Peter G Schultz

The California Institute for Biomedical Research, San Diego, California, United States

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Publications (584)4878.41 Total impact

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    ABSTRACT: Limb development requires the coordinated growth of several tissues and structures including long bones, joints and tendons, but the underlying mechanisms are not wholly clear. Recently, we identified a small drug-like molecule -we named Kartogenin (KGN)- that greatly stimulates chondrogenesis in marrow-derived mesenchymal stem cells (MSCs) and enhances cartilage repair in mouse osteoarthritis (OA) models. To determine whether limb developmental processes are regulated by KGN, we tested its activity on committed preskeletal mesenchymal cells from mouse embryo limb buds and whole limb explants. KGN did stimulate cartilage nodule formation and more strikingly, boosted digit cartilaginous anlaga elongation, synovial joint formation and interzone compaction, tendon maturation as monitored by ScxGFP, and interdigit invagination. To identify mechanisms, we carried out gene expression analyses and found that several genes, including those encoding key signaling proteins, were up-regulated by KGN. Amongst highly up-regulated genes were those encoding hedgehog and TGFβ superfamily members, particularly TFGβ1. The former response was verified by increases in Gli1-LacZ activity and Gli1 mRNA expression. Exogenous TGFβ1 stimulated cartilage nodule formation to levels similar to KGN, and KGN and TGFβ1 both greatly enhanced expression of lubricin/Prg4 in articular superficial zone cells. KGN also strongly increased the cellular levels of phospho-Smads that mediate canonical TGFβ and BMP signaling. Thus, limb development is potently and harmoniously stimulated by KGN. The growth effects of KGN appear to result from its ability to boost several key signaling pathways and in particular TGFβ signaling, working in addition to and/or in concert with the filamin A/CBFβ/RUNX1 pathway we identified previously to orchestrate overall limb development. KGN may thus represent a very powerful tool not only for OA therapy, but also limb regeneration and tissue repair strategies.
    Developmental biology. 09/2014;
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    ABSTRACT: A chemically defined anti-CXCR4–auristatin antibody–drug conjugate (ADC) was synthesized that selectively eliminates tumor cells overexpressing the CXCR4 receptor. The unnatural amino acid p-acetylphenylalanine (pAcF) was site-specifically incorporated into an anti-CXCR4 immunoglobulin G (IgG) and conjugated to an auristatin through a stable, non-cleavable oxime linkage to afford a chemically homogeneous ADC. The full-length anti-CXCR4 ADC was selectively cytotoxic to CXCR4+ cancer cells in vitro (half maximal effective concentration (EC50)≈80–100 pM). Moreover, the anti-CXCR4 ADC eliminated pulmonary lesions from human osteosarcoma cells in a lung-seeding tumor model in mice. No significant overt toxicity was observed but there was a modest decrease in the bone-marrow-derived CXCR4+ cell population. Because CXCR4 is highly expressed in a majority of metastatic cancers, a CXCR4–auristatin ADC may be useful for the treatment of a variety of metastatic malignancies.
    Angewandte Chemie 09/2014;
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    ABSTRACT: A sensitive and highly multiplex method to directly measure RNA sequence abundance without requiring reverse transcription would be of value for a number of biomedical applications, including high throughput small molecule screening, pathogen transcript detection and quantification of short/degraded RNAs.
    Nucleic Acids Research 07/2014; · 8.81 Impact Factor
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    ABSTRACT: Acute myeloid leukemia (AML), which is the most common acute adult leukemia and the second most common pediatric leukemia, still has a poor prognosis. Human C-type lectin-like molecule-1 (CLL1) is a recently identified myeloid lineage restricted cell surface marker, which is overexpressed in over 90 % of AML patient myeloid blasts and in leukemic stem cells. Here, we describe the synthesis of a novel bispecific antibody, αCLL1-αCD3, using the genetically encoded unnatural amino acid, p-acetylphenylalanine. The resulting αCLL1-αCD3 recruits cytotoxic T cells to CLL1 positive cells, and demonstrates potent and selective cytotoxicity against several human AML cell lines and primary AML patient derived cells in vitro. Moreover, αCLL1-αCD3 treatment completely eliminates established tumors in an U937 AML cell line xenograft model. These results validate the clinical potential of CLL1 as an AML-specific antigen for the generation of a novel immunotherapeutic for AML.
    Angewandte Chemie International Edition 07/2014; · 11.34 Impact Factor
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    ABSTRACT: Acute myeloid leukemia (AML), which is the most common acute adult leukemia and the second most common pediatric leukemia, still has a poor prognosis. Human C-type lectin-like molecule-1 (CLL1) is a recently identified myeloid lineage restricted cell surface marker, which is overexpressed in over 90 % of AML patient myeloid blasts and in leukemic stem cells. Here, we describe the synthesis of a novel bispecific antibody, αCLL1-αCD3, using the genetically encoded unnatural amino acid, p-acetylphenylalanine. The resulting αCLL1-αCD3 recruits cytotoxic T cells to CLL1 positive cells, and demonstrates potent and selective cytotoxicity against several human AML cell lines and primary AML patient derived cells in vitro. Moreover, αCLL1-αCD3 treatment completely eliminates established tumors in an U937 AML cell line xenograft model. These results validate the clinical potential of CLL1 as an AML-specific antigen for the generation of a novel immunotherapeutic for AML.
    Angewandte Chemie 07/2014;
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    ABSTRACT: The bovine antibody (BLV1H12) which has an ultralong heavy chain complementarity determining region 3 (CDRH3) provides a novel scaffold for antibody engineering. By substituting the extended CDRH3 of BLV1H12 with modified CXCR4 binding peptides that adopt a β-hairpin conformation, we generated antibodies specifically targeting the ligand binding pocket of CXCR4 receptor. These engineered antibodies selectively bind to CXCR4 expressing cells with binding affinities in the low nanomolar range. In addition, they inhibit SDF-1-dependent signal transduction and cell migration in a transwell assay. Finally, we also demonstrate that a similar strategy can be applied to other CDRs and show that a CDRH2-peptide fusion binds CXCR4 with a Kd of 0.9 nM. This work illustrates the versatility of scaffold-based antibody engineering and could greatly expand the antibody functional repertoire in the future.
    Journal of the American Chemical Society 07/2014; · 10.68 Impact Factor
  • Sophie B. Sun, Peter G. Schultz, Chan Hyuk Kim
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    ABSTRACT: To date, over 100 noncanonical amino acids (ncAAs) have been genetically encoded in living cells in order to expand the functional repertoire of the canonical 20 amino acids. More recently, this technology has been expanded to the field of protein therapeutics, where traditional chemical methods typically result in heterogeneous mixtures of proteins. The site-specific incorporation of ncAAs with orthogonal chemical groups allows unprecedented control over the site of conjugation and the stoichiometry, thus facilitating the rational optimization of the biological functions and/or pharmacokinetics of biologics. Herein, we discuss the recent contribution of ncAA technology in enhancing the pharmacological properties of current protein therapeutics as well as developing novel therapeutic modalities.
    ChemBioChem 07/2014; · 3.74 Impact Factor
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    ABSTRACT: The addition of noncanonical amino acids to the genetic code requires unique codons not assigned to the 20 canonical amino acids. Among the 64 triplet codons, only the three nonsense “stop” codons have been used to encode non-native amino acids. Use of quadruplet “frame-shift” suppressor codons provides an abundant alternative but suffers from low suppression efficiency as a result of competing recognition of their first three bases by endogenous host tRNAs or release factors. Deletion of release factor 1 in a genomically recoded strain of E. coli (E. coli C321), in which all endogenous amber stop codons (UAG) are replaced with UAA, abolished UAG mediated translation termination. Here we show that a Methanocaldococcus jannaschii-derived frame-shift suppressor tRNA/aminoacyl-tRNA synthetase pair enhanced UAGN suppression efficiency in this recoded bacterial strain. These results demonstrate that efficient quadruplet codons for encoding non-native amino acids can be generated by eliminating competing triplet codon recognition at the ribosome.
    ChemBioChem 05/2014; · 3.74 Impact Factor
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    ABSTRACT: Selective covalent bond formation at a protein-protein interface potentially can be achieved by genetically introducing into a protein an appropriately "tuned" electrophilic unnatural amino acid that reacts with a native nucleophilic residue in its cognate receptor upon complex formation. We have evolved orthogonal aminoacyl-tRNA synthetase/tRNACUA pairs that genetically encode three aza-Michael acceptor amino acids, Nε-acryloyl-(S)-lysine (AcrK, 1), p-acrylamido-(S)-phenylalanine (AcrF, 2), and p-vinylsulfonamido-(S)-phenylalanine (VSF, 3), in response to the amber stop codon in Escherichia coli. Using an αErbB2 Fab-ErbB2 antibody-receptor pair as an example, we demonstrate covalent bond formation between an αErbB2-VSF mutant and a specific surface lysine ε-amino group of ErbB2, leading to near quantitative crosslinking to either purified ErbB2 in vitro or to native cellular ErbB2 at physiological pH. This efficient biocompatible reaction may be useful for creating novel cell biological probes, diagnostics, or therapeutics that selectively and irreversibly bind a target protein in vitro or in living cells.
    Journal of the American Chemical Society 05/2014; · 10.68 Impact Factor
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    ABSTRACT: We report the engineering of zinc-finger-like motifs containing the unnatural amino acid (2,2'-bipyridin-5-yl)alanine (Bpy-Ala). A phage-display library was constructed in which five residues in the N-terminal finger of zif268 were randomized to include both canonical amino acids and Bpy-Ala. Panning of this library against a nine-base-pair DNA binding site identified several Bpy-Ala-containing functional Zif268 mutants. These mutants bind the Zif268 recognition site with affinities comparable to that of the wild-type protein. Further characterization indicated that the mutant fingers bind low-spin Fe(II) rather than Zn(II) . This work demonstrates that an expanded genetic code can lead to new metal ion binding motifs that can serve as structural, catalytic, or regulatory elements in proteins.
    ChemBioChem 03/2014; · 3.74 Impact Factor
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    ABSTRACT: A deficiency in C5 protects against arthritis development. However, there is currently no approach successfully translating these findings into arthritis therapy, as by targeting the key component, C5a. The aim of this study was to develop a vaccination strategy targeting C5a as therapy for patients with rheumatoid arthritis. An anti-C5a vaccine was generated by incorporating the unnatural amino acid p-nitrophenylalanine (4NPA) into selected sites in the murine C5a molecule. C5a-4NPA variants were screened for their immunogenicity in mice on different arthritis-susceptible class II major histocompatibility complex (MHC) backgrounds. A candidate vaccine was tested for its impact on disease in a murine model of collagen-induced arthritis (CIA). Immunity toward endogenous C5a as well as type II collagen was monitored and characterized. Replacing a single tyrosine residue in position 35 (Y(35) ) with 4NPA allowed the generation of an anti-C5a vaccine, which partly protected mice against the development of CIA while strongly ameliorating the severity of clinical disease. Although differing in just 3 atoms from wild-type C5a (wtC5a), C5aY(35) 4NPA induced loss of T cell and B cell tolerance toward the endogenous protein in mice expressing class II MHC H-2(q) molecules. Despite differential B cell epitope recognition, antibodies induced by both wtC5a and C5aY(35) 4NPA neutralized C5a. Thus, anti-wtC5a IgG titers during arthritis priming were potentially of critical importance for disease protection, because high titers of C5a-neutralizing antibodies after disease onset were unable to reverse the course of arthritis. The results of this study suggest that the most effective anti-C5a treatment in arthritis can be accomplished using a preventive vaccination strategy, and that treatment using conventional biologic or small molecule strategies targeting the C5a/C5aR axis may miss the optimal window for therapeutic intervention during the subclinical priming phase of the disease.
    Arthritis & rheumatology (Hoboken, N.J.). 03/2014; 66(3):610-21.
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    ABSTRACT: A polyspecific amber suppressor aminoacyl-tRNA synthetase/tRNA pair was evolved that genetically encodes a series of histidine analogs in both E. coli and mammalian cells. In combination with tRNACUAPyl, a pyrrolysyl-tRNA synthetase mutant was able to site-specifically incorporate 3-methyl-histidine, 3-pyridyl-alanine, 2-furyl-alanine, and 3-(2-thienyl)-alanine into proteins in response to an amber codon. Substitution of His66 in the blue fluorescent protein (BFP) with these histidine analogs created mutant proteins with distinct spectral properties. This work further expands the structural and chemical diversity of UAAs that can be genetically encoded in prokaryotic and eukaryotic organisms, and affords new probes of protein structure and function.
    ACS Chemical Biology 02/2014; · 5.44 Impact Factor
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    ABSTRACT: We found that Methanocaldococcus jannaschii DSM2661 tyrosyl-tRNA synthetase (Mj E9RS), specifically evolved to charge its cognate tRNA with the unnatural amino acid p-acetylphenylalanine (pAcF) in E coli, misaminoacylates the endogenous E. coli prolyl-tRNAs with pAcF at a low level (0.5% per proline frequency) in both the absence or presence of its coevolved amber suppressor tRNA (M. jannaschii tyrosyl-tRNA, ). In contrast to other E. coli tRNAs, the identity elements for recognition of the proly-tRNAs by the E. coli prolyl-tRNA synthetase (C1, G72, and A73) are similar to those in . Although the unique acceptor stem identity elements of the prolyl-tRNAs likely lower their recognition by the other endogenous aaRSs in E. coli, resulting in enhanced fidelity in the wild type strain, they lead to misaminoacylation by the archae-derived E9RS. Misincorporation of pAcF for proline was resolved to below detectable levels by overexpression of the endogenous E. coli prolyl-tRNA synthetase (proS) gene in combination with additional genomic manipulations to further increase the intracellular ratio of the ProS over its cognate proline tRNA's. These experiments suggest another mechanism by which the cell maintains the high fidelity of protein biosynthesis.
    ACS Chemical Biology 01/2014; · 5.44 Impact Factor
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    ABSTRACT: Using an expanded genetic code, antibodies with site-specifically incorporated nonnative amino acids were produced in stable cell lines derived from a CHO cell line with titers over 1 g/L. Using anti-5T4 and anti-Her2 antibodies as model systems, site-specific antibody drug conjugates (NDCs) were produced, via oxime bond formation between ketones on the side chain of the incorporated nonnative amino acid and hydroxylamine functionalized monomethyl auristatin D with either protease-cleavable or noncleavable linkers. When noncleavable linkers were used, these conjugates were highly stable and displayed improved in vitro efficacy as well as in vivo efficacy and pharmacokinetic stability in rodent models relative to conventional antibody drug conjugates conjugated through either engineered surface-exposed or reduced interchain disulfide bond cysteine residues. The advantages of the oxime-bonded, site-specific NDCs were even more apparent when low-antigen-expressing (2+) target cell lines were used in the comparative studies. NDCs generated with protease-cleavable linkers demonstrated that the site of conjugation had a significant impact on the stability of these rationally designed prodrug linkers. In a single-dose rat toxicology study, a site-specific anti-Her2 NDC was well tolerated at dose levels up to 90 mg/kg. These experiments support the notion that chemically defined antibody conjugates can be synthesized in commercially relevant yields and can lead to antibody drug conjugates with improved properties relative to the heterogeneous conjugates formed by nonspecific chemical modification.
    Proceedings of the National Academy of Sciences 01/2014; · 9.81 Impact Factor
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    ABSTRACT: High-throughput screening of 700,000 small molecules has identified 235 inhibitors of the GroEL/GroES-mediated refolding cycle. Dose-response analysis of a subset of these hits revealed that 21 compounds are potent inhibitors of GroEL/GroES-mediated refolding (IC50 <10μM). The screening results presented herein represent the first steps in a broader aim of developing molecular probes to study chaperonin biochemistry and physiology.
    Bioorganic & medicinal chemistry letters 01/2014; · 2.65 Impact Factor
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    ABSTRACT: An enhanced suppression system enables the expression of proteins in mammalian cells incorporating one unnatural amino acid (UAA) into multiple sites, as well as two different UAAs into distinct sites in a protein of interest. The utility of this technology was demonstrated by generating a full-length antibody, site-specifically conjugated to a drug and a fluorophore, and characterizing its activity in vitro.
    Angewandte Chemie International Edition 12/2013; 52(52):14080-3. · 11.34 Impact Factor
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    ABSTRACT: Protein arginine methyltransferase 1 (PRMT1)-dependent methylation contributes to the onset and progression of numerous diseases (e.g., cancer, heart disease, ALS), however, the regulatory mechanisms that control PRMT1 activity are relatively unexplored. We therefore set out to decipher how phosphorylation regulates PRMT1 activity. Curated mass spectrometry data identified Y291, a residue adjacent to the conserved THW loop, as being phosphorylated. Natural and unnatural amino acid mutagenesis, including the incorporation of p-carboxymethyl-L-phenylalanine (pCmF) as a phosphotyrosine mimic, were used to show that Y291 phosphorylation alters the substrate specificity of PRMT1. Additionally, p-benzoyl-L-phenylalanine (pBpF) was incorporated at the Y291 position and crosslinking experiments with K562 cell extracts identified several proteins (e.g., hnRNPA1 and hnRNP H3) that bind specifically to this site. Moreover, we also demonstrate that Y291 phosphorylation impairs PRMT1's ability to bind and methylate both proteins. In total, these studies demonstrate that Y291 phosphorylation alters both PRMT1 substrate specificity and protein-protein interactions.
    ACS Chemical Biology 12/2013; · 5.44 Impact Factor
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    ABSTRACT: Wnt signaling is one of the key oncogenic pathways in multiple cancers, and targeting this pathway is an attractive therapeutic approach. However, therapeutic success has been limited because of the lack of therapeutic agents for targets in the Wnt pathway and the lack of a defined patient population that would be sensitive to a Wnt inhibitor. We developed a screen for small molecules that block Wnt secretion. This effort led to the discovery of LGK974, a potent and specific small-molecule Porcupine (PORCN) inhibitor. PORCN is a membrane-bound O-acyltransferase that is required for and dedicated to palmitoylation of Wnt ligands, a necessary step in the processing of Wnt ligand secretion. We show that LGK974 potently inhibits Wnt signaling in vitro and in vivo, including reduction of the Wnt-dependent LRP6 phosphorylation and the expression of Wnt target genes, such as AXIN2. LGK974 is potent and efficacious in multiple tumor models at well-tolerated doses in vivo, including murine and rat mechanistic breast cancer models driven by MMTV-Wnt1 and a human head and neck squamous cell carcinoma model (HN30). We also show that head and neck cancer cell lines with loss-of-function mutations in the Notch signaling pathway have a high response rate to LGK974. Together, these findings provide both a strategy and tools for targeting Wnt-driven cancers through the inhibition of PORCN.
    Proceedings of the National Academy of Sciences 11/2013; · 9.81 Impact Factor
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    ABSTRACT: The X-ray crystal structure of a bovine antibody (BLV1H12) revealed a unique structure in its ultralong heavy chain complementarity determining region 3 (CDR3H) that folds into a solvent-exposed β-strand "stalk" fused to a disulfide crosslinked "knob" domain. We have substituted an antiparallel heterodimeric coiled-coil motif for the β-strand stalk in this antibody. The resulting antibody (Ab-coil) expresses in mammalian cells and has a stability similar to that of the parent bovine antibody. MS analysis of H-D exchange supports the coiled-coil structure of the substituted peptides. Substitution of the knob-domain of Ab-coil with bovine granulocyte colony-stimulating factor (bGCSF) results in a stably expressed chimeric antibody, which proliferates mouse NFS-60 cells with a potency comparable to that of bGCSF. This work demonstrates the utility of this novel coiled-coil CDR3 motif as a means for generating stable, potent antibody fusion proteins with useful pharmacological properties.
    Angewandte Chemie International Edition 11/2013; · 11.34 Impact Factor
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    ABSTRACT: A Fab-ulous killer: An anti-CD3 Fab-folate conjugate that targets cytotoxic T cells to folate-receptor-positive (FR(+) ) tumors results in efficient killing of tumor cells by activated T cells. This chemical approach to the synthesis of bispecific antibodies using unnatural amino acids with orthogonal chemical reactivity affords homogenous conjugates with precise control over the relative geometry of the antibody binding sites in excellent yields.
    Angewandte Chemie International Edition 11/2013; 52(46):12101-4. · 11.34 Impact Factor

Publication Stats

25k Citations
4,878.41 Total Impact Points


  • 2013–2014
    • The California Institute for Biomedical Research
      San Diego, California, United States
  • 1999–2014
    • The Scripps Research Institute
      • • Department of Chemistry
      • • Skaggs Institute for Chemical Biology
      La Jolla, California, United States
  • 2009–2012
    • University of California, San Diego
      • Division of Biological Sciences
      San Diego, CA, United States
  • 2008–2012
    • Genomics Institute of the Novartis Research Foundation
      San Diego, California, United States
  • 2011
    • Whitehead Institute for Biomedical Research
      Cambridge, Massachusetts, United States
    • Yale University
      • Department of Molecular, Cellular and Developmental Biology
      New Haven, CT, United States
  • 2005–2006
    • North Carolina State University
      • Department of Chemistry
      Raleigh, NC, United States
    • University of Maryland, College Park
      • Department of Chemistry and Biochemistry
      College Park, MD, United States
  • 1988–2006
    • University of California, Berkeley
      • • Department of Chemistry
      • • Department of Physics
      Berkeley, MO, United States
  • 1996–1999
    • Lawrence Berkeley National Laboratory
      • • Materials Sciences Division
      • • Geochemistry Department
      Berkeley, CA, United States
    • Howard Hughes Medical Institute
      Ashburn, Virginia, United States
  • 1995–1998
    • CSU Mentor
      Long Beach, California, United States
  • 1994
    • Lawrence University
      • Chemistry
      Berkeley, California, United States