1
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Yin X, Dong L, Wang X, Qin Z, Ma Y, Ke X, Li Y, Wang Q, Mi Y, Lyu Q, Xu X, Zheng P, Tang Y. Perilipin 5 regulates hepatic stellate cell activation and high-fat diet-induced non-alcoholic fatty liver disease. Animal Model Exp Med 2024; 7:166-178. [PMID: 37202925 PMCID: PMC11079159 DOI: 10.1002/ame2.12327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/21/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases globally. Hepatic stellate cells (HSCs) are the major effector cells of liver fibrosis. HSCs contain abundant lipid droplets (LDs) in their cytoplasm during quiescence. Perilipin 5 (PLIN 5) is a LD surface-associated protein that plays a crucial role in lipid homeostasis. However, little is known about the role of PLIN 5 in HSC activation. METHODS PLIN 5 was overexpressed in HSCs of Sprague-Dawley rats by lentivirus transfection. At the same time, PLIN 5 gene knockout mice were constructed and fed with a high-fat diet (HFD) for 20 weeks to study the role of PLIN 5 in NAFLD. The corresponding reagent kits were used to measure TG, GSH, Caspase 3 activity, ATP level, and mitochondrial DNA copy number. Metabolomic analysis of mice liver tissue metabolism was performed based on UPLC-MS/MS. AMPK, mitochondrial function, cell proliferation, and apoptosis-related genes and proteins were detected by western blotting and qPCR. RESULTS Overexpression of PLIN 5 in activated HSCs led to a decrease in ATP levels in mitochondria, inhibition of cell proliferation, and a significant increase in cell apoptosis through AMPK activation. In addition, compared with the HFD-fed C57BL/6J mice, PLIN 5 knockout mice fed with HFD showed reduced liver fat deposition, decreased LD abundance and size, and reduced liver fibrosis. CONCLUSION These findings highlight the unique regulatory role of PLIN 5 in HSCs and the role of PLIN 5 in the fibrosis process of NAFLD.
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Affiliation(s)
- Xuecui Yin
- Department of Internal Medicinethe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Lin Dong
- Department of Pediatricsthe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Xiaohan Wang
- Department of Pediatricsthe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Zhenzhen Qin
- Department of Internal Medicinethe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yuying Ma
- Department of Internal Medicinethe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Xiaofei Ke
- Department of Pediatricsthe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Ya Li
- Department of Internal Medicinethe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Qingde Wang
- Department of Internal Medicinethe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yang Mi
- Department of Internal Medicinethe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Quanjun Lyu
- Department of Clinical Nutritionthe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Xia Xu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Co‐innovation Center of Henan Province for New drug R & D and Preclinical Safety, School of Pharmaceutical SciencesZhengzhou UniversityZhengzhouChina
| | - Pengyuan Zheng
- Department of Internal Medicinethe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Youcai Tang
- Department of Internal Medicinethe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
- Department of Pediatrics, Gastroenterology, Henan Key Laboratory of Rehabilitation Medicine, Henan Joint International Research Laboratory of Chronic Liver Injury and Henan Provincial Outstanding Overseas Scientists Chronic Liver Injury Studiothe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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2
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Gai C, Harnor SJ, Zhang S, Cano C, Zhuang C, Zhao Q. Advanced approaches of developing targeted covalent drugs. RSC Med Chem 2022; 13:1460-1475. [PMID: 36561076 PMCID: PMC9749957 DOI: 10.1039/d2md00216g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
In recent years, the development of targeted covalent inhibitors has gained popularity around the world. Specific groups (electrophilic warheads) form irreversible bonds with the side chain of nucleophilic amino acid residues, thus changing the function of biological targets such as proteins. Since the first targeted covalent inhibitor was disclosed in the 1990s, great efforts have been made to develop covalent ligands from known reversible leads or drugs by addition of tolerated electrophilic warheads. However, high reactivity and "off-target" toxicity remain challenging issues. This review covers the concept of targeted covalent inhibition to diseases, discusses traditional and interdisciplinary strategies of cysteine-focused covalent drug discovery, and exhibits newly disclosed electrophilic warheads majorly targeting the cysteine residue. Successful applications to address the challenges of designing effective covalent drugs are also introduced.
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Affiliation(s)
- Conghao Gai
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Suzannah J Harnor
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Shihao Zhang
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Céline Cano
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Chunlin Zhuang
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Qingjie Zhao
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
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3
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Abstract
Covalent drugs offer higher efficacy and longer duration of action than their noncovalent counterparts. Significant advances in computational methods for modeling covalent drugs are poised to shift the paradigm of small molecule therapeutics within the next decade. This viewpoint discusses the advantages of a two-state model for ranking reversible and irreversible covalent ligands and of more complex models for dissecting reaction mechanisms. The relation between these models highlights the complexity and diversity of covalent drug binding and provides opportunities for mechanism-based rational design.
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Affiliation(s)
- Yun Lyna Luo
- Department of Pharmaceutical Sciences, Western University of Health Sciences, Pomona, California 91709, United States
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4
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Dhuria NV, Haro B, Kapadia A, Lobo KA, Matusow B, Schleiff MA, Tantoy C, Sodhi JK. Recent developments in predicting CYP-independent metabolism. Drug Metab Rev 2021; 53:188-206. [PMID: 33941024 DOI: 10.1080/03602532.2021.1923728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
As lead optimization efforts have successfully reduced metabolic liabilities due to cytochrome P450 (CYP)-mediated metabolism, there has been an increase in the frequency of involvement of non-CYP enzymes in the metabolism of investigational compounds. Although there have been numerous notable advancements in the characterization of non-CYP enzymes with respect to their localization, reaction mechanisms, species differences and identification of typical substrates, accurate prediction of non-CYP-mediated clearance, with a particular emphasis with the difficulties in accounting for any extrahepatic contributions, remains a challenge. The current manuscript comprehensively summarizes the recent advancements in the prediction of drug metabolism and the in vitro to in vitro extrapolation of clearance for substrates of non-CYP drug metabolizing enzymes.
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Affiliation(s)
- Nikhilesh V Dhuria
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bianka Haro
- School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Amit Kapadia
- California Poison Control Center, University of California San Francisco, San Diego, CA, USA
| | | | - Bernice Matusow
- Department of Drug Metabolism and Pharmacokinetics, Plexxikon Inc, Berkeley, CA, USA
| | - Mary A Schleiff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Christina Tantoy
- Department of Drug Metabolism and Pharmacokinetics, Plexxikon Inc, Berkeley, CA, USA
| | - Jasleen K Sodhi
- Department of Drug Metabolism and Pharmacokinetics, Plexxikon Inc, Berkeley, CA, USA.,Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, CA, USA
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5
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Wen C, Yan X, Gu Q, Du J, Wu D, Lu Y, Zhou H, Xu J. Systematic Studies on the Protocol and Criteria for Selecting a Covalent Docking Tool. Molecules 2019; 24:molecules24112183. [PMID: 31185706 PMCID: PMC6600387 DOI: 10.3390/molecules24112183] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 12/28/2022] Open
Abstract
With the resurgence of drugs with covalent binding mechanisms, much attention has been paid to docking methods for the discovery of targeted covalent inhibitors. The existence of many available covalent docking tools has inspired development of a systematic and objective procedure and criteria with which to evaluate these programs. In order to find a tool appropriate to studies of a covalently binding system, protocols and criteria are proposed for protein–ligand covalent docking studies. This paper consists of three sections: (1) curating a standard data set to evaluate covalent docking tools objectively; (2) establishing criteria to measure the performance of a tool applied for docking ligands into a complex system; and (3) creating a protocol to evaluate and select covalent binding tools. The protocols were applied to evaluate four covalent docking tools (MOE, GOLD, CovDock, and ICM-Pro) and parameters affecting covalent docking performance were investigated.
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Affiliation(s)
- Chang Wen
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China.
| | - Xin Yan
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China.
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China.
| | - Jiewen Du
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China.
| | - Di Wu
- National Supercomputer Center in Guangzhou & School of Data and Computer Science, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China.
| | - Yutong Lu
- National Supercomputer Center in Guangzhou & School of Data and Computer Science, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China.
| | - Huihao Zhou
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China.
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China.
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6
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Yuan X, Xu Y. Recent Trends and Applications of Molecular Modeling in GPCR⁻Ligand Recognition and Structure-Based Drug Design. Int J Mol Sci 2018; 19:ijms19072105. [PMID: 30036949 PMCID: PMC6073596 DOI: 10.3390/ijms19072105] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled receptors represent the largest family of human membrane proteins and are modulated by a variety of drugs and endogenous ligands. Molecular modeling techniques, especially enhanced sampling methods, have provided significant insight into the mechanism of GPCR–ligand recognition. Notably, the crucial role of the membrane in the ligand-receptor association process has earned much attention. Additionally, docking, together with more accurate free energy calculation methods, is playing an important role in the design of novel compounds targeting GPCRs. Here, we summarize the recent progress in the computational studies focusing on the above issues. In the future, with continuous improvement in both computational hardware and algorithms, molecular modeling would serve as an indispensable tool in a wider scope of the research concerning GPCR–ligand recognition as well as drug design targeting GPCRs.
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Affiliation(s)
- Xiaojing Yuan
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
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7
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Sotriffer C. Docking of Covalent Ligands: Challenges and Approaches. Mol Inform 2018; 37:e1800062. [PMID: 29927068 DOI: 10.1002/minf.201800062] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/01/2018] [Indexed: 01/08/2023]
Abstract
Covalent ligands have recently regained considerable attention in drug discovery. The rational design of such ligands, however, is still faced with particular challenges, mostly related to the fact that covalent bond formation is a quantum mechanical phenomenon which cannot adequately be handled by the force fields or empirical approaches typically used for noncovalent protein-ligand interactions. Although the necessity for quantum chemical approaches is clear, they cannot yet routinely be applied on large data sets of ligands or for a broader exploration of binding modes in docking calculations. On the other hand, technical solutions for performing docking calculations with covalent ligands are available, but their scope is normally quite limited. Scoring functions typically neglect the contribution from covalent bond formation completely. In this situation, the question arises how to approach covalent ligands and which methods to choose for their docking and design.
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Affiliation(s)
- Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, D-, 97074, Würzburg, Germany
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8
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Dos Santos Vasconcelos CR, de Lima Campos T, Rezende AM. Building protein-protein interaction networks for Leishmania species through protein structural information. BMC Bioinformatics 2018; 19:85. [PMID: 29510668 PMCID: PMC5840830 DOI: 10.1186/s12859-018-2105-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/01/2018] [Indexed: 12/21/2022] Open
Abstract
Background Systematic analysis of a parasite interactome is a key approach to understand different biological processes. It makes possible to elucidate disease mechanisms, to predict protein functions and to select promising targets for drug development. Currently, several approaches for protein interaction prediction for non-model species incorporate only small fractions of the entire proteomes and their interactions. Based on this perspective, this study presents an integration of computational methodologies, protein network predictions and comparative analysis of the protozoan species Leishmania braziliensis and Leishmania infantum. These parasites cause Leishmaniasis, a worldwide distributed and neglected disease, with limited treatment options using currently available drugs. Results The predicted interactions were obtained from a meta-approach, applying rigid body docking tests and template-based docking on protein structures predicted by different comparative modeling techniques. In addition, we trained a machine-learning algorithm (Gradient Boosting) using docking information performed on a curated set of positive and negative protein interaction data. Our final model obtained an AUC = 0.88, with recall = 0.69, specificity = 0.88 and precision = 0.83. Using this approach, it was possible to confidently predict 681 protein structures and 6198 protein interactions for L. braziliensis, and 708 protein structures and 7391 protein interactions for L. infantum. The predicted networks were integrated to protein interaction data already available, analyzed using several topological features and used to classify proteins as essential for network stability. Conclusions The present study allowed to demonstrate the importance of integrating different methodologies of interaction prediction to increase the coverage of the protein interaction of the studied protocols, besides it made available protein structures and interactions not previously reported. Electronic supplementary material The online version of this article (10.1186/s12859-018-2105-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Crhisllane Rafaele Dos Santos Vasconcelos
- Microbiology Department of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil. .,Genetics Department of Universidade Federal de Pernambuco, Recife, PE, Brazil.
| | - Túlio de Lima Campos
- Microbiology Department of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil.,Bioinformatics Plataform of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil
| | - Antonio Mauro Rezende
- Microbiology Department of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil. .,Bioinformatics Plataform of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil. .,Genetics Department of Universidade Federal de Pernambuco, Recife, PE, Brazil.
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9
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Dixit VA, Lal LA, Agrawal SR. Recent advances in the prediction of non‐
CYP450
‐mediated drug metabolism. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1323] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmaceutical Chemistry, School of Pharmacy & Technology Management (SPTM)Shri Vile Parle Kelavani Mandal's (SVKM's), Narsee Monjee Institute of Management Studies (NMIMS)ShirpurIndia
| | - L. Arun Lal
- Department of Pharmaceutical Chemistry, School of Pharmacy & Technology Management (SPTM)Shri Vile Parle Kelavani Mandal's (SVKM's), Narsee Monjee Institute of Management Studies (NMIMS)ShirpurIndia
| | - Simran R. Agrawal
- Department of Pharmaceutical Chemistry, School of Pharmacy & Technology Management (SPTM)Shri Vile Parle Kelavani Mandal's (SVKM's), Narsee Monjee Institute of Management Studies (NMIMS)ShirpurIndia
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10
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Knutson ST, Westwood BM, Leuthaeuser JB, Turner BE, Nguyendac D, Shea G, Kumar K, Hayden JD, Harper AF, Brown SD, Morris JH, Ferrin TE, Babbitt PC, Fetrow JS. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Sci 2017; 26:677-699. [PMID: 28054422 PMCID: PMC5368075 DOI: 10.1002/pro.3112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 12/22/2016] [Indexed: 01/11/2023]
Abstract
Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results.
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Affiliation(s)
- Stacy T. Knutson
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
- Department of Computer ScienceWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Brian M. Westwood
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
- Department of Computer ScienceWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Janelle B. Leuthaeuser
- Molecular Genetics and Genomics ProgramWake Forest School of MedicineWinston‐SalemNorth Carolina27157
| | - Brandon E. Turner
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Don Nguyendac
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Gabrielle Shea
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Kiran Kumar
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Julia D. Hayden
- Biochemistry Program, Dickinson CollegeCarlislePennsylvania17013
| | - Angela F. Harper
- Department of PhysicsWake Forest UniversityWinston‐SalemNorth Carolina27106
| | - Shoshana D. Brown
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
| | - John H. Morris
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
| | - Thomas E. Ferrin
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
| | - Patricia C. Babbitt
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCalifornia94158
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11
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Yao Z, Zhang L, Gao B, Cui D, Wang F, He X, Zhang JZH, Wei D. A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with Candida antarctica Lipase B. J Chem Inf Model 2016; 56:1979-1994. [DOI: 10.1021/acs.jcim.5b00585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhiqiang Yao
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Lujia Zhang
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Bei Gao
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Dongbing Cui
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Fengqing Wang
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Xiao He
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - John Z. H. Zhang
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Dongzhi Wei
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
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12
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Abstract
It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years.
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Affiliation(s)
- John J Irwin
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
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13
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Ahmed FH, Carr PD, Lee BM, Afriat-Jurnou L, Mohamed AE, Hong NS, Flanagan J, Taylor MC, Greening C, Jackson CJ. Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria. J Mol Biol 2015; 427:3554-3571. [PMID: 26434506 DOI: 10.1016/j.jmb.2015.09.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 12/11/2022]
Abstract
The deazaflavin cofactor F420 enhances the persistence of mycobacteria during hypoxia, oxidative stress, and antibiotic treatment. However, the identities and functions of the mycobacterial enzymes that utilize F420 under these conditions have yet to be resolved. In this work, we used sequence similarity networks to analyze the distribution of the largest F420-dependent protein family in mycobacteria. We show that these enzymes are part of a larger split β-barrel enzyme superfamily (flavin/deazaflavin oxidoreductases, FDORs) that include previously characterized pyridoxamine/pyridoxine-5'-phosphate oxidases and heme oxygenases. We show that these proteins variously utilize F420, flavin mononucleotide, flavin adenine dinucleotide, and heme cofactors. Functional annotation using phylogenetic, structural, and spectroscopic methods revealed their involvement in heme degradation, biliverdin reduction, fatty acid modification, and quinone reduction. Four novel crystal structures show that plasticity in substrate binding pockets and modifications to cofactor binding motifs enabled FDORs to carry out a variety of functions. This systematic classification and analysis provides a framework for further functional analysis of the roles of FDORs in mycobacterial pathogenesis and persistence.
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Affiliation(s)
- F Hafna Ahmed
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Paul D Carr
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Brendon M Lee
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Livnat Afriat-Jurnou
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - A Elaaf Mohamed
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Nan-Sook Hong
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Jack Flanagan
- University of Auckland Faculty of Medical and Health Sciences, 85 Park Road, Grafton, Auckland 2013, New Zealand
| | - Matthew C Taylor
- Commonwealth Scientific and Industrial Research Organisation Land and Water Flagship, Clunies Ross Street, Acton, ACT 2060, Australia
| | - Chris Greening
- Commonwealth Scientific and Industrial Research Organisation Land and Water Flagship, Clunies Ross Street, Acton, ACT 2060, Australia
| | - Colin J Jackson
- Australian National University Research School of Chemistry, Sullivans Creek Road, Acton, ACT 2601, Australia.
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14
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Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL. Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1019-37. [PMID: 25900361 DOI: 10.1016/j.bbapap.2015.04.015] [Citation(s) in RCA: 562] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/30/2015] [Accepted: 04/14/2015] [Indexed: 11/19/2022]
Abstract
The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymefunction.org/), is focused on devising and disseminating bioinformatics and computational tools as well as experimental strategies for the prediction and assignment of functions (in vitro activities and in vivo physiological/metabolic roles) to uncharacterized enzymes discovered in genome projects. Protein sequence similarity networks (SSNs) are visually powerful tools for analyzing sequence relationships in protein families (H.J. Atkinson, J.H. Morris, T.E. Ferrin, and P.C. Babbitt, PLoS One 2009, 4, e4345). However, the members of the biological/biomedical community have not had access to the capability to generate SSNs for their "favorite" protein families. In this article we announce the EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool (http://efi.igb.illinois.edu/efi-est/) that is available without cost for the automated generation of SSNs by the community. The tool can create SSNs for the "closest neighbors" of a user-supplied protein sequence from the UniProt database (Option A) or of members of any user-supplied Pfam and/or InterPro family (Option B). We provide an introduction to SSNs, a description of EFI-EST, and a demonstration of the use of EFI-EST to explore sequence-function space in the OMP decarboxylase superfamily (PF00215). This article is designed as a tutorial that will allow members of the community to use the EFI-EST web tool for exploring sequence/function space in protein families.
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Affiliation(s)
- John A Gerlt
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA.
| | - Jason T Bouvier
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Daniel B Davidson
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Heidi J Imker
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Boris Sadkhin
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - David R Slater
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Katie L Whalen
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
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15
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Theory and applications of covalent docking in drug discovery: merits and pitfalls. Molecules 2015; 20:1984-2000. [PMID: 25633330 PMCID: PMC6272664 DOI: 10.3390/molecules20021984] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/19/2014] [Accepted: 01/12/2015] [Indexed: 11/17/2022] Open
Abstract
The present art of drug discovery and design of new drugs is based on suicidal irreversible inhibitors. Covalent inhibition is the strategy that is used to achieve irreversible inhibition. Irreversible inhibitors interact with their targets in a time-dependent fashion, and the reaction proceeds to completion rather than to equilibrium. Covalent inhibitors possessed some significant advantages over non-covalent inhibitors such as covalent warheads can target rare, non-conserved residue of a particular target protein and thus led to development of highly selective inhibitors, covalent inhibitors can be effective in targeting proteins with shallow binding cleavage which will led to development of novel inhibitors with increased potency than non-covalent inhibitors. Several computational approaches have been developed to simulate covalent interactions; however, this is still a challenging area to explore. Covalent molecular docking has been recently implemented in the computer-aided drug design workflows to describe covalent interactions between inhibitors and biological targets. In this review we highlight: (i) covalent interactions in biomolecular systems; (ii) the mathematical framework of covalent molecular docking; (iii) implementation of covalent docking protocol in drug design workflows; (iv) applications covalent docking: case studies and (v) shortcomings and future perspectives of covalent docking. To the best of our knowledge; this review is the first account that highlights different aspects of covalent docking with its merits and pitfalls. We believe that the method and applications highlighted in this study will help future efforts towards the design of irreversible inhibitors.
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16
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London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry 2015; 54:528-37. [PMID: 25513739 PMCID: PMC4303301 DOI: 10.1021/bi501140k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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Enzyme function prediction remains
an important open problem. Though
structure-based modeling, such as metabolite docking, can identify
substrates of some enzymes, it is ill-suited to reactions that progress
through a covalent intermediate. Here we investigated the ability
of covalent docking to identify substrates that pass through such
a covalent intermediate, focusing particularly on the haloalkanoate
dehalogenase superfamily. In retrospective assessments, covalent docking
recapitulated substrate binding modes of known cocrystal structures
and identified experimental substrates from a set of putative phosphorylated
metabolites. In comparison, noncovalent docking of high-energy intermediates
yielded nonproductive poses. In prospective predictions against seven
enzymes, a substrate was identified for five. For one of those cases,
a covalent docking prediction, confirmed by empirical screening, and
combined with genomic context analysis, suggested the identity of
the enzyme that catalyzes the orphan phosphatase reaction in the riboflavin
biosynthetic pathway of Bacteroides.
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Affiliation(s)
- Nir London
- Department of Pharmaceutical Chemistry, and §Department of Bioengineering and Therapeutic Sciences, University of California San Francisco , San Francisco, California 94158, United States
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