Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease

The COVID-19 pandemic has highlighted the urgent need for the identification of new antiviral drug therapies for a variety of diseases. COVID-19 is caused by infection with the human coronavirus SARS-CoV-2, while other related human coronaviruses cause diseases ranging from severe respiratory infections to the common cold. We developed a computational approach to identify new antiviral drug targets and repurpose clinically-relevant drug compounds for the treatment of a range of human coronavirus diseases. Our approach is based on graph convolutional networks (GCN) and involves multiscale host-virus interactome analysis coupled to off-target drug predictions. Cell-based experimental assessment reveals several clinically-relevant drug repurposing candidates predicted by the in silico analyses to have antiviral activity against human coronavirus infection. In particular, we identify the MET inhibitor capmatinib as having potent and broad antiviral activity against several coronaviruses in a MET-independent manner, as well as novel roles for host cell proteins such as IRAK1/4 in supporting human coronavirus infection, which can inform further drug discovery studies.

Lipophilicity of the Cystic Fibrosis Drug, Ivacaftor (VX-770), and Its Destabilizing Effect on the Major CF-causing Mutation: F508del

Deletion of phenylalanine at position 508 (F508del) in cystic fibrosis transmembrane conductance regulator (CFTR) is the most common cystic fibrosis (CF)-causing mutation. Recently, ORKAMBI, a combination therapy that includes a corrector of the processing defect of F508del-CFTR (lumacaftor or VX-809) and a potentiator of channel activity (ivacaftor or VX-770), was approved for CF patients homozygous for this mutation. However, clinical studies revealed that the effect of ORKAMBI on lung function is modest and it was proposed that this modest effect relates to a negative impact of VX-770 on the stability of F508del-CFTR. In the current studies, we showed that this negative effect of VX-770 at 10 μM correlated with its inhibitory effect on VX-809-mediated correction of the interface between the second membrane spanning domain and the first nucleotide binding domain bearing F508del. Interestingly, we found that VX-770 exerted a similar negative effect on the stability of other membrane localized solute carriers (SLC26A3, SLC26A9, and SLC6A14), suggesting that this negative effect is not specific for F508del-CFTR. We determined that the relative destabilizing effect of a panel of VX-770 derivatives on F508del-CFTR correlated with their predicted lipophilicity. Polarized total internal reflection fluorescence microscopy on a supported lipid bilayer model shows that VX-770, and not its less lipophilic derivative, increased the fluidity of and reorganized the membrane. In summary, our findings show that there is a potential for nonspecific effects of VX-770 on the lipid bilayer and suggest that this effect may account for its destabilizing effect on VX-809- rescued F508del-CFTR.

Synthesis and properties of molecular probes for the rescue site on mutant cystic fibrosis transmembrane conductance regulator

Cystic fibrosis is a genetic disease caused by mutations in the gene for the cystic fibrosis transmembrane conductance regulator (CFTR) protein. In vitro experiments have demonstrated that 4-methyl-2-(5-phenyl-1H-pyrazol-3-yl)phenol (VRT-532, 1) is able to partially restore the function of mutant CFTR proteins. To help elucidate the nature of the interactions between 1 and mutant CFTR, molecular probes based on the structure of 1 have been prepared. These include a photoreactive aryl azide derivative 11 and a fluorescent dansyl sulfonamide 15. Additionally, a method for hydrogen isotope exchange on 1 has been developed, which could be used for the incorporation of radioactive tritium. Using iodide efflux assays, the probe molecules have been demonstrated to modulate the activity of mutant CFTR in the same manner as 1. These probe molecules enable a number of biochemical experiments aimed at understanding how 1 rescues the function of mutant CFTR. This understanding can in turn aid in the design and development of more efficacious compounds which may serve as therapeutic agents in the treatment of cystic fibrosis.

N,1-Bis(4-chloro-2-methylbenzyl)-3-methyl-2-oxo-1,2,3,4-tetrahydroquinoline-3-carboxamide

In the title mol­ecule, C₂₇H₂₆Cl₂N₂O₂, the chloro-substituted benzene rings make dihedral angles of 83.29 (9) and 80.81 (9)° with the benzene ring of the tetra­hydro­quinoline group. The dihedral angle formed by the two chloro-substituted benzene rings is 40.87 (12)°. The six-membered N-containing ring is in a half-chair conformation. In the crystal structure, inter­molecular N—H⋯O hydrogen bonds link mol­ecules into centrosymmetric dimers.

meso-4,5-Diphenyl-imidazolidin-2-one

The crystal structure determination of the title compound, C₁₅H₁₄N₂O, confirms the cis relationship between the phenyl groups at the 4- and 5-positions on the imidazolidine ring. The dihedral angle between the two phenyl rings is 48.14 (6)°. In the crystal structure, inter­molecular N—H⋯O hydrogen bonds link mol­ecules into centrosymmetric dimers. These dimers are, in turn, linked into a two-dimensional network via weak N—H⋯π(arene) inter­actions and π–π stacking inter­actions with centroid–centroid distances of 3.6937 (11) Å.

A direct synthesis of pyrrolocytosine from 5-iodocytosine

We have employed a tandem Sonogashira/annulation reaction between 5-iodocytosine derivatives and terminal alkynes to yield the fluorescent bicyclic nucleobase pyrrolcytosine. Pyrrolocytosine bearing substituents only on the pyrrole ring are conveniently synthesized from 5-iodocytosine. Water soluble pyrrolocytosines are being investigated as reporter groups in SNP analysis.

Progress towards a submonomer synthesis of peptide nucleic acid

We report recent developments in the optimization of a submonomer synthesis of peptide nucleic acid based on the Fukuyama-Mitsunobu reaction. The key steps in the submonomer synthesis are the installation of an appropriately protected 2-aminoethyl group on the alpha-nitrogen of an amino acid and its subsequent acylation with a protected nucleobase derivative. The aggressive alkylation conditions require a scheme of maximal protection for the nucleobases and that is proposed herein for the pyrimidines.

Nucleobase modified peptide nucleic acid

The Pd0/Cu1 catalyzed cross-coupling of terminal alkynes onto peptide nucleic acid monomers or submonomers bearing iodinated nucleobases has been utilized as a route to base-modified oligomers. Both 5-iodouracil and 5-iodocytosine derivatives undergo the cross-coupling to give the expected products in moderate to good yields. However, depending on the particular substrates and reaction conditions, the cross-coupling may be followed by a ring closing reaction to give the fluorescent furano- and pyrrolo-fused uracil and cytosine derivatives, respectively.

A convenient and scalable synthesis of ethyl N-[(2-Boc-amino)ethyl]glycinate and its hydrochloride. Key intermediates for peptide nucleic acid synthesis

An improved synthesis of ethyl N-[(2-Boc-amino)ethyl]glycinate and its hydrochloride salt is reported. The synthesis is based on the reductive alkylation of Boc-ethylenediamine with ethyl glyoxylate hydrate and furnishes the title compound in near quantitative yield and high purity without chromatography. This compound is suitable, as is, for the synthesis peptide nucleic acid monomers. Further, conversion to the hydrochloride salt provides a stable, nonhygroscopic solid that is a convenient form for handling and storage.

Optimization of a solid-phase synthesis of a PNA monomer

A new scheme for the synthesis of peptide nucleic acid (PNA) is described. First, a resin-bound amino acid is alkylated under Fukuyama-Mitsunobu conditions. A nucleobase is then incorporated via an acid fluoride. Subsequently, oligomerization may be achieved by deprotection, coupling of another amino acid, and repetition of the cycle. Each step of the submonomer synthesis has been optimized to provide essentially quantitative yield. [reaction: see text]