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Cardenal Peralta C, Vandroux P, Neumann-Arnold L, Panvert M, Fagart J, Seufert W, Mechulam Y, Schmitt E. Binding of human Cdc123 to eIF2γ. J Struct Biol 2023; 215:108006. [PMID: 37507029 DOI: 10.1016/j.jsb.2023.108006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Eukaryotic initiation factor 2 (eIF2) plays a key role in protein synthesis and in its regulation. The assembly of this heterotrimeric factor is facilitated by Cdc123, a member of the ATP grasp family that binds the γ subunit of eIF2. Notably, some mutations related to MEHMO syndrome, an X-linked intellectual disability, affect Cdc123-mediated eIF2 assembly. The mechanism of action of Cdc123 is unclear and structural information for the human protein is awaited. Here, the crystallographic structure of human Cdc123 (Hs-Cdc123) bound to domain 3 of human eIF2γ (Hs-eIF2γD3) was determined. The structure shows that the domain 3 of eIF2γ is bound to domain 1 of Cdc123. In addition, the long C-terminal region of Hs-Cdc123 provides a link between the ATP and Hs-eIF2γD3 binding sites. A thermal shift assay shows that ATP is tightly bound to Cdc123 whereas the affinity of ADP is much smaller. Yeast cell viability experiments, western blot analysis and two-hybrid assays show that ATP is important for the function of Hs-Cdc123 in eIF2 assembly. These data and recent findings allow us to propose a refined model to explain the mechanism of action of Cdc123 in eIF2 assembly.
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Affiliation(s)
- Cristina Cardenal Peralta
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Paul Vandroux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Lea Neumann-Arnold
- Department of Genetics, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Michel Panvert
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Jérôme Fagart
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Wolfgang Seufert
- Department of Genetics, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France.
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2
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Ford A, Breitgoff F, Pasquini M, MacKenzie A, McElroy S, Baker S, Abrusci P, Varzandeh S, Bird L, Gavard A, Damerell D, Redhead M. Application of particle swarm optimization to understand the mechanism of action of allosteric inhibitors of the enzyme HSD17β13. PATTERNS (NEW YORK, N.Y.) 2023; 4:100733. [PMID: 37223265 PMCID: PMC10201303 DOI: 10.1016/j.patter.2023.100733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/06/2022] [Accepted: 03/24/2023] [Indexed: 05/25/2023]
Abstract
Understanding a drug candidate's mechanism of action is crucial for its further development. However, kinetic schemes are often complex and multi-parametric, especially for proteins in oligomerization equilibria. Here, we demonstrate the use of particle swarm optimization (PSO) as a method to select between different sets of parameters that are too far apart in the parameter space to be found by conventional approaches. PSO is based upon the swarming of birds: each bird in the flock assesses multiple landing spots while at the same time sharing that information with its neighbors. We applied this approach to the kinetics of HSD17β13 enzyme inhibitors, which displayed unusually large thermal shifts. Thermal shift data for HSD17β13 indicated that the inhibitor shifted the oligomerization equilibrium toward the dimeric state. Validation of the PSO approach was provided by experimental mass photometry data. These results encourage further exploration of multi-parameter optimization algorithms as tools in drug discovery.
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Affiliation(s)
- Amy Ford
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Frauke Breitgoff
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Miriam Pasquini
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | | | - Stuart McElroy
- Bioascent, Bo'Ness Road, Chapelhall, Motherwell ML1 5SH, UK
| | - Steve Baker
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Patrizia Abrusci
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Simon Varzandeh
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Louise Bird
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Angeline Gavard
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - David Damerell
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Martin Redhead
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
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3
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Froes TQ, Chaves BT, Mendes MS, Ximenes RM, da Silva IM, da Silva PBG, de Albuquerque JFC, Castilho MS. Synthesis and biological evaluation of thiazolidinedione derivatives with high ligand efficiency to P. aeruginosa PhzS. J Enzyme Inhib Med Chem 2021; 36:1217-1229. [PMID: 34080514 PMCID: PMC8186431 DOI: 10.1080/14756366.2021.1931165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 01/07/2023] Open
Abstract
The thiazolidinone ring is found in compounds that have widespan biology activity and there is mechanism-based evidence that compounds bearing this moiety inhibit P. aeruginosa PhzS (PaPzhS), a key enzyme in the biosynthesis of the virulence factor named pyocyanin. Ten novel thiazolidinone derivatives were synthesised and screened against PaPhzS, using two orthogonal assays. The biological results provided by these and 28 other compounds, whose synthesis had been described, suggest that the dihydroquinazoline ring, found in the previous hit (A- Kd = 18 µM and LE = 0.20), is not required for PaPzhS inhibition, but unsubstituted nitrogen at the thiazolidinone ring is. The molecular simplification approach, pursued in this work, afforded an optimised lead compound (13- 5-(2,4-dimethoxyphenyl)thiazolidine-2,4-dione) with 10-fold improvement in affinity (Kd= 1.68 µM) and more than 100% increase in LE (0.45), which follows the same inhibition mode as the original hit compound (competitive to NADH).Executive summaryPhzS is a key enzyme in the pyocyanin biosynthesis pathway in P. aeruginosa.Orthogonal assays (TSA and FITC) show that fragment-like thiazolidinedione derivatives bind to PaPhzS with one-digit micromolar affinity.Fragment-like thiazolidinedione derivatives bind to the cofactor (NADH) binding site in PaPhzS.The molecular simplification optimised the ligand efficiency and affinity of the lead compound.
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Affiliation(s)
- Thamires Quadros Froes
- Programa de Pós-graduação em biotecnologia da, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Marina Sena Mendes
- Faculdade de Farmácia da, Universidade Federal da Bahia, Salvador, Brazil
| | - Rafael Matos Ximenes
- Departamento de Antibióticos da, Universidade Federal de Pernambuco. Av. Prof. Moraes Rego, Recife-Pe, Brazil
| | - Ivanildo Mangueira da Silva
- Departamento de Antibióticos da, Universidade Federal de Pernambuco. Av. Prof. Moraes Rego, Recife-Pe, Brazil
| | | | | | - Marcelo Santos Castilho
- Programa de Pós-graduação em biotecnologia da, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
- Faculdade de Farmácia da, Universidade Federal da Bahia, Salvador, Brazil
- Programa de Pós-Graduação em Farmácia da, Universidade Federal da Bahia, Salvador, Brazil
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4
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Nunes-Alves A, Ormersbach F, Wade RC. Prediction of the Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis. J Chem Inf Model 2021; 61:3708-3721. [PMID: 34197096 DOI: 10.1021/acs.jcim.1c00639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is growing consensus that the optimization of the kinetic parameters for drug-protein binding leads to improved drug efficacy. Therefore, computational methods have been developed to predict kinetic rates and to derive quantitative structure-kinetic relationships (QSKRs). Many of these methods are based on crystal structures of ligand-protein complexes. However, a drawback is that each ligand-protein complex is usually treated as having a single structure. Here, we present a modification of COMparative BINding Energy (COMBINE) analysis, which uses the structures of ligand-protein complexes to predict binding parameters. We introduce the option of using multiple structures to describe each ligand-protein complex in COMBINE analysis and apply this to study the effects of protein flexibility on the derivation of dissociation rate constants (koff) for inhibitors of p38 mitogen-activated protein (MAP) kinase, which has a flexible binding site. Multiple structures were obtained for each ligand-protein complex by performing docking to an ensemble of protein configurations obtained from molecular dynamics simulations. Coefficients to scale ligand-protein interaction energies determined from energy-minimized structures of ligand-protein complexes were obtained by partial least squares regression, and they allowed for the computation of koff values. The QSKR model obtained using single, energy-minimized crystal structures for each ligand-protein complex had higher predictive power than the QSKR model obtained with multiple structures from ensemble docking. However, incorporation of ligand-protein flexibility helped to highlight additional ligand-protein interactions that lead to longer residence times, such as interactions with residues Arg67 and Asp168, which are close to the ligand in many crystal structures. These results show that COMBINE analysis is a promising method to guide the design of compounds that bind to flexible proteins with improved binding kinetics.
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Affiliation(s)
- Ariane Nunes-Alves
- Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Fabian Ormersbach
- Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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5
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A novel scaffold to fight Pseudomonas aeruginosa pyocyanin production: early steps to novel antivirulence drugs. Future Med Chem 2020; 12:1489-1503. [PMID: 32772556 DOI: 10.4155/fmc-2019-0351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: Although bacterial resistance is a growing concern worldwide, the development of antibacterial drugs has been steadily decreasing. One alternative to fight this issue relies on reducing the bacteria virulence without killing it. PhzS plays a pivotal role in pyocyanin production in Pseudomonas aeruginosa. Results: A total of 31 thiazolidinedione derivatives were evaluated as putative PhzS inhibitors, using thermo shift assays. Compounds that significantly shifted PhzS's Tm had their mode of inhibition (cofactor competitor) and affinity calculated by thermo shift assays as well. The most promising compound (E)-5-(4-((4-oxo-3-phenyl-3,4-dihydroquinazolin-2-yl)methoxy)benzylidene)thiazolidine-2,4-dione had their affinity confirmed by microscale thermophoresis (Kd = 18 μM). Cellular assays suggest this compound reduces pyocyanin production in vitro, but does not affect P. aeruginosa viability. Conclusion: The first inhibitor of PhzS is described.
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6
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Huang S, Chen L, Mei H, Zhang D, Shi T, Kuang Z, Heng Y, Xu L, Pan X. In Silico Prediction of the Dissociation Rate Constants of Small Chemical Ligands by 3D-Grid-Based VolSurf Method. Int J Mol Sci 2020; 21:ijms21072456. [PMID: 32252223 PMCID: PMC7177943 DOI: 10.3390/ijms21072456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/30/2020] [Indexed: 12/26/2022] Open
Abstract
Accumulated evidence suggests that binding kinetic properties—especially dissociation rate constant or drug-target residence time—are crucial factors affecting drug potency. However, quantitative prediction of kinetic properties has always been a challenging task in drug discovery. In this study, the VolSurf method was successfully applied to quantitatively predict the koff values of the small ligands of heat shock protein 90α (HSP90α), adenosine receptor (AR) and p38 mitogen-activated protein kinase (p38 MAPK). The results showed that few VolSurf descriptors can efficiently capture the key ligand surface properties related to dissociation rate; the resulting models demonstrated to be extremely simple, robust and predictive in comparison with available prediction methods. Therefore, it can be concluded that the VolSurf-based prediction method can be widely applied in the ligand-receptor binding kinetics and de novo drug design researches.
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Affiliation(s)
- Shuheng Huang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), Chongqing University, Chongqing 400044, China; (S.H.); (L.C.)
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Linxin Chen
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), Chongqing University, Chongqing 400044, China; (S.H.); (L.C.)
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Hu Mei
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), Chongqing University, Chongqing 400044, China; (S.H.); (L.C.)
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
- Correspondence: (H.M.); (X.P.); Tel.: +86-23-65112677 (H.M.)
| | - Duo Zhang
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Tingting Shi
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Zuyin Kuang
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Yu Heng
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Lei Xu
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
| | - Xianchao Pan
- College of Bioengineering, Chongqing University, Chongqing 400044, China; (D.Z.); (T.S.); (Z.K.); (Y.H.); (L.X.)
- Department of Medicinal Chemistry, College of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Correspondence: (H.M.); (X.P.); Tel.: +86-23-65112677 (H.M.)
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7
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Braka A, Garnier N, Bonnet P, Aci-Sèche S. Residence Time Prediction of Type 1 and 2 Kinase Inhibitors from Unbinding Simulations. J Chem Inf Model 2019; 60:342-348. [DOI: 10.1021/acs.jcim.9b00497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Abdennour Braka
- Institut de Chimie Organique et Analytique (ICOA), UMR7311 Université d’Orléans-CNRS, Rue de Chartres—BP 6759, 45067 Orléans Cedex 2, France
- Centre de Biophysique Moléculaire (CBM) UPR 4301, CNRS, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Norbert Garnier
- Centre de Biophysique Moléculaire (CBM) UPR 4301, CNRS, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR7311 Université d’Orléans-CNRS, Rue de Chartres—BP 6759, 45067 Orléans Cedex 2, France
| | - Samia Aci-Sèche
- Institut de Chimie Organique et Analytique (ICOA), UMR7311 Université d’Orléans-CNRS, Rue de Chartres—BP 6759, 45067 Orléans Cedex 2, France
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8
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
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9
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Zhang D, Huang S, Mei H, Kevin M, Shi T, Chen L. Protein-ligand interaction fingerprints for accurate prediction of dissociation rates of p38 MAPK Type II inhibitors. Integr Biol (Camb) 2019; 11:53-60. [PMID: 30855664 DOI: 10.1093/intbio/zyz004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/20/2018] [Accepted: 02/01/2019] [Indexed: 12/22/2022]
Abstract
Binding/unbinding kinetics are key determinants of drug potencies. However, there are still a lot of challenges in predicting kinetic properties during early-stage drug development. In this work, position-restrained molecular dynamics simulations combined with energy decomposition were applied to extract protein-ligand interaction (PLI) fingerprints along the unbinding pathway of 20 p38 mitogen-activated protein kinase (p38 MAPK) Type II inhibitors. The results showed that the electrostatic and/or van der Waals interaction fingerprints at three key positions can be used for accurate prediction of the dissociation rate constants (koff) of p38 MAPK Type II inhibitors. The strategy proposed in this paper can provide not only an efficient method of predicting the dissociation rates of the p38 MAPK Type II inhibitors, but also the atom-level mechanism of enthalpy-driven unbinding process.
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Affiliation(s)
- Duo Zhang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), Chongqing University, Chongqing, China
- College of Bioengineering, Chongqing University, Chongqing, China
| | - Shuheng Huang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), Chongqing University, Chongqing, China
- College of Bioengineering, Chongqing University, Chongqing, China
| | - Hu Mei
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), Chongqing University, Chongqing, China
- College of Bioengineering, Chongqing University, Chongqing, China
| | | | - Tingting Shi
- College of Bioengineering, Chongqing University, Chongqing, China
| | - Linxin Chen
- College of Bioengineering, Chongqing University, Chongqing, China
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10
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Screening Pyridine Derivatives against Human Hydrogen Sulfide-synthesizing Enzymes by Orthogonal Methods. Sci Rep 2019; 9:684. [PMID: 30679627 PMCID: PMC6346012 DOI: 10.1038/s41598-018-36994-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022] Open
Abstract
Biosynthesis of hydrogen sulfide (H2S), a key signalling molecule in human (patho)physiology, is mostly accomplished by the human enzymes cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE) and 3-mercaptopyruvate sulfurtransferase (MST). Several lines of evidence have shown a close correlation between increased H2S production and human diseases, such as several cancer types and amyotrophic lateral sclerosis. Identifying compounds selectively and potently inhibiting the human H2S-synthesizing enzymes may therefore prove beneficial for pharmacological applications. Here, the human enzymes CBS, CSE and MST were expressed and purified from Escherichia coli, and thirty-one pyridine derivatives were synthesized and screened for their ability to bind and inhibit these enzymes. Using differential scanning fluorimetry (DSF), surface plasmon resonance (SPR), circular dichroism spectropolarimetry (CD), and activity assays based on fluorimetric and colorimetric H2S detection, two compounds (C30 and C31) sharing structural similarities were found to weakly inhibit both CBS and CSE: 1 mM C30 inhibited these enzymes by approx. 50% and 40%, respectively, while 0.5 mM C31 accounted for CBS and CSE inhibition by approx. 40% and 60%, respectively. This work, while presenting a robust methodological platform for screening putative inhibitors of the human H2S-synthesizing enzymes, highlights the importance of employing complementary methodologies in compound screenings.
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11
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Salehabadi H, Khajeh K, Dabirmanesh B, Biglar M, Amanlou M. Evaluation of angiotensin converting enzyme inhibitors by SPR biosensor and theoretical studies. Enzyme Microb Technol 2018; 120:117-123. [PMID: 30396392 DOI: 10.1016/j.enzmictec.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 06/13/2018] [Accepted: 10/19/2018] [Indexed: 01/01/2023]
Abstract
Surface plasmon resonance (SPR) biosensor has been utilized for monitoring analyte-ligand interactions in modern drug discovery processes. SPR biosensors measure the change in refractive indexes over the course of analyte molecules' binding to a specific immobilized ligand on sensor chip. This effort highlights a comprehensive SPR study besides enzymatic assay for discovery of new Angiotensin Converting Enzyme (ACE) inhibitors via screening of medicinal plants. At first, five medicinal plants were selected as potential sources for developing new ACE inhibitors through hydrolyzing hippuryl-L-histidyl-L-leucine (HHL) assay. The interaction of selected extracts with immobilized ACE on the sensor chip (500D) confirmed that the Onopordum acanthium L. had the greatest ACE inhibition activity among the set of compounds and its active compound (onopordia) was isolated. SPR biosensor used to evaluate binding affinity of onopordia and ACE. Equilibrium constant (KD), and changes in Gibb's free energy of the binding (ΔGbinding) values for the interaction of onopordia with ACE were found to be 10.24 μM and -28.48 kJ/mol, respectively. Computational analysis supported the binding of onopordia to the ACE active site. Kinetic and thermodynamic parameters of binding revealed that onopordia is an acceptable ACE inhibitor and could treat hypertension. SPR biosensor can be used to improve the drug discovery process for many important classes of drug targets due to its great sensitivity.
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Affiliation(s)
- Hafezeh Salehabadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 14176-53955, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-111, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-111, Iran
| | - Mahmood Biglar
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, 14176-53955, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 14176-53955, Iran; Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, 14176-53955, Iran.
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12
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Carroll B, Otten EG, Manni D, Stefanatos R, Menzies FM, Smith GR, Jurk D, Kenneth N, Wilkinson S, Passos JF, Attems J, Veal EA, Teyssou E, Seilhean D, Millecamps S, Eskelinen EL, Bronowska AK, Rubinsztein DC, Sanz A, Korolchuk VI. Oxidation of SQSTM1/p62 mediates the link between redox state and protein homeostasis. Nat Commun 2018; 9:256. [PMID: 29343728 PMCID: PMC5772351 DOI: 10.1038/s41467-017-02746-z] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
Cellular homoeostatic pathways such as macroautophagy (hereinafter autophagy) are regulated by basic mechanisms that are conserved throughout the eukaryotic kingdom. However, it remains poorly understood how these mechanisms further evolved in higher organisms. Here we describe a modification in the autophagy pathway in vertebrates, which promotes its activity in response to oxidative stress. We have identified two oxidation-sensitive cysteine residues in a prototypic autophagy receptor SQSTM1/p62, which allow activation of pro-survival autophagy in stress conditions. The Drosophila p62 homologue, Ref(2)P, lacks these oxidation-sensitive cysteine residues and their introduction into the protein increases protein turnover and stress resistance of flies, whereas perturbation of p62 oxidation in humans may result in age-related pathology. We propose that the redox-sensitivity of p62 may have evolved in vertebrates as a mechanism that allows activation of autophagy in response to oxidative stress to maintain cellular homoeostasis and increase cell survival. The cellular mechanisms underlying autophagy are conserved; however it is unclear how they evolved in higher organisms. Here the authors identify two oxidation-sensitive cysteine residues in the autophagy receptor SQSTM1/p62 in vertebrates which allow activation of pro-survival autophagy in stress conditions.
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Affiliation(s)
- Bernadette Carroll
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Elsje G Otten
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Diego Manni
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Rhoda Stefanatos
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Fiona M Menzies
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Graham R Smith
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK.,Bioinformatics Support Unit (BSU); Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, NE2 4HH, UK
| | - Diana Jurk
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Niall Kenneth
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Simon Wilkinson
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Joao F Passos
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Johannes Attems
- Institute of Neuroscience (IoN); Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Elizabeth A Veal
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Elisa Teyssou
- Institut du Cerveau et de la Moelle épinière (ICM), INSERM U1127, CNRS UMR7225, Sorbonne Universités, Université Pierre et Marie Curie, University of Paris 06, UPMC-P6 UMRS1127, Hôpital Pitié-Salpêtrière, Paris, France
| | - Danielle Seilhean
- Institut du Cerveau et de la Moelle épinière (ICM), INSERM U1127, CNRS UMR7225, Sorbonne Universités, Université Pierre et Marie Curie, University of Paris 06, UPMC-P6 UMRS1127, Hôpital Pitié-Salpêtrière, Paris, France.,Département de Neuropathologie, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Stéphanie Millecamps
- Institut du Cerveau et de la Moelle épinière (ICM), INSERM U1127, CNRS UMR7225, Sorbonne Universités, Université Pierre et Marie Curie, University of Paris 06, UPMC-P6 UMRS1127, Hôpital Pitié-Salpêtrière, Paris, France
| | | | | | - David C Rubinsztein
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.,UK Dementia Research Institute, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - Alberto Sanz
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Viktor I Korolchuk
- Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University Institute for Ageing (NUIA), Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL, UK.
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13
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Liu Q, Sun NN, Wu ZZ, Fan DH, Cao MQ. Chaihu-Shugan-San exerts an antidepressive effect by downregulating miR-124 and releasing inhibition of the MAPK14 and Gria3 signaling pathways. Neural Regen Res 2018; 13:837-845. [PMID: 29863014 PMCID: PMC5998613 DOI: 10.4103/1673-5374.232478] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Dysregulation of miR-124 has been reported to be involved in the pathophysiology of depression. Chaihu-Shugan-San, a traditional Chinese medicine, has antidepressive activity; however, the underlying mechanisms remain unclear. In this study, to generate a rodent model of depression, rats were subjected to a combination of solitary confinement and chronic unpredictable mild stress for 28 days. Rats were intragastrically administered Chaihu-Shugan-San (2.835 mL/kg/d) for 4 weeks, once a day. Real-time reverse-transcription quantitative polymerase chain reaction, miRNA microarray, western blot assay and transmission electron microscopy demonstrated that Chaihu-Shugan-San downregulated miR-124 expression and upregulated the mRNA and protein levels of mitogen-activated protein kinase 14 (MAPK14) and glutamate receptor subunit 3 (Gria3). Chaihu-Shugan-San also promoted synapse formation in the hippocampus. The open field test, sucrose consumption test and forced swimming test were used to assess depression-like behavior. After intragastric administration of Chaihu-Shugan-San, sucrose consumption increased, while the depressive behaviors were substantially reduced. Together, these findings suggest that Chaihu-Shugan-San exerts an antidepressant-like effect by downregulating miR-124 expression and by releasing the inhibition of the MAPK14 and Gria3 signaling pathways.
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Affiliation(s)
- Qiong Liu
- Department of Cardiovascular Medicine, XiangYa Hospital of Central South University, Changsha, Hunan Province, China
| | - Ning-Ning Sun
- Shenzhen Institute of Geriatrics, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong Province, China
| | - Zheng-Zhi Wu
- Shenzhen Institute of Geriatrics, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong Province, China
| | - Da-Hua Fan
- The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen; Chinese and Wsetern Integrative Medicine, Shcool of Medicine, Jinan University, Guangzhou, Guangdong Province, China
| | - Mei-Qun Cao
- Shenzhen Institute of Geriatrics, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong Province, China
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14
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Redhead M, Satchell R, McCarthy C, Pollack S, Unitt J. Thermal Shift as an Entropy-Driven Effect. Biochemistry 2017; 56:6187-6199. [DOI: 10.1021/acs.biochem.7b00860] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Martin Redhead
- Bioscience
Department, Sygnature Discovery, Nottingham NG1 1GF, U.K
| | - Rupert Satchell
- Bioscience
Department, Sygnature Discovery, Nottingham NG1 1GF, U.K
| | - Ciara McCarthy
- Bioscience
Department, Sygnature Discovery, Nottingham NG1 1GF, U.K
| | - Scott Pollack
- Bioscience
Department, Sygnature Discovery, Nottingham NG1 1GF, U.K
| | - John Unitt
- Bioscience
Department, Sygnature Discovery, Nottingham NG1 1GF, U.K
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15
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Klumpp M. Non-stoichiometric inhibition in integrated lead finding - a literature review. Expert Opin Drug Discov 2015; 11:149-62. [PMID: 26653534 DOI: 10.1517/17460441.2016.1128892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Non-stoichiometric inhibition summarizes different mechanisms by which low-molecular weight compounds can reproducibly inhibit high-throughput screening (HTS) and other lead finding assays without binding to a structurally defined site on their molecular target. This disqualifies such molecules from optimization by medicinal chemistry, and therefore their rapid elimination from screening hit lists is essential for productive and effective drug discovery. AREAS COVERED This review covers recent literature that either investigates the various mechanisms behind non-stoichiometric inhibition or suggests assays and readouts to identify them. In addition, combination of the various methods to distill promising molecules out of raw primary hit lists step-by-step is considered. Emerging technologies to demonstrate target engagement in cells are also discussed. EXPERT OPINION Over the last few years, awareness of non-stoichiometric inhibitors within screening libraries and HTS hit lists has considerably increased, not only in the pharmaceutical industry but also in the academic drug discovery community. This has resulted in a variety of methods to detect and handle such compounds. These range from in silico approaches to flag suspicious compounds, and counterassays to measure non-stoichiometric inhibition, to biophysical methods that positively demonstrate stoichiometric binding. In addition, novel technologies to verify target engagement within cells are becoming available. While still a time- and resource-consuming nuisance, non-stoichiometric inhibitors therefore do not fundamentally jeopardize the discovery of low molecular weight lead and drug candidates. Rather, they should be viewed as a manageable issue that with appropriate expertise can be overcome through integration of the above-mentioned approaches.
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Affiliation(s)
- Martin Klumpp
- a Novartis Institute of Biomedical Research Basel, Novartis Pharma AG , Basel , Switzerland
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16
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Abstract
Nonspecific bioactivity and assay artifacts have gained increasing attention in recent years. This focus has arisen primarily from the publication of a set of chemical substructures, termed pan assay interference compounds (PAINS), which are associated with promiscuous bioactivity and assay interference in real and virtual high-throughput screening (HTS) campaigns. Despite an increasing awareness in the HTS and medicinal chemistry communities about the liabilities of these compounds, articles featuring PAINS and PAINS-like compounds are still being published. In this perspective, we describe some of the factors we believe are driving this resource-sapping trend. We also provide what we hope are helpful insights that may lead to the earlier recognition of these generally nontranslatable compounds, thus preventing the propagation of PAINS-full costly research.
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Affiliation(s)
- Jayme L Dahlin
- 1 Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic College of Medicine , Rochester, Minnesota.,2 Medical Scientist Training Program, Mayo Clinic College of Medicine, Mayo Clinic College of Medicine , Rochester, Minnesota
| | - Michael A Walters
- 3 Institute for Therapeutics Discovery and Development, University of Minnesota , Minneapolis, Minnesota
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