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Chemical Evolution of Natural Product Structure

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

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Summary: In this study, the differences between ring systems from bioactive molecules and common synthetic molecules are analyzed by processing the ring systems extracted from one billion molecules. The bioactive rings are found to be distributed throughout the chemical space, but not uniformly, with several dense regions and empty areas. Additionally, a web tool for interactive navigation and identification of bioisosteric ring analogs in the ring chemical space is described.

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Identification of Inhibitors of Cholesterol Transport Proteins Through the Synthesis of a Diverse, Sterol-Inspired Compound Collection

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Design, Synthesis, and Biological Evaluation of Chemically and Biologically Diverse Pyrroquinoline Pseudo Natural Products

Jie Liu et al.

Summary: This study presents the design and synthesis of a collection of 155 pyrroquinoline pseudo-NPs, combining fragments characteristic of tetrahydroquinoline and pyrrolidine classes in novel arrangements. Cheminformatic analysis and biological evaluation revealed chemically diverse pseudo-NP classes with distinct bioactivity patterns, dependent on fragment connectivity and regioisomeric arrangement.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

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Privileged Biorenewable Secologanin-Based Diversity-Oriented Synthesis for Pseudo-Natural Alkaloids: Uncovering Novel Neuroprotective and Antimalarial Frameworks

Huajian Zhu et al.

Summary: Utilizing secologanin as a starting material, a diversity-oriented synthesis approach was developed to successfully synthesize novel pseudo-natural alkaloids, laying the foundation for producing polycyclic products with multiple chiral centers. These newly constructed molecules showed antimalarial and highly potent neuroprotective properties after preliminary activity screening.

CHEMSUSCHEM (2021)

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Article Chemistry, Medicinal

Pseudonatural Products Occur Frequently in Biologically Relevant Compounds

Jose-Manuel Gally et al.

Summary: This study introduces a new methodology for classifying fragment combinations and characterizing pseudonatural products using Python package. By analyzing the pairwise relative position of fragments within molecules, 18 different possible fragment combination categories were identified. Comparison with natural product references revealed that approximately 23% of biologically relevant compounds in the database comply with the PNP definition.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

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Review Chemistry, Multidisciplinary

Natural Product Synthesis through the Lens of Informatics

Stone Woo et al.

Summary: Retrosynthetic analysis emerged as a teaching tool in the 1960s and remains important in total synthesis; computer-assisted retrosynthesis can accelerate the synthesis of complex structures; the dynamic approach in synthetic target analysis has potential for further development and application.

ACCOUNTS OF CHEMICAL RESEARCH (2021)

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Pseudo Natural Products-Chemical Evolution of Natural Product Structure

George Karageorgis et al.

Summary: PNPs are compounds formed by combining NP fragments in unique ways, inheriting important biological characteristics of NPs while exhibiting unprecedented bioactivity. The importance of design principles, synthesis, and biological research on PNP scaffolds is emphasized. PNPs are considered as a human-driven branch of the evolution of natural product structure.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

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JOURNAL OF MEDICINAL CHEMISTRY (2021)

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Natural products in drug discovery: advances and opportunities

Atanas G. Atanasov et al.

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Trends in Hit-to-Lead Optimization Following DNA-Encoded Library Screens

Christopher A. Reiher et al.

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Yiran Huang et al.

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CHEMBIOCHEM (2021)

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Natural product fragment combination to performance-diverse pseudo-natural products

Michael Grigalunas et al.

Summary: Natural product structure and fragment-based compound development inspire the design of pseudo-natural products through combinations of fragments to create chemically and biologically diverse compound classes. A library of 244 pseudo-natural products was synthesized and evaluated in cell painting essays, revealing the phenotypic role of individual fragments in determining bioactivity.

NATURE COMMUNICATIONS (2021)

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Article Chemistry, Multidisciplinary

Combination of Pseudo-Natural Product Design and Formal Natural Product Ring Distortion Yields Stereochemically and Biologically Diverse Pseudo-Sesquiterpenoid Alkaloids

Jie Liu et al.

Summary: This study describes the synthesis and biological evaluation of a new compound class inspired by natural products, combining the pseudo-natural product design strategy and ring distortion approach. The resulting pseudo-sesquiterpenoid alkaloids are chemically and biologically diverse, with their biological performance dependent on the structure of sesquiterpene lactone-derived scaffolds and the stereochemistry of pyrrolidine fragments. The compound collection led to the discovery of a novel chemotype inhibiting Hedgehog-dependent osteoblast differentiation.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

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Identification of isoform/domain-selective fragments from the selection of DNA-encoded dynamic library

Yu Zhou et al.

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Synthesis of Indofulvin Pseudo-Natural Products Yields a New Autophagy Inhibitor Chemotype

Annina Burhop et al.

Summary: By combining fragments derived from natural products in new ways, a collection of pseudo-NPs known as indofulvins has been created. These compounds define a new chemotype of autophagy inhibitors targeting mitochondrial respiration, showing potential pharmacological properties.

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Slava Ziegler et al.

Summary: Profiling approaches like gene expression or proteome profiling generate unbiased small-molecule bioactivity profiles, which are essential tools in evaluating bioactive compounds. Automated imaging and image analysis can detect morphological alterations induced by small molecules through the detection of hundreds of morphological features in high-throughput experiments. Morphological profiling has gained attention in academia and pharmaceutical industry for predicting compound bioactivity and uncovering unanticipated activities.

CELL CHEMICAL BIOLOGY (2021)

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The chemistry and biology of fungal meroterpenoids (2009-2019)

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Summary: Fungal meroterpenoids are secondary metabolites with diverse chemical structures and potential bioactivities, classified into four categories mainly consisting of polyketide-terpenoids and shikimate-terpenoids. Basidiomycota are major producers of meroterpenoids, with genera like Ganoderma, Penicillium, Aspergillus, and Stachybotrys being dominant. Around 56% of meroterpenoids exhibit significant bioactivities, and some have been developed into clinically used drugs, indicating their potential in drug discovery.

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Natural product-informed exploration of chemical space to enable bioactive molecular discovery

Adam Nelson et al.

Summary: This minireview discusses methods that draw inspiration from natural products to focus on biologically-relevant areas of chemical space, potentially leading to more systematic discovery of unexplored regions in biologically-relevant chemical space.

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Pseudo-natural products and natural product-inspired methods in chemical biology and drug discovery

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Natural product-inspired cascade synthesis yields modulators of centrosome integrity

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Hybrid Molecules Incorporating Natural Products: Applications in Cancer Therapy, Neurodegenerative Disorders and Beyond

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A Small Nonrule of 3 Compatible Fragment Library Provides High Hit Rate of Endothiapepsin Crystal Structures with Various Fragment Chemotypes

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Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success

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Paul A. Wender et al.

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Natural product-likeness score and its application for prioritization of compound libraries

Peter Ertl et al.

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Cheminformatic analysis of natural products and their chemical space

Stefan Wetzel et al.

CHIMIA (2007)

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Charting biologically relevant chemical space: A structural classification of natural products (SCONP)

MA Koch et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

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Purmorphamine induces osteogenesis by activation of the hedgehog signaling pathway

X Wu et al.

CHEMISTRY & BIOLOGY (2004)

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Chemical space and biology

CM Dobson

NATURE (2004)

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Molecular shape diversity of combinatorial libraries: A prerequisite for broad bioactivity

WHB Sauer et al.

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2003)

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Natural product hybrids as new leads for drug discovery

LF Tietze et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2003)

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Property distributions: Differences between drugs, natural products, and molecules from combinatorial chemistry

M Feher et al.

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2003)

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Review Biotechnology & Applied Microbiology

Drug discovery by dynamic combinatorial libraries

O Ramstrom et al.

NATURE REVIEWS DRUG DISCOVERY (2002)

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