Naturally Occurring Organohalogen Compounds-A Comprehensive Review

Rare Chlorinated C19 Steroids Hocarnoids A and B from Hoya carnosa: Isolation, Semisynthesis, and Anti-inflammation

Steroids have consistently drawn scientific attention due to their diverse structures and exceptional pharmacological activities. However, halogenated natural steroids remain relatively rare, especially for those derived from plants. In this study, two chlorinated C19 steroids hocarnoids A (1) and B (2) were identified from the folk medicinal plant Hoya carnosa, representing the first examples of plant derived C-16 chlorinated steroids. Semisynthesis of compounds 1 and 2 was completed in 4 and 5 linear steps with 28.2% and 25.3% overall yields through a modified approach, corroborating further their structures. A total collection of 11 C19 steroids, including intermediates obtained during the synthesis, were evaluated for the anti-inflammatory activity against lipopolysaccharide (LPS)-induced inflammation-related RAW 264.7 macrophages. Among them, the natural product hocarnoid A (1) displayed the strongest anti-inflammatory activity with an IC50 value of 3.62 ± 0.08 μM, which also attenuated the mRNA levels of proinflammatory cytokines IL-1β, IL-6, IL-10, and TNF-α.

Unveiling organohalide respiration potential in River Nile sediments via 16S rRNA gene amplicon sequencing of endogenous bacterial communities

BACKGROUND

Industrial waste, agricultural runoff and untreated sewage contaminate the Nile, leaving a toxic legacy in its sediments. Organohalides-polluted sediment in particular poses serious public health risks and detrimental effects on aquatic life. Sediment microbiomes may harbor bacterial strains that could be utilized in bioremediation of such toxic pollutants.

MATERIAL AND METHODS

Two microbiomes from polluted River Nile sediments were analyzed by using 16S rRNA gene amplicon sequencing. In addition, PICRUSt analysis based on 16S rRNA data was used to explore the organohalide respiring bacteria (OHRB) genera and their corresponding organohalide respiration (OHR) activity. Microcosm studies were performed to validate the potential for dechlorination activity of River Nile sediment. Dechlorination of the parent chloroethenes into daughter end product were detected by gas chromatography coupled with flame ionization detection analysis.

RESULTS

Analysis of 16S rRNA gene amplicon sequences using the EZ-biocloud server identified Proteobacteria as the dominant phylum in both microbiomes, with Bacteroidetes and Chloroflexi prevalent in RNS1 sediment and Chlorobi in RNS2 sediment. EZ-biocloud and PCR analyses detected several potential OHRB genera, including Dehalococcoides, Dehalogenimonas, Desulfomonile, Desulfovibrio, and Geobacter, suggesting potential OHR activity. Further evidence for potential OHR activity was provided by PICRUSt functional prediction analysis, which suggested the presence of reductive dehalogenases as functional biomarkers associated with OHR in the sediment samples. Specifically, PICRUSt analysis predicted the presence of potential genes of tetrachloroethene reductive dehalogenase and 3-chloro-4-hydroxyphenylacetate reductive dehalogenase, previously linked to OHR. Microcosm studies confirmed the dechlorination potential of tetrachloroethene to dichloroethene.

CONCLUSION

This study demonstrates that River Nile sediment in industrialized area harbors distinct microbiomes enclosing various OHRB genera, providing substantial evidence for potential reductive dechlorination activity. It also provides potential functional biomarkers for OHR activity.

Iodide Enhances the Production of Pseurotin D over Pseurotin A by Inverting the Preference for the SN2 versus the SN2' Product in the Final Nonenzymatic Step

Nonenzymatic reactions, though critical in natural product biosynthesis, are significantly challenging to control. Adding 3% NaI to the culture medium of Penicillium janczewskii significantly increased pseurotin D (1) production and decreased pseurotin A (2) production. Previously, 1 and 2 were suggested to be produced via a nonenzymatic reaction, where the epoxide at C-10 undergoes SN2 (2) or SN2' (1) reactions. We confirmed that 1 was isolated as a 1:1 mixture of C-13 epimers by spectral elucidation via CP3 analysis aided by selective excitation NMR methods, which supported that 1 was produced through a nonenzymatic SN2' reaction. We propose that NaI increased the ratio of 1 by causing steric hindrance at the C-11 position of the transient intermediate, which makes C-13 more preferred in the SN2/SN2' competition.

Organohalide respiration: retrospective and perspective through bibliometrics

Organohalide-respiring bacteria (OHRB) play a pivotal role in the transformation of organohalogens in diverse environments. This bibliometric analysis provides a timely overview of OHRB research trends and identifies knowledge gaps. Publication numbers have steadily increased since the process was discovered in 1982, with fluctuations in total citations and average citations per publication. The past decade witnessed a peak in publications, underscoring heightened research activity and extensive collaboration. Thematic analysis identified two primary research foci: mechanistic exploration of OHRB and their interplay with environmental factors. Future research should prioritize elucidating the roles OHRB's play in biogeochemical cycling, utilizing synthetic biology tools for enhanced biotransformation, deciphering OHRB's ecological interactions, unraveling their evolutionary pathways, and investigating dehalogenation capabilities in other microorganisms, including archaea. These research directions promise to advance our understanding of microbially-driven organohalide transformations, microbial ecology, and genetic engineering potential, ultimately informing natural organohalide cycling and environmental management strategies.

Fe-Catalyzed Structurally Divergent γ-Polyhaloalkylation of Siloxydienes

Regioselective γ-polyhaloalkylation is achieved using tetrahalomethanes or α,α,α-trihaloalkyl compounds and siloxydienes via Fe(II) catalysis. A range of siloxydienes are functionalized in good yields with high stereoselectivity under mild reaction conditions. Structural divergence is observed as either haloalkylated or haloalkenylated products are formed on the basis of the substitution pattern of the siloxydiene. The halogenated products show utility in further synthetic transformations, selective reduction, and cross-coupling reactions.

MecE, MecB, and MecC proteins orchestrate methyl group transfer during dichloromethane fermentation

Dichloromethane (DCM), a common hazardous industrial chemical, is anaerobically metabolized by four bacterial genera: Dehalobacter, Dehalobacterium, Ca. Dichloromethanomonas, and Ca. Formimonas. However, the pivotal methyltransferases responsible for DCM transformation have remained elusive. In this study, we investigated the DCM catabolism of Dehalobacterium formicoaceticum strain EZ94, contained in an enriched culture, using a combination of biochemical approaches. Initially, enzymatic assays were conducted with cell-free protein extracts, after protein separation by blue native polyacrylamide gel electrophoresis. In the slices with the highest DCM transformation activity, a high absolute abundance of the methyltransferase MecC was revealed by mass spectrometry. Enzymatic activity assays with heterologously expressed MecB, MecC, and MecE from strain EZ94 showed complete DCM transformation only when all three enzymes were present. Our experimental results, coupled with the computational analysis of MecB, MecC, and MecE sequences, enabled us to assign specific roles in DCM transformation to each of the proteins. Our findings reveal that both MecE and MecC are zinc-dependent methyltransferases responsible for DCM demethylation and re-methylation of a product, respectively. MecB functions as a cobalamin-dependent shuttle protein transferring the methyl group between MecE and MecC. This study provides the first biochemical evidence of the enzymes involved in the anaerobic metabolism of DCM.IMPORTANCEDichloromethane (DCM) is a priority regulated pollutant frequently detected in groundwater. In this work, we identify the proteins responsible for the transformation of DCM fermentation in Dehalobacterium formicoaceticum strain EZ94 using a combination of biochemical approaches, heterologous expression of proteins, and computational analysis. These findings provide the basis to apply these proteins as biological markers to monitor bioremediation processes in the field.

EFSA Panel on Contaminants in the Food Chain (CONTAM), Knutsen HK, Åkesson A, Bampidis V, Bignami M, Bodin L, Chipman JK, Degen G, Hernández‐Jerez A, Hofer T, Landi S, Leblanc J, Machera K, Ntzani E, Rychen G, Sand S, Schwerdtle T, Vejdovszky K, Viviani B, Benford D, Hart A, Rose M, Schroeder H, Vleminckx C, Vrijheid M, Gkimprixi E, Kouloura E, Riolo F, Bordajandi LR, Hogstrand C. Update of the risk assessment of brominated phenols and their derivatives in food

The European Commission asked EFSA to update its 2012 risk assessment on brominated phenols and their derivatives in food, focusing on five bromophenols and one derivative: 2,4,6-tribromophenol (2,4,6-TBP), 2,4-dibromophenol (2,4-DBP), 4-bromophenol (4-BP), 2,6-dibromophenol (2,6-DBP), tetrabrominated bisphenol S (TBBPS), tetrabromobisphenol S bismethyl ether (TBBPS-BME). Based on the overall evidence, the CONTAM Panel considered in vivo genotoxicity of 2,4,6-TBP to be unlikely. Effects in liver and kidney were considered as the critical effects of 2,4,6-tribromophenol (2,4,6-TBP) in studies in rats. A BMDL10 of 353 mg/kg body weight (bw) per day for kidney papillary necrosis in male rats was identified and was selected as the reference point for the risk characterisation. The derivation of a health-based guidance value was not considered appropriate due to major limitations in the toxicological database. Instead, the margin of exposure (MOE) approach was applied to assess possible health concerns. Around 78,200 analytical results for 2,4,6-TBP in food were used to estimate dietary exposure for the European population. Considering the resulting MOE values, all far above an MOE of 6000 that does not raise a health concern, and accounting for the uncertainties affecting the exposure and hazard assessments, the CONTAM Panel concluded with at least 95% probability that the current dietary exposure to 2,4,6-TBP does not raise a health concern. Due to lack of occurrence data, no risk assessment could be performed for breastfed or formula-fed infants. No risk characterisation could be performed for any of the other brominated phenols and derivatives included in the assessment, due to lack of data both on the toxicity and occurrence.

A Survey of Recently Discovered Naturally Occurring Organohalogen Compounds

The discovery of naturally occurring organohalogen compounds has increased astronomically in the 55 years since they were first discovered─from fewer than 50 in 1968 to a combined 7,958 described examples in three comprehensive reviews. The present survey, which covers the period 2021-2023, brings the number of known natural organohalogens to approximately 8,400. The organization is according to species origin, and coverage includes marine and terrestrial plants, fungi, bacteria, marine sponges, corals, cyanobacteria, tunicates, and other marine organisms.

High Amounts of Halogenated Natural Products in Sperm Whales (Physeter macrocephalus) from Two Italian Regions in the Mediterranean Sea

Halogenated natural products (HNPs) are considered to be emerging contaminants whose environmental distribution and fate are only incompletely known. Therefore, several persistent and bioaccumulative HNP groups, together with man-made polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), were quantified in the blubber of nine sperm whales (Physeter macrocephalus) stranded on the coast of the Mediterranean Sea in Italy. The naturally occurring polybrominated hexahydroxanthene derivatives (PBHDs; sum of TetraBHD and TriBHD) were the most prominent substance class with up to 77,000 ng/g blubber. The mean PBHD content (35,800 ng/g blubber) even exceeded the one of PCBs (28,400 ng/g blubber), although the region is known to be highly contaminated with man-made contaminants. Based on mean values, Q1 ∼ PBDEs > MeO-BDEs ∼ 2,2'-diMeO-BB 80 and several other HNPs followed with decreasing amounts. All blubber samples contained an abundant compound whose molecular formula (C16H19Br3O2) was verified using high-resolution mass spectrometry. The only plausible matching isomer was (2S,4'S,9R,9'S)-2,7-dibromo-4'-bromomethyl-1,1-dimethyl-2,3,4,4',9,9'-9,9'-hexahydro-1H-xanthen-9-ol (OH-TriBHD), a hydroxylated secondary metabolite previously detected together with TriBHD and TetraBHD in a sponge known to be a natural producer of PBHDs. The estimated mean amount of the presumed OH-TriBHD was 3000 ng/g blubber, which is unexpectedly high for hydroxylated compounds in the lipids of marine mammals.

Informatics and Computational Approaches for the Discovery and Optimization of Natural Product-Inspired Inhibitors of the SARS-CoV-2 2'-O-Methyltransferase

The urgent need for new classes of orally available, safe, and effective antivirals─covering a breadth of emerging viruses─is evidenced by the loss of life and economic challenges created by the HIV-1 and SARS-CoV-2 pandemics. As frontline interventions, small-molecule antivirals can be deployed prophylactically or postinfection to control the initial spread of outbreaks by reducing transmissibility and symptom severity. Natural products have an impressive track record of success as prototypic antivirals and continue to provide new drugs through synthesis, medicinal chemistry, and optimization decades after discovery. Here, we demonstrate an approach using computational analysis typically used for rational drug design to identify and develop natural product-inspired antivirals. This was done with the goal of identifying natural product prototypes to aid the effort of progressing toward safe, effective, and affordable broad-spectrum inhibitors of Betacoronavirus replication by targeting the highly conserved RNA 2'-O-methyltransferase (2'-O-MTase). Machaeriols RS-1 (7) and RS-2 (8) were identified using a previously outlined informatics approach to first screen for natural product prototypes, followed by in silico-guided synthesis. Both molecules are based on a rare natural product group. The machaeriols (3-6), isolated from the genus Machaerium, endemic to Amazonia, inhibited the SARS-CoV-2 2'-O-MTase more potently than the positive control, Sinefungin (2), and in silico modeling suggests distinct molecular interactions. This report highlights the potential of computationally driven screening to leverage natural product libraries and improve the efficiency of isolation or synthetic analog development.

Identifying imprints of externally derived dust and halogens in the sedimentary record of an Iberian alpine lake for the past ∼13,500 years - Lake Peixão, Serra da Estrela (Central Portugal)

Iberian lacustrine sediments are a valuable archive to document environmental changes since the last glacial termination, seen as key for anticipating future climate/environmental changes and their far-reaching implications for generations to come. Herein, multi-proxy-based indicators of a mountain lake record from Serra da Estrela were used to reconstruct atmospheric (in)fluxes and associated climatic/environmental changes over the last ∼13.5 ka. Depositions of long-range transported dust (likely from the Sahara) and halogens (primarily derived from seawater) were higher for the pre-Holocene, particularly in the late Bølling-Allerød-Younger Dryas period, compared to the Holocene. This synchronous increase could be related to a recognized dust-laden atmosphere, along with the combined effect of (i) an earlier proposed effective transport of Sahara dust for higher latitudes during cold periods and (ii) the progressive Polar Front expansion southwards, with the amplification of halogen activation reactions in lower latitudes due to greater closeness to snow/sea ice (halide-laden) surfaces. Additionally, the orographic blocking of Serra da Estrela may have played a critical role in increasing precipitation of Atlantic origin at higher altitudes, with the presence of snow prompting physical and chemical processes involving halogen species. In the Late Holocene, the dust proxy records highlighted two periods of enhanced input to Lake Peixão, the first (∼3.5-2.7 ka BP) after the end of the last African Humid Period and the second, from the 19th century onwards, agreeing with the advent of commercial agriculture, and human contribution to land degradation and dust emission in the Sahara/Sahel region. The oceanic imprints throughout the Holocene matched well with North Atlantic rapid climatic changes that, in turn, coincided with ice-rafted debris or Bond events and other records of increased storminess for the European coasts. Positive parallel peaks in halogens were found in recent times, probably connected to fire extinction by halogenated alkanes and roadway de-icing.