Structural Elucidation of Cryptic Algaecides in Marine Algal-Bacterial Symbioses by NMR Spectroscopy and MicroED

Applying 3D ED/MicroED workflows toward the next frontiers

We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small molecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation.

Marine natural products

Covering: January to the end of December 2022This review covers the literature published in 2022 for marine natural products (MNPs), with 645 citations (633 for the period January to December 2022) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, the submerged parts of mangroves and other intertidal plants. The emphasis is on new compounds (1417 in 384 papers for 2022), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of NP structure class diversity in relation to biota source and biome is discussed.

MicroED in drug discovery

The cryo-electron microscopy (cryo-EM) method microcrystal electron diffraction (MicroED) was initially described in 2013 and has recently gained attention as an emerging technique for research in drug discovery. As compared to other methods in structural biology, MicroED provides many advantages deriving from the use of nanocrystalline material for the investigations. Here, we review the recent advancements in the field of MicroED and show important examples of small molecule, peptide and protein structures that has contributed to the current development of this method as an important tool for drug discovery.

Ecological Niche-Inspired Genome Mining Leads to the Discovery of Crop-Protecting Nonribosomal Lipopeptides Featuring a Transient Amino Acid Building Block

Investigating the ecological context of microbial predator-prey interactions enables the identification of microorganisms, which produce multiple secondary metabolites to evade predation or to kill the predator. In addition, genome mining combined with molecular biology methods can be used to identify further biosynthetic gene clusters that yield new antimicrobials to fight the antimicrobial crisis. In contrast, classical screening-based approaches have limitations since they do not aim to unlock the entire biosynthetic potential of a given organism. Here, we describe the genomics-based identification of keanumycins A-C. These nonribosomal peptides enable bacteria of the genus Pseudomonas to evade amoebal predation. While being amoebicidal at a nanomolar level, these compounds also exhibit a strong antimycotic activity in particular against the devastating plant pathogen Botrytis cinerea and they drastically inhibit the infection of Hydrangea macrophylla leaves using only supernatants of Pseudomonas cultures. The structures of the keanumycins were fully elucidated through a combination of nuclear magnetic resonance, tandem mass spectrometry, and degradation experiments revealing an unprecedented terminal imine motif in keanumycin C extending the family of nonribosomal amino acids by a highly reactive building block. In addition, chemical synthesis unveiled the absolute configuration of the unusual dihydroxylated fatty acid of keanumycin A, which has not yet been reported for this lipodepsipeptide class. Finally, a detailed genome-wide microarray analysis of Candida albicans exposed to keanumycin A shed light on the mode-of-action of this potential natural product lead, which will aid the development of new pharmaceutical and agrochemical antifungals.

Technical and engineering considerations for designing therapeutics and delivery systems

The newly-emerged pathological conditions and increased rates of drug resistance necessitate application of the state-of-the-art technologies for accelerated discovery of the therapeutic candidates and obtaining comprehensive knowledge about their targets, action mechanisms, and interactions within the body including those between the receptors and drugs. Using the physics- and chemistry-based modern techniques for theranostic purposes, preparing smart carriers, local delivery of genes or drugs, and enhancing pharmaceutical bioavailability could be of great value against the hard-to-treat diseases and growing drug resistance. Besides the artificial intelligence- and quantum-based techniques, crystal engineering capable of designing new molecules with appropriate characteristics, improving the stability and bioavailability of poorly soluble drugs, and efficient carrier development could play a crucial role in manufacturing efficient pharmaceuticals and reducing the adverse events. In this context, identifying the structures and behaviors of crystals and predicting their characteristics are of great value. Electron diffraction by accelerated analysis of the chemicals and sensitivity to charge alterations, electromechanical tools for controlled delivery of therapeutics, mechatronics via fabrication of multi-functional smart products including the organ-on-chip devices for healthcare applications, and optomechatronics by overcoming the limitations of conventional biomedical techniques could address the unmet biomedical requirements and facilitate development of more effective theranostics with improved outcomes.

Electron Diffraction of 3D Molecular Crystals

Electron crystallography has a storied history which rivals that of its more established X-ray-enabled counterpart. Recent advances in data collection and analysis have sparked a renaissance in the field, opening a new chapter for this venerable technique. Burgeoning interest in electron crystallography has spawned innovative methods described by various interchangeable labels (3D ED, MicroED, cRED, etc.). This Review covers concepts and findings relevant to the practicing crystallographer, with an emphasis on experiments aimed at using electron diffraction to elucidate the atomic structure of three-dimensional molecular crystals.

The Small-Molecule Language of Dynamic Microbial Interactions

Although microbes are routinely grown in monocultures in the laboratory, they are almost never encountered as single species in the wild. Our ability to detect and identify new microorganisms has advanced significantly in recent years, but our understanding of the mechanisms that mediate microbial interactions has lagged behind. What makes this task more challenging is that microbial alliances can be dynamic, consisting of multiple phases. The transitions between phases, and the interactions in general, are often mediated by a chemical language consisting of small molecules, also referred to as secondary metabolites or natural products. In this microbial lexicon, the molecules are like words and through their effects on recipient cells they convey meaning. The current review highlights three dynamic microbial interactions in which some of the words and their meanings have been characterized, especially those that mediate transitions in selected multiphasic associations. These systems provide insights into the principles that govern microbial symbioses and a playbook for interrogating similar associations in diverse ecological niches. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.