Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 57
Filter
1.
ACS Appl Bio Mater ; 4(11): 7921-7931, 2021 11 15.
Article in English | MEDLINE | ID: covidwho-1500415

ABSTRACT

The advent of COVID-19 pandemic has made it necessary to wear masks across populations. While the N95 mask offers great performance against airborne infections, its multilayered sealed design makes it difficult to breathe for a longer duration of use. The option of using highly breathable cloth or silk masks especially for a large populace is fraught with the danger of infection. As a normal cloth or silk mask absorbs airborne liquid, it can be a source of plausible infection. We demonstrate the chemical modification of one such mask, Eri silk, to make it hydrophobic (contact angle of water is 143.7°), which reduces the liquid absorption capacity without reducing the breathability of the mask significantly. The breathability reduces only 22% for hydrophobic Eri silk compared to the pristine Eri silk, whereas N95 shows a 59% reduction of breathability. The modified hydrophobic silk can repel the incoming aqueous liquid droplets without wetting the surface. The results indicate that a multilayered modified silk mask to make it hydrophobic can be an affordable and breathable alternative to the N95 mask.


Subject(s)
COVID-19/prevention & control , Masks , Nanostructures/chemistry , Breath Tests , COVID-19/virology , Humans , Hydrophobic and Hydrophilic Interactions , Porosity , Respiratory Protective Devices/virology , SARS-CoV-2/isolation & purification , Silanes/chemistry , Silk/chemistry
2.
Eur Phys J E Soft Matter ; 44(11): 132, 2021 Oct 30.
Article in English | MEDLINE | ID: covidwho-1495656

ABSTRACT

Understanding the physical and chemical properties of viral infections at molecular scales is a major challenge for the scientific community more so with the outbreak of global pandemics. There is currently a lot of effort being placed in identifying molecules that could act as putative drugs or blockers of viral molecules. In this work, we computationally explore the importance in antiviral activity of a less studied class of molecules, namely surfactants. We employ all-atoms molecular dynamics simulations to study the interaction between the receptor-binding domain of the SARS-CoV-2 spike protein and the phospholipid lecithin (POPC), in water. Our microsecond simulations show a preferential binding of lecithin to the receptor-binding motif of SARS-CoV-2 with binding free energies significantly larger than [Formula: see text]. Furthermore, hydrophobic interactions involving lecithin non-polar tails dominate these binding events, which are also accompanied by dewetting of the receptor binding motif. Through an analysis of fluctuations in the radius of gyration of the receptor-binding domain, its contact maps with lecithin molecules, and distributions of water molecules near the binding region, we elucidate molecular interactions that may play an important role in interactions involving surfactant-type molecules and viruses. We discuss our minimal computational model in the context of lecithin-based liposomal nasal sprays as putative mitigating therapies for COVID-19.


Subject(s)
Lecithins/chemistry , Molecular Docking Simulation , Phosphatidylcholines/chemistry , Spike Glycoprotein, Coronavirus/chemistry , Surface-Active Agents/chemistry , Binding Sites , Hydrophobic and Hydrophilic Interactions , Nasal Sprays , Protein Binding , Spike Glycoprotein, Coronavirus/metabolism
3.
Nanotechnology ; 33(6)2021 Nov 19.
Article in English | MEDLINE | ID: covidwho-1493587

ABSTRACT

Wearing a face mask has become a necessity following the outbreak of the coronavirus (COVID-19) disease, where its effectiveness in containing the pandemic has been confirmed. Nevertheless, the pandemic has revealed major deficiencies in the ability to manufacture and ramp up worldwide production of efficient surgical-grade face masks. As a result, many researchers have focused their efforts on the development of low cost, smart and effective face covers. In this article, following a short introduction concerning face mask requirements, the different nanotechnology-enabled techniques for achieving better protection against the SARS-CoV-2 virus are reviewed, including the development of nanoporous and nanofibrous membranes in addition to triboelectric nanogenerators based masks, which can filter the virus using various mechanisms such as straining, electrostatic attraction and electrocution. The development of nanomaterials-based mask coatings to achieve virus repellent and sterilizing capabilities, including antiviral, hydrophobic and photothermal features are also discussed. Finally, the usability of nanotechnology-enabled face masks is discussed and compared with that of current commercial-grade N95 masks. To conclude, we highlight the challenges associated with the quick transfer of nanomaterials-enabled face masks and provide an overall outlook of the importance of nanotechnology in counteracting the COVID-19 and future pandemics.


Subject(s)
COVID-19/prevention & control , Masks , Nanotechnology , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19/transmission , Filtration , Humans , Hydrophobic and Hydrophilic Interactions , Nanofibers/chemistry , Nanostructures/chemistry , User-Centered Design
4.
J Am Chem Soc ; 143(43): 17975-17982, 2021 11 03.
Article in English | MEDLINE | ID: covidwho-1483092

ABSTRACT

Targeted and efficient delivery of nucleic acids with viral and synthetic vectors is the key step of genetic nanomedicine. The four-component lipid nanoparticle synthetic delivery systems consisting of ionizable lipids, phospholipids, cholesterol, and a PEG-conjugated lipid, assembled by microfluidic or T-tube technology, have been extraordinarily successful for delivery of mRNA to provide Covid-19 vaccines. Recently, we reported a one-component multifunctional sequence-defined ionizable amphiphilic Janus dendrimer (IAJD) synthetic delivery system for mRNA relying on amphiphilic Janus dendrimers and glycodendrimers developed in our laboratory. Amphiphilic Janus dendrimers consist of functional hydrophilic dendrons conjugated to hydrophobic dendrons. Co-assembly of IAJDs with mRNA into dendrimersome nanoparticles (DNPs) occurs by simple injection in acetate buffer, rather than by microfluidic devices, and provides a very efficient system for delivery of mRNA to lung. Here we report the replacement of most of the hydrophilic fragment of the dendron from IAJDs, maintaining only its ionizable amine, while changing its interconnecting group to the hydrophobic dendron from amide to ester. The resulting IAJDs demonstrated that protonated ionizable amines play dual roles of hydrophilic fragment and binding ligand for mRNA, changing delivery from lung to spleen and/or liver. Replacing the interconnecting ester with the amide switched the delivery back to lung. Delivery predominantly to liver is favored by pairs of odd and even alkyl groups in the hydrophobic dendron. This simple structural change transformed the targeted delivery of mRNA mediated with IAJDs, from lung to liver and spleen, and expands the utility of DNPs from therapeutics to vaccines.


Subject(s)
Dendrimers/chemistry , RNA, Messenger/chemistry , Amines/chemistry , Animals , Esters/chemistry , Hydrophobic and Hydrophilic Interactions , Ions/chemistry , Mice , Nanoparticles/chemistry , RNA, Messenger/immunology , RNA, Messenger/metabolism , Vaccines, Synthetic/chemistry , Vaccines, Synthetic/immunology , Vaccines, Synthetic/metabolism
5.
Cells ; 10(10)2021 10 14.
Article in English | MEDLINE | ID: covidwho-1470797

ABSTRACT

Prediction of linear B cell epitopes is of interest for the production of antigen-specific antibodies and the design of peptide-based vaccines. Here, we present BCEPS, a web server for predicting linear B cell epitopes tailored to select epitopes that are immunogenic and capable of inducing cross-reactive antibodies with native antigens. BCEPS implements various machine learning models trained on a dataset including 555 linearized conformational B cell epitopes that were mined from antibody-antigen protein structures. The best performing model, based on a support vector machine, reached an accuracy of 75.38% ± 5.02. In an independent dataset consisting of B cell epitopes retrieved from the Immune Epitope Database (IEDB), this model achieved an accuracy of 67.05%. In BCEPS, predicted epitopes can be ranked according to properties such as flexibility, accessibility and hydrophilicity, and with regard to immunogenicity, as judged by their predicted presentation by MHC II molecules. BCEPS also detects if predicted epitopes are located in ectodomains of membrane proteins and if they possess N-glycosylation sites hindering antibody recognition. Finally, we exemplified the use of BCEPS in the SARS-CoV-2 Spike protein, showing that it can identify B cell epitopes targeted by neutralizing antibodies.


Subject(s)
COVID-19/prevention & control , Computational Biology/methods , Databases, Factual , Epitopes, B-Lymphocyte/chemistry , SARS-CoV-2 , Animals , Antigens , COVID-19/immunology , Cross Reactions , Glycosylation , Histocompatibility Antigens Class II , Humans , Hydrophobic and Hydrophilic Interactions , Internet , Machine Learning , Mice , Peptides/chemistry , Protein Domains , Proteins/chemistry , Reproducibility of Results , Software , Spike Glycoprotein, Coronavirus/chemistry
6.
Phys Chem Chem Phys ; 23(40): 22957-22971, 2021 Oct 20.
Article in English | MEDLINE | ID: covidwho-1462045

ABSTRACT

The identification of chemical compounds able to bind specific sites of the human/viral proteins involved in the SARS-CoV-2 infection cycle is a prerequisite to design effective antiviral drugs. Here we conduct a molecular dynamics study with the aim to assess the interactions of ivermectin, an antiparasitic drug with broad-spectrum antiviral activity, with the human Angiotensin-Converting Enzyme 2 (ACE2), the viral 3CLpro and PLpro proteases, and the viral SARS Unique Domain (SUD). The drug/target interactions have been characterized in silico by describing the nature of the non-covalent interactions found and by measuring the extent of their time duration along the MD simulation. Results reveal that the ACE2 protein and the ACE2/RBD aggregates form the most persistent interactions with ivermectin, while the binding with the remaining viral proteins is more limited and unspecific.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , Antiviral Agents/metabolism , Coronavirus 3C Proteases/metabolism , Coronavirus Papain-Like Proteases/metabolism , Ivermectin/metabolism , Angiotensin-Converting Enzyme 2/chemistry , Antiviral Agents/chemistry , Binding Sites , Coronavirus 3C Proteases/chemistry , Coronavirus Papain-Like Proteases/chemistry , G-Quadruplexes , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Ivermectin/chemistry , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Domains , RNA/genetics , RNA/metabolism , SARS-CoV-2
7.
Soft Matter ; 17(41): 9457-9468, 2021 Oct 27.
Article in English | MEDLINE | ID: covidwho-1454830

ABSTRACT

The possibility of contamination of human skin by infectious virions plays an important role in indirect transmission of respiratory viruses but little is known about the fundamental physico-chemical aspects of the virus-skin interactions. In the case of coronaviruses, the interaction with surfaces (including the skin surface) is mediated by their large glycoprotein spikes that protrude from (and cover) the viral envelope. Here, we perform all atomic simulations between the SARS-CoV-2 spike glycoprotein and human skin models. We consider an "oily" skin covered by sebum and a "clean" skin exposing the stratum corneum. The simulations show that the spike tries to maximize the contacts with stratum corneum lipids, particularly ceramides, with substantial hydrogen bonding. In the case of "oily" skin, the spike is able to retain its structure, orientation and hydration over sebum with little interaction with sebum components. Comparison of these results with our previous simulations of the interaction of SARS-CoV-2 spike with hydrophilic and hydrophobic solid surfaces, suggests that the "soft" or "hard" nature of the surface plays an essential role in the interaction of the spike protein with materials.


Subject(s)
Protein Binding , Skin/virology , Spike Glycoprotein, Coronavirus , COVID-19 , Humans , Hydrophobic and Hydrophilic Interactions , Molecular Dynamics Simulation , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/metabolism
8.
J Ovarian Res ; 14(1): 126, 2021 Sep 27.
Article in English | MEDLINE | ID: covidwho-1440942

ABSTRACT

BACKGROUND: Infections by the SARS-CoV-2 virus causing COVID-19 are presently a global emergency. The current vaccination effort may reduce the infection rate, but strain variants are emerging under selection pressure. Thus, there is an urgent need to find drugs that treat COVID-19 and save human lives. Hence, in this study, we identified phytoconstituents of an edible vegetable, Bitter melon (Momordica charantia), that affect the SARS-CoV-2 spike protein. METHODS: Components of Momordica charantia were tested to identify the compounds that bind to the SARS-CoV-2 spike protein. An MTiOpenScreen web-server was used to perform docking studies. The Lipinski rule was utilized to evaluate potential interactions between the drug and other target molecules. PyMol and Schrodinger software were used to identify the hydrophilic and hydrophobic interactions. Surface plasmon resonance (SPR) was employed to assess the interaction between an extract component (erythrodiol) and the spike protein. RESULTS: Our in-silico evaluations showed that phytoconstituents of Momordica charantia have a low binding energy range, -5.82 to -5.97 kcal/mol. A docking study revealed two sets of phytoconstituents that bind at the S1 and S2 domains of SARS-CoV-2. SPR showed that erythrodiol has a strong binding affinity (KD = 1.15 µM) with the S2 spike protein of SARS-CoV-2. Overall, docking, ADME properties, and SPR displayed strong interactions between phytoconstituents and the active site of the SARS-CoV-2 spike protein. CONCLUSION: This study reveals that phytoconstituents from bitter melon are potential agents to treat SARS-CoV-2 viral infections due to their binding to spike proteins S1 and S2.


Subject(s)
COVID-19/drug therapy , Momordica charantia/chemistry , Plant Extracts/pharmacology , Spike Glycoprotein, Coronavirus/genetics , Binding Sites/drug effects , COVID-19/genetics , COVID-19/virology , Humans , Hydrophobic and Hydrophilic Interactions/drug effects , Molecular Docking Simulation , Oleanolic Acid/analogs & derivatives , Oleanolic Acid/chemistry , Oleanolic Acid/pharmacology , Plant Extracts/chemistry , Protein Binding/drug effects , SARS-CoV-2/drug effects , SARS-CoV-2/pathogenicity , Spike Glycoprotein, Coronavirus/antagonists & inhibitors , Surface Plasmon Resonance
9.
J Mol Biol ; 433(10): 166946, 2021 05 14.
Article in English | MEDLINE | ID: covidwho-1386061

ABSTRACT

Coronaviruses are a major infectious disease threat, and include the zoonotic-origin human pathogens SARS-CoV-2, SARS-CoV, and MERS-CoV (SARS-2, SARS-1, and MERS). Entry of coronaviruses into host cells is mediated by the spike (S) protein. In our previous ESR studies, the local membrane ordering effect of the fusion peptide (FP) of various viral glycoproteins including the S of SARS-1 and MERS has been consistently observed. We previously determined that the sequence immediately downstream from the S2' cleavage site is the bona fide SARS-1 FP. In this study, we used sequence alignment to identify the SARS-2 FP, and studied its membrane ordering effect. Although there are only three residue differences, SARS-2 FP induces even greater membrane ordering than SARS-1 FP, possibly due to its greater hydrophobicity. This may be a reason that SARS-2 is better able to infect host cells. In addition, the membrane binding enthalpy for SARS-2 is greater. Both the membrane ordering of SARS-2 and SARS-1 FPs are dependent on Ca2+, but that of SARS-2 shows a greater response to the presence of Ca2+. Both FPs bind two Ca2+ ions as does SARS-1 FP, but the two Ca2+ binding sites of SARS-2 exhibit greater cooperativity. This Ca2+ dependence by the SARS-2 FP is very ion-specific. These results show that Ca2+ is an important regulator that interacts with the SARS-2 FP and thus plays a significant role in SARS-2 viral entry. This could lead to therapeutic solutions that either target the FP-calcium interaction or block the Ca2+ channel.


Subject(s)
Calcium/metabolism , Cell Membrane/metabolism , SARS Virus/metabolism , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Viral Fusion Proteins/metabolism , Amino Acid Sequence , Binding Sites , Calcium/pharmacology , Calorimetry , Cell Membrane/drug effects , Cell Membrane/virology , Hydrogen-Ion Concentration , Hydrophobic and Hydrophilic Interactions , SARS Virus/drug effects , SARS-CoV-2/drug effects , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Thermodynamics , Viral Fusion Proteins/chemistry , Viral Fusion Proteins/genetics , Virus Internalization/drug effects
10.
Nat Commun ; 12(1): 3201, 2021 05 27.
Article in English | MEDLINE | ID: covidwho-1387343

ABSTRACT

Fragment-based drug design has introduced a bottom-up process for drug development, with improved sampling of chemical space and increased effectiveness in early drug discovery. Here, we combine the use of pharmacophores, the most general concept of representing drug-target interactions with the theory of protein hotspots, to develop a design protocol for fragment libraries. The SpotXplorer approach compiles small fragment libraries that maximize the coverage of experimentally confirmed binding pharmacophores at the most preferred hotspots. The efficiency of this approach is demonstrated with a pilot library of 96 fragment-sized compounds (SpotXplorer0) that is validated on popular target classes and emerging drug targets. Biochemical screening against a set of GPCRs and proteases retrieves compounds containing an average of 70% of known pharmacophores for these targets. More importantly, SpotXplorer0 screening identifies confirmed hits against recently established challenging targets such as the histone methyltransferase SETD2, the main protease (3CLPro) and the NSP3 macrodomain of SARS-CoV-2.


Subject(s)
Coronavirus 3C Proteases/chemistry , Coronavirus Papain-Like Proteases/chemistry , Drug Development/methods , Drug Discovery/methods , High-Throughput Screening Assays/methods , Histone-Lysine N-Methyltransferase/chemistry , Animals , Cell Survival , Chlorocebus aethiops , Computational Chemistry , Crystallography, X-Ray , Databases, Protein , Drug Design , HEK293 Cells , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Ligands , Protein Binding , Receptors, G-Protein-Coupled/chemistry , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , Small Molecule Libraries , Vero Cells
11.
J Am Chem Soc ; 143(23): 8543-8546, 2021 06 16.
Article in English | MEDLINE | ID: covidwho-1387162

ABSTRACT

The S protein of SARS-CoV-2 is a type I membrane protein that mediates membrane fusion and viral entry. A vast amount of structural information is available for the ectodomain of S, a primary target by the host immune system, but much less is known regarding its transmembrane domain (TMD) and its membrane-proximal regions. Here, we determined the NMR structure of the S protein TMD in bicelles that closely mimic a lipid bilayer. The TMD structure is a transmembrane α-helix (TMH) trimer that assembles spontaneously in a membrane. The trimer structure shows an extensive hydrophobic core along the 3-fold axis that resembles that of a trimeric leucine/isoleucine zipper, but with tetrad, not heptad, repeats. The trimeric core is strong in bicelles, resisting hydrogen-deuterium exchange for weeks. Although highly stable, structural guided mutagenesis identified single mutations that can completely dissociate the TMD trimer. Multiple studies have shown that the membrane anchors of viral fusion proteins can form highly specific oligomers, but the exact function of these oligomers remains unclear. Our findings should guide future experiments to address the above question for SARS coronaviruses.


Subject(s)
Cell Membrane/metabolism , Hydrophobic and Hydrophilic Interactions , Protein Multimerization , Spike Glycoprotein, Coronavirus/chemistry , Models, Molecular , Protein Structure, Quaternary , Spike Glycoprotein, Coronavirus/metabolism
12.
J Phys Chem B ; 124(44): 9785-9792, 2020 11 05.
Article in English | MEDLINE | ID: covidwho-1387110

ABSTRACT

Over 50 peptides, which were known to inhibit SARS-CoV-1, were computationally screened against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. Based on the binding affinity and interaction, 15 peptides were selected, which showed higher affinity compared to the α-helix of the human ACE2 receptor. Molecular dynamics simulation demonstrated that two peptides, S2P25 and S2P26, were the most promising candidates, which could potentially block the entry of SARS-CoV-2. Tyr489 and Tyr505 residues present in the "finger-like" projections of the RBD were found to be critical for peptide interaction. Hydrogen bonding and hydrophobic interactions played important roles in prompting peptide-protein binding and interaction. Structure-activity relationship indicated that peptides containing aromatic (Tyr and Phe), nonpolar (Pro, Gly, Leu, and Ala), and polar (Asn, Gln, and Cys) residues were the most significant contributors. These findings can facilitate the rational design of selective peptide inhibitors targeting the spike protein of SARS-CoV-2.


Subject(s)
Antiviral Agents/metabolism , Betacoronavirus/chemistry , Peptides/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Antiviral Agents/chemistry , Binding Sites , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Molecular Docking Simulation , Molecular Dynamics Simulation , Molecular Structure , Peptides/chemistry , Protein Binding , Protein Domains , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Structure-Activity Relationship
13.
J Am Chem Soc ; 143(33): 13205-13211, 2021 08 25.
Article in English | MEDLINE | ID: covidwho-1349637

ABSTRACT

The receptor binding and proteolysis of Spike of SARS-CoV-2 release its S2 subunit to rearrange and catalyze viral-cell fusion. This deploys the fusion peptide for insertion into the cell membranes targeted. We show that this fusion peptide transforms from intrinsic disorder in solution into a wedge-shaped structure inserted in bilayered micelles, according to chemical shifts, 15N NMR relaxation, and NOEs. The globular fold of three helices contrasts the open, extended forms of this region observed in the electron density of compact prefusion states. In the hydrophobic, narrow end of the wedge, helices 1 and 2 contact the fatty acyl chains of phospholipids, according to NOEs and proximity to a nitroxide spin label deep in the membrane mimic. The polar end of the wedge may engage and displace lipid head groups and bind Ca2+ ions for membrane fusion. Polar helix 3 protrudes from the bilayer where it might be accessible to antibodies.


Subject(s)
Micelles , Peptides/metabolism , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/chemistry , COVID-19/pathology , COVID-19/virology , Humans , Hydrophobic and Hydrophilic Interactions , Peptides/chemistry , Phospholipids/chemistry , Phospholipids/metabolism , Protein Binding , Protein Conformation, alpha-Helical , Protein Subunits/chemistry , Protein Subunits/metabolism , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/metabolism
14.
Talanta ; 235: 122691, 2021 Dec 01.
Article in English | MEDLINE | ID: covidwho-1313446

ABSTRACT

The nucleocapsid protein (NP) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for several steps of the viral life cycle, and is abundantly expressed during infection, making it an ideal diagnostic target protein. This protein has a strong tendency for dimerization and interaction with nucleic acids. For the first time, high titers of NP were expressed in E. coli with a CASPON tag, using a growth-decoupled protein expression system. Purification was accomplished by nuclease treatment of the cell homogenate and a sequence of downstream processing (DSP) steps. An analytical method consisting of native hydrophobic interaction chromatography hyphenated to multi-angle light scattering detection (HIC-MALS) was established for in-process control, in particular, to monitor product fragmentation and multimerization throughout the purification process. 730 mg purified NP per liter of fermentation could be produced by the optimized process, corresponding to a yield of 77% after cell lysis. The HIC-MALS method was used to demonstrate that the NP product can be produced with a purity of 95%. The molecular mass of the main NP fraction is consistent with dimerized protein as was verified by a complementary native size-exclusion separation (SEC)-MALS analysis. Peptide mapping mass spectrometry and host cell specific enzyme-linked immunosorbent assay confirmed the high product purity, and the presence of a minor endogenous chaperone explained the residual impurities. The optimized HIC-MALS method enables monitoring of the product purity, and simultaneously access its molecular mass, providing orthogonal information complementary to established SEC-MALS methods. Enhanced resolving power can be achieved over SEC, attributed to the extended variables to tune selectivity in HIC mode.


Subject(s)
COVID-19 , Nucleocapsid Proteins , Chromatography , Escherichia coli/genetics , Humans , Hydrophobic and Hydrophilic Interactions , Nucleocapsid Proteins/genetics , SARS-CoV-2
15.
Int J Mol Sci ; 22(13)2021 Jul 01.
Article in English | MEDLINE | ID: covidwho-1304671

ABSTRACT

Hollow vesicles made from a single or double layer of block-copolymer molecules, called polymersomes, represent an important technological platform for new developments in nano-medicine and nano-biotechnology. A central aspect in creating functional polymersomes is their combination with proteins, especially through encapsulation in the inner cavity of the vesicles. When producing polymersomes by techniques such as film rehydration, significant proportions of the proteins used are trapped in the vesicle lumen, resulting in high encapsulation efficiencies. However, because of the difficulty of scaling up, such methods are limited to laboratory experiments and are not suitable for industrial scale production. Recently, we developed a scalable polymersome production process in stirred-tank reactors, but the statistical encapsulation of proteins resulted in fairly low encapsulation efficiencies of around 0.5%. To increase encapsulation in this process, proteins were genetically fused with hydrophobic membrane anchoring peptides. This resulted in encapsulation efficiencies of up to 25.68%. Since proteins are deposited on the outside and inside of the polymer membrane in this process, two methods for the targeted removal of protein domains by proteolysis with tobacco etch virus protease and intein splicing were evaluated. This study demonstrates the proof-of-principle for production of protein-functionalized polymersomes in a scalable process.


Subject(s)
Cell Encapsulation/methods , Nanotechnology/methods , Peptides/chemistry , Polymers/chemistry , Proteins/chemistry , Hydrophobic and Hydrophilic Interactions , Membranes/chemistry
16.
Molecules ; 26(13)2021 Jun 23.
Article in English | MEDLINE | ID: covidwho-1295887

ABSTRACT

A possible inhibitor of proteases, which contains an indole core and an aromatic polar acetylene, was designed and synthesized. This indole derivative has a molecular architecture kindred to biologically relevant species and was obtained through five synthetic steps with an overall yield of 37% from the 2,2'-(phenylazanediyl)di(ethan-1-ol). The indole derivative was evaluated through docking assays using the main protease (SARS-CoV-2-Mpro) as a molecular target, which plays a key role in the replication process of this virus. Additionally, the indole derivative was evaluated as an inhibitor of the enzyme kallikrein 5 (KLK5), which is a serine protease that can be considered as an anticancer drug target.


Subject(s)
Acetylene/chemistry , Antiviral Agents/chemistry , Antiviral Agents/chemical synthesis , Indoles/chemistry , Protease Inhibitors/chemistry , Protease Inhibitors/chemical synthesis , SARS-CoV-2/enzymology , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Antiviral Agents/pharmacology , COVID-19/drug therapy , Coronavirus 3C Proteases/antagonists & inhibitors , Drug Discovery , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Kallikreins/antagonists & inhibitors , Models, Molecular , Molecular Docking Simulation , Protease Inhibitors/pharmacology , SARS-CoV-2/drug effects
17.
J Phys Chem Lett ; 12(27): 6252-6261, 2021 Jul 15.
Article in English | MEDLINE | ID: covidwho-1290145

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is mainly mediated through the interaction between the spike protein (S-pro) of the virus and the host angiotensin-converting enzyme II (ACE2). The attachment of heparan sulfate (HS) to S-pro is necessary for its binding to ACE2. In this study, the binding process of the receptor-binding domain (RBD) of S-pro to ACE2 was explored by enhanced sampling simulations. The free-energy landscape was characterized to elucidate the binding mechanism of S-pro to ACE2 with and without HS fragment DP4. We found that the stability of the T470-F490 loop and the hydrophobic interactions contributed from F486/Y489 in the T470-F490 loop of S-pro are quite crucial for the binding, which is enhanced by the presence of DP4. Our study provides valuable insights for rational drug design to prevent the invasion of SARS-CoV-2.


Subject(s)
Angiotensin-Converting Enzyme Inhibitors/metabolism , Host Microbial Interactions , Models, Molecular , Spike Glycoprotein, Coronavirus/metabolism , Drug Design , Hydrophobic and Hydrophilic Interactions , Protein Binding , Protein Domains , Spike Glycoprotein, Coronavirus/chemistry , Thermodynamics
18.
J Am Chem Soc ; 143(23): 8543-8546, 2021 06 16.
Article in English | MEDLINE | ID: covidwho-1258540

ABSTRACT

The S protein of SARS-CoV-2 is a type I membrane protein that mediates membrane fusion and viral entry. A vast amount of structural information is available for the ectodomain of S, a primary target by the host immune system, but much less is known regarding its transmembrane domain (TMD) and its membrane-proximal regions. Here, we determined the NMR structure of the S protein TMD in bicelles that closely mimic a lipid bilayer. The TMD structure is a transmembrane α-helix (TMH) trimer that assembles spontaneously in a membrane. The trimer structure shows an extensive hydrophobic core along the 3-fold axis that resembles that of a trimeric leucine/isoleucine zipper, but with tetrad, not heptad, repeats. The trimeric core is strong in bicelles, resisting hydrogen-deuterium exchange for weeks. Although highly stable, structural guided mutagenesis identified single mutations that can completely dissociate the TMD trimer. Multiple studies have shown that the membrane anchors of viral fusion proteins can form highly specific oligomers, but the exact function of these oligomers remains unclear. Our findings should guide future experiments to address the above question for SARS coronaviruses.


Subject(s)
Cell Membrane/metabolism , Hydrophobic and Hydrophilic Interactions , Protein Multimerization , Spike Glycoprotein, Coronavirus/chemistry , Models, Molecular , Protein Structure, Quaternary , Spike Glycoprotein, Coronavirus/metabolism
19.
Genes (Basel) ; 12(6)2021 05 27.
Article in English | MEDLINE | ID: covidwho-1256475

ABSTRACT

The genomic diversity of SARS-CoV-2 has been a focus during the ongoing COVID-19 pandemic. Here, we analyzed the distribution and character of emerging mutations in a data set comprising more than 95,000 virus genomes covering eight major SARS-CoV-2 lineages in the GISAID database, including genotypes arising during COVID-19 therapy. Globally, the C>U transitions and G>U transversions were the most represented mutations, accounting for the majority of single-nucleotide variations. Mutational spectra were not influenced by the time the virus had been circulating in its host or medical treatment. At the amino acid level, we observed about a 2-fold excess of substitutions in favor of hydrophobic amino acids over the reverse. However, most mutations constituting variants of interests of the S-protein (spike) lead to hydrophilic amino acids, counteracting the global trend. The C>U and G>U substitutions altered codons towards increased amino acid hydrophobicity values in more than 80% of cases. The bias is explained by the existing differences in the codon composition for amino acids bearing contrasting biochemical properties. Mutation asymmetries apparently influence the biochemical features of SARS CoV-2 proteins, which may impact protein-protein interactions, fusion of viral and cellular membranes, and virion assembly.


Subject(s)
COVID-19/virology , Genome, Viral , Hydrophobic and Hydrophilic Interactions , Mutation , SARS-CoV-2/genetics , Viral Proteins/chemistry , Viral Proteins/genetics , APOBEC Deaminases , Alleles , Amino Acid Substitution , Amino Acids/chemistry , Amino Acids/genetics , Evolution, Molecular , Genetic Variation , Genotype , Host-Pathogen Interactions , Humans , Phylogeny , Polymorphism, Single Nucleotide , Protein Binding , Protein Interaction Domains and Motifs , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics
20.
Biomolecules ; 11(6)2021 05 28.
Article in English | MEDLINE | ID: covidwho-1256422

ABSTRACT

The urgent need for novel and effective drugs against the SARS-CoV-2 coronavirus pandemic has stimulated research worldwide. The Papain-like protease (PLpro), which is essential for viral replication, shares a similar active site structural architecture to other cysteine proteases. Here, we have used representatives of the Ovarian Tumor Domain deubiquitinase family OTUB1 and OTUB2 along with the PLpro of SARS-CoV-2 to validate and rationalize the binding of inhibitors from previous SARS-CoV candidate compounds. By forming a new chemical bond with the cysteine residue of the catalytic triad, covalent inhibitors irreversibly suppress the protein's activity. Modeling covalent inhibitor binding requires detailed knowledge about the compounds' reactivities and binding. Molecular Dynamics refinement simulations of top poses reveal detailed ligand-protein interactions and show their stability over time. The recently discovered selective OTUB2 covalent inhibitors were used to establish and validate the computational protocol. Structural parameters and ligand dynamics are in excellent agreement with the ligand-bound OTUB2 crystal structures. For SARS-CoV-2 PLpro, recent covalent peptidomimetic inhibitors were simulated and reveal that the ligand-protein interaction is very dynamic. The covalent and non-covalent docking plus subsequent MD refinement of known SARS-CoV inhibitors into DUBs and the SARS-CoV-2 PLpro point out a possible approach to target the PLpro cysteine protease from SARS-CoV-2. The results show that such an approach gives insight into ligand-protein interactions, their dynamic character, and indicates a path for selective ligand design.


Subject(s)
Deubiquitinating Enzymes/antagonists & inhibitors , Protease Inhibitors/chemistry , SARS-CoV-2/metabolism , Viral Proteases/chemistry , Binding Sites , COVID-19/pathology , Catalytic Domain , Deubiquitinating Enzymes/metabolism , Drug Design , Female , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Ligands , Molecular Dynamics Simulation , Ovarian Neoplasms/metabolism , Ovarian Neoplasms/pathology , Protease Inhibitors/metabolism , SARS-CoV-2/isolation & purification , Viral Proteases/metabolism
SELECTION OF CITATIONS
SEARCH DETAIL
...