Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic.

Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein-protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein-protein and protein-nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.

Stereoelectronic Features of a Complex Ketene Dimerization Reaction.

The amidation reaction of a tetrahydroisoquinolin-1-one-4-carboxylic acid is a key step in the multi-kilogram-scale preparation of the antimalarial drug SJ733, now in phase 2 clinical trials. In the course of investigating THIQ carboxamidations, we found that propanephosphonic acid anhydride (T3P) is an effective reagent, although the yield and byproducts vary with the nature and quantity of the base. As a control, the T3P reaction of a 3-(2-thienyl) THIQ was performed in the absence of the amine, and the products were characterized: among them are three dimeric allenes and two dimeric lactones. A nucleophile-promoted ketene dimerization process subject to subtle steric and stereoelectronic effects accounts for their formation. Two novel monomeric products, a decarboxylated isoquinolone and a purple, fused aryl ketone, were also isolated, and mechanisms for their formation from the ketene intermediate are proposed.

The Stability of the Complex and the Basicity of the Anion Impact the Selectivity and Affinity of Tripodal Gadolinium Complexes for Anions.

The affinities and selectivities of lanthanide complexes with open coordination sites for anions vary considerably with the chelate. In order to determine the effect of the stability of a lanthanide complex on its affinity for anions, five different complexes featuring different bidentate chelating moieties were synthesized, and their affinity for anions in water at neutral pH were evaluated by longitudinal relaxometry measurements. The chelates comprise both oxygen and nitrogen donors including maltol, 1,2-hydroxypyridinone, hydroxamic acid, pyridin-2-ylmethanol, and carbamoylmethylphosphonate diester. They were chosen to span a range of basicities all the while maintaining a similar tripodal tris-bidentate architecture, thereby allowing for a direct study of the role of the coordinating motif on the supramolecular recognition of anions by the corresponding GdIII complex. Overall, for ligands containing the same number of protonation steps, and therefore the same charge at neutral pH, the lower the acidity of the chelate (higher ∑pKa's), the less stable the corresponding GdIII complex, and the higher its affinity for anions. Regardless of the number of protonation steps, the more stable GdIII complexes form ternary or quaternary assemblies with coordinating anions. In contrast, the same anions readily displace the chelate of the least stable complexes, resulting instead in the formation of GdIII·anion precipitates. Irrespective of the chelate, in the absence of steric hindrance at the open coordination site, the affinity of GdIII complexes for anions follows the order phosphate > arsenate > bicarbonate > fluoride. Hence, the selectivity and affinity of GdIII complexes of tripodal tris-bidentate chelates for anions is a function of the stability of the GdIII complex and the basicity of the anion.

Gadolinium Complex for the Catch and Release of Phosphate from Water.

The ability of complexes of hard and labile metal ions with one or more open coordination sites to capture phosphates with high affinity and selectivity directly in water at neutral pH and release them under acidic conditions is evaluated with Gadolinium- 2,2',2''-(((nitrilotris(ethane-2,1-diyl))tris(azanediyl))tris(carbonyl))tris(4-oxo-4H-pyran-3-olate) (Gd-TREN-MAM). This model lanthanide complex has two open coordination sites that, at neutral pH, are filled with water molecules. In water at neutral pH, Gd-TREN-MAM binds phosphate with high affinity (Ka = 1.3 × 104) via the formation of a ternary complex in which one phosphate replaces both inner-sphere water molecules. The formation of this complex is highly pH-dependent; the phosphate is completely released from Gd-TREN-MAM below pH 2. Because the GdIII ion remains complexed by its ligand, even under strong acidic conditions, Gd-TREN-MAM can be used at least 10 times in a pH-based recycling scheme that enables the catch and release of one phosphate per cycle. Gd-TREN-MAM is highly selective for phosphate over other anions of environmental concerns, including HCO3-, HCO2-, CH3CO2-, SO42-, NO3-, NO2-, BrO3-, AsO4-, F-, Cl-, and Br- and, to a lesser extent, ClO3-. The development of such receptors that bind phosphate reversibly in a pH-dependent manner opens the possibility to design catch-and-release systems for the purification of surface waters.

Protocol for building synthetic protocell membranes that sense redox using synthetic phospholipids and natural lipids.

Sensing is a critical function of artificial cells; however, this is challenging to realize using bottom-up approaches. Here, we present a protocol for building protocell membranes that sense cues important for redox biochemistry and signaling by combining synthetic phospholipids and natural lipids. We detail procedures for building giant unilamellar vesicles as protocell models that fluoresce in response to the biologically significant redox agents peroxynitrite, hydrogen peroxide, and hydrogen sulfide. For complete details on the use and execution of this protocol, please refer to (i) Gutierrez and Aggarwal et al.1 as well as (ii) Erguven and Wang et al.2.

Incorporation of an Isohexide Subunit Improves the Drug-like Properties of Bioactive Compounds.

An enhanced ability to pre-engineer favorable drug-likeness qualities into bioactive molecules would focus and streamline the drug development process. We find that phenols, carboxylic acids, and a purine react with isosorbide ("GRAS" designated) under Mitsunobu coupling conditions to deliver the isoidide conjugates selectively and efficiently. Such conjugates show improved solubility and permeability properties compared with the bare scaffold compounds themselves, and the purine adduct may have applications as a 2'-deoxyadenosine isostere. We anticipate additional benefits, implied by their structures, in metabolic stability and reduced toxicity of the isoidide conjugates as well.

Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic.

Three-dimensional structures of SARS-CoV-2 and other coronaviral proteins archived in the Protein Data Bank were used to analyze viral proteome evolution during the first six months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48,000 viral proteome sequences showed how each one of the 29 viral study proteins have undergone amino acid changes. Structural models computed for every unique sequence variant revealed that most substitutions map to protein surfaces and boundary layers with a minority affecting hydrophobic cores. Conservative changes were observed more frequently in cores versus boundary layers/surfaces. Active sites and protein-protein interfaces showed modest numbers of substitutions. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for six drug discovery targets and four structural proteins comprising the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and functional interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.