Alzheimer's disease (AD) is a multifactorial disease with mixed pathologies. Consequentially, drugs targeting multiple pathological processes may offer synergistic benefits. While histone deacetylase (HDAC) inhibitors have demonstrated efficacy in alleviating AD-related pathologies in animal models, the neuroprotective Wnt/β-catenin signaling pathway remains compromised in AD brain. CI-994 is a class I HDAC inhibitor containing N-(2-aminophenyl)-benzamide. Our recent studies indicate that CI-994 is also an activator of Wnt/β-catenin signaling by stabilizing Wnt co-receptor LRP6. We herein use CI-994 as a scaffold to develop novel potent dual modulators of class I HDACs and Wnt/β-catenin signaling for AD therapy. Our lead compound, W2A-28, selectively inhibits class I HDAC1, 2 and 3 with IC50 values of 0.51 μM, 0.68 μM and 0.22 μM, respectively, and shows no inhibitory activities on other HDACs. Furthermore, W2A-28 potently activates Wnt reporter activity with an EC50 value of 1.61 μM in Wnt-3A-expressing HEK293 cells. As expected, activation of Wnt/β-catenin signaling by W2A-28 is associated with elevated LRP6 protein level. Importantly, W2A-28 displays excellent microsomal stability in both mouse and human liver microsomal stability assays, alongside high permeability and a lack of active efflux in MDR1-MDCKII models. Critically, W2A-28 treatment significantly enhances histone acetylation, activates Wnt/β-catenin signaling, suppresses tau phosphorylation, and reduces Aβ levels in AD patient-specific cerebral organoids carrying APOE ε4/ε4 or APOE ε3/ε4 with PSEN1 M146V mutation. Our findings position W2A-28 as a promising multi-target drug candidate for AD therapy.

Advances in genomic medicine accelerate the identification of mutations in disease-associated genes, but the pathogenicity of many mutations remains unknown, hindering their use in diagnostics and clinical decision-making. Predictive AI models are generated to combat this issue, but current tools display low accuracy when tested against functionally validated datasets. We show that integrating detailed conformational data extracted from molecular dynamics simulations (MDS) into advanced AI-based models increases their predictive power. We carry out an exhaustive mutational analysis of the disease gene PMM2 and subject structural models of each variant to MDS. AI models trained on this dataset outperform existing tools when predicting the known pathogenicity of mutations. Our best performing model, a neuronal networks model, also predicts the pathogenicity of several PMM2 mutations currently considered of unknown significance. We believe this model helps alleviate the burden of unknown variants in genomic medicine.

Selective inhibition of the more than 100 S1 family serine proteases is a long-standing challenge due to their active site similarity. Mesotrypsin, implicated in cancer progression, exemplifies these difficulties; no current inhibitors achieve selectivity over other human trypsins. We found an unexpected autoinhibited conformation of mesotrypsin via x-ray crystallography, revealing a cryptic pocket adjacent to the active site. Using high-throughput virtual screening targeting this cryptic pocket, we identified a conformationally selective small-molecule inhibitor that stabilizes the inactive state of mesotrypsin. This inhibitor demonstrates selectivity for mesotrypsin over other trypsins. Our findings challenge the accepted view of digestive trypsins as constitutively active enzymes lacking potential for allosteric regulation. Furthermore, analyses of other structures suggest that dynamic sampling of closed states with analogous allosteric cryptic pockets appears widespread among S1 serine proteases. These observations point to a potentially generalizable strategy to achieve selective inhibition, offering broad implications for drug development targeting serine proteases in cancer and other diseases.

Alzheimer’s disease (AD) is a multifactorial disease often with mixed pathologies. As such, drugs targeting multiple pathological processes simultaneously could have synergistic therapeutic effects. The histone acetylation homeostasis is greatly impaired in AD, and histone deacetylase (HDAC) inhibitors have been known to alleviate AD-relevant pathologies in various animal models. In addition, Wnt/β-catenin signaling is compromised in AD, and restoring Wnt/β-catenin signaling is an attractive therapeutic strategy for AD treatment. CI-994 is a class I HDAC inhibitor containing N-(2-aminophenyl)-benzamide. Our recent studies indicate that CI-994 is also an activator of Wnt/β-catenin signaling by stabilizing Wnt co-receptor LRP6. We use CI-994 as a scaffold to develop novel potent dual modulators for class I HDAC inhibition and Wnt/β-catenin signaling activation, and then determine the therapeutic potential of the lead compound W2A-28 in AD patient-specific iPSC-derived cerebral organoids. W2A-28 inhibits class I HDAC1, 2 and 3 activities with IC 50 values of 512 nM, 675 nM and 217 nM, respectively, with no inhibitory activities on other HDACs and Sirtuin family members. Furthermore, W2A-28 greatly increases Wnt reporter activity with an EC 50 value of 1.61 µM in Wnt-3A-expressing HEK293 cells. As expected, activation of Wnt/β-catenin signaling by W2A-28 is associated with elevated Wnt co-receptor LRP6 protein level by reducing LRP6 degradation. Importantly, W2A-28 displays excellent aqueous solubility and microsomal stability. Further, W2A-28 shows high permeability with no active efflux in MDR1-MDCKII permeability assays and is not a P-gp substrate. Finally, W2A-28 significantly reduces Aβ40 and Aβ42 levels and suppresses tau phosphorylation in AD patient-specific iPSC-derived cerebral organoids carrying APOE4. Our studies suggest that W2A-28 is a potential drug candidate for the treatment of AD.

Alzheimer's disease (AD) is marked by the pathological accumulation of amyloid beta-42 (Aβ42), contributing to synaptic dysfunction and neurodegeneration. While extracellular amyloid plaques are well-studied, increasing evidence highlights intracellular Aβ42 as an early and toxic driver of disease progression. In this study, we present a novel, Generative AI-based drug design approach to promote targeted degradation of Aβ42 via the ubiquitin-proteasome system (UPS), using E3 ligase-directed molecular glues. We systematically evaluated the ternary complex formation potential of Aβ42 with three E3 ligases (CRBN, VHL, and MDM2) through structure-based modeling, ADMET screening, and docking. We then developed a Ligase-Conditioned Junction Tree Variational Autoencoder (LC-JT-VAE) to generate ligase-specific small molecules, incorporating protein sequence embeddings and torsional angle-aware molecular graphs. Our results demonstrate that this generative model can produce chemically valid, novel, and target-specific molecular glues capable of facilitating Aβ42 degradation. This integrated approach offers a promising framework for designing UPS-targeted therapies for neurodegenerative diseases.

Complete loss-of-function mutations in the PRKN gene are a major cause of early-onset Parkinson’s disease (PD). PRKN encodes the Parkin protein, an E3 ubiquitin ligase that works in conjunction with the ubiquitin kinase PINK1 in a distinct quality control pathway to tag damaged mitochondria for autophagic clearance, i.e., mitophagy. According to previous structural investigations, Parkin protein is typically kept in an inactive conformation via several intramolecular, auto-inhibitory interactions. Here, we performed molecular dynamics simulations (MDS) to provide insights into conformational changes occurring during the de-repression of Parkin and the gain of catalytic activity. We analyzed four different Parkin-activating mutations that are predicted to disrupt certain aspects of its auto-inhibition. All four variants showed greater conformational motions compared to wild-type protein, as well as differences in distances between domain interfaces and solvent-accessible surface area, which are thought to play critical roles as Parkin gains catalytic activity. Our findings reveal that the studied variants exert a notable influence on Parkin activation as they alter the opening of its closed inactive structure, a finding that is supported by recent structure- and cell-based studies. These findings not only helped further characterize the hyperactive variants but overall improved our understanding of Parkin’s catalytic activity and nominated targets within Parkin’s structure for potential therapeutic designs.

Aggregated α-synuclein (α-SYN) proteins, encoded by the SNCA gene, are hallmarks of Lewy body disease (LBD), affecting multiple brain regions. However, the specific mechanisms underlying α-SYN pathology in cortical neurons, crucial for LBD-associated dementia, remain unclear. Here, we recapitulated α-SYN pathologies in human induced pluripotent stem cells (iPSCs)–derived cortical organoids generated from patients with LBD with SNCA gene triplication. Single-cell RNA sequencing, combined with functional and molecular validation, identified synaptic and mitochondrial dysfunction in excitatory neurons exhibiting high expression of the SNCA gene, aligning with observations in the cortex of autopsy-confirmed LBD human brains. Furthermore, we screened 1280 Food and Drug Administration–approved drugs and identified four candidates (entacapone, tolcapone, phenazopyridine hydrochloride, and zalcitabine) that inhibited α-SYN seeding activity in real-time quaking-induced conversion assays with human brains, reduced α-SYN aggregation, and alleviated mitochondrial dysfunction in SNCA triplication organoids and excitatory neurons. Our findings establish human cortical LBD models and suggest potential therapeutic drugs targeting α-SYN aggregation for LBD.

Neurodegenerative diseases are commonly associated with the formation of aberrant protein aggregates within the brain, and ultrastructural analyses have revealed that the proteins within these inclusions often assemble into amyloid filaments. Cryoelectron microscopy (cryo-EM) has emerged as an effective method for determining the near-atomic structure of these disease-associated filamentous proteins, and the resulting structures have revolutionized the way we think about aberrant protein aggregation and propagation during disease progression. These structures have also revealed that individual fibril conformations may dictate different disease conditions, and this newfound knowledge has improved disease modeling in the lab and advanced the ongoing pursuit of clinical tools capable of distinguishing and targeting different pathogenic entities within living patients. In this review, we summarize some of the recently developed cryo-EM structures of ex vivo α-synuclein, tau, β-amyloid (Aβ), TAR DNA-binding protein 43 (TDP-43), and transmembrane protein 106B (TMEM106B) fibrils and discuss how these structures are being leveraged toward mechanistic research and therapeutic development.

Background: While ‘immuno-competence’ is a well-known term, it lacks an operational definition. To address this omission, this study explored whether the temporal and structured data of the complete blood cell count (CBC) can rapidly estimate immuno-competence. To this end, one or more ratios that included data on all monocytes, lymphocytes and neutrophils were investigated. Materials and methods: Longitudinal CBC data collected from 101 COVID-19 patients (291 observations) were analyzed. Dynamics were estimated with several approaches, which included non-structured (the classic CBC format) and structured data. Structured data were assessed as complex ratios that capture multicellular interactions among leukocytes. In comparing survivors with non-survivors, the hypothesis that immuno-competence may exhibit feedback-like (oscillatory or cyclic) responses was tested. Results: While non-structured data did not distinguish survivors from non-survivors, structured data revealed immunological and statistical differences between outcomes: while survivors exhibited oscillatory data patterns, non-survivors did not. In survivors, many variables (including IL-6, hemoglobin and several complex indicators) showed values above or below the levels observed on day 1 of the hospitalization period, displaying L-shaped data distributions (positive kurtosis). In contrast, non-survivors did not exhibit kurtosis. Three immunologically defined data subsets included only survivors. Because information was based on visual patterns generated in real time, this method can, potentially, provide information rapidly. Discussion: The hypothesis that immuno-competence expresses feedback-like loops when immunological data are structured was not rejected. This function seemed to be impaired in immuno-suppressed individuals. While this method rapidly informs, it is only a guide that, to be confirmed, requires additional tests. Despite this limitation, the fact that three protective (survival-associated) immunological data subsets were observed since day 1 supports many clinical decisions, including the early and personalized prognosis and identification of targets that immunomodulatory therapies could pursue. Because it extracts more information from the same data, structured data may replace the century-old format of the CBC.

The maturation of brain microvascular endothelial cells leads to the formation of a tightly sealed monolayer, known as the blood-brain barrier (BBB). The BBB damage is associated with the pathogenesis of age-related neurodegenerative diseases including vascular cognitive impairment and Alzheimer's disease. Growing knowledge in the field of epigenetics can enhance the understanding of molecular profile of the BBB and has great potential for the development of novel therapeutic strategies or targets to repair a disrupted BBB. Histone deacetylases (HDACs) inhibitors are epigenetic regulators that can induce acetylation of histones and induce open chromatin conformation, promoting gene expression by enhancing the binding of DNA with transcription factors. We investigated how HDAC inhibition influences the barrier integrity using immortalized human endothelial cells (HCMEC/D3) and the human induced pluripotent stem cell (iPSC)-derived brain vascular endothelial cells. The endothelial cells were treated with or without a novel compound named W2A-16. W2A-16 not only activates Wnt/β-catenin signaling but also functions as a class I HDAC inhibitor. We demonstrated that the administration with W2A-16 sustained barrier properties of the monolayer of endothelial cells, as evidenced by increased trans-endothelial electrical resistance (TEER). The BBB-related genes and protein expression were also increased compared with non-treated controls. Analysis of transcript profiles through RNA-sequencing in hCMEC/D3 cells indicated that W2A-16 potentially enhances BBB integrity by influencing genes associated with the regulation of the extracellular microenvironment. These findings collectively propose that the HDAC inhibition by W2A-16 plays a facilitating role in the formation of the BBB. Pharmacological approaches to inhibit HDAC may be a potential therapeutic strategy to boost and/or restore BBB integrity.

This letter demonstrates the potential of novel cryptic proteins resulting from TAR DNA-binding protein 43 (TDP-43) dysfunction as markers of TDP-43 pathology in neurodegenerative diseases.

Mutations in the PINK1 and PRKN genes are the most frequent genetic cause of early-onset Parkinson disease. The pathogenic p.R275W substitution in PRKN is the most frequent substitution observed in patients, and thus far has been characterized mostly through overexpression models that suggest a possible gain of toxic misfunction. However, its effects under endogenous conditions are largely unknown. We used patient fibroblasts, isogenic neurons, and post-mortem human brain samples from carriers with and without PRKN p.R275W to assess functional impact. Immunoblot analysis and immunofluorescence were used to study mitophagy activation, and mitophagy execution was analyzed by flow cytometry of the reporter mitoKeima. The functional analysis was accompanied by structural investigation of PRKN p.R275W. We observed lower PRKN protein in fibroblasts with compound heterozygous p.R275W mutations. Isogenic neurons showed an allele-dose dependent decrease in PRKN protein. Lower PRKN protein levels were accompanied by diminished phosphorylated ubiquitin and decreased MFN2 modification. Mitochondrial degradation was also allele-dose dependently impaired. Consistently, PRKN protein levels were drastically reduced in human brain samples from p.R275W carriers. Finally, structural simulations showed significant changes in the closed form of PRKN p.R275W. Our data suggest that under endogenous conditions the p.R275W mutation results in a loss-of-function by destabilizing PRKN.

Tumor necrosis factor-α (TNFα) is a master cytokine which induces expression of chemokines and adhesion molecules, such as intercellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion molecule 1 (VCAM-1), in endothelial cells to initiate the vascular inflammatory response. In this study, we identified neuropilin-1 (NRP1), a co-receptor of several structurally diverse ligands, as a modulator of TNFα-induced inflammatory response of endothelial cells. NRP1 shRNA expression suppressed TNFα-stimulated leukocyte adhesion and expression of ICAM-1 and VCAM-1 in human umbilical vein endothelial cells (HUVECs). Likewise, it reduced TNFα-induced phosphorylation of MAPK p38 but did not significantly affect other TNF-induced signaling pathways, such as the classical NFκB and the AKT pathway. Immunofluorescent staining demonstrated co-localization of NRP1 with the two receptors of TNF, TNFR1 and TNFR2. Co-immunoprecipitation further confirmed that NRP1 was in the same protein complex or membrane compartment as TNFR1 and TNFR2, respectively. Modulation of NRP1 expression, however, neither affected TNFR levels in the cell membrane nor the receptor binding affinities of TNFα. Although a direct interface between NRP1 and TNFα/TNFR1 appeared possible from a protein docking model, a direct interaction was not supported by binding assays in cell-free microplates and cultured cells. Furthermore, TNFα was shown to downregulate NRP1 in a time-dependent manner through TNFR1-NFκB pathway in HUVECs. Taken together, our study reveals a novel reciprocal crosstalk between NRP1 and TNFα in vascular endothelial cells.

Mesotrypsin is an S1 family serine protease which promotes invasiveness of several human cancers. Other S1 family members play important roles in digestion, coagulation, and other critical biological processes. The active sites of these enzymes are highly similar, and selective targeting of specific serine proteases via conventional orthosteric small molecules is a technical challenge that is often not achieved. Allosteric sites tend to proffer greater variability than active sites to allow for selective targeting among similar proteins. However, until recently, there had been no reported allosteric site for the regulation of mesotrypsin activity. Our group has recently solved an x-ray crystal structure of unliganded mesotrypsin that revealed a loop of residues obscuring the active site, identified as an autoinhibitory loop. The structure also exhibited an allosteric binding pocket in this novel conformation which possessed two residues that differed among the three human trypsin isoforms. We hypothesized that the loop might be stabilized in the autoinhibitory conformation via a small molecule ligand targeting the exposed allosteric binding site. We further posited that the allosteric site might permit selective inhibition of mesotrypsin, due to the sequence differences lining the pocket. To explore this hypothesis, we subjected the mesotrypsin allosteric binding site and altered morphology of the active site to high-throughput virtual screening, resulting in collectively 58 hit compounds that met multiple cutoff criteria. The hits were then tested for inhibitory capability towards mesotrypsin using enzyme kinetics with a chromogenic substrate. Four of the compounds demonstrated mesotrypsin inhibition and were similarly tested against cationic trypsin and anionic trypsin. A single compound displayed approximately 5-fold selectivity for mesotrypsin over the other trypsins, to date the most selective small molecule targeting mesotrypsin. Additionally, we evaluated the compound selectivity against various coagulation pathway serine proteases that represent clinically relevant off-targets. The results demonstrated a strong preference for mesotrypsin. Our approach for selective allosteric inhibition of mesotrypsin may represent a paradigm shifting mode for targeting other S1 family serine proteases. Examination of publicly available structures of serine proteases indicates conformational heterogeneity the 220 loop, analogous to the mesotrypsin autoinhibitory loop. There appears to be a single well-defined uninhibited conformation that is poised for substrate access and catalytic activity. However, there are multiple autoinhibited conformations with differing levels of occlusion of the active site observed in different enzymes. Structural profiling of these autoinhibited conformations reveals prospective allosteric binding pockets with differential morphologies, suggesting potential for selective inhibition. Taken together, our findings support our hypothesis that selective inhibition of mesotrypsin, and perhaps other serine proteases, may be achieved by exploiting a cryptic allosteric binding site, locking the enzymes in an inactive conformation. The authors would like to acknowledge funding support under NIH R01GM144393, as well as synchrotron access from Lawrence Berkeley National Laboratory under ALS-11671.

Serine Protease Inhibitor Family AS (SERPINA5), also known as PCI (Protein C Inhibitor) or PAl3 (plasminogen activator inhibitor 3), is a member of the serine proteinase inhibitor family. Our previous studies have shown that increased expression of the SERPINA5 gene is associated with tau expression in the brain and Alzheimer's disease. We hypothesize selective targeting of SERPINA5 has potential as a therapy for Alzheimer's disease. Since the full-length 3D human SERPINA5 structure is still unknown, we performed computational modeling in silico using Schrodinger Suite 2022-2 (Prime software), AlphaFold 2 and OpenFold (trainable PyTorch reproduction of DeepMind's AlphaFold). Molecular mapping was used to identify binding hot spots, which are regions of the protein surface that can bind small molecules or drug fragments and was calculated by ATLAS (FTMap) software. The best structures with different conformational states were selected and molecular mapping was performed for each of them. The druggability hot spots were determined, then ranked according to their ability to bind small molecules and peptides on the SERPINA5 protein surface. These results will be used in molecular docking, molecular dynamics simulations and biological testing research.

We have previously shown computationally that Mycolactone (MLN), a toxin produced by Mycobacterium ulcerans, strongly binds to Munc18b and other proteins, presumably blocking degranulation and exocytosis of blood platelets and mast cells. We investigated the effect of MLN on endocytosis using similar approaches, and it bound strongly to the N-terminal of the clathrin protein and a novel SARS-CoV-2 fusion protein. Experimentally, we found 100% inhibition up to 60 nM and 84% average inhibition at 30 nM in SARS-CoV-2 live viral assays. MLN was also 10× more potent than remdesivir and molnupiravir. MLN's toxicity against human alveolar cell line A549, immortalized human fetal renal cell line HEK293, and human hepatoma cell line Huh7.1 were 17.12%, 40.30%, and 36.25%, respectively. The cytotoxicity IC50 breakpoint ratio versus anti-SARS-CoV-2 activity was more than 65-fold. The IC50 values against the alpha, delta, and Omicron variants were all below 0.020 µM, and 134.6 nM of MLN had 100% inhibition in an entry and spread assays. MLN is eclectic in its actions through its binding to Sec61, AT2R, and the novel fusion protein, making it a good drug candidate for treating and preventing COVID-19 and other similarly transmitted enveloped viruses and pathogens.

ID 18265 Poster Board 329 Matrix MetalloProteinases (MMPs) are a family of 23 multidomain zinc-dependent endopeptidases that primarily target extracellular matrix proteins for degradation. An array of physiological functions rely on MMP activity; dysfunction results in diseases/disorders, including cancers, cardiovascular and pulmonary disease, and arthritis. Despite considerable long-term efforts towards MMP-targeted pharmacology, most potential therapeutics fail in clinical trials due to off-target toxicity against MMPs and other zinc-dependent endopeptidases. Our group has been applying protein engineering efforts towards endogenous Tissue Inhibitors of MetalloProteinases (TIMPs) to create high-affinity and selective inhibitors for disease-associated MMPs. We previously utilized semi-random mutagenesis and yeast surface display to identify an ultrabinder variant of TIMP1 with enhanced affinity towards MMP3, a target in cancer and lung fibrotic diseases, and solved a co-crystal structure of MMP3 bound to this engineered ultrabinder TIMP variant. Here, we employ modeling and molecular dynamics simulations on unbound and MMP3-bound TIMP1 and the ultrabinder variant to investigate the biophysical etiology of MMP-TIMP molecular recognition and of mutation-induced affinity improvements. Our simulations reveal localized induced fit at the zinc-chelating portion of TIMP upon binding MMP, whereas other binding interface regions seem to rely more on innate shape complementarity and conformational selection. Inter-residue motion covariance matrices reveal that MMP binding also reorganizes motion coupling throughout TIMP globally; this suggests that allosteric regulation of the binding interface differs between the unbound and MMP-bound states. Comparisons of molecular dynamics trajectories were made between WT TIMP1 and the ultrabinder TIMP1 variant. Time-resolved analyses of ultrabinder TIMP1 shows that it possesses stable secondary structural alterations that increase TIMP interdomain interactions, as well as protein-protein interactions with MMP3. Dynamical network analyses show that the engineered TIMP1 is able to propagate internal motions with greater efficiency, which appears to suppress motions perturbing TIMP from MMP-congruent configurations. In both the unbound and the MMP-bound states, variant TIMP1 has reduced conformational variability compared to WT TIMP1, with greater representation of conformations resembling that of the bound crystal structure, and more favorable predicted binding energy to MMP3. Overall, our results show that the engineered ultrabinder TIMP1 variant possesses altered protein dynamics that promote MMP3 compatibility in multiple ways, both via preconfiguration of unbound TIMP and via maintenance of the MMP/TIMP complex. These data suggest strategies that utilize intrinsic protein dynamics to improve affinity and selectivity of TIMPs in future engineering efforts towards biopharmaceutical development. This research is supported by NIH R01GM132100

Abstract BACKGROUND Mutations of NFkB1 are a known cause of inborn errors of immunity resulting in immunodeficiency due to the role of NFkB1 as a transcriptional regulator of immunomodulating proteins. We present a patient with a diagnosis of common variable immunodeficiency (CVID), cytopenias with massive splenomegaly, and nodular regenerative hyperplasia of the liver. Our proband, a 22-year-old male, presents with a clinical picture of immunodeficiency, and has a maternal cousin with a similar gene mutation but differing phenotype. Next generation panel sequencing (NGPS) was utilized to discover a novel, single point mutation variant in NFkB1, V213E, that is present in our proband. METHODS The novel single-point mutation V213E in the NFkB gene was modeled in-silico using the I-TASSER homology modeling software. Molecular dynamics simulations of both the wild type and variant mutant form fitted to accommodate the novel mutation were conducted and analyzed to assess for possible pathogenicity of the novel mutation. RESULTS This variant replaces Valine with Glutamic Acid at position 213 in the transcription regulator’s sequence. We perform molecular modeling to analyze the proteomic impact and difference in molecular dynamics (MDS) which depicted suppressed dynamics in the ankyrin region and death domain of the protein complex. Analysis of the proband’s family showed no significant family history except for the maternal cousin with a mutation in NFkB1. CONCLUSION This case both highlights the heterogeneity in phenotype of NFkB1 pathogenic variants as shown in this patient, full penetrance of the variant mutation, and suggests the pathogenicity of a new variant through protein modeling techniques and molecular dynamic simulations.

The 2,5-diketopiperazines are a prominent class of bioactive molecules. The nocardioazines are actinomycete natural products that feature a pyrroloindoline diketopiperazine scaffold composed of two D-tryptophan residues functionalized by N - and C -methylation, prenylation, and diannulation. Here we identify and characterize the nocardioazine B biosynthetic pathway from marine Nocardiopsis sp. CMB-M0232 by using heterologous biotransformations, in vitro biochemical assays, and macromolecular modeling. Assembly of the cyclo -L-Trp-L-Trp diketopiperazine precursor is catalyzed by a cyclodipeptide synthase. A separate genomic locus encodes tailoring of this precursor and includes an aspartate/glutamate racemase homolog as an unusual D/L isomerase acting upon diketopiperazine substrates, a phytoene synthase-like prenyltransferase as the catalyst of indole alkaloid diketopiperazine prenylation, and a rare dual function methyltransferase as the catalyst of both N - and C -methylation as the final steps of nocardioazine B biosynthesis. The biosynthetic paradigms revealed herein showcase Nature’s molecular ingenuity and lay the foundation for diketopiperazine diversification via biocatalytic approaches.