Target-directed synthesis and screening of antiviral (anti-SARS-CoV) and antibacterial compounds based on non-proteinogenic amino acids, peptides and polymers.
Yerevan State University (YSU)
Agricultural University of Georgia (AUG, DIBB)
Scientific and Production Center "Armbiotechnology" NAS RA
University of California San Diego
University of Texas at San Antonio (UTSA)
University of Paris-Saclay
Nagoya Institute of Technology
Universite de Nantes
The goal of the proposed project is the targeted synthesis and study of non-proteinogenic amino acids, peptides and other polymeric compounds capable of suppressing the activity of RNA-dependent RNA polymerase and SARS-COV-2 protease, human hTMPRSS2 protease, epithelial growth factor receptor (EGFR), mitogen-activated protein kinase (MAPK14), clostridial collagenases, as well as inhibiting the growth of pathogenic strains of Pseudomonas aeruginosa, Streptococcus pneumoniae, Stenotrophomonas maltophilia, Staphylococcus aureus, which have multiple antibiotic resistance. The most active compounds will be recommended for the development of antiviral and antibacterial drugs, including drugs against COVID-19.
Currently there is a wide range of antibacterial and antiviral medicines used in treatment of infectious diseases. Nevertheless some infections, especially caused by multiple-drug resistant pathogens and viruses, are not suppressed by existing drugs. As the COVID-19 pandemic has shown modern scientific achievements turn out insufficient to overcome this disease. It became obvious that results of detailed studies of emerging infections should be immediately used in targeted synthesis of pharmacologically active compounds which are able to stop virus propagation.
The main targets for drugs against viral infections are enzymes involved in the replication of viral genomes (DNA and RNA polymerases) and ensuring the biological activity of viruses (viral proteases, host proteases ((hTMPRSS2). In the case of SARS-COV-2, the viral RNA-dependent RNA polymerase (RdRp) is the most interesting therapeutic target since the enzyme is very specific to coronaviruses and is absent in humans. Currently, a number of antiviral drugs have been developed based on the serine protease inhibitors of the hepatitis C virus, such as Simeprevir, Grazoprevir, Glecaprevir, inhibitors of HIV aspartic protease Ritonavir, Darunavir, Tipranavir. The search for inhibitors of the SARS-CoV2 3CLpro cysteine protease is under development. Host (human) protease inhibitors deserve special attention as candidate targets for antiviral drugs. It has been shown that the hTMPRSS2 transmembrane protease is actively involved in infection with SARS-CoV and SARS-CoV-2 viruses.
The protein kinase IA?E14, which is considered as a target for anti-inflammatory drugs and tyrosine kinase associated with the epidermal growth factor receptor are of particular interest. It is known that interrupting EGFR signaling by blocking EGFR binding sites in the extracellular domain of the receptor or inhibiting the intracellular tyrosine kinase activity can prevent the growth of EGER- induced tumors.
As antibacterial agents, preference is given to compounds that inhibit the growth of antibiotic-resistant pathogenic bacteria, as well as inhibitors of collagenases of Clostridia genus bacteria.
The proposed research is based on the results obtained in the framework of previous ISTC Projects A-1247, A-1677 and A-2289, in the course of which numerous non-protein amino acids, peptides and polymers based on them were synthesized and studied. Under these projects universal methods for the asymmetric synthesis of amino acids were developed and about 200 names of not described in the literature non-protein amino acids and peptides on their basis, containing various aliphatic, aromatic, heterocyclic, unsaturated and other groups in the side radical, were synthesized. The study of their biological activity made it possible to identify a number of inhibitors of serine proteases, collagenase and metalloprotease MMP2, as well as growth inhibitors of antibiotic resistant bacteria of Pseudomonas genus and Stenotrophomonas maltophilia strains, which can be targets for creating new efficient antiviral and antibacterial drugs. The intraspecific and interspecific transfer of antibiotic resistance genes was studied. Some genes that cause antibiotic resistance were identified, their localization in the bacterial genome was revealed. A high level of stability trait of bacterial antibiotic resistance in the absence of selective pressure was noted.
Docking analysis also revealed non-protein amino acids and peptides that can interact with the proteases of the SARS-COV and Dangue viruses, which is an important object for further research. Undoubtedly, the theoretical and experimental skills of the team of performers, as well as extensive experience in research and organizational work can guarantee success in obtaining new active antibacterial and antiviral drugs within the proposed project, in particular, for the use against COVID-19.
Thus, the use of previously obtained results and modeling followed by the synthesis of new non-protein amino acids, peptides and polymers based on them make it quite realistic to achieve the goals of the proposed project. In accordance with this goal, it is supposed to evaluate the already synthesized compounds as potential RdRp inhibitors against SARS-CoV2 and model new structures on their basis. A database (library) of compounds interacting with the target enzymes selected for this study will be created. Further, a targeted synthesis of optically active non-protein amino acids, peptides and other polymeric compounds selected in silico – SARS-CoV2 RdRp inhibitors, the SARS-CoV2 cysteine protease 3CLpro, inhibitors of human serine protease TMPRSS2, inhibitors of MAPK14, clostridial collagenase and catalytic EGFR domain -will be carried out. To do this, it is planned to use the possibilities of both the stoichiometric methods for the asymmetric synthesis of amino acids, previously developed by us, and to synthesize new efficient chiral catalysts and on their basis to elaborate catalytic methods for the asymmetric synthesis of amino acids (Scheme 2). The newly synthesized compounds selected by modeling will be investigated for inhibiting SARS-CoV2 RdRp, 3CLpro and TMPRSS2 proteases, clostridial collagenase, MAPK14, as well as EGFR in vitro experiments. The mechanisms of enzyme inhibition will be identified. Also, molecular-genetic characteristics of multiple antibiotic resistance of pathogenic strains of P. aeruginosa, St. pneumoniae, S. maltophilia, St. aureus will be studied, new compounds that suppress their growth will be identified. It is envisaged to study the effect of new inhibitors of viral enzymes on the reproduction of viruses in cell culture.