4. Chemical space of naturally occurring compounds

2020 ◽  
pp. 103-124
Keyword(s):  
Chemical Space ◽  
Naturally Occurring

Chemical space of naturally occurring compounds

2018 ◽  
Vol 4 (5) ◽  
Author(s):  
Fernanda I. Saldívar-González ◽  
B. Angélica Pilón-Jiménez ◽  
José L. Medina-Franco
Keyword(s):  
Data Mining ◽  
Natural Products ◽  
Small Molecules ◽  
Chemical Space ◽  
Chemical Diversity ◽  
Diversity Analysis ◽  
Naturally Occurring ◽  
Systematic Exploration ◽  
Chemical Descriptors ◽  
Different Sources

AbstractThe chemical space of naturally occurring compounds is vast and diverse. Other than biologics, naturally occurring small molecules include a large variety of compounds covering natural products from different sources such as plant, marine, and fungi, to name a few, and several food chemicals. The systematic exploration of the chemical space of naturally occurring compounds have significant implications in many areas of research including but not limited to drug discovery, nutrition, bio- and chemical diversity analysis. The exploration of the coverage and diversity of the chemical space of compound databases can be carried out in different ways. The approach will largely depend on the criteria to define the chemical space that is commonly selected based on the goals of the study. This chapter discusses major compound databases of natural products and cheminformatics strategies that have been used to characterize the chemical space of natural products. Recent exemplary studies of the chemical space of natural products from different sources and their relationships with other compounds are also discussed. We also present novel chemical descriptors and data mining approaches that are emerging to characterize the chemical space of naturally occurring compounds.

scholarly journals Computational Approaches to Identify Natural Products as Inhibitors of DNA Methyltransferases

2018 ◽  
Author(s):  
Fernanda I. Saldívar-González ◽  
Alejandro Gómez-García ◽  
Norberto Sánchez-Cruz ◽  
Javier Ruiz-Rios ◽  
B. Angélica Pilón-Jiménez ◽  
...  
Keyword(s):  
Natural Products ◽  
Molecular Modeling ◽  
Small Molecules ◽  
Chemical Space ◽  
Pharmacophore Modeling ◽  
Dna Methyltransferases ◽  
Computational Approaches ◽  
Naturally Occurring ◽  
Epigenetic Drug ◽  
Different Sources

Naturally occurring small molecules include a large variety of natural products from different sources that have confirmed activity against epigenetic targets. In this work we review chemoinformatic, molecular modeling and other computational approaches that have been used to uncover natural products as inhibitors of DNA metiltransferases, a major family of epigenetic targets with significant potential for the treatment of cancer and several other diseases. Examples of these computational approaches include docking, similarity-based virtual screening, and pharmacophore modeling. It is also commented the chemoinformatic-based exploration of the chemical space of naturally occurring compounds as epigenetic modulators which may have significant implications in epigenetic drug discovery and nutriepigenetics.

“Drug-likeness” properties of natural compounds

2019 ◽  
Vol 4 (11) ◽  
Author(s):  
Fidele Ntie-Kang ◽  
Kennedy D. Nyongbela ◽  
Godfred A. Ayimele ◽  
Suhaib Shekfeh
Keyword(s):  
Natural Product ◽  
Chemical Space ◽  
Natural Compounds ◽  
Quantitative Structure Activity Relationship ◽  
Learning Approaches ◽  
Naturally Occurring ◽  
Chemical Concepts ◽  
Approved Drugs ◽  
Physical And Chemical ◽  
Fundamental Physical

Abstract Our previous work was focused on the fundamental physical and chemical concepts behind “drug-likeness” and “natural product (NP)-likeness”. Herein, we discuss further details on the concepts of “drug-likeness”, “lead-likeness” and “NP-likeness”. The discussion will first focus on NPs as drugs, then a discussion of previous studies in which the complexities of the scaffolds and chemical space of naturally occurring compounds have been compared with synthetic, semisynthetic compounds and the Food and Drug Administration-approved drugs. This is followed by guiding principles for designing “drug-like” natural product libraries for lead compound discovery purposes. In addition, we present a tool for measuring “NP-likeness” of compounds and a brief presentation of machine-learning approaches. A binary quantitative structure–activity relationship for classifying drugs from nondrugs and natural compounds from nonnatural ones is also described. While the studies add to the plethora of recently published works on the “drug-likeness” of NPs, it no doubt increases our understanding of the physicochemical properties that make NPs fall within the ranges associated with “drug-like” molecules.

scholarly journals Chalcones: Synthetic Chemistry Follows Where Nature Leads

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1203
Author(s):  
Hiba A. Jasim ◽  
Lutfun Nahar ◽  
Mohammad A. Jasim ◽  
Sharon A. Moore ◽  
Kenneth J. Ritchie ◽  
...  
Keyword(s):  
Critical Appraisal ◽  
Chemical Space ◽  
Structural Features ◽  
Structural Modifications ◽  
Chalcone Derivatives ◽  
Bioactive Natural Products ◽  
Bioinspired Synthesis ◽  
Naturally Occurring ◽  
Reduced Toxicity ◽  
Unique Chemical

Chalcones belong to the flavonoid class of phenolic compounds. They form one of the largest groups of bioactive natural products. The potential anticancer, anti-inflammatory, antimicrobial, antioxidant, and antiparasitic properties of naturally occurring chalcones, and their unique chemical structural features inspired the synthesis of numerous chalcone derivatives. In fact, structural features of chalcones are easy to construct from simple aromatic compounds, and it is convenient to perform structural modifications to generate functionalized chalcone derivatives. Many of these synthetic analogs were shown to possess similar bioactivities as their natural counterparts, but often with an enhanced potency and reduced toxicity. This review article aims to demonstrate how bioinspired synthesis of chalcone derivatives can potentially introduce a new chemical space for exploitation for new drug discovery, justifying the title of this article. However, the focus remains on critical appraisal of synthesized chalcones and their derivatives for their bioactivities, linking to their interactions at the biomolecular level where appropriate, and revealing their possible mechanisms of action.

scholarly journals Computational Analysis of Naturally Occurring Aristolochic Acid Analogues and Their Biological Sources

Biomolecules ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1344
Author(s):  
Tingjun Xu ◽  
Weiming Chen ◽  
Junhong Zhou ◽  
Jingfang Dai ◽  
Yingyong Li ◽  
...  
Keyword(s):  
Aristolochic Acid ◽  
Chemical Space ◽  
Herbal Medicines ◽  
Wide Distribution ◽  
Potential Hazard ◽  
Multiple Cancer ◽  
Aristolochic Acids ◽  
Biological Source ◽  
Naturally Occurring ◽  
Biological Sources

Aristolochic acids are known for nephrotoxicity, and implicated in multiple cancer types such as hepatocellular carcinomas demonstrated by recent studies. Natural products that are analogues to aristolochic acids have been constantly isolated from organisms; a larger chemical space of these compounds and a wider coverage of biological sources should be determined in consideration of the potential hazard of aristolochic acid analogues and the wide distribution of their biological sources in the nature. Therefore, we carried out an in silico research of naturally occurring aristolochic acid analogues and their biological sources, as a supplement to existing studies. The result shows a chemical space of 238 naturally occurring aristolochic acid analogues that are present in 175 species of biological sources including 44 traditional medicines. With the computational estimation for toxicity and the implication in hazard assessment of a biological source with the presence of aristolochic acid analogues, we propose that additional awareness should be raised to the public for avoidance of toxic species, especially those that are used as herbal medicines and easily accessible.

scholarly journals “Drug-Likeness” versus “Natural Product-Likeness”

2018 ◽  
Author(s):  
Fidele Ntie-Kang ◽  
Kennedy D. Nyongbela ◽  
Godfred A. Ayimele ◽  
Suhaib Shekfeh
Keyword(s):  
Natural Product ◽  
Chemical Space ◽  
Quantitative Structure Activity Relationship ◽  
Learning Approaches ◽  
Lead Compound ◽  
Synthetic Compounds ◽  
Naturally Occurring ◽  
Structure Activity ◽  
Approved Drugs ◽  
Fda Approved Drugs

We discuss further details on the concepts of “drug-likeness”, “lead-likeness”, and “natural product-likeness”. The discussion will first focus on natural products as drugs, then a discussion of previous studies in which the complexities of the scaffolds and chemical space of naturally occurring compounds have been compared with synthetic, semi-synthetic compounds and FDA-approved drugs. This is followed by guiding principles for designing “drug-like” natural product libraries for lead compound discovery purposes. We end up by presenting a tool for measuring “natural product-likeness” of compounds and a brief presentation of machine learning approaches and a binary quantitative structure-activity relationship (QSAR) for classifying drugs from non-drugs and natural compounds from non-natural ones, respectively.

Pathology of Bone Cells in Pigs with Experimental Turbinate Osteoporosis (Atrophic Rhinitis)

1971 ◽  
Vol 29 ◽  
pp. 304-305
Author(s):  
A. W. Fetter ◽  
C. C. Capen
Keyword(s):  
Mucous Membrane ◽  
Bone Cells ◽  
Atrophic Rhinitis ◽  
Infectious Agents ◽  
Metabolic Disturbances ◽  
Progressive Reduction ◽  
Naturally Occurring ◽  
Fundamental Cause ◽  
Osteocytic Osteolysis ◽  
Uncertain Etiology

Atrophic rhinitis in swine is a disease of uncertain etiology in which infectious agents, hereditary predisposition, and metabolic disturbances have been reported to be of primary etiologic importance. It shares many similarities, both clinically and pathologically, with ozena in man. The disease is characterized by deformity and reduction in volume of the nasal turbinates. The fundamental cause for the localized lesion of bone in the nasal turbinates has not been established. Reduced osteogenesis, increased resorption related to inflammation of the nasal mucous membrane, and excessive resorption due to osteocytic osteolysis stimulated by hyperparathyroidism have been suggested as possible pathogenetic mechanisms.The objectives of this investigation were to evaluate ultrastructurally bone cells in the nasal turbinates of pigs with experimentally induced atrophic rhinitis, and to compare these findings to those in control pigs of the same age and pigs with the naturally occurring disease, in order to define the fundamental lesion responsible for the progressive reduction in volume of the osseous core.

High Resolution Replication of Organoclay Surfaces

1982 ◽  
Vol 40 ◽  
pp. 576-577
Author(s):  
W. W. Barker ◽  
W. E. Rigsby ◽  
V. J. Hurst ◽  
W. J. Humphreys
Keyword(s):  
Clay Mineral ◽  
Organic Molecule ◽  
Organic Molecules ◽  
X Ray Diffraction ◽  
Xrd Pattern ◽  
X Ray ◽  
Naturally Occurring ◽  
Silicate Layers ◽  
Mineral Identification

Experimental clay mineral-organic molecule complexes long have been known and some of them have been extensively studied by X-ray diffraction methods. The organic molecules are adsorbed onto the surfaces of the clay minerals, or intercalated between the silicate layers. Natural organo-clays also are widely recognized but generally have not been well characterized. Widely used techniques for clay mineral identification involve treatment of the sample with H2 O2 or other oxidant to destroy any associated organics. This generally simplifies and intensifies the XRD pattern of the clay residue, but helps little with the characterization of the original organoclay. Adequate techniques for the direct observation of synthetic and naturally occurring organoclays are yet to be developed.

SEM study of the morphological effects of kinetin and zeatin on the growth and development of the apical meristem in wheat

1995 ◽  
Vol 53 ◽  
pp. 978-979
Author(s):  
G. M. Hutchins ◽  
J. S. Gardner
Keyword(s):  
Growth And Development ◽  
Furfuryl Alcohol ◽  
Apical Meristem ◽  
Plant Cells ◽  
Triticum Aestivum L ◽  
Morphological Development ◽  
Naturally Occurring ◽  
Chinese Spring Wheat ◽  
Sem Study ◽  
Moist Environment

Cytokinins are plant hormones that play a large and incompletely understood role in the life-cycle of plants. The goal of this study was to determine what roles cytokinins play in the morphological development of wheat. To achieve any real success in altering the development and growth of wheat, the cytokinins must be applied directly to the apical meristem, or spike of the plant. It is in this region that the plant cells are actively undergoing mitosis. Kinetin and Zeatin were the two cytokinins chosen for this experiment. Kinetin is an artificial hormone that was originally extracted from old or heated DNA. Kinetin is easily made from the reaction of adenine and furfuryl alcohol. Zeatin is a naturally occurring hormone found in corn, wheat, and many other plants.Chinese Spring Wheat (Triticum aestivum L.) was used for this experiment. Prior to planting, the seeds were germinated in a moist environment for 72 hours.

Fine structure and properties of defects in naturally occurring silicates and oxides

1990 ◽  
Vol 48 (4) ◽  
pp. 460-461
Author(s):  
David R. Veblen
Keyword(s):  
Chemical Reactions ◽  
High Resolution Electron Microscopy ◽  
Extended Defects ◽  
Single Chain ◽  
Naturally Occurring ◽  
Resolution Electron ◽  
Fine Structures ◽  
Image Simulations ◽  
Similar Crystal Structure

Extended defects and interfaces control many processes in rock-forming minerals, from chemical reactions to rock deformation. In many cases, it is not the average structure of a defect or interface that is most important, but rather the structure of defect terminations or offsets in an interface. One of the major thrusts of high-resolution electron microscopy in the earth sciences has been to identify the role of defect fine structures in reactions and to determine the structures of such features. This paper will review studies using HREM and image simulations to determine the structures of defects in silicate and oxide minerals and present several examples of the role of defects in mineral chemical reactions. In some cases, the geological occurrence can be used to constrain the diffusional properties of defects.The simplest reactions in minerals involve exsolution (precipitation) of one mineral from another with a similar crystal structure, and pyroxenes (single-chain silicates) provide a good example. Although conventional TEM studies have led to a basic understanding of this sort of phase separation in pyroxenes via spinodal decomposition or nucleation and growth, HREM has provided a much more detailed appreciation of the processes involved.

Sign in / Sign up

Export Citation Format

Share Document