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Welsh CL, Madan LK. Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. J Chem Inf Model 2024; 64:1331-1346. [PMID: 38346324 PMCID: PMC11144062 DOI: 10.1021/acs.jcim.3c01615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Dynamics-driven allostery provides important insights into the working mechanics of proteins, especially enzymes. In this study, we employ this paradigm to answer a basic question: in enzyme superfamilies, where the catalytic mechanism, active sites, and protein fold are conserved, what accounts for the difference in the catalytic prowess of the individual members? We show that when subtle changes in sequence do not translate to changes in structure, they do translate to changes in dynamics. We use sequentially diverse PTP1B, TbPTP1, and YopH as representatives of the conserved protein tyrosine phosphatase (PTP) superfamily. Using amino acid network analysis of group behavior (community analysis) and influential node dominance on networks (eigenvector centrality), we explain the dynamic basis of the catalytic variations seen between the three proteins. Importantly, we explain how a dynamics-based blueprint makes PTP1B amenable to allosteric control and how the same is abstracted in TbPTP1 and YopH.
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Affiliation(s)
- Colin L Welsh
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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2
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Welsh CL, Madan LK. Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.23.550226. [PMID: 37547015 PMCID: PMC10402003 DOI: 10.1101/2023.07.23.550226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Dynamics-driven allostery provides important insights into the working mechanics of proteins, especially enzymes. In this study we employ this paradigm to answer a basic question: in enzyme superfamilies where the catalytic mechanism, active sites and protein fold are conserved, what accounts for the difference in the catalytic prowess of the individual members? We show that when subtle changes in sequence do not translate to changes in structure, they do translate to changes in dynamics. We use sequentially diverse PTP1B, TbPTP1, and YopH as the representatives of the conserved Protein Tyrosine Phosphatase (PTP) superfamily. Using amino acid network analysis of group behavior (community analysis) and influential node dominance on networks (eigenvector centrality), we explain the dynamic basis of catalytic variations seen between the three proteins. Importantly, we explain how a dynamics-based blueprint makes PTP1B amenable to allosteric control and how the same is abstracted in TbPTP1 and YopH.
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Zhang Y, Luo M, Wu P, Wu S, Lee TY, Bai C. Application of Computational Biology and Artificial Intelligence in Drug Design. Int J Mol Sci 2022; 23:13568. [PMID: 36362355 PMCID: PMC9658956 DOI: 10.3390/ijms232113568] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 08/24/2023] Open
Abstract
Traditional drug design requires a great amount of research time and developmental expense. Booming computational approaches, including computational biology, computer-aided drug design, and artificial intelligence, have the potential to expedite the efficiency of drug discovery by minimizing the time and financial cost. In recent years, computational approaches are being widely used to improve the efficacy and effectiveness of drug discovery and pipeline, leading to the approval of plenty of new drugs for marketing. The present review emphasizes on the applications of these indispensable computational approaches in aiding target identification, lead discovery, and lead optimization. Some challenges of using these approaches for drug design are also discussed. Moreover, we propose a methodology for integrating various computational techniques into new drug discovery and design.
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Affiliation(s)
- Yue Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Mengqi Luo
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Peng Wu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518055, China
| | - Song Wu
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Tzong-Yi Lee
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
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Menegatti ACO. Targeting protein tyrosine phosphatases for the development of antivirulence agents: Yersinia spp. and Mycobacterium tuberculosis as prototypes. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140782. [PMID: 35470106 DOI: 10.1016/j.bbapap.2022.140782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
Protein phosphorylation mediated by protein kinases and phosphatases has a central regulatory function in many cellular processes in eukaryotes and prokaryotes. As a result, several diseases caused by imbalance in phosphorylation levels are known, especially due to protein tyrosine phosphatases (PTPs) activity, an important family of signaling enzymes. Furthermore, over the last decades several studies have shown the main role of PTPs in pathogenic bacteria: they are associated with growth, cell division, cell wall biosynthesis, biofilm formation, metabolic processes, as well as virulence factor. In this way, PTPs have ascended as targets for antibacterial drug design, particularly in view of the antibiotic resistance in pathogenic bacteria, which demands novel therapeutics strategies. Targeting secreted PTPs is an antivirulence strategy to combat the emergence of antimicrobial resistance (AMR). This review focuses on the recent advances in understanding the role of PTPs and the approaches to target them, with an emphasis in Yersinia spp. and Mycobacterium tuberculosis pathogenesis.
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Affiliation(s)
- Angela Camila Orbem Menegatti
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, Paraíba, Brazil.
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Liu X, Shi D, Zhou S, Liu H, Liu H, Yao X. Molecular dynamics simulations and novel drug discovery. Expert Opin Drug Discov 2017; 13:23-37. [DOI: 10.1080/17460441.2018.1403419] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xuewei Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | | | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
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Fonseca EMB, Trivella DBB, Scorsato V, Dias MP, Bazzo NL, Mandapati KR, de Oliveira FL, Ferreira-Halder CV, Pilli RA, Miranda PCML, Aparicio R. Crystal structures of the apo form and a complex of human LMW-PTP with a phosphonic acid provide new evidence of a secondary site potentially related to the anchorage of natural substrates. Bioorg Med Chem 2015; 23:4462-4471. [PMID: 26117648 DOI: 10.1016/j.bmc.2015.06.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/29/2015] [Accepted: 06/05/2015] [Indexed: 12/22/2022]
Abstract
Low molecular weight protein tyrosine phosphatases (LMW-PTP, EC 3.1.3.48) are a family of single-domain enzymes with molecular weight up to 18 kDa, expressed in different tissues and considered attractive pharmacological targets for cancer chemotherapy. Despite this, few LMW-PTP inhibitors have been described to date, and the structural information on LMW-PTP druggable binding sites is scarce. In this study, a small series of phosphonic acids were designed based on a new crystallographic structure of LMW-PTP complexed with benzylsulfonic acid, determined at 2.1Å. In silico docking was used as a tool to interpret the structural and enzyme kinetics data, as well as to design new analogs. From the synthesized series, two compounds were found to act as competitive inhibitors, with inhibition constants of 0.124 and 0.047 mM. We also report the 2.4Å structure of another complex in which LMW-PTP is bound to benzylphosphonic acid, and a structure of apo LMW-PTP determined at 2.3Å resolution. Although no appreciable conformation changes were observed, in the latter structures, amino acid residues from an expression tag were found bound to a hydrophobic region at the protein surface. This regions is neighbored by positively charged residues, adjacent to the active site pocket, suggesting that this region might be not a mere artefact of crystal contacts but an indication of a possible anchoring region for the natural substrate-which is a phosphorylated protein.
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Affiliation(s)
- Emanuella M B Fonseca
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil
| | - Daniela B B Trivella
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil; Department of Organic Chemistry, Institute of Chemistry, University of Campinas, CP 6154, CEP 13083-970, Campinas, SP, Brazil
| | - Valéria Scorsato
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil
| | - Mariana P Dias
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil
| | - Natália L Bazzo
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil
| | - Kishore R Mandapati
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil; Department of Organic Chemistry, Institute of Chemistry, University of Campinas, CP 6154, CEP 13083-970, Campinas, SP, Brazil
| | - Fábio L de Oliveira
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil
| | - Carmen V Ferreira-Halder
- Department of Biochemistry, Institute of Biology, University of Campinas, CEP 13083-862, Campinas, SP, Brazil
| | - Ronaldo A Pilli
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, CP 6154, CEP 13083-970, Campinas, SP, Brazil
| | - Paulo C M L Miranda
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, CP 6154, CEP 13083-970, Campinas, SP, Brazil
| | - Ricardo Aparicio
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil.
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Oxoindolinylidene Derivatives of Thiazolidin-4-ones: Methods of Synthesis and Biological Activity (Review). Chem Heterocycl Compd (N Y) 2015. [DOI: 10.1007/s10593-014-1619-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Abstract
SIGNIFICANCE Protein tyrosine phosphatases (PTPs) are important enzymes that are involved in the regulation of cellular signaling. Evidence accumulated over the years has indicated that PTPs present exciting opportunities for drug discovery against diseases such as diabetes, cancer, autoimmune diseases, and tuberculosis. However, the highly conserved and partially positive charge of the catalytic sites of PTPs is a major challenge in the development of potent and highly selective PTP inhibitors. RECENT ADVANCES Here, we examine the strategy of developing bidentate inhibitors for selective inhibition of PTPs. Bidentate inhibitors are small-molecular-weight compounds with the ability to bind to both the active site and a non-conserved secondary phosphate binding site. This secondary phosphate binding site was initially discovered in protein tyrosine phosphatase 1B (PTP1B), and, hence, most of the bidentate inhibitors reported in this review are PTP1B inhibitors. CRITICAL ISSUES Although bidentate inhibition is a good strategy for developing potent and selective inhibitors, the cell membrane permeability and pharmacokinetic properties of the inhibitors are also important for successful drug development. In this review, we will also summarize the various efforts made toward the development of phosphotyrosine (pTyr) mimetics for increasing cellular permeability. FUTURE DIRECTIONS Even though the secondary phosphate binding site was initially found in PTP1B, structural data have shown that a secondary binding site can also be found in other PTPs, albeit with varying degrees of accessibility. Along with improvements in pTyr mimetics, we believe that the future will see an increase in the number of orally bioavailable bidentate inhibitors against the various classes of PTPs.
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Affiliation(s)
- Joo-Leng Low
- 1 Institute of Chemical and Engineering Sciences , Agency for Science Technology and Research, Singapore, Singapore
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Xu F, Yang ZZ, Xi LM, Jiang JR, Ke ZL, Wu HG. Synthesis of 10-phenyl-[1,2,4]Triazolo[1,5- b] [2,7]Naphthyridin-5(3 H)-One Derivatives. JOURNAL OF CHEMICAL RESEARCH 2014. [DOI: 10.3184/174751914x13976543689677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Several new 10-phenyl-[1,2,4]triazolo[1,5- b][2,7]naphthyridin-5(3 H)-one derivatives were synthesised by condensation of 2,3-diamino-4-phenyl-2,7-naphthyridin-1(2 H)-one with aldehydes and also with acid anhydrides. Their structures were confirmed by 1H NMR, 13C NMR, IR, mass spectra and elemental analysis. The key starting material 4-[a-cyano(phenyl)methyl]nicotinic acid was easily cyclised to give 3-amino-4-phenyl-1 H-pyrano[3,4- c]pyridin-1-one under alkaline conditions, the structure of which was confirmed by X-ray crystallography following conversion to the corresponding N,N-dimethylformamidine derivative.
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Affiliation(s)
- Feng Xu
- Biopharmaceutical Research and Development Centre, Taizhou Vocational & Technical College, Taizhou 318000, P.R. China
| | - Zhen-Zhen Yang
- Biopharmaceutical Research and Development Centre, Taizhou Vocational & Technical College, Taizhou 318000, P.R. China
| | - Li-Min Xi
- Biopharmaceutical Research and Development Centre, Taizhou Vocational & Technical College, Taizhou 318000, P.R. China
| | - Jun-Rong Jiang
- Biopharmaceutical Research and Development Centre, Taizhou Vocational & Technical College, Taizhou 318000, P.R. China
| | - Zhong-Lu Ke
- Biopharmaceutical Research and Development Centre, Taizhou Vocational & Technical College, Taizhou 318000, P.R. China
| | - Han-Gui Wu
- Biopharmaceutical Research and Development Centre, Taizhou Vocational & Technical College, Taizhou 318000, P.R. China
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