1
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Kumar V, Peter JJ, Sagar A, Ray A, Jha MP, Rebeaud ME, Tiwari S, Goloubinoff P, Ashish F, Mapa K. Interdomain communication suppressing high intrinsic ATPase activity of Sse1 is essential for its co-disaggregase activity with Ssa1. FEBS J 2019; 287:671-694. [PMID: 31423733 DOI: 10.1111/febs.15045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/08/2019] [Accepted: 08/16/2019] [Indexed: 01/19/2023]
Abstract
In eukaryotes, Hsp110s are unambiguous cognates of the Hsp70 chaperones, in primary sequence, domain organization, and structure. Hsp110s function as nucleotide exchange factors (NEFs) for the Hsp70s although their apparent loss of Hsp70-like chaperone activity, nature of interdomain communication, and breadth of domain functions are still puzzling. Here, by combining single-molecule FRET, small angle X-ray scattering measurements (SAXS), and MD simulation, we show that yeast Hsp110, Sse1 lacks canonical Hsp70-like interdomain allostery. However, the protein exhibits unique noncanonical conformational changes within its domains. Sse1 maintains an open-lid substrate-binding domain (SBD) in close contact with its nucleotide-binding domain (NBD), irrespective of its ATP hydrolysis status. To further appreciate such ATP-hydrolysis-independent exhaustive interaction between two domains of Hsp110s, NBD-SBD chimera was constructed between Hsp110 (Sse1) and Hsp70 (Ssa1). In Sse1/Ssa1 chimera, we observed undocking of two domains leading to complete loss of NEF activity of Sse1. Interestingly, chimeric proteins exhibited significantly enhanced ATPase rate of Sse1-NBD compared to wild-type protein, implying that intrinsic ATPase activity of the protein remains mostly repressed. Apart from repressing the high ATPase activity of its NBD, interactions between two domains confer thermal stability to Sse1 and play critical role in the (co)chaperoning function of Sse1 in Ssa1-mediated disaggregation activity. Altogether, Sse1 exhibits a unique interdomain interaction, which is essential for its NEF activity, suppression of high intrinsic ATPase activity, co-chaperoning activity in disaggregase machinery, and stability of the protein.
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Affiliation(s)
- Vignesh Kumar
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSir), CSIR-HRDC, Ghaziabad, India
| | - Joshua Jebakumar Peter
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Amin Sagar
- CSIR-Institute of Microbial Technology, Chandigarh, Uttar Pradesh, India
| | - Arjun Ray
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSir), CSIR-HRDC, Ghaziabad, India
| | - Mainak Pratim Jha
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Mathieu E Rebeaud
- Department of Plant Molecular Biology, University of Lausanne, Switzerland
| | - Satyam Tiwari
- Department of Plant Molecular Biology, University of Lausanne, Switzerland
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, University of Lausanne, Switzerland
| | - Fnu Ashish
- CSIR-Institute of Microbial Technology, Chandigarh, Uttar Pradesh, India
| | - Koyeli Mapa
- Academy of Scientific and Innovative Research (AcSir), CSIR-HRDC, Ghaziabad, India.,Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
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2
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Structure-affinity properties of a high-affinity ligand of FKBP12 studied by molecular simulations of a binding intermediate. PLoS One 2014; 9:e114610. [PMID: 25502559 PMCID: PMC4264844 DOI: 10.1371/journal.pone.0114610] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/10/2014] [Indexed: 11/19/2022] Open
Abstract
With a view to explaining the structure-affinity properties of the ligands of the protein FKBP12, we characterized a binding intermediate state between this protein and a high-affinity ligand. Indeed, the nature and extent of the intermolecular contacts developed in such a species may play a role on its stability and, hence, on the overall association rate. To find the binding intermediate, a molecular simulation protocol was used to unbind the ligand by gradually decreasing the biasing forces introduced. The intermediate was subsequently refined with 17 independent stochastic boundary molecular dynamics simulations that provide a consistent picture of the intermediate state. In this state, the core region of the ligand remains stable, notably because of the two anchoring oxygen atoms that correspond to recurrent motifs found in all FKBP12 ligand core structures. Besides, the non-core regions participate in numerous transient intermolecular and intramolecular contacts. The dynamic aspect of most of the contacts seems important both for the ligand to retain at least a part of its configurational entropy and for avoiding a trapped state along the binding pathway. Since the transient and anchoring contacts contribute to increasing the stability of the intermediate, as a corollary, the dissociation rate constant of this intermediate should be decreased, resulting in an increase of the affinity constant . The present results support our previous conclusions and provide a coherent rationale for explaining the prevalence in high-affinity ligands of (i) the two oxygen atoms found in carbonyl or sulfonyl groups of dissimilar core structures and of (ii) symmetric or pseudo-symmetric mobile groups of atoms found as non-core moieties. Another interesting aspect of the intermediate is the distortion of the flexible 80 s loop of the protein, mainly in its tip region, that promotes the accessibility to the bound state.
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3
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Maciejewski A, Pasenkiewicz-Gierula M, Cramariuc O, Vattulainen I, Rog T. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration. J Phys Chem B 2014; 118:4571-81. [PMID: 24745688 DOI: 10.1021/jp5016627] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM).
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Affiliation(s)
- Arkadiusz Maciejewski
- Department of Physics, Tampere University of Technology , PO Box 692, FI-33101 Tampere, Finland
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4
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Procacci P, Bizzarri M, Marsili S. Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations. J Chem Theory Comput 2013; 10:439-50. [DOI: 10.1021/ct400809n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Piero Procacci
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Marco Bizzarri
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Simone Marsili
- Centro Nacional de Investigaciones Oncologicas, Calle de Melchor Fernández Almagro, 3, E-28029 Madrid, Spain
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5
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General IJ, Meirovitch H. Absolute Free Energy of Binding and Entropy of the FKBP12-FK506 Complex: Effects of the Force Field. J Chem Theory Comput 2013; 9:4609-19. [PMID: 26589173 DOI: 10.1021/ct400484u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hypothetical scanning molecular dynamics (HSMD) method combined with thermodynamic integration (HSMD-TI) has been extended recently for calculating ΔA(0)-the absolute free energy of binding of a ligand to a protein. With HSMD-TI, ΔA(0) is obtained in a new way as a sum of several components, among them is ΔSligand-the change in the conformational entropy as the ligand is transferred from the bulk solvent to the active site-this entropy is obtained by a specific reconstruction procedure. This unique aspect of HSMD (which is useful in rational drug design) is in particular important for treating large ligands, where ΔSligand might be significant. Technically, one should verify that the results for ΔSligand converge-a property that might become more difficult for large ligands; therefore, studying ligands of increasing size would define the range of applicability of HSMD-TI for binding. In this paper, we check the performance of HSMD-TI by applying it to the relatively large ligand FK506 (126 atoms) complexed with the protein FKBP12, where ΔA(0) = -12.8 kcal/mol is known experimentally as well as the crystal structure of the complex. This structure was initially equilibrated by carrying out a 100 ns molecular dynamics trajectory, where the system is modeled by the AMBER force field, TIP3P water, and Particle Mesh Ewald. HSMD-TI calculations were carried out in three conformational regions defined by the intervals [0.2,2], [2,5], and [5,100] ns along the trajectory, where local equilibration of the total energy has been observed; we obtained ΔA(0) = -13.6 ± 1.1, -16.6 ± 1.4, and -16.7 ± 1.4 kcal/mol, respectively indicating the following: (1) The second and third regions belong to the same conformational subspace of the complex, which is different from the [0.2,2] ns subspace. (2) The unsatisfactory result for ΔA(0) obtained in the well equilibrated (hence theoretically preferred) latter regions reflects the nonperfect modeling used, which however (3) has led to the experimental ΔA(0) in the [0.2,2] ns region close to the crystal structure. Keeping the complex near its crystal structure has been a successful approach in the literature. To check this avenue further, we applied harmonic restraints on backbone atoms and obtained unsatisfactory results for ΔA(0), suggesting that implementation of this approach is not straightforward. Converging results for ΔSligand were obtained in all regions, where the result ΔSligand([0.2,2]) = 7.1 ± 1.2 kcal/mol is less region dependent than ΔA(0) and is relatively large probably due to the large ligand.
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Affiliation(s)
- Ignacio J General
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , 3059 BST3, Pittsburgh, Pennsylvania 15260, United States
| | - Hagai Meirovitch
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , 3059 BST3, Pittsburgh, Pennsylvania 15260, United States.,Department of Physics, Bar-Ilan University , Ramat Gan, 52900, Israel
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6
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Bizzarri M, Marsili S, Procacci P. Intraligand Hydrophobic Interactions Rationalize Drug Affinities for Peptidyl−Prolyl Cis−Trans Isomerase Protein. J Phys Chem B 2011; 115:6193-201. [DOI: 10.1021/jp110585p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Bizzarri
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Simone Marsili
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Piero Procacci
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
- Centro Interdipartimentale per lo Studio delle Dinamiche Complesse (CSDC), Via Sansone 1, I-50019 Sesto Fiorentino, Italy
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7
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Olivieri L, Gardebien F. Molecular Dynamics Simulations of a Binding Intermediate between FKBP12 and a High-Affinity Ligand. J Chem Theory Comput 2011; 7:725-41. [DOI: 10.1021/ct100394d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lilian Olivieri
- DSIMB, INSERM, U665, Paris, F-75015, France, DSIMB, INSERM, U665, Faculté des Sciences et Technologies, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France, INTS, Paris, F-75015, France, and Laboratoire de Biochimie et Génétique Moléculaire, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France
| | - Fabrice Gardebien
- DSIMB, INSERM, U665, Paris, F-75015, France, DSIMB, INSERM, U665, Faculté des Sciences et Technologies, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France, INTS, Paris, F-75015, France, and Laboratoire de Biochimie et Génétique Moléculaire, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France
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8
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Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125939.ch4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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9
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Shirts MR, Mobley DL, Chodera JD. Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time? ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1016/s1574-1400(07)03004-6] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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10
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Jayachandran G, Shirts MR, Park S, Pande VS. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. J Chem Phys 2006; 125:084901. [PMID: 16965051 DOI: 10.1063/1.2221680] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a technique for biomolecular free energy calculations that exploits highly parallelized sampling to significantly reduce the time to results. The technique combines free energies for multiple, nonoverlapping configurational macrostates and is naturally suited to distributed computing. We describe a methodology that uses this technique with docking, molecular dynamics, and free energy perturbation to compute absolute free energies of binding quickly compared to previous methods. The method does not require a priori knowledge of the binding pose as long as the docking technique used can generate reasonable binding modes. We demonstrate the method on the protein FKBP12 and eight of its inhibitors.
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Affiliation(s)
- Guha Jayachandran
- Computer Science Department, Stanford University, Stanford, CA 94305, USA
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11
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Xu Y, Wang R. A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method. Proteins 2006; 64:1058-68. [PMID: 16838311 DOI: 10.1002/prot.21044] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The FK506-binding proteins have been targets of pharmaceutical interests over years. We have studied the binding of a set of 12 nonimmunosuppressive small-molecule inhibitors to FKBP12 through molecular dynamics simulations. Each complex was subjected to 1-ns MD simulation conducted in an explicit solvent environment under constant temperature and pressure. The binding free energy of each complex was then computed by the MM-PB/SA method in the AMBER program. Our MM-PB/SA computation produced a good correlation between the experimentally determined and the computed binding free energies with a correlation coefficient (R(2)) of 0.93 and a standard deviation as low as 0.30 kcal/mol. The vibrational entropy term given by the normal mode analysis was found to be helpful for achieving this correlation. Moreover, an adjustment to one weight factor in the PB/SA model was essential to correct the absolute values of the final binding free energies to a reasonable range. A head-to-head comparison of our MM-PB/SA model with a previously reported Linear Response Approximation (LRA) model suggested that the MM-PB/SA method is more robust in binding affinity prediction for this class of compounds.
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Affiliation(s)
- Yong Xu
- State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, People's Republic of China
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12
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Leitgeb M, Schröder C, Boresch S. Alchemical free energy calculations and multiple conformational substates. J Chem Phys 2006; 122:84109. [PMID: 15836022 DOI: 10.1063/1.1850900] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Thermodynamic integration (TI) was combined with (adaptive) umbrella sampling to improve the convergence of alchemical free energy simulations in which multiple conformational substates are present. The approach, which we refer to as non-Boltzmann TI (NBTI), was tested by computing the free energy differences between three five-atomic model systems, as well as the free energy difference of solvation between leucine and asparagine. In both cases regular TI failed to give converged results, whereas the NBTI results were free from hysteresis and had standard deviations well below +/-0.7 kcal/mole. We also present theoretical considerations that make it possible to compute free energy differences between simple molecules, such as the five-atomic model systems, by numerical integration of the partition functions at the respective end points.
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Affiliation(s)
- Martin Leitgeb
- Department of Biomolecular Structural Chemistry, Biomolecular Simulation Group, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
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13
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Jorgensen WL, Tirado-Rives J. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. J Comput Chem 2005; 26:1689-700. [PMID: 16200637 DOI: 10.1002/jcc.20297] [Citation(s) in RCA: 314] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An overview is provided of the capabilities for the current versions of the BOSS and MCPRO programs for molecular modeling of organic and biomolecular systems. Recent applications are noted, particularly for QM/MM studies of organic and enzymatic reactions and for protein-ligand binding.
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14
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Smith MBK, Ruby S, Horouzhenko S, Buckingham B, Richardson J, Puleri I, Potts E, Jorgensen WL, Arnold E, Zhang W, Hughes SH, Michejda CJ, Smith RH. HIV-1 reverse transcriptase variants: molecular modeling of Y181C, V106A, L100I, and K103N mutations with nonnucleoside inhibitors using Monte Carlo simulations in combination with a linear response method. ACTA ACUST UNITED AC 2004; 18:151-63. [PMID: 15553926 DOI: 10.3109/10559610390484203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The energies and physical descriptors for the binding of 21 novel 1-(2,6-difluorobenzyl)-2-(2,6-difluorophenyl)-benzimidazole (BPBI) analogs to HIV-1 reverse transcriptase (RT) variants Y181C, L100I, V106A, and K103N have been determined using Monte Carlo (MC) simulations. The crystallographic structure of the lead compound, 4-methyl BPBI, was used as a starting point to model the inhibitors in both the mutant bound and the unbound states. The energy terms and physical descriptors obtained from the calculations were reasonably correlated with the respective experimental EC50 values for the inhibitors against the various mutant RTs. Using the linear response correlations from the calculations, 2 novel BPBI inhibitors have been designed and simulations have been carried out. The results show the computed deltaG(binding) values match the experimental data for the analogs. Given the ongoing problem with drug resistance, the ability to predict the activity of novel analogs against variants prior to synthesis is highly advantageous.
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15
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Wissner A, Hamann PR, Nilakantan R, Greenberger LM, Ye F, Rapuano TA, Loganzo F. Syntheses and EGFR kinase inhibitory activity of 6-substituted-4-anilino [1,7] and [1,8] naphthyridine-3-carbonitriles. Bioorg Med Chem Lett 2004; 14:1411-6. [PMID: 15006373 DOI: 10.1016/j.bmcl.2004.01.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2003] [Accepted: 01/15/2004] [Indexed: 10/26/2022]
Abstract
The syntheses and EGFR kinase inhibitory activity of a series of 6-substituted-4-anilino [1,7] and [1,8] naphthyridine-3-carbonitriles are described. Both reversible and irreversible binding inhibitors were prepared. These series were compared with each other and with the corresponding 4-anilinoquinoline-3-carbonitriles. Compounds having a 1,7-naphthyridine core structure can retain high potency while those with a 1,8-naphthyridine core are significantly less active. These results are consistent with molecular modeling observations.
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Affiliation(s)
- Allan Wissner
- Chemical and Screening Sciences and Oncology Research, Wyeth Research, 401N. Middletown Road, Pearl River, NY 10965, USA.
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16
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Affiliation(s)
- A A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
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17
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Orozco M, Luque FJ. Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems. Chem Rev 2000; 100:4187-4226. [PMID: 11749344 DOI: 10.1021/cr990052a] [Citation(s) in RCA: 454] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franqués 1, E-08028 Barcelona, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda. Diagonal s/n, E-08028 Barcelona, Spain
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18
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Sich C, Improta S, Cowley DJ, Guenet C, Merly JP, Teufel M, Saudek V. Solution structure of a neurotrophic ligand bound to FKBP12 and its effects on protein dynamics. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:5342-55. [PMID: 10951192 DOI: 10.1046/j.1432-1327.2000.01551.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The structure of a recently reported neurotrophic ligand, 3-(3-pyridyl)-1-propyl(2S)-1-(3,3-dimethyl-1, 2-dioxopentyl)-2-pyrrolidinecarboxylate, in complex with FKBP12 was determined using heteronuclear NMR spectroscopy. The inhibitor exhibits a binding mode analogous to that observed for the macrocycle FK506, used widely as an immunosuppressant, with the prolyl ring replacing the pipecolyl moiety and the amide bond in a trans conformation. However, fewer favourable protein-ligand interactions are detected in the structure of the complex, suggesting weaker binding compared with the immunosuppressant drug. Indeed, a micromolar dissociation constant was estimated from the NMR ligand titration profile, in contrast to the previously published nanomolar inhibition activity. Although the inhibitor possesses a remarkable structural simplicity with respect to FK506, 15N relaxation studies show that it induces similar effects on the protein dynamics, stabilizing the conformation of solvent-exposed residues which are important for mediating the interaction of immunophilin/ligand complexes with molecular targets and potentially for the transmission of the neurotrophic action of FKBP12 inhibitors.
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Affiliation(s)
- C Sich
- Department of Structural Biology and Cheminformatics, Department of Biotechnology, Sanofi-Synthelabo, Strasbourg, France
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19
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Kahn K, Bruice TC. Alpha-ketoamides and alpha-ketocarbonyls: conformational analysis and development of all-atom OPLS force field. Bioorg Med Chem 2000; 8:1881-91. [PMID: 11003132 DOI: 10.1016/s0968-0896(00)00122-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The molecular structures and barriers for the internal rotation around the OC-CO single bond in four alpha-ketoamides and eight alpha-ketocarbonyls have been determined from the MP3/aug-cc-pVDZ and MP2/aug-cc-pVDZ calculations. Alpha-ketocarbonyls with non-bulky substituents adopt planar conformations with two carbonyl oxygens in s-trans arrangement. The s-cis conformation is significantly less stable due to the electrostatic repulsion between the two carbonyl groups. Primary and secondary alpha-ketoamides are planar when the substituent at the carbonyl carbon is hydrogen or methyl group but tertiary alpha-ketoamides adopt a conformation where the OC-CO unit is significantly bent. Based on current ab initio structural data, a set of OPLS-AA force field parameters has been derived. These parameters can be used for the modeling of a variety of alpha-ketoamide or alpha-ketocarbonyl containing drugs such as novel protease inhibitors or neuroregenerative polyketides.
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Affiliation(s)
- K Kahn
- Department of Chemistry and Biochemistry, University of California-Santa Barbara, 93106, USA
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20
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Smith MB, Lamb ML, Tirado-Rives J, Jorgensen WL, Michejda CJ, Ruby SK, Smith RH. Monte Carlo calculations on HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor 8-Cl TIBO: contribution of the L100I and Y181C variants to protein stability and biological activity. PROTEIN ENGINEERING 2000; 13:413-21. [PMID: 10877852 DOI: 10.1093/protein/13.6.413] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A computational model of the non-nucleoside inhibitor 8-Cl TIBO complexed with HIV-1 reverse transcriptase (RT) was constructed in order to determine the binding free energies. Using Monte Carlo simulations, both free energy perturbation and linear response calculations were carried out for the transformation of wild-type RT to two key mutants, Y181C and L100I. The newer linear response method estimates binding free energies based on changes in electrostatic and van der Waals energies and solvent-accessible surface areas. In addition, the change in stability of the protein between the folded and unfolded states was estimated for each of these mutations, which are known to emerge upon treatment with the inhibitor. Results from the calculations revealed that there is a large hydrophobic contribution to protein stability in the native, folded state. The calculated absolute free energies of binding from both the linear response, and also the more rigorous free energy perturbation method, gave excellent agreement with the experimental differences in activity. The success of the relatively rapid linear response method in predicting experimental activities holds promise for estimating the activity of the inhibitors not only against the wild-type RT, but also against key protein variants whose emergence undermines the efficacy of the drugs.
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Affiliation(s)
- M B Smith
- National Cancer Institute-FCRDC, P.O. Box B, Frederick, MD 21702, USA
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Abstract
The large enzyme families of protein disulfide isomerases and peptidyl prolyl cis/trans isomerases have been shown to assist polypeptide restructuring. Various folding states of polypeptides may serve as substrates of the catalysed reaction. Our understanding of the cellular function of these enzymes is increasing as a result of the availability of more specific inhibitors, the discovery of natural substrates and the use of genetically modified organisms. Further highlights of these studies include insights into the three-dimensional structures of enzyme-ligand complexes, as well as into the mechanism of slow folding phases on the atomic level.
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Affiliation(s)
- C Schiene
- Research Unit Enzymology of Protein Folding, Max-Planck Society, Halle/Saale, D-06120, Germany
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22
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Qian Y, Marugan JJ, Fossum RD, Vogt A, Sebti SM, Hamilton AD. Probing the hydrophobic pocket of farnesyltransferase: aromatic substitution of CAAX peptidomimetics leads to highly potent inhibitors. Bioorg Med Chem 1999; 7:3011-24. [PMID: 10658608 DOI: 10.1016/s0968-0896(99)00252-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cysteine farnesylation at the carboxylate terminal tetrapeptide CAAX of Ras protein is catalyzed by farnesyltransferase. This lipid modification is necessary for regulatory function of both normal and oncogenic Ras. The high frequency of Ras mutation in human cancers has prompted an intensive study on finding ways of controlling oncogenic Ras function. Inhibition of farnesyltransferase is among the most sought after targets for cancer chemotherapy. We report here the design, synthesis and biological characterization of a series of peptidomimetics as farnesyltransferase inhibitors. These compounds are extremely potent towards farnesyltransferase with IC50 values ranging from subnanomolar to low nanomolar concentrations. They have a high selectivity for farnesyltransferase over the closely related geranylgeranyltransferase-I. Structure-activity relationship studies demonstrated that a properly positioned hydrophobic group significantly enhanced inhibition potency, reflecting an improved complementarity to the large hydrophobic pocket in the CAAX binding site.
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Affiliation(s)
- Y Qian
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
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23
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Lamb ML, Tirado-Rives J, Jorgensen WL. Estimation of the binding affinities of FKBP12 inhibitors using a linear response method. Bioorg Med Chem 1999; 7:851-60. [PMID: 10400338 DOI: 10.1016/s0968-0896(99)00015-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A series of non-immunosuppressive inhibitors of FK506 binding protein (FKBP12) are investigated using Monte Carlo statistical mechanics simulations. These small molecules may serve as scaffolds for chemical inducers of protein dimerization, and have recently been found to have FKBP12-dependent neurotrophic activity. A linear response model was developed for estimation of absolute binding free energies based on changes in electrostatic and van der Waals energies and solvent-accessible surface areas, which are accumulated during simulations of bound and unbound ligands. With average errors of 0.5 kcal/mol, this method provides a relatively rapid way to screen the binding of ligands while retaining the structural information content of more rigorous free energy calculations.
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Affiliation(s)
- M L Lamb
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
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