Themed collection Chemical Biology in OBC
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From pirates and killers: does metabolite diversity drive bacterial competition?
This article discusses interspecies competition by sets of closely related metabolites with significantly different biological activities.
Org. Biomol. Chem., 2018,16, 2814-2819
https://doi.org/10.1039/C8OB00150B
Hybridization-specific chemical reactions to create interstrand crosslinking and threaded structures of nucleic acids
This review introduces the creation of interstrand crosslinking and threaded structures based on the hybridization-specific chemical reactions and their functions and perspectives in oligonucleotide therapeutics, chemical biology and nanotechnology.
Org. Biomol. Chem., 2022,20, 4699-4708
https://doi.org/10.1039/D2OB00551D
Recent developments in the utility of saturated azaheterocycles in peptidomimetics
This review summarizes applications of 3-, 4-, 5-, and 6-membered azaheterocycles as tools to introduce conformational restrictions in the design of peptidomimetics.
Org. Biomol. Chem., 2022,20, 963-979
https://doi.org/10.1039/D1OB01329G
Deoxy sugars. General methods for carbohydrate deoxygenation and glycosidation
The methods for the synthesis of deoxy sugars, involving deoxygenation and glycosidation, give access to useful molecules for multiple purposes.
Org. Biomol. Chem., 2022,20, 934-962
https://doi.org/10.1039/D1OB02001C
Organocatalysis applied to carbohydrates: from roots to current developments
This review is devoted to the broad application of organocatalysis in the synthesis of (un)natural carbohydrates as well as organocatalyzed glycosylation and the aldol reaction for the synthesis of C-glycosides.
Org. Biomol. Chem., 2022,20, 919-933
https://doi.org/10.1039/D1OB01919H
Molecular platforms based on biocompatible photoreactions for photomodulation of biological targets
In this paper, we summarize molecular platforms based on ultraviolet (UV), visible (Vis) or near-infrared (NIR) photoreactions. Recent applications for spatiotemporal photomodulation of various biomolecules in living objects are also discussed.
Org. Biomol. Chem., 2021,19, 9358-9368
https://doi.org/10.1039/D1OB01613J
Photoaffinity labelling strategies for mapping the small molecule–protein interactome
We review the development of photoaffinity labeling (PAL) chemistries and the application of PAL to chemoproteomic target deconvolution for small molecules, lipids, and metabolites.
Org. Biomol. Chem., 2021,19, 7792-7809
https://doi.org/10.1039/D1OB01353J
Antitumor activity of tridentate pincer and related metal complexes
Pincer and related metal complexes containing tunable tridentate ligand frameworks display promising antitumor activity.
Org. Biomol. Chem., 2021,19, 5254-5273
https://doi.org/10.1039/D1OB00577D
Optically superior fluorescent probes for selective imaging of cells, tumors, and reactive chemical species
Fluorescent probes with superior optical properties have been summarized along with the mechanisms used for their development and the challenges faced in their synthesis.
Org. Biomol. Chem., 2021,19, 5208-5236
https://doi.org/10.1039/D1OB00509J
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Asparaginyl endopeptidases: enzymology, applications and limitations
The potentials of using asparaginyl endopeptidases (AEP) as tools for polypeptide modifications have been discussed.
Org. Biomol. Chem., 2021,19, 5048-5062
https://doi.org/10.1039/D1OB00608H
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Chemical probes targeting the kinase CK2: a journey outside the catalytic box
An up-to-date and comprehensive review on chemical probes targeting the important kinase CK2.
Org. Biomol. Chem., 2021,19, 4380-4396
https://doi.org/10.1039/D1OB00257K
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Approaches for peptide and protein cyclisation
Polypeptide cyclisation can enhance thermal stability, proteolytic resistance and membrane permeability. Cyclisation can be achieved by methods including chemical, enzyme and protein tag approaches. Each has strengths and limitations.
Org. Biomol. Chem., 2021,19, 3983-4001
https://doi.org/10.1039/D1OB00411E
Harnessing methylation and AdoMet-utilising enzymes for selective modification in cascade reactions
This review summarizes the recent findings and developments in the emerging area of (chemo)-enzymatic cascades using MTases and AdoMet-generating enzymes.
Org. Biomol. Chem., 2021,19, 3756-3762
https://doi.org/10.1039/D1OB00354B
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Metabolic labeling probes for interrogation of the host–pathogen interaction
Metabolic labeling of intracellular pathogens can provide new methods of studying host pathogen interactions.
Org. Biomol. Chem., 2021,19, 2856-2870
https://doi.org/10.1039/D0OB02517H
Chemistry and biology of spiroacetals from myxobacteria
This review details the isolation, biosynthesis, biological activity and synthesis of spiroacetals from the myxobacterium Sorangium cellulosum.
Org. Biomol. Chem., 2021,19, 2871-2890
https://doi.org/10.1039/D1OB00026H
Artificial enzymes bringing together computational design and directed evolution
This manuscript reviews the combination of computational enzyme design and directed evolution and its advantages in the development of artificial enzymes.
Org. Biomol. Chem., 2021,19, 1915-1925
https://doi.org/10.1039/D0OB02143A
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Silicon phthalocyanines: synthesis and resurgent applications
Their unique axial bonds and NIR optical properties have made silicon phthalocyanines (SiPcs) valuable compounds. Herein, we present key synthetic strategies and emerging applications of SiPcs over the past decade.
Org. Biomol. Chem., 2021,19, 1168-1190
https://doi.org/10.1039/D0OB02299C
Recent advances in the direct O-arylation of carbohydrates
An emerging approach for the synthesis of O-aryl glycosides and carbohydrate-derived aryl ethers via C(sp2)–O bond formation is reviewed.
Org. Biomol. Chem., 2021,19, 514-524
https://doi.org/10.1039/D0OB02009E
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Recent highlights of biosynthetic studies on marine natural products
Marine bacteria are excellent yet often underexplored sources of structurally unique bioactive natural products.
Org. Biomol. Chem., 2021,19, 123-140
https://doi.org/10.1039/D0OB01677B
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Glycosyl disulfides: importance, synthesis and application to chemical and biological systems
This review explores methodologies for the preparation of glycosyl disulfides, their utility as intermediates in carbohydrate synthesis, and evaluates their biological impact in glycoscience and beyond.
Org. Biomol. Chem., 2021,19, 82-100
https://doi.org/10.1039/D0OB02079F
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Tyrosine bioconjugation – an emergent alternative
A review of the heretofore less explored approach of tyrosine bioconjugation, which is rapidly becoming a constructive alternative/complement to the more well-established strategies, is provided.
Org. Biomol. Chem., 2020,18, 9018-9028
https://doi.org/10.1039/D0OB01912G
Recent advances in the synthesis of C-terminally modified peptides
A go-to compilation of recent strategies to access C-terminally modified peptides contextualized by a discussion of the major synthetic challenges that have historically hampered progress in this area.
Org. Biomol. Chem., 2020,18, 7253-7272
https://doi.org/10.1039/D0OB01417F
Development and utilization of peptide-based quorum sensing modulators in Gram-positive bacteria
This review discusses the development of peptide-based quorum sensing modulators and their use as potential therapeutics.
Org. Biomol. Chem., 2020,18, 7273-7290
https://doi.org/10.1039/D0OB01421D
Rational design of small molecule fluorescent probes for biological applications
Guidelines based on photophysical tuning, reactivity, isomerization, and energy transfer for rational design of synthetic fluorescent probes for biological systems.
Org. Biomol. Chem., 2020,18, 5747-5763
https://doi.org/10.1039/D0OB01131B
Structural advances of Siglecs: insight into synthetic glycan ligands for immunomodulation
This review summarizes the natural and synthetic glycan ligands of Siglecs and the growing body of knowledge for structural features governing sialic acid recognition.
Org. Biomol. Chem., 2020,18, 5784-5797
https://doi.org/10.1039/D0OB01116A
The curious yellow colouring matter of the Iceland poppy
This account provides an chronological overview of the fascinating history of the pigment responsible for the yellow colour of the Iceland poppy (Papaver nudicaule).
Org. Biomol. Chem., 2020,18, 5278-5286
https://doi.org/10.1039/D0OB01162B
TLR2 agonists and their structure–activity relationships
We review the structure–activity relationships and synthetic studies of TLR2 agonists – important chemical targets in immunotherapy.
Org. Biomol. Chem., 2020,18, 5073-5094
https://doi.org/10.1039/D0OB00942C
Recent development in the synthesis of C-glycosides involving glycosyl radicals
C-Glycosylation involving glycosyl radical intermediates is a particularly effective approach to access C-glycosides, which are core units of a great number of natural products, bioactive compounds and marketed drugs.
Org. Biomol. Chem., 2020,18, 5095-5109
https://doi.org/10.1039/D0OB00711K
Chemical methods for modification of proteins
The field of protein bioconjugation draws attention from stakeholders in chemistry, biology, and medicine. This review provides an overview of the present status, challenges, and opportunities for organic chemists.
Org. Biomol. Chem., 2020,18, 4669-4691
https://doi.org/10.1039/D0OB00857E
Enzymatic glycosylation involving fluorinated carbohydrates
This contribution reviews the enzymatic synthesis, including optimisation efforts, of fluorinated carbohydrates involving fluorinated donors and/or acceptors, as well as the enzymatic activation of the fluorinated donors.
Org. Biomol. Chem., 2020,18, 3423-3451
https://doi.org/10.1039/D0OB00436G
Multiphosphorylated peptides: importance, synthetic strategies, and applications for studying biological mechanisms
Advances in the synthesis of multiphosphorylated peptides and peptide libraries: tools for studying the effects of phosphorylation patterns on protein function and regulation.
Org. Biomol. Chem., 2020,18, 3405-3422
https://doi.org/10.1039/D0OB00499E
Recent advances in β-L-rhamnosylation
This review describes various methodologies for the stereoselective 1,2-cis glycosylation of L-rhamnose leading to β-L-rhamnosides and their applications in oligosaccharide synthesis.
Org. Biomol. Chem., 2020,18, 3216-3228
https://doi.org/10.1039/D0OB00297F
Synthesis of trehalose glycolipids
Chemical synthesis of trehalose glycolipids such as DAT, TDM, SL-1, SL-3, and Ac2SGL from MTb, emmyguyacins from fungi, succinoyl trehalose from rhodococcus, and maradolipids from worms, as well as mycobacterial oligosaccharides is reviewed.
Org. Biomol. Chem., 2020,18, 2013-2037
https://doi.org/10.1039/D0OB00041H
Structure elucidation of bacterial nonribosomal lipopeptides
We provide a summary of the tools, which allow elucidate the structures of nonribosomal lipopetides.
Org. Biomol. Chem., 2020,18, 1710-1727
https://doi.org/10.1039/C9OB02539A
Insights into DNA catalysis from structural and functional studies of the 8-17 DNAzyme
The review examines functional knowledge gathered over two decades of research on the 8-17 DNAzyme, focusing on three aspects: the structural requirements for catalysis, the role of metal ions and the participation of general acid-base catalysis.
Org. Biomol. Chem., 2020,18, 1697-1709
https://doi.org/10.1039/C9OB02453K
Staphylococcus aureus capsular polysaccharides: a structural and synthetic perspective
This review surveys known structures of staphylococcal polysaccharides and summarizes all synthetic efforts to obtain these sequences.
Org. Biomol. Chem., 2020,18, 783-798
https://doi.org/10.1039/C9OB02546D
Mechanistic and structural studies into the biosynthesis of the bacterial sugar pseudaminic acid (Pse5Ac7Ac)
The nonulosonic acid sugar pseudaminic acid, Pse5Ac7Ac, is present on the surface of a number of human pathogens, herein we review the mechanistic and structural characterisation of the enzymes responsible for its biosynthesis in bacteria.
Org. Biomol. Chem., 2020,18, 799-809
https://doi.org/10.1039/C9OB02433F
G-quadruplexes as versatile scaffolds for catalysis
This review summarizes the beginning, progress, and prospects of non-canonical DNA-based hybrid catalysts focusing on G-quadruplexes as versatile scaffolds for catalysis.
Org. Biomol. Chem., 2019,17, 9547-9561
https://doi.org/10.1039/C9OB01876J
Stabilization of the triple helix in collagen mimicking peptides
The review classifies existing chemical approaches towards stronger triple helical assemblies in peptides.
Org. Biomol. Chem., 2019,17, 8031-8047
https://doi.org/10.1039/C9OB01646E
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Chemical ADP-ribosylation: mono-ADPr-peptides and oligo-ADP-ribose
A review of recent advances towards synthetic ADP-ribosylated proteins and oligo-ADP-ribose chains.
Org. Biomol. Chem., 2019,17, 5460-5474
https://doi.org/10.1039/C9OB00501C
Synthetic strategies for fluorination of carbohydrates
Different synthetic strategies for accomplishing regio- and stereoselective fluorinations of carbohydrate scaffolds are discussed in light of the biological implications arising from such substitutions.
Org. Biomol. Chem., 2019,17, 5173-5189
https://doi.org/10.1039/C9OB00405J
Synthesis of carbohydrate building blocks via regioselective uniform protection/deprotection strategies
Scope 1: sugar is uniformly protected leaving only one (or two) free hydroxyl group; scope 2: uniformly protected sugar is deprotected to liberate only one (or two) hydroxyl group.
Org. Biomol. Chem., 2019,17, 4934-4950
https://doi.org/10.1039/C9OB00573K
Chemical composition of DNA-encoded libraries, past present and future
We discuss here the chemical composition of DNA-encoded libraries likely to be made in the near future.
Org. Biomol. Chem., 2019,17, 4676-4688
https://doi.org/10.1039/C9OB00581A
Versatility of glycals in synthetic organic chemistry: coupling reactions, diversity oriented synthesis and natural product synthesis
Versatility of glycals in the stereoselective synthesis of natural products.
Org. Biomol. Chem., 2019,17, 4153-4182
https://doi.org/10.1039/C9OB00343F
Saturated bioisosteres of benzene: where to go next?
Saturated bioisosteres for ortho- and meta-substituted benzenes remain a current challenge for chemists.
Org. Biomol. Chem., 2019,17, 2839-2849
https://doi.org/10.1039/C8OB02812E
The expanding spectrum of diketopiperazine natural product biosynthetic pathways containing cyclodipeptide synthases
Tailoring enzymes decorate diketopiperazines to yield unique structures and biological functions.
Org. Biomol. Chem., 2019,17, 2305-2314
https://doi.org/10.1039/C8OB03063D
Emerging applications of peptide–oligonucleotide conjugates: bioactive scaffolds, self-assembling systems, and hybrid nanomaterials
Peptide–oligonucleotide conjugates (POCs) are covalent constructs that link a molecule like DNA to a synthetic peptide sequences.
Org. Biomol. Chem., 2019,17, 1668-1682
https://doi.org/10.1039/C8OB02436G
Rearranged ergostane-type natural products: chemistry, biology, and medicinal aspects
Rearranged ergostane-type natural products are structurally intriguing and exhibit biologically relevant properties.
Org. Biomol. Chem., 2019,17, 1624-1633
https://doi.org/10.1039/C8OB02325E
One-pot multi-segment condensation strategies for chemical protein synthesis
This paper describes recent advances of one-pot multi-segment condensation strategies based on kinetically controlled strategies and/or protecting group-removal strategies in chemical protein synthesis.
Org. Biomol. Chem., 2019,17, 727-744
https://doi.org/10.1039/C8OB02610F
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Fluorogenic probes for super-resolution microscopy
Fluorogenic probes efficiently reduce non-specific background signals, which often results in highly improved signal-to-noise ratios.
Org. Biomol. Chem., 2019,17, 215-233
https://doi.org/10.1039/C8OB02711K
Azobenzene-based small molecular photoswitches for protein modulation
This review highlights the design strategies of azobenzene photoswitches as well as their applications in the manipulation of biological systems.
Org. Biomol. Chem., 2018,16, 8434-8445
https://doi.org/10.1039/C8OB02157K
Lasso peptides: chemical approaches and structural elucidation
The diverse functionality and the extraordinary stability of lasso peptides make these molecules attractive scaffolds for drug discovery. The ability to generate lasso peptides chemically remains a challenging endeavor.
Org. Biomol. Chem., 2018,16, 5065-5080
https://doi.org/10.1039/C8OB01304G
Biosynthesis of the teleocidin-type terpenoid indole alkaloids
Teleocidin B is a terpenoid indole alkaloid with unique structures including indolactam and cyclic terpenoid, and is a strong protein kinase C activator. In this review, we describe the isolation and biosynthetic studies of teleocidins.
Org. Biomol. Chem., 2018,16, 4746-4752
https://doi.org/10.1039/C8OB00803E
The synthesis of mono-alkyl phosphates and their derivatives: an overview of their nature, preparation and use, including synthesis under plausible prebiotic conditions
Nucleic acids, phospholipids and other organic phosphates play central roles in biological pathways.
Org. Biomol. Chem., 2018,16, 3068-3086
https://doi.org/10.1039/C8OB00469B
C8-Guanine modifications: effect on Z-DNA formation and its role in cancer
Participation of Z DNA in normal and disease related biological processes.
Org. Biomol. Chem., 2018,16, 2198-2209
https://doi.org/10.1039/C8OB00030A
Recent progress of C-glycosylation methods in the total synthesis of natural products and pharmaceuticals
C-Glycosylation has found widespread use in the synthesis of biomedically important natural products and pharmaceuticals.
Org. Biomol. Chem., 2018,16, 1791-1806
https://doi.org/10.1039/C8OB00032H
Cas9-mediated DNA cleavage guided by enzymatically prepared 4′-thio-modified RNA
The 4′-thio sgRNA, which is enzymatically prepared by T7 transcription using 4′-thiopyrimidine nucleoside 5′- triphosphates, induces Cas9-mediated DNA cleavage.
Org. Biomol. Chem., 2022,20, 5245-5248
https://doi.org/10.1039/D2OB00742H
N-Methoxy-1,3-oxazinane nucleic acids (MOANAs) – a configurationally flexible backbone modification allows post-synthetic incorporation of base moieties
A (2R,3S)-4-(methoxyamino)butane-1,2,3-triol residue within forms N-methoxy-1,3-oxazinanes with a variety of aldehydes, providing easy and pH-controllable access to base-modified oligonucleotides.
Org. Biomol. Chem., 2022,20, 3480-3485
https://doi.org/10.1039/D2OB00465H
Evaluation of DNA-mediated electron transfer using a hole-trapping nucleobase under crowded conditions
Decompositions of hole-trapping nucleobases in noncondensed DNA and liquid crystalline DNA showed that efficient electron transfer occurred under crowded conditions.
Org. Biomol. Chem., 2022,20, 2043-2047
https://doi.org/10.1039/D1OB01669E
Small molecule peptidomimetic trypsin inhibitors: validation of an EKO binding mode, but with a twist
A commonality noticed between structures of trypsin and natural trypsin inhibitors leads to a new small molecule inhibitor design strategy.
Org. Biomol. Chem., 2022,20, 2075-2080
https://doi.org/10.1039/D1OB02127C
Harnessing an emissive guanine surrogate to design small-molecule fluorescent chemosensors of O6-methylguanine-DNA-methyltransferase (MGMT)
Activity of O6-methylguanine-DNA-methyltransferase (MGMT) can be monitored in real time using chemosensors that generate an emissive guanine analogue thienoguanine (thGN).
Org. Biomol. Chem., 2022,20, 1888-1892
https://doi.org/10.1039/D2OB00208F
Pyrrovobasine, hybrid alkylated pyrraline monoterpene indole alkaloid pseudodimer discovered using a combination of mass spectral and NMR-based machine learning annotations
The MS2-guided phytochemical investigation of Voacanga africana stem bark resulted in the isolation of pyrrovobasine, the first pyrraline-containing MIA.
Org. Biomol. Chem., 2022,20, 98-105
https://doi.org/10.1039/D1OB01791H
A comprehensive study on the effect of backbone stereochemistry of a cyclic hexapeptide on membrane permeability and microsomal stability
The effect of backbone stereochemistry of a cyclic hexapeptide on membrane permeability and metabolic stability was comprehensively evaluated. Besides, the effect of side chain structures on the pharmacokinetic properties was investigated.
Org. Biomol. Chem., 2021,19, 10326-10331
https://doi.org/10.1039/D1OB02090K
Streptomyces aureorectus DSM 41692 and Streptomyces virens DSM 41465 are producers of the antibiotic nucleocidin and 4′-fluoroadenosine is identified as a co-product
Genome homologies led to the identification of Streptomyces aureorectus DSM 41692 and Streptomyces virens DSM 41465 as producers of the antibiotic nucleocidin, and also 4’-fluoroadenosine.
Org. Biomol. Chem., 2021,19, 10081-10084
https://doi.org/10.1039/D1OB01898A
Synthesis, proteolytic stability, and in vitro evaluation of DOTA conjugated p160 peptide based radioconjugates: [177Lu]Lu–DOTA–p160
Synthesis, spectroscopic characterization, and in vitro biological evaluation of Lu-177 radiolabeled DOTA conjugated p160 peptide derivatives: potential candidates for breast tumor imaging and therapy.
Org. Biomol. Chem., 2021,19, 9849-9854
https://doi.org/10.1039/D1OB01812D
Pentacyclic spermidine alkaloids with radioprotective and anti-inflammatory activities from Orychophragmus violaceus
Two pairs of novel pentacyclic spermidine alkaloid enantiomers, (±)-orychoviolines A and B, were isolated from the seeds of Orychophragmus violaceus and represented the first example of a 2-piperidinone-fused hydrodibenzofuran skeleton.
Org. Biomol. Chem., 2021,19, 9844-9848
https://doi.org/10.1039/D1OB01973B
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Automated glycan assembly of peptidoglycan backbone fragments
The automated glycan assembly of different oligosaccharide fragments of the bacterial peptidoglycan backbone is reported.
Org. Biomol. Chem., 2021,19, 9829-9832
https://doi.org/10.1039/D1OB01987B
Perforalactones D and E, two new C-20 quassinoids with potential activity to induce lysosomal biogenesis from the twigs of Harrisonia perforata (Blanco) Merr.
Two new quassinoids, perforalactones D and E, from Harrisonia perforata, could promote the expression of lysosomal genes and induce lysosomal biogenesis.
Org. Biomol. Chem., 2021,19, 9637-9640
https://doi.org/10.1039/D1OB01927A
Methyl to trifluoromethyl substitution as a strategy to increase the membrane permeability of short peptides
CH3 to CF3 substitution on a side chain of proteiogenic amino acids increases the membrane permeability of peptides.
Org. Biomol. Chem., 2021,19, 9386-9389
https://doi.org/10.1039/D1OB01565F
Solitumergosterol A, a unique 6/6/6/6/5 steroid from the deep-sea-derived Penicillium solitum MCCC 3A00215
An unprecedented C30 steroid, solitumergosterol A (1), from the deep-sea-derived Penicillium solitum inhibited the proliferation of MB231 tumor cells by a RXRα-dependent mechanism.
Org. Biomol. Chem., 2021,19, 9369-9372
https://doi.org/10.1039/D1OB01392K
About this collection
The latest articles published in Organic and Biomolecular Chemistry related to chemical biology research.