
Marcos Pires
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Isolation and Synthesis of a Bacterially Produced Inhibitor of Rosette Development in Choanoflagellates
Routes of Synthesis of Carbapenems for Optimizing Both the Inactivation of l,d-Transpeptidase LdtMt1 of Mycobacterium tuberculosis and the Stability toward Hydrolysis by β-Lactamase BlaC
Structure and mechanism of the essential two-component signal-transduction system WalKR in Staphylococcus aureus
Article
The WalKR signal transduction system is involved in extracellular signal recognition, but the details of this function are not well established. Here, the authors report the crystal structure of this two-component system alongside the characterisation of a small-molecule activator.
Nature Communications doi: 10.1038/ncomms11000
Authors: Quanjiang Ji, Peter J. Chen, Guangrong Qin, Xin Deng, Ziyang Hao, Zdzislaw Wawrzak, Won-Sik Yeo, Jenny Winjing Quang, Hoonsik Cho, Guan-Zheng Luo, Xiaocheng Weng, Qiancheng You, Chi-Hao Luan, Xiaojing Yang, Taeok Bae, Kunqian Yu, Hualiang Jiang, Chuan He
Versatile protein tagging in cells with split fluorescent protein
Article
Tagging proteins with fluorescent proteins is a powerful method for both imaging and non-imaging applications. Here the authors use the eleventh β-strand of sfGFP and sfCherry as epitope tags for multicolour imaging and amplified signals by tandem arrangement; shortness of the tag enabled introduction into genomic loci using CRISPR/Cas9.
Nature Communications doi: 10.1038/ncomms11046
Authors: Daichi Kamiyama, Sayaka Sekine, Benjamin Barsi-Rhyne, Jeffrey Hu, Baohui Chen, Luke A. Gilbert, Hiroaki Ishikawa, Manuel D. Leonetti, Wallace F. Marshall, Jonathan S. Weissman, Bo Huang
Chemoproteomic profiling of host and pathogen enzymes active in cholera

Nature Chemical Biology 12, 268 (2016). doi:10.1038/nchembio.2025
Authors: Stavroula K Hatzios, Sören Abel, Julianne Martell, Troy Hubbard, Jumpei Sasabe, Diana Munera, Lars Clark, Daniel A Bachovchin, Firdausi Qadri, Edward T Ryan, Brigid M Davis, Eranthie Weerapana & Matthew K Waldor
A Host-Produced Autoinducer-2 Mimic Activates Bacterial Quorum Sensing
Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk
Probing Polytopic Membrane Protein–Substrate Interactions by Luminescence Resonance Energy Transfer
An injectable nanoparticle generator enhances delivery of cancer therapeutics
Nature Biotechnology. doi:10.1038/nbt.3506
Authors: Rong Xu, Guodong Zhang, Junhua Mai, Xiaoyong Deng, Victor Segura-Ibarra, Suhong Wu, Jianliang Shen, Haoran Liu, Zhenhua Hu, Lingxiao Chen, Yi Huang, Eugene Koay, Yu Huang, Jun Liu, Joe E Ensor, Elvin Blanco, Xuewu Liu, Mauro Ferrari & Haifa Shen
The efficacy of cancer drugs is often limited because only a small fraction of the administered dose accumulates in tumors. Here we report an injectable nanoparticle generator (iNPG) that overcomes multiple biological barriers to cancer drug delivery. The iNPG is a discoidal micrometer-sized particle that can be loaded with chemotherapeutics. We conjugate doxorubicin to poly(L-glutamic acid) by means of a pH-sensitive cleavable linker, and load the polymeric drug (pDox) into iNPG to assemble iNPG-pDox. Once released from iNPG, pDox spontaneously forms nanometer-sized particles in aqueous solution. Intravenously injected iNPG-pDox accumulates at tumors due to natural tropism and enhanced vascular dynamics and releases pDox nanoparticles that are internalized by tumor cells. Intracellularly, pDox nanoparticles are transported to the perinuclear region and cleaved into Dox, thereby avoiding excretion by drug efflux pumps. Compared to its individual components or current therapeutic formulations, iNPG-pDox shows enhanced efficacy in MDA-MB-231 and 4T1 mouse models of metastatic breast cancer, including functional cures in 40–50% of treated mice.
Targeting the Bacterial Division Protein FtsZ
Enzyme-Instructed Self-Assembly of Small d-Peptides as a Multiple-Step Process for Selectively Killing Cancer Cells
Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk
[Report] Schedule-dependent interaction between anticancer treatments
Peptide based hydrogels for cancer drug release: modulation of stiffness, drug release and proteolytic stability of hydrogels by incorporating D-amino acid residue(s)
DOI: 10.1039/C6CC01744D, Communication
This is a novel example of tailor-made design of hydrogels for anticancer drug release.
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On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry
Macrocyclization of Unprotected Peptide Isocyanates
Preparation and Evaluation of Radiolabeled Antibody Recruiting Small Molecules That Target Prostate-Specific Membrane Antigen for Combined Radiotherapy and Immunotherapy
Multifunctional Coating Improves Cell Adhesion on Titanium by using Cooperatively Acting Peptides
Abstract
Promotion of cell adhesion on biomaterials is crucial for the long-term success of a titanium implant. Herein a novel concept is highlighted combining very stable and affine titanium surface adhesive properties with specific cell binding moieties in one molecule. A peptide containing l-3,4-dihydroxyphenylalanine was synthesized and affinity to titanium was investigated. Modification with a cyclic RGD peptide and a heparin binding peptide (HBP) was realized by an efficient on-resin combination of Diels–Alder reaction with inverse electron demand and CuI catalyzed azide–alkyne cycloaddition. The peptide was fluorescently labeled by thiol Michael addition. Conjugating the cyclic RGD and HBP in one peptide gave improved spreading, proliferation, viability, and the formation of well-developed actin cytoskeleton and focal contacts of osteoblast-like cells.
Let′s stick together: An efficient on-resin combination of a Diels–Alder reaction with inverse electron demand and a CuI catalyzed azide–alkyne cycloaddition is used to link a stable and affine TiO2-binding peptide to two cell adhesive motifs. The multifunctional construct improved the cell adhesion of osteoblast-like cells through the cooperative action of the peptides. DOPA=l-3,4-dihydroxylphenylalanine.
Structure and Energetic Contributions of a Designed Modular Peptide-Binding Protein with Picomolar Affinity
Stapled Peptides with γ-Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction
Abstract
“Stapled” peptides are typically designed to replace two non-interacting residues with a constraining, olefinic staple. To mimic interacting leucine and isoleucine residues, we have created new amino acids that incorporate a methyl group in the γ-position of the stapling amino acid S5. We have incorporated them into a sequence derived from steroid receptor coactivator 2, which interacts with estrogen receptor α. The best peptide (IC50=89 nm) replaces isoleucine 689 with an S-γ-methyl stapled amino acid, and has significantly higher affinity than unsubstituted peptides (390 and 760 nm). Through X-ray crystallography and molecular dynamics studies, we show that the conformation taken up by the S-γ-methyl peptide minimizes the syn-pentane interactions between the α- and γ-methyl groups.
Branching out: γ-Branched stapling amino acids were synthesized and incorporated into peptides to produce high-affinity inhibitors of the estrogen receptor/steroid receptor coactivator interaction. Some branched stapled peptides were more effective than the unfunctionalized peptide. The influence of 1,5-interactions on peptide conformation was analyzed by circular dichroism, X-ray crystallography, and molecular dynamics.
Cytotoxic T Cells Use Mechanical Force to Potentiate Target Cell Killing
A p-Hydroxyphenacyl–Benzothiazole–Chlorambucil Conjugate as a Real-Time-Monitoring Drug-Delivery System Assisted by Excited-State Intramolecular Proton Transfer
Abstract
Among the well-known phototriggers, the p-hydroxyphenacyl (pHP) group has consistently enabled the very fast, efficient, and high-conversion release of active molecules. Despite this unique behavior, the pHP group has been ignored as a delivery agent, particularly in the area of theranostics, because of two major limitations: Its excitation wavelength is below 400 nm, and it is nonfluorescent. We have overcome these limitations by incorporating a 2-(2′-hydroxyphenyl)benzothiazole (HBT) appendage capable of rapid excited-state intramolecular proton transfer (ESIPT). The ESIPT effect also provided two unique advantages: It assisted the deprotonation of the pHP group for faster release, and it was accompanied by a distinct fluorescence color change upon photorelease. In vitro studies showed that the p-hydroxyphenacyl–benzothiazole–chlorambucil conjugate presents excellent properties, such as real-time monitoring, photoregulated drug delivery, and biocompatibility.
Let it go… The two major limitations for theranostics of the p-hydroxyphenacyl (pHP) phototrigger were overcome by incorporating a benzothiazole appendage to enable rapid excited-state intramolecular proton transfer (ESIPT; see picture). The ESIPT effect had two key advantages: It assisted the deprotonation of pHP group for faster release of the anticancer drug chlorambucil and led to a fluorescence color change upon photorelease.
Redirecting immunity via covalently incorporated immunogenic sialic acid on the tumor cell surface
DOI: 10.1039/C5SC04133C, Edge Article
Open Access
  This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.
Anti-tumor immunity was achieved via metabolically incorporated non-self antigen-labelled sialic acid on the tumor surface glycocalyx.
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Dual Genetic Encoding of Acetyl-lysine and Non-deacetylatable Thioacetyl-lysine Mediated by Flexizyme
Abstract
Acetylation of lysine residues is an important post-translational protein modification. Lysine acetylation in histones and its crosstalk with other post-translational modifications in histone and non-histone proteins are crucial to DNA replication, DNA repair, and transcriptional regulation. We incorporated acetyl-lysine (AcK) and the non-hydrolyzable thioacetyl-lysine (ThioAcK) into full-length proteins in vitro, mediated by flexizyme. ThioAcK and AcK were site-specifically incorporated at different lysine positions into human histone H3, either individually or in pairs. We demonstrate that the thioacetyl group in histone H3 could not be removed by the histone deacetylase sirtuin type 1. This method provides a powerful tool to study protein acetylation and its role in crosstalk between post-translational modifications.
Director′s cut: The Flexizyme technique is used to incorporate acetyl-lysine and the non-hydrolyzable thioacetyl-lysine into full-length proteins in vitro and site-specifically into human histone H3, either individually or in pairs. The thioacetyl group of the modified histone H3 could not be removed by the histone deacetylase sirtuin.
Fast and Tight Boronate Formation for Click Bioorthogonal Conjugation
Abstract
A new click bioorthogonal reaction system was devised to enable the fast ligation (kON≈340 m−1 s−1) of conjugatable derivatives of a rigid cyclic diol (nopoldiol) and a carefully optimized boronic acid partner, 2-methyl-5-carboxymethylphenylboronic acid. Using NMR and fluorescence spectroscopy studies, the corresponding boronates were found to form reversibly within minutes at low micromolar concentration in water, providing submicromolar equilibrium constant (Keq≈105–106 m−1). Efficient protein conjugation under physiological conditions was demonstrated with model proteins thioredoxin and albumin, and characterized by mass spectrometry and gel electrophoresis.
A click bioorthogonal reaction system was devised for the fast ligation of conjugatable derivatives of a rigid cyclic diol (nopoldiol) with an optimal boronic acid partner, 2-methyl-5-carboxymethylphenylboronic acid. The resulting boronates form reversibly within minutes at low concentrations in water. Efficient protein conjugation under physiological conditions was demonstrated with model proteins thioredoxin and albumin.
Aptamer and Antisense-Mediated Two-Dimensional Isolation of Specific Cancer Cell Subpopulations
Inclusion of Strep-tag II in design of antigen receptors for T-cell immunotherapy
Nature Biotechnology. doi:10.1038/nbt.3461
Authors: Lingfeng Liu, Daniel Sommermeyer, Alexandra Cabanov, Paula Kosasih, Tyler Hill & Stanley R Riddell
Adoptive immunotherapy with genetically engineered T cells has the potential to treat cancer and other diseases. The introduction of Strep-tag II sequences into specific sites in synthetic chimeric antigen receptors or natural T-cell receptors of diverse specificities provides engineered T cells with a marker for identification and rapid purification, a method for tailoring spacer length of chimeric receptors for optimal function, and a functional element for selective antibody-coated, microbead-driven, large-scale expansion. These receptor designs facilitate cGMP manufacturing of pure populations of engineered T cells for adoptive T-cell therapies and enable in vivo tracking and retrieval of transferred cells for downstream research applications.
Glycopeptide antibiotic analogs for selective inactivation and two-photon imaging of vancomycin-resistant strains
DOI: 10.1039/C5CC10230H, Communication
Theranostic divalent vancomycin systems exhibit selective antibacterial activity against vancomycin-resistant strains and can be applied for two-photon fluorescence imaging.
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Selective labelling and eradication of antibiotic-tolerant bacterial populations in Pseudomonas aeruginosa biofilms
Article
Pathogenic bacteria can aggregate to form biofilms and develop tolerance to antibiotics. Here, the authors use a proteomics approach to study the development of tolerance to the antibiotic colistin in Pseudomonas aeruginosa biofilms, and show that co-treatment with a second compound kills the tolerant cells.
Nature Communications doi: 10.1038/ncomms10750
Authors: Song Lin Chua, Joey Kuok Hoong Yam, Piliang Hao, Sunil S. Adav, May Margarette Salido, Yang Liu, Michael Givskov, Siu Kwan Sze, Tim Tolker-Nielsen, Liang Yang









