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 12th January 2022

  • 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 DOI: 10.1056/NEJMoa2021436

.

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

Drug candidate

CSD Refcode

Source of interest

Clofazimine

DAKXUI

Nature article

Astemizole 

ZENREP

Nature article

Apilimod

CARCAC

Nature article

8-(3-Chlorostyryl)caffeine

KASVUW

Nature article

Tretinoin

VITAAC01

Nature article

Acitretin

NAZLAC01

Nature article

Ibrutinib

BETWUV/BETXEG

www.technologynetworks.com

Oleandrin

BAVJEN/ZAMSOV

cen.acs.org

Zuclopenthixol

CLPNXA

Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19  

Ambroxol

FIYBEV

Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19

Amodiaquine

GIWLII01

Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19

rac-Nebivolol hydrochloride

WEBCEL01

Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19

Vorinostat

IQILAW

Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19

Isoxsuprine hydrochloride

BAHFAR01

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

DOI: 10.1007/s00406-020-01231-x 

Decitabine

EYOJUZ

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

DOI: 10.1016/j.mencom.2020.07.004

Salinomycin (benzylammonium salinomycinate)

IYIJIL

DOI: 10.1038/s41586-021-03491-6

Amantadine

BASCOQ

DOI: 10.1016/j.mehy.2020.109755

Quercetin monohydrate

AKIJEK

DOI: 10.1186/s12950-021-00268-6

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

DOI: 10.1211/PJ.2020.20208609

Bicalutamide

JAYCES

DOI: 10.1038/s41598-020-77794-5 

Tizoxanide

HEVZAL

DOI: 10.1038/s41598-020-71634-2 

Voriconazole

CEXMAU

DOI: 10.1186/s13054-021-03568-8

Dutasteride

SONPAO02

DOI: 10.7759/cureus.13047

Enzalutamide

YEXGEQ

https://clinicaltrials.gov/ct2/show/NCT04475601

2-Deoxy-d-glucose

BECGUL01

DOI: 10.1080/09553002.2020.1818865

TEMPOL

MHPIPO

https://clinicaltrials.gov/ct2/show/NCT04729595

Halofantrine hydrochloride

SATRAG

DOI: 10.1038/s41467-021-23328-0

Mitoguazone sulfate

FEMPAO

DOI: 10.1038/s41467-021-23328-0

22,23-dihydro-avermectin B1a  (Main ivermectin component)

BIFYOF

DOI: 10.1016/j.eclinm.2021.100959

Liothyronine

TITHYN10

DOI: 10.1186/s13054-020-02934-2

Mycophenolate Mofetil

WAJYUC

DOI: 10.1126/sciadv.abh3032

Trimethoprim

AMXBPM

DOI: 10.1126/sciadv.abh3032

Enalaprilat

CIYNIH

DOI: 10.1126/sciadv.abh3032

Moexipril hydrochloride

DOQBUI

DOI: 10.1126/sciadv.abh3032

bazedoxifene acetate

IZOJUF

DOI: 10.1021/acs.chemmater.1c00584

Pentoxifylline

JAKGEH

DOI: 10.1111/crj.13363

Theophylline

THEOPH05

DOI: 10.1111/crj.13363

Dihydromyricetin

SIMVOA

DOI: 10.1016/j.phymed.2021.153704

Artemisinin

QNGHSU

DOI: 10.1038/s41598-021-93361-y

Nafamostat mesylate

HAMJAK

DOI: 10.1128/AAC.00754-20

Blonanserin

MUSRUN

DOI: 10.1073/pnas.2024302118

Hypericin pyridinium

PIRLUX

DOI: 10.1073/pnas.2024302118

Emodin

ETANIY

DOI: 10.1073/pnas.2024302118

N4-Hydroxycytidine

BAMYEX

DOI: 10.1038/s41467-021-23328-0

Metenkefalin

FABJIB

https://clinicaltrials.gov/ct2/show/NCT04374032

triglycidyl isocyanurate

QEVVUI

DOI: 10.1126/science.abf7945

Pterostilbene

QAHWUU

DOI: 10.3390/v13071335

Sulfasalazine

QIJZOY

DOI: 10.1126/sciadv.abh3032

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)

Raltegravir potassium

URAVIU

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