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Статті в журналах з теми "Chimical Diversity"

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Автор: Grafiati

Опубліковано: 9 березня 2024

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Awale, Mahendra, Ricardo Visini, Daniel Probst, Josep Arús-Pous, and Jean-Louis Reymond. "Chemical Space: Big Data Challenge for Molecular Diversity." CHIMIA International Journal for Chemistry 71, no. 10 (October 25, 2017): 661–66. http://dx.doi.org/10.2533/chimia.2017.661.

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Schröder, Jens A., and Pauline E. Jullien. "The Diversity of Plant Small RNAs Silencing Mechanisms." CHIMIA International Journal for Chemistry 73, no. 5 (May 29, 2019): 362–67. http://dx.doi.org/10.2533/chimia.2019.362.

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Small RNAs gene regulation was first discovered about 20 years ago. It represents a conserve gene regulation mechanism across eukaryotes and is associated to key regulatory processes. In plants, small RNAs tightly regulate development, but also maintain genome stability and protect the plant against pathogens. Small RNA gene regulation in plants can be divided in two canonical pathways: Post-transcriptional Gene Silencing (PTGS) that results in transcript degradation and/or translational inhibition or Transcriptional Gene Silencing (TGS) that results in DNA methylation. In this review, we will focus on the model plant Arabidopsis thaliana. We will provide a brief overview of the molecular mechanisms involved in canonical small RNA pathways as well as introducing more atypical pathways recently discovered.

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Fabrizio, Alberto, Ksenia Briling, Andrea Grisafi, and Clémence Corminboeuf. "Learning (from) the Electron Density: Transferability, Conformational and Chemical Diversity." CHIMIA International Journal for Chemistry 74, no. 4 (April 29, 2020): 232–36. http://dx.doi.org/10.2533/chimia.2020.232.

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Machine-learning in quantum chemistry is currently booming, with reported applications spanning all molecular properties from simple atomization energies to complex mathematical objects such as the many-body wavefunction. Due to its central role in density functional theory, the electron density is a particularly compelling target for non-linear regression. Nevertheless, the scalability and the transferability of the existing machine-learning models of ρ(r) are limited by its complex rotational symmetries. Recently, in collaboration with Ceriotti and coworkers, we combined an efficient electron density decomposition scheme with a local regression framework based on symmetry-adapted Gaussian process regression able to accurately describe the covariance of the electron density spherical tensor components. The learning exercise is performed on local environments, allowing high transferability and linear-scaling of the prediction with respect to the number of atoms. Here, we review the main characteristics of the model and show its predictive power in a series of applications. The scalability and transferability of the trained model are demonstrated through the prediction of the electron density of Ubiquitin.

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Wolfender, Jean-Luc, and Emerson Ferreira Queiroz. "Chemical Diversity of Natural Resources and the Bioactivity of their Constituents." CHIMIA International Journal for Chemistry 66, no. 5 (May 30, 2012): 324–29. http://dx.doi.org/10.2533/chimia.2012.324.

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Ila, Hiriyakkanavar, and Hiriyakkanavar Junjappa. "Molecular Diversity through Novel Organosulfur Synthons: Versatile Templates for Heterocycle Synthesis." CHIMIA International Journal for Chemistry 67, no. 1 (February 27, 2013): 17–22. http://dx.doi.org/10.2533/chimia.2013.17.

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Kang, Chengjun, and Andrei Honciuc. "A Diversity of Asymmetric Nano-/Microcolloidal Architectures Grown by ATRP from Janus Seeds." CHIMIA International Journal for Chemistry 73, no. 4 (April 24, 2019): 324–28. http://dx.doi.org/10.2533/chimia.2019.324.

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Muñiz, Manuel, and Auxiliadora Aguilera-Romero. "A Role for Lipids in Protein Sorting?" CHIMIA 75, no. 12 (December 9, 2021): 1026. http://dx.doi.org/10.2533/chimia.2021.1026.

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Lipid and protein diversity provides structural and functional identity to the membrane compartments that define the eukaryotic cell. This compositional heterogeneity is maintained by the secretory pathway, which feeds newly synthesized proteins and lipids to the endomembrane systems. The precise sorting of lipids and proteins through the pathway guarantees the achievement of their correct delivery. Although proteins have been shown to be key for sorting mechanisms, whether and how lipids contribute to this process is still an open discussion. Our laboratory, in collaboration with other groups, has recently addressed the long-postulated role of membrane lipids in protein sorting in the secretory pathway, by investigating in yeast how a special class of lipid-linked cell surface proteins are differentially exported from the endoplasmic reticulum. Here we comment on this interdisciplinary study that highlights the role of lipid diversity and the importance of protein-lipid interactions in sorting processes at the cell membrane.

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Probst, Daniel. "The Societal and Scientific Importance of Inclusivity, Diversity, and Equity in Machine Learning for Chemistry." CHIMIA 77, no. 1/2 (February 22, 2023): 56. http://dx.doi.org/10.2533/chimia.2023.56.

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While the introduction of practical deep learning has driven progress across scientific fields, recent research highlighted that the requirement of deep learning for ever-increasing computational resources and data has potential negative impacts on the scientific community and society as a whole. An ever-growing need for more computational resources may exacerbate the concentration of funding, the exclusiveness of research, and thus the inequality between countries, sectors, and institutions. Here, I introduce recent concerns and considerations of the machine learning research community that could affect chemistry and present potential solutions, including more detailed assessments of model performance, increased adherence to open science and open data practices, an increase in multinational and multi-institutional collaboration, and a focus on thematic and cultural diversity.

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Wennemers, Helma. "Peptides – Molecular Allrounders." CHIMIA International Journal for Chemistry 75, no. 6 (June 30, 2021): 525–29. http://dx.doi.org/10.2533/chimia.2021.525.

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The enormous structural and functional diversity available through combining different amino acids into peptides offers numerous exciting opportunities. This article summarizes recent research highlights from my laboratory in the areas of asymmetric catalysis, supramolecular chemistry, and chemical biology. This scope includes the development of bioinspired peptide catalysts, synthetic collagen peptides, supramolecular porous assemblies, and cell-penetrating peptides.

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Simon, Clémence, Suihan Feng, and Howard Riezman. "Chemical Biology Tools to Study Lipids and their Metabolism with Increased Spatial and Temporal Resolution." CHIMIA 75, no. 12 (December 9, 2021): 1012. http://dx.doi.org/10.2533/chimia.2021.1012.

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Lipids are important cellular components providing many essential functions. To fulfill these various functions evolution has selected for a diverse set of lipids and this diversity is seen at the organismal, cellular and subcellular level. Understanding how cells maintain this complex lipid organization is a very challenging problem, which for lipids, is not easily addressed using biochemical and genetic techniques. Therefore, chemical tools have an important role to play in our quest to understand the complexities of lipid metabolism. Here we discuss new chemical tools to study lipids, their distribution and metabolism with increased spatial and temporal resolution.

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Frey, Johanna, Sabine Choppin, Françoise Colobert, and Joanna Wencel-Delord. "Towards Atropoenantiopure N–C Axially Chiral Compounds via Stereoselective C–N Bond Formation." CHIMIA International Journal for Chemistry 74, no. 11 (November 25, 2020): 883–89. http://dx.doi.org/10.2533/chimia.2020.883.

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N–C axial chirality, although disregarded for decades, is an interesting type of chirality with appealing applications in medicinal chemistry and agrochemistry. However, atroposelective synthesis of optically pure compounds is extremely challenging and only a limited number of synthetic routes have been designed. In particular, asymmetric N-arylation reactions allowing atroposelective N–C bond forming events remain scarce, although great advances have been achieved recently. In this minireview we summarize the synthetic approaches towards synthesis of N–C axially chiral compounds via stereocontrolled N–C bond forming events. Both organo-catalyzed and metal-catalyzed transformations are described, thus illustrating the diversity and specificity of both strategies.

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Raed, Anas Abo, Vasudevan Dhayalan, Shahar Barkai, and Anat Milo. "N-Heterocyclic Carbene Triazolium Salts Containing Brominated Aromatic Motifs: Features and Synthetic Protocol." CHIMIA International Journal for Chemistry 74, no. 11 (November 25, 2020): 878–82. http://dx.doi.org/10.2533/chimia.2020.878.

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In this work, we provide a brief overview of the role of N-aryl substituents on triazolium N-heterocyclic carbene (NHC) catalysis. This synopsis provides context for the disclosed synthetic protocol for new chiral N-heterocyclic carbene (NHC) triazolium salts with brominated aromatic motifs. Incorporating brominated aryl rings into NHC structures is challenging, probably due to the substantial steric and electronic influence these substituents exert throughout the synthetic protocol. However, these exact characteristics make it an interesting N-aryl substituent, because the electronic and steric diversity it offers could find broad use in organometallic- and organo-catalysis. Following the synthetic reaction by NMR guided the extensive modification of a known protocol to enable the preparation of these challenging NHC pre-catalysts.

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Robert, Christelle A. M., and Pierre Mateo. "The Chemical Ecology of Benzoxazinoids." CHIMIA 76, no. 11 (November 30, 2022): 928. http://dx.doi.org/10.2533/chimia.2022.928.

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Benzoxazinoids are specialized metabolites that modulate plant physiology and plant interactions with their environment. In this review, we synthesize their multiple functions and ecological relevance. We first provide an overview of benzoxazinoid biosynthesis and highlight known regulatory elements involved in modulating their production. We then outline the role of benzoxazinoids in plant nutrition, vegetative and reproductive growth, and defense. We further summarize benzoxazinoid response to environmental factors such as temperature, drought, CO2, light, or nutrient levels and emphasize their potential role in tolerating abiotic stresses. Finally, we argue that benzoxazinoids act as a strong selective force on different trophic levels by shaping the plant interactions with microbes, insect herbivores, and competitor plants. Understanding the pivotal role of benzoxazinoids in plant biology is crucial to apprehend their impact on (agro)ecosystem functioning and diversity.

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Arús-Pous, Josep, Mahendra Awale, Daniel Probst, and Jean-Louis Reymond. "Exploring Chemical Space with Machine Learning." CHIMIA International Journal for Chemistry 73, no. 12 (December 18, 2019): 1018–23. http://dx.doi.org/10.2533/chimia.2019.1018.

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Chemical space is a concept to organize molecular diversity by postulating that different molecules occupy different regions of a mathematical space where the position of each molecule is defined by its properties. Our aim is to develop methods to explicitly explore chemical space in the area of drug discovery. Here we review our implementations of machine learning in this project, including our use of deep neural networks to enumerate the GDB13 database from a small sample set, to generate analogs of drugs and natural products after training with fragment-size molecules, and to predict the polypharmacology of molecules after training with known bioactive compounds from ChEMBL. We also discuss visualization methods for big data as means to keep track and learn from machine learning results. Computational tools discussed in this review are freely available at http://gdb.unibe.ch and https://github.com/reymond-group.

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Edwardson, Thomas G. W., Mikail D. Levasseur, and Donald Hilvert. "The OP Protein Cage: A Versatile Molecular Delivery Platform." CHIMIA International Journal for Chemistry 75, no. 4 (April 28, 2021): 323–28. http://dx.doi.org/10.2533/chimia.2021.323.

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Well-defined containers constructed from multiple protein subunits are a unique class of nanomaterial useful in supramolecular chemistry and biology. These protein cages are widespread in nature, where they are responsible for a diversity of important tasks. As such, producing our own designer protein cages, complete with bespoke functionalities, is a promising avenue to new nanodevices, biotechnology and therapies. Herein, we describe how an artificial, computationally designed protein cage can be rationally engineered using supramolecular intuition to produce new functional capsules. Positive supercharging the interior cavity of this porous protein cage enables the efficient encapsulation of oligonucleotides by electrostatically-driven self-assembly. Moreover, the resulting cargo-loaded cages enter mammalian cells and release their cargo, for example siRNA which modulates gene expression. To expand the cargo scope of this proteinaceous container, a higher level of supramolecular complexity can also be introduced. Encapsulation of anionic surfactants affords protein-scaffolded micelles, which are capable of sequestering poorly water-soluble small molecules within their hydrophobic cores. These hybrid particles stably carry bioactive cargo and deliver it intracellularly, thereby increasing potency. Further development of these genetically-encoded materials is ongoing towards specific applications ranging from cell biology to medicine.

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"Poly(triacetylene)s: A New Class of Linearly π-Conjugated Oligomers and Polymers with an All-carbon Backbone". CHIMIA 55, № 3 (28 березня 2001): 132. http://dx.doi.org/10.2533/chimia.2001.132.

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Linearly π-conjugated polymers are intensively investigated in both academia and industry for a diversity of advanced materials applications. Polyacetylenes (PAs) and poly(diacetylene)s (PDAs) were among the earliest investigated linearly π-conjugated polymers possessing an all-carbon backbone. They actually represent the first members in an entire progression of linear all-carbon polymers which starts with polyacetylene and ultimately extends to carbyne. Here, we describe the discovery and systematic investigation of poly(triacetylene)s (PTAs), the third class of compounds in this progression. We report both the preparation of longer-chain polydisperse PTA polymers as well as the synthesis, characterization, and physical study of monodisperse oligomers with record lengths extending up to 18 nm. We show how molecular properties evolve into the saturation range with increasing oligomeric length and report several direct determinations of the effective conjugation length (ECL), i.e. the oligomeric length at which saturation of molecular properties occurs. Finally, we present a new class of hybrid oligomers and polymers, with a diversity of chromophores inserted as functional spacers into the PTA backbone for further enhancement of optoelectronic properties.

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"The Alkaloids of Triphyophyllum peltatum (Dioncophyllaceae)." CHIMIA 52, no. 1-2 (February 25, 1998): 18. http://dx.doi.org/10.2533/chimia.1998.18.

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A great diversity of naphthylisoquinolines, presumably acetogenic biaryl alkaloids, has been obtained from the West-African liana Triphyophyllum peltatum. By the example of dioncophylline A, the main alkaloid from T. peltatum, we illustrate the various methods of structural elucidation established in our laboratory. The structural peculiarities of some of the minor alkaloids from the same species are discussed. A perspective on the interesting biological activities of various alkaloids from T. peltatum and related plants is given. The most promising lead is dioncophylline C, marked by pronounced antiplasmodial activity. Chemical syntheses, especially dimerization of naphthylisoquinolines, and QSAR-guided modifications of the most active structures are featured as rewarding strategies in the search for improved drugs. A chemotaxonomic summary is presented.

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"The Development of Enzymes for the Preparation of Chemicals." CHIMIA 53, no. 12 (December 22, 1999): 613. http://dx.doi.org/10.2533/chimia.1999.613.

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The use of enzymes as catalysts for the preparation of novel organic molecules is becoming more widespread every year. The science of biotransformation has matured, and biocatalysts now stand alongside other forms of catalysts to be considered as viable options for the promotion of a particular reaction. Of great importance for the breakthrough of biocatalysts was the availability of enzymes and the increasing demand for enantiomerically pure compounds. Especially, hydrolytic enzymes, lyases, and oxidoreductases are of technical importance today. The potential of enzymes for the synthesis of chemical compounds is by no means exhausted, and the enormous diversity of microorganisms is an almost unlimited pool for new enzymes. In this paper, different strategies are discussed to find and develop new enzymes for the application in organic synthesis.

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"Research Topics." CHIMIA 50, no. 12 (December 18, 1996): 655. http://dx.doi.org/10.2533/chimia.1996.655.

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Quantum-mechanical calculations have been applied to predict thermodynamic and reactivity properties of unknown organic molecules, being stable compounds or reactive intermediates. Through synthesis some of the theoretical systems become real compounds that can be synthons (synthetic intermediates) or chirons (optically pure synthetic intermediates) useful in the preparation of natural products and analogues of biological interest (anti-cancer, anti-virus, antibiotic, anti-diabetes agents). Our interests concentrate on remote substituent effects as we want to play with them together with polyfunctional systems and reactions that constitute new synthetic approaches. These have to be convergent, highly stereoselective, and versatile (applicable to a large variety of derivatives: molecular diversity). We often rely on tandem reactions or/and reaction cascades. Sometimes the new compounds and their new reactions send us back to the theory and to mechanistic studies.

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"Feed Stuffs Analysis at the Swiss Federal Research Station for Animal Production (RAP), Posieux : Die Futtermittelanalytik an der Eidgenössischen Forschungsanstalt für Nutztiere (RAP) in Posieux." CHIMIA 51, no. 10 (October 29, 1997): 777. http://dx.doi.org/10.2533/chimia.1997.777.

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Agricultural research and associated control or service activities are carried out, in Switzerland, in six federal research stations. The Swiss Federal Research Station for Animal Production (RAP) focuses on the optimal conversion of feed stuffs into milk and meat, taking into account animal requirements as well as ecological and economic considerations. The station also operates the official Swiss feed stuffs control laboratory. Its analytical chemistry section carries out over 100 000 tests/year, using chemical, physical and microbiological methods, and authenticity procedures based on molecular biology. Sample diversity combined with a multitude of test incentives requires a broad range of state-of-the-art methods for the determination of nutrients, minerals, noxious substances and residues. Evaluating, adapting, and validating analytical methods and testing equipment, are therefore essential tasks of this section. Being accreditaded according to European standards (EN 45001), the laboratory has furthermore to meet the high quality management criteria.

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"Directed Evolution with Fast and Efficient Selection Technologies." CHIMIA 55, no. 4 (April 25, 2001): 325. http://dx.doi.org/10.2533/chimia.2001.325.

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Directed molecular evolution has proven to be a very powerful concept for the generation of proteins with improved properties, such as increased activity, binding affinity, folding efficiency or enhanced chemical and/or thermodynamic stability. We review here advances in the selection of proteins carrying desired mutations from pools of proteins that mostly carry unfavourable alterations. A short overview of the concept of directed evolution with a discussion of randomisation strategies is given first. Two technologies for the selection of proteins, each with its own advantages, are then discussed: In Ribosome Display, all steps are carried out in a cell-free system, which allows one to create very large libraries (diversity > 1011), rapidly introduce mutations and thus obtain an iterative evolution. Examples with antibodies evolved for affinity or stability are discussed. In the Protein Fragment Complementation Assay, a library-versus-library selection is possible, that is, a simultaneous selection of binders against many targets. Examples with peptide and antibody libraries are discussed.

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"Enhanced Enzyme Performance by DNA Shuffling." CHIMIA 53, no. 12 (December 22, 1999): 617. http://dx.doi.org/10.2533/chimia.1999.617.

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In the quest for enhanced enzyme performance in non-natural applications, directed evolution emulates natural processes for the generation of diversity and selection of desirable traits. Classical methods for improving protein characteristics rely upon point mutation or cassette mutagenesis of a selected region within a desired sequence (i.e., focusing on a narrow sequence space). However, computer simulations of the evolution of linear sequences have demonstrated the importance of recombination of blocks of related sequences rather than sequence mutation alone. DNA shuffling includes in vivo and in vitro methods for recombination of nucleic acid sequences. In one format, DNA shuffling involves methods for in vitro homologous recombination of pools of related genes. For example, fragmentation of nucleic acid sequences that encode genes, can be followed by reassembly using the polymerase chain reaction (PCR). As the complete gene sequence can be shuffled, a wider sequence space can be accessed in searching for the desired, improved variant. Repeated cycles of recombination, optionally together with error-prone PCR to introduce point mutations, allow efficient molecular evolution of complex sequences in vitro, to provide biological molecules with improved properties.

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"Extended Substrate Acceptance of Herpes Simplex Virus Type 1 Thymidine Kinase: a New Chance for Gene and Antiviral Therapy." CHIMIA 54, no. 11 (November 1, 2000): 663. http://dx.doi.org/10.2533/chimia.2000.663.

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Herpes simplex virus type 1 thymidine kinase (HSV1-TK) has become increasingly important as a target in medicinal chemistry because of its links to therapy of viral infection, gene therapy of cancer and allogeneic transplantation. These applications are based on the differences in binding properties between the human and the viral enzyme. Several problems have been encountered in the clinic, e.g. the increase of resistance for antiviral drugs and the immunosuppressive effects of the dosages needed for tumor regression. Thus intensive efforts have been directed towards understanding substrate diversity to overcome the clinical limitations. In this context, kinetic and thermodynamic studies revealed that substrates bind in compulsory order and that the binding event is enthalpy driven. The structural evaluation of aciclovir resistant HSV strains shows that loss of electrostatic interactions, change in steric accessibility and modification of the 3D conformation of HSV1-TK are responsible for the encountered resistance. Further crystallography studies revealed the role of water in substrate binding, the advantage of a fixed ribose ring and that substrate acceptance of HSV1-TK is extended to all five nucleobases. The reviewed results give new rationale for the design of novel prodrugs and engineered HSV1-TK for antiviral and gene therapy.

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