25COVID-19 virus is the cause of a debilitating and life-threatening infectious 26 pulmonary disease that is now responsible for a global pandemic. Currently, there are 27 no specific drugs or vaccines to contain this virus. The main protease (M pro ) of COVID-28 19 virus is a key enzyme, which plays an essential role in viral replication and 29 transcription, making it an ideal drug target. An FDA-approved antineoplastic drug, 30 carmofur, has been identified as an inhibitor that targets COVID-19 virus M pro .
31However, its inhibitory mechanism is unknown. Here, we report the 1.6-Ă
crystal 32 structure of COVID-19 virus M pro in complex with carmofur. The crystal structure 33 shows that carmofur contains an electrophilic carbonyl reactive group, which 34 covalently binds to C145, a member of the catalytic dyad. As a result, its fatty acid tail 35 occupies the hydrophobic S2 subsite of M pro whilst its 5-fluorouracil head is cleaved as 36 product of the new covalent bond that has formed. Carmofur is active in a cell based 37 antiviral assay with an EC50 of 24.87 ÎŒM. It is therefore a promising lead compound 38 for the development of new antivirals to target COVID-19. : bioRxiv preprint 41 Starting in December 2019, a highly infectious viral disease has now spread and 42 reached over 200 countries leading to a global public health emergency and pandemic.
43The etiological agent of the disease is a coronavirus (identified as .
44According to the WHO COVID-2019 Situation Report-77, there were 1,210,956 45 confirmed cases and 67,594 deaths, with a mortality rate at 5.58%. The number of 46 confirmed cases worldwide continues to grow at a rapid rate and is far from peaking.
47However, there are no specific drugs or vaccines available to control symptoms or the 48 spread of this disease.
49The COVID-19 virus has a ~30,000 nt RNA genome encoded with two translation 50 products, polyproteins 1a and 1ab (pp1a and pp1ab) which are crucial for replication 51 and transcription 1,2 . These polyproteins become matured non-structural and structural 52 proteins through auto-cleavage by the main protease (M pro ) and by a papain-like 53 protease 3 . Because of this, M pro is an excellent target for anti-coronavirus (CoV) drug 54 development 4-6 . In order to rapidly discover new drug leads that target COVID-19 virus 55 M pro , our group screened over 10,000 compounds from a library that consisted of 56 approved drugs, drug candidates in clinical trials, and other pharmacologically active 57 compounds. Amongst these we identified carmofur as compound that can inhibit M pro 58 with an IC50 of 1.82 ÎŒM 7 .
59Carmofur is an FDA-approved antineoplastic drug, and a derivative of 5-60 fluorouracil (5-FU) a widely drug used against solid cancers. 5-FU is especially 61 efficient for controlling head, neck, and gastrointestinal tumors 8 . Carmofur (Figure 1A) 62 is a derivative of this compound and has been used in colon cancer therapy since 1981 9 .
63Clinical research has also shown that carmofur has a curative effect on breast, gastri...