A chemoinformatic analysis of atoms, scaffolds and functional groups in natural products

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Joelle Ngo Hanna ◽  
Boris D. Bekono ◽  
Luc C. O. Owono ◽  
Flavien A. A. Toze ◽  
James A. Mbah ◽  
...  
Keyword(s):  
Natural Products ◽  
Drug Discovery ◽  
Physicochemical Properties ◽  
Functional Groups ◽  
Atomic Composition ◽  
Synthetic Compounds ◽  
Chemical Libraries ◽  
Synthetic Drugs ◽  
Drugs Analysis ◽  
Chemical Class

Abstract In the quest to know why natural products (NPs) have often been considered as privileged scaffolds for drug discovery purposes, many investigations into the differences between NPs and synthetic compounds have been carried out. Several attempts to answer this question have led to the investigation of the atomic composition, scaffolds and functional groups (FGs) of NPs, in comparison with synthetic drugs analysis. This chapter briefly describes an atomic enumeration method for chemical libraries that has been applied for the analysis of NP libraries, followed by a description of the main differences between NPs of marine and terrestrial origin in terms of their general physicochemical properties, most common scaffolds and “drug-likeness” properties. The last parts of the work describe an analysis of scaffolds and FGs common in NP libraries, focusing on huge NP databases, e.g. those in the Dictionary of Natural Products (DNP), NPs from cyanobacteria and the largest chemical class of NP – terpenoids.

scholarly journals Fragment Library of Natural Products and Compound Databases for Drug Discovery

Biomolecules ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1518 ◽  
Author(s):  
Ana L. Chávez-Hernández ◽  
Norberto Sánchez-Cruz ◽  
José L. Medina-Franco
Keyword(s):  
Natural Products ◽  
Drug Discovery ◽  
Synthetic Compounds ◽  
Drug Candidates ◽  
Compound Libraries ◽  
Chemical Database ◽  
Fragment Library ◽  
Further Development ◽  
Fragment Libraries ◽  
Fragment Based Drug Discovery

Natural products and semi-synthetic compounds continue to be a significant source of drug candidates for a broad range of diseases, including coronavirus disease 2019 (COVID-19), which is causing the current pandemic. Besides being attractive sources of bioactive compounds for further development or optimization, natural products are excellent substrates of unique substructures for fragment-based drug discovery. To this end, fragment libraries should be incorporated into automated drug design pipelines. However, public fragment libraries based on extensive collections of natural products are still limited. Herein, we report the generation and analysis of a fragment library of natural products derived from a database with more than 400,000 compounds. We also report fragment libraries of a large food chemical database and other compound datasets of interest in drug discovery, including compound libraries relevant for COVID-19 drug discovery. The fragment libraries were characterized in terms of content and diversity.

scholarly journals BIOFACQUIM: A Mexican Compound Database of Natural Products

Biomolecules ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 31 ◽  
Author(s):  
B. Pilón-Jiménez ◽  
Fernanda Saldívar-González ◽  
Bárbara Díaz-Eufracio ◽  
José Medina-Franco
Keyword(s):  
Natural Products ◽  
Drug Discovery ◽  
Physicochemical Properties ◽  
Chemical Space ◽  
Structural Diversity ◽  
Proof Of Concept ◽  
Molecular Fingerprints ◽  
The Public ◽  
Compound Database

Compound databases of natural products have a major impact on drug discovery projects and other areas of research. The number of databases in the public domain with compounds with natural origins is increasing. Several countries, Brazil, France, Panama and, recently, Vietnam, have initiatives in place to construct and maintain compound databases that are representative of their diversity. In this proof-of-concept study, we discuss the first version of BIOFACQUIM, a novel compound database with natural products isolated and characterized in Mexico. We discuss its construction, curation, and a complete chemoinformatic characterization of the content and coverage in chemical space. The profile of physicochemical properties, scaffold content, and diversity, as well as structural diversity based on molecular fingerprints is reported. BIOFACQUIM is available for free.

scholarly journals Natural Products Are a Promising Source for Anthelmintic Drug Discovery

Biomolecules ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1457
Author(s):  
K. L. T. Dilrukshi Jayawardene ◽  
Enzo A. Palombo ◽  
Peter R. Boag
Keyword(s):  
Natural Products ◽  
Drug Discovery ◽  
Folk Medicine ◽  
Parasitic Nematodes ◽  
Control Cost ◽  
Synthetic Compounds ◽  
Anthelmintic Drug ◽  
Drug Classes ◽  
Almost All ◽  
Promising Source

Parasitic nematodes infect almost all forms of life. In the human context, parasites are one of the major causative factors for physical and intellectual growth retardation in the developing world. In the agricultural setting, parasites have a great economic impact through a reduction in livestock performance or control cost. The main method of controlling these devastating conditions is the use of anthelmintic drugs. Unfortunately, there are only a few anthelmintic drug classes available in the market and significant resistance has developed in most of the parasitic species of livestock. Therefore, development of new anthelmintics with different modes of action is critical for sustainable parasitic control in the future. The drug development pipeline is broadly limited to two types of molecules, namely synthetic compounds and natural plant products. Compared to synthetic compounds, natural products are highly diverse, and many have historically proven valuable in folk medicine to treat various gastrointestinal ailments. This review focus on the use of traditional knowledge-based plant extracts in the development of new therapeutic leads, the approaches used as screening techniques, and common bottlenecks and opportunities in plant-based anthelmintic drug discovery.

scholarly journals A review on antifungal agents against Candida albicans and Aspergillus niger

2021 ◽  
Vol 2 (1) ◽  
pp. 042-054
Author(s):  
Vishnuvardhini R ◽  
Priya R Iyer
Keyword(s):  
Cell Wall ◽  
Natural Products ◽  
Candida Albicans ◽  
Aspergillus Niger ◽  
Amphotericin B ◽  
Antifungal Agents ◽  
Fungal Infections ◽  
Natural Compounds ◽  
Synthetic Compounds ◽  
Synthetic Drugs

Candidiasis is the fungal infection caused by Candida albicans. It causes different type of candidiasis infections in the blood, heart, eyes, brain, bones also other parts of our body. Different types of candidiasis are vaginal candidiasis, pulmonary candidiasis, oral candidiasis. It may be acute or chronic. It can be cured by using natural compounds or synthetic compounds or semisynthetic compounds. Apergillosis is the fungal infections in human caused by Aspergillus niger. Aspergillosis infections are classified into allergic pulmonary sinusitis, cutaneous aspergillosis, invasive aspergillosis, chronic necrotising pulmonary aspergillosis can be cured by using synthetic compounds like intravenous injections, oral medicines of capsules, tropical medicines like creams and some other natural products from plants. Natural products like saponins, flavonoids, alkaloids, xanthones, lectins and polypeptides, quinones, terpenoids, coumarins, essential oils and other compounds are the secondary metabolites extracted from the plants. Those plants are effective against fungal infections. Synthetic drugs like Azole group of drugs composed of imidazoles which includes miconazole, clotrimazole, ketoconazole, and triazoles include itraconazole, Posaconazole, isavuconazole are used to inhibit the ergosterol synthesis of cell membrane of fungi. Echinocandins are antifungal agent and it is used to disrupt the cell wall of fungi and inhibiting the synthesis of beta- 1,3 glucan fungal cell wall. Echinocandins are classified into caspofungin, anidulafungin, micafungin which having antifungal activity and amphotericin B used to treat both candidiasis and aspergillosis. Combination of drugs like synthetic drugs and natural compounds used to treat Candidiasis and Aspergillosis. Comparison and effectiveness of drugs depends upon the infections they are getting affected. Amphotericin B and azole group of drugs are commonly more effective than other group of drugs, but ketoconazole is widely used. Adverse effects of antifungal agents include, skin rashes, irritation, itching, nausea and vomiting, fever, abdominal pain, muscle and joint pain, etc.

scholarly journals BIOFACQUIM: A Mexican Compound Database of Natural Products

2018 ◽  
Author(s):  
B. Angélica Pilón-Jiménez ◽  
Fernanda I. Saldívar-González ◽  
Bárbara I. Díaz-Eufracio ◽  
José L. Medina-Franco
Keyword(s):  
Natural Products ◽  
Drug Discovery ◽  
Physicochemical Properties ◽  
Chemical Space ◽  
Structural Diversity ◽  
Molecular Fingerprints ◽  
Natural Origin ◽  
The Public ◽  
Compound Database

Compound databases of natural products have a major impact on drug discovery projects and other areas of research. The number of databases in the public domain with compounds from natural origin is increasing. Several countries have initiatives in place to construct and maintain compound databases that are representative of their diversity. Examples are Brazil, France, Panama and recently Vietnam. Herein, we discuss the first version of BIOFACQUIM, a novel compound database with natural products isolated and characterized in Mexico. We discuss its construction, curation, and a complete chemoinformatic characterization of the content and coverage in chemical space. It is reported the profile of physicochemical properties, scaffold content, and diversity, as well as structural diversity based on molecular fingerprints. BIOFACQUIM is freely available.

Potential for Treatment of Neurodegenerative Diseases with Natural Products or Synthetic Compounds that Stabilize Microtubules

2020 ◽  
Vol 26 (35) ◽  
pp. 4362-4372
Author(s):  
John H. Miller ◽  
Viswanath Das
Keyword(s):  
Natural Products ◽  
Neurodegenerative Diseases ◽  
In Vivo Models ◽  
Synthetic Compounds ◽  
Stabilizing Agents ◽  
Animal Models Of Disease ◽  
Model Studies ◽  
Models Of Disease

No effective therapeutics to treat neurodegenerative diseases exist, despite significant attempts to find drugs that can reduce or rescue the debilitating symptoms of tauopathies such as Alzheimer’s disease, Parkinson’s disease, frontotemporal dementia, amyotrophic lateral sclerosis, or Pick’s disease. A number of in vitro and in vivo models exist for studying neurodegenerative diseases, including cell models employing induced-pluripotent stem cells, cerebral organoids, and animal models of disease. Recent research has focused on microtubulestabilizing agents, either natural products or synthetic compounds that can prevent the axonal destruction caused by tau protein pathologies. Although promising results have come from animal model studies using brainpenetrant natural product microtubule-stabilizing agents, such as paclitaxel analogs that can access the brain, epothilones B and D, and other synthetic compounds such as davunetide or the triazolopyrimidines, early clinical trials in humans have been disappointing. This review aims to summarize the research that has been carried out in this area and discuss the potential for the future development of an effective microtubule stabilizing drug to treat neurodegenerative disease.

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