Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling

A mutated KRAS protein is frequently observed in human cancers. Traditionally, the oncogenic properties of KRAS missense mutants at position 12 (G12X) have been considered as equal. Here, by assessing the probabilities of occurrence of all KRAS G12X mutations and KRAS dynamics we show that this assumption does not hold true. Instead, our findings revealed an outstanding mutational bias. We conducted a thorough mutational analysis of KRAS G12X mutations and assessed to what extent the observed mutation frequencies follow a random distribution. Unique tissue-specific frequencies are displayed with specific mutations, especially with G12R, which cannot be explained by random probabilities. To clarify the underlying causes for the nonrandom probabilities, we conducted extensive atomistic molecular dynamics simulations (170 its) to study the differences of G12X mutations on a molecular level. The simulations revealed an allosteric hydrophobic signaling network in KRAS, and that protein dynamics is altered among the G12X mutants and as such differs from the wild-type and is mutation-specific. The shift in long-timescale conformational dynamics was confirmed with Markov state modeling. A G12X mutation was found to modify KRAS dynamics in an allosteric way, which is especially manifested in the switch regions that are responsible for the effector protein binding. The findings provide a basis to understand better the oncogenic properties of KRAS G12X mutants and the consequences of the observed nonrandom frequencies of specific G12X mutations.Peer reviewe

Selective targeting of the αC and DFG-out pocket in p38 MAPK

The p38 MAPK cascade is a key signaling pathway linked to a multitude of physiological functions and of central importance in inflammatory and autoimmune diseases. Although studied extensively, little is known about how conformation-specific inhibitors alter signaling outcomes. Here, we have explored the highly dynamic back pocket of p38 MAPK with allosteric urea fragments. However, screening against known off-targets showed that these fragments maintained the selectivity issues of their parent compound BIRB-796, while combination with the hinge-binding motif of VPC-00628 greatly enhanced inhibitor selectivity. Further efforts focused therefore on the exploration of the αC-out pocket of p38 MAPK, yielding compound 137 as a highly selective type-II inhibitor. Even though 137 is structurally related to a recent p38 type-II chemical probe, SR-318, the data presented here provide valuable insights into back-pocket interactions that are not addressed in SR-318 and it provides an alternative chemical tool with good cellular activity targeting also the p38 back pocket

Exploiting lipotoxicity for the treatment of liver cancer

Metabolic alterations occur frequently in solid tumours, but metabolic cancer therapies are limited by the complexity and plasticity of metabolic networks. We could recently show that activation of the liver X receptor alpha (LXRα) and inhibition of a Raf-1-SCD1 protein complex induces an intracellular accumulation of saturated free fatty acids leading to lethal lipotoxicity in tumour cells and allows for an efficient treatment of liver carcinomas

The Influence of Knee and Ankle Bracing on Lower Extremity Kinematics During a Cutting Maneuver

PURPOSE: To determine the effect of four brace conditions on the lower extremity kinematics during a jogging cutting maneuver. METHODS: 18 subjects (9 male and 9 female, age = 22.8±2.0 yrs, ht = 174.7±7.6 cm, wt = 74.9±14.5 kg) participated in this study. Each subject performed 7–10 jogging cutting trials while wearing each of the four brace conditions; ankle brace only (AB), knee brace only (KB), ankle and knee brace together (ABKB) and no brace (NB). Hip and knee sagittal and frontal plane kinematics and ankle sagittal plane kinematics were assessed for each subject during each of the brace conditions. RESULTS: ANOVA (α = .05) revealed that sagittal plane ankle and hip ROM were not influenced by brace condition. Sagittal plane knee ROM was significantly reduced in the KB compared to the NB condition. Frontal plane knee ROM revealed a more varus position during the KB and ABKB conditions compared to the NB and AB conditions. The results also revealed that the hip was significantly more abducted during the KB and ABKB conditions when compared to the AB and NB conditions. CONCLUSIONS: The results indicate that the KB and the ABKB significantly influenced frontal plane hip and knee ROM and sagittal plane knee ROM during a jogging cutting maneuver. These braces may be beneficial in preventing excessive motion at the respective joint however it is important to consider their impact at the hip joint as a result of these bracing techniques. It is possible that these changes in ROM may result in subsequent changes in joint moments and or ground reaction forces