The proposal ¿Rational Quest toolkit for therapeUtics and risk assEssmEnt in the nCoV coNtext¿ (acronym: QUEEN) has been submitted in response to the H2020 Call: SC1-PHE-CORONAVIRUS-2020, with the participation of the Sapienza Unit leaded by prof. Guido Antonelli. The main aim of the proposal was to develop a powerful tool (the QUEEN Hit Finder tool) to quickly screen among thousands of available drugs contained in online databases through computational molecular modeling. This extensive virtual screening campaign would be supported by a massive set of wet-lab experiments (from proteins binding affinity assays to in vivo experiments). In the QUEEN project, the group of Sapienza University proposed to investigate on sensitive cell culture models, the efficacy of compounds selected by the partner¿s computational tool and perform transcriptome analysis of infected cells in the presence of the candidate drug(s).
The identification of natural compounds able to act as antiviral drugs that can inhibit SARS-CoV-2 infection and/or replication would represent a powerful step to enhance the response to a possible second wave of the pandemic virus. We will utilize experimental in vitro CoV infections, first with the low-pathogenic CoV OC43, and NL63, and then with SARS-CoV-2, to test for inhibition of viral infection, decrease in replication and activation of the innate immune response using molecular and cellular biology techniques. In particular, we here propose: 1) to screen in silico the in house library of the Department of Chemistry and Technology of Drugs (plant-derived natural compounds and antimicrobial peptides) for interactions with the processes of SARS-CoV-2 entry and replication; 2) infecting permissive cells with the CoVs OC43, NL63, and SARS-CoV-2, in the presence of the selected compounds in order to evaluate their antiviral activity; 3) studying the impact of the selected compounds on innate immunity.
A component of the present project, Guglielmi Roberto, belongs to the Department of Chemistry and Technology of Drugs (DCTD), headed by Prof. Bruno Botta. Given the expertise of the group, the innovative aspect is the virtual screening of an in-house natural compounds¿ library, recently used for discovery of highly valued pharmaceutical intermediates and development of new environment-friendly methodologies to be employed in their production. In particular, DCTD is involved in developing several disciplines such as: Bioactive Natural Products, Organic Synthesis, Organometallic chemistry, Lead Optimization, Isolation, Structure elucidation, Drug Discovery and Enantioselective separations. Their main research efforts have been the isolation, biotransformation, structure elucidation and synthesis of biologically active compounds from medicinal plants. The screening of this library has been successfully employed in several multidisciplinary projects, as consolidated strategy for drug discovery. The organometallic reaction schemes based on green metric parameters have been considered as the milestone for the synthesis of precursors of active pharmaceutical ingredients (API). The organometallic research activities over the years have been directed to the development of ¿green¿ methodological synthetic approaches and to design and synthesis of new Pd- and Au-based catalysts. In addition, the analytical tools developed using high efficiency techniques, such as high performance liquid chromatography (HPLC) and supercritical fluid chromatography (SFC), have provided scientific and technical support for the separation of chiral bioactive compounds. Since natural products can offer unprecedented source for finding novel hits or leads against a wide range of biological targets, the combined organometallic green processes and enantioselective separation skills, as well as the international network launched by COST Action CM1407 (Challenging Organic Syntheses Inspired by Nature: from Natural Products Chemistry to Drug Discovery), will effective support the synthetic scale-up on the base of green chemistry principles. On this basis, the research will proceed by developing novel, environmentally safe, synthetic routes based on the coupling of enzymes and organometallic catalysis. In recent years, this unit has been involved in several innovative drug research projects with the purpose of discovering natural products as lead structures. As a result, a library composed of more than 1000 unique bioactive natural compounds is available in the laboratories of the Department and has been successfully employed in multidisciplinary projects, as consolidated strategy for drug discovery. Moreover, a computational tool for bioinformatic analysis has been established at DCTD and will be used in the project, helping state-of-the-art structure-based drug design approach and cheminformatics studies.
Relying on the group expertise on antiviral drugs and the IFN system, the DMM Virology Unit proposes to analyze two components derived from the innate arm of the immune system, the type I/III IFNs activation and the Inflammasome pathway, leading to cytokine production. Experimentally elucidating these two components could be the basis for a drug therapy with anti-viral effects and a synergistic activation of the IFN response with a reduced chance to overactivate proinflammatory cytokines. Moreover, we will compare, using state-of-the-art statistical tools, the different level of activation of the IFNs and the inflammasome pathways among three CoVs that differ in the severity of the disease they cause in the infected host. This original approach may shed light onto which pathways are responsible of the cytokine storm induced in severe COVID-19 patients. In fact, it¿s being recognized that different respiratory virus infections can induce the production of various types of cytokines in vitro and these differences may be associated with the pathophysiology of each respiratory virus infection in vivo . Moreover, a detailed characterization of the innate arm immune system when evaluating the efficacy of a novel drug, may lead to an increase of its therapeutic effectiveness adding to the antiviral effect, a positive modulation of the host response.