Molecules of interest in the fight against COVID-19

At the CCDC we have been deeply saddened by the devastating impact that COVID-19 has had around the world. During these difficult times it has, however, been heart-warming to see the scientific community coming together to try to find a cure and a vaccine.

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.

Blog last updated 3rd February 2021

  • New molecules and additional structures added
  • Cross-link to related blog added.

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:

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.

.

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.

.

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

.

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 

Drug Candidate CSD Refcode
Tranexamic acid AMMCHC10
Dipyridamole BIRKES01
Naproxen COYRUD
Celecoxib DIBBUL
Colchicine DIHSAO (S enantiomer)
Zidovudine FIXGAU
Escin GACZIT
Azvudine HAMCOP
Fingolimod HUCHEU
Camostat JAMREU
Valsartan KIPLIG
Ciclesonide KOJPIJ - solvate EMIQAU, EMIQEY
Pirfenidone KOMJOO
Dexmedetomidine LADTIT
Vitamin c LASCAC
Mefloquine LEBYAT
Tranilast MCMYAN
Methylprednisolone MTHPRG
Acetylcysteine NALCYS
losartan OCAHAC
Azithromycin PILQIN, PILQUZ 
Ebastine QATJIF
Sildenafil QEGTUT
Levamisole SAWJIJ
Nadolol TAYGAC
Itraconazole TEHZIP
Tetrandrine TETRIN11
Thalidomide THALID01
Alpha lipoic acid THOCAR
Lenflunomide VIFQIL
Imatinib mesilate XAVTOF
Tacrolimus FINWEE
Dapagliflozin CIMNUJ, CINSEZ
Hydrocorisone CORTSL, CORTMS
Simvastatin EJEQAL
Sirolimus RAPMCN
Spironolactone ATPRCL01
Indomethacin INDMET
Telmisartan XUYHOO (01)
Famotidine FOGVIG (01-08)
Doxycycline LATQAA - 02 (monohydrate)
Diltiazem GAJKAG
Niclosamide HEBFUR - 01
Atazanavir LISTEP, (also LUQRAS, LUQREW)
Trifluoprazine ZZMHQ
Chlorpromazine , chlorpromazine CPROMZ, 01
Captopril MCPRPL, 01
Etoposide LEZREO
Almitrine KEHBAA
Estradiol ESOURE12
Prazosin WAHJAR
Methotrexate DOJZAD, DOJZAD01
Isotretinoin TUDSIU
Atovaquorine UMOMAL (-03)
Trihexyphenidyl THEXPL
Ramipril QOQWAU
Cyclosporine DEKSAN
Cotrimoxazole SMZTMP
Verapamil CURHOM
Amiodarone DUTRUF

Moxidectin

GETBOW
Artesunate FAHFAV
Colchicine PALYOQ
Melatonin MELATN
Clevudine TEYDAC05
Clavulanate BICLAV10 (Benzyl ester)
Losartan potassium

MOPHAA

Bismuth Potassium Citrate

REGSUS

Oseltamivir

WETLOY (Phosphate)

Amoxicillin

AMOXCT10 (zwitterionic, trihydrate) 

Metformin

ETIVUY (N,N-Dimethylbiguanidium bromide)
JAMRIY (N,N-Dimethylbiguanide hydrochloride)

Noscapine

PUJMOX (rac-β-Noscapine) 

BOVPUA (rac-α-Noscapine)


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

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

Drug candidate CSD Refcode Source of interest
Amantadine BASCOQ DOI: 10.1016/j.mehy.2020.109755
Quercetin monohydrate AKIJEK
Asunaprevir MIYWOI DOI: 10.1016/j.lfs.2020.117652
Bromhexine hydrochloride CUXYID DOI: 10.26633/RPSP.2020.40
Resveratrol DALGON DOI: 10.1080/07391102.2020.1762743 
E)-1-(2,4-di­chloro­phen­yl)-3-[4-(morpholin-4-yl)phen­yl]prop-2-en-1-one TACXOO DOI: 10.1107/S2053229620014217 
Fenofibrate TADLIU DOI: 10.1080/20905068.2020.1785144 
Apremilast (benzoic acid) BOVNUY DOI: 10.1111/dth.13961 
Raloxifene (hydrochloride) SAQYIR DOI: 10.21873/invivo.12135 
Telaprevir  LERJID DOI: 10.1016/j.compbiomed.2020.104186 
Sitagliptin phosphate URAWUH DOI: 10.1016/j.mehy.2020.110111 
Budesonide RHBUXP10 / SHBUXP10 Inhaled corticosteroid added to COVID-19 PRINCIPLE trial 
Bicalutamide JAYCES DOI: 10.1038/s41598-020-77794-5 
Tizoxanide HEVZAL DOI: 10.1038/s41598-020-71634-2