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de la Fuente-Nunez, C.

Publications and source records attributed to de la Fuente-Nunez, C..

At least 19 recordsLinked to original sources

Designing antimicrobials with programmable mechanism and safety

Antimicrobial peptides (AMPs) are a promising solution to antimicrobial resistance, yet generative models for their design cannot control the physicochemical properties and motifs that shape activity and selectivity. Here, we present OmegAMP, a conditional diffusion framework controlling net charge, mean hydrophobicity, and sequence length, supporting de novo, analog, and motif-guided design. Across 204 wet-lab characterized peptides, de novo generation yielded antimicrobials with broad activity against multidrug-resistant Gram-negative isolates. Analog generation converted six inactive prototypes into antimicrobials, with the prototype determining each analog's membrane-disruption mode and mammalian-cell safety. Motif-guided analog generation preserved lipopolysaccharide engagement of active prototypes, and a redesigned non-antimicrobial leucine zipper acquired antimicrobial activity while retaining DNA-perturbing character in vitro. In murine skin and thigh infection models, leads reduced bacterial burden, with a motif-guided DNA-perturbing lead matching the fluoroquinolone control systemically. OmegAMP opens a programmable route to new peptide antibiotics whose mechanism and safety follow from the chosen prototype.

bioinformatics↗

Ancient human mitochondrial genomes encode antimicrobial peptides

Mitochondria are bacteria-derived organelles that coordinate major innate immune pathways, but whether mitochondrial genomes themselves encode direct antimicrobial functions is underexplored. Here, we test the hypothesis that ancient human mitochondrial DNA is not only an evolutionary record, but also contains encrypted peptide sequences with the capacity to contribute to host defense. Because mitochondria descend from a bacterial endosymbiont and retain bacterial-like molecular features, we reasoned that their compact genomes might preserve sequence fragments capable of engaging bacterial-like membranes or bacterial physiology. We mined 2,025 ancient human mitochondrial genomes using a computational pipeline that couples ORF extraction and deep learning, identifying 65 candidate peptides that we term mitochondrins. We synthesized 38 candidates and experimentally validated 14 as antimicrobials against clinically relevant Gram-negative and Gram-positive bacteria. Active mitochondrins were not defined by length, charge, or helicity alone; instead, potency depended on precise hydrophobic-cationic patterning, with nested peptide families revealing how single motif-level changes can switch activity on or off. Mechanistic assays showed that mitochondrins span multiple antibacterial modalities, from strong membrane disruption to potent activity with limited membrane perturbation, suggesting noncanonical or multi-step killing mechanisms. Several peptides displayed low cytotoxicity toward human cells, and one representative mitochondrin reduced bacterial burden in a murine skin abscess model. These findings provide a biochemical basis for the hypothesis that mitochondrial genomes may contribute to innate immunity.

bioengineering↗

Peptide structural plasticity is predictable from sequence and environment

Many peptides often do not have a single dominant structure. Instead, many remain disordered in water and fold when they encounter membranes or other chemical environments, a property that underlies diverse biological functions but is difficult to predict. Here we introduce ApexFold, a machine-learning frame-work that predicts how peptide secondary structure change across environments. ApexFold uses peptide sequence and features together with physicochemical descriptors of the surrounding medium to estimate the fractions of helical, {beta}-like and disordered structure expected in each condition. Trained on circular-dichroism measurements from 1,187 peptides assayed in water, co-solvents and membrane-mimicking micelles, ApexFold predicted solvent-induced structural shifts in independent peptide panels and outperformed static structure predictors that return a single conformation. These results show that peptide structural plasticity can be learned from sequence and environment, providing a way to prioritize peptides and experimental conditions before synthesis and structural characterization.

bioengineering↗

Integrated kidney and urine proteomics define encrypted antimicrobial peptides as effectors of host defence in human pyelonephritis

Antimicrobial peptides (AMPs) are key effectors of host defence, however, their functional deployment across renal tissue and urine in pyelonephritis (PN) remains incompletely understood. Here, we integrate kidney and urine proteomics with urinary peptidomics and computational prediction to define AMP organisation and function. Proteomic analysis indicated coordinated induction of multiple AMPs in infected kidneys. These patterns were recapitulated in the urinary proteome, where AMP abundance correlated with leukocyte counts. Multiplex immunofluorescence microscopy localised these AMPs to myeloid cells, identifying them as central effector sources. Importantly, analysis of the urine peptidome revealed multiple encrypted AMPs (EPs), which arise from proteolytic processing of precursor proteins. To systematically assess their relevance for host defence, we applied an ensemble of machine learning-based predictors to prioritise candidates with activity in the urinary environment. This approach identified several potential EPs, among which the S100A12-derived peptide Calcitermin was confirmed in patient urine. Furthermore, it exerts antibacterial activity against uropathogenic E. coli (UPEC) and modulates myeloid cell responses. Together, these findings define a coordinated and compartmentalised AMP defence programme in human PN that extends beyond increased peptide expression, highlighting EPs as functionally relevant effectors with therapeutic potential.

immunology↗

Integrative machine learning predicts activating kinase mutations for precision oncology

Kinases are enzymes that catalyze phosphorylation and play crucial roles in a myriad of cellular regulatory processes and hemostasis. Patient-specific genetic mutations that aberrantly activate kinases can profoundly influence cancer progression and alter drug efficacy. Predicting the impact of such missense mutations across the human kinome on protein function and cellular signaling is therefore a critical step toward personalized targeted therapy. Here, we present Kinome-AI, an integrative machine learning framework that classifies kinase missense mutations as activating or non-activating. Kinome-AI is trained on a rich multi-modal feature set, including residue-level biochemical changes, sequence embeddings from a protein language model, and structural descriptors of kinase-ATP-substrate complexes derived from molecular modeling. Notably, detailed structural features were available for only 21% of mutants; we leverage these as privileged information during training to impute missing structural data for the remaining [~]79. This strategy boosts performance without requiring structural inputs for new (unseen) mutations. The resulting classifier achieves an area under the receiver operating characteristic curve (AUROC) of 0.85 and a balanced accuracy (BACC) of 0.76 across 1,003 mutations spanning 110 different kinases --substantially outperforming existing bioinformatics and general-purpose variant effect predictors. This work provides a robust approach to quantify sequence-structure- function relationships of cancer-driving kinase mutations, paving the way for improved personalized cancer treatment. Significance StatementIn cancer patients, numerous mutations in diverse protein kinases lead to marked differences in disease progression and drug response. Identifying which kinase mutations are activating in individual patients is therefore critical for precision oncology. Drawing inspiration from teacher- student (privileged information) learning, we developed a deep learning framework that integrates structural features from molecular simulations with sequence embeddings from protein language models. This approach enables accurate binary classification of the activation status of kinase mutations. Our study demonstrates how data-driven algorithms can leverage accumulated sequence and structural knowledge of known mutations to predict the effects of novel variants a priori. The model, termed Kinome-AI, shows significant promise for incorporation into personalized cancer therapy decision pipelines.

cancer biology↗

Atom-level backbone engineering preserves peptide function while enhancing stability

Peptide therapeutics offer unmatched potency and selectivity but are limited by rapid proteolysis and poor pharmacokinetics. Backbone engineering provides a rational approach to enhance stability while preserving function, yet direct comparisons across strategies remain scarce. Using bradykinin as a model, we systematically evaluated four backbone modifications--D-amino acid substitution, N-methylation, -methylation, and azapeptide incorporation. Each modification produced distinct outcomes in synthesis, conformation, proteolytic stability, and receptor pharmacology. While D- and N-methyl substitutions yielded high stability, they compromised receptor binding and in vivo function. In contrast, the azapeptide analogue maintained native-like affinity and physiological activity while achieving an enhanced stability profile. These findings highlight the need to balance stability and function in peptide design and position azapeptides as an underexplored class with strong therapeutic potential. More broadly, this study establishes a framework for systematic, data-driven peptide design and optimization.

biochemistry↗

Molecular response to the non-lytic peptide bac7 (1-35) triggers disruption of Klebsiella pneumoniae biofilm

Klebsiella pneumoniae is becoming increasingly difficult to treat as multidrug-resistant (MDR) strains become more prevalent. The formation of biofilm heightens this threat by embedding bacterial cells in a polysaccharide-rich matrix that limits antibiotic penetration. Here we dissect the anti-biofilm bovine host-defense cathelicidin peptide fragment bac7 (1-35), exploring its anti-biofilm mechanism, evaluating its ability to curb dissemination of hypervirulent K. pneumoniae, and testing its breadth of activity against diverse clinical isolates. Transcriptomic profiling revealed that bac7(1-35) simultaneously compromises the bacterial membrane and inhibits ribosomal function, a dual assault that precipitates rapid biofilm collapse and blocks bacterial spread. Further, the peptide eradicated biofilms produced by the strongest MDR clinical isolates in the Multidrug-Resistant Organism Repository and Surveillance Network (MRSN) diversity panel. Although bac7 (1-35) kills bacterial cells via a cytosolic mechanism, membrane interaction profiles varied among MRSN isolates, correlating with differential peptide translocation. In a delayed-treatment murine skin-abscess model, bac7 (1-35) halted in vivo dissemination of the hypervirulent strain NTUH-K2044. Collectively, these results delineate a multifaceted mode of action for bac7 (1-35) and underscore its therapeutic promise against biofilm-associated MDR K. pneumoniae infections. Author SummaryKlebsiella pneumoniae is a top-priority pathogen for new therapies, with many strains already approaching pan-drug resistant status. Biofilm formation further complicates treatment, yet biofilm-active therapeutics have not reached the clinic, in part because we still lack a detailed understanding of how to disrupt these impenetrable structures. Antimicrobial peptides are promising candidates and have shown biofilm-disruption potential. Here we provide mechanistic insight into how a host defense peptide dismantles pre-formed K. pneumoniae biofilms. We find that the peptides dual targeting of bacterial membranes and ribosomes triggers dispersal from the biofilm state and concomitantly downregulates factors required for surface attachment and extracellular matrix production. This mechanism involves a protein that, to our knowledge, has not been characterized in K. pneumoniae. Our findings reveal a switch that can be leveraged to reprogram biofilm maintenance toward dispersal in K. pneumoniae, advancing the path to peptide-based antibiofilm therapeutics.

microbiology↗

Defining the importance of the arginine loop region of protegrin-1 for antimicrobial activity towards colistin-resistant Klebsiella pneumoniae.

Carbapenem resistant Klebsiella pneumoniae extreme drug resistance has warranted the use of colistin as a last-resort antibiotic but these isolates are now displaying increasing rates of colistin resistance. This is in large part due to the modifications made to the lipid A by the PhoPQ two component system. Host defense peptides (HDPs) are like colistin in that they are both positively charged and display amphipathic character, however are not impacted by lipid A modifications to the extent of colistin. To understand how HDPs can penetrate colistin resistant membranes we performed a deep mutational scanning analysis of protegrin-1 and revealed that amino acids mutations that resulted in alteration of peptide structure had more impact on antimicrobial activity than a reduction in charge. Probing single and double amino acid variants using membrane analysis and molecular modeling revealed the loss of antimicrobial activity correlated with decreased inner membrane leakage and pore modeling predicting decreased pore size,

microbiology↗

Proteasome-derived antimicrobial peptides discovered via deep learning

Recent computational discoveries have identified numerous bioactive peptides within the human proteome, as well as across the broader tree of life, which were previously unrecognized for their roles in host immunity. These findings have led us to propose the "cross-talk hypothesis", suggesting that many molecules, such as proteins and peptides, traditionally viewed as extraneous to immune function may in fact actively contribute to immunity. Building on our earlier studies, which uncovered proteasome-derived peptides with putative antimicrobial activity in the human proteome, here we systematically interrogated the proteasome, a large protein complex responsible for degrading and recycling damaged or surplus proteins, for additional antimicrobial peptides. Using deep learning, we systematically mined ProteasomeDB, a curated repository of proteasomal cleavage and splicing events, to predict antibiotic activity against 11 clinically relevant pathogens. This deep learning approach uncovered 59 candidate peptides ("proteasomins") with a median minimum inhibitory concentration (MIC) of [≤]64LmolLLL1. Refinement yielded 21 sequence-diverse proteasomins, which were characterized for their physicochemical properties. These peptides were enriched in cationic residues and exhibit enhanced amphiphilicity, key attributes for disrupting microbial membranes. Dimensionality reduction via UMAP further showed that proteasomins are sequence-distinct from known antimicrobial peptides, underscoring their novelty and potential for unique mechanisms of action. Moreover, comparative analyses revealed that cis- and trans-spliced proteasomins exhibit similar predicted antimicrobial activities, suggesting that critical structural determinants remain conserved irrespective of splicing modality. Collectively, these findings expand our understanding of the proteasome, underscore the extensive, previously unrecognized repertoire of innate immune peptides, and provide a promising foundation for developing innovative therapeutics to combat multidrug-resistant pathogens.

microbiology↗

Generative latent diffusion language modeling yields anti-infective synthetic peptides

Generative artificial intelligence (AI) offers a powerful avenue for peptide design, yet this process remains challenging due to the vast sequence space, complex structure-activity relationships, and the need to balance antimicrobial potency with low toxicity. Traditional approaches often rely on trial-and-error screening and fail to efficiently navigate the immense diversity of potential sequences. Here, we introduce AMP-Diffusion, a novel latent diffusion model fine-tuned on antimicrobial peptide (AMP) sequences using embeddings from protein language models. By systematically exploring sequence space, AMP-Diffusion enables the rapid discovery of promising antibiotic candidates. We generated 50,000 candidate sequences, which were subsequently filtered and ranked using our APEX predictor model. From these, 46 top candidates were synthesized and experimentally validated. The resulting AMP-Diffusion peptides demonstrated broad-spectrum antibacterial activity, targeting clinically relevant pathogens--including multidrug-resistant strains--while exhibiting low cytotoxicity in human cell assays. Mechanistic studies revealed bacterial killing via membrane permeabilization and depolarization, and the peptides showed favorable physicochemical profiles. In preclinical mouse models of infection, lead peptides effectively reduced bacterial burdens, displaying efficacy comparable to polymyxin B and levofloxacin, with no detectable adverse effects. This study highlights the potential of AMP-Diffusion as a robust generative platform for designing novel antibiotics and bioactive peptides, offering a promising strategy to address the escalating challenge of antimicrobial resistance.

microbiology↗

Improving functional protein generation via foundation model-derived latent space likelihood optimization

A variety of deep generative models have been adopted to perform de novo functional protein generation. Compared to 3D protein design, sequence-based generation methods, which aim to generate amino acid sequences with desired functions, remain a major approach for functional protein generation due to the abundance and quality of protein sequence data, as well as the relatively low modeling complexity for training. Although these models are typically trained to match protein sequences from the training data, exact matching of every amino acid is not always essential. Certain amino acid changes (e.g., mismatches, insertions, and deletions) may not necessarily lead to functional changes. This suggests that maximizing the training data likelihood beyond the amino acid sequence space could yield better generative models. Pre-trained protein large language models (PLMs) like ESM2 can encode protein sequences into a latent space, potentially serving as functional validators. We propose training functional protein sequence generative models by simultaneously optimizing the likelihood of training data in both the amino acid sequence space and the latent space derived from a PLM. This training scheme can also be viewed as a knowledge distillation approach that dynamically re-weights samples during training. We applied our method to train GPT- like models (i.e., autoregressive transformers) for antimicrobial peptide (AMP) and malate dehydrogenase (MDH) generation tasks. Computational experiments confirmed that our method outperformed various deep generative models (e.g., generative adversarial net, variational autoencoder, and GPT model without the proposed training strategy) on these tasks, demonstrating the effectiveness of our multi-likelihood optimization strategy.

bioinformatics↗

Key-cutting machine: A novel optimization framework for tailored protein and peptide design

Computational protein and peptide design is emerging as a transformative framework for engineering macromolecules with precise structures and functions, offering innovative solutions in medicine, biotechnology, and materials science. However, current methods predominantly rely on generative models, which are expensive to train and inflexible to modify. Here, we introduce the Key-Cutting Machine (KCM), a novel optimization-based platform that iteratively leverages structure prediction to match desired backbone geometries. KCM requires only a single GPU and enables seamless incorporation of user-defined requirements into the objective function, circumventing the high retraining costs typical of generative models while allowing straightforward assessment of measurable properties. By employing an Estimation of Distribution Algorithm, KCM optimizes sequences based on geometric, physicochemical, and energetic criteria. We benchmarked its performance on -helices, {beta}-sheets, and unstructured regions, demonstrating precise backbone geometry design. As a proof of concept, we applied KCM to antimicrobial peptide (AMP) design by using a template AMP as the "key", yielding a candidate with potent in vitro activity against multiple bacterial strains and efficacy in a murine infection model. KCM thus emerges as a robust tool for de novo protein and peptide design, offering a flexible paradigm for replicating and extending the structure-function relationships of existing templates.

bioengineering↗

Design of multimodal antibiotics against intracellular infections using deep learning

The rise of antimicrobial resistance has rendered many treatments ineffective, posing serious public health challenges. Intracellular infections are particularly difficult to treat since conventional antibiotics fail to neutralize pathogens hidden within human cells. However, designing molecules that penetrate human cells with preserved antimicrobial activity has historically been a major challenge. Here, we introduce ApexDuo, a multimodal artificial intelligence (AI) model for generating peptides with both cell- penetrating and antimicrobial properties. From a library of 50 million AI-generated compounds, we selected and characterized several candidates. Our lead, Turingcin-46, penetrated mammalian cells and reduced intracellular Staphylococcus aureus and Listeria monocytogenes. In mouse models of skin abscess and peritonitis, Turingcin-46 reduced bacterial loads by up to two orders of magnitude. In sum, ApexDuo generated multimodal peptide antibiotics, opening new avenues for designing molecules with more than one function.

synthetic biology↗

Venomics AI: a computational exploration of global venoms for antibiotic discovery

The relentless emergence of antibiotic-resistant pathogens, particularly Gram-negative bacteria, highlights the urgent need for novel therapeutic interventions. Drug-resistant infections account for approximately 5 million deaths annually, yet the antibiotic development pipeline has largely stagnated. Venoms, representing a remarkably diverse reservoir of bioactive molecules, remain an underexploited source of potential antimicrobials. Venom-derived peptides, in particular, hold promise for antibiotic discovery due to their evolutionary diversity and unique pharmacological profiles. In this study, we mined comprehensive global venomics datasets to identify new antimicrobial candidates. Using machine learning, we explored 16,123 venom proteins, generating 40,626,260 venom-encrypted peptides (VEPs). Using APEX, a deep learning model combining a peptide-sequence encoder with neural networks for antimicrobial activity prediction, we identified 386 VEPs structurally and functionally distinct from known antimicrobial peptides. Our analyses showed that these VEPs possess high net charge and elevated hydrophobicity, characteristics conducive to bacterial membrane disruption. Structural studies revealed considerable conformational flexibility, with many VEPs transitioning to -helical conformations in membrane-mimicking environments, indicative of their antimicrobial potential. Of the 58 VEPs selected for experimental validation, 53 displayed potent antimicrobial activity. Mechanistic assays indicated that VEPs primarily exert their effects through bacterial membrane depolarization, mirroring AMP-like mechanisms. In vivo studies using a mouse model of Acinetobacter baumannii infection demonstrated that lead VEPs significantly reduced bacterial burdens without notable toxicity. This study highlights the value of venoms as a resource for new antibiotics. By integrating computational approaches and experimental validation, venom-derived peptides emerge as promising candidates to combat the global challenge of antibiotic resistance.

bioengineering↗

A generative artificial intelligence approach for antibiotic optimization

Antimicrobial resistance (AMR) poses a critical global health threat, underscoring the urgent need for innovative antibiotic discovery strategies. While recent advances in peptide design have yielded numerous antimicrobial agents, optimizing these molecules experimentally remains challenging due to unpredictable and resource-intensive trial-and-error approaches. Here, we introduce APEX Generative Optimization (APEXGO), a generative artificial intelligence (AI) framework that integrates a transformer-based variational autoencoder with Bayesian optimization to design and optimize antimicrobial peptides. Unlike traditional supervised learning approaches that screen fixed databases of existing molecules, APEXGO generates entirely novel peptide sequences through arbitrary modifications of template peptides, representing a paradigm shift in peptide design and antibiotic discovery. Our framework introduces a new peptide variational autoencoder with design and diversity constraints to maintain similarity to specific templates while enabling sequence innovation. This work represents the first in vitro and in vivo experimental validation of generative Bayesian optimization in any setting. Using ten de-extinct peptides as templates, APEXGO generated optimized derivatives with enhanced antimicrobial properties. We synthesized 100 of these optimized peptides and conducted comprehensive in vitro characterizations, including assessments of antimicrobial activity, mechanism of action, secondary structure, and cytotoxicity. Notably, APEXGO achieved an outstanding 85% ground-truth experimental hit rate and a 72% success rate in enhancing antimicrobial activity against clinically relevant Gram-negative pathogens, outperforming previously reported methods for antibiotic discovery and optimization. In preclinical mouse models of Acinetobacter baumannii infection, several AI-optimized molecules--most notably derivatives of mammuthusin-3 and mylodonin-2--exhibited potent anti-infective activity comparable to or exceeding that of polymyxin B, a widely used last-resort antibiotic. These findings highlight the potential of APEXGO as a novel generative AI approach for peptide design and antibiotic optimization, offering a powerful tool to accelerate antibiotic discovery and address the escalating challenge of AMR.

microbiology↗

Dual quorum-sensing control of purine biosynthesis drives pathogenic fitness of Enterococcus faecalis

Enterococcus faecalis is a resident of the human gut, though upon translocation to the blood or body tissues, it can be pathogenic. Here we discover and characterize two peptide-based quorum-sensing systems that transcriptionally modulate de novo purine biosynthesis in E. faecalis. Using a comparative genomic analysis, we find that most enterococcal species do not encode this system; E. moraviensis, E. haemoperoxidus and E. caccae, three species that are closely related to E. faecalis, encode one of the two systems, and only E. faecalis encodes both systems. We show that these systems are important for the intracellular survival of E. faecalis within macrophages and for the fitness of E. faecalis in a murine wound infection model. Taken together, we combine comparative genomics, microbiological, bacterial genetics, transcriptomics, targeted proteomics and animal model experiments to describe a paired quorum sensing mechanism that directly influences central metabolism and impacts the pathogenicity of E. faecalis.

microbiology↗

Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning

Molecular de-extinction could offer new avenues for drug discovery by reintroducing bioactive molecules that are no longer encoded by extant organisms. To prospect for antimicrobial peptides encrypted as subsequences of extinct and extant human proteins, we introduce the panCleave random forest model for proteome-wide cleavage site prediction. Our model outperformed multiple protease-specific cleavage site classifiers for three modern human caspases, despite its pan-protease design. Antimicrobial activity was observed in vitro for modern and archaic protein fragments identified with panCleave. Lead peptides were tested for mechanism of action, resistance to proteolysis, and anti-infective efficacy in two pre-clinical mouse models. These results suggest that machine learning-based encrypted peptide prospection can identify stable, nontoxic antimicrobial peptides. Moreover, we establish molecular de-extinction through paleoproteome mining as a framework for antibacterial drug discovery. HighlightsO_LIMachine learning guides bioinspired prospection for encrypted antimicrobial peptides. C_LIO_LIModern and extinct human proteins harbor antimicrobial subsequences. C_LIO_LIAncient encrypted peptides display in vitro and in vivo activity with low host toxicity. C_LIO_LIPaleoproteome mining offers a new framework for antibiotic discovery. C_LI

bioengineering↗

Autonomous treatment of bacterial infections in vivo using antimicrobial micro- and nanomachines

The increasing resistance of bacteria to existing antibiotics constitutes a major public health threat globally. Most current antibiotic treatments are hindered by poor delivery to the infection site, leading to undesired off-target effects and drug resistance development and spread. Here, we describe micro- and nanomachines that effectively and autonomously deliver antibiotic payloads to the target area. The active motion and antimicrobial activity of the silica-based robots are driven by catalysis of the enzyme urease and antimicrobial peptides, respectively. These antimicrobial machines show micromolar bactericidal activity in vitro against different Gram-positive and Gram-negative pathogenic bacterial strains and act by rapidly depolarizing their membrane. Finally, they demonstrated autonomous anti-infective efficacy in vivo in a clinically relevant abscess infection mouse model. In summary, our machines combine navigation, catalytic conversion, and bactericidal capacity to deliver antimicrobial payloads to specific infection sites. This technology represents a much-needed tool to direct therapeutics to their target to help combat drug-resistant infections.

bioengineering↗