymatic Catalysis in N-Acetylhexosamine 1-Kinase: Concerted Mechanism of Two-Magnesium-Ion-Assisted GlcNAc Phosphorylation, Flexibility Behavior of Lid Motif upon Substrate Recognition, and Water-Assisted GlcNAc-1-P Release. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Nai She
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Yiming Ma
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of China
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15
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Zhang F, Wang YH, Tang X, Wu R. Catalytic promiscuity of the non-native FPP substrate in the TEAS enzyme: non-negligible flexibility of the carbocation intermediate. Phys Chem Chem Phys 2018; 20:15061-15073. [DOI: 10.1039/c8cp02262c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
By QM(DFT)/MM MD simulations, it has been revealed that the non-native substrate catalytic promiscuity of TEAS (one of the sesquiterpene cyclases) is mostly attributable to its notable conformational flexibility of the branching intermediate bisabolyl cation.
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Affiliation(s)
- Fan Zhang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Yong-Heng Wang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Xiaowen Tang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Ruibo Wu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
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16
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Zhao Y, She N, Zhang X, Wang C, Mo Y. Product release mechanism and the complete enzyme catalysis cycle in yeast cytosine deaminase (yCD): A computational study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1020-1029. [PMID: 28478051 DOI: 10.1016/j.bbapap.2017.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/02/2017] [Indexed: 11/24/2022]
Abstract
Yeast cytosine deaminase (yCD) is critical in gene-directed enzyme prodrug therapy as it catalyzes the hydrolytic deamination of cytosine. The product (uracil) release process is considered as rate-limiting in the whole enzymatic catalysis and includes the cleavage of the uracil-metal bond and the delivery of free uracil out of the reactive site. Herein extensive combined random acceleration molecular dynamics (RAMD) and molecular dynamics (MD) simulations coupled with the umbrella sampling technique have been performed to study the product transport mechanism. Five channels have been identified, and the thermodynamic and dynamic characterizations for the two most favorable channels have been determined and analyzed. The free energy barrier for the most beneficial pathway is about 13kcal/mol and mainly results from the cleavage of hydrogen bonds between the ligand uracil and surrounding residues Asn51, Glu64, and Asp155. The conjugated rings of Phe114 and Trp152 play gating and guiding roles in the product delivery via π⋯π van der Waals interactions with the product. Finally, the full cycle of the enzymatic catalysis has been determined, making the whole process computationally more precise.
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Affiliation(s)
- Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China.
| | - Nai She
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China
| | - Xin Zhang
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China.
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
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