Patients with indolent lymphoma undertaking recurrent or continuous B cell suppression are at risk of severe COVID‐19. Patients and healthy controls (HC; N = 13) received two doses of BNT162b2: follicular lymphoma (FL; N = 35) who were treatment naïve (TN; N = 11) or received immunochemotherapy (ICT; N = 23) and Waldenström's macroglobulinemia (WM; N = 37) including TN ( N = 9), ICT ( N = 14), or treated with Bruton's tyrosine kinase inhibitors (BTKi; N = 12). Anti‐spike immunoglobulin G (IgG) was determined by a high‐sensitivity flow‐cytometric assay, in addition to live‐virus neutralization. Antigen‐specific T cells were identified by coexpression of CD69/CD137 and CD25/CD134 on T cells. A subgroup ( N = 29) were assessed for third mRNA vaccine response, including omicron neutralization. One month after second BNT162b2, median anti‐spike IgG mean fluorescence intensity (MFI) in FL ICT patients (9977) was 25‐fold lower than TN (245 898) and HC (228 255, p = .0002 for both). Anti‐spike IgG correlated with lymphocyte count ( r = .63; p = .002), and time from treatment ( r = .56; p = .007), on univariate analysis, but only with lymphocyte count on multivariate analysis ( p = .03). In the WM cohort, median anti‐spike IgG MFI in BTKi patients (39 039) was reduced compared to TN (220 645, p = .0008) and HC ( p < .0001). Anti‐spike IgG correlated with neutralization of the delta variant ( r = .62, p < .0001). Median neutralization titer for WM BTKi (0) was lower than HC (40, p < .0001) for early‐clade and delta. All cohorts had functional T cell responses. Median anti‐spike IgG decreased 4‐fold from second to third dose ( p = .004). Only 5 of 29 poor initial responders assessed after third vaccination demonstrated seroconversion and improvement in neutralization activity, including to the omicron variant.

Noble gases are chemically inert, and it was therefore thought they would have little effect on biology. Paradoxically, it was found that they do exhibit a wide range of biological effects, many of which are target-specific and potentially useful and some of which have been demonstrated in vivo. The underlying mechanisms by which useful pharmacology, such as tissue and neuroprotection, anti-addiction effects, and analgesia, is elicited are relatively unexplored. Experiments to probe the interactions of noble gases with specific proteins are more difficult with gases than those with other chemicals. It is clearly impractical to conduct the large number of gas–protein experiments required to gain a complete picture of noble gas biology. Given the simplicity of atoms as ligands, in silico methods provide an opportunity to gain insight into which noble gas–protein interactions are worthy of further experimental or advanced computational investigation. Our previous validation studies showed that in silico methods can accurately predict experimentally determined noble gas binding sites in X-ray structures of proteins. Here, we summarize the largest reported in silico reverse docking study involving 127 854 protein structures and the five nonradioactive noble gases. We describe how these computational screening methods are implemented, summarize the main types of interactions that occur between noble gases and target proteins, describe how the massive data set that this study generated can be analyzed (freely available at group18.csiro.au), and provide the NDMA receptor as an example of how these data can be used to understand the molecular pharmacology underlying the biology of the noble gases. We encourage chemical biologists to access the data and use them to expand the knowledge base of noble gas pharmacology, and to use this information, together with more efficient delivery systems, to develop “atomic drugs” that can fully exploit their considerable and relatively unexplored potential in medicine.

F420 is a low-potential redox cofactor used by diverse bacteria and archaea. In mycobacteria, this cofactor has multiple roles, including adaptation to redox stress, cell wall biosynthesis, and activation of the clinical antitubercular prodrugs pretomanid and delamanid. A recent biochemical study proposed a revised biosynthesis pathway for F420 in mycobacteria; it was suggested that phosphoenolpyruvate served as a metabolic precursor for this pathway, rather than 2-phospholactate as long proposed, but these findings were subsequently challenged. In this work, we combined metabolomic, genetic, and structural analyses to resolve these discrepancies and determine the basis of F420 biosynthesis in mycobacterial cells. We show that, in whole cells of Mycobacterium smegmatis, phosphoenolpyruvate rather than 2-phospholactate stimulates F420 biosynthesis. Analysis of F420 biosynthesis intermediates present in M. smegmatis cells harboring genetic deletions at each step of the biosynthetic pathway confirmed that phosphoenolpyruvate is then used to produce the novel precursor compound dehydro-F420-0. To determine the structural basis of dehydro-F420-0 production, we solved high-resolution crystal structures of the enzyme responsible (FbiA) in apo-, substrate-, and product-bound forms. These data show the essential role of a single divalent cation in coordinating the catalytic precomplex of this enzyme and demonstrate that dehydro-F420-0 synthesis occurs through a direct substrate transfer mechanism. Together, these findings resolve the biosynthetic pathway of F420 in mycobacteria and have significant implications for understanding the emergence of antitubercular prodrug resistance. IMPORTANCE Mycobacteria are major environmental microorganisms and cause many significant diseases, including tuberculosis. Mycobacteria make an unusual vitamin-like compound, F420, and use it to both persist during stress and resist antibiotic treatment. Understanding how mycobacteria make F420 is important, as this process can be targeted to create new drugs to combat infections like tuberculosis. In this study, we show that mycobacteria make F420 in a way that is different from other bacteria. We studied the molecular machinery that mycobacteria use to make F420, determining the chemical mechanism for this process and identifying a novel chemical intermediate. These findings also have clinical relevance, given that two new prodrugs for tuberculosis treatment are activated by F420.

Lichen associations, a classic model for successful and sustainable interactions between micro-organisms, have been studied for many years. However, there are significant gaps in our understanding about how the lichen symbiosis operates at the molecular level. This review addresses opportunities for expanding current knowledge on signalling and metabolic interplays in the lichen symbiosis using the tools and approaches of systems biology, particularly network modelling. The largely unexplored nature of symbiont recognition and metabolic interdependency in lichens could benefit from applying a holistic approach to understand underlying molecular mechanisms and processes. Together with ‘omics’ approaches, the application of signalling and metabolic network modelling could provide predictive means to gain insights into lichen signalling and metabolic pathways. First, we review the major signalling and recognition modalities in the lichen symbioses studied to date, and then describe how modelling signalling networks could enhance our understanding of symbiont recognition, particularly leveraging omics techniques. Next, we highlight the current state of knowledge on lichen metabolism. We also discuss metabolic network modelling as a tool to simulate flux distribution in lichen metabolic pathways and to analyse the co-dependence between symbionts. This is especially important given the growing number of lichen genomes now available and improved computational tools for reconstructing such models. We highlight the benefits and possible bottlenecks for implementing different types of network models as applied to the study of lichens.

28F420 is a low-potential redox cofactor used by diverse bacteria and archaea. In mycobacteria, 29 this cofactor has multiple roles, including adaptation to redox stress, cell wall biosynthesis, and 30 activation of the clinical antitubercular prodrugs pretomanid and delamanid. A recent 31 biochemical study proposed a revised biosynthesis pathway for F420 in mycobacteria; it was 32 suggested that phosphoenolpyruvate served as a metabolic precursor for this pathway, rather 33 than 2-phospholactate as long proposed, but these findings were subsequently challenged. In 34 this work, we combined metabolomic, genetic, and structural analyses to resolve these 35 discrepancies and determine the basis of F420 biosynthesis in mycobacterial cells. We show that, 36 in whole cells of Mycobacterium smegmatis, phosphoenolpyruvate rather than 2-37 phospholactate stimulates F420 biosynthesis. Analysis of F420 biosynthesis intermediates 38 present in M. smegmatis cells harboring genetic deletions at each step of the biosynthetic 39 pathway confirmed that phosphoenolpyruvate is then used to produce the novel precursor 40 compound dehydro-F420-0. To determine the structural basis of dehydro-F420-0 production, we 41 solved high-resolution crystal structures of the enzyme responsible (FbiA) in apo, substrate, 42 and product bound forms. These data show the essential role of a single divalent cation in 43 coordinating the catalytic pre-complex of this enzyme and demonstrate that dehydro-F420-0 44 synthesis occurs through a direct substrate transfer mechanism. Together, these findings 45 resolve the biosynthetic pathway of F420 in mycobacteria and have significant implications for 46 understanding the emergence of antitubercular prodrug resistance. 47 48 49 50 51 52 53 54 55 56Factor 420 (F420) is a deazaflavin cofactor that mediates diverse redox reactions in bacteria and 57 archaea (1). Chemically, F420 consists of a redox-active deazaflavin headgroup (derived from 58 the chromophore Fo) that is conjugated to a variable-length polyglutamate tail via a 59 phosphoester linkage (2). While the Fo headgroup of F420 superficially resembles flavins (e.g. 60FAD, FMN), three chemical substitutions in the isoalloxazine ring give it distinct chemical 61 properties more reminiscent of nicotinamides (e.g. NADH, NADPH) (1). These include a low 62 standard potential (-350 mV) and obligate two-electron (hydride) transfer chemistry (3, 4). The 63 electrochemical properties of F420 make it ideal to reduce a wide range of otherwise 64 recalcitrant organic compounds (5-7). Diverse prokaryotes are known to synthesize F420, but 65 the compound is best characterised for its roles in methanogenesis in archaea, antibiotic 66 biosynthesis in streptomycetes, and metabolic adaptation of mycobacteria (1,(8)(9)(10)(11). In 67 mycobacteria, F420 is involved in a plethora of processes: central carbon metabolism, cell wall 68 synthesis, recovery from dormancy, resistance to oxidative stress, and inactivation of certain 69 bactericidal agents (7,(12)(13)(1...