COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to more than 6 million deaths worldwide. SARS-CoV-2 is a betacoronavirus and possesses a positive-sense single- stranded RNA genome that contains 14 open reading frames (ORFs) and encodes 29 viral proteins divided into a series of structural proteins and non, including the spike (S), membrane (M), envelope (E), and nucleocapsid (N) proteins. In the SARS-CoV-2 lifecycle, S protein, which recognizes the human ACE2 receptor and is cleaved by host proteases, is responsible for virus binding and entry into host cells. Subsequently, Mpro and PLpro are necessary for the production and function of non-structural proteins (NSPs). The key RNA-dependent RNA polymerase (RdRp, also known as NSP12) catalyzes the synthesis of viral RNA and plays a central role in the lifecycle of SARS-CoV-2 Therefore, targeting these functional proteins is a rational strategy to inhibit infection and the replication of SARS-CoV-2. In this context, our research focused on the design and synthesis of different molecular entities as SARS- COV-2 entry inhibitors and viral polymerase inhibitors, respectively. Starting with the assumption that similar viruses often use the same host protein to infect cells and that the mutation rate of the host target is often lower than that of viral RNA, we decided to identify novel molecules that could target the binding between S protein and ACE2 as SARS-COV-2 entry inhibitors. We performed HTS screening to identify some HITs that were further optimized to reduce their cytotoxicity. Their affinity with both ACE2 and S was determinate and furthermore their antiviral activity was proven into a pseudovirus model of infection on Vero E6 cells. For the polymerase inhibitors, the same approach was used. We decided to perform a large screening of the antiviral in-house compounds previously synthetized to identify the hit for this class. RDS2153 was selected for the optimization process to understand more about structure-activity relationships (SARs) and to improve the antiviral activity in vitro (IC 50 ). Analogues were designed, synthetized, and tested against SARs COV2 polymerase. On the best compounds proved to be polymerase inhibitors the binding mode was also investigated. More detail of both the projects will be showed and discussed.
Different approaches to target SARS-CoV-2: discovery of new small molecules as antiviral agents / Ruggieri, G.; Madia, V. N.; Patacchini, E.; Albano, A.; Arpacioglu, M.; Ialongo, D.; Messore, A.; Saccoliti, F.; De Leo, A.; Malune, P.; Esposito, F.; Michelini, Z.; Cara, A.; Scipione, L.; Tramontano, E.; Di Santo, R.; Costi, R.. - (2024). (Intervento presentato al convegno 1NF-ACT Meeting 2024 tenutosi a Pavia, Italy).
Different approaches to target SARS-CoV-2: discovery of new small molecules as antiviral agents.
Madia, V. N.;Patacchini, E.;Albano, A.;Arpacioglu, M.;Ialongo, D.;Messore, A.;Saccoliti, F.;Scipione, L.;Tramontano, E.;Di Santo, R.;Costi, R.
2024
Abstract
COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to more than 6 million deaths worldwide. SARS-CoV-2 is a betacoronavirus and possesses a positive-sense single- stranded RNA genome that contains 14 open reading frames (ORFs) and encodes 29 viral proteins divided into a series of structural proteins and non, including the spike (S), membrane (M), envelope (E), and nucleocapsid (N) proteins. In the SARS-CoV-2 lifecycle, S protein, which recognizes the human ACE2 receptor and is cleaved by host proteases, is responsible for virus binding and entry into host cells. Subsequently, Mpro and PLpro are necessary for the production and function of non-structural proteins (NSPs). The key RNA-dependent RNA polymerase (RdRp, also known as NSP12) catalyzes the synthesis of viral RNA and plays a central role in the lifecycle of SARS-CoV-2 Therefore, targeting these functional proteins is a rational strategy to inhibit infection and the replication of SARS-CoV-2. In this context, our research focused on the design and synthesis of different molecular entities as SARS- COV-2 entry inhibitors and viral polymerase inhibitors, respectively. Starting with the assumption that similar viruses often use the same host protein to infect cells and that the mutation rate of the host target is often lower than that of viral RNA, we decided to identify novel molecules that could target the binding between S protein and ACE2 as SARS-COV-2 entry inhibitors. We performed HTS screening to identify some HITs that were further optimized to reduce their cytotoxicity. Their affinity with both ACE2 and S was determinate and furthermore their antiviral activity was proven into a pseudovirus model of infection on Vero E6 cells. For the polymerase inhibitors, the same approach was used. We decided to perform a large screening of the antiviral in-house compounds previously synthetized to identify the hit for this class. RDS2153 was selected for the optimization process to understand more about structure-activity relationships (SARs) and to improve the antiviral activity in vitro (IC 50 ). Analogues were designed, synthetized, and tested against SARs COV2 polymerase. On the best compounds proved to be polymerase inhibitors the binding mode was also investigated. More detail of both the projects will be showed and discussed.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
