scholarly journals Sanitize It Yourself: human-based sanitization checker against machine-generated chemical structures

2021 ◽  
Author(s):  
Naruki Yoshikawa ◽  
Kentaro Rikimaru ◽  
Kazuki Yamamoto
Keyword(s):  
Deep Learning ◽  
Drug Design ◽  
Web Application ◽  
Chemical Space ◽  
Computer Aided Drug Design ◽  
Chemical Structures ◽  
Structural Formulas ◽  
Computer Aided ◽  
Novel Structures

Many computer-aided drug design (CADD) methods using deep learning have recently been proposed to explore the chemical space toward novel scaffolds efficiently. However, there is a tradeoff between the ease of generating novel structures and the chemical feasibility of structural formulas. To overcome the limitations of computational filtering, we have implemented a web application that allows easy compound sanitization by humans. The application is available at https://sanitizer.chemical.space/.

scholarly journals Sanitize It Yourself: Web-based molecular sanitization for machine-generated chemical structures

2021 ◽  
Author(s):  
Naruki Yoshikawa ◽  
Kentaro Rikimaru ◽  
Kazuki Yamamoto
Keyword(s):  
Deep Learning ◽  
Web Service ◽  
Chemical Space ◽  
Computer Aided Drug Design ◽  
Web Based ◽  
Chemical Structures ◽  
Structural Formulas ◽  
Computer Aided ◽  
Novel Structures ◽  
The Web

Many computer-aided drug design (CADD) methods using deep learning have recently been proposed to explore the chemical space toward novel scaffolds efficiently. However, there is a tradeoff between the ease of generating novel structures and the chemical feasibility of structural formulas. To overcome the limitations of computational filtering, we have implemented a web-based software in which users can share and evaluate computer-generated compounds. The web service is available at https://sanitizer.chemical.space/.

Computer-Aided Drug Design Applied to Secondary Metabolites as Anticancer Agents

2020 ◽  
Vol 20 (19) ◽  
pp. 1677-1703
Author(s):  
Rodrigo Santos Aquino de Araújo ◽  
Edeildo Ferreira da Silva-Junior ◽  
Thiago Mendonça de Aquino ◽  
Marcus Tullius Scotti ◽  
Hamilton M. Ishiki ◽  
...  
Keyword(s):  
Drug Design ◽  
Anticancer Agents ◽  
Cost Reduction ◽  
Computer Aided Drug Design ◽  
Structure Based Drug Design ◽  
Chemical Structures ◽  
Computer Aided ◽  
Low Costs ◽  
New Compounds

: Computer-Aided Drug Design (CADD) techniques have garnered a great deal of attention in academia and industry because of their great versatility, low costs, possibilities of cost reduction in in vitro screening and in the development of synthetic steps; these techniques are compared with highthroughput screening, in particular for candidate drugs. The secondary metabolism of plants and other organisms provide substantial amounts of new chemical structures, many of which have numerous biological and pharmacological properties for virtually every existing disease, including cancer. In oncology, compounds such as vimblastine, vincristine, taxol, podophyllotoxin, captothecin and cytarabine are examples of how important natural products enhance the cancer-fighting therapeutic arsenal. : In this context, this review presents an update of Ligand-Based Drug Design and Structure-Based Drug Design techniques applied to flavonoids, alkaloids and coumarins in the search of new compounds or fragments that can be used in oncology. : A systematical search using various databases was performed. The search was limited to articles published in the last 10 years. : The great diversity of chemical structures (coumarin, flavonoids and alkaloids) with cancer properties, associated with infinite synthetic possibilities for obtaining analogous compounds, creates a huge chemical environment with potential to be explored, and creates a major difficulty, for screening studies to select compounds with more promising activity for a selected target. CADD techniques appear to be the least expensive and most efficient alternatives to perform virtual screening studies, aiming to selected compounds with better activity profiles and better “drugability”.

Computer Aided Drug Design Approaches for Identification of Novel Autotaxin (ATX) Inhibitors

2016 ◽  
Vol 23 (17) ◽  
pp. 1708-1724 ◽  
Author(s):  
Eleni Vrontaki ◽  
Georgia Melagraki ◽  
Eleanna Kaffe ◽  
Thomas Mavromoustakos ◽  
George Kokotos ◽  
...  
Keyword(s):  
Drug Design ◽  
Computer Aided Drug Design ◽  
Computer Aided

Prospects for Discovering the Secondary Metabolites of Cordyceps Sensu Lato by the Integrated Strategy

2020 ◽  
Vol 17 (2) ◽  
pp. 97-120
Author(s):  
Shabana Bibi ◽  
Yuan-Bing Wang ◽  
De-Xiang Tang ◽  
Mohammad Amjad Kamal ◽  
Hong Yu
Keyword(s):  
Drug Design ◽  
Biological Activities ◽  
Design Methods ◽  
Chinese Herbs ◽  
Active Metabolites ◽  
Computer Aided Drug Design ◽  
Design Concepts ◽  
Conventional Drug ◽  
Computer Aided ◽  
Design Techniques

: Some species of Cordyceps sensu lato are famous Chinese herbs with significant biological activities, often used as edible food and traditional medicine in China. Cordyceps represents the largest entomopathogenic group of fungi, including 40 genera and 1339 species in three families and incertae sedis of Hypocreales. Objective: Most of the Cordyceps-derivatives have been approved clinically for the treatment of various diseases such as diabetes, cancers, inflammation, cardiovascular, renal and neurological disorders and are used worldwide as supplements and herbal drugs, but there is still need for highly efficient Cordyceps-derived drugs for fatal diseases with approval of the U.S. Food and Drug Administration. Methods: Computer-aided drug design concepts could improve the discovery of putative Cordyceps- derived medicine within less time and low budget. The integration of computer-aided drug design methods with experimental validation has contributed to the successful discovery of novel drugs. Results: This review focused on modern taxonomy, active metabolites, and modern drug design techniques that could accelerate conventional drug design and discovery of Cordyceps s. l. Successful application of computer-aided drug design methods in Cordyceps research has been discussed. Conclusion: It has been concluded that computer-aided drug design techniques could influence the multiple target-focused drug design, because each metabolite of Cordyceps has shown significant activities for the various diseases with very few or no side effects.

Zoning in on Tankyrases: A Brief Review on the Past, Present and Prospective Studies

2020 ◽  
Vol 19 (16) ◽  
pp. 1920-1934
Author(s):  
Xylia Q. Peters ◽  
Thembeka H. Malinga ◽  
Clement Agoni ◽  
Fisayo A. Olotu ◽  
Mahmoud E.S. Soliman
Keyword(s):  
Drug Design ◽  
Small Molecule ◽  
Small Molecule Inhibitors ◽  
Design Methods ◽  
Selective Inhibitors ◽  
Computer Aided Drug Design ◽  
Cellular Processes ◽  
Conventional Drug ◽  
Computer Aided ◽  
Tankyrase 1

Background: Tankyrases are known for their multifunctionalities within the poly(ADPribose) polymerases family and playing vital roles in various cellular processes which include the regulation of tumour suppressors. Tankyrases, which exist in two isoforms; Tankyrase 1 and 2, are highly homologous and an integral part of the Wnt β -catenin pathway that becomes overly dysregulated when hijacked by pro-carcinogenic machineries. Methods: In this review, we cover the distinct roles of the Tankyrase isoforms and their involvement in the disease pathogenesis. Also, we provide updates on experimentally and computationally derived antagonists of Tankyrase whilst highlighting the precedence of integrative computer-aided drug design methods towards the discovery of selective inhibitors. Results: Despite the high prospects embedded in the therapeutic targeting and blockade of Tankyrase isoforms, the inability of small molecule inhibitors to achieve selective targeting has remained a major setback, even until date. This explains numerous incessant drug design efforts geared towards the development of highly selective inhibitors of the respective Tankyrase isoforms since they mediate distinct aberrancies in disease progression. Therefore, considering the setbacks of conventional drug design methods, can computer-aided approaches actually save the day? Conclusion: The implementation of computer-aided drug design techniques in Tankyrase research could help complement experimental methods and facilitate ligand/structure-based design and discovery of small molecule inhibitors with enhanced selectivity.

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