Small-molecule compounds structural properties

Three-dimensional quantitative structure-aaivity relationships (3D-QSARs) are quantitative models that relate the biological activity of small molecules with their properties calculated in 3D space.All 3D-QSAR methods combine molecular modeling and statistical analysis of the relative biological potency within a set of compounds. In this chapter, we provide... 

Precisely defined collections of different chemical compounds are denominated as chemical libraries that can be efficiently prepared by methods of combinatorial chemistry. Each chemical compound owes specific structural, steiic, and electronic properties that determine all possible interactions of the small molecule with a given protein or receptor. The molecule s properties are based on the steiic arrangement of functional groups, including the conformations that can be attained by a specific structure. 

Characterization of structural, spectroscopic, and reactivity properties of model compounds—that is, metal cofactor small molecule analogs. 

The thermal polymerization of reactive polyimide oligomers is a critical part of a number of currently important polymers. Both the system in which we are interested, PMR-15, and others like it (LARC-13, HR-600), are useful high temperature resins. They also share the feature that, while the basic structure and chemistry of their imide portions is well defined, the mode of reaction and ultimately the structures that result from their thermally activated end-groups is not clear. Since an understanding of this thermal cure would be an important step towards the improvement of both the cure process and the properties of such systems, we have approached our study of PMR-15 with a focus only on this higher temperature thermal curing process. To this end, we have used small molecule model compounds with pre-formed imide moieties and have concentrated on the chemistry of the norbornenyl end-cap (1). 

Robust peptide-derived approaches aim to identify a small drug-like molecule to mimic the peptide interactions. The primary peptide molecule is considered in these approaches as a tool compound to demonstrate that small molecules can compete with a given interaction. A variety of chemical, 3D structural and molecular modeling approaches are used to validate the essential 3D pharmacophore model which in turn is the basis for the design of the mimics. The chemical approaches include in addition to N- and C-terminal truncations a variety of positional scanning methods. Using alanine scans one can identify the key pharmacophore points D-amino-acid or proline scans allow stabilization of (i-turn structures cyclic scans bias the peptide or portions of the peptide in a particular conformation (a-helix, (i-turn and so on) other scans, like N-methyl-amino-acid scans and amide-bond-replacement (depsi-peptides) scans aim to improve the ADME properties." ... 

Abstract Piperazines and its congeners, (di)keto piperazines are valuable tools in drug discovery, providing a natural path for the process peptide > peptidomimetic > small molecule also called depeptisation. Moreover, they can provide molecular probes to understand molecular pathways for diseases of unmet medical need. However, in order to better understand the design of such value added compounds, the detailed understanding of scope and limitation of their synthesis as well as their 3D structures and associated physicochemical properties is indispensables. Isocyanide multicomponent reaction (MCR) chemistry provides a prime tool for entering the chemical space of (di)(keto)piperazines since not less then 20 different ways exist to access a diversity of related scaffolds. 

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