ArticleProceedings of the National Academy of Sciences of the United States of America2021
Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 75 citations in OpenAlex.
- Cyclic Peptides as Modulators of Protein-Protein Interactions: A Survival Guide from Discovery Platforms to AI-Driven Design.International journal of molecular sciences · 2026Review
- Review
- Machine learning-based prediction of peptide aggregation during chemical synthesis.Nature chemistry · 2026Article
- CyclicMPNN: Stable Cyclic Peptide Sequence Generation.bioRxiv : the preprint server for biology · 2026Article
- Accurate de novo design of high-affinity protein-binding macrocycles using deep learning.Nature chemical biology · 2025Article
- The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design.bioRxiv : the preprint server for biology · 2025Article
- Rapid clearance of achiral small-molecule drugs using de novo-designed proteins and their cyclic and mirror-image variants.Nature biomedical engineering · 2025Article
- Computational structure prediction of lanthipeptides with NMR data reveals underappreciated peptide flexibility.Protein science : a publication of the Protein Society · 2025Article
- Heuristic energy-based cyclic peptide design.PLoS computational biology · 2025Article
- Heuristic energy-based cyclic peptide design.bioRxiv : the preprint server for biology · 2025Article
- CYCLICCAE: A CONFORMATIONAL AUTOENCODER FOR EFFICIENT HETEROCHIRAL MACROCYCLIC BACKBONE SAMPLING.bioRxiv : the preprint server for biology · 2025Article
- Mechanism of Ampicillin Hydrolysis by New Delhi Metallo-β-Lactamase 1: Insight From QM/MM MP2 Calculation.Journal of computational chemistry · 2025Article
- Parameterizing non-canonical amino acids for cyclic peptide simulations.Methods in enzymology · 2025Article
- Accurate de novo design of heterochiral protein-protein interactions.Cell research · 2024Article
- AccuratebioRxiv : the preprint server for biology · 2024Article
- Integrating Computational Design and Experimental Approaches for Next-Generation Biologics.Biomolecules · 2024Review
- HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer.Bioinformatics (Oxford, England) · 2024Article
- Machine Learning Models Identify Inhibitors of New Delhi Metallo-β-lactamase.Journal of chemical information and modeling · 2024Article
- Toward high-resolution modeling of small molecule-ion channel interactions.Frontiers in pharmacology · 2024Article
- Design and structural validation of peptide-drug conjugate ligands of the kappa-opioid receptor.Nature communications · 2023Article
Corrections and comments
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Authors and funding
17 authors at 8 institutions in 2 countries.
Funding
Abstract
The rise of antibiotic resistance calls for new therapeutics targeting resistance factors such as the New Delhi metallo-β-lactamase 1 (NDM-1), a bacterial enzyme that degrades β-lactam antibiotics. We present structure-guided computational methods for designing peptide macrocycles built from mixtures of l- and d-amino acids that are able to bind to and inhibit targets of therapeutic interest. Our methods explicitly consider the propensity of a peptide to favor a binding-competent conformation, which we found to predict rank order of experimentally observed IC
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.