Sequence, Structure and Energetic Determinants of Phosphopeptide Selectivity of SH2 Domains

Sheinerman, Felix B.; Al‐Lazikani, Bissan; Honig, Barry

doi:10.1016/j.jmb.2003.09.075

Cited by 45 publications

(61 citation statements)

References 102 publications

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“…Although SH2 domains have been noted to have a high sequence similarity in their 100 amino acids (31,32), S3I-201 has preference for Stat3 in that at concentrations that inhibit Stat3, S3I-201 has a low effect on Stat1 and Stat5, no interaction with the Src family proteins, weak inhibition of Erk1/2 and Shc activation, and low toxicity to cells with no aberrant Stat3. Our study supports computational modeling application in structure-based virtual screening for identifying Stat3 inhibitors from chemical libraries, and together with another report (15) is among the first to identify Stat3 inhibitors by this approach.…”

Section: Discussionmentioning

confidence: 99%

Selective chemical probe inhibitor of Stat3, identified through structure-based virtual screening, induces antitumor activity

Siddiquee

Zhang

Guida

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

685

669

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P roteins of the STAT (signal transducer and activator of transcription) family are activated in response to cytokines and growth factors and promote proliferation, survival, and other biological processes (1-3). STATs are activated by phosphorylation of a critical tyrosine residue, which is mediated by growth factor receptor tyrosine kinases, Janus kinases, or the Src family kinases. Upon tyrosine phosphorylation, dimers of STATs formed between two phosphorylated monomers translocate to the nucleus, bind to specific DNA-response elements in the promoters of target genes, and induce gene expression. Aberrant activity of one of the family members, Stat3, contributes to carcinogenesis and tumor progression by up-regulating gene expression and promoting dysregulated growth, survival, and angiogenesis and modulating immune responses (2-9).As a critical step in STAT activation (10), the dimerization between two STAT monomers presents an attractive target to abolish Stat3 DNA-binding and transcriptional activity and to inhibit Stat3 biological functions (11, 12). Stat3 dimerization relies on the reciprocal binding of the SH2 domain of one monomer to the Pro-pTyr-Leu-Lys-Thr-Lys sequence of the other Stat3 monomer. To pursue the development of inhibitors of Stat3 signaling, key structural information gleaned from the x-ray crystal structure of the Stat3␤ homodimer (13) was used in the computational modeling and automated docking of small molecules into the SH2 domain of a Stat3 monomer, relative to the bound native pTyr peptide, to identify binders of the Stat3 SH2 domain, and potentially disruptors of Stat3⅐Stat3 dimers (14, 15).Structure-based high-throughput virtual screening of the National Cancer Institute (NCI) chemical libraries identified the high-scoring compound NSC 74859 (resynthesized as a pure sample and named S3I-201), which selectively inhibits Stat3 DNA-binding activity in vitro with an IC 50 value of 86 Ϯ 33 M. Furthermore, S3I-201 induces growth inhibition and apoptosis of malignant cells in part by constitutively inhibiting active Stat3 and induces human breast tumor regression in xenograft models. ResultsComputational Modeling and Virtual Screening. Our computational modeling and virtual screening study used the GLIDE (Grid-based Ligand Docking from Energetics) software (16, 17) (available from Schrödinger, Portland, OR) for the docking simulations and relied on the x-ray crystal structure of the Stat3␤ homodimer bound to DNA (13) determined at 2.25-Å resolution (1BG1 in the Protein Data Bank). For the virtual screening, DNA was removed and only one of the two monomers was used (see Fig. 1). To validate the docking approach, the native pTyr (pY) peptide, APpYLKT, was extracted from the crystal structure of one of the monomers and docked to the other monomer, whereby GLIDE produced a docking mode that closely resembled the x-ray crystal structure (data not shown). Three-dimensional structures of compounds from the NCI's chemical libraries were downloaded from the NCI Developmental Therapeutics Progra...

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Section: Discussionmentioning

confidence: 99%

Selective chemical probe inhibitor of Stat3, identified through structure-based virtual screening, induces antitumor activity

Siddiquee

Zhang

Guida

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

685

669

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“…These values correspond to an absolute binding free energy in the range of approximately Ϫ8 kcal͞mol. The determinants of the phosphopeptide selectivity of SH2 domains have been characterized previously by using various empirical approaches (22,26,27).Our ability to understand many aspects concerning the specificity of SH2 domains for phosphotyrosyl peptides of particular sequences would benefit from all-atom MD͞FEP computations, although a straightforward application of current approaches appears to be problematic for a number of reasons. First, the sheer magnitude of the electrostatics interactions arising from the doubly charged phosphotyrosine side chain (28) suggests that the standard FEP technique used to compute absolute binding free energies, which consists of reversibly decoupling the ligand from its surrounding (12-17), is essentially impractical.…”

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confidence: 99%

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confidence: 99%

“…SH2 domains are highly conserved noncatalytic proteins of Ϸ100-aa residues, which can bind phosphotyrosine-containing polypeptide sequences with high affinity and specificity. They are found in a wide variety of intracellular signal transduction pathways involving tyrosine kinases (18)(19)(20)(21)(22), and inappropriate cellular signaling caused by malfunctions of SH2-mediated process has been linked to many pathologic conditions (e.g., cancer, autoimmune diseases, asthma, allergies, etc.). SH2 domains are highly selective toward the sequence phosphotyrosine-Glu-Glu-Ile (pYEEI) (23), with dissociation constants ranging from micromolar to nanomolar ranges (19,24; for a review, see ref.…”

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confidence: 99%

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Calculation of absolute protein–ligand binding free energy from computer simulations

Woo

Roux²

2005

Proc. Natl. Acad. Sci. U.S.A.

634

896

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A general methodology for calculating the equilibrium binding constant of a flexible ligand to a protein receptor is formulated on the basis of potentials of mean force. The overall process is decomposed into several stages that can be computed separately: the free ligand in the bulk is first restrained into the conformation it adopts in the bound state, position, and orientation by applying biasing potentials, then it is translated into the binding site, where it is released completely. The conformational restraining potential is based on the root-mean-square deviation of the peptide coordinates relative to its average conformation in the bound complex. Free energy contributions from each stage are calculated by means of free energy perturbation potential of mean force techniques by using appropriate order parameters. The present approach avoids the need to decouple the ligand from its surrounding (bulk solvent and receptor protein) as is traditionally performed in the doubledecoupling scheme. It is believed that the present formulation will be particularly useful when the solvation free energy of the ligand is very large. As an application, the equilibrium binding constant of the phosphotyrosine peptide pYEEI to the Src homology 2 domain of human Lck has been calculated. The results are in good agreement with experimental values. Approaches at different levels of complexity and sophistication have been used to calculate binding free energies in complex biomolecular systems. Screening of large molecular databases of compounds to identify potential lead drug molecules typically relies on very simplified scoring schemes to achieve the needed efficiency (6). The binding free energy may be estimated on the basis of a continuum solvent approximation assuming quadratic fluctuations around a unique configuration (7,8). The Molecular Mechanics͞ Poisson-Boltzmann (PB) and Surface Area (MM͞PB-SA) method is a popular approach that relies on a mixed scheme combining configurations sampled from molecular dynamics (MD) simulations with explicit solvent, together with free energy estimators based on an implicit continuum solvent model (9). MM͞PB-SA shares some similarities with the linear interaction energy method, which also uses averages calculated from explicit solvent simulations within a linear response framework (10). Despite their usefulness, such approximate schemes can be limited, and how to improve the results is unclear because they do not offer a rigorous route to compute the equilibrium binding constant.In principle, treatments based on MD free energy perturbation (FEP) simulations with explicit solvent molecules offer the most powerful and promising approach to estimate the binding free energies of ligands to macromolecules (11). Nonetheless, although previous studies have provided many of the fundamental elements necessary for the calculation of binding free energy by means of MD (12-17), the computations so far have been limited mostly to fairly small and rigid ligands [e.g., rare gas atom (12, 15), water (14)...

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“…On the other hand, a multiple structural alignment is a form of sequence alignment based on comparison of shape. Multiple structural alignments has been proven to be helpfulin protein structure classification and structure-based functionprediction by highlighting structurally conserved regions of functional significance as well as selectivity determinants [12,13]. Examples of most current multiple structural alignment softwares include CAALIGN [14], Vorolign [15], Matt [16] and POSA [17].…”

Section: Introductionmentioning

confidence: 99%

An Optimal Mesh Algorithm for Remote Protein Homology Detection

Abdullah

Othman

Kasim

et al. 2011

Communications in Computer and Information Science

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Sequence, Structure and Energetic Determinants of Phosphopeptide Selectivity of SH2 Domains

Cited by 45 publications

References 102 publications

Selective chemical probe inhibitor of Stat3, identified through structure-based virtual screening, induces antitumor activity

Selective chemical probe inhibitor of Stat3, identified through structure-based virtual screening, induces antitumor activity

Calculation of absolute protein–ligand binding free energy from computer simulations

An Optimal Mesh Algorithm for Remote Protein Homology Detection

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