Molecules of interest in the fight against COVID-19

Please note: these molecules are still being investigated and are not currently approved for treatment. This article presents early stage research for information only, and is not intended to give any medical advice.

Various teams at the CCDC are already working on several ideas to support global COVID-19 efforts and have been delighted to hear from some of our users about research they are doing using the Cambridge Structural Database (CSD) and our software to help fight the COVID-19 pandemic.

Amazingly there are already several potential vaccines and small molecule drug candidates for COVID-19 and so we thought we would seek out some of these structures in the CSD in case they are of use to others. Each individual structure is freely available in the CSD with curated chemical information such as a 2D diagram as well as the underlying dataset with coordinates from our free Access Structures service.

The table at the bottom of this page shows some of the structures we have found in the CSD so far.

About the data

For structures where we have identified that the compound is being investigated as a potential candidate, we have also added additional text in the bioactivity field to make the structures as easy as possible for users to find. For example, CSD Refcode DOHVED now has “Favipiravir was investigated in 2020 as a potential candidate to target COVID-19 (coronavirus)” added to the bioactivity field in the CSD.

You can also use the CSD to find similar structures, for example a similarity search for Chloroquine results in 26 hits with a number of the similar structures already having known bioactivity, these include CSD Refcode GOMRIJ which is an active anti-malarial aminoquinoline, CSD Refcode LURGUA which is a potent bisquinoline anti-malarial agent and CSD Refcode BIDSIS which has antitumour and antimycobacterial activity.

If you would like more information about how to perform similarity searches using our advanced online WebCSD search system we have a number of FAQs to help to get you started including:

• How does the similarity search work?
• What should I sketch for a similarity search?
• What are the strengths/weaknesses of similarity searching in WebCSD?
• WebCSD information page

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Keep in touch and get involved

We will try to keep up with research activities to help ensure the CSD is as informative as possible. If you spot a new candidate small molecule structure then you can tweet us using @ccdc_cambridge or email us to let us know.

Anyone can also freely search the CSD based on a Drug Name on our Access Structures service where they can also download the associated CIF.

Do let us know if you are using the CSD and software to help fight COVID-19, or if you want to collaborate with us get in touch using hello@ccdc.cam.ac.uk.

.You may also be interested in our other blogs on COVID-19.

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These structures are of interest in early stage research only.

This article is not to be taken as medical advice.

Drug Candidate	CSD Refcode	Are there other structures containing this drug candidate?	Reference to COVID-19 research	Image of the structure in CSD
Ritonavir	YIGPIO	Yes	Liu et al, ACS Cent. Sci. 2020, 6, 3, 315-331
Darunavir	NISTIV	Yes	Liu et al, ACS Cent. Sci. 2020, 6, 3, 315-331
Favipiravir	DOHVED	No	Liu et al, ACS Cent. Sci. 2020, 6, 3, 315-331
Remdesivir	ZARNAK	No	Liu et al, ACS Cent. Sci. 2020, 6, 3, 315-331
Ribavirin	VIRAZL	Yes	Liu et al, ACS Cent. Sci. 2020, 6, 3, 315-331
Arbidol	SAJPOK	Yes	Liu et al, ACS Cent. Sci. 2020, 6, 3, 315-331
Chloroquine	CDMQUI	Yes	Liu et al, ACS Cent. Sci. 2020, 6, 3, 315-331
Nitazoxanide	QUZWOY	Yes	Liu et al, ACS Cent. Sci. 2020, 6, 3, 315-331
Umifenovir	SIYSEA	Yes	Lu, H., BioSci Trends, 2020, 16;14(1), 69-71
Triazavirin	NOXCUB	No	Vincent, M. J. et al, Virol J., 2005, 2, 69
Penciclovir	YACGUE	Yes	Wang, M. et al, Cell Research, 2020, 30, 269-271
Indinavir	DIJWOJ	Yes	Chang,Y. et al, Pharmacology & Toxicology, preprint, February 2020
Ebselen	SENGOH	Yes	Jin, Z. et al, BioRXiv preprint, March 2020
Sofosbuvir	CUZROG	Yes	Elfiky, A., Life Sciences, 2020, 248, 117477
Dexamethasone	DEXMET11	Yes
Clofazimine	DAKXUI	Yes
Astemizole	ZENREP
Apilimod	CARCAC

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Additional structures identified from 'Global Coronavirus COVID-19 Clinical Trial Tracker' (www.covid19-trials.com) by Cytel

Every structure in the table below can be accessed freely by searching for the CSD Refcode in our Access Structures service - www.ccdc.cam.ac.uk/structures 

The articles we used to compile this list so far are:

• https://pubs.acs.org/doi/10.1021/acscentsci.0c00272Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases, ACS Cent. Sci.
• https://blog.drugbankplus.com/data-driven-approaches-to-identify-potential-covid-19-therapies/DrugBank white paper
• https://doi.org/10.1038/s41422-020-0282-0
• http://www.ox.ac.uk/news/2020-03-23-first-patients-enrolled-new-clinical-trial-possible-covid-19-treatments(oxford clinical trial)
• https://www.preprints.org/manuscript/202002.0242/v2
• https://arxiv.org/abs/2003.00163
• https://doi.org/10.1101/2020.02.26.964882