Mutant-Selective Allosteric EGFR Degraders are Effective Against a Broad Range of Drug-Resistant Mutations

Targeting epidermal growth factor receptor (EGFR) through an allosteric mechanism provides a potential therapeutic strategy to overcome drug-resistant EGFR mutations that emerge within the ATP binding site. Here, we develop an allosteric EGFR degrader, DDC-01-163, which can selectively inhibit the proliferation of L858R/T790M (L/T) mutant Ba/F3 cells while leaving wildtype EGFR Ba/F3 cells unaffected. DDC-01-163 is also effective against osimertinib-resistant cells with L/T/C797S and L/T/L718Q EGFR mutations. When combined with an ATP-site EGFR inhibitor, osimertinib, the anti-proliferative activity of DDC-01-163 against L858R/T790M EGFR-Ba/F3 cells is enhanced. Collectively, DDC-01-163 is a promising allosteric EGFR degrader with selective activity against various clinically relevant EGFR mutants as a single agent and when combined with an ATP-site inhibitor. Our data suggests that targeted protein degradation is a promising drug development approach for mutant EGFR.     

Microseparation techniques for the study of the enantioselectivity of drug–plasma protein binding

Stereoselectivity in protein binding can have a significant effect on the pharmacokinetic and pharmacodynamic properties of chiral drugs. The investigation of enantioselectivity of drugs in their binding with human plasma proteins and the identification of the molecular mechanisms involved in the stereodiscrimination by the proteins represent a great challenge for clinical pharmacology. In this review, the separation techniques used for enantioselective protein binding experiments are described and compared. An overview of studies on enantiomer–protein interactions, enantiomer–enantiomer interactions as well as chiral drug–drug interactions, including allosteric effects, is presented. The contribution of individual plasma proteins to the overall enantioselective binding and the animal species variability in drug–plasma protein binding stereoselectivity are reviewed. Copyright © 2008 John Wiley & Sons, Ltd.     

Thermodynamic and kinetic effects of Lewis acid complexation on a Schiff base present in two tautomeric forms

The effect of complexation with Lewis acids on the tautomeric equilibrium of a derivative of pyridoxal has been explored using density functional theory. Three complexation sites (pyridine nitrogen, aromatic ring, and carbonyl group) have been considered. The tautomeric equilibrium can be modulated with the formation of complexes at the different sites. The changes observed in the geometric, energetic and electronic properties of the tautomers and transition states have been analyzed. Relationships have been found between those parameters, including a relationship between energetic and geometric parameters in agreement with the Hammond postulate. Copyright © 2010 John Wiley & Sons, Ltd.     

De Novo Design and Synthesis of a γ‐Turn Peptidomimetic Scaffold and Its Application as JNK3 Allosteric Ligand

As a way to develop a neuroprotective agent for the JNK3‐JIP1‐binding site, peptidomimetics of JIP‐1 as JNK3 allosteric regulators have been examined. The study consisted of in silico scaffold hopping, molecular docking, solution and solid‐phase peptide syntheses, and K_d measurements using surface plasmon resonance. As a peptidomimetic of JIP1, heptamer mimetic 16 (K_d=2.72 μm ) displayed a higher affinity than decamer JIP1 (K_d=23.6 μm ). The high affinity of 16 implies that the characteristic γ‐turn mimetic structure, “”Φ‐X‐Φ“ hydrophobic motif in 16 , increased its affinity toward the JIP‐site of JNK3.     

Parameterization of Org27569: An allosteric modulator of the cannabinoid CB1 G protein‐coupled receptor

The cannabinoid CB₁ receptor is a class A G protein‐coupled receptor (GPCR) that is the most widely expressed GPCR in the brain. Many GPCRs contain allosteric binding sites for endogenous and/or synthetic ligands, which are topographically distinct from the agonist‐binding site that is known as the orthosteric site. While both endogenous and synthetic ligands that act at the CB₁ orthosteric site have been known for some time, compounds that act at a CB₁ allosteric site have only recently been discovered. The most studied of these is 5‐chloro‐3‐ethyl‐1H‐indole‐2‐carboxylic acid [2‐(4‐piperidin‐1‐ylphenyl)ethyl]amide (Org27569). Because allosteric ligands are thought to act through conformational changes in the receptor that are transmitted from the allosteric to the orthosteric site, computational studies of the structural and dynamic interactions of Org27569 with the CB₁ receptor are crucial to achieve a molecular level understanding of the basis of action of this important new class of compounds. To date, such computational studies have not been possible due to the lack of a complete set of molecular mechanics force field parameters for Org27569. Here, we present the development of missing CHARMM force field parameters for Org27569 using previously published methods and the validation and application of these new parameters using normal mode analysis and molecular dynamics simulations combined with experimental infrared measurements. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Optimizing departure times in vehicle routes

Most solution methods for the vehicle routing problem with time windows (VRPTW) develop routes from the earliest feasible departure time. In practice, however, temporary traffic congestion make such solutions non-optimal with respect to minimizing the total duty time. Furthermore, the VRPTW does not account for driving hours regulations, which restrict the available travel time for truck drivers. To deal with these problems, we consider the vehicle departure time optimization (VDO) problem as a post-processing of a VRPTW. We propose an ILP formulation that minimizes the total duty time. The results of a case study indicate that duty time reductions of 15% can be achieved. Furthermore, computational experiments on VRPTW benchmarks indicate that ignoring traffic congestion or driving hours regulations leads to practically infeasible solutions. Therefore, new vehicle routing methods should be developed that account for these common restrictions. We propose an integrated approach based on classical insertion heuristics.     

Study on the Model for Regulation of the Allosteric Enzyme Activity

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Chiral Sensing Using Circularly Polarized Luminescence of Bis(phenanthroline dicarboxylic acid) EuIII Complex Induced by Allosteric‐type Interaction with Amino Acid Molecules

[Eu(pda)₂]^? and [Eu(bda)₂]^? (pda=1,10‐phenanthroline‐2, 9‐dicarboxylic acid; bda=2,2′ bipyridine 5,5′‐dicarboxylic acid) have an achiral D_2d structure in crystals. These complexes exhibit circularly polarized luminescence (CPL) in water containing chiral amino acids. In this work, induced CPL of [Eu(pda)₂]^? and [Eu(bda)₂]^? in water solutions containing a mixture of d ‐ and l ‐ amino acids were examined. Plots of g_lum values of the induced CPL as a function of mol‐fraction of l ‐ and d ‐ arginine reveal that [Eu(pda)₂]^? favors homo‐association ([Eu(pda)₂]^?‐(l ‐arginine)₂ or [Eu(pda)₂]^?‐(d ‐arginine)₂) over hetero‐association {[Eu(pda)₂]^?‐(l ‐arginine)?(d ‐arginine)}. This suggests that association of an arginine molecule induces a structural change in [Eu(pda)₂]^? to promote chiral selective association to another arginine, i.e., homo‐allosteric association. On the other hand, the system of [Eu(pda)₂]^? with histidine favors hetero‐allosteric association over homo‐association. No allosteric effect is recognized in CPL from [Eu(bda)₂]^?.     

Insights into Allosteric Control of Human Blood Group A and B Glycosyltransferases from Dynamic NMR

Human blood group A and B glycosyltransferases (GTA, GTB) are retaining glycosyltransferases, requiring a catalytic mechanism that conserves the anomeric configuration of the hexopyranose moiety of the donor substrate (UDP-GalNAc, UDP-Gal). Previous studies have shown that GTA and GTB cycle through structurally distinct states during catalysis. Here, we link binding and release of substrates, substrate-analogs, and products to transitions between open, semi-closed, and closed states of the enzymes. Methyl TROSY based titration experiments in combination with zz-exchange experiments uncover dramatic changes of binding kinetics associated with allosteric interactions between donor-type and acceptor-type ligands. Taken together, this highlights how allosteric control of on- and off-rates correlates with conformational changes, driving catalysis to completion.