GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data

• Thomas Barillot,
• Baptiste Schindler,
• Baptiste Moge,
• Elisa Fadda,
• Franck Lépine and
• Isabelle Compagnon

Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134

• , which results in modulated peaks amplitudes. This was simulated as a linear variation of the signal amplitude across the spectral range. The variation was contained in a uniform distribution bounded by ±10%. Spectra can be recorded at increased speed for rapid analytical diagnostics, which traduces into

Anomeric 1,2,3-triazole-linked sialic acid derivatives show selective inhibition towards a bacterial neuraminidase over a trypanosome trans-sialidase

• Peterson de Andrade,
• Sanaz Ahmadipour and
• Robert A. Field

Beilstein J. Org. Chem. 2022, 18, 208–216, doi:10.3762/bjoc.18.24

• Biotechnology and Biological Sciences Research Council (BBSRC) as part of UK Research and Innovation. This work was also supported by Innovate UK grant 76242: Sugars, Enzymes And Diagnostics (SEAD).

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA’s binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA

• for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications. Keywords: antisense; chemical modifications; diagnostics; peptide nucleic acid; PNA; Introduction Peptide nucleic acid (PNA) is a DNA mimic where the sugar–phosphate backbone of DNA is replaced with

• enabling component of many assays and diagnostics [4][7][8][9]. On the other hand, development of PNA based therapeutics has notably lagged behind other nucleic acid technologies [10][11]. In the present review, we summarize the remarkable journey of PNA from the initial design, through many chemical

A comprehensive review of flow chemistry techniques tailored to the flavours and fragrances industries

• Guido Gambacorta,
• James S. Sharley and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2021, 17, 1181–1312, doi:10.3762/bjoc.17.90

• processing safety (lowered inventory, improved control of heat/mass transfer), enhanced process diagnostics (PAT, inventory management), upgraded yields and selectivity (improved mixing and energetics) as well as allowing access to expanded processing windows (greater temperature, pressure and reaction time

• direct diagnostics to be obtained facilitating rapid analysis of the content and assessment of the extent of reaction in real-time. Several in-line monitoring tools, for example, ReactIR [58][59][60][61][62] and flow based NMR [63][64][65][66] which allow for substrate specific, non-consuming analysis

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• sensing is an active area of research which has developed tremendously in the last few decades [1][2][3][4]. The importance of anion sensing stems from its importance in various practical applications which range from identifying and detecting environmentally toxic anions to medical diagnostics. In recent

Synthesis of new fluorescent molecules having an aggregation-induced emission property derived from 4-fluoroisoxazoles

• Kazuyuki Sato,
• Akira Kawasaki,
• Yukiko Karuo,
• Atsushi Tarui,
• Kentaro Kawai and
• Masaaki Omote

Beilstein J. Org. Chem. 2020, 16, 1411–1417, doi:10.3762/bjoc.16.117

• ; Introduction Fluorescence bioprobes based on conventional organic dyes are used for enzyme activity measurements and in bioimaging systems with promising applications in the field of clinical diagnostics [1][2][3][4][5][6][7]. Most of the fluorescence bioprobes are mainly excited with near-ultraviolet or blue

Development of fluorinated benzils and bisbenzils as room-temperature phosphorescent molecules

• Shigeyuki Yamada,
• Takuya Higashida,
• Yizhou Wang,
• Masato Morita,
• Takuya Hosokai,
• Kaveendra Maduwantha,
• Kaveenga Rasika Koswattage and
• Tsutomu Konno

Beilstein J. Org. Chem. 2020, 16, 1154–1162, doi:10.3762/bjoc.16.102

• materials, and biosensors in biomedical diagnostics [1][2][3][4] and as organic light-emitting diodes in the technological field [5][6][7][8]. Among the organic light-emitting molecules developed thus far, extended π-conjugated compounds (e.g., pyrenes and perylenes) emit fluorescence, which is a radiative

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

• . Petersburg, 197101, Russian Federation 10.3762/bjoc.16.100 Abstract Nowadays a variety of biosensors are widely used in different fields, including biomedical diagnostics and self-testing. Nucleic acid-based biosensors are typically applied to detect another nucleic acid, proteins, ions, and several other

• diagnosis. Keywords: androgen receptor; 10–23 deoxyribozyme; nucleic acid sensor; malachite green aptamer; RNA cleavage; Introduction The fast and precise diagnostics of diseases are one of the key factors that allow choosing the most effective method of treatment. Disease markers can be found at a few

Automated glycan assembly of arabinomannan oligosaccharides from Mycobacterium tuberculosis

• Alonso Pardo-Vargas,
• Priya Bharate,
• Martina Delbianco and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2019, 15, 2936–2940, doi:10.3762/bjoc.15.288

• ]. Identification of novel anti-TB agents that specifically target AMs with high sensitivity are required. Pure AM oligosaccharides may help to identify new lead compounds for the development of diagnostics. Since the isolation of pure oligosaccharides from MTB strains in sufficient quantities is challenging, the

Dyes in modern organic chemistry

• Heiko Ihmels

Beilstein J. Org. Chem. 2019, 15, 2798–2800, doi:10.3762/bjoc.15.272

• properties. Traditionally, organic dyes are the basis of well-established color indicators for qualitative and quantitative analysis. Nowadays, we cannot imagine research in the life sciences or in medical diagnostics without the sophisticated applications of organic dyes as fluorescent probes, dye labels

Fluorescent phosphorus dendrimers excited by two photons: synthesis, two-photon absorption properties and biological uses

• Anne-Marie Caminade,
• Artem Zibarov,
• Eduardo Cueto Diaz,
• Aurélien Hameau,
• Maxime Klausen,
• Kathleen Moineau-Chane Ching,
• Jean-Pierre Majoral,
• Jean-Baptiste Verlhac,
• Olivier Mongin and
• Mireille Blanchard-Desce

Beilstein J. Org. Chem. 2019, 15, 2287–2303, doi:10.3762/bjoc.15.221

• nanocrystals [6]), widely used for imaging live cells, for in vivo imaging and diagnostics [7]. Even if the properties of quantum dots have been compared with those of classical organic fluorophores [8], organic fluorophores having giant TPA properties are far less common [9], although there are noticeable

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time

• areas, including clinical diagnostics and drug discovery amongst others. Molecular probes generally consist of a recognition element that can bind to the specific target, and a reporter group that, in combination with an appropriate signal transduction mechanism, translates the molecular interaction

• [24]. Overall, these properties enable the use of PNA for several applications, including therapeutics and diagnostics [25], and as a unique tool for DNA manipulation, such as PCR clamping [26] and PNA openers [27]. Ironically, the very same uncharged nature of PNA that is the basis of several of the

Intramolecular glycosylation

• Xiao G. Jia and
• Alexei V. Demchenko

Beilstein J. Org. Chem. 2017, 13, 2028–2048, doi:10.3762/bjoc.13.201

• proteins in the human body are glycosylated [3], and cells display a multitude of glycostructures [4]. Since glycan and glycoconjugate biomarkers are present in all body fluids, they offer a fantastic opportunity for diagnostics. Changes in the level of glycans, as well as changes in glycosylation and

Biomimetic molecular design tools that learn, evolve, and adapt

• David A Winkler

Beilstein J. Org. Chem. 2017, 13, 1288–1302, doi:10.3762/bjoc.13.125

• evolutionary transition of life. Establishing ethical principles for artificial life. Development of advanced computational AI methods is likely to cause social disruption in the next two decades but they should bring unprecedented benefits, such as improved medical diagnostics, and cheaper more efficient

Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• because they can be employed to enhance the intensity of Raman signals close to the NP surface, widely explored in biomedical diagnostics (surface enhanced Raman spectroscopy, SERS). This effect is even more intense when the nanoparticles possess an irregular shape, generating an anisotropic distribution

Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

• Srikala Pangannaya,
• Neethu Padinchare Purayil,
• Shweta Dabhi,
• Venu Mankad,
• Prafulla K. Jha,
• Satyam Shinde and
• Darshak R. Trivedi

Beilstein J. Org. Chem. 2017, 13, 222–238, doi:10.3762/bjoc.13.25

• −, F− and AcO− ions through hydrogen bond interaction followed by a deprotonation process [27][28][29]. The design of molecular logic gates with chemical and biological molecules has been at the forefront creating a new avenue to advanced diagnostics and therapeutics through molecular computers. As an

Synthesis, dynamic NMR characterization and XRD studies of novel N,N’-substituted piperazines for bioorthogonal labeling

• Constantin Mamat,
• Marc Pretze,
• Matthew Gott and
• Martin Köckerling

Beilstein J. Org. Chem. 2016, 12, 2478–2489, doi:10.3762/bjoc.12.242

• bioorthogonal 18F-containing building blocks The development of new 18F-based radiotracers remains an ongoing goal in the field of radiopharmacy and provides tools for specific cancer diagnostics using positron emission tomography (PET) [31][32][33]. When radiotracers are based on tumor-specific peptides

Organic chemistry meets polymers, nanoscience, therapeutics and diagnostics

• Vincent M. Rotello

Beilstein J. Org. Chem. 2016, 12, 1638–1646, doi:10.3762/bjoc.12.161

The role of alkyl substituents in deazaadenine-based diarylethene photoswitches

• Christopher Sarter,
• Michael Heimes and
• Andres Jäschke

Beilstein J. Org. Chem. 2016, 12, 1103–1110, doi:10.3762/bjoc.12.106

• up new and innovative applications in materials sciences, bionanotechnology, synthetic biology, and biomedical diagnostics, and reversible photoswitching is a particularly attractive goal [1][2][3][4][5][6][7][8][9][10][11][12]. Light is a powerful and convenient trigger for manipulating structure

Self and directed assembly: people and molecules

• Tony D. James

Beilstein J. Org. Chem. 2016, 12, 391–405, doi:10.3762/bjoc.12.42

• , Defence Science and Technology Laboratory (DSTL), the Nuffield Foundation, Prostate Cancer UK, Dunhill Medical Trust, Alzheimer's Research UK (ARUK), Beckman-Coulter Inc, Zeneca Group PLC, Unipath Ltd, Smart Holograms, Glysure Ltd, Quotient Diagnostics, the Royal Society and the Royal Society of Chemistry

Bright molecules for sensing, computing and imaging: a tale of two once-troubled cities

• A. Prasanna de Silva

Beilstein J. Org. Chem. 2015, 11, 2774–2784, doi:10.3762/bjoc.11.298

• design tool has been taken up by about 330 laboratories (Figure 1, PET maps) so far. A bit of medical diagnostics While it was clear from the beginning that fluorescent PET sensors would be useful, we saw no practical path to such development. Serendipity had to smile in the form of the interest and the

• commercial will of Roche Diagnostics before such a path would open. The molecular engineering capabilities of the fluorescent PET sensor design were initially put to the test to quantitatively plan an ‘off-on’ sensor for sodium in whole untreated blood. Since the normal Na+ level is 0.1 M, our receptor

Learning from the unexpected in life and DNA self-assembly

• Jennifer M. Heemstra

Beilstein J. Org. Chem. 2015, 11, 2713–2720, doi:10.3762/bjoc.11.292

• demonstrated that we could use our split aptamer ligation method to measure the concentration of a small-molecule target, but doing so required analysis via gel electrophoresis. Thus, we sought to create an assay that would be capable of the high throughput needed for clinical diagnostics applications, and we

Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• controlled assembly of nanoparticles by means of biomolecules is crucial for biological and medical applications such as sensing [4], bioimaging [5], and medical diagnostics [6]. Although nanoparticles are also applied as targeted biomarkers and drug-delivery agents to tumor cells [7], only very little is

Detonation nanodiamonds biofunctionalization and immobilization to titanium alloy surfaces as first steps towards medical application

• Juliana P. L. Gonçalves,
• Afnan Q. Shaikh,
• Manuela Reitzig,
• Daria A. Kovalenko,
• Jan Michael,
• René Beutner,
• Gianaurelio Cuniberti,
• Dieter Scharnweber and
• Jörg Opitz

Beilstein J. Org. Chem. 2014, 10, 2765–2773, doi:10.3762/bjoc.10.293

• Juliana P. L. Goncalves Afnan Q. Shaikh Manuela Reitzig Daria A. Kovalenko Jan Michael Rene Beutner Gianaurelio Cuniberti Dieter Scharnweber Jorg Opitz Inspection and Diagnosis Methods, Fraunhofer Institute for Ceramic Technologies and Systems –Materials Diagnostics, Maria-Reiche-Str. 2, 01109