Dimerization of the adaptor Gads facilitates antigen receptor signaling by promoting the cooperative binding of Gads to the adaptor LAT

The accurate assembly of signalosomes centered on the adaptor protein LAT (linker of activated T cells) is required for antigen receptor signaling in T cells and mast cells. During signalosome assembly, members of the growth factor receptor-bound protein 2 (Grb2) family of cytosolic adaptor proteins bind cooperatively to LAT through interactions with its phosphorylated tyrosine (pTyr) residues. We demonstrated the Src homology 2 (SH2) domain-mediated dimerization of the Grb2 family member, Grb2-related adaptor downstream of Shc (Gads). Gads dimerization was mediated by an SH2 domain interface, which is distinct from the pTyr binding pocket and which promoted cooperative, preferential binding of paired Gads to LAT. This SH2 domain-intrinsic mechanism of cooperativity, which we quantified by mathematical modeling, enabled Gads to discriminate between dually and singly phosphorylated LAT molecules. Mutational inactivation of the dimerization interface reduced cooperativity and abrogated Gads signaling in T cells and mast cells. The dimerization-dependent, cooperative binding of Gads to LAT may increase antigen receptor sensitivity by reducing signalosome formation at incompletely phosphorylated LAT molecules, thereby prioritizing the formation of complete signalosomes.

Abstract A24: ZAP-70 and SYK regulation in the B cell receptor pathway in chronic lymphocytic leukemia

Recent discoveries of inhibitors for Syk (spleen tyrosine kinase) family protein kinases provide promising therapeutic options for patients with chronic lymphocytic leukemia (CLL). However, molecular mechanisms of these inhibitors in the B cell receptor (BCR) signaling pathway are not well understood. This study investigates functionality of Syk family protein kinases and their inhibitors in the BCR signaling pathway in CLL cells. In this work, we tested several computational models of ZAP-70 (ζ chain–associated protein kinase of 70 kD) and SYK regulation in the BCR signaling pathway to explain the observed differences in the clinical behaviors of ZAP-70+ / ZAP-70- phenotypes of CLL patients. Specifically, we characterized the effects of different ZAP-70 and SYK expression and phosphorylation levels on the BCR activation threshold. Using stochastic simulations of BCR signaling network, we reproduced the correlations between the observed and calculated trends quantitatively. We find that an increased ZAP-70 expression is correlated with decreased levels of phosphorylated ZAP-70 and SYK, depending on the amount of SYK that is expressed in cells. Our calculations also show that ZAP-70 is able to compensate for a missing SYK functionality with an increased BCR activation threshold in SYK-deficient B-CLL cells, similar to SYK-deficient B cells. Furthermore, our computational model predicts a dual inhibition of ZAP-70 and SYK for the treatment of ZAP-70+ patients, as a selective inhibition of either ZAP-70 or SYK results in disease relapse. Our findings uncover molecular mechanisms of ZAP-70 and SYK regulation in the BCR signaling pathway for the development of CLL immunotherapies.

Citation Format: Maria P. Frushicheva. ZAP-70 and SYK regulation in the B cell receptor pathway in chronic lymphocytic leukemia. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A24.

Abstract B131: Quantitative modeling of Syk regulation in B cell chronic lymphocytic leukemia

Spleen tyrosine kinases (Syk) are initiators of B cell receptor-mediated (BCR) signaling events, enabling cells to drive chronic lymphocytic leukemia (CLL) progression. However, the mechanistic principles of biochemical signaling pathways that contribute to CLL pathogenesis are poorly understood. This study investigates Syk-mediated molecular pathways of the BCR signaling network using computational modeling. An expression of ζ chain-associated protein kinase of 70 kD (ZAP-70, Syk-family protein kinase) in the BCR signaling pathway is an adverse prognostic marker in CLL. Therefore, we need a better understanding of molecular mechanisms of Syk family protein kinases and effects of their inhibitors in the BCR signaling pathway. In this work, we dissected several computational models of ZAP-70 and SYK regulation to design an integrated mechanistic description of the BCR signaling pathway, and to explain the observed differences in the clinical behaviors of ZAP-70+ / ZAP-70- phenotypes of CLL patients. Specifically, we characterized the effects of different ZAP-70 and SYK expression and phosphorylation levels on the BCR activation threshold, using stochastic simulations of the BCR signaling network. Preliminary findings suggest that ZAP-70 serves as an adaptor protein that facilitates the recruitment of SYK to the BCR complex. We find that the expression of ZAP-70 enhances the BCR signaling, and therefore correlates with a more aggressive disease course. Our results will help in the development of novel therapies targeting Syk functions to regulate B-CLL responses.

Citation Format: Maria P. Frushicheva. Quantitative modeling of Syk regulation in B cell chronic lymphocytic leukemia [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr B131.

Abstract B039: In silico models for B cell receptor signaling in chronic lymphocytic leukemia

Recent discoveries of ZAP-70 (ζ chain–associated protein kinase of 70 kD) and Syk (spleen tyrosine kinase) inhibitors (gefitinib1 and fostamatinib2 respectively) provide promising therapeutic options for patients with chronic lymphocytic leukemia (CLL). However, the precise action of these inhibitors in the B cell receptor (BCR) signaling pathway is not well understood. This study designs an integrated mechanistic description of the BCR signaling pathway in CLL cells, and investigates the effects of possible inhibitors on this pathway. In this work, we examined several computational models of ZAP-70 and Syk regulation in the BCR signaling pathway to explain the observed differences in the clinical behaviors of ZAP+ / ZAP- phenotypes of B-CLL patients. Specifically, we characterized the effects of different ZAP-70 and Syk expression and phosphorylation levels on the BCR activation threshold. The correlations between the observed and calculated trends are reproduced quantitatively.

Our calculations show that depending on the amount of Syk that is expressed in cells, increased ZAP-70 expression is correlated with decreased levels of phosphorylated ZAP-70 and Syk, and vice versa. ZAP-70 and Syk phosphorylation occur independently, but is dependent on the amount of ZAP-70 and Syk that is expressed in cells. These results support reported experimental observations.3 We also find that ZAP-70 is able to compensate for a missing Syk functionality with an increased BCR activation threshold in Syk-deficient B-CLL cells, similar to Syk-deficient B cell study.4 In addition, we find that selective inhibition of either Syk or ZAP-70 will result in a disease relapse. This suggests the used of two inhibitors rather than one for the treatment of ZAP-70+ patients, based on our model. Lastly, we find that enhanced or reduced BCR signaling is observed at low amounts of Syk expression in CLL cells. However, this computational prediction needs to be verified experimentally in order to identify a viable physiological range of the amount of Syk that is expressed in B-CLL cells for ZAP-70+ and ZAP-70- phenotypes.

Our results uncover molecular mechanisms of ZAP-70 and Syk regulation in the BCR signaling pathway for its future therapeutic use in B-CLL. Our in silico network analysis will help in the development of immunotherapies targeting ZAP-70 and Syk functions to regulate B-CLL responses. Furthermore, our study provides information about responses to certain cancer therapies, and tumor progression.

References:

1 Dielschneider, R. F. et al. Cell Death Dis. 2014, 5 (10), e1439.

2 Friedberg, J. W. et al. Blood 2010, 115 (13), 2578.

3 Kaplan, D. et al. Cytometry B Clin. Cytom. 2010, 78 (2), 115.

4 Kong, G. H. et al. Immunity 1995, 2 (5), 485.

Citation Format: Maria P. Frushicheva, Arup K. Chakraborty. In silico models for B cell receptor signaling in chronic lymphocytic leukemia. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr B039.

The catalytic activity of the kinase ZAP-70 mediates basal signaling and negative feedback of the T cell receptor pathway

T cell activation by antigens binding to the T cell receptor (TCR) must be properly regulated to ensure normal T cell development and effective immune responses to pathogens and transformed cells while avoiding autoimmunity. The Src family kinase Lck and the Syk family kinase ZAP-70 (ζ chain-associated protein kinase of 70 kD) are sequentially activated in response to TCR engagement and serve as critical components of the TCR signaling machinery that leads to T cell activation. We performed a mass spectrometry-based phosphoproteomic study comparing the quantitative differences in the temporal dynamics of phosphorylation in stimulated and unstimulated T cells with or without inhibition of ZAP-70 catalytic activity. The data indicated that the kinase activity of ZAP-70 stimulates negative feedback pathways that target Lck and thereby modulate the phosphorylation patterns of the immunoreceptor tyrosine-based activation motifs (ITAMs) of the CD3 and ζ chain components of the TCR and of signaling molecules downstream of Lck, including ZAP-70. We developed a computational model that provides a mechanistic explanation for the experimental findings on ITAM phosphorylation in wild-type cells, ZAP-70-deficient cells, and cells with inhibited ZAP-70 catalytic activity. This model incorporated negative feedback regulation of Lck activity by the kinase activity of ZAP-70 and predicted the order in which tyrosines in the ITAMs of TCR ζ chains must be phosphorylated to be consistent with the experimental data.

Computer aided enzyme design and catalytic concepts

Gaining a deeper understanding of enzyme catalysis is of great practical and fundamental importance. Over the years it has become clear that despite advances made in experimental mutational studies, a quantitative understanding of enzyme catalysis will not be possible without the use of computer modeling approaches. While we believe that electrostatic preorganization is by far the most important catalytic factor, convincing the wider scientific community of this may require the demonstration of effective rational enzyme design. Here we make the point that the main current advances in enzyme design are basically advances in directed evolution and that computer aided enzyme design must involve approaches that can reproduce catalysis in well-defined test cases. Such an approach is provided by the empirical valence bond method.

Monovalent engagement of the BCR activates ovalbumin-specific transnuclear B cells

Monovalent engagement can trigger BCR signal transduction, and fine-tuning of BCR-ligand recognition can lead to B cell nonresponsiveness, activation, or inhibition.

Valency requirements for B cell activation upon antigen encounter are poorly understood. OB1 transnuclear B cells express an IgG1 B cell receptor (BCR) specific for ovalbumin (OVA), the epitope of which can be mimicked using short synthetic peptides to allow antigen-specific engagement of the BCR. By altering length and valency of epitope-bearing synthetic peptides, we examined the properties of ligands required for optimal OB1 B cell activation. Monovalent engagement of the BCR with an epitope-bearing 17-mer synthetic peptide readily activated OB1 B cells. Dimers of the minimal peptide epitope oriented in an N to N configuration were more stimulatory than their C to C counterparts. Although shorter length correlated with less activation, a monomeric 8-mer peptide epitope behaved as a weak agonist that blocked responses to cell-bound peptide antigen, a blockade which could not be reversed by CD40 ligation. The 8-mer not only delivered a suboptimal signal, which blocked subsequent responses to OVA, anti-IgG, and anti-kappa, but also competed for binding with OVA. Our results show that fine-tuning of BCR-ligand recognition can lead to B cell nonresponsiveness, activation, or inhibition.

Electrostatic origin of the catalytic effect of a supramolecular host catalyst

The development of enzyme mimetic catalysts as well as the analysis of the catalytic effects of such catalysts has been a major challenge for synthetic chemists. One of the impressive examples of artificial catalysts has been the development of a highly charged host compound that provides a significant acceleration to the hydrolysis of orthoformates and other systems. However, the origin of the catalytic effect has not been quantified, and its origin remains somewhat unclear. The understanding of the corresponding supramolecular catalysis has thus become a major challenge, both in terms of computational modeling and in terms of the analysis of the corresponding acid-catalyzed reaction. Here we present a computer simulation study and kinetic analyses that reproduce the experimentally observed catalytic effect, establishing that this effect is due to electrostatic stabilization of the positively charged transition state (relative to the uncharged bound complex). Our study illustrates the crucial need for careful analysis of the complex kinetics of the catalytic effect and the host system, as well as the need for computational modeling in analyzing the catalytic effect and in the potential design of better catalysts. Finally, our finding of the large stabilization of the bound H(3)O(+) points out the very low "local pH" inside the host system even when the solvent is kept at a high pH.

Validating the vitality strategy for fighting drug resistance

The current challenge in designing effective drugs against HIV-1 is to find novel candidates with high potency, but with a lower susceptibility to mutations associated with drug resistance. Trying to address this challenge, we developed in our previous study (Ishikita and Warshel, Angew Chem Int Ed Engl 2008; 47:697-700) a novel computational strategy for fighting drug resistance by predicting the likely moves of the virus through constraints on binding and catalysis. This has been based on calculating the ratio between the vitality values ((K(i) k(cat)/K(M))(mutant)/(K(i) k(cat)/K(M))(wild-type)) and using it as a guide for predicting the moves of the virus. The corresponding calculations of the binding affinity, K(i), were carried out using the semi-macroscopic version of the protein dipole Langevin dipole (PDLD/S) in its linear response approximation (LRA) in its β version (PDLD/S-LRA/β). We also calculate the proteolytic efficiency, k(cat)/K(M), by evaluating the transition state (TS) binding free energies using the PDLD/S-LRA/β method. Here we provide an extensive validation of our strategy by calculating the vitality of six existing clinical and experimental drug candidates. It is found that the computationally determined vitalities correlate reasonably well with those derived from the corresponding experimental data. This indicates that the calculated vitality may be used to identify mutations that would be most effective for the survival of the virus. Thus, it should be possible to use our approach in screening for mutations that would provide the most effective resistance to any proposed antiviral drug. This ability should be very useful in guiding the design of drug molecules that will lead to the slowest resistance.

Towards quantitative computer-aided studies of enzymatic enantioselectivity: the case of Candida antarctica lipase A

The prospect for consistent computer-aided refinement of stereoselective enzymes is explored by simulating the hydrolysis of enantiomers of an α-substituted ester by wild-type and mutant Candida antarctica lipase A, using several strategies. In particular, we focused on the use of the empirical valence bond (EVB) method in a quantitative screening for enantioselectivity, and evaluate both k(cat) and k(cat)/K(M) of the R and S stereoisomers. We found that an extensive sampling is essential for obtaining converging results. This requirement points towards possible problems with approaches that use a limited conformational sampling. However, performing the proper sampling appears to give encouraging results and to offer a powerful tool for the computer-aided design of enantioselective enzymes. We also explore faster strategies for identifying mutations that will help in augmenting directed-evolution experiments, but these approaches require further refinement.

Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis

One of the fundamental challenges in biotechnology and biochemistry is the ability to design effective enzymes. Despite recent progress, most of the advances on this front have been made by placing the reacting fragments in the proper places, rather than by optimizing the preorganization of the environment, which is the key factor in enzyme catalysis. Thus, rational improvement of the preorganization would require approaches capable of evaluating reliably the actual catalytic effect. This work considers the catalytic effects in different Kemp eliminases as a benchmark for a computer-aided enzyme design. It is shown that the empirical valence bond provides a powerful screening tool, with significant advantages over current alternative strategies. The insights provided by the empirical valence bond calculations are discussed with an emphasis on the ability to analyze the difference between the linear free energy relationships obtained in solution and those found in the enzymes. We also point out the trade-off between the reliability and speed of the calculations and try to determine what it takes to realize reliable computer-aided screening.