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The structure of the E. coli LexA repressor complex was studied by affinity cleavage and affinity photo-cross-linking. Cysteine residues were introduced in 7, 28, 38, or 52 positions of the protein with arginine as the original amino acid. The cysteine side chains were incorporated with EDTA-iron or phenyl azide. Alkali/heat treatment determined cross-linking in the phenyl azide derivatives while EDTA-iron derivatives cleaved with DNA near the amino acid.

An ethylenediaminetetraaceticacid (EDTA)-iron complex was incorporated at the second amino acid of the catabolite gene activator protein and the bacteriophage Cro in two steps. A unique solvent-accessible cysteine residue was introduced at the site of interest using site-directed mutagenesis. An S-(2-pyridylthio)cysteaminyl-EDTA-iron complex, was used to produce the resulting protein derivatives. The protein derivatives had sequence-specific DNA cleavage properties.

Research has been conducted on antibacterial peptide microcin J25. The authors have demonstrated that this peptide is a 21-residue lariat protoknot which consists of cyclic segment followed by a linear segment that loops back and threads through the cyclic segment.

A strategy that permits labeling of termini or internal sites, that permits in situ labeling, and that is compatible with a range of fluorochromes with different spectroscopic and photophysical properties is reported. It is hypothesized that the hexahistidine tag should interact tightly with [Ni(super 2+):nitrilotriacetic acid](sub n)-fluorescent labeling.

TNP-2198, a stable conjugate of a rifamycin pharmacophore and a nitroimidazole pharmacophore, has been designed, synthesized, and evaluated as a novel dual-targeted antibacterial agent for the treatment of microaerophilic and anaerobic bacterial infections. TNP-2198 exhibits greater activity than a 1:1 molar mixture of the parent drugs and exhibits activity against strains resistant to both rifamycins and nitroimidazoles. A crystal structure of TNP-2198 bound to a Mycobacterium tuberculosis RNA polymerase transcription initiation complex reveals that the rifamycin portion of TNP-2198 binds to the rifamycin binding site on RNAP and the nitroimidazole portion of TNP-2198 interacts directly with the DNA template-strand in the RNAP active-center cleft, forming a hydrogen bond with a base of the DNA template strand. TNP-2198 is currently in Phase 2 clinical development for the treatment of Helicobacter pylori infection, Clostridioides difficile infection, and bacterial vaginosis.

The growing prevalence of drug resistant bacteria is a significant global threat to human health. The antibacterial drug rifampin, which functions by inhibiting bacterial RNA polymerase (RNAP), is an important part of the antibacterial armamentarium. Here, in order to identify novel inhibitors of bacterial RNAP, we used affinity-selection mass spectrometry to screen a chemical library for compounds that bind to Escherichia coli RNAP. We identified a novel small molecule, MRL-436, that binds to RNAP, inhibits RNAP, and exhibits antibacterial activity. MRL-436 binds to RNAP through a binding site that differs from the rifampin binding site, inhibits rifampin-resistant RNAP derivatives, and exhibits antibacterial activity against rifampin-resistant strains. Isolation of mutants resistant to the antibacterial activity of MRL-436 yields a missense mutation in codon 622 of the rpoC gene encoding the RNAP β' subunit or a null mutation in the rpoZ gene encoding the RNAP ω subunit, confirming that RNAP is the functional cellular target for the antibacterial activity of MRL-436, and indicating that RNAP β' subunit residue 622 and the RNAP ω subunit are required for the antibacterial activity of MRL-436. Similarity between the resistance determinant for MRL-436 and the resistance determinant for the cellular alarmone ppGpp suggests a possible similarity in binding site and/or induced conformational state for MRL-436 and ppGpp.