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.     

X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno-oncology.     

Replacement of the Cobalt Center of Vitamin B12 by Nickel: Nibalamin and Nibyric Acid Prepared from Metal-Free B12 Ligands Hydrogenobalamin and Hydrogenobyric Acid

The (formal) replacement of Co in cobalamin ( Cbl ) by Ni^II generates nibalamin ( Nibl ), a new transition-metal analogue of vitamin B₁₂. Described here is Nibl , synthesized by incorporation of a Ni^II ion into the metal-free B₁₂ ligand hydrogenobalamin ( Hbl ), itself prepared from hydrogenobyric acid ( Hby ). The related Ni^II corrin nibyric acid ( Niby ) was similarly synthesized from Hby , the metal-free cobyric acid ligand. The solution structures of Hbl , and Niby and Nibl , were characterized by spectroscopic studies. Hbl features two inner protons bound at N2 and N4 of the corrin ligand, as discovered in Hby . X-ray analysis of Niby shows the structural adaptation of the corrin ligand to Ni^II ions and the coordination behavior of Ni^II. The diamagnetic Niby and Nibl , and corresponding isoelectronic Co^I corrins, were deduced to be isostructural. Nibl is a structural mimic of four-coordinate base-off Cbls , as verified by its ability to act as a strong inhibitor of bacterial adenosyltransferase.     

Catalyst-Controlled Transannular Polyketide Cyclization Cascades: Selective Folding of Macrocyclic Polyketides

The biomimetic synthesis of aromatic polyketides from macrocyclic substrates by means of catalyst-controlled transannular cyclization cascades is described. The macrocyclic substrates, which feature increased stability and fewer conformational states, were thereby transformed into several distinct polyketide scaffolds. The catalyst-controlled transannular cyclizations selectively led to aromatic polyketides with a defined folding and oxygenation pattern, thus emulating β-keto-processing steps of polyketide biosynthesis.     

Experimental validation of corrections factors for γ–γ and γ–X coincidence summing of 133Ba, 152Eu,and 125Sb in volume sources

True coincidence summing correction factors for ¹³³Ba, ¹⁵²Eu and ¹²⁵Sb were determined experimentally for a small volume source and compared with correction factors obtained with three softwares (EFFTRAN-X, GESPECOR and VGSL). The radionuclides investigated have a relatively challenging decay scheme and their spectra are known to suffer from losses due to summation (γ–γ, γ–X and X–X) when measured at close distances on a HPGe detector sensitive to low energy photons. This study shows that the softwares were in good agreement with each other and the experimental data and the calculated activity was consistent with the activity in the volume source.

     

Physicochemical properties of SARS-CoV-2 for drug targeting,virus inactivation and attenuation,vaccine formulation and quality control

The material properties of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its proteins are discussed. We review the viral structure, size, rigidity, lipophilicity, isoelectric point, buoyant density and centrifugation conditions, stability against pH, temperature, UV light, gamma radiation, and susceptibility to various chemical agents including solvents and detergents. Possible inactivation, downstream, and formulation conditions are given including suitable buffers and some first ideas for quality-control methods. This information supports vaccine development and discussion with competent authorities during vaccine approval and is certainly related to drug-targeting strategies and hygienics. Several instructive tables are given, including the pI and grand average of hydropathicity (GRAVY) of SARS-CoV-1 and -2 proteins in comparison. SARS-CoV-1 and SARS-CoV-2 are similar in many regards, so information can often be derived. Both are unusually stable, but sensitive at their lipophilic membranes. However, since seemingly small differences can have strong effects, for example, on immunologically relevant epitope settings, unevaluated knowledge transfer from SARS-CoV-1 to SARS-CoV-2 cannot be advised. Published knowledge regarding downstream processes, formulations and quality assuring methods is, as yet, limited. However, standard approaches employed for other viruses and vaccines seem to be feasible including virus inactivation, centrifugation conditions, and the use of adjuvants.     

Supramolecular Ammine-Copper rac-BINOLAT Salts through in-situ R- or S-BINOL Racemization

The molecule rac-1,1'-binaphthalene-2,2'-diol (rac-1,1'-bi-2-naphthol, rac-BINOL) shows a propensity for supramolecular, charge-assisted O–H ··· O^– hydrogen-bonded strand formation when crystallized with its deprotonated form BINOLAT^2– and Cu²⁺ in conc. ammonia. The naphthyl-paneled cavities in the {(rac-BINOLAT^2–)(rac-BINOL)₂} strands host the [Cu(NH₃)₅]²⁺-guest cation through second-sphere N–H ··· O hydrogen bonding in the structure of [Cu(NH₃)₅]²⁺(rac-BINOLAT^2–)(rac-BINOL)₂. Decreasing the copper(II) and ammonia concentrations in the crystallization leads to {(rac-BINOLAT^2–)(rac-BINOL)} strands, in which rac-BINOLAT^2– coordinates to two copper(II) atoms in the structure of [Cu(NH₃)₂(μ-rac-BINOLAT^2–-κ²O,O':κO)]₂(rac-BINOL)₂. In the {Cu²⁺(NH₃)₂} moiety two BINOLAT-oxide atoms act as bridging ligands. Both copper structures could be obtained by using the racemic rac-BINOL or the enantiomeric R- or S-BINOL, through an in-situ racemization of the latter.