03 Oct 18:16
by Flavia Fontana, Dongfei Liu, Jouni Hirvonen, Hélder A. Santos
The application of nanotechnology to the treatment of cancer or other diseases has been boosted during the last decades due to the possibility to precise deliver drugs where needed, enabling a decrease in the drug's side effects. Nanocarriers are particularly valuable for potentiating the simultaneous co-delivery of multiple drugs in the same particle for the treatment of heavily burdening diseases like cancer. Immunotherapy represents a new concept in the treatment of cancer and has shown outstanding results in patients treated with check-point inhibitors. Thereby, researchers are applying nanotechnology to cancer immunotherapy toward the development of nanocarriers for delivery of cancer vaccines and chemo-immunotherapies. Cancer nanovaccines can be envisioned as nanocarriers co-delivering antigens and adjuvants, molecules often presenting different physicochemical properties, in cancer therapy. A wide range of nanocarriers (e.g., polymeric, lipid-based and inorganic) allow the co-formulation of these molecules, or the delivery of chemo- and immune-therapeutics in the same system. Finally, there is a trend toward the use of biologically inspired and derived nanocarriers. In this review, we present the recent developments in the field of immunotherapy, describing the different systems proposed by categories: polymeric nanoparticles, lipid-based nanosystems, metallic and inorganic nanosystems and, finally, biologically inspired and derived nanovaccines. WIREs Nanomed Nanobiotechnol 2017, 9:e1421. doi: 10.1002/wnan.1421
For further resources related to this article, please visit the WIREs website.
19 Aug 19:25
by Volz, P., Krause, N., Balke, J., Schneider, C., Walter, M., Schneider, F., Schlesinger, R., Alexiev, U.
A variant of the cation channel channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) was selectively labeled at position Cys-79 at the end of the first cytoplasmic loop and the beginning of transmembrane helix B with the fluorescent dye fluorescein (acetamidofluorescein). We utilized (i) time-resolved fluorescence anisotropy experiments to monitor the structural dynamics at the cytoplasmic surface close to the inner gate in the dark and after illumination in the open channel state and (ii) time-resolved fluorescence quenching experiments to observe the solvent accessibility of helix B at pH 6.0 and 7.4. The light-induced increase in final anisotropy for acetamidofluorescein bound to the channel variant with a prolonged conducting state clearly shows that the formation of the open channel state is associated with a large conformational change at the cytoplasmic surface, consistent with an outward tilt of helix B. Furthermore, results from solute accessibility studies of the cytoplasmic end of helix B suggest a pH-dependent structural heterogeneity that appears below pH 7. At pH 7.4 conformational homogeneity was observed, whereas at pH 6.0 two protein fractions exist, including one in which residue 79 is buried. This inaccessible fraction amounts to 66% in nanodiscs and 82% in micelles. Knowledge about pH-dependent structural heterogeneity may be important for CrChR2 applications in optogenetics.
18 Aug 20:29
by Matthias Fach, Lydia Radi and Peter R. Wich

Journal of the American Chemical Society
DOI: 10.1021/jacs.6b06243
18 Aug 20:28
by Peter V. Robinson, Cheng-ting Tsai, Amber E. de Groot, Julia L. McKechnie and Carolyn R. Bertozzi

Journal of the American Chemical Society
DOI: 10.1021/jacs.6b03861
17 Aug 17:58
by Anna Brezden, Mohamed F. Mohamed, Manish Nepal, John S. Harwood, Jerrin Kuriakose, Mohamed N. Seleem and Jean Chmielewski

Journal of the American Chemical Society
DOI: 10.1021/jacs.6b04831
17 Aug 13:41
by Hao Wu, Guillaume Mousseau, Sonia Mediouni, Susana T. Valente, Thomas Kodadek
Abstract
We present here an efficient alternative to N-methylation for the purpose of morphing protein-binding peptides into more serum-stable and cell-permeable compounds. This involves the incorporation of a cycloalanine (CyAla) into a peptide in a way that avoids difficult coupling steps. We demonstrate the utility of this chemistry in creating a cell-permeable derivative of a high-affinity HIV Rev protein-binding peptide.
Introducing sites of N-alkylation into peptides improves serum stability and cell permeability. The most common strategy, N-methylation, requires harsh peptide-coupling reactions. An alternative strategy is proposed involving the efficient incorporation of cycloalanine residues into peptides. This approach was employed to create a cell-permeable version of a HIV Rev peptide antagonist.
17 Aug 13:40
by Nitin A. Patil, Julien Tailhades, John A. Karas, Frances Separovic, John D. Wade, Mohammed Akhter Hossain
Abstract
Heterodimeric peptides linked by disulfide bonds are attractive drug targets. However, their chemical assembly can be tedious, time-consuming, and low yielding. Inspired by the cellular synthesis of pro-insulin in which the two constituent peptide chains are expressed as a single-chain precursor separated by a connecting C-peptide, we have developed a novel chemically cleavable bis-linker tether which allows the convenient assembly of two peptide chains as a single “pro”-peptide on the same solid support. Following the peptide cleavage and post-synthetic modifications, this bis-linker tether can be removed in one-step by chemical means. This method was used to synthesize a drug delivery-cargo conjugate, TAT-PKCi peptide, and a two-disulfide bridged heterodimeric peptide, thionin (7-19)-(24-32R), a thionin analogue. To our knowledge, this is the first report of a one-pot chemically cleavable bis-linker strategy for the facile synthesis of cross-bridged two-chain peptides.
Tethered together: A dimedone-based N-terminal linker was developed for use in a bis-linker tether strategy for efficient synthesis of heterodimeric peptides. Sequential solid-phase synthesis of two peptide chains on the same solid support, separated by the tether, followed by their folding and the chemical cleavage of the bis-linker tether yielded the heterodimeric peptide.
12 Aug 14:59
by Alvin Kung, Ying-Chu Chen, Marianne Schimpl, Feng Ni, Jianfa Zhu, Maurice Turner, Henrik Molina, Ross Overman and Chao Zhang

Journal of the American Chemical Society
DOI: 10.1021/jacs.6b05483
08 Aug 13:25
by Julian Engel, Christian Becker, Jonas Lategahn, Marina Keul, Julia Ketzer, Thomas Mühlenberg, Laxmikanth Kollipara, Carsten Schultz-Fademrecht, René P. Zahedi, Sebastian Bauer, Daniel Rauh
Abstract
Targeting acquired drug resistance represents the major challenge in the treatment of EGFR-driven non-small-cell lung cancer (NSCLC). Herein, we describe the structure-based design, synthesis, and biological evaluation of a novel class of covalent EGFR inhibitors that exhibit excellent inhibition of EGFR-mutant drug-resistant cells. Protein X-ray crystallography combined with detailed kinetic studies led to a deeper understanding of the mode of inhibition of EGFR-T790M and provided insight into the key principles for effective inhibition of the recently discovered tertiary mutation at EGFR-C797S.
Methods against mutants: Targeting acquired drug resistance represents the major challenge in the treatment of EGFR-driven non-small-cell lung cancer. Complex crystal structures of new covalent inhibitors and detailed kinetic studies provide insight into the key features required for targeting EGFR mutations, including EGFR-L858R/T790M/C797S.
01 Aug 17:48
by Derek P. Ng and Charles M. Deber

Biochemistry
DOI: 10.1021/acs.biochem.6b00380
20 Jul 18:26
by Heidi Ledford
The unsung heroes of CRISPR
Nature 535, 7612 (2016). http://www.nature.com/doifinder/10.1038/535342a
Author: Heidi Ledford
The soaring popularity of gene editing has made celebrities of the principal investigators who pioneered the field — but their graduate students and postdocs are often overlooked.
20 Jul 17:14
by Haya Jamali, Hasan A. Khan, Caroline C. Tjin and Jonathan A. Ellman

ACS Medicinal Chemistry Letters
DOI: 10.1021/acsmedchemlett.6b00215
08 Jul 14:06
by Frank Versluis, Daphne M. van Elsland, Serhii Mytnyk, Dayinta L. Perrier, Fanny Trausel, Jos M. Poolman, Chandan Maity, Vincent A. A. le Sage, Sander I. van Kasteren, Jan H. van Esch and Rienk Eelkema

Journal of the American Chemical Society
DOI: 10.1021/jacs.6b03853
08 Jul 14:05
by Sumati Bhatia, Luis Cuellar Camacho and Rainer Haag

Journal of the American Chemical Society
DOI: 10.1021/jacs.5b12950
24 Jun 14:44
by Burns KE, McCleerey TP, Thévenin D
pH-Selective Cytotoxicity of pHLIP-Antimicrobial Peptide Conjugates.
Sci Rep. 2016;6:28465
Authors: Burns KE, McCleerey TP, Thévenin D
Abstract
Positively charged antimicrobial peptides have become promising agents for the treatment of cancer by inducing apoptosis though their preferential binding and disruption of negatively charged membranes, such as the mitochondrial membrane. (KLAKLAK)2 is such a peptide but due to its polarity, it cannot cross the cellular membrane and therefore relies on the use of a delivery agent. For targeted delivery, previous studies have relied on cell penetrating peptides, nanoparticles or specific biomarkers. Herein, we investigated the first use of pHLIP to selectively target and directly translocate (KLAKLAK)2 into the cytoplasm of breast cancer cells, based on the acidic tumor micro-environment. With the goal of identifying a lead conjugate with optimized selective cytotoxicity towards cancer cells, we analyzed a family of (KLAKLAK)2 analogs with varying size, polarity and charge. We present a highly efficacious pHLIP conjugate that selectively induces concentration- and pH-dependent toxicity in breast cancer cells.
PMID: 27334357 [PubMed - in process]
24 Jun 13:04
by Haijun Zhao, Qian Li and Zehui Hong

Molecular Pharmaceutics
DOI: 10.1021/acs.molpharmaceut.6b00164
23 Jun 17:35
by Arnaud C. Tiberghien, Jean-Noel Levy, Luke A. Masterson, Neki V. Patel, Lauren R. Adams, Simon Corbett, David G. Williams, John A. Hartley and Philip W. Howard

ACS Medicinal Chemistry Letters
DOI: 10.1021/acsmedchemlett.6b00062
03 Jun 23:53
by Carlos Mas-Moruno, Roberta Fraioli, Florian Rechenmacher, Stefanie Neubauer, Tobias G. Kapp, Horst Kessler
Abstract
Engineering biomaterials with integrin-binding activity is a very powerful approach to promote cell adhesion, modulate cell behavior, and induce specific biological responses at the surface level. The aim of this Review is to illustrate the evolution of surface-coating molecules in this field: from peptides and proteins with relatively low integrin-binding activity and receptor selectivity to highly active and selective peptidomimetic ligands. In particular, we will bring into focus the difficult challenge of achieving selectivity between the two closely related integrin subtypes αvβ3 and α5β1. The functionalization of surfaces with such peptidomimetics opens the way for a new generation of highly specific cell-instructive surfaces to dissect the biological role of integrin subtypes and for application in tissue engineering and regenerative medicine.
An active and evolving area: Surface coating has evolved from RGD-based peptides and proteins with relatively poor integrin-binding activity and selectivity to peptidomimetics with high affinity and receptor subtype selectivity. This Review highlights the most representative milestones in this amazing journey.
30 May 12:27
by Maria Panagiotopoulou, Yolanda Salinas, Selim Beyazit, Stephanie Kunath, Luminita Duma, Elise Prost, Andrew G. Mayes, Marina Resmini, Bernadette Tse Sum Bui, Karsten Haupt
Abstract
Advanced tools for cell imaging are of great interest for the detection, localization, and quantification of molecular biomarkers of cancer or infection. We describe a novel photopolymerization method to coat quantum dots (QDs) with polymer shells, in particular, molecularly imprinted polymers (MIPs), by using the visible light emitted from QDs excited by UV light. Fluorescent core–shell particles specifically recognizing glucuronic acid (GlcA) or N-acetylneuraminic acid (NANA) were prepared. Simultaneous multiplexed labeling of human keratinocytes with green QDs conjugated with MIP-GlcA and red QDs conjugated with MIP-NANA was demonstrated by fluorescence imaging. The specificity of binding was verified with a non-imprinted control polymer and by enzymatic cleavage of the terminal GlcA and NANA moieties. The coating strategy is potentially a generic method for the functionalization of QDs to address a much wider range of biocompatibility and biorecognition issues.
Labels to tell them apart: The visible light emitted from quantum dots excited by UV light was used to photopolymerize a molecularly imprinted polymer (MIP) shell around the QDs. The use of different quantum dots with MIP shells that recognize glucuronic acid (green) or N-acetylneuraminic acid (red) enabled the multiplexed labeling and imaging of keratinocytes. The labels could be differentiated and quantified on and in the cells.
26 May 00:54
by Huy N. Hoang, Russell W. Driver, Renée L. Beyer, Timothy A. Hill, Aline D. de Araujo, Fabien Plisson, Rosemary S. Harrison, Lena Goedecke, Nicholas E. Shepherd, David P. Fairlie
Abstract
Cyclic pentapeptides (e.g. Ac-(cyclo-1,5)-[KAXAD]-NH2; X=Ala, 1; Arg, 2) in water adopt one α-helical turn defined by three hydrogen bonds. NMR structure analysis reveals a slight distortion from α-helicity at the C-terminal aspartate caused by torsional restraints imposed by the K(i)–D(i+4) lactam bridge. To investigate this effect on helix nucleation, the more water-soluble 2 was appended to N-, C-, or both termini of a palindromic peptide ARAARAARA (≤5 % helicity), resulting in 67, 92, or 100 % relative α-helicity, as calculated from CD spectra. From the C-terminus of peptides, 2 can nucleate at least six α-helical turns. From the N-terminus, imperfect alignment of the Asp5 backbone amide in 2 reduces helix nucleation, but is corrected by a second unit of 2 separated by 0–9 residues from the first. These cyclic peptides are extremely versatile helix nucleators that can be placed anywhere in 5–25 residue peptides, which correspond to most helix lengths in protein–protein interactions.
Pep up your peptide: When an α-helical cyclic pentapeptide 1 was appended to one or both ends of a palindromic peptide ARAARAARA (≤5 % helicity), 67, 92, or 100 % α-helicity of the resulting peptide was observed (see picture). From the C-terminus of peptides, 1 nucleated at least six α-helical turns. Imperfect alignment of a backbone amide in 1 reduced helix nucleation when 1 was attached to the N-terminus, but was corrected by a second unit of 1.
25 May 15:41
by Van Bavel JJ, Mende-Siedlecki P, Brady WJ, Reinero DA
Contextual sensitivity in scientific reproducibility.
Proc Natl Acad Sci U S A. 2016 May 23;
Authors: Van Bavel JJ, Mende-Siedlecki P, Brady WJ, Reinero DA
Abstract
In recent years, scientists have paid increasing attention to reproducibility. For example, the Reproducibility Project, a large-scale replication attempt of 100 studies published in top psychology journals found that only 39% could be unambiguously reproduced. There is a growing consensus among scientists that the lack of reproducibility in psychology and other fields stems from various methodological factors, including low statistical power, researcher's degrees of freedom, and an emphasis on publishing surprising positive results. However, there is a contentious debate about the extent to which failures to reproduce certain results might also reflect contextual differences (often termed "hidden moderators") between the original research and the replication attempt. Although psychologists have found extensive evidence that contextual factors alter behavior, some have argued that context is unlikely to influence the results of direct replications precisely because these studies use the same methods as those used in the original research. To help resolve this debate, we recoded the 100 original studies from the Reproducibility Project on the extent to which the research topic of each study was contextually sensitive. Results suggested that the contextual sensitivity of the research topic was associated with replication success, even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines. These results suggest that researchers, replicators, and consumers should be mindful of contextual factors that might influence a psychological process. We offer several guidelines for dealing with contextual sensitivity in reproducibility.
PMID: 27217556 [PubMed - as supplied by publisher]
23 May 19:17
by Ramin A. Morshed, Megan E. Muroski, Qing Dai, Michelle L. Wegscheid, Brenda Auffinger, Dou Yu, Yu Han, Lingjiao Zhang, Meijing Wu, Yu Cheng and Maciej S. Lesniak

Molecular Pharmaceutics
DOI: 10.1021/acs.molpharmaceut.6b00004
14 May 16:14
by David P. Fairlie, Aline Dantas de Araujo
Abstract
Stapled peptides are an emerging class of cyclic peptide molecules with enhanced biophysical properties such as conformational and proteolytic stability, cellular uptake and elevated binding affinity and specificity for their biological targets. Among the limited number of chemistries available for their synthesis, the cysteine-based stapling strategy has received considerable development in the last few years driven by facile access from cysteine-functionalized peptide precursors. Here we present some recent advances in peptide and protein stapling where the side-chains of cysteine residues are covalently connected with a range of different crosslinkers affording bisthioether macrocyclic peptides of varying topology and biophysical properties. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 843–852, 2016.
11 May 13:42
by Francesco Cardarelli
The intracellular trafficking mechanism of Lipofectamine-based transfection reagents and its implication for gene delivery
Scientific Reports, Published online: 11 May 2016; doi:10.1038/srep25879
06 May 20:06
by Cezary Treda
by Cezary Treda, Marta Popeda, Magdalena Ksiazkiewicz, Dawid P. Grzela, Maciej P. Walczak, Mateusz Banaszczyk, Joanna Peciak, Ewelina Stoczynska-Fidelus, Piotr Rieske
The Epidermal Growth Factor Receptor (EGFR) and its mutations contribute in various ways to tumorigenesis and biology of human cancers. They are associated with tumor proliferation, progression, drug resistance and the process of apoptosis. There are also reports that overexpression and activation of wild-type EGFR may lead to cell apoptosis. To study this phenomenon, we overexpressed in an AD293 cell line two most frequently observed forms of the EGFR receptor: wild-type and the constitutively active mutant–EGFR variant III (EGFRvIII). Then, we compared the effect of EGF stimulation on cell viability and downstream EGFR signaling. AD293 cells overexpressing wild-type EGFR, despite a significant proliferation increase in serum supplemented medium, underwent apoptosis after EGF stimulation in serum free conditions. EGFRvIII expressing cells, however, were unaffected by either serum starvation or EGF treatment. The effect of EGF was completely neutralized by tyrosine kinase inhibitors (TKIs), indicating the specificity of this observation. Moreover, apoptosis was not prevented by inhibiting EGFR downstream proteins (PI3K, AKT and mTOR). Here we showed another EGFR function, dependent on environmental factors, which could be employed in therapy and drug design. We also proposed a new tool for EGFR inhibitor analysis.
06 May 19:15
by Simon Beaudoin, Andreanne Rondeau, Olivier Martel, Marc-Andre Bonin, Johan E. van Lier and Jeffrey V. Leyton

Molecular Pharmaceutics
DOI: 10.1021/acs.molpharmaceut.6b00075
06 May 14:18
by Shutao Guo, Yoshiyuki Nakagawa, Aoune Barhoumi, Weiping Wang, Changyou Zhan, Rong Tong, Claudia Santamaria and Daniel S. Kohane

Journal of the American Chemical Society
DOI: 10.1021/jacs.6b02435
05 May 00:48
by Dominik Paquet
Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9
Nature 533, 7601 (2016). doi:10.1038/nature17664
Authors: Dominik Paquet, Dylan Kwart, Antonia Chen, Andrew Sproul, Samson Jacob, Shaun Teo, Kimberly Moore Olsen, Andrew Gregg, Scott Noggle & Marc Tessier-Lavigne
The bacterial CRISPR/Cas9 system allows sequence-specific gene editing in many organisms and holds promise as a tool to generate models of human diseases, for example, in human pluripotent stem cells. CRISPR/Cas9 introduces targeted double-stranded breaks (DSBs) with high efficiency, which are typically repaired by non-homologous end-joining (NHEJ) resulting in nonspecific insertions, deletions or other mutations (indels). DSBs may also be repaired by homology-directed repair (HDR) using a DNA repair template, such as an introduced single-stranded oligo DNA nucleotide (ssODN), allowing knock-in of specific mutations. Although CRISPR/Cas9 is used extensively to engineer gene knockouts through NHEJ, editing by HDR remains inefficient and can be corrupted by additional indels, preventing its widespread use for modelling genetic disorders through introducing disease-associated mutations. Furthermore, targeted mutational knock-in at single alleles to model diseases caused by heterozygous mutations has not been reported. Here we describe a CRISPR/Cas9-based genome-editing framework that allows selective introduction of mono- and bi-allelic sequence changes with high efficiency and accuracy. We show that HDR accuracy is increased dramatically by incorporating silent CRISPR/Cas-blocking mutations along with pathogenic mutations, and establish a method termed ‘CORRECT’ for scarless genome editing. By characterizing and exploiting a stereotyped inverse relationship between a mutation’s incorporation rate and its distance to the DSB, we achieve predictable control of zygosity. Homozygous introduction requires a guide RNA targeting close to the intended mutation, whereas heterozygous introduction can be accomplished by distance-dependent suboptimal mutation incorporation or by use of mixed repair templates. Using this approach, we generated human induced pluripotent stem cells with heterozygous and homozygous dominant early onset Alzheimer’s disease-causing mutations in amyloid precursor protein (APPSwe) and presenilin 1 (PSEN1M146V) and derived cortical neurons, which displayed genotype-dependent disease-associated phenotypes. Our findings enable efficient introduction of specific sequence changes with CRISPR/Cas9, facilitating study of human disease.
03 May 19:59
by Xiong-Jie Jiang, Janet T. F. Lau, Qiong Wang, Dennis K. P. Ng, Pui-Chi Lo
Abstract
A diiodo distyryl boron dipyrromethene (BODIPY) core was conjugated to two ferrocenyl quenchers through acid-labile ketal and/or thiol-cleavable disulfide linkers, of which the fluorescence and photosensitizing properties were significantly quenched through a photoinduced electron-transfer process. The two symmetrical analogues that contained either the ketal or disulfide linkers could only be activated by a single stimulus, whereas the unsymmetrical analogue was responsive to dual stimuli. Upon interaction with acid and/or dithiothreitol (DTT), these linkers were cleaved selectively. The separation of the BODIPY core and the ferrocenyl moieties restored the photoactivities of the former in phosphate buffered saline and inside the MCF-7 breast cancer cells, rendering these compounds as potential activable photosensitizers for targeted photodynamic therapy. The dual activable analogue exhibited the greatest enhancement in intracellular fluorescence intensity in both an acidic environment (pH 5) and the presence of DTT (4 mm). Its photocytotoxicity against MCF-7 cells also increased by about twofold upon preincubation with 4 mm of DTT. The activation of this compound was also demonstrated in nude mice bearing a HT29 human colorectal carcinoma. A significant increase in fluorescence intensity in the tumor was observed over 9 h after intratumoral injection.
Call to action: Three bisferrocenyl distyryl boron dipyrromethene (BODIPY) derivatives have been prepared, the photoactivities of which can be activated by acid and/or dithiothreitol (DTT) both in phosphate buffered saline and at the cellular level (see figure). The in vivo activation of the dual activable analogue has also been demonstrated.
03 May 13:34
by Xiaoding Xu, Jun Wu, Yanlan Liu, Mikyung Yu, Lili Zhao, Xi Zhu, Sushant Bhasin, Qing Li, Emily Ha, Jinjun Shi, Omid C. Farokhzad
Abstract
RNA interference (RNAi) gene silencing technologies have shown significant potential for treating various diseases, including cancer. However, clinical success in cancer therapy remains elusive, mainly owing to suboptimal in vivo delivery of RNAi therapeutics such as small interference RNA (siRNA) to tumors. Herein, we developed a library of polymers that respond to a narrow pH change (ultra-pH-responsive), and demonstrated the utility of these materials in targeted and deep tumor-penetrating nanoparticle (NP) for in vivo RNAi. The new NP platform is mainly composed of the following key components: i) internalizing RGD (iRGD) to enhance tumor targeting and tissue penetration; ii) polyethylene glycol (PEG) chains to prolong blood circulation; and iii) sharp pH-responsive hydrophobic polymer to improve endosome escape. Through systematic studies of structure–function relationship, the optimized RNAi NPs (<70 nm) showed efficient gene silencing and significant inhibition of tumor growth with negligible toxicities in vivo.
A tumor-penetrating and pH-responsive nanoplatform was developed for targeted siRNA delivery. This platform could efficiently use tumor-penetrating and pH-responsive abilities to deliver therapeutic siRNA to the cytoplasm, leading to a significant inhibition of tumor growth. This platform shows great promise as a siRNA delivery vehicle for cancer therapy.