At the crossroads of chemistry and biology

The life sciences are molecular and the harnessing of information gleaned from genomics and proteomics will require interdisciplinary research integrating chemistry and biology. This approach is illustrated by the synthesis and biological evaluation of lipidated peptides and proteins and the delineation of a concept arguing for natural product guided combinatorial chemistry.     

Genetic engineering of structural protein polymers.

Genetic and protein engineering are components of a new polymer chemistry that provide the tools for producing macromolecular polyamide copolymers of diversity and precision far beyond the current capabilities of synthetic polymer chemistry. The genetic machinery allows molecular control of chemical and physical chain properties. Nature utilizes this control to formulate protein polymers into materials with extraordinary mechanical properties, such as the strength and toughness of silk and the elasticity and resilience of mammalian elastin. The properties of these materials have been attributed to the presence of short repeating oligopeptide sequences contained in the proteins, fibroin, and elastin. We have produced homoblock protein polymers consisting exclusively of silk-like crystalline blocks and elastin-like flexible blocks. We have demonstrated that each homoblock polymer as produced by microbial fermentation exhibits measurable properties of crystallinity and elasticity. Additionally, we have produced alternating block copolymers of various amounts of silk-like and elastin-like blocks, ranging from a ratio of 1:4 to 2:1, respectively. The crystallinity of each copolymer varies with the amount of crystalline block interruptions. The production of fiber materials with custom-engineered mechanical properties is a potential outcome of this technology.     

Architectural self-construction in nature and chemical synthesis

The chemistry of squalene oxide (1) exemplifies that architectural complexity can be encoded in the structures of relatively simple, polyunsaturated molecules. When the concept of architectural self-construction is an integral part of the design of a chemical synthesis, powerful strategies can be uncovered. this article addresses studies which showed that polyunsaturated, 19-membered ring carbocycle contains all of the molecular information that is required to give the stereochemically complex polycyclic architecture of the cytotoxic natural product FR182877.     

Bioelementology as an interdisciplinary integrative approach in life sciences: Terminology,classification, perspectives

The article presents the proposed concept of bioelements and the basic postulates of bioelementology for assessing and discussing them in the scientific community. It is known that chemical elements exist in the organism not by themselves, but in certain species having close interaction with other components. Such units are proposed to be called bioelements: the elementary functioning units of living matter, which are biologically active complexes of chemical elements as atoms, ions or nanoparticles with organic compounds of exogenous or biogenous origin. The scientific discipline that studies bioelements, is proposed to be called bioelementology. This discipline could lay the foundation for the integration of bioorganic chemistry, bioinorganic chemistry, biophysics, molecular biology and other parts of life sciences.     

Structure-based drug design with geometric deep learning

Structure-based drug design uses three-dimensional geometric information of macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric deep learning, an emerging concept of neural-network-based machine learning, has been applied to macromolecular structures. This review provides an overview of the recent applications of geometric deep learning in bioorganic and medicinal chemistry, highlighting its potential for structure-based drug discovery and design. Emphasis is placed on molecular property prediction, ligand binding site and pose prediction, and structure-based de novo molecular design. The current challenges and opportunities are highlighted, and a forecast of the future of geometric deep learning for drug discovery is presented.     

Bioinspired polymeric materials: in-between proteins and plastics

Chemical and biological researchers are making rapid progress in the design and synthesis of non-natural oligomers and polymers that emulate the properties of natural proteins. Whereas molecular biologists are exploring biosynthetic routes to non-natural proteins with controlled material properties, synthetic polymer chemists are developing bioinspired materials with well-defined chemical and physical properties that function or self-organize according to defined molecular architectures. Bioorganic chemists, on the other hand, are developing several new classes of non-natural oligomers that are bridging the gap between molecular biology and polymer chemistry. These synthetic oligomers have both sidechain and length specificity, and, in some cases, demonstrate capability for folding, self-assembly, and specific biorecognition. Continued active exploration of diverse backbone and sidechain chemistries and connectivities in bioinspired oligomers will offer the potential for self-organized materials with greater chemical diversity and biostability than natural peptides. Taken together, advances in molecular bioengineering, polymer chemistry, and bioorganic chemistry are converging towards the creation of useful bioinspired materials with defined molecular properties.     

The Proton Trap Technology—Toward High Potential Quinone‐Based Organic Energy Storage

An organic cathode material based on a copolymer of poly(3,4‐ethylenedioxythiophene) containing pyridine and hydroquinone functionalities is described as a proton trap technology. Utilizing the quinone to hydroquinone redox conversion, this technology leads to electrode materials compatible with lithium and sodium cycling chemistries. These materials have high inherent potentials that in combination with lithium give a reversible output voltage of above 3.5 V (vs Li^0/+) without relying on lithiation of the material, something that is not showed for quinones previously. Key to success stems from coupling an intrapolymeric proton transfer, realized by an incorporated pyridine proton donor/acceptor functionality, with the hydroquinone redox reactions. Trapping of protons in the cathode material effectively decouples the quinone redox chemistry from the cycling chemistry of the anode, which makes the material insensitive to the nature of the electrolyte cation and hence compatible with several anode materials. Furthermore, the conducting polymer backbone allows assembly without any additives for electronic conductivity. The concept is demonstrated by electrochemical characterization in several electrolytes and finally by employing the proton trap material as the cathode in lithium and sodium batteries. These findings represent a new concept for enabling high potential organic materials for the next generation of energy storage systems.     

Nanomaterials in controlled drug release

In past years with the advances of chemistry and material sciences, the development of nanotechnology brought generations of nanomaterials with specific biomedical properties. These include the nanoparticle-based drug delivery, nanosized drugs, and nanomaterials for tissue engineering. The present article focuses on the use of nanomaterials in controlled drug release. The applications of nanomaterials with nano-enabled drug release characteristics brought many benefits when compared to the traditional (bulk) materials. We discuss the current advances and propose some future directions for the technology development.     

生物质谱分析的研究进展及临床应用

质谱分析技术已应用于化学、化工、环境、能源、医药、运动医学、刑侦科学、生命科学、材料科学等各个领域。阐述目前生物质谱技术的类型、原理以及在医学领域中的应用,进而分析质谱技术在未来发展的前景。     

Asymmetric induction under confinement

Confinement may efficiently condition the stereochemical outcome of a reaction through space constriction and molecular close contact. This article briefly reviews recent approaches of supramolecular chemistry to achieve chiral confinement. Crystallization is not always possible and the use of chiral crystals or clathrates lacks generality. The construction of solid supramolecular assemblies circumvents some of the problems of the crystal chemistry. In this regard, molecular imprinting of polymeric matrices with orifices mimicking the transition state of an enantioselective process is a very young, promising technique. Zeolites provide porous, rigid environments to host molecules without the need of lucky crystallizations, yet zeolites are not chiral per se and must be chirally modified. Besides, the limited dimension of their pores restricts the size of the guest molecules. Despite these problems, useful asymmetric photochemical reactions have been performed on zeolites. Finally, the formation of pillared lamellar structures, from inorganic salts of tetravalent transition metals covalently grafted with organic chains, is considered. The adequate selection of functionality and chirality of the organic pillars would afford custom-made, highly porous, 3D hybrid organo-inorganic scaffolds. However, the production of asymmetric processes within these layered materials still remains to be seen.     

Design and analysis of nanoscale bioassemblies

Bionanotechnology is an emerging field in nanotechnology. In general, it uses concepts from chemistry, biochemistry, and molecular biology to identify components and processes for the construction of self-assembling materials and devices. Distant goals of the science of bionanotechnology range from developing programmable nanoscale devices that can sample or alter their environments to developing assemblies capable of Darwinian evolution. At the heart of these approaches is the concept of the production of supramolecular assemblies (SMAs; also known as supramolecular aggregates) by programmed self-assembly in an aqueous medium. Ordered arrays, planar and closed-shell tilings, dynamic machines, and switches have been designed and constructed by using DNA-DNA, protein-protein, and protein-nucleic acid biospecificities. We review the designs and the analytical techniques that have been employed in the production of SMAs that do not occur in nature.     

Carotenoid research: History and new perspectives for chemistry in biological systems

The history of carotenoid research as this progressed from chemistry to biochemistry and biology is outlined. Proposed roles of carotenoids in eye health, as antioxidants, and in protection against cancer and other degenerative diseases, as well as stimulatory effects on the immune system and metabolism are covered. Proposed biological actions must be consistent with the chemistry of carotenoids in the largely aqueous biological systems, which may differ from the known chemistry of carotenoids in organic solvents. In particular, carotenoids tend to form aggregates. The effects of this aggregation and of other molecular interactions in vivo are likely to be crucial to biological activity. These perspectives of the chemistry of carotenoids and carotenoid free radicals are examined and the need for carotenoid samples used in experimental work to be pure and free from breakdown products and pro-oxidant peroxides is emphasised.This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.     

Extending the concept of template-assembled synthetic proteins.

The creation of native-like macromolecules in copying nature's way represents a fascinating challenge in protein chemistry today. In the absence of a detailed knowledge of the complex folding pathway the ultimate goal in protein de novo design, the construction of artificial proteins with predetermined three-dimensional structure and tailor-made functions based on a defined, generally valid set of rules, appears to be still out of reach. With progress in synthesis strategies and biostructural characterization methods, topological templates have become a versatile tool for inducing and stabilizing secondary and tertiary structures, such as protein loops, beta-turns, alpha-helices, beta-sheets and a variety of folding motifs. In this article, we extend the concept of template-assembled synthetic proteins for the construction of protein-like topologies with multiply bridged, oligocyclic chain architectures termed locked-in tertiary folds that exhibit unique physicochemical and folding properties because of the highly confined conformational space. Furthermore, we show that some fundamental questions in protein assembly can be approached applying the template concept. Using covalent template trapping of self-associated peptide assemblies in aqueous solution the structural and physical forces guiding protein folding, supramolecular assembly and molecular recognition processes can be studied on a molecular level.     

Bacterial enzymes for lignin depolymerisation: new biocatalysts for generation of renewable chemicals from biomass

The conversion of polymeric lignin from plant biomass into renewable chemicals is an important unsolved problem in the biorefinery concept. This article summarises recent developments in the discovery of bacterial enzymes for lignin degradation, our current understanding of their molecular mechanism of action, and their use to convert lignin or lignocellulose into aromatic chemicals. The review also discusses the recent developments in screening of metagenomic libraries for new biocatalysts, and the use of protein engineering to enhance lignin degradation activity.     

Some considerations on the proper use of computational tools in transition metal chemistry

The current understanding of transition metal chemistry is reviewed placing the attention at the applications and applicability of computational quantum chemistry to the calculation and prediction of spectroscopic properties of transition metal complexes and molecular magnets.     

Opportunities at the interface of chemistry and biology

The combination of the tools and principles of chemistry, together with the tools of modern molecular biology, allow us to create complex synthetic and natural molecules, and processes with novel biological, chemical and physical properties. This article illustrates the tremendous opportunity that lies at this interface of chemistry and biology by describing a number of examples, ranging from efforts to expand the genetic code of living organisms to the use of combinatorial methods to generate biologically active synthetic molecules.     

Opportunities at the interface of chemistry and biology

The combination of the tools and principles of chemistry, together with the tools of modern molecular biology, allow us to create complex synthetic and natural molecules, and processes with novel biological, chemical and physical properties. This article illustrates the tremendous opportunity that lies at this interface of chemistry and biology by describing a number of examples, ranging from efforts to expand the genetic code of living organisms to the use of combinatorial methods to generate biologically active synthetic molecules.     

Opportunities at the interface of chemistry and biology

The combination of the tools and principles of chemistry, together with the tools of modern molecular biology, allow us to create complex synthetic and natural molecules, and processes with novel biological, chemical and physical properties. This article illustrates the tremendous opportunity that lies at this interface of chemistry and biology by describing a number of examples, ranging from efforts to expand the genetic code of living organisms to the use of combinatorial methods to generate biologically active synthetic molecules.     

Electronic control of helical chirality.

Chiral phenomena are common in living systems. Despite the fact that development of materials has often been inspired by chemistry from the biological world, materials that take advantage of inherent chirality have found relatively few applications. It is therefore probable that much remains to be gained from novel applications of molecular, macromolecular and supramolecular chirality. Among the most intriguing recent advances in studies of chiral materials is the development of mechanisms to control the shape and properties of chiral molecules. Photo-induced helical chirality inversions have been studied for several years and significant achievements have been reported. Recently, electronically triggered systems have drawn significant attention. These technologies offer the potential for development of novel materials that take advantage of photonic or electronic modulation of molecular recognition, optical or mechanical properties.