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

Note: you can now access the structures through the COVID-19 drug subset on our desktop software, and in the CSD-Python API. Learn more here.

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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	Yes	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	Nature article
Astemizole	ZENREP		Nature article
Apilimod	CARCAC		Nature article
8-(3-Chlorostyryl)caffeine	KASVUW		Nature article
Tretinoin	VITAAC01	Yes	Nature article
Acitretin	NAZLAC01	Yes	Nature article
Ibrutinib	BETWUV/BETXEG	Yes	www.technologynetworks.com
Oleandrin	BAVJEN/ZAMSOV	Yes	cen.acs.org
Zuclopenthixol	CLPXNA		Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19
Ambroxol	FIYBEV	Yes	Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19
Amodiaquine	GIWLII01	Yes	Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19
rac-Nebivolol hydrochloride	WEBCEL01	Yes	Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19
Vorinostat	IQILAW	Yes	Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19
Isoxsuprine hydrochloride	BAHFAR01	Yes	Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19
Ciprofloxacin	COVPIN01		Ciprofloxacin and moxifloxacin article Azithromycin and ciprofloxacin article
Moxifloxacin hydrochloride	ABABIQ		Scientific Report
Ganciclovir	UGIVAI01		J. Thorac Imaging article
Bepridil hydrochloride	CEZBAK		DOI:10.1073/pnas.2012201118
Pimozide perchlorate	PIMOZD		DOI:10.1073/pnas.2012201118
Rimonabant	RIFBAL		DOI:10.1073/pnas.2012201118
Zopiclone	CUHNEY23		DOI:10.1073/pnas.2012201118
Saquinavir chloride	WUTSUB		DOI:10.1073/pnas.2012201118
Clemastine hydrogen fumarate	CLEMAS02		DOI:10.1073/pnas.2012201118
Metixene hydrochloride	METHIX10		DOI:10.1073/pnas.2012201118
Duloxetine hydrochloride	MUCDUK		DOI:10.1073/pnas.2012201118
Donepezil	SUBTIS(01-05)		DOI: 10.1007/s00406-020-01231-x
Decitabine	EYOJUZ(01)		ClinicalTrials.gov
Tramadol	BUFPAV		DOI: 10.1016/j.mehy.2020.110468 clinicaltrials.gov
Emtricitabine	HAKJIM		DOI:10.1093/ofid/ofaa455
Tenofovir disoproxil (fumaric acid)	DUXSAR		DOI:10.1093/ofid/ofaa455
Tenofovir alafenamide	BUKQOQ		DOI: 10.1093/ofid/ofaa455
Fluoxetine hydrochloride	FUDCOW		DOI: 10.1111/bph.15418
Ifenprodil	KAHFAB		DOI: 10.1126/science.abf7945
Tolperisone hydrochloride	SIFGIY		DOI: 10.1126/science.abf7945
Disulfiram	ETHUSS(01-05)		DOI: 10.1016/j.mencom.2020.07.004
Salinomycin (benzylammonium salinomycinate )	IYIJIL		DOI: 10.1038/s41586-021-03491-6

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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

Other structures of interest to COVID-19 based on research papers are listed below: