Evaluation of the Antiviral Potential of Modified Heterocyclic Base and 5’-Norcarbocyclic Nucleoside Analogs Against SARS-CoV-2

Abstract

The pandemic caused by the novel betacoronavirus SARS-CoV-2 has already claimed more than 3.5 million lives. Despite the development and use of anti-COVID-19 vaccines, the disease remains a major public health challenge throughout the world. Large-scale screening of the drugs already approved for the treatment of other viral, bacterial, and parasitic infections, as well as autoimmune, oncological, and other diseases is currently underway as part of their repurposing for development of effective therapeutic agents against SARS-CoV-2. In this work, we present the results of a phenotypic screening of libraries of modified heterocyclic bases and 5-norcarbocyclic nucleoside analogs previously synthesized by us. We identified two leading compounds with apparent potential to inhibit SARS-CoV-2 replication and EC50 values in a range of 2070 M. The structures of these compounds can be further optimized to develop an antiviral drug.

Nucleoside Analogs and Perylene Derivatives Modulate Phase Separation of SARS-CoV-2 N Protein and Genomic RNA In Vitro

“…Initially designed as molecular probes for studying RNA/DNA-recognizing enzymes, fleximers have shown significant promise in antiviral research, including the development of coronavirus inhibitors [ 27 ]. Among the available fleximers, we selected the ATP mimetic Flex-nt10 (analog of 8-aza-7-deazaadenosine 5'-triphosphate), the adenosine mimetics Flex-ns10 (8-aza-7-deazaadenosine analog) and Flex-ns12 (8-aza-3,7-dideazaadenosine analog), and the deoxyadenosine mimetic Flex-dns12 [ 28 , 29 ].…”

“…In addition to purine nucleoside derivatives, we considered a well-known cytidine analog NHC (β-D-N 4 -hydroxycytidine, Figure 4 a) [ 30 ] and several recently reported pyrimidine derivatives ( Figure 4 c,d) that inhibited SARS-CoV-2 in vitro. These derivatives included 5′-norcarbocyclic (NorC) analogs of 3H-pirrolo[2,3-d]-pyrimidine-2-one (NorC-24p) and 3H-furano[2,3-d]-pyrimidine-2-one (NorC-24f) nucleosides with a hydrophobic 4-pentylphenyl substituent ( Figure 4 c) [ 29 ] and perylene-harboring uridine analogs Peryl-8 and Peryl-5 (neutral and positively charged derivatives, respectively, Figure 4 d) [ 31 ]. To verify the importance of charged and hydrophobic fragments, we also tested the non-nucleoside neutral perylene derivatives Peryl-2a and Peryl-2b, their positively charged analogs Peryl-3a and Peryl-3b, and an additional positively charged compound with in vivo-confirmed antiviral activity Peryl-10 ( Figure 4 d) [ 31 ].…”

“…To verify the importance of charged and hydrophobic fragments, we also tested the non-nucleoside neutral perylene derivatives Peryl-2a and Peryl-2b, their positively charged analogs Peryl-3a and Peryl-3b, and an additional positively charged compound with in vivo-confirmed antiviral activity Peryl-10 ( Figure 4 d) [ 31 ]. The codes of all small molecules were taken from the previous works [ 29 , 31 ] and the prefixes indicate small molecule types.…”

“… Code Effects on the N-RNA Condensates a Antiviral Activity, IC50 ± SD, µM b S/S control ± SD Count/Count control ± SD ATP 0.4 ± 0.1 0.5 ± 0.2 - NHC 0.5 ± 0.3 0.4 ± 0.1 8 ± 5, refs. [ 29 , 31 ] c NorC-24p 11 ± 1 6.2 ± 0.8 21 ± 6, ref. [ 29 ] c NorC-24f 15 ± 1 9 ± 2 ≥50 c Flex-nt10 b 2 ± 1 4.7 ± 0.3 - Flex-ns10 2.9 ± 0.9 2.4 ± 0.4 >100 c Flex-ns12 0.4 ± 0.1 0.4 ± 0.1 >100 c Flex-dns12 3 ± 1 4 ± 1 >100 c Peryl-8 23 ± 7 1.4 ± 0.4 1.3 ± 0.4, ref.…”

New Analogues of Uridine as Possible Anti-Viral Agents Specific to SARS-CoV-2

“…As a result, the nitrogenous base retains the necessary hydrogen bonds and aromatic properties that are required for recognition, while gaining the flexibility to adapt to the enzyme binding site and potential mutations. It has been shown that such compounds are able to inhibit the replication of HCoV-NL63 and MERS-CoV coronaviruses in cell culture [ 11 , 12 ]. The idea of fleximer compounds was developed further in the form of the synthesis of “reverse” fleximers ( Fig.…”