Post Date
Jul 23 2024

Discovering Direct-Acting Anti-viral Potential Drugs by Targeting Dengue Virus Protease and SARS-CoV-2 Main Protease

Dr. Muhammad Saeed
Farwa Batool
Reference / Filters
Chemistry & Chemical Engineering


Pakistan has been experiencing frequent epidemics of viral infections due to the prevalence of several pathogenic viruses including but not limited to flavivirus (Dengue virus, DENV), hepatitis C virus (HCV), and most recently the severe acute respiratory syndrome-corona virus-2 (SARS-COV-2). The lack of both universally effective pan-DENV vaccine and specific anti-dengue drugs has caused flaviviral infection as serious public health concern. A very recent global pandemic of COVID-19, caused by a special bat-transmitted strain of corona viruses, has further aggravated the situation, and calls for an earnest effort towards the development of antiviral therapeutics.

The research presented in this thesis aims at discovering direct-acting antivirals against Dengue virus (DENV) and Coronavirus by targeting their reproductively essential proteins, commonly known as proteases. Owing to the immense utility of small molecule inhibitors in drug discovery approach, 2 libraries of small molecule inhibitors, belonging to the heterocyclic class of organic compounds, namely 1,2-benzisothiazolones (BITs) and 1,3-benzothiazinones (BTZs), were synthesized via a novel one-pot two-step synthetic route. To extend the chemical landscape, 4 additional libraries of heterocyclic rings containing privileged scaffolds such as sulfonamides, oxadiazoles, and phthalimides were included in the synthetic library of more than 50 compounds. Initial screening using the biochemical assays against dengue virus protease resulted in the identification of several BITS, and oxadiazole-sulfonamide hybrids as hits. The compounds showing promising DENV protease inhibition in the biochemical assay were further tested for the replication inhibition of infectious DENV in cell culture-based infectivity assay. Two of the synthesized BITs and none of the oxadiazol-sulfonamide hybrids were found to suppress DENV replication and viral infectivity rendering their potential to develop into new anti-dengue therapeutics. All the synthesized compounds were subjected to screening for drug-like properties using online SwissADME model, demonstrating favorable pharmaceutical properties.

Amidst the COVID-19 pandemic associated lockdown, from March-August 2020, in Pakistan, we diverted our attention towards the discovery of inhibitors of SARS-COV-2 main protease. In this context, multiple libraries of synthesized flavonoids, thioflavonoids, and BITs were subjected to in-silico screening against SARS-CoV-2 main protease (3C-Like protease or Mpro) to find potential therapeutics against the COVID-19. The compounds were short-listed by virtual screening and then filtered through the SwissADME modelling tool to eliminate the compounds with unfavorable pharmacokinetics. The top binders of SARS-CoV-2 Mpro with favorable drug-like properties were selected using iterative docking analyses. A thioflavonol derivative was found to be a potential hit for the inhibition of Mpro after molecular dynamic (MD) simulation studies and free binding energy calculations. Further computational modelling revealed the mode of binding and atomic level interactions between the Mpro and the identified hits. These in silico studies demonstrated that the flavonols have a potential of inhibiting the Mpro and in turn may inhibit the replication of SARS-COV-2. This thesis significantly contributes to the field of medicinal chemistry by demonstrating novel findings about potential therapeutics against flaviviruses and corona virus by 

(i) efficiently synthesizing and evaluating different libraries of heterocyclic compounds against flaviviruses, 

(ii) providing a detailed computational assessment of the selectively designed inhibitors against corona viruses. These accomplishments may pave the way towards the development of anti-dengue and anti-COVID-19 therapeutics.


1. Batool, F.; Saeed, M.; Saleem, H. N.; Kirschner, L.; Bodem, J., Facile Synthesis and In Vitro Activity of N-Substituted 1, 2-Benzisothiazol-3 (2H)-ones against Dengue Virus NS2BNS3 Protease. Pathogens 2021,10 (4), 464.

2. Batool, F.; Mughal, E. U.; Zia, K.; Sadiq, A.; Naeem, N.; Javid, A.; Ul-Haq, Z.; Saeed, M., Synthetic flavonoids as potential antiviral agents against SARS-CoV-2 main protease. Journal of Biomolecular Structure and Dynamics 2020, 1-12.

3. Saleem, H. N.; Batool, F.; Mansoor, H. J.; Shahzad-ul-Hussan, S.; Saeed, M., Inhibition of Dengue Virus Protease by Eugeniin, Isobiflorin, and Biflorin Isolated from the Flower Buds of Syzygium aromaticum (Cloves). Acs Omega 2019, 4 (1), 1525-1533.

4. Hamdani, S. S.; Khan, B. A.; Hameed, S.; Batool, F.; Saleem, H. N.; Mughal, E. U.; Saeed, M., Synthesis and evaluation of novel S-benzyl-and S-alkylphthalimide-oxadiazolebenzenesulfonamide hybrids as inhibitors of dengue virus protease. Bioorganic Chemistry 2020, 96, 103567.

5. Younus, H. A.; Hameed, A.; Mahmood, A.; Khan, M. S.; Saeed, M.; Batool, F.; Asari, A.; Mohamad, H.; Pelletier, J.; Sévigny, J., Sulfonylhydrazones: Design, Synthesis and Investigation of Ectonucleotidase (ALP & e5′ NT) Inhibition Activities. Bioorganic Chemistry 2020, 103827.

6. Batool, R.; Kazmi, S. A. R.; Khurshid, S.; Saeed, M.; Ali, S.; Adnan, A.; Altaf, F.; Hameed, A.; Batool, F.; Fatima, N., Postharvest shelf-life enhancement of peach fruit treated with glucose oxidase immobilized on ZnO nanoparticles. Food Chemistry 2022, 366, 130591