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Zaidi N, Ahmad O, Khursheed M, Nabi F, Uversky VN, Khan RH. Furosemide Derails Human Lysozyme Fibrillation by Interacting with Aggregation Hot Spots: A Biophysical Comprehension. J Phys Chem B 2024. [PMID: 38683125 DOI: 10.1021/acs.jpcb.3c02613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Kidney-associated human lysozyme amyloidosis leads to renal impairments;thus, patients are often prescribed furosemide. Based on this fact, the effect of furosemide on induced human lysozyme fibrillation, in vitro, is evaluated by spectroscopic, calorimetric, computational, and cellular-based assays/methods. Results show that furosemide increases the lag phase and decreases the apparent rate of aggregation of human lysozyme, thereby decelerating the nucleation phase and amyloid fibril formation, as confirmed by the decrease in the level of Thioflavin-T fluorescence. Fewer entities of hydrodynamic radii of ∼171 nm instead of amyloid fibrils (∼412 nm) are detected in human lysozyme in the presence of furosemide by dynamic light scattering. Moreover, furosemide decreases the extent of conversion of the α/β structure of human lysozyme into a predominant β-sheet. The isothermal titration calorimetry established that furosemide forms a complex with human lysozyme, which was also confirmed through fluorescence quenching and computational studies. Also, human lysozyme lytic activity is inhibited competitively by furosemide due to the involvement of amino acid residues of the active site in catalysis, as well as complex formation. Conclusively, furosemide interacts with Gln58, Ile59, Asn60, Ala108, and Trp109 of aggregation-prone regions 2 and 4 of human lysozyme, thereby masking its sites of aggregation and generating only lower-order entities that are less toxic to red blood cells than the fibrils. Thus, furosemide slows the progression of amyloid fibrillation in human lysozyme.
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Affiliation(s)
- Nida Zaidi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Owais Ahmad
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Maryam Khursheed
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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2
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Wang R, Zhang W, Ma H, Zou D, Zhang Z, Wang S. Structural insights into the binding of zoledronic acid with RANKL via computational simulations. Front Mol Biosci 2022; 9:992473. [PMID: 36200071 PMCID: PMC9527314 DOI: 10.3389/fmolb.2022.992473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/05/2022] [Indexed: 12/03/2022] Open
Abstract
Zoledronic acid (ZOL) inhibits receptor activator of nuclear factor-κB ligand (RANKL) and reduces bone turnover. This plays an important role in the development of bisphosphonate-related osteonecrosis of the jaw (BRONJ). Previous reports have shown that ZOL binds to the enzyme farnesyl pyrophosphate synthase (FPPS) to block its activity. However, the mechanism of action of ZOL and its interaction with RANKL is still unclear. In this study, we confirmed that ZOL significantly suppressed the bone remodeling in ZOL-treated rats, investigated whether ZOL could bind to RANKL and examined the interactions between these molecules at the atomic level. Surface plasmon resonance (SPR) assay was performed to validate that ZOL could directly bind to RANKL in a dose dependent manner, and the equilibrium constant was calculated (KD = 2.28 × 10−4 M). Then, we used molecular docking simulation to predict the binding site and analyze the binding characteristics of ZOL and RANKL. Through molecular dynamics simulation, we confirmed the stable binding between ZOL and RANKL and observed their dynamic interactions over time. Binding free energy calculations and its decomposition were conducted to obtain the binding free energy −70.67 ± 2.62 kJ/mol for the RANKL–ZOL complex. We identified the key residues of RANKL in the binding region, and these included Tyr217(A), Val277(A), Gly278(A), Val277(B), Gly278(B), and Tyr215(C). Taken together, our results demonstrated the direct interaction between ZOL and RANKL, indicating that the pharmacological action of ZOL might be closely related to RANKL. The design of novel small molecules targeting RANKL might reduce the occurrence of BRONJ.
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Affiliation(s)
- Ruijie Wang
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, College of Stomatology, Chinese Academy of Medical Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Wenjie Zhang
- Shanghai Key Laboratory of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, College of Stomatology, Chinese Academy of Medical Sciences, Shanghai Jiao Tong University, Shanghai, China
- Department of Prosthodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hailong Ma
- Shanghai Key Laboratory of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, College of Stomatology, Chinese Academy of Medical Sciences, Shanghai Jiao Tong University, Shanghai, China
- Department of Oral Maxillofacial-Head and Neck Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Duohong Zou
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, College of Stomatology, Chinese Academy of Medical Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiyuan Zhang
- Shanghai Key Laboratory of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, College of Stomatology, Chinese Academy of Medical Sciences, Shanghai Jiao Tong University, Shanghai, China
- Department of Oral Maxillofacial-Head and Neck Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Zhiyuan Zhang, ; Shaoyi Wang,
| | - Shaoyi Wang
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, National Center for Stomatology, National Clinical Research Center for Oral Diseases, College of Stomatology, Chinese Academy of Medical Sciences, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Zhiyuan Zhang, ; Shaoyi Wang,
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3
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Liu W, Jiang J, Lin Y, You Q, Wang L. Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization. J Med Chem 2022; 65:10809-10847. [PMID: 35969687 DOI: 10.1021/acs.jmedchem.2c00682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-activity relationships (SARs) and structure-property relationships (SPRs) have been considered the most important factors during the drug optimization process. For medicinal chemists, improvements in the potencies and druglike properties of small molecules are regarded as their major goals. Among them, the binding affinity and selectivity of small molecules on their targets are the most important indicators. In recent years, there has been growing interest in using thermodynamic and kinetic profiles to analyze ligand-receptor interactions, which could provide not only binding affinities but also detailed binding parameters for small-molecule optimization. In this perspective, we are trying to provide an insight into thermodynamic and kinetic profiles in small-molecule optimization. Through a highlight of strategies on the small-molecule optimization with specific cases, we aim to put forward the importance of structure-thermodynamic relationships (STRs) and structure-kinetic relationships (SKRs), which could provide more guidance to find safe and effective small-molecule drugs.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jingsheng Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yating Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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4
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Spectral and molecular modelling studies of sulfadoxine interaction with bovine serum albumin. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.111871] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Savino S, Toscano A, Purgatorio R, Profilo E, Laghezza A, Tortorella P, Angelelli M, Cellamare S, Scala R, Tricarico D, Marobbio CMT, Perna F, Vitale P, Agamennone M, Dimiccoli V, Tolomeo A, Scilimati A. Novel bisphosphonates with antiresorptive effect in bone mineralization and osteoclastogenesis. Eur J Med Chem 2018; 158:184-200. [PMID: 30216851 DOI: 10.1016/j.ejmech.2018.08.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/18/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
Bisphosphonates such as zoledronic, alendronic and risedronic acids are a class of drugs clinically used to prevent bone density loss and osteoporosis. Novel P-C-P bisphosphonates were synthesized for targeting human farnesyl pyrophosphate synthase (hFPPS) and human geranylgeranyl pyrophosphate synthase (hGGPPS), key enzymes of the mevalonate pathway, and capable of anti-proliferative action on a number of cell lines (PC3, MG63, MC3T3, RAW 264.7, J774A.1, bone marrow cells and their co-colture with PC3) involved in bone homeostasis, bone formation and death. Among sixteen compounds, [1-hydroxy-2-(pyrimidin-2-ylamino)ethane-1,1-diyl]bis(phosphonic acid) (10) was effective in reducing PC3 and RAW 264.7 cell number in crystal-violet and cell-dehydrogenase activity assays at 100 μM concentration. 10 reduced differentiated osteoclasts number similarly with zoledronic acid in osteoclastogenesis assay. At nanomolar concentrations, 10 was more effective than zoledronic acid in inducing mineralization in MC3T3 and murine bone marrow cells. Further, 10 significantly inhibited the activity of hFPPS showing an IC50 of 0.31 μM and a remarkable hydroxyapatite binding of 90%. Docking calculations were performed identifying putative interactions between some representative novel bisphosphonates and both hFPPS and hGGPPS. Then, 10 was found to behave similarly or even better than zoledronic acid as a anti-resorptive agent.
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Affiliation(s)
- Salvatore Savino
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Annamaria Toscano
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Rosa Purgatorio
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Emanuela Profilo
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Antonio Laghezza
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Paolo Tortorella
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Mariacristina Angelelli
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Saverio Cellamare
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Rosa Scala
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Domenico Tricarico
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Carlo Marya Thomas Marobbio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Filippo Perna
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Paola Vitale
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy
| | - Mariangela Agamennone
- Department of Pharmacy, University of Chieti "Gabriele d'Annunzio", Via dei Vestini, 31, 66100, Chieti, Italy
| | - Vincenzo Dimiccoli
- ITEL Telecomunicazioni S.r.l., Via A. Labriola, 70037, Ruvo di Puglia, Bari, Italy
| | - Anna Tolomeo
- ITEL Telecomunicazioni S.r.l., Via A. Labriola, 70037, Ruvo di Puglia, Bari, Italy
| | - Antonio Scilimati
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125, Bari, Italy.
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6
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Hasan A, Waibhaw G, Pandey LM. Conformational and Organizational Insights into Serum Proteins during Competitive Adsorption on Self-Assembled Monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8178-8194. [PMID: 29936836 DOI: 10.1021/acs.langmuir.8b01110] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Physicochemical interactions of proteins with surfaces mediate the interactions between the implant and the biological system. Surface chemistry of the implant is crucial as it regulates the events at the interface. The objective of this study was to explore the performance of modified surfaces for such interactions relevant to various biomedical applications. Because of a wide range of surface wettability, we aimed to study protein behavior (i.e., conformational changes and their packing) during competitive protein adsorption. Three serum proteins (bovine serum albumin, BSA; fibrinogen, FB; and immunoglobulin G, IgG) were tested for their conformational changes and orientation upon adsorption on hydrophilic (COOH and amine), moderately hydrophobic (mixed and hybrid), and hydrophobic (octyl) surfaces generated via silanization. Modified surfaces were characterized using Fourier-transform infrared spectroscopy, contact angle, and atomic force microscopy (AFM) techniques. Adsorbed masses of proteins from single and binary protein solutions on different surfaces were quantified along with their secondary structure analyses. Maximum adsorbed protein masses were found to be on negatively charged and hydrophobic (octyl) surfaces because of ionic and hydrophobic interactions between protein molecules and surfaces, respectively. Side-on and end-on orientations of adsorbed protein molecules were analyzed using theoretical and AFM analyses. We observed compact and elongated forms of BSA molecules on hydrophilic and hydrophobic surfaces, respectively. We further found a linear increase in the α-helix content of BSA and β-sheet contents of FB and IgG proteins with the increasing side-on (%)-oriented protein molecules on the surfaces. This indicates that side-on orientations of adsorbed FB and IgG lead to the formation of β-sheets. Sodium dodecyl sulfate polyacrylamide gel electrophoresis was employed to quantify the protein types and their ratio in competitively adsorbed proteins on different surfaces. A theoretical analysis was also used to determine the % secondary structures of competitively adsorbed proteins from BSA/FB and BSA/IgG solutions, which very well agreed with experimental results. The competitive protein adsorption from both BSA/FB and BSA/IgG solutions was found to be entropy-driven, as revealed by thermodynamic studies performed using isothermal titration calorimetry.
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Affiliation(s)
- Abshar Hasan
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Gyan Waibhaw
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
| | - Lalit M Pandey
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam 781039 , India
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7
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Gałȩzowska J, Czapor-Irzabek H, Janicki R, Chmielewska E, Janek T. New aspects of coordination chemistry and biological activity of NTMP-related diphosphonates containing a heterocyclic ring. NEW J CHEM 2017. [DOI: 10.1039/c7nj02415k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two aminodiphosphonic chelating agents are studied toward a series of metal ions (Cu2+, Ni2+, Zn2+, Ca2+, Mg2+) to give a thermodynamic picture of their binding abilities and the influence of free ligands and their complexes on human melanoma and human colon adenocarcinoma cells.
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Affiliation(s)
- J. Gałȩzowska
- Department of Inorganic Chemistry
- Wrocław Medical University
- 50-556 Wroclaw
- Poland
| | - H. Czapor-Irzabek
- Laboratory of Elemental Analysis and Structural Research
- Wrocław Medical University
- 50-556 Wroclaw
- Poland
| | - R. Janicki
- Faculty of Chemistry
- University of Wrocław
- F. Joliot-Curie 14
- 50-383 Wrocław
- Poland
| | - E. Chmielewska
- Department of Bioorganic Chemistry
- Faculty of Chemistry
- Wrocław University of Science and Technology
- Wrocław
- Poland
| | - T. Janek
- Department of Inorganic Chemistry
- Wrocław Medical University
- 50-556 Wroclaw
- Poland
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8
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In Vitro and In Vivo Investigation of the Inhibition of Trypanosoma brucei Cell Growth by Lipophilic Bisphosphonates. Antimicrob Agents Chemother 2015; 59:7530-9. [PMID: 26392508 DOI: 10.1128/aac.01873-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/16/2015] [Indexed: 12/18/2022] Open
Abstract
We report the results of a screen of a library of 925 potential prenyl synthase inhibitors against Trypanosoma brucei farnesyl diphosphate synthase (TbFPPS) and against T. brucei, the causative agent of human African trypanosomiasis. The most potent compounds were lipophilic analogs of the bone resorption drug zoledronate, some of which had submicromolar to low micromolar activity against bloodstream form T. brucei and selectivity indices of up to ∼ 300. We evaluated the effects of two such inhibitors on survival and parasitemia in a T. brucei mouse model of infection and found that survival increased by up to 16 days. We also investigated the binding of three lipophilic bisphosphonates to an expressed TbFPPS using crystallography and investigated the thermodynamics of binding using isothermal titration calorimetry.
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9
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Fernández D, Ortega-Castro J, Mariño L, Perelló J, Frau J. Mechanistic insights into protonation state as a critical factor in hFPPS enzyme inhibition. J Comput Aided Mol Des 2015; 29:667-80. [PMID: 26081258 DOI: 10.1007/s10822-015-9853-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/10/2015] [Indexed: 10/23/2022]
Abstract
Zoledronate and risedronate are the most powerful available nitrogen-containing bisphosphonates used in the treatment of bone-resorption disorders. Knowledge about inhibition mechanisms of these molecules is based on available crystallographic structures of human farnesyl pyrophosphate synthase (hFPPS). However, there is a lack of information explaining the inhibition potency of these two molecules compared to the natural substrate, dimethylallyl pyrophosphate. We carried out a molecular dynamics study that shown: (1) that NBPs potency is related to higher electrostatic interactions with the metallic cluster of the active site than to the natural substrate, and (2) the protonation of the R2 side chain is a critical factor to stabilize the NBPs into a closely irreversible ternary complex with the hFPPS.
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Affiliation(s)
- David Fernández
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122, Palma de Mallorca, Spain
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10
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Schmidberger JW, Schnell R, Schneider G. Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase from Pseudomonas aeruginosa. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:721-31. [PMID: 25760619 PMCID: PMC4356374 DOI: 10.1107/s1399004715001121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/19/2015] [Indexed: 12/23/2022]
Abstract
Locus PA4043 in the genome of Pseudomonas aeruginosa PAO1 has been annotated as coding for a farnesyl pyrophosphate synthase (FPPS). This open reading frame was cloned and expressed recombinantly in Escherichia coli. The dimeric enzyme shows farnesyl pyrophosphate synthase activity and is strongly inhibited by ibandronate and zoledronate, drugs that are presently in clinical use. The structures of the unliganded enzyme and complexes with the substrate geranyl diphosphate (GPP), the inhibitor ibandronate and two compounds obtained from a differential scanning fluorimetry-based screen of a fragment library were determined by X-ray crystallography to resolutions of better than 2.0 Å. The enzyme shows the typical α-helical fold of farnesyl pyrophosphate synthases. The substrate GPP binds in the S1 substrate site in an open conformation of the enzyme. In the enzyme-ibandronate complex three inhibitor molecules are bound in the active site of the enzyme. One inhibitor molecule occupies the allylic substrate site (S1) of each subunit, as observed in complexes of nitrogen-containing bisphosphonate inhibitors of farnesyl synthases from other species. Two (in subunit A) and one (in subunit B) additional ibandronate molecules are bound in the active site. The structures of the fragment complexes show two molecules bound in a hydrophobic pocket adjacent to the active site. This allosteric pocket, which has previously only been described for FPPS from eukaryotic organisms, is thus also present in enzymes from pathogenic prokaryotes and might be utilized for the design of inhibitors of bacterial FPPS with a different chemical scaffold to the highly charged bisphosphonates, which are less likely to pass bacterial membranes.
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Affiliation(s)
- Jason W. Schmidberger
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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11
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Ashouri M, Maghari A, Karimi-Jafari MH. Hydrogen bonding motifs in a hydroxy-bisphosphonate moiety: revisiting the problem of hydrogen bond identification. Phys Chem Chem Phys 2015; 17:13290-300. [DOI: 10.1039/c5cp00693g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Relative energy of conformers are highly correlated with their sum of local density of potential energy at H-bond critical points.
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Affiliation(s)
- Mitra Ashouri
- Department of Physical Chemistry
- School of Chemistry
- College of Science
- University of Tehran
- Tehran
| | - Ali Maghari
- Department of Physical Chemistry
- School of Chemistry
- College of Science
- University of Tehran
- Tehran
| | - M. H. Karimi-Jafari
- Department of Bioinformatics
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
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12
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Shang N, Li Q, Ko TP, Chan HC, Li J, Zheng Y, Huang CH, Ren F, Chen CC, Zhu Z, Galizzi M, Li ZH, Rodrigues-Poveda CA, Gonzalez-Pacanowska D, Veiga-Santos P, de Carvalho TMU, de Souza W, Urbina JA, Wang AHJ, Docampo R, Li K, Liu YL, Oldfield E, Guo RT. Squalene synthase as a target for Chagas disease therapeutics. PLoS Pathog 2014; 10:e1004114. [PMID: 24789335 PMCID: PMC4006925 DOI: 10.1371/journal.ppat.1004114] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/28/2014] [Indexed: 12/20/2022] Open
Abstract
Trypanosomatid parasites are the causative agents of many neglected tropical diseases and there is currently considerable interest in targeting endogenous sterol biosynthesis in these organisms as a route to the development of novel anti-infective drugs. Here, we report the first x-ray crystallographic structures of the enzyme squalene synthase (SQS) from a trypanosomatid parasite, Trypanosoma cruzi, the causative agent of Chagas disease. We obtained five structures of T. cruzi SQS and eight structures of human SQS with four classes of inhibitors: the substrate-analog S-thiolo-farnesyl diphosphate, the quinuclidines E5700 and ER119884, several lipophilic bisphosphonates, and the thiocyanate WC-9, with the structures of the two very potent quinuclidines suggesting strategies for selective inhibitor development. We also show that the lipophilic bisphosphonates have low nM activity against T. cruzi and inhibit endogenous sterol biosynthesis and that E5700 acts synergistically with the azole drug, posaconazole. The determination of the structures of trypanosomatid and human SQS enzymes with a diverse set of inhibitors active in cells provides insights into SQS inhibition, of interest in the context of the development of drugs against Chagas disease. Chagas disease is caused by the protozoan parasite Trypanosoma cruzi and affects eight million individuals, primarily in Latin America. Currently there is no cure for chronic T. cruzi infections. Unlike humans, this parasite use a variety of sterols (e.g. ergosterol, 24-ethyl-cholesta-5,7,22-trien-3 beta ol, and its 22-dihydro analogs), rather than cholesterol in their cell membranes, so inhibiting endogenous sterol biosynthesis is an important therapeutic target. Here, we report the first structure of the parasite's squalene synthase, which catalyzes the first committed step in sterol biosynthesis, as well as the structures of a broad range of squalene synthase inhibitors active against the clinically relevant intracellular stages, opening the way to new approaches to treating this neglected tropical disease.
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Affiliation(s)
- Na Shang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Qian Li
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tzu-Ping Ko
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hsiu-Chien Chan
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jikun Li
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yingying Zheng
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Chun-Hsiang Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Feifei Ren
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Chun-Chi Chen
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhen Zhu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Melina Galizzi
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Zhu-Hong Li
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Carlos A. Rodrigues-Poveda
- Instituto de Parasitología y Biomedicina “Lopez-Neyra”, Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - Dolores Gonzalez-Pacanowska
- Instituto de Parasitología y Biomedicina “Lopez-Neyra”, Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - Phercyles Veiga-Santos
- Laboratório de Ultraestrutura Celular Hertha Meyer, CCS, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, Brazil
- Diretoria de Programa, Instituto Nacional de Metrologia, Normalização e Qualidade Industrial–INMETRO, Duque de Caxias, Rio de Janeiro, Brazil
| | - Tecia Maria Ulisses de Carvalho
- Laboratório de Ultraestrutura Celular Hertha Meyer, CCS, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, Brazil
- Diretoria de Programa, Instituto Nacional de Metrologia, Normalização e Qualidade Industrial–INMETRO, Duque de Caxias, Rio de Janeiro, Brazil
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, CCS, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, Brazil
- Diretoria de Programa, Instituto Nacional de Metrologia, Normalização e Qualidade Industrial–INMETRO, Duque de Caxias, Rio de Janeiro, Brazil
| | - Julio A. Urbina
- Instituto Venezolano de Investigaciones Cientificas, Caracas, Venezuela
| | | | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Kai Li
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yi-Liang Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Eric Oldfield
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (EO); (RTG)
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- * E-mail: (EO); (RTG)
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13
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Kawasaki Y, Sekiguchi M, Kawasaki M, Hirakura Y. Thermodynamic Evaluation of the Binding of Bisphosphonates to Human Farnesyl Pyrophosphate Synthase. Chem Pharm Bull (Tokyo) 2014; 62:77-83. [DOI: 10.1248/cpb.c13-00710] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yuko Kawasaki
- Institute for Drug Discovery Research, Astellas Pharma Inc
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14
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Fei Y, Landry JP, Li Y, Yu H, Lau K, Huang S, Chokhawala HA, Chen X, Zhu XD. An optics-based variable-temperature assay system for characterizing thermodynamics of biomolecular reactions on solid support. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:114102. [PMID: 24289409 PMCID: PMC3838479 DOI: 10.1063/1.4826352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/07/2013] [Indexed: 06/02/2023]
Abstract
A biological state is equilibrium of multiple concurrent biomolecular reactions. The relative importance of these reactions depends on physiological temperature typically between 10 °C and 50 °C. Experimentally the temperature dependence of binding reaction constants reveals thermodynamics and thus details of these biomolecular processes. We developed a variable-temperature opto-fluidic system for real-time measurement of multiple (400-10,000) biomolecular binding reactions on solid supports from 10 °C to 60 °C within ±0.1 °C. We illustrate the performance of this system with investigation of binding reactions of plant lectins (carbohydrate-binding proteins) with 24 synthetic glycans (i.e., carbohydrates). We found that the lectin-glycan reactions in general can be enthalpy-driven, entropy-driven, or both, and water molecules play critical roles in the thermodynamics of these reactions.
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Affiliation(s)
- Yiyan Fei
- Department of Physics, University of California, One Shields Avenue, Davis, California 95616, USA
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15
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16
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Arabieh M, Karimi-Jafari MH, Ghannadi-Maragheh M. Low-energy conformers of pamidronate and their intramolecular hydrogen bonds: a DFT and QTAIM study. J Mol Model 2012; 19:427-38. [DOI: 10.1007/s00894-012-1564-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/06/2012] [Indexed: 10/27/2022]
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17
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Cai G, Deng L, Fryszczyn BG, Brown NG, Liu Z, Jiang H, Palzkill T, Song Y. Thermodynamic Investigation of Inhibitor Binding to 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase. ACS Med Chem Lett 2012; 3:496-500. [PMID: 23050057 PMCID: PMC3462030 DOI: 10.1021/ml300071w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 05/07/2012] [Indexed: 11/29/2022] Open
Abstract
Isothermal titration calorimetry (ITC) was used to investigate the binding of six inhibitors to 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), a target for developing novel anti-infectives. The binding of hydroxamate inhibitors to E. coli DXR is Mg(2+)-dependent, highly endothermic (ΔH: 22.7-24.3 kJ/mol) and entropy-driven, while that of non-hydroxamate compounds is metal ion independent and exothermic (ΔH: -19.4- -13.8 kJ/mol), showing hydration/dehydration of the enzyme metal ion binding pocket account for the drastic ΔH change. However, for DXRs from Plasmodium falciparum and Mycobacterium tuberculosis, the binding of all inhibitors is exothermic (ΔH: -24.9 - -9.2 kJ/mol), suggesting the metal ion binding sites of these two enzymes are considerably less hydrated. The dissociation constants measured by ITC are well correlated with those obtained by enzyme inhibition assays (R(2) = 0.75). Given the rapid rise of antibiotic resistance, this work is of interest since it provides novel structural implications for rational development of potent DXR inhibitors.
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Affiliation(s)
- Guobin Cai
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Lisheng Deng
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Bartlomiej G. Fryszczyn
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Nicholas G. Brown
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Zhen Liu
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Hong Jiang
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Timothy Palzkill
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Yongcheng Song
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
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18
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Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity. Proc Natl Acad Sci U S A 2012; 109:4058-63. [PMID: 22392982 DOI: 10.1073/pnas.1118215109] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the results of an in vitro screening assay targeting the intraerythrocytic form of the malaria parasite Plasmodium falciparum using a library of 560 prenyl-synthase inhibitors. Based on "growth-rescue" and enzyme-inhibition experiments, geranylgeranyl diphosphate synthase (GGPPS) is shown to be a major target for the most potent leads, BPH-703 and BPH-811, lipophilic analogs of the bone-resorption drugs zoledronate and risedronate. We determined the crystal structures of these inhibitors bound to a Plasmodium GGPPS finding that their head groups bind to the [Mg(2+)](3) cluster in the active site in a similar manner to that found with their more hydrophilic parents, whereas their hydrophobic tails occupy a long-hydrophobic tunnel spanning both molecules in the dimer. The results of isothermal-titration-calorimetric experiments show that both lipophilic bisphosphonates bind to GGPPS with, on average, a ΔG of -9 kcal mol(-1), only 0.5 kcal mol(-1) worse than the parent bisphosphonates, consistent with the observation that conversion to the lipophilic species has only a minor effect on enzyme activity. However, only the lipophilic species are active in cells. We also tested both compounds in mice, finding major decreases in parasitemia and 100% survival. These results are of broad general interest because they indicate that it may be possible to overcome barriers to cell penetration of existing bisphosphonate drugs in this and other systems by simple covalent modification to form lipophilic analogs that retain their enzyme-inhibition activity and are also effective in vitro and in vivo.
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19
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Kang SO, Lynch VM, Day VW, Anslyn EV. Enthalpy vs Entropy Driven Complexation of Homoallylic Alcohols by Rh(I) Complexes. Organometallics 2011; 30:6233-6240. [PMID: 22328800 PMCID: PMC3274780 DOI: 10.1021/om200793p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The thermodynamics of binding between several homoallylic alcohols and simple olefinic Rh(I) compounds was examined with (1)H NMR spectroscopy and ITC. (1)H NMR titrations revealed moderate binding of these alcohols with [Rh(COD)(2)](+) (1) and [Rh(COD)(CH(3)CN)(2)](+) (3), but weaker binding with [Rh(NBD)(2)](+) (2). ITC indicated that the complexation with [Rh(COD)(2)](+) is mainly governed by enthalpy whereas binding with [Rh(COD)(CH(3)CN)(2)](+) is entirely driven by entropy. The thermodynamic parameters for the homoallylic alcohol binding of Rh(I) complexes 1-3 are consistent with crystallographic data.
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Affiliation(s)
- Sung Ok Kang
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712
| | - Vincent M. Lynch
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712
| | - Victor W. Day
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
| | - Eric V. Anslyn
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712
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20
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Gordo S, Martos V, Vilaseca M, Menéndez M, de Mendoza J, Giralt E. On the role of flexibility in protein-ligand interactions: the example of p53 tetramerization domain. Chem Asian J 2011; 6:1463-9. [PMID: 21626703 DOI: 10.1002/asia.201000938] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The recognition of protein surfaces by designed ligands has become an attractive approach in drug discovery. However, the variable nature and irregular behavior of protein surfaces defy this new area of research. The easy to understand "lock-and-key" model is far from being the ideal paradigm in biomolecular interactions and, hence, any new finding on how proteins and ligands behave in recognition events paves a step of the way. Herein, we illustrate a clear example on how an increase in flexibility of both protein and ligand can result in an increase in the stability of the macromolecular complex. The biophysical study of the interaction between a designed flexible tetraguanidinium-calix[4]arene and the tetramerization domain of protein p53 (p53TD) and its natural mutant p53TD-R337H shows how the floppy mutant domain interacts more tightly with the ligand than the well-packed wild-type protein. Moreover, the flexible calixarene ligand interacts with higher affinity to both wild-type and mutated protein domains than a conformationally rigid calixarene analog previously reported. These findings underscore the crucial role of flexibility in molecular recognition processes, for both small ligands and large biomolecular surfaces.
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Affiliation(s)
- Susana Gordo
- Institute for Research in Biomedicine, Baldiri Reixac 10, 08028 Barcelona, Spain
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21
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Ohno K, Mori K, Orita M, Takeuchi M. Computational insights into binding of bisphosphates to farnesyl pyrophosphate synthase. Curr Med Chem 2011; 18:220-33. [PMID: 21110804 PMCID: PMC3343387 DOI: 10.2174/092986711794088335] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 11/21/2010] [Indexed: 12/01/2022]
Abstract
Bisphosphonates (BPs) are the most widely used and effective treatment for osteoporosis and Paget's disease. Non-nitrogen containing BPs (non-N-BPs), namely etidronate, clodronate, tiludronate, as well as nitrogen-containing BPs (N-BPs), namely pamidronate, alendronate, ibandronate, risedronate, zoledronate and minodronate have been launched on the market to date. N-BPs act by inhibiting the enzyme farnesyl pyrophosphate synthase (FPPS), and several crystal structures of complexes between FPPS and N-BPs have been revealed. Understanding the physical basis of the binding between protein and small molecules is an important goal in both medicinal chemistry and structural biology. In this review, we analyze in detail the energetic basis of molecular recognition between FPPS and N-BPs. First, we summarize the interactions between ligands and proteins observed in N-BPs-FPPS complexes in the Protein Data Bank (PDB). Second, we present an interaction energy analysis on the basis of full quantum mechanical calculation of FPPS and N-BP complexes using the fragment molecular orbital (FMO) method. The FMO result revealed that not only hydrogen bond and electrostatic interaction but also CH-O and π-π interaction with FPPS are important for N-BP’s potency. Third, we describe a binding site analysis of FPPS on the basis of the inhomogeneous solvation theory which, by clustering the results from an explicit solvent molecular dynamics simulation (MD), is capable of describing the entropic and enthalpic contributions to the free energies of individual hydration sites. Finally, we also discuss the structure-activity relationship (SAR) of the series of minodronate derivatives.
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Affiliation(s)
- K Ohno
- Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan
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22
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Huang CH, Gabelli SB, Oldfield E, Amzel LM. Binding of nitrogen-containing bisphosphonates (N-BPs) to the Trypanosoma cruzi farnesyl diphosphate synthase homodimer. Proteins 2010; 78:888-99. [PMID: 19876942 DOI: 10.1002/prot.22614] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Bisphosphonates (BPs) are a class of compounds that have been used extensively in the treatment of osteoporosis and malignancy-related hypercalcemia. Some of these compounds act through inhibition of farnesyl diphosphate synthase (FPPS), a key enzyme in the synthesis of isoprenoids. Recently, nitrogen-containing bisphosphonates (N-BPs) used in bone resorption therapy have been shown to be active against Trypanosoma cruzi, the parasite that causes American trypanosomiasis (Chagas disease), suggesting that they may be used as anti-trypanosomal agents. The crystal structures of TcFPPS in complex with substrate (isopentenyl diphosphate, IPP) and five N-BP inhibitors show that the C-1 hydroxyl and the nitrogen-containing groups of the inhibitors alter the binding of IPP and the conformation of two TcFPPS residues, Tyr94 and Gln167. Isothermal titration calorimetry experiments suggest that binding of the first N-BPs to the homodimeric TcFPPS changes the binding properties of the second site. This mechanism of binding of N-BPs to TcFPPS is different to that reported for the binding of the same compounds to human FPPS. Proteins 2010. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Chuan-Hsiang Huang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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23
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Gao J, Chu X, Qiu Y, Wu L, Qiao Y, Wu J, Li D. Discovery of potent inhibitor for farnesyl pyrophosphate synthase in the mevalonate pathway. Chem Commun (Camb) 2010; 46:5340-2. [DOI: 10.1039/c0cc00992j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Implications of fast-time scale dynamics of human DNA/RNA cytosine methyltransferases (DNMTs) for protein function. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0681-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Abstract
A variety of new treatments for osteoporosis have become available within the last several years, and a number of emerging treatments remain in late clinical stage development. New and emerging treatments include more potent members, or more convenient formulations, of existing classes of therapy, but a number of the emerging treatments are first-generation compounds addressing specific therapeutic targets based on recent advances in understanding of basic bone biology. These new and emerging treatments include agents with anticatabolic effects, compounds with anabolic effects, and one agent possibly containing both anticatabolic and anabolic effects. The increasing variety of new and emerging treatments increases the possibility that effective therapy will be targeted to the specific needs of the individual patient.
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Affiliation(s)
- Bart L Clarke
- Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Mayo Clinic, Rochester, MN 55905, USA.
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26
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Mukherjee S, Huang C, Guerra F, Wang K, Oldfield E. Thermodynamics of bisphosphonates binding to human bone: a two-site model. J Am Chem Soc 2009; 131:8374-5. [PMID: 19489581 DOI: 10.1021/ja902895p] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used isothermal titration calorimetry (ITC) to study the thermodynamics of binding of 12 bisphosphonates to human bone. The ITC results show that there are two binding sites. Site A is the weak, highly populated site seen by NMR and is characterized by an average DeltaG of binding of -5.2 kcal. Site B is a strong binding site characterized by a DeltaG of binding of -8.5 kcal. Binding to both sites is overwhelmingly entropy driven. Using a thermodynamic group approach and a linear regression method, we predict the DeltaG of binding of all 12 compounds with an R(2) = 0.95 (a 0.19 kcal error variance estimate, approximately 3% of the total DeltaG range), opening up the way to designing novel chemotherapy, immunotherapy, and anti-infectious disease drugs having weak bone binding affinity.
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Affiliation(s)
- Sujoy Mukherjee
- Center for Biophysics & Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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27
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Zhang Y, Cao R, Yin F, Hudock MP, Guo RT, Krysiak K, Mukherjee S, Gao YG, Robinson H, Song Y, No JH, Bergan K, Leon A, Cass L, Goddard A, Chang TK, Lin FY, Van Beek E, Papapoulos S, Wang AHJ, Kubo T, Ochi M, Mukkamala D, Oldfield E. Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation. J Am Chem Soc 2009; 131:5153-62. [PMID: 19309137 DOI: 10.1021/ja808285e] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Considerable effort has focused on the development of selective protein farnesyl transferase (FTase) and protein geranylgeranyl transferase (GGTase) inhibitors as cancer chemotherapeutics. Here, we report a new strategy for anticancer therapeutic agents involving inhibition of farnesyl diphosphate synthase (FPPS) and geranylgeranyl diphosphate synthase (GGPPS), the two enzymes upstream of FTase and GGTase, by lipophilic bisphosphonates. Due to dual site targeting and decreased polarity, the compounds have activities far greater than do current bisphosphonate drugs in inhibiting tumor cell growth and invasiveness, both in vitro and in vivo. We explore how these compounds inhibit cell growth and how cell activity can be predicted based on enzyme inhibition data, and using X-ray diffraction, solid state NMR, and isothermal titration calorimetry, we show how these compounds bind to FPPS and/or GGPPS.
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Affiliation(s)
- Yonghui Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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28
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Cao R, Chen CKM, Guo RT, Wang AHJ, Oldfield E. Structures of a potent phenylalkyl bisphosphonate inhibitor bound to farnesyl and geranylgeranyl diphosphate synthases. Proteins 2009; 73:431-9. [PMID: 18442135 DOI: 10.1002/prot.22066] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We report the X-ray crystallographic structures of the bisphosphonate N-[methyl(4-phenylbutyl)]-3-aminopropyl-1-hydroxy-1,1-bisphosphonate (BPH-210), a potent analog of pamidronate (Aredia), bound to farnesyl diphosphate synthase (FPPS) from Trypanosoma brucei as well as to geranylgeranyl diphosphate synthase from Saccharomyces cerevisiae. BPH-210 binds to FPPS, together with 3 Mg(2+), with its long, hydrophobic phenylbutyl side-chain being located in the same binding pocket that is occupied by allylic diphosphates and other bisphosphonates. Binding is overwhelmingly entropy driven, as determined by isothermal titration calorimetry. The structure is of interest since it explains the lack of potency of longer chain analogs against FPPS, since these would be expected to have a steric clash with an aromatic ring at the distal end of the binding site. Unlike shorter chain FPPS inhibitors, such as pamidronate, BPH-210 is also found to be a potent inhibitor of human geranylgeranyl diphosphate synthase. In this case, the bisphosphonate binds only to the GGPP product inhibitory site, with only 1 (chain A) or 0 (chain B) Mg(2+), and DeltaS is much smaller and DeltaH is approximately 6 k cal more negative than in the case of FPPS binding. Overall, these results are of general interest since they show that some bisphosphonates can bind to more than one trans-prenyl synthase enzyme which, in some cases, can be expected to enhance their overall activity in vitro and in vivo.
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Affiliation(s)
- Rong Cao
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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29
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Biological Activity of Aminophosphonic Acids and Their Short Peptides. TOPICS IN HETEROCYCLIC CHEMISTRY 2009. [DOI: 10.1007/7081_2008_14] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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30
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Davis AM, St-Gallay SA, Kleywegt GJ. Limitations and lessons in the use of X-ray structural information in drug design. Drug Discov Today 2008; 13:831-41. [PMID: 18617015 PMCID: PMC7185550 DOI: 10.1016/j.drudis.2008.06.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 05/23/2008] [Accepted: 06/04/2008] [Indexed: 12/04/2022]
Affiliation(s)
- Andrew M Davis
- Department of Medicinal Chemistry, AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leicestershire LE11 5RH, United Kingdom.
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31
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Quadir MA, Radowski MR, Kratz F, Licha K, Hauff P, Haag R. Dendritic multishell architectures for drug and dye transport. J Control Release 2008; 132:289-94. [PMID: 18639596 DOI: 10.1016/j.jconrel.2008.06.016] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Revised: 06/13/2008] [Accepted: 06/16/2008] [Indexed: 12/21/2022]
Abstract
Here we present the efficiency and versatility of newly developed core-multishell nanoparticles (CMS NPs), to encapsulate and transport the antitumor drugs doxorubicin hydrochloride (Dox), methotrexate (Mtx) and sodium ibandronate (Ibn) as well as dye molecules, i.e., a tetrasulfonated indotricarbocyanine (ITCC) and nile red. Structurally, the CMS NPs are composed of hyperbranched poly(ethylene imine) core functionalized by alkyl diacids connected to monomethyl poly(ethylene glycol). In order to evaluate their transport in aqueous media in vitro, we have used and compared SEC, UV, ITC, and NMR techniques. We observed that the CMS NPs were able to spontaneously encapsulate and transport Dox, Mtx and nile red in both organic and aqueous media as determined by SEC and UV-VIS spectroscopy. For the VIS transparent Ibn Isothermal Titration Calorimetric (ITC) experiments show an exothermic interaction with the CMS NPs. The enthalpic stabilization (DeltaH) upon encapsulation was in the order of approximately 7 kcals/mol which indicates stable interaction between Ibn and nanoparticles. A T(1) inversion recovery NMR experiment was carried out for 31P and 1H nuclei of Ibn and an increment of spin-lattice relaxation time for respective nuclei was observed upon encapsulation. CMS NPs were also found to encapsulate ITCC dye with stoichiometry of 6-8 molecules/nanocarrier. For in vivo imaging studies the dye loaded CMS NPs were injected to F9 teratocarcinoma bearing mice and a strong contrast was observed in the tumor tissues compared to free dye after 6 h of administration.
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Affiliation(s)
- Mohiuddin A Quadir
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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Dunford JE, Kwaasi AA, Rogers MJ, Barnett BL, Ebetino FH, Russell RGG, Oppermann U, Kavanagh KL. Structure–Activity Relationships Among the Nitrogen Containing Bisphosphonates in Clinical Use and Other Analogues: Time-Dependent Inhibition of Human Farnesyl Pyrophosphate Synthase. J Med Chem 2008; 51:2187-95. [DOI: 10.1021/jm7015733] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James E. Dunford
- Structural Genomics Consortium, The Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom, Nuffield Department of Orthopaedic Surgery, The Botnar Research Centre, University of Oxford, Institute of Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, United Kingdom, Bone and Musculoskeletal Research Programme, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom, Chemistry Department, University of Cincinnati,
| | - Aaron A. Kwaasi
- Structural Genomics Consortium, The Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom, Nuffield Department of Orthopaedic Surgery, The Botnar Research Centre, University of Oxford, Institute of Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, United Kingdom, Bone and Musculoskeletal Research Programme, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom, Chemistry Department, University of Cincinnati,
| | - Michael J. Rogers
- Structural Genomics Consortium, The Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom, Nuffield Department of Orthopaedic Surgery, The Botnar Research Centre, University of Oxford, Institute of Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, United Kingdom, Bone and Musculoskeletal Research Programme, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom, Chemistry Department, University of Cincinnati,
| | - Bobby L. Barnett
- Structural Genomics Consortium, The Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom, Nuffield Department of Orthopaedic Surgery, The Botnar Research Centre, University of Oxford, Institute of Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, United Kingdom, Bone and Musculoskeletal Research Programme, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom, Chemistry Department, University of Cincinnati,
| | - Frank H. Ebetino
- Structural Genomics Consortium, The Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom, Nuffield Department of Orthopaedic Surgery, The Botnar Research Centre, University of Oxford, Institute of Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, United Kingdom, Bone and Musculoskeletal Research Programme, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom, Chemistry Department, University of Cincinnati,
| | - R. Graham G. Russell
- Structural Genomics Consortium, The Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom, Nuffield Department of Orthopaedic Surgery, The Botnar Research Centre, University of Oxford, Institute of Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, United Kingdom, Bone and Musculoskeletal Research Programme, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom, Chemistry Department, University of Cincinnati,
| | - Udo Oppermann
- Structural Genomics Consortium, The Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom, Nuffield Department of Orthopaedic Surgery, The Botnar Research Centre, University of Oxford, Institute of Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, United Kingdom, Bone and Musculoskeletal Research Programme, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom, Chemistry Department, University of Cincinnati,
| | - Kathryn L. Kavanagh
- Structural Genomics Consortium, The Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom, Nuffield Department of Orthopaedic Surgery, The Botnar Research Centre, University of Oxford, Institute of Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, United Kingdom, Bone and Musculoskeletal Research Programme, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom, Chemistry Department, University of Cincinnati,
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Guénin E, Monteil M, Bouchemal N, Prangé T, Lecouvey M. Syntheses of Phosphonic Esters of Alendronate, Pamidronate and Neridronate. European J Org Chem 2007. [DOI: 10.1002/ejoc.200601067] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Steuber H, Heine A, Klebe G. Structural and Thermodynamic Study on Aldose Reductase: Nitro-substituted Inhibitors with Strong Enthalpic Binding Contribution. J Mol Biol 2007; 368:618-38. [PMID: 17368668 DOI: 10.1016/j.jmb.2006.12.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 12/04/2006] [Accepted: 12/04/2006] [Indexed: 10/23/2022]
Abstract
To prevent diabetic complications derived from enhanced glucose flux via the polyol pathway the development of aldose reductase inhibitors (ARIs) has been established as a promising therapeutic concept. In order to identify novel lead compounds, a virtual screening (VS) was performed successfully suggesting carboxylate-type inhibitors of sub-micromolar to micromolar affinity. Here, we combine a structural characterization of the binding modes observed by X-ray crystallography with isothermal titration calorimetry (ITC) measurements providing insights into the driving forces of inhibitor binding, particularly of the first leads from VS. Characteristic features of this novel inhibitor type include a carboxylate head group connected via an alkyl spacer to a heteroaromatic moiety, which is linked to a further nitro-substituted aromatic portion. The crystal structures of two enzyme-inhibitor complexes have been determined at resolutions of 1.43 A and 1.55 A. Surprisingly, the carboxylic group of the most potent VS lead occupies the catalytic pocket differently compared to the interaction geometry observed in almost all other crystal structures with structurally related ligands and obtained under similar conditions, as an interstitial water molecule is picked up upon ligand binding. The nitro-aromatic moiety of both leads occupies the specificity pocket of the enzyme, however, adopting a different geometry compared to the docking prediction: unexpectedly, the nitro group binds to the bottom of the specificity pocket and provokes remarkable induced-fit adaptations. A peptide group located at the active site orients in such a way that H-bond formation to one nitro group oxygen atom is enabled, whereas a neighbouring tyrosine side-chain performs a slight rotation off from the binding cavity to accommodate the nitro group. Identically constituted ligands, lacking this nitro group, exhibit an affinity drop of one order of magnitude. In addition, thermodynamic data suggest a strongly favourable contribution to binding enthalpy in case the inhibitor is equipped with a nitro group at the corresponding position. To further investigate this phenomenon, we determined crystal structures and thermodynamic data of two similarly constituted IDD-type inhibitors addressing the specificity pocket with either a nitro or halogen-substituted aromatic moiety. As these data suggest, the nitro group provokes the enthalpic contribution, in addition to the H-bond mentioned above, by accepting two "non-classical" H-bonds donated by the aromatic tyrosine side-chain. In summary, this study provides the platform for further structure-guided design hypotheses of novel drug candidates with higher affinity and selectivity.
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Affiliation(s)
- Holger Steuber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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Moll D, Schweinsberg S, Hammann C, Herberg FW. Comparative thermodynamic analysis of cyclic nucleotide binding to protein kinase A. Biol Chem 2007; 388:163-72. [PMID: 17261079 DOI: 10.1515/bc.2007.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We have investigated the thermodynamic parameters and binding of a regulatory subunit of cAMP-dependent protein kinase (PKA) to its natural low-molecular-weight ligand, cAMP, and analogues thereof. For analysis of this model system, we compared side-by-side isothermal titration calorimetry (ITC) with surface plasmon resonance (SPR). Both ITC and SPR analyses revealed that binding of the protein to cAMP or its analogues was enthalpically driven and characterised by similar free energy values (DeltaG=-9.4 to -10.7 kcal mol-1) for all interactions. Despite the similar affinities, binding of the cyclic nucleotides used here was characterised by significant differences in the contribution of entropy (-TDeltaS) and enthalpy (DeltaH) to DeltaG. The comparison of ITC and SPR data for one cAMP analogue further revealed deviations caused by the method. These equilibrium parameters could be complemented by thermodynamic data of the transition state (DeltaHnot equal, DeltaGnot equal, DeltaSnot equal) for both association and dissociation measured by SPR. This direct comparison of ITC and SPR highlights method-specific advantages and drawbacks for thermodynamic analyses of protein/ligand interactions.
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Affiliation(s)
- Daniela Moll
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
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Grundner C, Perrin D, van Huijsduijnen RH, Swinnen D, Gonzalez J, Gee CL, Wells TN, Alber T. Structural basis for selective inhibition of Mycobacterium tuberculosis protein tyrosine phosphatase PtpB. Structure 2007; 15:499-509. [PMID: 17437721 PMCID: PMC2775457 DOI: 10.1016/j.str.2007.03.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 03/05/2007] [Accepted: 03/07/2007] [Indexed: 01/07/2023]
Abstract
Tyrosine kinases and phosphatases establish the crucial balance of tyrosine phosphorylation in cellular signaling, but creating specific inhibitors of protein Tyr phosphatases (PTPs) remains a challenge. Here, we report the development of a potent, selective inhibitor of Mycobacterium tuberculosis PtpB, a bacterial PTP that is secreted into host cells where it disrupts unidentified signaling pathways. The inhibitor, (oxalylamino-methylene)-thiophene sulfonamide (OMTS), showed an IC(50) of 440 +/- 50 nM and >60-fold specificity for PtpB over six human PTPs. The 2 A resolution crystal structure of PtpB in complex with OMTS revealed a large rearrangement of the enzyme, with some residues shifting >27 A relative to the PtpB:PO(4) complex. Extensive contacts with the catalytic loop provide a potential basis for inhibitor selectivity. Two OMTS molecules bound adjacent to each other, raising the possibility of a second substrate phosphotyrosine binding site in PtpB. The PtpB:OMTS structure provides an unanticipated framework to guide inhibitor improvement.
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Affiliation(s)
- Christoph Grundner
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | | | | | | | | | - Christine L. Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | | | - Tom Alber
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Corresponding author: 510-642-8758 (Voice), 510-643-9290 (FAX),
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