Biology subjects

Sherman, D. H.

Publications and source records attributed to Sherman, D. H..

14 recordsLinked to original sources

bioRxiv2026

Chemoselective Halogenation of Premarineosin A for Next-Generation Antimalarial Development

Premarineosin A undergoes rapid, chemoselective C12 halogenation under mild conditions, providing brominated, chlorinated, fluorinated, and iodinated analogs. These derivatives retained potent antiplasmodial activity against both chloroquine-sensitive and -resistant Plasmodium falciparum strains and displayed smaller reductions in potency against the resistant strain than the parent compound.

biochemistry↗

bioRxiv2025

The gut microbiome of the Passalid beetle has high cellulolytic potential and constitutes an unrecognized system for production of greenhouse gasses in neotropical forests

Herbivores, and their associated microbiomes, play a major role in the global carbon cycle. Recalcitrant cellulose molecules are broken down by microorganisms that colonize the herbivore gut, releasing greenhouse gasses in the process. Passalid beetles are tropical herbivores that feed only on decaying wood and present subsocial behavior that may lead to the acquisition and sharing of microbial symbionts for efficient biomass and energy production. We collected five groups of Veturius sp. Passalid beetles from different logs in the Costa Rican rainforest and analyzed the microbial communities of larval and adult guts, as well as the substrate material in which they resided (partially chewed wood material mixed with feces that covers their tunnels). Adults, larvae, and substrate harbor different microbial communities, with substrate showing the highest diversity and richness, and larvae gut comprising a high abundance of methanogenic archaea. Reconstructed metagenome assembled genomes (MAGs) revealed that larvae and adults are enriched in genomes encoding a myriad of glycosyl hydrolases. Methanogenic taxa were enriched within the larval MAGs and bins, suggesting that larval microbiota participate in the final steps of cellulose decomposition in the system. Finally, we assessed methane production rates by Passalid beetles and compared them with termites. Our results show that Passalid larvae and adults produce methane at rates comparable to termites. Passalid and other beetle larvae are potentially underappreciated contributors to the carbon cycle and the biotic production of the greenhouse gas methane.

microbiology↗

bioRxiv2025

Advancing (-)-Premarineosin A as a Potent Antimalarial Therapeutic via Metabolic Engineering and Late-Stage Derivatization

Diversification of structurally complex natural products remains a key challenge in the discovery of next-generation therapeutics. Premarineosin A, a potent and selective antimalarial natural product, is a promising yet underexplored scaffold due to limited availability and synthetic complexity. In this work, we overcome both barriers by coupling metabolic engineering with late-stage derivatization, enabling the first systematic exploration of the premarineosin A scaffold. Rational engineering of Streptomyces eitanensis, encoding a (-)-premarineosin A biosynthetic gene cluster, increased titers over 200-fold. Sustainable production of (-)-premarineosin A enabled a unique semi-synthetic and biocatalytic derivatization campaign. In this first structure-activity relationship study of premarineosin A, we accessed a suite of novel analogs, including a C12-brominated derivative with nanomolar potency (EC50 < 5 nM). This work establishes (-)-premarineosin A as a tractable and evolvable antimalarial scaffold, demonstrating how chemical biology approaches can unlock new structural and pharmacological space from complex microbial metabolites.

microbiology↗

bioRxiv2024

Engineering a Biosynthetic Pathway for the Production of (+)-Brevianamides A and B in Escherichia coli

The privileged fused-ring system comprising the bicyclo[2.2.2]diazaoctane (BDO) core is prevalent in diketopiperazine (DKP) natural products with potent and diverse biological activities, with some being explored as drug candidates. Typically, only low yields of these compounds can be extracted from native fungal producing strains and the available synthetic routes remain challenging due to their structural complexity. BDO-containing DKPs including (+)-brevianamides A and B are assembled via multi-component biosynthetic pathways incorporating non-ribosomal peptide synthetases, prenyltransferases, flavin monooxygenases, cytochrome P450s and semi-pinacolases. To simplify access to this class of alkaloids, we designed an engineered biosynthetic pathway in Escherichia coli, composed of six enzymes sourced from different kingdoms of life. The pathway includes a cyclodipeptide synthase (NascA), a cyclodipeptide oxidase (DmtD2/DmtE2), a prenyltransferase (NotF), a flavin-dependent monooxygenase (BvnB), and kinases (PhoN and IPK). Cultivated in glycerol supplemented with prenol, the engineered E. coli strain produces 5.3 mg/L of (-)-dehydrobrevianamide E (4), which undergoes a terminal, ex vivo lithium hydroxide catalyzed rearrangement reaction to yield (+)-brevianamides A and B with a 46% yield and a 92:8 diastereomeric ratio. Additionally, titers of 4 were increased eight-fold by enhancing NADPH pools in the engineered E. coli strain. Our study combines synthetic biology, biocatalysis and synthetic chemistry approaches to provide a five-step engineered biosynthetic pathway for producing complex indole alkaloids in E. coli. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/627567v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@399e92org.highwire.dtl.DTLVardef@d98faaorg.highwire.dtl.DTLVardef@1671ac1org.highwire.dtl.DTLVardef@d7bc6_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

Ultra-high-throughput screening of antimicrobial combination therapies using a two-stage transparent machine learning model

Here, we present M2D2, a two-stage machine learning (ML) pipeline that identifies promising antimicrobial drug combinations, which are crucial for combating drug resistance. M2D2 addresses key challenges in drug combination discovery by predicting drug synergies using computationally generated drug-protein interaction data, thereby circumventing the need for expensive omics data. The model improves the accuracy of drug target identification using high-throughput experimental and computational methods via feedback between ML stages. M2D2s transparent framework provides mechanistic insights into drug interactions and was benchmarked against chemogenomics, transcriptomics, and metabolomics datasets. We experimentally validated M2D2 using high-throughput screening of 946 combinations of Food and Drug Administration (FDA)- approved drugs and antibiotics against Escherichia coli. We discovered synergy between a cerebrovascular drug and a widely used penicillin antibiotic and validated predicted mechanisms of action using genome-wide CRISPR inhibition screens. M2D2 offers a transparent ML tool for rapidly designing combination therapies and guides repurposing efforts while providing mechanistic insights.

systems biology↗

bioRxiv2024

Structure of a Putative Terminal Amidation Domain in Natural Product Biosynthesis

Bacteria are rich sources of pharmaceutically valuable natural products, many crafted by modular polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). PKS and NRPS systems typically contain a thioesterase (TE) to offload a linear or cyclized product from a carrier protein, but alternative chemistry is needed for products with a terminal amide. Several pathways with amidated products also possess an uncharacterized 400-amino acid terminal domain. We present the characterization and structure of this putative terminal amidation domain (TAD). TAD binds NAD with the nicotinamide near an invariant cysteine that is also accessible to an intermediate on a carrier protein, indicating a catalytic role. The TAD structure resembles cyanobacterial acyl-ACP reductase (AAR), which binds NADPH near an analogous catalytic cysteine. Bioinformatic analysis reveals that TADs are broadly distributed across bacterial phyla and often occur at the end of terminal NRPS modules, suggesting many amidated products may yet be discovered.

biochemistry↗

bioRxiv2024

Substrate Trapping in Polyketide Synthase Thioesterase Domains: Structural Basis for Macrolactone Formation

Emerging antibiotic resistance requires continual improvement in the arsenal of antimicrobial drugs, especially the critical macrolide antibiotics. Formation of the macrolactone scaffold of these polyketide natural products is catalyzed by a modular polyketide synthase (PKS) thioesterase (TE). The TE accepts a linear polyketide substrate from the termina PKS acyl carrier protein to generate an acyl-enzyme adduct that is resolved by attack of a substrate hydroxyl group to form the macrolactone. Our limited mechanistic understanding of TE selectivity for a substrate nucleophile and/or water has hampered development of TEs as biocatalysts that accommodate a variety of natural and non-natural substrates. To understand how TEs direct the substrate nucleophile for macrolactone formation, acyl-enzyme intermediates were trapped as stable amides by substituting the natural serine OH with an amino group. Incorporation of the unnatural amino acid, 1,3-diaminopropionic acid (DAP), was tested with five PKS TEs. DAP-modified TEs (TEDAP) from the pikromycin and erythromycin pathways were purified and tested with six full-length polyketide intermediates from three pathways. The erythromycin TE had permissive substrate selectivity, whereas the pikromycin TE was selective for its native hexaketide and heptaketide substrates. In a crystal structure of a native substrate trapped in pikromycin TEDAP, the linear heptaketide was curled in the active site with the nucleophilic hydroxyl group positioned 4 [A] from the amide-enzyme linkage. The curled heptaketide displayed remarkable shape complementarity with the TE acyl cavity. The strikingly different shapes of acyl cavities in TEs of known structure, including those reported here for juvenimicin, tylosin and fluvirucin biosynthesis, provide new insights to facilitate TE engineering and optimization.

biochemistry↗

bioRxiv2023

Investigating Metabolic Trends in the Oral Cavity to Identify Novel Metabolites

The human oral microbiome typically contains over 700 different microbial species. These interactions between the microorganisms within this community can shape the microenvironment throughout the human body, as these interactions are paramount to maintaining oral and overall systemic health. Recent advances in technology, such as next-generation sequencing (NGS), have revealed the complexities of the oral microbiome, linking dysbiosis of the oral microbiome with several chronic ailments such as cardiovascular disease, diabetes, and inflammatory bowel disease. However, the role of microbial secondary metabolites in oral and systemic disease progression remains poorly understood. Here, we conducted a metabolomics study on the human salivary secondary metabolome during the induction of gingival inflammation (gingivitis), the precursor to periodontal disease. In this study, we sought to assess the changes in the oral secondary metabolome during disease progression by emulating dysbiosis of the oral microbiome through a twenty-one-day induction of gingivitis in twenty human participants. We identified secondary metabolites, cyclo(L-Tyr-L-Pro) with regulatory properties for quorum sensing and inflammatory marker secretion, indicating a specialized role for secondary metabolites in oral health maintenance. Surprisingly, we also uncovered a previously unknown metabolic lag that occurs during dysbiosis recovery of the oral cavity, which indicates a lingering presence of signaling molecules for pathogenic microbe proliferation or a total oral metabolome modification following microenvironmental stress in the oral cavity. This work represents a high-resolution metabolomic landscape for understanding oral health during gingivitis that opens new opportunities for combating progressive periodontal diseases and sepsis due to the translocation of oral microbes in the human body.

molecular biology↗

bioRxiv2022

Expression of Microcystis biosynthetic gene clusters in natural populations suggests temporally dynamic synthesis of novel and known secondary metabolites in western Lake Erie

SummaryMicrocystis spp. produces diverse secondary metabolites within freshwater cyanoHABs around the world. In addition to the biosynthetic gene clusters (BGCs) encoding known compounds, Microcystis genomes harbor numerous BGCs of unknown function, indicating its poorly understood chemical repertoire. While recent studies show that Microcystis produces several metabolites in the lab and field, little work has focused on analyzing the abundance and expression of its broader suite of BGCs during cyanoHAB events. Here, we use metagenomic and metatranscriptomic approaches to track the relative abundance of Microcystis BGCs and their transcripts throughout the 2014 western Lake Erie cyanoHAB. Results indicate the presence of several transcriptionally active BGCs that are predicted to synthesize both known and novel secondary metabolites. The abundance and expression of these BGCs shifted throughout the bloom, with transcript abundance levels correlating with temperature, nitrate and phosphorus concentrations, and the abundance of co-occurring predatory and competitive eukaryotic microorganisms, suggesting the importance of both abiotic and biotic controls in regulating expression. This work highlights the need for understanding the chemical ecology and potential risks to human and environmental health posed by secondary metabolites that are produced but unmonitored, as well as the potential discovery of pharmaceutical compounds from cyanoHAB-derived BGCs. Originality-Statement of SignificanceMicrocystis spp. dominate cyanobacterial harmful algal blooms (cyanoHABs) worldwide and pose significant threats to water quality through the production of numerous secondary metabolites, many of which are toxic. While the toxicity and biochemistry of microcystins and several other compounds have been well studied, the broader suite of secondary metabolites produced by Microcystis remains poorly understood, leaving gaps in our understanding of their impacts on ecology, human and ecosystem health, or potential pharmaceutical application. In this study, we use metagenomic and transcriptomic datasets to examine the diversity of genes encoding synthesis of secondary metabolites in natural Microcystis populations and assess their patterns of transcription in the context of biotic and abiotic conditions in western Lake Erie cyanoHABs. Our results reveal the presence of a large diversity of both known gene clusters that encode toxic secondary metabolites as well as novel ones that encode cryptic compounds. This research highlights the need for targeted studies of the secondary metabolite diversity in western Lake Erie, a vital freshwater source to the United States and Canada.

microbiology↗

bioRxiv2021

Directed biosynthesis of fluorinated polyketides

Modification of polyketides with fluorine offers a promising approach to develop new pharmaceuticals. While synthetic chemical methods for site-specific incorporation of fluorine in complex molecules have improved in recent years, approaches for the direct biosynthetic fluorination of natural compounds are still rare. Herein, we present a broadly applicable approach for site-specific, biocatalytic derivatization of polyketides with fluorine. Specifically, we exchanged the native acyltransferase domain (AT) of a polyketide synthase (PKS), which acts as the gatekeeper for selection of extender units, with an evolutionarily related but substrate tolerant domain from metazoan type I fatty acid synthase (FAS). The resulting PKS/FAS hybrid can utilize fluoromalonyl coenzyme A and fluoromethylmalonyl coenzyme A for polyketide chain extension, introducing fluorine or fluoro-methyl disubstitutions in polyketide scaffolds. Addition of a fluorine atom is often a decisive factor toward developing superior properties in next-generation antibiotics, including the macrolide solithromycin. We demonstrate the feasibility of our approach in the semisynthesis of a fluorinated derivative of the macrolide antibiotic YC-17.

biochemistry↗

bioRxiv2020

Computationally-guided exchange of substrate selectivity motifs in a modular polyketide synthase acyltransferase

Acyltransferases (ATs) of modular polyketide synthases catalyze the installation of malonyl-CoA extenders into polyketide scaffolds. Subsequently, AT domains have been targeted extensively to site-selectively introduce various extenders into polyketides. Yet, a complete inventory of AT residues responsible for substrate selection has not been established, critically limiting the efficiency and scope of AT engineering. Here, molecular dynamics simulations were used to prioritize ~50 mutations in the active site of EryAT6 from erythromycin biosynthesis. Following detailed in vitro studies, 13 mutations across 10 residues were identified to significantly impact extender unit selectivity, including nine residues that were previously unassociated with AT specificity. Unique insights gained from the MD studies and the novel EryAT6 mutations led to identification of two previously unexplored structural motifs within the AT active site. Remarkably, exchanging both motifs in EryAT6 with those from ATs with unusual extender specificities provided chimeric PKS modules with expanded and inverted substrate specificity. Our enhanced understanding of AT substrate selectivity and application of this motif-swapping strategy is expected to advance our ability to engineer PKSs towards designer polyketides.

synthetic biology↗

bioRxiv2019

DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases

SummaryDDAP is a tool for predicting the biosynthetic pathways of the products of type I modular polyketide synthase (PKS) with the focus on providing a more accurate prediction of the ordering of proteins and substrates in the pathway. In this study, the module docking domain (DD) affinity prediction performance on a hold-out testing data set reached AUC = 0.88; the MRR of pathway prediction reached 0.67. DDAP has advantages compared to previous informatics tools in several aspects: (i) it does not rely on large databases, making it a high efficiency tool, (ii) the predicted DD affinity is represented by a probability (0 to 1), which is more intuitive than raw scores, (iii) its performance is competitive compared to the current popular rule-based algorithm. To the best of our knowledge, DDAP is so far the first machine learning based algorithm for type I PKS pathway prediction. We also established the first database of type I modular PKSs, featuring a comprehensive annotation of available docking domains information in bacterial biosynthetic pathways.\n\nAvailability and implementationThe DDAP database is available at https://tylii.github.io/ddap. The prediction algorithm DDAP is freely available on GitHub (https://github.com/tylii/ddap) and released under the MIT license.\n\nContactukarvind@umich.edu

bioinformatics↗

bioRxiv2018

Petrobactin protects against oxidative stress and enhances sporulation efficiency in Bacillus anthracis Sterne

Bacillus anthracis is a gram-positive bacillus that under conditions of environmental stress, such as low nutrients, can convert from a vegetative bacillus to a highly durable spore that enables long-term survival. The sporulation process is regulated by a sequential cascade of dedicated transcription factors but requires key nutrients to complete, one of which is iron. Iron acquisition by the iron-scavenging siderophore petrobactin is the only such system known to be required for vegetative growth of B. anthracis in iron-depleted conditions, e.g., in the host. However, the extent to which petrobactin is involved in spore formation is unknown. This work shows that efficient in vitro sporulation of B. anthracis requires petrobactin, that the petrobactin biosynthesis operon (asbA-F) is induced prior to sporulation, and that petrobactin itself is associated with spores. Petrobactin is also required for both oxidative stress protection during late stage growth and wild-type levels of sporulation in sporulation medium. When considered with the petrobactin-dependent sporulation in bovine blood also described in this work, these effects on in vitro growth and sporulation suggest that petrobactin is required for B. anthracis transmission via the spore during natural infections in addition to its key functions during active anthrax infections.\n\nImportanceBacillus anthracis causes the disease anthrax, which is transmitted via its dormant, spore phase. However, converting from bacilli to spore is a complex, energetically costly process that requires many nutrients including iron. B. anthracis requires the siderophore petrobactin to scavenge iron from host environments. We show that in the Sterne strain, petrobactin is required also for efficient sporulation, even when ample iron is available. The petrobactin biosynthesis operon is expressed during sporulation, and petrobactin is biosynthesized during growth in high iron sporulation medium but instead of being exported, the petrobactin remains intracellular to protect against oxidative stress and improve sporulation. It is also required for full growth and sporulation in blood (bovine), an essential step for anthrax transmission between mammalian hosts.

microbiology↗

bioRxiv2017

Structural basis of the Cope rearrangement and C-C bond-forming cascade in hapalindole/fischerindole biogenesis

STRUCTURESThe atomic coordinates and structure factors for:\n\nHpiC1 W73M/K132M SeMet (P212121) -1.7 [A]\n\nHpiC1 native (C2) -1.5 [A]\n\nHpiC1 native (P42) -2.1 [A]\n\nHpiC1 Y101F (C2) -1.4 [A]\n\nHpiC1 Y101S (C2) -1.4 [A]\n\nHpiC1 F138S (P21) -1.7 [A]\n\nHpiC1 Y101F/F138S (P21 -1.65 [A] have been deposited with the Research Collaboratory for Structural Bioinformatics as Protein Data Bank entries 5WPP, 5WPR, 6AL6, 5WPR, 5WPU, 6AL7, and 6AL8 (www.rcsb.org).\n\nGRANTSThis work was supported by: The authors thank the National Science Foundation under the CCI Center for Selective C-H Functionalization (CHE-1205646), the National Institutes of Health (CA70375 to RMW and DHS), R35 GM118101, R01 GM076477 and the Hans W. Vahlteich Professorship (to DHS) for financial support. M.G-B. thanks the Ramon Areces Foundation for a postdoctoral fellowship. J.N.S. acknowledges the support of the National Institute of General Medical Sciences of the National Institutes of Health under Award Number F32GM122218. Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575). The content does not necessarily represent the official views of the National Institutes of Health.\n\nABSTRACTHapalindole alkaloids are a structurally diverse class of cyanobacterial natural products defined by their varied polycyclic ring systems and diverse biological activities. These polycyclic scaffolds are generated from a common biosynthetic intermediate by the Stig cyclases in three mechanistic steps, including a rare Cope-rearrangement, 6-exo-trig cyclization, and electrophilic aromatic substitution. Here we report the structure of HpiC1, a Stig cyclase that catalyzes the formation of 12-epi-hapalindole U in vitro. The 1.5 [A] structure reveals a dimeric assembly with two calcium ions per monomer and the active sites located at the distal ends of the protein dimer. Mutational analysis and computational methods uncovered key residues for an acid catalyzed [3,3]-sigmatropic rearrangement and specific determinants that control the position of terminal electrophilic aromatic substitution leading to a switch from hapalindole to fischerindole alkaloids.

biochemistry↗