ACS Bio & Med Chem Au最新文献

The ΔG affinity of drugs with biopolymers and the underling noncovalent interactions play an essential role in drug discovery. Supramolecular complexes can be designed for the identification and quantification of specific interactions, including their dependence on the medium; they also secure the additivity of ΔΔG increments. Such analyses have helped to clarify hydrophobic effects in intermolecular associations, which are barely measurable with small alkyl groups, but large in the presence of curved surfaces in which the replacement of hydrogen bond-deficient water molecules by a ligand leads to sizable enthalpy gain. Difficult to predict entropy contributions TΔS to ΔG vary between 5% and over 90%, particularly in drug associations, as is obvious from literature data. As illustrated with several drug complexes, many so-called hydrophobic effects involve in fact van der Waals or dispersive interactions. Measurements with supramolecular porphyrin complexes allowed us to derive dispersive binding contributions for many groups, which exhibit a correlation with polarizability. In consequence, heteroatoms or π-systems always lead to enhanced van der Waals contributions, while for hydrophobic effects the opposite is expected. Binding contributions from supramolecular complexes can in the future also help artificial intelligence approaches in drug discovery, by expansion of hybrid databases with potential ligands containing groups with desired binding contributions.

The human transcriptome contains secondary RNA structures like RNA G-quadruplexes (rG4s) which regulate biological processes such as translation by ribosome stalling. Canonical rG4s, which are stabilized by both Hoogsteen hydrogen bonds and potassium ions, are known to hinder translation in the 5' untranslated region (5'UTR) of mRNAs. In neurodegenerative diseases, including Parkinson's disease (PD), rG4s have been shown to influence protein synthesis. However, the impact of rG4s in nonmutated therapeutic targets like monoamine oxidase B (MAOB), an enzyme involved in dopamine metabolism, remains unexplored. In this study, an rG4 located in the MAOB mRNA's 5'UTR was identified, and ways to either stabilize or reprogram this rG4 were explored. The translation inhibitory role of the rG4 was demonstrated both in vitro and in cellulo and was shown to be further accentuated in the presence of the PhenDC3 ligand. As an alternative to ligands, which cannot specifically stabilize only one G4, the MOAB rG4 was reprogrammed with G-rich antisense oligonucleotides (G-ASOs) from a two-quartets to three-quartets G4. The G-ASOs, either unmodified DNA or 2'OMe, were shown to both induce a new rG4 folding through intermolecular interactions and to specifically reduce the translation of MAOB both in vitro and in cellulo. These findings propose a targeted approach with which to modulate rG4 structures for therapeutics, suggesting that rG4 folding, when stabilized by G-ASOs, could regulate protein synthesis and even potentially alleviate PD symptoms by reducing MAOB activity. This approach opens new avenues as it could be used to reduce the expression of many therapeutic protein targets.

Allosteric regulation is a pivotal mechanism governing a wide array of cellular functions. Essential to this process is a flexible biomolecule allowing distant sites to interact through coordinated or sequential conformational shifts. Phosphoinositide-dependent kinase 1 (PDK1) possesses a conserved allosteric binding site, the PIF-pocket, which regulates the kinase's ATP binding, catalytic activity, and substrate interactions. We elucidated the allosteric mechanisms of PDK1 by comparing conformational ensembles of the kinase bound with different small-molecule allosteric modulators in the PIF-pocket with that of the modulator-free kinase. Analysis of over 48 μs of simulations consistently shows that the allosteric modulators predominantly influence the conformational dynamics of specific distal regions from the PIF-pocket, driving allosteric activation. Furthermore, a recently developed advanced difference contact network community analysis is employed to elucidate allosteric communications. This approach integrates multiple conformational ensembles into a single community network, offering a valuable tool for future studies aimed at identifying function-related dynamics in proteins.

Spiniferin is a 13-mer scorpion-origin antimicrobial peptide having poor antimicrobial activity. To augment Spiniferin's antimicrobial activity, we enhanced its net positive charge by replacing a glutamic acid residue with an arginine residue toward its amino terminus. We envisaged that a cation-π interaction could be introduced between this arginine residue and the tryptophan residue located near the middle of Spiniferin. This cation-π interaction could promote stronger interaction of the peptide with a negatively charged bacterial membranes, resulting in its increased antimicrobial activity. Though glutamic acid-to-arginine substitution [Spiniferin-(E4R)] enhanced both the antimicrobial and toxic properties of Spiniferin, the same replacement with a d-arginine residue [Spiniferin-(E4dR)] significantly enhanced its antimicrobial activity against selected Gram-negative/positive bacteria and a MRSA strain while maintaining low hemolytic/cytotoxic properties. Interestingly, Spiniferin-(E4dR) analogs, with its aromatic-tryptophan residue substituted with an aromatic phenylalanine or an aliphatic valine residue, and its d-arginine residue replaced with a d-lysine residue, showed much lesser antibacterial activity than Spiniferin-(E4dR) or Spiniferin-(E4R). The results indicated a crucial role of the tryptophan and l-/d-arginine combination in augmenting the antimicrobial activity of Spiniferin analogs, Spiniferin-(E4R) and Spiniferin-(E4dR). Spiniferin-(E4dR) showed bactericidal properties against selected Gram-positive/negative bacteria. It permeabilized bacterial membranes and induced damages in bacterial membrane organization, suggesting that the bacterial plasma membrane is its target for exhibiting antimicrobial activity. Further, Spiniferin-(E4dR) in the intravenous route demonstrated the survival of E. coli ATCC 25922-infected mice and the clearance of bacteria from the visceral organs of these mice. Computational studies showed the requisite distance between the arginine's cationic side chain and the π-electron site of the tryptophan residue for a possible intramolecular cation-π interaction in Spiniferin-(E4dR)/Spiniferin-(E4R).

Drug-resistant bacterial infections impose a major threat to human health, as current antibiotic treatments are becoming increasingly ineffective. Priority has been given to the development of alternative medications to curb the development of resistance or agents that can work on the resistance strains. Among various promising approaches, 1,2,3-triazole-based molecular hybrids have emerged as excellent candidates owing to their ease of synthesis, high structural diversity, functional tunability, and biocompatibility. The rapid advancement of biological understanding of 1,2,3-triazole has been greatly aided by the discovery of the Click reaction. Drugs with a single molecular target often fail to kill the bacteria effectively, and even if they do, the bacteria eventually become resistant by virtue of mutations or other mechanisms. In this context, the 1,2,3-triazole group has been explored to design novel molecular hybrids to combat antimicrobial resistance in an effective manner. Different types of 1,2,3-triazole-based hybrids have been developed that have shown inhibitory effects on critical bacterial enzymes, the ability to produce intracellular reactive oxygen species, and the ability to disrupt the cell membrane. Herein, we discuss the strategic design principles of triazole-based hybrids, their antibacterial potential, especially focusing on the drug resistance issue, and future perspectives to critically assess their potential for multitargeting antibacterial agents. The presented information can lead to the development of novel multifaceted antibacterial agents in the future by means of their unique chemical features to address the growing challenge of drug resistance.

We present a comprehensive analysis of the initial α,β-dehydrogenation step in long-chain fatty acid β-oxidation (FAO). We focused on palmitoyl-CoA oxidized by two mitochondrial acyl-CoA dehydrogenases, very-long-chain acyl-CoA dehydrogenase (VLCAD) and acyl-CoA dehydrogenase family member 9 (ACAD9), both implicated in mitochondrial diseases. By combining MS and NMR, we identified the (2E)-hexadecenoyl-CoA as the expected α-β-dehydrogenation product and also the E and Z stereoisomers of 3-hexadecenoyl-CoA: a "γ-oxidation" product. This finding reveals an alternative catalytic pathway in mitochondrial FAO, suggesting a potential regulatory role for ACAD9 and VLCAD during fatty acid metabolism.

Iron and 2-oxoglutarate dependent (Fe/2OG) enzymes utilize an Fe^IV=O species to catalyze the functionalization of otherwise chemically inert C-H bonds. In addition to the more familiar canonical reactions of hydroxylation and chlorination, they also catalyze several other types of reactions that contribute to the diversity and complexity of natural products. In the past decade, several new Fe/2OG enzymes that catalyze C-C and C-N bond formation have been reported in the biosynthesis of structurally complex natural products. Compared with hydroxylation and chlorination, the catalytic cycles of these Fe/2OG enzymes involve distinct mechanistic features to enable noncanonical reaction outcomes. This Review summarizes recent discoveries of Fe/2OG enzymes involved in C-C and C-N bond formation with a focus on reaction mechanisms and their roles in natural product biosynthesis.

The antibiotic alaremycin (5-acetamido-4-oxo-5-hexenoic acid, 1), isolated from Streptomyces sp. A012304, structurally resembles 5-aminolevulinic acid (ALA), a precursor in porphyrin biosynthesis, and inhibits porphobilinogen synthase, the enzyme responsible for catalyzing the first common step of this pathway. In our previous study, the biosynthetic gene cluster responsible for alaremycin production-composed of almA (ALA synthase homologue), almB (N-acetyltransferase), almC (oxidoreductase), and almE (MFS-type transporter)-was identified, and a potential biosynthetic pathway was proposed. In this study, the biosynthetic pathway of 1 was confirmed by detecting intermediates using the liquid chromatography-mass spectrometry/MS (LC-MS/MS) analysis of extracts from Escherichia coli cells transformed with the biosynthetic genes, followed by in vitro reconstitution of the biosynthetic reactions using purified enzymes. AlmA catalyzed the condensation of l-serine and succinyl-CoA to produce 5-amino-6-hydroxy-4-oxohexanoic acid (2), AlmB catalyzed the N-acetylation of 2 to produce 5-acetamido-6-hydroxy-4-oxohexanoic acid (3), and AlmC catalyzed the dehydration of 3 to form 1. The AlmC-catalyzed reaction may involve a two-step mechanism including reduction by NADH and oxidation by Fe³⁺. Additionally, a novel derivative of 1 was identified in the culture broth of the producer strain, and its structure was determined as 5,6-dihydroalaremycin (5-acetamido-4-oxohexanoic acid, 4). It was revealed that 4 is synthesized via the same biosynthetic pathway but with AlmA and AlmB utilizing l-alanine as the amino acid precursor instead of l-serine.