From MERS-Cov to SARS-Cov-2: Another good idea for anti-coronavirus inhibitor design

What is PPI?? A: PPI, also known as protein-to-protein interactions, is often a key regulatory factor for intercellular communication, and these interactions often lead to diseases such as cancerTherefore, by regulating these interaction sites is conducive to the exploration of new methods of disease treatmentAt present, most studies have focused on naturally occurring interprotein-protein interactions under physiological conditions as targets for drug development, while studies that regulate non-natural protein-to-protein interaction targets (non-native-protein-protein interactions) are rarely reportedResearch HighlightsRecently, the team from Taiwan's National ZTE University, Hu Minghong, analyzed the non-natural dipolymer crystal configuration of MERS-CoV N-NTD (N-end domain in the MerS-CoSsyndrome Coronary Virus-Nuclear Shell (N) protein) and used its non-natural protein-to-natural protein contact interface as a screening target to screen the progenitor compound P3 (5-palatinate) from the Acros and Drug DatabaseThis work was published in Journal of Medcine Chemistry1: Reference 1 Screenshotresearch ideas
MERS-CoV wraps its genome in a nuclear shell (N) protein to form a ribonucleoprotein (RNP) complexRNP is essential for the transcription and assembly of virusesTherefore, it is a feasible antiviral drug development strategy to destroy the formation of viral ribonucleoprotein (RNP) complex by regulating MERS-CoV nuclear shell (N) protein oligomers by small moleculesThe MERS-CoV nuclear shell (N) protein contains the N end domain (NTD) and the C end domain (CTD), both of which are involved in RNA bindingThe MERS-CoV N-NTD structure (n-end domain in the nuclear crust (N) protein) is folded in a monomerMERS-CoVN-CTD (C-end domain in nuclear crust (N) protein) is always a natural dipoly, and through protein-protein interaction leads to the nucleocrust (N) protein oligopolyIn general, the design idea of this work is to use the characteristics of MERS-CoV N-CTD natural interprotein interaction to bring the single MERS-CoVN-NTD close to each other, thus forming an unnatural protein-protein-protein-inter-protein action site, and then use this point as a target for antiviral drug designFigure 2: Anti-coronavirus drug design strategyThe images are derived from reference 1 the analysis of crystal structures in the interface of non-natural dipolymers
in order to better understand the specific characteristics of the target and the screening inhibitors, the team first analyzed the crystal structure of MERS-CoV N-NTD non-natural protein interprotein sites The authors named the interacting MERSCoV N-NTD protein dipolymer monomer 1 and 2, and divided the dipolymer interface into two regions: one in the n-end flexible zone and the other on the ring between the N-protein beta 4 and beta 5 In the first area, the W43, N66, N68, Y102 and F135 of monomer 1 produce a conservative dredging pocket, while the side chain of the M38 of monomer 2 can enter the dredging pocket of monomer 1 through hydrophobic contact In addition, the H37 and N39 of the monomer 2 are stacked with the W43 and F135 of the monomer 1 respectively, and contribute to the hydrophobic effect of the interface The hydrogen bond between monomer 2 and monomer 1 mainly includes the formation of hydrogen bonds between the side chain of N39 and the primary chain of N68, as well as the main chain oxygen of residual G104, F135 and T137 forming three hydrogen bonds with the side chains of Q73 and T134 In a further study, the team found that the dipolymer state was stable and needed to maintain the dipolymer state through residual h37, M38 on monomer 2 In addition, if the W43A mutation can significantly reduce the n-NTD oligopoly trend Another important feature is that the interface of the two-body is hydrophobic Here, the author can not help but say that for the design of drugs, the analysis of the target structure is often very important, can make us more targeted and direction Just as sick to take medicine, must be drugged, in order to cure the disease From the crystal structure we can understand the active site of the target, the structure of the properties, the location of the interaction and so on, for the next new drug design has a good guiding significance Figure 3: Non-natural dipolymer interface structure of MERS-CoV N-NTD The image sits from reference 1 screening strategy for pilot compounds
So, what inspiration should the analysis of the interaction of non-natural dipolymer interface and the hydrophobic nature of the interface give any inspiration to the screening of the next pilot compound? And how did the team design a screening strategy? first based on the analysis of non-natural dipolymer interface interaction sites, the research team removed H37 and M38 from the template to identify compounds that can replace carrier fusion residues, and carried out structural-based virtual screening in the hydrophobic pockets of n-NTD dipolymer interface, and initially screened the series of ligands According to the author's analysis, the main reason for adopting this strategy is that W43 will affect the oligomepoly of MERS-Cov N-NTD protein, and H37 and M38 are the main remnants of maintaining the stability of the dipolymer interface then based on the hydrophobic nature of the non-natural dipolymer interface, the team virtually screened three candidate compounds: pyridine-2-2-(hydroxymethyl)-1 dihydropyridine (P1), clinical drug-dependent acid (P2) and 5-Pasciacoxy (P2) and 5-Pasciamine (P2) as the criteria for hydrophobic complementation (SL/L) and low topological polarsurface area (TPSA) Compared with the compounds P1 and P2, 5-pyreoxyglutamine (P3) has a higher protoliceic matching surface (SL/L), butt fraction (Socre) and lower topological polarity surface area (TPSA), and can increase the rigidity, hydrophosofability and stable MERS-CoVN-NTD dipolymer structure around the protein tryptophan environment Importantly, the results of the experiments on cytotoxic concentrations (CC50 s 805.32 m) and effective concentrations (EC50 s 32.1?M) also showed that P3 had a good therapeutic index Therefore, P3 is an excellent anti-MERS-CoV candidate inhibitor Figure 4: Structural of the candidate compounds P1, P2 and P3 P3 induced MERS-CoVN protein aggregation after screening out the optimal pilot compound P3, the next team first proved that the question is whether the compound is the same as the expected design strategy, can it induce coronavirus N protein aggregation? the team used Small Angle X-ray scattering (Small Angle X-Ray Scattering, SAXS) to study the effects of P3 on the structure of the full-length MERSCoV N protein When combined with the pilot compound P3, the full-length MERS-CoV N protein forms a large protein aggregate and naturally forms a topologically enclosed octosphere through n-CTD (C-end domain in the n-cinclin (N) protein in the aggregate, thus inducing N protein aggregation and inhibiting the formation of MERS-CoV RNP (Middle East Respiratory Syndrome coronavirus ribonucleic protein complex) Figure 5: Protein aggregates combined with the compound P3 The image sits from reference 1 antiviral activity research
further cell experiments show that p3 of 50 m has little effect on viral titer (the toxicity of the virus, the amount of active virus in the unit volume) after 48 hours, but can significantly inhibit the replication of viral RNA The P3 of 100 m completely inhibits the production and replication of the virus after 48 hours In addition, the immunofluorescent results also show that the compound P3 inhibits MERS-CoV activity by inducing abnormal aggregation of the cell core shell (N) protein Figure 6: Study of antiviral activity of the compound P3 The images are drawn from references 1 the inspiration for the design of SARS-Cov-2 inhibitors
researchers from the Chinese Academy of Sciences and other institutions recently published in the journal Cell (Cell, 2020, doi:1016/j.cell.2020.03.045) shows that the structural characteristics of MERS-Co and SARS-CoV-2 proteins are consistent In addition, they found that the protoglobulin (S protein) on the surface of SARS-CoV S, like MERS-CoV, was cut by host proteases into S1 and S2 sub-synosis responsible for receptor identification and membrane fusion, respectively S1 can be further divided into N-end domain (N-NTD) and C-end domain (N-CTD) in the nucleocrust (N) protein, and the genome of SARS-Cov-2 is packaged in the nucleoid (N) protein to form a ribonucleoprotein (RNP) complex This is not to give us some hints, is it possible to also with SARS-Cov-2N-NTD (new coronavirus-nuclear shell (N) protein n-end domain) as a target to screen the whole-length N protein oligomer sedation induced abnormal at the cellular level and small molecular compounds with anti-new coronavirus (SARS-Cov-2) effect Of course, we also have to analyze more specifically the characteristics of the non-natural interprotein interprotein interface of SARS-Cov-2N-NTD (N-end domain in the new coronavirus-nuclear shell (N) protein Because the genes and characteristics of the new coronavirus SARS-Cov-2 are very similar to MERS-Cov, but some changes will cause their ability to bind to the human body's host cells, infectious capacity, disease-causing capacity to change dramatically, thereby seriously endangering the health of thousands of people conclusion
the global new coronary pneumonia epidemic is so severe today, the new anti-coronavirus drug design strategy is currently in the wild and future coronavirus treatment is of great significance At present, the drugs targeted to coronavirus are mainly angiotensin conversion enzyme 2 (ACE2), RNA polymerase, viral protease and virus 3CL hydrolysis, while the non-natural protein interaction interface (non-native-interaction protein-protein-protein-protein) of coronavirus escloser is a new breakthrough as an antiviral inhibitor screening target related references Structure-Based Stabilization of Non-Protein-Protein Interactions of CoronaVirusoNuclecaps Native Proteins inViral Drug Design Journal of Medicine.
J?rgen Bosch PPIpon and aller development in human diseases DrugDiscovery Today: Technologies 3, Wang Qihui et al Construct and functional of SARS-CoV-2 entry by using human ACE2 Cell.