Drug Discovery Inspired by Mother Nature: Seeking Natural Biochemotypes and the Natural Assembly Rules of the Biochemome
Purpose. The Human Genome Project is producing a new biological ‘periodic table’, which defines all genes for making macromolecules (proteins, DNA, RNA, etc) and the relations between genes and their biological functions. We now need to consider whether to initiate a biochemome project aimed at disc...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2013-08-01
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| Series: | Journal of Pharmacy & Pharmaceutical Sciences |
| Online Access: | https://journals.library.ualberta.ca/jpps/index.php/JPPS/article/view/19137 |
| _version_ | 1797758795926994944 |
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| author | Qiong Gu Xin Yan Jun Xu |
| author_facet | Qiong Gu Xin Yan Jun Xu |
| author_sort | Qiong Gu |
| collection | DOAJ |
| description | Purpose. The Human Genome Project is producing a new biological ‘periodic table’, which defines all genes for making macromolecules (proteins, DNA, RNA, etc) and the relations between genes and their biological functions. We now need to consider whether to initiate a biochemome project aimed at discovering biochemistry’s ‘periodic table’, which would define all molecular parts for making small molecules (natural products) and the relations between the parts and their functions to regulate genes. By understanding the Biochemome, we might be able to design biofunctional molecules based upon a set of molecular parts for drug innovation. Methods. A number of algorithms for processing chemical structures are used to systematically derive chemoyls (natural building blocks) from a database of compounds identified in Traditional Chinese Medicine (TCM). The rules to combine chemoyls for biological activities are then deduced by mining an annotated TCM structure-activity database (ATCMD). Based upon the rules and the basic chemoyls, a chemical library can be biochemically profiled, virtual synthetic routes can be planned, and lead compounds can be identified for a specific drug target. Conclusions. The Biochemome is the complete set of molecular components (chemoyls) in an organism and Biochemomics studies the rules governing their assembly and their evolution, together with the relations between the Biochemome and drug targets. This approach provides a new paradigm for drug discovery that is based on a comprehensive knowledge of the synthetic origins of biochemical diversity, and helps to direct biomimetic syntheses aimed at assembling quasi-natural product libraries for drug screening.
This article is open to POST-PUBLICATION REVIEW. Registered readers (see “For Readers”) may comment by clicking on ABSTRACT on the issue’s contents page. |
| first_indexed | 2024-03-12T18:35:17Z |
| format | Article |
| id | doaj.art-be6e649e1b414a42af11452271b058de |
| institution | Directory Open Access Journal |
| issn | 1482-1826 |
| language | English |
| last_indexed | 2024-03-12T18:35:17Z |
| publishDate | 2013-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Journal of Pharmacy & Pharmaceutical Sciences |
| spelling | doaj.art-be6e649e1b414a42af11452271b058de2023-08-02T08:04:03ZengFrontiers Media S.A.Journal of Pharmacy & Pharmaceutical Sciences1482-18262013-08-0116210.18433/J3C31SDrug Discovery Inspired by Mother Nature: Seeking Natural Biochemotypes and the Natural Assembly Rules of the BiochemomeQiong Gu0Xin Yan1Jun Xu2Research Center for Drug Discovery, School of Pharmaceutical Sciences, and Institute of Human Virology, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou, China.Research Center for Drug Discovery, School of Pharmaceutical Sciences, and Institute of Human Virology, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou, China.Research Center for Drug Discovery, School of Pharmaceutical Sciences, and Institute of Human Virology, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou, China.Purpose. The Human Genome Project is producing a new biological ‘periodic table’, which defines all genes for making macromolecules (proteins, DNA, RNA, etc) and the relations between genes and their biological functions. We now need to consider whether to initiate a biochemome project aimed at discovering biochemistry’s ‘periodic table’, which would define all molecular parts for making small molecules (natural products) and the relations between the parts and their functions to regulate genes. By understanding the Biochemome, we might be able to design biofunctional molecules based upon a set of molecular parts for drug innovation. Methods. A number of algorithms for processing chemical structures are used to systematically derive chemoyls (natural building blocks) from a database of compounds identified in Traditional Chinese Medicine (TCM). The rules to combine chemoyls for biological activities are then deduced by mining an annotated TCM structure-activity database (ATCMD). Based upon the rules and the basic chemoyls, a chemical library can be biochemically profiled, virtual synthetic routes can be planned, and lead compounds can be identified for a specific drug target. Conclusions. The Biochemome is the complete set of molecular components (chemoyls) in an organism and Biochemomics studies the rules governing their assembly and their evolution, together with the relations between the Biochemome and drug targets. This approach provides a new paradigm for drug discovery that is based on a comprehensive knowledge of the synthetic origins of biochemical diversity, and helps to direct biomimetic syntheses aimed at assembling quasi-natural product libraries for drug screening. This article is open to POST-PUBLICATION REVIEW. Registered readers (see “For Readers”) may comment by clicking on ABSTRACT on the issue’s contents page.https://journals.library.ualberta.ca/jpps/index.php/JPPS/article/view/19137 |
| spellingShingle | Qiong Gu Xin Yan Jun Xu Drug Discovery Inspired by Mother Nature: Seeking Natural Biochemotypes and the Natural Assembly Rules of the Biochemome Journal of Pharmacy & Pharmaceutical Sciences |
| title | Drug Discovery Inspired by Mother Nature: Seeking Natural Biochemotypes and the Natural Assembly Rules of the Biochemome |
| title_full | Drug Discovery Inspired by Mother Nature: Seeking Natural Biochemotypes and the Natural Assembly Rules of the Biochemome |
| title_fullStr | Drug Discovery Inspired by Mother Nature: Seeking Natural Biochemotypes and the Natural Assembly Rules of the Biochemome |
| title_full_unstemmed | Drug Discovery Inspired by Mother Nature: Seeking Natural Biochemotypes and the Natural Assembly Rules of the Biochemome |
| title_short | Drug Discovery Inspired by Mother Nature: Seeking Natural Biochemotypes and the Natural Assembly Rules of the Biochemome |
| title_sort | drug discovery inspired by mother nature seeking natural biochemotypes and the natural assembly rules of the biochemome |
| url | https://journals.library.ualberta.ca/jpps/index.php/JPPS/article/view/19137 |
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