Protein-ligand Docking Simulations with AutoDock4 Focused on the Main Protease of SARS-CoV-2

2021 ◽  
Vol 28 ◽  
Author(s):  
Walter Filgueira de Azevedo Junior ◽  
Gabriela Bitencourt-Ferreira ◽  
Joana Retzke Godoy ◽  
Hilda Mayela Aran Adriano ◽  
Wallyson André dos Santos Bezerra ◽  
...  
Keyword(s):  
Scientific Evidence ◽  
Three Dimensional ◽  
Structural Data ◽  
Ligand Docking ◽  
Dimensional Structure ◽  
Computational Approaches ◽  
Docking Simulations ◽  
Protein Target ◽  
Main Protease ◽  
Docking Protocol

Background: The main protease of SARS-CoV-2 (Mpro) is one of the targets identified in SARS-CoV-2, the causative agent of COVID-19. The application of X-ray diffraction crystallography made available the three-dimensional structure of this protein target in complex with ligands, which paved the way for docking studies. Objective: Our goal here is to review recent efforts in the application of docking simulations to identify inhibitors of the Mpro using the program AutoDock4. Method: We searched PubMed to identify studies that applied AutoDock4 for docking against this protein target. We used the structures available for Mpro to analyze intermolecular interactions and reviewed the methods used to search for inhibitors. Results: The application of docking against the structures available for the Mpro found ligands with an estimated inhibition in the nanomolar range. Such computational approaches focused on the crystal structures revealed potential inhibitors of Mpro that might exhibit pharmacological activity against SARS-CoV-2. Nevertheless, most of these studies lack the proper validation of the docking protocol. Also, they all ignored the potential use of machine learning to predict affinity. Conclusion: The combination of structural data with computational approaches opened the possibility to accelerate the search for drugs to treat COVID-19. Several studies used AutoDock4 to search for inhibitors of Mpro. Most of them did not employ a validated docking protocol, which lends support to critics of their computational methodology. Furthermore, one of these studies reported the binding of chloroquine and hydroxychloroquine to Mpro. This study ignores the scientific evidence against the use of these antimalarial drugs to treat COVID-19.

scholarly journals SphereCon—a method for precise estimation of residue relative solvent accessible area from limited structural information

2020 ◽  
Vol 36 (11) ◽  
pp. 3372-3378
Author(s):  
Alexander Gress ◽  
Olga V Kalinina
Keyword(s):  
Protein Function ◽  
Structural Information ◽  
Solvent Accessibility ◽  
Three Dimensional ◽  
Structural Data ◽  
Supplementary Information ◽  
Dimensional Structure ◽  
Relative Solvent Accessibility ◽  
Precise Measure ◽  
The Impact

Abstract Motivation In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. Availability and implementation https://github.com/kalininalab/spherecon. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

Mapping of monoclonal antibodies specific to P64k: A common antigen of several isolates of Neisseria meningitidis

2001 ◽  
Vol 47 (2) ◽  
pp. 158-164 ◽  
Author(s):  
C Nazábal ◽  
T Carmenate ◽  
S Cruz ◽  
S González ◽  
R Silva ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Neisseria Meningitidis ◽  
Three Dimensional ◽  
Structural Data ◽  
Dimensional Structure ◽  
Bacterial Surface ◽  
A Minor ◽  
The Relationship ◽  
Cell Elisa ◽  
Competition Assays

P64k is a minor outer membrane protein from Neisseria meningitidis. This protein has been produced at high levels in Escherichia coli. We generated a group of monoclonal antibodies (mAbs) against recombinant P64k, which recognise four non-overlapping epitopes, as shown using competition assays with biotinylated mAbs. The P64k sequences involved in mAbs binding were mapped with synthetic overlapping peptides derived from the P64k protein, and located in the previously determined three-dimensional structure of the protein. These antibodies were also characterised by whole-cell ELISA and bactericidal tests against N. meningitidis. Only two of the recognised epitopes were exposed on the bacterial surface, and none of the mAbs showed bactericidal activity. The relationship between these results and the structural data on the epitopes bound by the mAbs is discussed.Key words: Neisseria meningitidis, P64k, monoclonal antibodies, epitope mapping.

scholarly journals Virtual High Throughput Screening Based Prediction of Potential Drugs for COVID-19

2020 ◽  
Author(s):  
Sekhar Talluri
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Viral Infections ◽  
Genomic Sequence ◽  
Reproduction Number ◽  
Three Dimensional ◽  
Drug Repurposing ◽  
Dimensional Structure ◽  
Main Protease ◽  
Approved Drugs

SARS-CoV-2 is a betacoronavirus that was first identified during the Wuhan COVID-19 epidemic in 2019. It was listed as a potential global health threat by WHO due to high mortality, high basic reproduction number and lack of clinically approved drugs and vaccines for COVID-19. The genomic sequence of the virus responsible for COVID-19, as well as the experimentally determined three dimensional structure of the Main protease (Mpro) are available. The reported structure of the target Mpro was utilized in this study to identify potential drugs for COVID-19 using virtual high throughput screening. The results of this study confirm earlier preliminary reports based on studies of homologs that some of the drugs approved for treatment of other viral infections also have the potential for treatment of COVID-19. Approved anti-viral drugs that target proteases were ranked for potential effectiveness against COVID-19 and novel candidates for drug repurposing were identified.

scholarly journals RNA 3D modeling with FARFAR2, online

2020 ◽  
Author(s):  
Andrew Watkins ◽  
Rhiju Das
Keyword(s):  
Rna Structure ◽  
Structure Prediction ◽  
Chemical Shifts ◽  
Three Dimensional ◽  
Structural Data ◽  
Dimensional Structure ◽  
Rna Structures ◽  
Beet Western Yellows Virus ◽  
H Nmr ◽  
Sampling Algorithms

AbstractUnderstanding the three-dimensional structure of an RNA molecule is often essential to understanding its function. Sampling algorithms and energy functions for RNA structure prediction are improving, due to the increasing diversity of structural data available for training statistical potentials and testing structural data, along with a steady supply of blind challenges through the RNA Puzzles initiative. The recent FARFAR2 algorithm enables near-native structure predictions on fairly complex RNA structures, including automated selection of final candidate models and estimation of model accuracy. Here, we describe the use of a publicly available webserver for RNA modeling for realistic scenarios using FARFAR2, available at https://rosie.rosettacommons.org/farfar2. We walk through two cases in some detail: a simple model pseudoknot from the frameshifting element of beet western yellows virus modeled using the “basic interface” to the webserver, and a replication of RNA-Puzzle 20, a metagenomic twister sister ribozyme, using the “advanced interface.” We also describe example runs of FARFAR2 modeling including two kinds of experimental data: a c-di-GMP riboswitch modeled with low resolution restraints from MOHCA-seq experiments and a tandem GA motif modeled with 1H NMR chemical shifts.

scholarly journals Natural Compounds Activities against SARS-CoV-2 Mpro through Bioinformatics Approaches for Development of Antivirus Candidates

2021 ◽  
Vol 24 (5) ◽  
pp. 170-176
Author(s):  
Taufik Muhammad Fakih
Keyword(s):  
Binding Free Energy ◽  
Natural Compounds ◽  
Protein Docking ◽  
Ligand Docking ◽  
Angiotensin Converting Enzyme 2 ◽  
Docking Simulations ◽  
Main Protease ◽  
Alternative Approach ◽  
Therapeutic Mechanism ◽  
Almost All

Coronavirus infection (COVID-19) caused by SARS-CoV-2 appears as a pandemic that has spread to almost all countries in the world. Antiviral therapy using natural compounds is one alternative approach to overcome this infectious disease. The therapeutic mechanism is proven effective against the main protease (Mpro) of SARS-CoV-2. This research aims to perform bioinformatics studies, including ligand-docking simulations and protein-protein docking simulations, to identify, evaluate, and explore five compounds' activity on SARS-CoV-2 Mpro and their effects against Angiotensin-Converting Enzyme 2 (ACE-2). Protein-ligand docking simulations show kaempferol, flavonol, and their glycosides (Afzelin and Juglanin) and other flavonoids (Quercetin, Naringenin, and Genistein) have a high affinity towards SARS-CoV-2 Mpro. These results were then confirmed using protein-protein docking simulations to observe the ability of five compounds to prevent the attachment of ACE-2 to the active site. Based on the results of the bioinformatics studies, Quercetin has the best affinity, with a binding free energy value of −33.18 kJ/mol. The five compounds are predicted to be able to interact strongly with SARS-CoV-2. The results in this research are useful for further studies in the development of novel anti-infective drugs for COVID-19 that target SARS-CoV-2 Mpro.

Thickness measurement of glucose-embedded crotoxin complex crystals by EELS

1993 ◽  
Vol 51 ◽  
pp. 686-687
Author(s):  
R.D. Leapman ◽  
J. Brink ◽  
W. Chiu
Keyword(s):  
Energy Loss ◽  
Three Dimensional ◽  
Structural Data ◽  
Mean Free Path ◽  
Thickness Measurement ◽  
Dimensional Structure ◽  
Specimen Thickness ◽  
Electron Dose ◽  
Cell Layers ◽  
Complex Crystals

In three-dimensional structure determination of macromolccules by electron crystallography it is necessary to combine diffraction patterns and images recorded at various tilt angles from different crystals. In order to merge these data sets successfully all the crystals should have the same thickness. It has been proposed that parallel electron energy loss spectroscopy (EELS) might provide a useful means of assessing the thickness of a beam-sensitive organic crystal prior to recording the high-resolution structural data. This can be achieved by measuring the fraction of the total transmitted electrons that do not lose energy, i.e., the zero-loss intensity. If Iz is the integrated zero-loss intensity and Itot is the total integrated intensity in the energy loss spectrum, then the specimen thickness, t, is given in terms of the total inelastic mean free path, λi, by, t/λi = ln(Itot/Iz). Results recently obtained from n-paraffin crystals have shown that it is feasible to determine the number of unit cell layers under low electron dose conditions.

Structure–function relationships in Gan42B, an intracellular GH42 β-galactosidase fromGeobacillus stearothermophilus

2015 ◽  
Vol 71 (12) ◽  
pp. 2433-2448 ◽  
Author(s):  
Hodaya V. Solomon ◽  
Orly Tabachnikov ◽  
Shifra Lansky ◽  
Rachel Salama ◽  
Hadar Feinberg ◽  
...  
Keyword(s):  
Active Sites ◽  
Plant Cell Wall ◽  
Three Dimensional ◽  
Gel Permeation Chromatography ◽  
Structural Data ◽  
Dimensional Structure ◽  
Cell Wall Polysaccharides ◽  
Small Opening ◽  
Three Dimensional Structure ◽  
Tim Barrel

Geobacillus stearothermophilusT-6 is a Gram-positive thermophilic soil bacterium that contains a battery of degrading enzymes for the utilization of plant cell-wall polysaccharides, including xylan, arabinan and galactan. A 9.4 kb gene cluster has recently been characterized inG. stearothermophilusthat encodes a number of galactan-utilization elements. A key enzyme of this degradation system is Gan42B, an intracellular GH42 β-galactosidase capable of hydrolyzing short β-1,4-galactosaccharides into galactose units, making it of high potential for various biotechnological applications. The Gan42B monomer is made up of 686 amino acids, and based on sequence homology it was suggested that Glu323 is the catalytic nucleophile and Glu159 is the catalytic acid/base. In the current study, the detailed three-dimensional structure of wild-type Gan42B (at 2.45 Å resolution) and its catalytic mutant E323A (at 2.50 Å resolution), as determined by X-ray crystallography, are reported. These structures demonstrate that the three-dimensional structure of the Gan42B monomer generally correlates with the overall fold observed for GH42 proteins, consisting of three main domains: an N-terminal TIM-barrel domain, a smaller mixed α/β domain, and the smallest all-β domain at the C-terminus. The two catalytic residues are located in the TIM-barrel domain in a pocket-like active site such that their carboxylic functional groups are about 5.3 Å from each other, consistent with a retaining mechanism. The crystal structure demonstrates that Gan42B is a homotrimer, resembling a flowerpot in general shape, in which each monomer interacts with the other two to form a cone-shaped tunnel cavity in the centre. The cavity is ∼35 Å at the wide opening and ∼5 Å at the small opening and ∼40 Å in length. The active sites are situated at the interfaces between the monomers, so that every two neighbouring monomers participate in the formation of each of the three active sites of the trimer. They are located near the small opening of the cone tunnel, all facing the centre of the cavity. The biological relevance of this trimeric structure is supported by independent results obtained from gel-permeation chromatography. These data and their comparison to the structural data of related GH42 enzymes are used for a more general discussion concerning structure–activity aspects in this GH family.

Structure–specificity relationships in Abp, a GH27 β-L-arabinopyranosidase fromGeobacillus stearothermophilusT6

2014 ◽  
Vol 70 (11) ◽  
pp. 2994-3012 ◽  
Author(s):  
Shifra Lansky ◽  
Rachel Salama ◽  
Hodaya V. Solomon ◽  
Hadar Feinberg ◽  
Hassan Belrhali ◽  
...  
Keyword(s):  
Active Sites ◽  
Critical Role ◽  
Three Dimensional ◽  
Structural Data ◽  
Size Exclusion ◽  
Dimensional Structure ◽  
Structural Basis ◽  
X Ray ◽  
Three Dimensional Structure ◽  
Tim Barrel

L-Arabinose sugar residues are relatively abundant in plants and are found mainly in arabinan polysaccharides and in other arabinose-containing polysaccharides such as arabinoxylans and pectic arabinogalactans. The majority of the arabinose units in plants are present in the furanose form and only a small fraction of them are present in the pyranose form. The L-arabinan-utilization system inGeobacillus stearothermophilusT6, a Gram-positive thermophilic soil bacterium, has recently been characterized, and one of the key enzymes was found to be an intracellular β-L-arabinopyranosidase (Abp). Abp, a GH27 enzyme, was shown to remove β-L-arabinopyranose residues from synthetic substrates and from the native substrates sugar beet arabinan and larch arabinogalactan. The Abp monomer is made up of 448 amino acids, and based on sequence homology it was suggested that Asp197 is the catalytic nucleophile and Asp255 is the catalytic acid/base. In the current study, the detailed three-dimensional structure of wild-type Abp (at 2.28 Å resolution) and its catalytic mutant Abp-D197A with (at 2.20 Å resolution) and without (at 2.30 Å resolution) a bound L-arabinose product are reported as determined by X-ray crystallography. These structures demonstrate that the three-dimensional structure of the Abp monomer correlates with the general fold observed for GH27 proteins, consisting of two main domains: an N-terminal TIM-barrel domain and a C-terminal all-β domain. The two catalytic residues are located in the TIM-barrel domain, such that their carboxylic functional groups are about 5.9 Å from each other, consistent with a retaining mechanism. An isoleucine residue (Ile67) located at a key position in the active site is shown to play a critical role in the substrate specificity of Abp, providing a structural basis for the high preference of the enzyme towards arabinopyranoside over galactopyranoside substrates. The crystal structure demonstrates that Abp is a tetramer made up of two `open-pincers' dimers, which clamp around each other to form a central cavity. The four active sites of the Abp tetramer are situated on the inner surface of this cavity, all opening into the central space of the cavity. The biological relevance of this tetrameric structure is supported by independent results obtained from size-exclusion chromatography (SEC), dynamic light-scattering (DLS) and small-angle X-ray scattering (SAXS) experiments. These data and their comparison to the structural data of related GH27 enzymes are used for a more general discussion concerning structure–selectivity aspects in this glycoside hydrolase (GH) family.

A unique octameric structure of Axe2, an intracellular acetyl-xylooligosaccharide esterase fromGeobacillus stearothermophilus

2014 ◽  
Vol 70 (2) ◽  
pp. 261-278 ◽  
Author(s):  
Shifra Lansky ◽  
Onit Alalouf ◽  
Hodaya Vered Solomon ◽  
Anat Alhassid ◽  
Lata Govada ◽  
...  
Keyword(s):  
Active Sites ◽  
Quaternary Structure ◽  
Gel Filtration ◽  
Three Dimensional ◽  
Structural Data ◽  
Catalytic Triad ◽  
Dimensional Structure ◽  
Internal Cavity ◽  
Three Dimensional Structure ◽  
New Family

Geobacillus stearothermophilusT6 is a thermophilic, Gram-positive soil bacterium that possesses an extensive and highly regulated hemicellulolytic system, allowing the bacterium to efficiently degrade high-molecular-weight polysaccharides such as xylan, arabinan and galactan. As part of the xylan-degradation system, the bacterium uses a number of side-chain-cleaving enzymes, one of which is Axe2, a 219-amino-acid intracellular serine acetylxylan esterase that removes acetyl side groups from xylooligosaccharides. Bioinformatic analyses suggest that Axe2 belongs to the lipase GDSL family and represents a new family of carbohydrate esterases. In the current study, the detailed three-dimensional structure of Axe2 is reported, as determined by X-ray crystallography. The structure of the selenomethionine derivative Axe2-Se was initially determined by single-wavelength anomalous diffraction techniques at 1.70 Å resolution and was used for the structure determination of wild-type Axe2 (Axe2-WT) and the catalytic mutant Axe2-S15A at 1.85 and 1.90 Å resolution, respectively. These structures demonstrate that the three-dimensional structure of the Axe2 monomer generally corresponds to the SGNH hydrolase fold, consisting of five central parallel β-sheets flanked by two layers of helices (eight α-helices and five 310-helices). The catalytic triad residues, Ser15, His194 and Asp191, are lined up along a substrate channel situated on the concave surface of the monomer. Interestingly, the Axe2 monomers are assembled as a `doughnut-shaped' homo-octamer, presenting a unique quaternary structure built of two staggered tetrameric rings. The eight active sites are organized in four closely situated pairs, which face the relatively wide internal cavity. The biological relevance of this octameric structure is supported by independent results obtained from gel-filtration, TEM and SAXS experiments. These data and their comparison to the structural data of related hydrolases are used for a more general discussion focusing on the structure–function relationships of enzymes of this category.

scholarly journals In silico Identification of Characteristics Spike Glycoprotein of SARS-CoV-2 in the Development Novel Candidates for COVID-19 Infectious Diseases

2020 ◽  
Vol 6 (2) ◽  
pp. 48-52
Author(s):  
Taufik Muhammad Fakih ◽  
Mentari Luthfika Dewi
Keyword(s):  
Infectious Diseases ◽  
In Silico ◽  
Three Dimensional ◽  
Protein Docking ◽  
Dimensional Structure ◽  
Spike Glycoprotein ◽  
Angiotensin Converting Enzyme 2 ◽  
Docking Simulations ◽  
Discovery Studio ◽  
Identification Evaluation

Background: The emergence of infectious diseases caused by SARS-CoV-2 has resulted in more than 90,000 infections and 3,000 deaths. The coronavirus spike glycoprotein encourages the entry of SARS-CoV-2 into cells and is the main target of antivirals. SARS-CoV-2 uses ACE2 to enter cells with an affinity similar to SARS-CoV, correlated with the efficient spread of SARS-CoV-2 among humans.Objective: In the research, identification, evaluation, and exploration of the structure of SARS-CoV and SARS-CoV-2 spike glycoprotein macromolecules and their effects on Angiotensin-Converting Enzyme 2 (ACE-2) using in silico studies.Methods: The spike glycoproteins of the two coronaviruses were prepared using the BIOVIA Discovery Studio 2020. Further identification of the three-dimensional structure and sequencing of the macromolecular spike glycoprotein structure using Chimera 1.14 and Notepad++. To ensure the affinity and molecular interactions between the SARS-CoV and SARS-CoV-2 spike glycoproteins against ACE-2 protein-protein docking simulations using PatchDock was accomplished. The results of the simulations were verified using the BIOVIA Discovery Studio 2020.Results: Based on the results of the identification of the macromolecular structure of the spike glycoprotein, it was found that there are some similarities in characteristics between SARS-CoV and SARS-CoV-2. Protein-protein docking simulations resulted that SARS-COV-2 spike glycoprotein has the strongest bond with ACE-2, with an ACE score of −1509.13 kJ/mol.Conclusion: Therefore, some information obtained from the results of this research can be used as a reference in the development of SARS-CoV-2 spike glycoprotein inhibitor candidates for the treatment of infectious diseases of COVID-19.

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