Expansive discovery of chemically diverse structured macrocyclic oligoamides

Science

Published On 2024/4/26

Small macrocycles with four or fewer amino acids are among the most potent natural products known, but there is currently no way to systematically generate such compounds. We describe a computational method for identifying ordered macrocycles composed of alpha, beta, gamma, and 17 other amino acid backbone chemistries, which we used to predict 14.9 million closed cycles composed of >42,000 monomer combinations. We chemically synthesized 18 macrocycles predicted to adopt single low-energy states and determined their x-ray or nuclear magnetic resonance structures; 15 of these were very close to the design models. We illustrate the therapeutic potential of these macrocycle designs by developing selective inhibitors of three protein targets of current interest. By opening up a vast space of readily synthesizable drug-like macrocycles, our results should considerably enhance structure-based drug …

Journal

Science

Volume

384

Issue

6,694

Page

420-428

Authors

David Baker

David Baker

University of Washington

H-Index

209

Research Interests

Protein Design

University Profile Page

Gaurav Bhardwaj

Gaurav Bhardwaj

University of Washington

H-Index

14

Research Interests

Protein and Peptide Design

Protein Engineering

Computational Chemistry

Computational Biology

Molecular Phylogenetics

University Profile Page

Patrick J. Salveson

Patrick J. Salveson

University of California, Irvine

H-Index

7

Research Interests

Chemical Biology

Structural Biology

Organic Chemistry

Peptides

University Profile Page

Other Articles from authors

David Baker

David Baker

University of Washington

The Shortest History of Sex: Two Billion Years of Procreation and Recreation (Shortest History)

A wild—and satisfying!—ride through two billion years of sexual evolution. The Shortest History books deliver thousands of years of history in one riveting, fast-paced read. From the first microbial exchanges of DNA to Tinder and sexbots, how did sex begin, and how did it evolve to be so varied and complex in humans? What influence do our genetic ancestors have on our current love lives? And what might sex look like in the future? With acuity, humor, and respect for human diversity, The Shortest History of Sex reveals where the many facets of our sexuality—chemical, anatomical, behavioral, social—come from. Chasing down our evolutionary family tree, from the first aquatic creatures to primate societies, David Baker sheds light on our baffling array of passions, impulses, and fetishes, and guides us toward a clear understanding of one of the deepest, most abiding forces of human nature. The Shortest History of Sex also charts how sex changed for humans across the foraging, agrarian, and modern eras, showing how, even as our biology and sexual instincts have remained the same, the current nature of our sex lives has no historical or evolutionary precedent. The result is a revealing, utterly unique insight into history and human behavior—and the profound forces of nature and nurture compelling our most intimate relationships.

David Baker

David Baker

University of Washington

Nature

Blueprinting extendable nanomaterials with standardized protein blocks

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures 1. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large …

David Baker

David Baker

University of Washington

Nature Computational Science

Machine learning-guided engineering of genetically encoded fluorescent calcium indicators

Here we used machine learning to engineer genetically encoded fluorescent indicators, protein-based sensors critical for real-time monitoring of biological activity. We used machine learning to predict the outcomes of sensor mutagenesis by analyzing established libraries that link sensor sequences to functions. Using the GCaMP calcium indicator as a scaffold, we developed an ensemble of three regression models trained on experimentally derived GCaMP mutation libraries. The trained ensemble performed an in silico functional screen on 1,423 novel, uncharacterized GCaMP variants. As a result, we identified the ensemble-derived GCaMP (eGCaMP) variants, eGCaMP and eGCaMP+, which achieve both faster kinetics and larger ∆F/F0 responses upon stimulation than previously published fast variants. Furthermore, we identified a combinatorial mutation with extraordinary dynamic range, eGCaMP2+, which …

David Baker

David Baker

University of Washington

Nature Communications

Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes

The organization of membrane proteins between and within membrane-bound compartments is critical to cellular function. Yet we lack approaches to regulate this organization in a range of membrane-based materials, such as engineered cells, exosomes, and liposomes. Uncovering and leveraging biophysical drivers of membrane protein organization to design membrane systems could greatly enhance the functionality of these materials. Towards this goal, we use de novo protein design, molecular dynamic simulations, and cell-free systems to explore how membrane-protein hydrophobic mismatch could be used to tune protein cotranslational integration and organization in synthetic lipid membranes. We find that membranes must deform to accommodate membrane-protein hydrophobic mismatch, which reduces the expression and co-translational insertion of membrane proteins into synthetic membranes. We …

David Baker

David Baker

University of Washington

bioRxiv

Plasmodium falciparum protein phosphatase PP7 is required for early ring-stage development

We previously reported that the Plasmodium falciparum putative serine/threonine protein phosphatase 7 (PP7) is a high confidence substrate of the cAMP-dependent protein kinase (PKA). Here we explore the function of PP7 in asexual P. falciparum blood stage parasites. We show that conditional disruption of PP7 leads to a severe growth arrest. We show that PP7 is a calcium-dependent phosphatase which interacts with calmodulin and calcium-dependent protein kinase 1 (CDPK1), consistent with a role in calcium signalling. Notably, PP7 was found to be dispensable for erythrocyte invasion, but was crucial for ring-stage development, with PP7-null parasites arresting shortly following invasion and showing no transition to ameboid forms. Phosphoproteomic analysis revealed that PP7 may regulate dephosphorylation of PKAc substrates, particularly in the presence of Ca2+. Its interaction with calmodulin and CDPK1 further emphasise a role in calcium signalling, while its impact on early ring development and PKAc substrate phosphorylation underscores its importance in parasite development.

David Baker

David Baker

University of Washington

Genome editing reagents and their use

The application discloses multimeric assemblies packaging one or more active component and their use to carry out nucleic acid regulation or gene editing.

David Baker

David Baker

University of Washington

De novo design of obligate ABC heterotrimeric proteins

Disclosed are polypeptides having an amino acid sequence at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of the amino acid sequences listed in Tables 1, 2, and 3, and heteropolymers formed from such polypeptides.

David Baker

David Baker

University of Washington

bioRxiv

Activation loop phosphorylation and cGMP saturation of PKG regulate egress of malaria parasites.

The cGMP-dependent protein kinase (PKG) is the sole cGMP sensor in malaria parasites, acting as an essential signalling hub to govern key developmental processes throughout the parasite life cycle. Despite the importance of PKG in the clinically relevant asexual blood stages, many aspects of malarial PKG regulation, including the importance of phosphorylation, remain poorly understood. Here we use genetic and biochemical approaches to show that reduced cGMP binding to cyclic nucleotide binding domain B does not affect in vitro kinase activity but prevents parasite egress. Similarly, we show that phosphorylation of a key threonine residue (T695) in the activation loop is dispensable for kinase activity in vitro but is essential for in vivo PKG function, with loss of T695 phosphorylation leading to aberrant phosphorylation events across the parasite proteome and changes to the substrate specificity of PKG. Our findings indicate that Plasmodium PKG is uniquely regulated to transduce signals crucial for malaria parasite development.

David Baker

David Baker

University of Washington

Nature Communications

Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the …

David Baker

David Baker

University of Washington

Σύντομη ιστορία του κόσμου

Σε αυτή την πανοραμική θεώρηση του κόσμου, ο David Baker καταγράφει τις ιστορικές μεταβολές στο Σύμπαν, αποκαλύπτοντας την τεράστια αύξηση της πολυπλοκότητας που συνοδεύει κάθε εξελικτική φάση του παρελθόντος, του παρόντος και του μέλλοντός μας. Καθώς συνδυάζει γνώσεις από τη φυσική, τη χημεία, τη βιολογία και άλλες επιστήμες, ο διακεκριμένος ιστορικός μάς βοηθάει να δούμε πέρα από τα στενά όρια και το χάος των ανθρώπινων προβλημάτων, απαντώντας στο θεμελιώδες ερώτημα: Από πού προερχόμαστε και πού πηγαίνουμε;

David Baker

David Baker

University of Washington

The Lancet Child & Adolescent Health

Immunomodulatory therapy in children with paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS, MIS-C; RECOVERY): a randomised …

BackgroundPaediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 (PIMS-TS), also known as multisystem inflammatory syndrome in children (MIS-C) emerged in April, 2020. The paediatric comparisons within the RECOVERY trial aimed to assess the effect of intravenous immunoglobulin or corticosteroids compared with usual care on duration of hospital stay for children with PIMS-TS and to compare tocilizumab (anti-IL-6 receptor monoclonal antibody) or anakinra (anti-IL-1 receptor antagonist) with usual care for those with inflammation refractory to initial treatment.MethodsWe did this randomised, controlled, open-label, platform trial in 51 hospitals in the UK. Eligible patients were younger than 18 years and had been admitted to hospital for PIMS-TS. In the first randomisation, patients were randomly assigned (1: 1: 1) to usual care (no additional treatments), usual care plus …

David Baker

David Baker

University of Washington

Nature Chemical Biology

Design of amyloidogenic peptide traps

Segments of proteins with high β-strand propensity can self-associate to form amyloid fibrils implicated in many diseases. We describe a general approach to bind such segments in β-strand and β-hairpin conformations using de novo designed scaffolds that contain deep peptide-binding clefts. The designs bind their cognate peptides in vitro with nanomolar affinities. The crystal structure of a designed protein−peptide complex is close to the design model, and NMR characterization reveals how the peptide-binding cleft is protected in the apo state. We use the approach to design binders to the amyloid-forming proteins transthyretin, tau, serum amyloid A1 and amyloid β1−42 (Aβ42). The Aβ binders block the assembly of Aβ fibrils as effectively as the most potent of the clinically tested antibodies to date and protect cells from toxic Aβ42 species.

David Baker

David Baker

University of Washington

Nature Nanotechnology

De novo design of pH-responsive self-assembling helical protein filaments

Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures that are environmentally responsive remains a challenge. Here we describe the de novo design of pH-responsive protein filaments built from subunits containing six or nine buried histidine residues that assemble into micrometre-scale, well-ordered fibres at neutral pH. The cryogenic electron microscopy structure of an optimized design is nearly identical to the computational design model for both the subunit internal geometry and the subunit packing into the fibre. Electron, fluorescent and atomic force microscopy characterization reveal a sharp and reversible transition from assembled to disassembled fibres over 0.3 pH units, and rapid fibre disassembly in less than 1 s following a drop in pH. The midpoint of the …

David Baker

David Baker

University of Washington

The Astronomical Journal

Identification of the Top TESS Objects of Interest for Atmospheric Characterization of Transiting Exoplanets with JWST

JWST has ushered in an era of unprecedented ability to characterize exoplanetary atmospheres. While there are over 5000 confirmed planets, more than 4000 Transiting Exoplanet Survey Satellite (TESS) planet candidates are still unconfirmed and many of the best planets for atmospheric characterization may remain to be identified. We present a sample of TESS planets and planet candidates that we identify as" best-in-class" for transmission and emission spectroscopy with JWST. These targets are sorted into bins across equilibrium temperature T eq and planetary radius R p and are ranked by a transmission and an emission spectroscopy metric (TSM and ESM, respectively) within each bin. We perform cuts for expected signal size and stellar brightness to remove suboptimal targets for JWST. Of the 194 targets in the resulting sample, 103 are unconfirmed TESS planet candidates, also known as TESS Objects …

David Baker

David Baker

University of Washington

bioRxiv

Computational stabilization of a non-heme iron enzyme enables efficient evolution of new function

Directed evolution has emerged as a powerful tool for engineering new biocatalysts. However, introducing new catalytic residues can be destabilizing, and it is generally beneficial to start with a stable enzyme parent. Here we show that the deep learning tool ProteinMPNN can be used to redesign an Fe(II)/alphaKG superfamily enzyme for greater stability, solubility, and expression while retaining both native activity and an industrially-relevant non-native function. We performed site-saturation mutagenesis with both the wild type and stabilized design variant and screened for activity increases in a non-native C-H hydroxylation reaction. We observed substantially larger increases in non-native activity for variants obtained from the stabilized scaffold compared to those from the wild-type enzyme. Deep learning tools like ProteinMPNN are user-friendly and widely-accessible, and relatively straightforward structural criteria were sufficient to obtain stabilized variants while preserving catalytic function. Our work suggests that stabilization by computational sequence redesign could be routinely implemented as a first step in directed evolution campaigns for novel biocatalysts.

David Baker

David Baker

University of Washington

De novo designed rotor (axle: ring) protein assemblies

Polypeptides that comprise axle or ring components of protein nanomachines, and kits and nanomachines including such polypeptides are disclosed herein.

David Baker

David Baker

University of Washington

Nature Methods

Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA

Protein–RNA and protein–DNA complexes play critical roles in biology. Despite considerable recent advances in protein structure prediction, the prediction of the structures of protein–nucleic acid complexes without homology to known complexes is a largely unsolved problem. Here we extend the RoseTTAFold machine learning protein-structure-prediction approach to additionally predict nucleic acid and protein–nucleic acid complexes. We develop a single trained network, RoseTTAFoldNA, that rapidly produces three-dimensional structure models with confidence estimates for protein–DNA and protein–RNA complexes. Here we show that confident predictions have considerably higher accuracy than current state-of-the-art methods. RoseTTAFoldNA should be broadly useful for modeling the structure of naturally occurring protein–nucleic acid complexes, and for designing sequence-specific RNA and DNA …

2023/11/23

Article Details
David Baker

David Baker

University of Washington

Proceedings of the National Academy of Sciences

De novo design of modular protein hydrogels with programmable intra-and extracellular viscoelasticity

Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency of de novo protein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric …

David Baker

David Baker

University of Washington

Identification of sars-cov-2 epitopes discriminating covid-19 infection from control and methods of use

The present invention is directed to peptides for use in the detection of antibodies against SARS-CoV-2, which are indicative of past SARS-CoV-2 infections. Additionally, assays and methods of distinguishing patients having had a prior infection from those vaccinated patients are also provided. Additionally, vaccine compositions for use in eliciting anti-SARS-CoV-2 immune response are provided along with methods of producing antibodies and methods of eliciting an immune response.

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Yuriy Román-Leshkov

Massachusetts Institute of Technology

Science

Electrically driven proton transfer promotes Brønsted acid catalysis by orders of magnitude

Electric fields play a key role in enzymatic catalysis and can enhance reaction rates by 100,000-fold, but the same rate enhancements have yet to be achieved in thermochemical heterogeneous catalysis. In this work, we probe the influence of catalyst potential and interfacial electric fields on heterogeneous Brønsted acid catalysis. We observed that variations in applied potential of ~380 mV led to a 100,000-fold rate enhancement for 1-methylcyclopentanol dehydration, which was catalyzed by carbon-supported phosphotungstic acid. Mechanistic studies support a model in which the interfacial electrostatic potential drop drives quasi-equilibrated proton transfer to the adsorbed substrate prior to rate-limiting C–O bond cleavage. Large increases in rate with potential were also observed for the same reaction catalyzed by Ti/TiOyHx and for the Friedel Crafts acylation of anisole with acetic anhydride by carbon …

Erle C. Ellis

Erle C. Ellis

University of Maryland, Baltimore County

Science

Data-driven hope for the planet

A data scientist offers an optimistic reality check for the Anthropocene

Erle C. Ellis

Erle C. Ellis

University of Maryland, Baltimore County

Science

Centering Earth in policy-making

A pair of authors advocate scaling governance structures to better address planetary crises