scholarly journals A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry

2021 ◽  
Vol 118 (50) ◽  
pp. e2112942118
Author(s):  
Julián Valero ◽  
Laia Civit ◽  
Daniel M. Dupont ◽  
Denis Selnihhin ◽  
Line S. Reinert ◽  
...  

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created an urgent need for new technologies to treat COVID-19. Here we report a 2′-fluoro protected RNA aptamer that binds with high affinity to the receptor binding domain (RBD) of SARS-CoV-2 spike protein, thereby preventing its interaction with the host receptor ACE2. A trimerized version of the RNA aptamer matching the three RBDs in each spike complex enhances binding affinity down to the low picomolar range. Binding mode and specificity for the aptamer–spike interaction is supported by biolayer interferometry, single-molecule fluorescence microscopy, and flow-induced dispersion analysis in vitro. Cell culture experiments using virus-like particles and live SARS-CoV-2 show that the aptamer and, to a larger extent, the trimeric aptamer can efficiently block viral infection at low concentration. Finally, the aptamer maintains its high binding affinity to spike from other circulating SARS-CoV-2 strains, suggesting that it could find widespread use for the detection and treatment of SARS-CoV-2 and emerging variants.

2020 ◽  
Vol 48 (14) ◽  
pp. e82-e82 ◽  
Author(s):  
Ryoga Ishida ◽  
Tatsuo Adachi ◽  
Aya Yokota ◽  
Hidehito Yoshihara ◽  
Kazuteru Aoki ◽  
...  

Abstract Aptamers are short single-stranded RNA/DNA molecules that bind to specific target molecules. Aptamers with high binding-affinity and target specificity are identified using an in vitro procedure called high throughput systematic evolution of ligands by exponential enrichment (HT-SELEX). However, the development of aptamer affinity reagents takes a considerable amount of time and is costly because HT-SELEX produces a large dataset of candidate sequences, some of which have insufficient binding-affinity. Here, we present RNA aptamer Ranker (RaptRanker), a novel in silico method for identifying high binding-affinity aptamers from HT-SELEX data by scoring and ranking. RaptRanker analyzes HT-SELEX data by evaluating the nucleotide sequence and secondary structure simultaneously, and by ranking according to scores reflecting local structure and sequence frequencies. To evaluate the performance of RaptRanker, we performed two new HT-SELEX experiments, and evaluated binding affinities of a part of sequences that include aptamers with low binding-affinity. In both datasets, the performance of RaptRanker was superior to Frequency, Enrichment and MPBind. We also confirmed that the consideration of secondary structures is effective in HT-SELEX data analysis, and that RaptRanker successfully predicted the essential subsequence motifs in each identified sequence.


2019 ◽  
Author(s):  
Ryoga Ishida ◽  
Tatsuo Adachi ◽  
Aya Yokota ◽  
Hidehito Yoshihara ◽  
Kazuteru Aoki ◽  
...  

AbstractAptamers are short single-stranded RNA/DNA molecules that bind to specific target molecules. Aptamers with high binding-affinity and target specificity are identified using an in vitro procedure called high throughput systematic evolution of ligands by exponential enrichment (HT-SELEX). However, the development of aptamer affinity reagents takes a considerable amount of time and is costly because HT-SELEX produces a large dataset of candidate sequences, some of which have insufficient binding-affinity. Here, we present RNA aptamer Ranker (RaptRanker), a novel in silico method for identifying high binding-affinity aptamers from HT-SELEX data by scoring and ranking. RaptRanker analyzes HT-SELEX data by evaluating the nucleotide sequence and secondary structure simultaneously, and by ranking according to scores reflecting local structure and sequence frequencies. To evaluate the performance of RaptRanker, we performed two new HT-SELEX experiments, and evaluated binding affinities of a part of sequences that include aptamers with low binding-affinity. In both datasets, the performance of RaptRanker was superior to Frequency, Enrichment and MPBind. We also confirmed that the consideration of secondary structures is effective in HT-SELEX data analysis, and that RaptRanker successfully predicted the essential subsequence motifs in each identified sequence.


Toxins ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 389 ◽  
Author(s):  
Marieke Sternkopf ◽  
Sven Thoröe-Boveleth ◽  
Tobias Beck ◽  
Kirsten Oleschko ◽  
Ansgar Erlenkötter ◽  
...  

Hydrophobic uremic toxins accumulate in patients with chronic kidney disease, contributing to a highly increased cardiovascular risk. The clearance of these uremic toxins using current hemodialysis techniques is limited due to their hydrophobicity and their high binding affinity to plasma proteins. Adsorber techniques may be an appropriate alternative to increase hydrophobic uremic toxin removal. We developed an extracorporeal, whole-blood bifunctional adsorber particle consisting of a porous, activated charcoal core with a hydrophilic polyvinylpyrrolidone surface coating. The adsorption capacity was quantified using analytical chromatography after perfusion of the particles with an albumin solution or blood, each containing mixtures of hydrophobic uremic toxins. A time-dependent increase in hydrophobic uremic toxin adsorption was depicted and all toxins showed a high binding affinity to the adsorber particles. Further, the particle showed a sufficient hemocompatibility without significant effects on complement component 5a, thrombin-antithrombin III complex, or thrombocyte concentration in blood in vitro, although leukocyte counts were slightly reduced. In conclusion, the bifunctional adsorber particle with cross-linked polyvinylpyrrolidone coating showed a high adsorption capacity without adverse effects on hemocompatibility in vitro. Thus, it may be an interesting candidate for further in vivo studies with the aim to increase the efficiency of conventional dialysis techniques.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Irene Carlon-Andres ◽  
Tomas Malinauskas ◽  
Sergi Padilla-Parra

AbstractThe HIV-1 envelope glycoprotein (Env) mediates viral entry into the host cell. Although the highly dynamic nature of Env intramolecular conformations has been shown with single molecule spectroscopy in vitro, the bona fide Env intra- and intermolecular mechanics when engaged with live T cells remains unknown. We used two photon fast fluorescence lifetime imaging detection of single-molecule Förster Resonance Energy Transfer occurring between fluorescent labels on HIV-1 Env on native virions. Our observations reveal Env dynamics at two levels: transitions between different intramolecular conformations and intermolecular interactions between Env within the viral membrane. Furthermore, we show that three broad neutralizing anti-Env antibodies directed to different epitopes restrict Env intramolecular dynamics and interactions between adjacent Env molecules when engaged with living T cells. Importantly, our results show that Env-Env interactions depend on efficient virus maturation, and that is disrupted upon binding of Env to CD4 or by neutralizing antibodies. Thus, this study illuminates how different intramolecular conformations and distribution of Env molecules mediate HIV-1 Env–T cell interactions in real time and therefore might control immune evasion.


Author(s):  
Michael Dominic Sacco ◽  
Chunlong Ma ◽  
Panagiotis Lagarias ◽  
Ang Gao ◽  
Julia Alma Townsend ◽  
...  

AbstractThe main protease (Mpro) of SARS-CoV-2, the pathogen responsible for the COVID-19 pandemic, is a key antiviral drug target. While most SARS-CoV-2 Mpro inhibitors have a γ-lactam glutamine surrogate at the P1 position, we recently discovered several Mpro inhibitors have hydrophobic moieties at the P1 site, including calpain inhibitors II/XII, which are also active against human cathepsin L, a host-protease that is important for viral entry. To determine the binding mode of these calpain inhibitors and establish a structure-activity relationship, we solved X-ray crystal structures of Mpro in complex with calpain inhibitors II and XII, and three analogues of GC-376, one of the most potent Mpro inhibitors in vitro. The structure of Mpro with calpain inhibitor II confirmed the S1 pocket of Mpro can accommodate a hydrophobic methionine side chain, challenging the idea that a hydrophilic residue is necessary at this position. Interestingly, the structure of calpain inhibitor XII revealed an unexpected, inverted binding pose where the P1’ pyridine inserts in the S1 pocket and the P1 norvaline is positioned in the S1’ pocket. The overall conformation is semi-helical, wrapping around the catalytic core, in contrast to the extended conformation of other peptidomimetic inhibitors. Additionally, the structures of three GC-376 analogues UAWJ246, UAWJ247, and UAWJ248 provide insight to the sidechain preference of the S1’, S2, S3 and S4 pockets, and the superior cell-based activity of the aldehyde warhead compared with the α-ketoamide. Taken together, the biochemical, computational, structural, and cellular data presented herein provide new directions for the development of Mpro inhibitors as SARS-CoV-2 antivirals.


Author(s):  
Dinakara Rao Ampasala ◽  
Bhagath Kumar Palaka ◽  
Anbumani Velmurugan Ilavarasi ◽  
Ishwar Patidar ◽  
Lakshmi Priya Poovadan ◽  
...  

Introduction: Insect growth and metamorphosis are strictly dependent on the structural changes that occur in chitin containing tissues and organs. Chitin synthase catalyzes chitin polymerization by β-(1, 4) glycosidic linkage of Nacetyl-D-glucosamine (GlcNAc) monomers; the major component of insect cuticles. Targeting this enzyme could be a promising strategy to control insect pests while avoiding adverse effects on coexisting populations. Nikkomycin Z and polyoxins are commercially available fungal inhibitors known to bind to the nucleotide-binding sites of insects and fungal chitin synthase. But the binding mode of chitin synthase has not been explored to date as its structure is not available yet. Methods: To understand the structural features of the Chilo partellus chitin synthase enzyme (CpCHS), the threedimensional (3D) structure of the CpCHS catalytic domain was modeled using ROBETTA webserver. The obtained model was used to investigate the binding mode of its substrate, uridine diphosphate-N-acetyl-D-glucosamine (UDPGlcNAc), and inhibitors (nikkomycin Z and polyoxins) by molecular docking approach using Schrödinger Suite-Maestro v9.2. The docked complexes were further investigated for their interaction stability by performing molecular dynamics (MD) simulations using GROMACS v5.1.2. Results: Our study highlighted the significance of various interactions made by CHS residues present in the Walker-B loop and donor-binding motifs with the substrate (UDP-GlcNAc), and GEDR motif with an acceptor (GlcNAc). Also, the interactions of the QRRRW motif while forming chitin polymer were explored. We observed that the inhibitors exhibited good binding affinity with these motifs, indicated by their docking and binding affinity scores. Conclusion: In vitro analysis suggested that nikkomycin Z showed higher inhibition of chitin synthase activity at a concentration of 2.5 µg.L-1 . Our study provided insights into the crucial interactions of chitin synthase while designing inhibitors against insect pests.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 4008-4008
Author(s):  
Chika Iwamoto ◽  
Katsuto Takenaka ◽  
Shingo Urata ◽  
Takahiro Shima ◽  
Katsuhiko Itoh ◽  
...  

Abstract Abstract 4008 Various immunodeficient mouse lines for human hematopoietic assay have been developed. It is well recognized that in addition to disruption of the lymphoid system, the strain background such as NOD and Balb/c is critical to achieve efficient xenotransplantation. We have reported that in the NOD strain, NOD-specific polymorphism of SIRPA allows the mouse SIRPA to bind human CD47, preventing activation of host macrophages to engulf human hematopoietic cells and/or to cytokine production, and therefore can inhibit graft rejection of human cells (Takenaka et al., Nature Immunology, 2007). Here we tested whether the efficient xenotransplantation capability in the Balb/c strain is decided also by the SIRPA-CD47 self-recognition system. We have also reported that the efficiency of human to mouse xenotransplantation in hematopoiesis can be measured by maintenance of human hematopoiesis in vitro in chimeric long-term culture (LTC) assay, where human hematopoietic cells are cultured in the presence of murine macrophages. Different doses of macrophages were seeded on MS-5 stromal cells with lineage negative cord blood cells, and 4–5 weeks after the initiation of culture, the number of colony-forming cells (CFCs) was counted. In this system the addition of B6-derived murine macrophages severely suppressed human LTC-initiating cells (LTC-IC), whereas replacement of B6-derived macrophages with NOD-derived macrophages significantly enhanced the maintenance of human LTC-IC in vitro. Interestingly, Balb/c-derived macrophages had an intermediate effect between those of B6 and NOD-derived macrophages. These results are reasonably corresponding to the efficiency of human hematopoietic cell engraftment in immunodeficient mice of each background strain. To test if this effect is derived from binding of murine SIRPA and human CD47, we performed protein-binding assays of these molecules. B6 SIRPA never binds to human CD47. NOD SIRPA showed a very high binding affinity, while Balb/c SIRPA showed an intermediate affinity (Kd=2.501 for NOD, 3.076E+2 for Balb/c, and 4.974E+10 for B6). We then cloned the SIRPA cDNA from Balb/c and NOD strains, and enforced to express these molecules in HeLa cells by using lentivirus vectors. HeLa cells with enforced NOD and Balb/c SIRPA also showed the similar strong and intermediate affinity to human CD47, respectively, indicating that strain-specific SIRPA decides its binding capability with human CD47. We then enforced to express SIRPA derived from B6, NOD, or Balb/c strains into B6 macrophages, and tested their inhibitory effect on the human LTC-IC assay. Again, the addition of macrophages with enforced B6 SIRPA into cultures inhibited human LTC-IC, whereas those with enforced NOD SIRPA promoted maintenance of human LTC-IC. The addition of macrophages with Balb/c SIRPA again showed an intermediate effect. Because we have also reported the high binding affinity to human CD47 in the NOD strain is caused by alteration of amino-acid sequences of the IgV domain of SIRPA caused by the NOD-specific single nucleotide polymorphisms (SNPs), DNA sequencing of the SIRPA domain in each strain was performed. We found 2 independent Balb/c-specific SNPs. One of the SNPs causes the exchange of the 29th amino acid leucine with valine (L29V). We then transduced the SIRPA with L29V mutation into HeLa cells, performed the binding assay for human CD47, and found that cells expressing L29V SIRPA had the affinity equivalent to HeLa cells transduced with Balb/c SIRPA. Thus, the Balb/c-specific L29V polymorphism of SIRPA allows moderate binding to human CD47, and SIRPA signaling evoked by this binding maintains human LTC-IC activity presumably by inhibiting Balb/c macrophages to engulf cultured human cells. These data collectively suggest that the efficiency of mouse to human xenotransplantation is decided by “macrophage tolerance” based on the binding affinity of human CD47 to strain-specific murine SIRPA. Our findings should be useful to establish a novel immunodeficient strain with more efficient xenotransplantation capability for human cells. Disclosures: No relevant conflicts of interest to declare.


2020 ◽  
Author(s):  
Annika Roth ◽  
Steffen Lütke ◽  
Denise Meinberger ◽  
Gabriele Hermes ◽  
Gerhard Sengle ◽  
...  

AbstractObjectiveSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the pathogen accountable for the coronavirus disease 2019 (COVID-19) pandemic. Viral entry via binding of the receptor binding domain (RBD) located within the S1 subunit of the SARS-CoV-2 Spike (S) protein to its target receptor angiotensin converting enzyme (ACE) 2 is a key step in cell infection. The efficient transition of the virus is linked to a unique protein called open reading frame (ORF) 8. As SARS-CoV-2 infections can develop into life-threatening lower respiratory syndromes, effective therapy options are urgently needed. Several publications propose vitamin D treatment, although its mode of action against COVID-19 is not fully elucidated. It is speculated that vitamin D’s beneficial effects are mediated by up-regulating LL-37, a well-known antimicrobial peptide with antiviral effects.MethodsRecombinantly expressed SARS-CoV-2 S protein, the extended S1 subunit (S1e), the S2 subunit (S2), the receptor binding domain (RBD), and ORF8 were used for surface plasmon resonance (SPR) studies to investigate LL-37’s ability to bind to SARS-CoV-2 proteins and to localize its binding site within the S protein. Binding competition studies were conducted to confirm an inhibitory action of LL-37 on the attachment of SARS-CoV-2 S protein to its entry receptor ACE2.ResultsWe could show that LL-37 binds to SARS-CoV-2 S protein (LL-37/SStrep KD = 410 nM, LL-37/SHis KD = 410 nM) with the same affinity, as SARS-CoV-2 binds to hACE2 (hACE2/SStrep KD = 370 nM, hACE2/SHis KD = 370 nM). The binding is not restricted to the RBD of the S protein, but rather distributed along the entire length of the protein. Interaction between LL-37 and ORF8 was detected with a KD of 290 nM. Further, inhibition of the binding of SStrep (IC50 = 740 nM), S1e (IC50 = 170 nM), and RBD (IC50 = 130 nM) to hACE2 by LL-37 was demonstrated.ConclusionsWe have revealed a biochemical link between vitamin D, LL-37, and COVID-19 severity. SPR analysis demonstrated that LL-37 binds to SARS-CoV-2 S protein and inhibits binding to its receptor hACE2, and most likely viral entry into the cell. This study supports the prophylactic use of vitamin D to induce LL-37 that protects from SARS-CoV-2 infection, and the therapeutic administration of vitamin D for the treatment of COVID-19 patients. Further, our results provide evidence that the direct use of LL-37 by inhalation and systemic application may reduce the severity of COVID-19.


Author(s):  
Qingxiu He ◽  
Xin Chen ◽  
Xi Yang ◽  
Guangpin Li ◽  
Haiqiong Guo ◽  
...  

: The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has attracted worldwide attention due to its high infectivity and pathogenicity. Objective: The purpose of this study is to develop drugs with therapeutic potentials for COVID-19. Methods: We selected the crystal structure of 3CL pro to perform virtual screening against natural products in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Then, molecular dynamics (MD) simulation was carried out to explore the binding mode between compounds and 3CL pro. Results and Discussion: A total of 6 candidates with good theoretical binding affinity to 3CL pro were identified. The binding mode after MD shows that hydrogen bonding and hydrophobic interaction play an important role in the binding process. Finally, based on the free binding energy analysis, the candidate natural product Gypenoside LXXV may bind to 3CL pro with high binding affinity. Conclusion: The natural product Gypenoside LXXV may have good potential anti-SARS-COV-2 activity.


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