Signal Transducer and Activator of Transcription 3 (STAT3) plays a crucial role in cancer development and thus is a viable target for cancer treatment. STAT3 functions as a dimer mediated by phosphorylation of the SRC-homology 2 (SH2) domain, a key target for therapeutic drugs. While great efforts have been employed towards the development of compounds that directly target the SH2 domain, no compound has yet been approved by the FDA due to a lack of specificity and pharmacologic efficacy. Studies have shown that allosteric regulation of SH2 via the coiled-coil domain (CCD) is an alternative drug design strategy. Several CCD effectors have been shown to modulate SH2 binding and affinity, and at the time of writing at least one drug candidate has entered phase I clinical trials. However, the mechanism for SH2 regulation via CCD is poorly understood. Here, we investigate structural and dynamic features of STAT3 and compare the wild type to the reduced function variant D170A in order to delineate mechanistic differences and propose allosteric pathways. Molecular dynamics simulations were employed to explore conformational space of STAT3 and the variant, followed by structural, conformation, and dynamic analysis. The trajectories explored show distinctive conformational changes in the SH2 domain for the D170A variant, indicating long range allosteric effects. Multiple analyses provide evidence for long range communication pathways between the two STAT3 domains, which seem to be mediated by a rigid core which connects the CCD and SH2 domains via the linker domain (LD) and transmits conformational changes through a network of short-range interactions. The proposed allosteric mechanism provides new insight into the understanding of intramolecular signaling in STAT3 and potential pharmaceutical control of STAT3 specificity and activity. In all living organisms, the proliferation and survival of cells are regulated by various proteins. Signal Transducers and Activators of Transcription 3 (STAT3) protein is one of these important proteins. However, the abnormal regulation of these proteins will contribute to the proliferation of cancer. The constitutive activation of STAT3 has been linked to several types of solid tumors, leukemia, and lymphomas. Consequently, STAT3 proteins have been a key target for cancer therapy. SH2 (SRC-homology 2) domain is the key interaction site, great efforts have been made to target SH2 domain. However, specificity has been a major challenge in drug discovery. Research showing regulation of SH2 domain via CCD (coiled-coil domain) has opened a new path for drug discovery, but progress is challenged by poor understanding of the allosteric mechanism. Here, we show that CCD regulates SH2 conformation via a rigid backbone. The perturbations in CCD are transmitted through an α-helix to the rigid core that orchestrate the movement of CCD and LD (link domain), leading to structural changes in the SH2 domain. The present findings provide an allosteric mechanism with atomistic details underlying the regulation of CCD to SH2 domain in STAT3 protein. A detailed allosteric pathway allows informed drug design targeting CCD for desired downstream effect on SH2 domain and the overall STAT3 function.

Equation-of-motion coupled-cluster theory with single and double excitations (EOM-CCSD) provides a robust framework for describing a wide range of electronically excited and open-shell states. Among its various formulations, the double electron-attachment (EOM-DEA-CCSD) and double ionization potential (EOM-DIP-CCSD) methods are particularly effective for treating diradicals and other types of open-shell species. To enable accurate geometry optimizations and property calculations, we present the derivation and implementation of analytic nuclear gradients for EOM-DEA-CCSD and EOM-DIP-CCSD. These new capabilities were illustrated by calculations of singlet–triplet gaps in benzyne diradicals as well as characterization of molecules relevant to quantum information science. We further extended the framework to include spin–orbit coupling calculations for EOM-DEA-CCSD states, allowing calculations of intensity borrowing and intersystem crossings.

Obtaining sub-chemical accuracy (1 kJ mol−1) for reaction energies of medium-sized gas-phase molecules is a longstanding challenge in the field of thermochemical modeling. The perturbative triples correction to coupled-cluster single double triple [CCSD(T)] constitutes an important component of all high-accuracy composite model chemistries that obtain this accuracy but can be a roadblock in the calculation of medium to large systems due to its O(N7) scaling, particularly in HEAT-like model chemistries that eschew separation of core and valence correlation. This study extends the work of Lesiuk [J. Chem. Phys. 156, 064103 (2022)] with new approximate methods and assesses the accuracy of five different approximations of (T) in the context of a subset of molecules selected from the W4-17 dataset. It is demonstrated that all of these approximate methods can achieve sub-0.1 kJ mol−1 accuracy with respect to canonical, density-fitted (T) contributions with a modest number of projectors. The approximation labeled Z̃T appears to offer the best trade-off between cost and accuracy and shows significant promise in an order-of-magnitude reduction in the computational cost of the CCSD(T) component of high-accuracy model chemistries.

Signal Transducer and Activator of Transcription 3 (STAT3) plays a crucial role in cancer development and thus is a viable target for cancer treatment. STAT3 functions as a dimer mediated by phosphorylation of the SRC-homology 2 (SH2) domain, a key target for therapeutic drugs. While great efforts have been employed towards the development of compounds that directly target the SH2 domain, no compound has yet been approved by the FDA due to a lack of specificity and pharmacologic efficacy. Studies have shown that allosteric regulation of SH2 via the coiled-coil domain (CCD) is an alternative drug design strategy. Several CCD effectors have been shown to modulate SH2 binding and affinity, and at the time of writing at least one drug candidate has entered phase I clinical trials. However, the mechanism for SH2 regulation via CCD is poorly understood. Here, we investigate structural and dynamic features of STAT3 and compare the wild type to the reduced function variant D170A in order to delineate mechanistic differences and propose allosteric pathways. Molecular dynamics simulations were employed to explore conformational space of STAT3 and the variant, followed by structural, conformation, and dynamic analysis. The trajectories explored show distinctive conformational changes in the SH2 domain for the D170A variant, indicating long range allosteric effects. Multiple analyses provide evidence for long range communication pathways between the two STAT3 domains, which seem to be mediated by a rigid core which connects the CCD and SH2 domains via the linker domain (LD) and transmits conformational changes through a network of short-range interactions. The proposed allosteric mechanism provides new insight into the understanding of intramolecular signaling in STAT3 and potential pharmaceutical control of STAT3 specificity and activity. Author Summary: In all living organisms, the proliferation and survival of cells are regulated by various proteins. Signal Transducers and Activators of Transcription 3(STAT3) protein is one of the important proteins. However, the abnormal regulation of these proteins will lead to cancer cell. The constitutive activation of STAT3 has been linked to several types of solid tumors, leukemia, and lymphomas. Consequently, STAT3 proteins have been a key target for cancer therapy. SH2(SRC-homology 2) domain is the key interaction site, great efforts have been attributed to target SH2 domain, which specificity has been a major challenge in drug discovery. Research showing regulation of SH2 domain via CCD has opened a new path for drug discovery, however is challenged by poor understanding of the allosteric mechanism. Here, we show that CCD regulates SH2 conformation via a rigid backbone. The perturbations in CCD is transmitted through α-helix to the rigid core that concert the movement of CCD and LD (Link domain), leading to structural changes in the SH2 domain. The present findings provide allosteric mechanism with atomistic details underlying the regulation of CCD to SH2 domain in STAT3 protein. Which allows informed drug design targeting CCD for desired downstream effect on SH2 domain and the overall STAT3 function.