scholarly journals Would It Be Possible to Stabilize Prefusion SARS-COV-2 Spikes with Ligands?

2021 ◽  
Author(s):  
Lorenzo, M.M. ◽  
Rafael Blasco ◽  
Julio Coll
Keyword(s):  
Membrane Fusion ◽  
Host Cells ◽  
Amino Acid Residues ◽  
Wild Type ◽  
Native Conformation ◽  
Infectivity Assay ◽  
Computational Screening ◽  
Binding Score ◽  
Host Membrane

<p>Fusion to host cells and infection caused by Severe Acute Respiratory Syndrome coronavirus (SARS)-CoV2 was inhibited <i>in vitro</i> by PP mutations stabilizing prefusion states of their spike (S) protein native conformation, as reported by several authors. However, the possible stabilization of S by binding-ligands, rather than by mutations, have not been explored, nor it is yet known if it would be possible. In this work, the so called “spring-loaded switch-folding” (SLSF) expanding S amino acid residues 960-1010 was computationally targeted because SLSF surrounded the previously described PP mutations. The SLSF trimeric prefusion conformation consisted in 3x3 α-helices that require a transition to 3 longer α-helices before viral/host membrane fusion, similarly to what occurs in other enveloped viruses. Results of a double computational screening among hundred of thousands of natural compounds for binding to the wild-type isolated SLSF conformer predicted more leads for its trimers than for monomers. Further ranked by the number of SLSF-conformers bound, some of the predicted top-leads may deserve experimental validation. Additional screening among thousands of drugs identified Tinosorb, an star-shaped molecule, as the lowest binding-score lead to SLSF in the low nM range. However, despite its lower binding-score, 3-fold molecular symmetry and fitting the inner part of the SLSF α-helices, we were unable to experimentally show any specific inhibition of S-mediated membrane fusion using an VSV-pseudotyped infectivity assay, nor any virtual binding to S-SLSF using docking to whole native S trimers. Further exploring the star-shaped features may provide new molecular alternatives to cross-bind the α-helices of S-SLSF to hypothetically inhibit coronavirus fusion.<b></b></p>

scholarly journals Would It Be Possible to Stabilize Prefusion SARS-COV-2 Spikes with Ligands?

2020 ◽  
Author(s):  
Julio Coll
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Membrane Fusion ◽  
Experimental Validation ◽  
Wild Type ◽  
Native Conformation ◽  
Enveloped Viruses ◽  
Computational Screening ◽  
Host Membrane ◽  
Nm Range

The<i> </i>infection by Severe Acute Respiratory Syndrome coronavirus (SARS)-CoV2 could be inhibited <i> in vitro </i>by mutations stabilizing their spike (S) native conformation in prefusion states, as reported by several authors. However, the possible S stabilization by binding-ligands, rather than by mutations, have not been computationally explored, nor it is known if that will be possible. Therefore, to first explore these possibilities, a binding target for predictive programs was focused to where the inhibiting mutations were described in the S coronavirus protein, in particular to the “spring-loaded switch-folding” (SLSF) segment of the S2 subunit, whose prefusion unfolding/refolding is required for viral/host membrane fusion. Similar SLSF prefusion mechanisms have been described in many other enveloped viruses. Results of a double computational screening of hundred of thousands of natural compounds for binding to wild-type SLSF conformer, predicted more leads in the low nM range for trimers than for monomers. Further ranked by the number of bound SLSF-conformers, some of the derived top-leads were predicted that may deserve experimental validation. Additionally, thousands of drugs were also included into the screening, resulting in a few top-lead drugs predicted to bind SLSF targets in the low nM range. All these potentially interacting S-ligands, similar structures and/or chemically improved designs, could be used to experimentally find out whether it will be possible to use them for inhibiting fusion and infection, offer new tools to investigate prefusion mechanism(s) and may contribute to therapeutic purposes.

Would It Be Possible to Stabilize Prefusion SARS-COV-2 Spikes with Ligands?

2020 ◽  
Author(s):  
Julio Coll
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Membrane Fusion ◽  
Experimental Validation ◽  
Wild Type ◽  
Native Conformation ◽  
Enveloped Viruses ◽  
Computational Screening ◽  
Host Membrane ◽  
Nm Range

The<i> </i>infection by Severe Acute Respiratory Syndrome coronavirus (SARS)-CoV2 could be inhibited <i> in vitro </i>by mutations stabilizing their spike (S) native conformation in prefusion states, as reported by several authors. However, the possible S stabilization by binding-ligands, rather than by mutations, have not been computationally explored, nor it is known if that will be possible. Therefore, to first explore these possibilities, a binding target for predictive programs was focused to where the inhibiting mutations were described in the S coronavirus protein, in particular to the “spring-loaded switch-folding” (SLSF) segment of the S2 subunit, whose prefusion unfolding/refolding is required for viral/host membrane fusion. Similar SLSF prefusion mechanisms have been described in many other enveloped viruses. Results of a double computational screening of hundred of thousands of natural compounds for binding to wild-type SLSF conformer, predicted more leads in the low nM range for trimers than for monomers. Further ranked by the number of bound SLSF-conformers, some of the derived top-leads were predicted that may deserve experimental validation. Additionally, thousands of drugs were also included into the screening, resulting in a few top-lead drugs predicted to bind SLSF targets in the low nM range. All these potentially interacting S-ligands, similar structures and/or chemically improved designs, could be used to experimentally find out whether it will be possible to use them for inhibiting fusion and infection, offer new tools to investigate prefusion mechanism(s) and may contribute to therapeutic purposes.

scholarly journals Brown Spiders’ Phospholipases-D with Potential Therapeutic Applications: Functional Assessment of Mutant Isoforms

Biomedicines ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 320
Author(s):  
Thaís Pereira da Silva ◽  
Fernando Jacomini de Castro ◽  
Larissa Vuitika ◽  
Nayanne Louise Costacurta Polli ◽  
Bruno César Antunes ◽  
...  
Keyword(s):  
Structural Changes ◽  
Capillary Permeability ◽  
Structural Data ◽  
Histopathological Analysis ◽  
Amino Acid Residues ◽  
Wild Type ◽  
Antigenic Properties ◽  
Harmful Effects

Phospholipases-D (PLDs) found in Loxosceles spiders’ venoms are responsible for the dermonecrosis triggered by envenomation. PLDs can also induce other local and systemic effects, such as massive inflammatory response, edema, and hemolysis. Recombinant PLDs reproduce all of the deleterious effects induced by Loxosceles whole venoms. Herein, wild type and mutant PLDs of two species involved in accidents—L. gaucho and L. laeta—were recombinantly expressed and characterized. The mutations are related to amino acid residues relevant for catalysis (H12-H47), magnesium ion coordination (E32-D34) and binding to phospholipid substrates (Y228 and Y228-Y229-W230). Circular dichroism and structural data demonstrated that the mutant isoforms did not undergo significant structural changes. Immunoassays showed that mutant PLDs exhibit conserved epitopes and kept their antigenic properties despite the mutations. Both in vitro (sphingomyelinase activity and hemolysis) and in vivo (capillary permeability, dermonecrotic activity, and histopathological analysis) assays showed that the PLDs with mutations H12-H47, E32-D34, and Y228-Y229-W230 displayed only residual activities. Results indicate that these mutant toxins are suitable for use as antigens to obtain neutralizing antisera with enhanced properties since they will be based on the most deleterious toxins in the venom and without causing severe harmful effects to the animals in which these sera are produced.

scholarly journals Novel Salmonella enterica Serovar Typhimurium Protein That Is Indispensable for Virulence and Intracellular Replication

2001 ◽  
Vol 69 (12) ◽  
pp. 7413-7418 ◽  
Author(s):  
Tahar van der Straaten ◽  
Angela van Diepen ◽  
Kitty Kwappenberg ◽  
Sjaak van Voorden ◽  
Kees Franken ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Function ◽  
Salmonella Enterica ◽  
Host Cells ◽  
Wild Type ◽  
Intracellular Replication ◽  
Oxygen Intermediates ◽  
Serovar Typhimurium

ABSTRACT Upon contact with host cells, the intracellular pathogenSalmonella enterica serovar Typhimurium promotes its uptake, targeting, and survival in intracellular niches. In this process, the bacterium evades the microbicidal effector mechanisms of the macrophage, including oxygen intermediates. This study reports the phenotypic and genotypic characterization of an S. enterica serovar Typhimurium mutant that is hypersusceptible to superoxide. The susceptible phenotype is due to a MudJ insertion-inactivation of a previously undescribedSalmonella gene designated sspJ that is located between 54.4 and 64 min of the Salmonellachromosome and encodes a 392-amino-acid protein. In vivo, upon intraperitoneal injection of 104 to 107bacteria in C3H/HeN and 101 to 104 bacteria in BALB/c mice, the mutant strain was less virulent than the wild type. Consistent with this finding, during the first hour after ingestion by macrophage-like J774 and RAW264.7 cells in vitro, the intracellular killing of the strain carrying sspJ::MudJ is enhanced fivefold over that of wild-type microorganisms. Wild-type salmonellae displayed significant intracellular replication during the first 24 h after uptake, but sspJ::MudJ mutants failed to do so. This phenotype could be restored to that of the wild type by sspJ complementation. The SspJ protein is found in the cytoplasmic membrane and periplasmic space. Amino acid sequence homology analysis did reveal a leader sequence and putative pyrroloquinoline quinone-binding domains, but no putative protein function. We excluded the possibility that SspJ is a scavenger of superoxide or has superoxide dismutase activity.

scholarly journals Role of Adhesin Release for Mucosal Colonization by a Bacterial Pathogen

2003 ◽  
Vol 197 (6) ◽  
pp. 735-742 ◽  
Author(s):  
Loïc Coutte ◽  
Sylvie Alonso ◽  
Nathalie Reveneau ◽  
Eve Willery ◽  
Brigitte Quatannens ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Bacterial Pathogen ◽  
Host Cells ◽  
Wild Type ◽  
Early Step ◽  
Bacterial Surface ◽  
Extracellular Milieu ◽  
Wild Type Parent

Pathogen attachment is a crucial early step in mucosal infections. This step is mediated by important virulence factors called adhesins. To exert these functions, adhesins are typically surface-exposed, although, surprisingly, some are also released into the extracellular milieu, the relevance of which has previously not been studied. To address the role of adhesin release in pathogenesis, we used Bordetella pertussis as a model, since its major adhesin, filamentous hemagglutinin (FHA), partitions between the bacterial surface and the extracellular milieu. FHA release depends on its maturation by the specific B. pertussis protease SphB1. We constructed SphB1-deficient mutants and found that they were strongly affected in their ability to colonize the mouse respiratory tract, although they adhered even better to host cells in vitro than their wild-type parent strain. The defect in colonization could be overcome by prior nasal instillation of purified FHA or by coinfection with FHA-releasing B. pertussis strains, but not with SphB1-producing FHA-deficient strains, ruling out a nonspecific effect of SphB1. These results indicate that the release of FHA is important for colonization, as it may facilitate the dispersal of bacteria from microcolonies and the binding to new sites in the respiratory tract.

scholarly journals Exocytosis induction in Paramecium tetraurelia cells by exogenous phosphoprotein phosphatase in vivo and in vitro: possible involvement of calcineurin in exocytotic membrane fusion.

1987 ◽  
Vol 105 (1) ◽  
pp. 181-189 ◽  
Author(s):  
M Momayezi ◽  
C J Lumpert ◽  
H Kersken ◽  
U Gras ◽  
H Plattner ◽  
...  
Keyword(s):  
Alkaline Phosphatase ◽  
Membrane Fusion ◽  
Paramecium Tetraurelia ◽  
Wild Type ◽  
Current Finding ◽  
Phosphoprotein Phosphatase ◽  
Negative Results ◽  
Molecular Components

Since it had been previously shown that in Paramecium cells exocytosis involves the dephosphorylation of a 65-kD phosphoprotein (PP), we tried to induce exocytotic membrane fusion by exogenous phosphatases (alkaline phosphatase or calcineurin [CaN]). The occurrence of calmodulin (CaM) at preformed exocytosis sites (Momayezi, M., H. Kersken, U. Gras, J. Vilmart-Seuwen, and H. Plattner, 1986, J. Histochem. Cytochem., 34:1621-1638) and the current finding of the presence of the 65-kD PP and of a CaN-like protein in cell surface fragments ("cortices") isolated from Paramecium cells led us to also test the effect of antibodies (Ab) against CaM or CaN on exocytosis performance. Microinjected anti-CaN Ab strongly inhibit exocytosis. (Negative results with microinjected anti-CaM Ab can easily be explained by the abundance of CaM.) Alternatively, microinjection of a Ca2+-CaM-CaN complex triggers exocytosis. The same occurs with alkaline phosphatase. All these effects can also be mimicked in vitro with isolated cortices. In vitro exocytosis triggered by adding Ca2+-CaM-CaN or alkaline phosphatase is paralleled by dephosphorylation of the 65-kD PP. Exocytosis can also be inhibited in cortices by anti-CaM Ab or anti-CaN Ab. In wild-type cells, compounds that inhibit phosphatase activity, but none that inhibit kinases or proteases, are able to inhibit exocytosis. Exocytosis cannot be induced by phosphatase injection in a membrane-fusion-deficient mutant strain (nd9-28 degrees C) characterized by a defective organization of exocytosis sites (Beisson, J., M. Lefort-Tran, M. Pouphile, M. Rossignol, and B. Satir, 1976, J. Cell Biol., 69:126-143). We conclude that exocytotic membrane fusion requires an adequate assembly of molecular components to allow for the dephosphorylation of a 65-kD PP and that this step is crucial for the induction of exocytotic membrane fusion in Paramecium cells. In vivo this probably involves a Ca2+-CaM-stimulated CaN-like PP phosphatase.

scholarly journals Structural Requirements of Tom40 for Assembly into Preexisting TOM Complexes of Mitochondria

2001 ◽  
Vol 12 (5) ◽  
pp. 1189-1198 ◽  
Author(s):  
Doron Rapaport ◽  
Rebecca D. Taylor ◽  
Michael Käser ◽  
Thomas Langer ◽  
Walter Neupert ◽  
...  
Keyword(s):  
Intermediate Stage ◽  
In Vivo Studies ◽  
Mitochondrial Outer Membrane ◽  
Amino Acid Residues ◽  
Wild Type ◽  
Tom Complex ◽  
Precursor Proteins ◽  
Blue Native

Tom40 is the major subunit of the translocase of the outer mitochondrial membrane (the TOM complex). To study the assembly pathway of Tom40, we have followed the integration of the protein into the TOM complex in vitro and in vivo using wild-type and altered versions of the Neurospora crassa Tom40 protein. Upon import into isolated mitochondria, Tom40 precursor proteins lacking the first 20 or the first 40 amino acid residues were assembled as the wild-type protein. In contrast, a Tom40 precursor lacking residues 41 to 60, which contains a highly conserved region of the protein, was arrested at an intermediate stage of assembly. We constructed mutant versions of Tom40 affecting this region and transformed the genes into a sheltered heterokaryon containing a tom40 null nucleus. Homokaryotic strains expressing the mutant Tom40 proteins had growth rate defects and were deficient in their ability to form conidia. Analysis of the TOM complex in these strains by blue native gel electrophoresis revealed alterations in electrophoretic mobility and a tendency to lose Tom40 subunits from the complex. Thus, both in vitro and in vivo studies implicate residues 41 to 60 as containing a sequence required for proper assembly/stability of Tom40 into the TOM complex. Finally, we found that TOM complexes in the mitochondrial outer membrane were capable of exchanging subunits in vitro. A model is proposed for the integration of Tom40 subunits into the TOM complex.

scholarly journals Fur Represses Adhesion to, Invasion of, and Intracellular Bacterial Community Formation within Bladder Epithelial Cells and Motility in Uropathogenic Escherichia coli

2016 ◽  
Vol 84 (11) ◽  
pp. 3220-3231 ◽  
Author(s):  
Kumiko Kurabayashi ◽  
Tomohiro Agata ◽  
Hirofumi Asano ◽  
Haruyoshi Tomita ◽  
Hidetada Hirakawa
Keyword(s):  
Escherichia Coli ◽  
Epithelial Cells ◽  
Antimicrobial Agents ◽  
Host Cells ◽  
Type I ◽  
Wild Type ◽  
Content Type ◽  
Type I Fimbriae ◽  
Tract Infections

Uropathogenic Escherichia coli (UPEC) is a major pathogen that causes urinary tract infections (UTIs). This bacterium adheres to and invades the host cells in the bladder, where it forms biofilm-like polymicrobial structures termed intracellular bacterial communities (IBCs) that protect UPEC from antimicrobial agents and the host immune systems. Using genetic screening, we found that deletion of the fur gene, which encodes an iron-binding transcriptional repressor for iron uptake systems, elevated the expression of type I fimbriae and motility when UPEC was grown under iron-rich conditions, and it led to an increased number of UPEC cells adhering to and internalized in bladder epithelial cells. Consequently, the IBC colonies that the fur mutant formed in host cells were denser and larger than those formed by the wild-type parent strain. Fur is inactivated under iron-restricted conditions. When iron was depleted from the bacterial cultures, wild-type UPEC adhesion, invasion, and motility increased, similar to the case with the fur mutant. The purified Fur protein bound to regions upstream of fimA and flhD , which encode type I fimbriae and an activator of flagellar expression that contributes to motility, respectively. These results suggest that Fur is a repressor of fimA and flhD and that its repression is abolished under iron-depleted conditions. Based on our in vitro experiments, we conclude that UPEC adhesion, invasion, IBC formation, and motility are suppressed by Fur under iron-rich conditions but derepressed under iron-restricted conditions, such as in patients with UTIs.

scholarly journals ATP keeps exocytosis sites in a primed state but is not required for membrane fusion: an analysis with Paramecium cells in vivo and in vitro.

1986 ◽  
Vol 103 (4) ◽  
pp. 1279-1288 ◽  
Author(s):  
J Vilmart-Seuwen ◽  
H Kersken ◽  
R Stürzl ◽  
H Plattner
Keyword(s):  
Membrane Fusion ◽  
Time Course ◽  
Paramecium Tetraurelia ◽  
Wild Type ◽  
Primed State ◽  
Different Strains ◽  
Exogenous Trigger ◽  
Free Media

We have tried to specify a widespread hypothesis on the requirement of ATP for exocytosis (membrane fusion). With Paramecium tetraurelia cells, synchronously (approximately 1 s) exocytosing trichocysts, ATP pools have been measured in different strains, including wild type cells, "non-discharge" (nd), "trichless" (tl), and other mutations. The occurrence of a considerable and rapid ATP consumption also in nd and tl mutations as well as its time course (with a maximum 3-5 s after exocytosis) in exocytosis-competent strains does not match the actual extent of exocytosis performance. However, from in vivo as well as from in vitro experiments, we came to the conclusion that ATP might be required to keep the system in a primed state and its removal might facilitate membrane fusion. (For the study of exocytosis in vitro we have developed a new system, consisting of isolated cortices). In vivo as well as in vitro exocytosis is inhibited by increased levels of ATP or by a nonhydrolyzable ATP analogue. In vitro exocytosis is facilitated in ATP-free media. In vivo-microinjected ATP retards exocytosis in response to chemical triggers, whereas microinjected apyrase triggers exocytosis without exogenous trigger. Experiments with this system also largely exclude any overlaps with other processes that normally accompany exocytosis. Our data also explain why it was frequently assumed that ATP would be required for exocytosis. We conclude that membrane fusion during exocytosis does not require the presence of ATP; the occurrence of membrane fusion might involve the elimination of ATP from primed fusogenic sites; most of the ATP consumption measured in the course of exocytosis may be due to other effects, probably to recovery phenomena.

scholarly journals The degree of polymerization and sulfation patterns in heparan sulfate are critical determinants of cytomegalovirus entry into host cells

2021 ◽  
Vol 17 (8) ◽  
pp. e1009803
Author(s):  
Dipanwita Mitra ◽  
Mohammad H. Hasan ◽  
John T. Bates ◽  
Michael A. Bierdeman ◽  
Dallas R. Ederer ◽  
...  
Keyword(s):  
Cell Surface ◽  
Heparan Sulfate ◽  
Virus Entry ◽  
Degree Of Polymerization ◽  
Host Cells ◽  
Virus Infectivity ◽  
Wild Type ◽  
Enveloped Viruses ◽  
Host Membrane ◽  
Mutant Cells

Several enveloped viruses, including herpesviruses attach to host cells by initially interacting with cell surface heparan sulfate (HS) proteoglycans followed by specific coreceptor engagement which culminates in virus-host membrane fusion and virus entry. Interfering with HS-herpesvirus interactions has long been known to result in significant reduction in virus infectivity indicating that HS play important roles in initiating virus entry. In this study, we provide a series of evidence to prove that specific sulfations as well as the degree of polymerization (dp) of HS govern human cytomegalovirus (CMV) binding and infection. First, purified CMV extracellular virions preferentially bind to sulfated longer chain HS on a glycoarray compared to a variety of unsulfated glycosaminoglycans including unsulfated shorter chain HS. Second, the fraction of glycosaminoglycans (GAG) displaying higher dp and sulfation has a larger impact on CMV titers compared to other fractions. Third, cell lines deficient in specific glucosaminyl sulfotransferases produce significantly reduced CMV titers compared to wild-type cells and virus entry is compromised in these mutant cells. Finally, purified glycoprotein B shows strong binding to heparin, and desulfated heparin analogs compete poorly with heparin for gB binding. Taken together, these results highlight the significance of HS chain length and sulfation patterns in CMV attachment and infectivity.

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