Bioorganic & Medicinal Chemistry Volume 21, Issue 12, 2013

Symposium-in-Print

Tetrahedron Young Investigator Award 2013

Ashraf Brik

Edited by:

Herbert Waldmann

Contents

Chemistry and biology of peptides, proteins and beyond pp 3398–3399

Ashraf Brik*

ARTICLES

Intracellular protein degradation: From a vague idea through the lysosome and the ubiquitin–proteasome systemand onto human diseases and drug targeting

pp 3400–3410

Aaron Ciechanover*

Gly76 is conjugated to the target molecule in all known ubiquitination reactions (to amino, hydroxyl, or sulfhydryl groups). Lys48 is conjugated by ubiquitin during the generationof a polyubiquitin chain that is recognized by the proteasome, resulting in degradation of the conjugated protein. All other Lys residues are conjugated to generate a chaininvolved in non-proteolytic functions. Met is the N-terminal residue.

Non-enzymatic synthesis of ubiquitin chains: Where chemistry makes a difference pp 3411–3420

Hosahalli P. Hemantha, Ashraf Brik*

Bioorganic & Medicinal Chemistry 21 (2013) 3389–3397

Contents lists available at SciVerse ScienceDirect

Bioorganic & Medicinal Chemistry

journal homepage: www.elsevier .com/locate /bmc

Nonenzymatic assembly of branched polyubiquitin chains for structural and biochemical studies pp 3421–3429

Emma K. Dixon, Carlos A. Castañeda, Tanuja R. Kashyap, Yan Wang, David Fushman*

Ub Ub

Ub

K33K11

Ub

K33K11

Ub2 x

Branched polyUb Chain

COSR

Ag+-mediatedCondensation

Ub

K33Boc

K11Boc

TFA

Improving bioorthogonal protein ubiquitylation by click reaction pp 3430–3435

Daniel Schneider, Tatjana Schneider, Daniel Rösner, Martin Scheffner*, Andreas Marx*

Total chemical synthesis of fully functional Photoactive Yellow Protein pp 3436–3442

Wendy R. Gordon, Duhee Bang, Wouter D. Hoff, Stephen B. H. Kent*

Total chemical synthesis of dengue 2 virus capsid protein via native chemical ligation: Role of the conserved salt-bridge pp 3443–3449

Changyou Zhan, Le Zhao, Xishan Chen, Wei-Yue Lu*, Wuyuan Lu*

3390 Contents / Bioorg. Med. Chem. 21 (2013) 3389–3397

Dynamic combinatorial libraries of artificial repeat proteins pp 3450–3457

Margarita Eisenberg, Inbal Shumacher, Rivka Cohen-Luria, Gonen Ashkenasy*

The role of reactivity in DNA templated native chemical PNA ligation during PCR pp 3458–3464

Alexander Roloff, Oliver Seitz*

Traceless Staudinger acetylation of azides in aqueous buffers pp 3465–3472

Sylwia Sowa, Michaela Mühlberg, K. Michal Pietrusiewicz*, Christian P. R. Hackenberger*

R = H R = -(CH2)2N(BH3)Me2

P

R

R

BH3 S

O TFA

rt, 1 h

N3

OEG

NH

OEG

O

Fmoc-NH-Nle(N3)AESG-OHFmoc

HN

HN

O

O

OHAESG

Traceless Staudinger ligation

boranedeprotection

aqueous buffer system

aqueous buffer system

Solid phase synthesis of peptide-selenoesters pp 3473–3478

Artin Ghassemian, Xavier Vila-Farrés, Paul F. Alewood, Thomas Durek*

Contents / Bioorg. Med. Chem. 21 (2013) 3389–3397 3391

Exploration of an imide capture/N,N-acyl shift sequence for asparagine native peptide bond formation pp 3479–3485

Reda Mhidia, Emmanuelle Boll, Fabien Fécourt, Mikhail Ermolenko, Nathalie Ollivier, Kaname Sasaki, David Crich,Bernard Delpech, Oleg Melnyk*

O

N3

HN

RHN

OHS

ONH O

OHN

R

ONH2

+PG

peptidepeptide

peptide peptide

Total synthesis of biotinylated N domain of human hepatocyte growth factor pp 3486–3494

Laurent Raibaut, Jérome Vicogne, Bérénice Leclercq, Hervé Drobecq, Rémi Desmet, Oleg Melnyk*

H-GQRKRRNTIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNK-NH2

31 70 96 12774 84

Biot

HGF N domain

Structure–activity studies on the upstream splice junction of a semisynthetic intein pp 3495–3503

Alexandra Wasmuth, Christina Ludwig, Henning D. Mootz*

Large scale modification of biomolecules using immobilized sortase A from Staphylococcus aureus pp 3504–3510

Max Steinhagen, Katja Zunker, Karoline Nordsieck, Annette G. Beck-Sickinger*

3392 Contents / Bioorg. Med. Chem. 21 (2013) 3389–3397

Employing directed evolution for the functional analysis of multi-specific proteins pp 3511–3516

Maxim Levin, Dotan Amar, Amir Aharoni*

Peptide-based hydrogel nanoparticles as effective drug delivery agents pp 3517–3522

Rafael Ischakov, Lihi Adler-Abramovich, Ludmila Buzhansky, Talia Shekhter, Ehud Gazit*

Mapping the Vif–A3G interaction using peptide arrays: A basis for anti-HIV lead peptides pp 3523–3532

Tali H. Reingewertz, Elena Britan-Rosich, Shahar Rotem-Bamberger, Mathias Viard, Amy Jacobs, Abigail Miller, Ji Youn Lee,Jeeseong Hwang, Robert Blumenthal, Moshe Kotler, Assaf Friedler*

Modified silaffin R5 peptides enable encapsulation and release of cargo molecules from biomimetic silica particles pp 3533–3541

Carolin C. Lechner, Christian F. W. Becker*

Contents / Bioorg. Med. Chem. 21 (2013) 3389–3397 3393

Impact of fluorination on proteolytic stability of peptides in human blood plasma pp 3542–3546

Vivian Asante, Jérémie Mortier, Hartmut Schlüter, Beate Koksch*

Stapled peptide-based membrane fusion inhibitors of hepatitis C virus pp 3547–3554

Hong-Kui Cui, Jie Qing, Ye Guo, Yu-Jia Wang, Li-Jia Cui, Tian-Hua He, Linqi Zhang*, Lei Liu*

E2

CD81

Cell

HCV

Cell

HCV

Stapled peptidedesigned from CD81

Synthesis and application of cNGR-containing imaging agents for detection of angiogenesis pp 3555–3564

Ingrid Dijkgraaf*, Pieter Van de Vijver, Anouk Dirksen, Tilman M. Hackeng

Conformational stability of triazolyl functionalized collagen triple helices pp 3565–3568

Roman S. Erdmann, Helma Wennemers*

3394 Contents / Bioorg. Med. Chem. 21 (2013) 3389–3397

Synthesis of peptides and glycopeptides with polyproline II helical topology as potential antifreeze molecules pp 3569–3581

Leo Corcilius, Gajan Santhakumar, Robin S. Stone, Chantelle J. Capicciotti, Soumya Joseph, Jacqueline M. Matthews,Robert N. Ben, Richard J. Payne*

R2

NH

O

N

O

HN

O

NH

O

N

O

HN

O

NH

O

N

O

HN

O

OH

O O OR1 R1 R1

R1 = H O

AcHNHO

OHHOO

AcHN

OH OH

OO

OHHO

OHOH

2

Conformational investigation of antibiotic proximicin by X-ray structure analysis and quantum studies suggest astretched conformation of this type of c-peptide

pp 3582–3589

Alexander Denisiuk, Vivien Schubert, Falko E. Wolter, Elisabeth Irran, Patrick Trouillas*, Roderich D. Süssmuth*

Sickle-shape conformation of netropsin

Stretched shape conformation of proximicins

versus

Efficient minor groove DNA binder Non-efficient DNA binder

The three-dimensional solution structure of mini-M conotoxin BtIIIA reveals a disconnection between disulfideconnectivity and peptide fold

pp 3590–3596

Muharrem Akcan, Ying Cao, Fan Chongxu, David J. Craik*

Bioavailable affinity label for collagen prolyl 4-hydroxylase pp 3597–3601

James D. Vasta, Joshua J. Higgin, Elizabeth A. Kersteen, Ronald T. Raines*

Contents / Bioorg. Med. Chem. 21 (2013) 3389–3397 3395

New repertoire of ‘donor-two-acceptor’ NIR fluorogenic dyes pp 3602–3608

Einat Kisin-Finfer, Doron Shabat*

A chiron approach towards the synthesis of 3-hydroxy lysine and its derivatives pp 3609–3613

K. S. Ajish Kumar

D-glucoseOON3

OOH N3

OH

O

N3

RO

R1HN OHO

R2

R3O

8, R = CHO9, R = H

10, R1 = H; R2 = NH2; R3 = H13, R1 = Cbz; R2 = N3; R3 =CHO

5

Investigation of the role of linker moieties in bifunctional tacrine hybrids pp 3614–3623

Todd J. Eckroat, Keith D. Green, Rebecca A. Reed, Joshua J. Bornstein, Sylvie Garneau-Tsodikova*

Di-alkylated paromomycin derivatives: Targeting the membranes of Gram positive pathogens that cause skin infections pp 3624–3631

Yifat Berkov-Zrihen, Ido M. Herzog, Mark Feldman, Adar Sonn-Segev, Yael Roichman, Micha Fridman*

O ONH3

OH

OH

H3N

OS O

OH

H3NNH3

OHO

OS

HO

H3NHO

3396 Contents / Bioorg. Med. Chem. 21 (2013) 3389–3397

OTHER CONTENT

Bioorganic & Medicinal Chemistry Reviews and Perspectives pp I–III

*Corresponding authorSupplementary data available via SciVerse ScienceDirect

COVER

The ubiquitin chains exhibit different structures and dynamics, which play key role in their diverse cellular functions. The chemical synthesisof ubiquitin conjugates in general and ubiquitin chains in particular are increasingly becoming vital to our ongoing efforts to understand thecomplexity of the ubiquitin signal at the molecular level.

Available online at www.sciencedirect.com

Indexed/Abstracted in: Beilstein, Biochemistry & Biophysics Citation Index, CANCERLIT, Chemical Abstracts, ChemistryCitation Index, Current Awareness in Biological Sciences/BIOBASE, Current Contents: Life Sciences, EMBASE/ExcerptaMedica, MEDLINE, PASCAL, Research Alert, Science Citation Index, SciSearch, TOXFILE. Also covered in the abstract and citationdatabase SciVerse Scopus�. Full text available on SciVerse ScienceDirect�

ISSN 0968-0896

Contents / Bioorg. Med. Chem. 21 (2013) 3389–3397 3397