bims-pimaco 2024-01-21 papers

Issue of 2024–01–21
six papers selected by
Lucas B. Zeiger

J Biol Chem. 2024 Jan 16. pii: S0021-9258(24)00026-7. [Epub ahead of print] 105650

Revealing the mechanism of action of a first-in-class covalent inhibitor of KRASG12C (ON) and other functional properties of oncogenic KRAS by 31P NMR.

Alok K Sharma, Jun Pei, Yue Yang, Marcin Dyba, Brian Smith, Dana Rabara, Erik Larsen, Felice C Lightstone, Dominic Esposito, Andrew G Stephen, Bin Wang, Pedro J Beltran, Eli Wallace, Dwight V Nissley, Frank McCormick, Anna E Maciag.

Individual oncogenic KRAS mutants confer distinct differences in biochemical properties and signaling for reasons that are not well understood. KRAS activity is closely coupled to protein dynamics and is regulated through two interconverting conformations: state 1 (inactive, effector binding deficient), and state 2 (active, effector binding enabled). Here we use 31P NMR to delineate the differences in state 1 and state 2 populations present in wild-type (WT) and common KRAS oncogenic mutants (G12C, G12D, G12V, G13D, and Q61L) bound to its natural substrate GTP or a commonly used nonhydrolyzable analogue GppNHp. Our results show that GppNHp-bound proteins exhibit significant state 1 population, whereas GTP-bound KRAS is primarily (90% or more) in the state 2 conformation. This observation suggests that the predominance of state 1 shown here and in other studies is related to GppNHp and is most likely nonexistent in cells. We characterize the impact of this differential conformational equilibrium of oncogenic KRAS on RAF1 kinase effector RBD (RAS Binding Domain) binding and intrinsic hydrolysis. Through a KRAS G12C drug discovery, we have identified a novel small molecule inhibitor, BBO-8956, which is effective against both GDP and GTP-bound KRAS G12C. We show that binding of this inhibitor significantly perturbs the state 1 - state 2 equilibrium and induces an inactive state 1 conformation in GTP-bound KRAS G12C. In the presence of BBO-8956, RAF1 RBD is unable to induce a signaling competent state 2 conformation within the ternary complex, demonstrating the mechanism of action (MOA) for this novel, active-conformation inhibitor.

Keywords: (31)P NMR; Cancer; GTP; GTPase KRAS; GppNHp; KRAS G12C selective small molecule inhibitor; Protein complex; nucleotide; state 1 (inactive) conformation; state 2 (active) conformation

DOI: https://doi.org/10.1016/j.jbc.2024.105650

Biochim Biophys Acta Gene Regul Mech. 2024 Jan 17. pii: S1874-9399(24)00001-4. [Epub ahead of print] 195005

Post-translational regulation of the mTORC1 pathway: A switch that regulates metabolism-related gene expression.

Yitao Wang, Tobias Engel, Xinchen Teng.

The mechanistic target of rapamycin complex 1 (mTORC1) is a kinase complex that plays a crucial role in coordinating cell growth in response to various signals, including amino acids, growth factors, oxygen, and ATP. Activation of mTORC1 promotes cell growth and anabolism, while its suppression leads to catabolism and inhibition of cell growth, enabling cells to withstand nutrient scarcity and stress. Dysregulation of mTORC1 activity is associated with numerous diseases, such as cancer, metabolic disorders, and neurodegenerative conditions. This review focuses on how post-translational modifications, particularly phosphorylation and ubiquitination, modulate mTORC1 signaling pathway and their consequential implications for pathogenesis. Understanding the impact of phosphorylation and ubiquitination on the mTORC1 signaling pathway provides valuable insights into the regulation of cellular growth and potential therapeutic targets for related diseases.

Keywords: Phosphorylation; Transcription factor; Ubiquitination; mTOR; mTORC1 signaling pathway

DOI: https://doi.org/10.1016/j.bbagrm.2024.195005

ACS Med Chem Lett. 2024 Jan 11. 15(1): 21-28

Structure-Based Design and Evaluation of Reversible KRAS G13D Inhibitors.

Christian Nilewski, Sharada Labadie, Binqing Wei, Sushant Malhotra, Steven Do, Lewis Gazzard, Li Liu, Cheng Shao, Jeremy Murray, Yevgeniy Izrayelit, Amy Gustafson, Nicholas F Endres, Fang Ma, Xin Ye, Jun Zou, Marie Evangelista.

Oncogenic KRAS mutations were identified decades ago, yet the selective inhibition of specific KRAS mutant proteins represents an ongoing challenge. Recent progress has been made in targeting certain P-loop mutant proteins, in particular KRAS G12C, for which the covalent inhibition of the GDP state via the Switch II pocket is now a clinically validated strategy. Inhibition of other KRAS mutant proteins such as KRAS G13D, on the other hand, still requires clinical validation. The remoteness of the D13 residue relative to the Switch II pocket in combination with the solvent exposure and conformational flexibility of the D13 side chain, as well as the difficulties of targeting carboxylate residues covalently, renders this specific protein particularly challenging to target selectively. In this report, we describe the design and evaluation of potent and KRAS G13D-selective reversible inhibitors. Subnanomolar binding to the GDP state Switch II pocket and biochemical selectivity over WT KRAS are achieved by leveraging a salt bridge with D13.

DOI: https://doi.org/10.1021/acsmedchemlett.3c00478

Mol Cancer Ther. 2024 Jan 15.

Cereblon-Based Bifunctional Degrader of SOS1, BTX-6654, Targets Multiple KRAS Mutations and Inhibits Tumor Growth.

Kyle Begovich, Angela Schoolmeesters, Navin Rajapakse, Elena Martinez-Terroba, Maneesh Kumar, Arvind Shakya, Chon Lai, Steven Greene, Brandon Whitefield, Akinori Okano, Venkat Mali, Shenlin Huang, Aparajita H Chourasia, Leah Fung.

Mutations within the oncogene KRAS drive an estimated 25% of all cancers. Only allele-specific KRAS G12C inhibitors are currently available and are associated with the emergence of acquired resistance, partly due to upstream pathway reactivation. Given its upstream role in the activation of KRAS, Son of Sevenless homologue 1 (SOS1), has emerged as an attractive therapeutic target. Agents that target SOS1 for degradation could represent a potential pan-KRAS modality that may be capable of circumventing certain acquired resistance mechanisms. Here, we report the development of two SOS1 cereblon-based bifunctional degraders, BTX-6654 and BTX-7312, cereblon-based bifunctional SOS1 degraders. Both compounds exhibited potent target-dependent and -specific SOS1 degradation. BTX-6654 and BTX-7312 reduced downstream signaling markers, pERK and pS6, and displayed antiproliferative activity in cells harboring various KRAS mutations. In two KRAS G12C xenograft models, BTX-6654 degraded SOS1 in a dose-dependent manner correlating with tumor growth inhibition, additionally exhibiting synergy with KRAS and MEK inhibitors. Altogether, BTX-6654 provided preclinical proof of concept for single-agent and combination use of bifunctional SOS1 degraders in KRAS-driven cancers.

DOI: https://doi.org/10.1158/1535-7163.MCT-23-0513

Cell Signal. 2024 Jan 17. pii: S0898-6568(24)00028-7. [Epub ahead of print] 111060

SPOP negatively regulates mTORC1 activity by ubiquitinating Sec13.

Yong Yang, Yan-Chun Han, Qi Cao, Xi Wang, Xiao-Dan Wei, Meng-Di Shang, Xiao-Gang Zhang, Xiao Li, Bin Hu, Cheng-Yang Tian, Zhen-Lin Yang, Ke-Hui Liu, Jiu-Qiang Wang.

The mammalian target of rapamycin complex1 (mTORC1) can response to amino acid to regulate metabolism and cell growth. GATOR2 act as important role in amino acid mediated mTORC1 signaling pathway by repressing GTPase activity (GAP) of GATOR1. However, it is still unclear how GATOR2 regulates mTORC1 signaling pathway. Here, we found that K63-ubiquitination of Sce13, one component of GAROR2, suppresses the mTORC1 activity by lessening the inter-interaction of GATOR2. Mechanistically, the ubiquitination of Sec13 was mediated by SPOP. Subsequently, the ubiquitination of Sec13 attenuated its interaction with the other component of GATOR2, thus suppressing the activity of mTORC1. Importantly, the deficiency of SPOP promoted the faster proliferation and migration of breast cancer cells, which was attenuated by knocking down of Sec13. Therefore, SPOP can act as a tumor suppressor gene by negatively regulating mTORC1 signaling pathway.

Keywords: GATOR2; SPOP; Sec13; Ubiquitin; mTORC1

DOI: https://doi.org/10.1016/j.cellsig.2024.111060

Mol Divers. 2024 Jan 19.

Discovery of novel Akt1 inhibitors by an ensemble-based virtual screening method, molecular dynamics simulation, and in vitro biological activity testing.

Wen Zhang, Mei-Ling Hu, Xiu-Yun Shi, Xiang-Long Chen, Xue Su, Hua-Zhao Qi, Li Yuan, Hui Zhang.

Akt1, as an important member of the Akt family, plays a controlled role in cancer cell growth and survival. Inhibition of Akt1 activity can promote cancer cell apoptosis and inhibit tumor growth. Therefore, in this investigation, a multilayer virtual screening approach, including receptor-ligand interaction-based pharmacophore, 3D-QSAR, molecular docking, and deep learning methods, was utilized to construct a virtual screening platform for Akt1 inhibitors. 17 representative compounds with different scaffolds were identified as potential Akt1 inhibitors from three databases. Among these 17 compounds, the Hit9 exhibited the best inhibitory activity against Akt1 with inhibition rate of 33.08% at concentration of 1 μM. The molecular dynamics simulations revealed that Hit9 and Akt1 could form a compact and stable complex. Moreover, Hit9 interacted with some key residues by hydrophobic, electrostatic, and hydrogen bonding interactions and induced substantial conformation changes in the hinge region of the Akt1 active site. The average binding free energies for the Akt1-CQU, Akt1-Ipatasertib, and Akt1-Hit9 systems were - 34.44, - 63.37, and - 39.14 kJ mol-1, respectively. In summary, the results obtained in this investigation suggested that Hit9 with novel scaffold may be a promising lead compound for developing new Akt1 inhibitor for treatment of various cancers with Akt1 overexpressed.

Keywords: 3D-QSAR model; Akt1 inhibitors; Biological activity; Deep-learning model; Molecular dynamics; Pharmacophore model

DOI: https://doi.org/10.1007/s11030-023-10788-3