Docking Complex Research Articles

Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies

A global crisis of coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has impacted millions of people’s lives throughout the world. In parallel to vaccine development, identifying potential antiviral agents against SARS-CoV-2 has become an urgent need to combat COVID-19. One of the most attractive drug targets for discovering anti-SARS-CoV-2 agents is the main protease (Mpro), which plays a pivotal role in the viral life cycle. This study aimed to elucidate a series of twenty-one 12-dithiocarbamate-14-deoxyandrographolide analogues as SARS-CoV-2 Mpro inhibitors using in vitro and in silico studies. These compounds were initially screened for the inhibitory activity toward SARS-CoV-2 Mpro by in vitro enzyme-based assay. We found that compounds 3k, 3l, 3m and 3t showed promising inhibitory activity against SARS-CoV-2 Mpro with >50% inhibition at 10 μM. Afterward, the binding mode of each compound in the active site of SARS-CoV-2 Mpro was explored by molecular docking. The optimum docked complexes were then chosen and subjected to molecular dynamic (MD) simulations. The MD results suggested that all studied complexes were stable along the simulation time, and most of the compounds could fit well with the SARS-CoV-2 Mpro active site, particularly at S1, S2 and S4 subsites. The per-residue decomposition free energy calculations indicated that the hot-spot residues essential for ligand binding were T25, H41, C44, S46, M49, C145, H163, M165, E166, L167, D187, R188, Q189 and T190. Therefore, the obtained information from the combined experimental and computational techniques could lead to further optimization of more specific and potent andrographolide analogues toward SARS-CoV-2 Mpro.

Protein–protein docking and molecular dynamics studies of sericin and cocoonase of silkworm: an insight for cocoon softening

Cocoonase is known to digest the sericin protein that encapsulates the silkworm cocoon's fibroin protein. Silk fibroin and sericin are two types of proteins that make up silk, and accounts for around 20–30% of the overall cocoon weight. The aim of the study was to see the protein–protein interaction (PPI) and molecular dynamic study of sericin, cocoonase and protein-protein docked complex of silkworm by computational approaches. Here motif analysis, phylogenetic analysis, principal component analysis, root-mean-square deviation (RMSD), root mean square fluctuation, radius of gyration, structural and functional study of cocoonase and sericin as well as molecular docking study were carried out. The 33 amino acid residues of cocoonase shows interaction with 38 aa residues of sericin involving 4 disulphide bonds, 22 hydrogen bonds and 319 non-bonded contacts. The confirmational stability and flexibility of both the proteins as well as protein–protein complex were achieved at 70 ns of MD simulation study. RMSD-based data indicated that cocoonase is more stable than sericin and complex, and complex has a greater fluctuation with more compact (higher Rg) value than cocoonase and sericin, inferring higher conformational stability and flexibility of protein-protein complex than cocoonase and sericin. This study provides a new dimension for PPI study by computational approaches. Communicated by Ramaswamy H. Sarma

Molecular Docking and Dynamics Investigations for Identifying Potential Inhibitors of the 3-Chymotrypsin-like Protease of SARS-CoV-2: Repurposing of Approved Pyrimidonic Pharmaceuticals for COVID-19 Treatment.

This study demonstrates the inhibitory effect of 42 pyrimidonic pharmaceuticals (PPs) on the 3-chymotrypsin-like protease of SARS-CoV-2 (3CLpro) through molecular docking, molecular dynamics simulations, and free binding energies by means of molecular mechanics–Poisson Boltzmann surface area (MM-PBSA) and molecular mechanics–generalized Born surface area (MM-GBSA). Of these tested PPs, 11 drugs approved by the US Food and Drug Administration showed an excellent binding affinity to the catalytic residues of 3CLpro of His41 and Cys145: uracil mustard, cytarabine, floxuridine, trifluridine, stavudine, lamivudine, zalcitabine, telbivudine, tipiracil, citicoline, and uridine triacetate. Their percentage of residues involved in binding at the active sites ranged from 56 to 100, and their binding affinities were in the range from −4.6 ± 0.14 to −7.0 ± 0.19 kcal/mol. The molecular dynamics as determined by a 200 ns simulation run of solvated docked complexes confirmed the stability of PP conformations that bound to the catalytic dyad and the active sites of 3CLpro. The free energy of binding also demonstrates the stability of the PP–3CLpro complexes. Citicoline and uridine triacetate showed free binding energies of −25.53 and −7.07 kcal/mol, respectively. Therefore, I recommend that they be repurposed for the fight against COVID-19, following proper experimental and clinical validation.

In silico assessment of chronic toxicity of a combination drug namely \u2018Olmesartan medoxomil and Hydrochlorothiazide\u2019, marketed in Bangladesh

BackgroundNowadays combination therapy has become more popular due to their additional effect, synergistic effect and antagonistic effect. Any of these can influence the treatment profile. Combination therapy is used to treat some chronic diseases like diabetes, hypertension, cancer etc. But recently India has banned some fixed dose drug combinations due to their increased chances of adverse drug effects and drug interactions. So it is the time to take a look on the present drug combinations available in Bangladesh. An in silico study may provide important information about their probable toxicities. Drugs available in the combination may deposit slowly in the body and may lead to toxicities. Here an antihypertensive drug combination ‘Olmesartan medoxomil and Hydrochlorothiazide’ had been studied.ResultsOlmesartan medoxomil and Hydrochlorothiazide have not been found to comply any similar protein to interact with each other, thus no possible chance of additional toxicity of the combination in case of long term use.ConclusionsAt first, using PubChem the ligand was searched for a canonical SMILE. By inputting the canonical SMILE in Protox, a basic information about toxicities was predicted. From Swiss Target Prediction, target proteins responsible for both efficacy and toxicity were identified. These protein structures were downloaded from Protein Data Bank and edited with Flare. Undesired amino acid, ligand–ligand complex, fatty acid, and water molecules were removed by PyMOL. Structurally modified proteins and ligands were inputted in Swiss PDB viewer for energy minimization. Energy minimization is a very important step because unfavorable bond length, bond strength and torsion angle between protein and ligand may interfere with docking procedure. Then docking between Olmesartan medoxomil (ligand) and the proteins responsible for efficacy and toxicity was performed by PyRx. Vina binding affinity provided the value of binding strength between the ligand and the proteins, which determines how strong the bond is. The more negative the vina binding affinity, the stronger the bond. Discovery studio software was used to visualize the docking complexes. Same steps were followed for Hydrochlorothiazide to identify proteins responsible for desired and undesired effects, but no toxic effect was found from protox.

Evaluation and Designing of Epitopic-Peptide Vaccine Against Bunyamwera orthobunyavirus Using M-Polyprotein Target Sequences.

Bunyamwera orthobunyavirus and its serogroup can cause several diseases in humans, cattle, ruminants, and birds. The viral M-polyprotein helps the virus to enter the host body. Therefore, this protein might serve as a potential vaccine target against Bunyamwera orthobunyavirus. The present study applied the immunoinformatics technique to design an epitopic vaccine component that could protect against Bunyamwera infection. Phylogenetic analysis revealed the presence of conserved patterns of M-polyprotein within the viral serogroup. Three epitopes common for both B-cell and T-cell were identified, i.e., YQPTELTRS, YKAHDKEET, and ILGTGTPKF merged with a specific linker peptide to construct an active vaccine component. The low atomic contact energy value of docking complex between human TLR4 (TLR4/MD2 complex) and vaccine construct confirms the elevated protein–protein binding interaction. Molecular dynamic simulation and normal mode analysis illustrate the docking complex’s stability, especially by the higher Eigenvalue. In silico cloning of the vaccine construct was applied to amplify the desired vaccine component. Structural allocation of both the vaccine and epitopes also show the efficacy of the developed vaccine. Hence, the computational research design outcomes support that the peptide-based vaccine construction is a crucial drive target to limit the infection of Bunyamwera orthobunyavirus to an extent.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10989-021-10322-9.

Virtual Screening and Molecular Dynamics Simulation Study of Influenza Polymerase PB2 Inhibitors.

Influenza A virus is the main cause of worldwide epidemics and annual influenza outbreaks in humans. In this study, a virtual screen was performed to identify compounds that interact with the PB2 cap-binding domain (CBD) of influenza A polymerase. A virtual screening workflow based on Glide docking was used to screen an internal database containing 8417 molecules, and then the output compounds were selected based on solubility, absorbance, and structural fingerprints. Of the 16 compounds selected for biological evaluation, six compounds were identified that rescued cells from H1N1 virus-mediated death at non-cytotoxic concentrations, with EC50 values ranging from 2.5–55.43 μM, and that could bind to the PB2 CBD of H1N1, with Kd values ranging from 0.081–1.53 μM. Molecular dynamics (MD) simulations of the docking complexes of our active compounds revealed that each compound had its own binding characteristics that differed from those of VX-787. Our active compounds have novel structures and unique binding modes with PB2 proteins, and are suitable to serve as lead compounds for the development of PB2 inhibitors. An analysis of the MD simulation also helped us to identify the dominant amino acid residues that play a key role in binding the ligand to PB2, suggesting that we should focus on increasing and enhancing the interaction between inhibitors and these major amino acids during lead compound optimization to obtain more active PB2 inhibitors.

In silico screening and epitope mapping of leptospiral outer membrane protein—Lsa46

Leptospirosis is one of the neglected diseases caused by the spirochete, Leptospira interrogans. Leptospiral surface adhesion (Lsa) proteins are surface exposed outer membrane proteins present in the pathogen. It acts as laminin and plasminogen binding proteins which enable them to infect host cells. The major target for the development of vaccine in the current era focuses on surface exposed outer membrane proteins, as they can induce strong and fast immune response in hosts. Therefore, the present study mapped the potential epitopes of the Leptospiral outer membrane proteins, mainly the surface adhesion proteins. Protein sequence analysis of Lsa proteins was done by in silico methods. The primary protein sequence analysis revealed Lsa46 as a suitable target which can be a potent Leptospiral vaccine candidate. Its structure was modelled by threading based method in I-TASSER server and validated by Ramachandran plot. The predicted epitope’s interactions with human IgG, IgM(Fab) and T-cell receptor TCR(αβ) were performed by molecular docking studies using Biovia Discovery studio 2018. One of the predicted B-cell epitopes and the IgG showed desirable binding interactions, while four of the predicted B-cell epitopes and T-cell epitopes showed desirable binding interactions with IgM and TCR respectively. The molecular dynamic simulation studies carried out with the molecular docked complexes gave minimized energies indicating stable interactions. The structural analysis of the entire simulated complex showed a stable nature except for one of the Epitope-IgM complex. Further the binding free energy calculation of eight receptor-ligand complex predicted them energetically stable. The results of the study help in elucidating the structural and functional characterization of Lsa46 for epitope-based vaccine design. Communicated by Ramaswamy H. Sarma.

Synthesis and characterization of Cu(II)-pyrazole complexes for possible anticancer agents; conformational studies as well as compatible in-silico and in-vitro assays

New pyrazole derivatives were prepared and used to synthesize new bioactive agents from Cu(II) complexes that have OSN donors. Analytical and spectral (IR, UV-Vis, MS, 1H NMR, ESR & XRD) instruments characterized these complexes as well as their corresponding ligands. The bonding mode has been modified from ligand to ligand and the molar ratio for isolated complexes has also varied (1:1/1:2, M:L). The geometry of isolated complexes was commonly proposed, based on electronic transitions and ESR spectral-parameters. Via computational approaches, these structures were optimized using standard programs (Gaussian 09 & HyperChem 8.1) under the required basis set. Consequently, important physical characteristics have been obtained after finishing the optimization process. Inhibition behavior of all new synthesizes was studied by MOE module as in-silico approach which conducted versus the crystal structure of NUDT5 protein (6gru) of breast cancer cells. The interaction features summarized from docking processes, reveal effective inhibition validity for new Cu(II) complexes versus breast cancer cells. This according to scoring energy values and the stability of docking complexes in true interaction path (bond length ≤3.5 Å) particularly with Cu(II)-L3 and Cu(II)-L4 complexes. This reflects the possibility of successful behavior during practical application through in-vitro assay that intended in this study. Finally, the degree of toxicity of such new compounds to the breast cancer cell line was determined by in-vitro screening. To judge perfectly on their toxicity, in-vitro screening must compared to positive control as Doxorubicin (reference drug). IC50 values were calculated and represent Cu(II) complexes as outstanding cytotoxic agents which revealed superiority on the reference drug itself.

Synergistic Effects of Natural Compounds Toward Inhibition of SARS-CoV-2 3CL Protease.

The biggest challenge in medical management and control of the COVID-19 pandemic is the nonavailability of the treatment molecules. While vaccines and other biotherapeutic products for managing COVID-19 have reached the market, a small-molecule cure is yet to be developed. This is relevant because the cost of production, storage, and ease of distribution of a small-molecule drug are significantly more favorable than those of biologics. In this paper, we present a multicompound approach, where two drug molecules are administered concurrently to offer an effective therapy for COVID-19. The co-action of the two compounds, each derived from natural origins, has been demonstrated against the 3CL protease, already recognized as a potential drug target for inhibiting SARS-CoV-2. The pair of compounds pursued in this study are flavonoid and naphthalene scaffold. Individually, they offer ∼30 to 35% inhibition at 10 μM. Comprehensive docking and molecular dynamics simulations elucidate that these compounds exhibit excellent binding in the process, which however quickly deteriorates, and the ligand is separated from the binding site. This suggests that while the ligands initially bind with the protease, they are unable to maintain it for an extended period. However, the simulation showed that a simultaneous docked complex of both the compounds together with the protein boosts the stronger binding for a sufficient time. The enzyme assay exhibited 97 and 85% inhibition activity when both compounds were used together at 100 and 50 μM, respectively. Later, a multiconcentration assay was used to determine the coinhibitory activity, and it was observed that the compounds have ∼20 to 30% inhibition activity even at lower concentrations of 0.5 and 1 μM. Surface plasmon resonance was used to measure the binding of the compounds, and when used together, the compounds had a 10-fold greater binding affinity. Thus, the results demonstrate a synergistic mechanism between the two compounds that enhances the inhibition activity against SARS-CoV-2 3CL protease.

LvCPG2 facilitated WSSV infection by interaction with VP26 and VP28

Chondroitin sulfate proteoglycans (CSP), widely distributed in extracellular matrices, have several important functions in vertebrates. In certain viruses, CSP acts as a receptor to promote infection. However, chondroitin proteoglycans lack sulfate are poorly understood in invertebrates. In this study, chondroitin proteoglycan 2 of Litopenaeus vannamei (LvCPG2) was cloned. The open reading frame of LvCPG2 cDNA is 2133 bp, which encodes a protein of 710 amino acids. LvCPG2 contained eight Chitin-binding domain type 2 (ChtBD2). LvCPG2 had the highest expression in lymphoid and significantly increased after WSSV challenge. The relative expression of IE1 and VP28, as well as the viral copy numbers were decreased significantly in LvCPG2-silenced shrimp. The far-western blotting result showed that LvCPG2 interacted with VP26 and VP28. Molecular docking complexes showed that N-terminal of LvCPG2 interacted with C-terminal VP26, while C-terminal of LvCPG2 combined with N-terminal of VP28. Flow cytometry analysis indicated that LvCPG2 could facilitate WSSV adhesion and penetration of shrimp hemocytes. Collectively, these findings suggested that LvCPG2 was involved in WSSV infection by interaction with VP26 and VP28.

Subtractive Proteomics and Immuno-informatics Approaches for Multi-peptide Vaccine Prediction Against Klebsiella oxytoca and Validation Through In Silico Expression.

Klebsiella oxytoca is a gram-negative bacterium. It is opportunistic in nature and causes hospital acquired infections. Subtractive proteomics and reverse vaccinology approaches were employed to screen out the best proteins for vaccine designing. Whole proteome of K. oxytoca strain ATCC 8724, consisting of 5483 proteins, was used for designing the vaccine. Total 1670 cytotoxic T lymphocyte (CTL) epitope were predicted through NetCTL while 1270 helper T lymphocyte (HTL) epitopes were predicted through IEDB server. The epitopes were screened for non-toxicity, allergenicity, antigenicity and water solubility. After epitope screening 300 CTL and 250 HTL epitopes were submitted to IFN-γ epitope server to predict their Interferon-γ induction response. The selected IFN-γ positive epitopes were tested for their binding affinity with MHCI-DRB1 by MHCPred. The 15 CTL and 13 HTL epitopes were joined by linkers AAY and GPGPG respectively in vaccine construct. Chain C of Pam3CSK4 (PDB ID; 2Z7X) was linked to the vaccine construct as an adjuvant. A 450aa long vaccine construct was submitted to I-TASSER server for 3D structure prediction. Thirteen Linear B cells were predicted by ABCPred server and 10 sets of discontinues epitopes for 3D vaccine structure were predicted by DiscoTope server. The modeled 3D vaccine construct was docked with human Toll-like receptor 2 (PDB ID: 6NIG) by PatchDock. The docked complexes were refined by FireDock. The selected docked complex showed five hydrogen bonds and one salt bridge. The vaccine sequence was reverse transcribed to get nucleotide sequence for In silico cloning. The reverse transcribed sequence strand was cloned in pET28a(+) expression vector. A clone containing 6586 bp was constructed including the 450 bp of query gene sequence.

Structural significance of Neprylysin from Streptococcus suis GZ1 in the degradation of Aβ peptides, a causative agent in Alzheimer's disease.

Alzheimer's disease (AD) is a progressive brain disorder. The accumulation of amyloid beta (Aβ) peptides in the human brain leads to AD. The cleavage of Aβ peptides by several enzymes is being considered as an essential aspect in the treatment of AD. Neprilysin (NEP) is an important enzyme that clears the Aβ plaques in the human brain. The human NEP activity has been found reduced due to mutations in NEP and the presence of inhibitors. However, the role of NEP in the degradation of Aβ peptides in detail at the molecular level is not yet clear. Hence, in the present study, we have investigated the structural significance of NEP from the bacterial source Streptococcus suis GZ1 using various bioinformatics approaches. The homology modelling technique was used to predict the three-dimensional structure of NEP. Further, molecular dynamic (MD) simulated model of NEP was docked with Aβ peptide. Analysis of MD simulated docked complex showed that the wild-type NEP-Aβ-peptide complex is more stable as compared to mutant complex. Hydrogen bonding interactions between NEP with Zn2+and Aβ peptide confirm the degradation of the Aβ peptide. The molecular docking and MD simulation results revealed that the active site residue Glu-538 of bacterial NEP along with Zn2+ interact with His-13 of Aβ peptide. This stable interaction confirms the involvement of NEP with Glu-538 in the degradation of the Aβ peptide. The other residues such as Glu203, Ser537, Gly140, Val587, and Val536 could also play an important role in the cleavage of Aβ peptide in between Asp1-Ala2, Arg5-His6, Val18-Phe19, Gly9-Tyr10, and Arg5-His6. Hence, the predicted model of the NEP enzyme of Streptococcus suis GZ1could be useful to understand the Aβ peptide degradation in detail at the molecular level. The information obtained from this study would be helpful in designing new lead molecules for the effective treatment of AD.

In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools

BackgroundThis world is currently witnessing a pandemic outbreak of ‘COVID-19′ caused by a positive-strand RNA virus ‘SARS-CoV-2’. Millions have succumbed globally to the disease, and the numbers are increasing day by day. The viral genome enters into the human host through interaction between the spike protein (S) and host angiotensin-converting enzyme-2 (ACE2) proteins. S is the common target for most recently rolled-out vaccines across regions. A recent surge in single/multiple mutations in S region is of great concern as it may escape vaccine induced immunity. So far, the treatment regime with repurposed drugs has not been too successful. HypothesisNatural compounds are capable of targeting mutated spike protein by binding to its active site and destabilizing the spike-host ACE2 interaction. Materials and methodsA hypothetical mutated spike protein was constructed by incorporating twelve different mutations from twelve geographical locations simultaneously into the receptor-binding domain (RBD) and docked with ACE2 and seven phytochemicals namely allicin, capsaicin, cinnamaldehyde, curcumin, gingerol, piperine and zingeberene. Molecular Dynamic (MD) simulation and Principal Component Analysis (PCA) were finally used for validation of the docking results. ResultThe docking results showed that curcumin and piperine were most potent to bind ACE2, mutated spike, and mutated spike-ACE2 complex, thereby restricting viral entry. ADME analysis also proved their drug candidature. The docking complexes were found to be stable by MD simulation. ConclusionThis result provides a significant insight about the phytochemicals' role, namely curcumin and piperine, as the potential therapeutic entities against mutated spike protein of SARS-CoV-2.

In-silico design of envelope based multi-epitope vaccine candidate against Kyasanur forest disease virus

Kyasanur forest disease virus (KFDV) causing tick-borne hemorrhagic fever which was earlier endemic to western Ghats, southern India, it is now encroaching into new geographic regions, but there is no approved medicine or effective vaccine against this deadly disease. In this study, we did in-silico design of multi-epitope subunit vaccine for KFDV. B-cell and T-cell epitopes were predicted from conserved regions of KFDV envelope protein and two vaccine candidates (VC1 and VC2) were constructed, those were found to be non-allergic and possess good antigenic properties, also gives cross-protection against Alkhurma hemorrhagic fever virus. The 3D structures of vaccine candidates were built and validated. Docking analysis of vaccine candidates with toll-like receptor-2 (TLR-2) by Cluspro and PatchDock revealed strong affinity between VC1 and TLR2. Ligplot tool was identified the intermolecular hydrogen bonds between vaccine candidates and TLR-2, iMOD server confirmed the stability of the docking complexes. JCAT sever ensured cloning efficiency of both vaccine constructs and in-silico cloning into pET30a (+) vector by SnapGene showed successful translation of epitope region. IMMSIM server was identified increased immunological responses. Finally, multi-epitope vaccine candidates were designed and validated their efficiency, it may pave the way for up-coming vaccine and diagnostic kit development.

In silico investigations of some Cyperus rotundus compounds as potential anti-inflammatory inhibitors of 5-LO and LTA4H enzymes

The present study aimed to experimentally identify the essential oil of Algerian Cyperus rotundus L. and to model the interaction of some known anti-inflammatory molecules with two key enzymes involved in inflammation, 5-Lypoxygenase (5-LO) and leukotriene A4 hydrolase (LTA4H). Gas chromatography/gas chromatography–mass spectrometry (GC/GC-MS) revealed that 92.7% of the essential oil contains 35 compounds, including oxygenated sesquiterpenes (44.2%), oxygenated monoterpenes (30.2%), monoterpene hydrocarbons (11.8%) and sesquiterpene hydrocarbons (6.5%). The major identified oxygenated terpenes are humulene oxide II, caryophyllene oxide, khusinol, agarospirol, spathulinol and trans-pinocarveol Myrtenol and α-terpineol are known to exhibit anti-inflammatory activities. Several complexes obtained after docking the natural terpenes with 5-LO and LTA4H have shown strong hydrogen bonding interactions. The best docking energies were found with α-terpineol, Myrtenol and khusinol. The interaction between the natural products and amino-acid residues HIS367, ILE673 and GLN363 appears to be critical for 5-LO inhibition, while the interaction with residues GLU271, HIS295, TYR383, TYR378, GLU318, GLU296 and ASP375 is critical for LTA4H inhibition. Molecular dynamics (MD) trajectories of the selected docked complexes showed stable backbone root mean square deviation (RMSD), supporting the stability of the natural product–enzyme interaction. Communicated by Ramaswamy H. Sarma

Remodeling and activation mechanisms of outer arm dyneins revealed by cryo-EM.

Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the trachea and protect the human body from viral infections. The main force generators of ciliary beating are the outer dynein arms (ODAs) which attach to the doublet microtubules. The bending of cilia is driven by the ODAs' conformational changes caused by ATP hydrolysis. Here, we report the native ODA complex structure attaching to the doublet microtubule by cryo-electron microscopy. The structure reveals how the ODA complex is attached to the doublet microtubule via the docking complex in its native state. Combined with coarse-grained molecular dynamic simulations, we present a model of how the attachment of the ODA to the doublet microtubule induces remodeling and activation of the ODA complex.

Synthesis and Identification of Novel Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach.

The novel coronavirus disease that arises in the end of 2019 (COVID-19) in Wuhan, China, has rapidly spread over the globe and was considered as a world pandemic. Currently, various antiviral therapies or vaccines are available, and many researches are ongoing for further treatments. Targeting the coronavirus’ main protease (key enzyme: 3CLpro) is growing in importance in anti-SARS-CoV-2 drug discovery process. The present study aims at predicting the antiviral activity of two novel compounds using in silico approaches that might become potential leads against SARS-CoV-2. The 3D structures of the new compounds are elucidated by single-crystal X-ray techniques. The interactions between different units of 4 and 5 were emphasized by analyzing their corresponding Hirshfeld surfaces and ESP plots. NBO and FMO analyses were investigated as well. Molecular docking combined with molecular dynamics simulations (MDs) was performed to investigate the binding modes and molecular interactions of 4 and 5 with the amino acids of coronavirus main protease (6LU7) protein. The best docking scores were obtained for both ligands through the major binding interactions via hydrogen/hydrophobic bonds with the key amino acids in the active site: HIS41, CYS145, MET49, MET165, HIS172, and GLU166 amino acids. A MD simulation study was also performed for 100 ns to validate the stability behavior of the main protease 3CLpro-ligand complexes. The MD simulation study successfully confirmed the stability of the ligands in the binding site as potent anti-SARS-CoV-2 (COVID-19) inhibitors. Additionally, MMPBSA energy of both docked complexes was determined as a validation assay of docking and MD simulations to validate compound conformation and interaction stability with 3CLpro. The synthesized compounds might be helpful in the fight against COVID-19 prior to biological activity confirmation in vitro and in vivo.

Reconstruction of the Fas-Based Death-Inducing Signaling Complex (DISC) Using a Protein–Protein Docking Meta-Approach

The death-inducing signaling complex (DISC) is a fundamental multiprotein complex, which triggers the extrinsic apoptosis pathway through stimulation by death ligands. DISC consists of different death domain (DD) and death effector domain (DED) containing proteins such as the death receptor Fas (CD95) in complex with FADD, procaspase-8, and cFLIP. Despite many experimental and theoretical studies in this area, there is no global agreement neither on the DISC architecture nor on the mechanism of action of the involved species. In the current work, we have tried to reconstruct the DISC structure by identifying key protein interactions using a new protein–protein docking meta-approach. We combined the benefits of five of the most employed protein–protein docking engines, HADDOCK, ClusPro, HDOCK, GRAMM-X, and ZDOCK, in order to improve the accuracy of the predicted docking complexes. Free energy of binding and hot spot interacting residues were calculated and determined for each protein–protein interaction using molecular mechanics generalized Born surface area and alanine scanning techniques, respectively. In addition, a series of in-cellulo protein-fragment complementation assays were conducted to validate the protein–protein docking procedure. The results show that the DISC formation initiates by dimerization of adjacent FasDD trimers followed by recruitment of FADD through homotypic DD interactions with the oligomerized death receptor. Furthermore, the in-silico outcomes indicate that cFLIP cannot bind directly to FADD; instead, cFLIP recruitment to the DISC is a hierarchical and cooperative process where FADD initially recruits procaspase-8, which in turn recruits and heterodimerizes with cFLIP. Finally, a possible structure of the entire DISC is proposed based on the docking results.

Structural Analysis of a Novel Aspartic-Type Endopeptidase from Moringa oleifera Seeds and Its Milk-Clotting Properties.

A novel aspartic-type endopeptidase was previously obtained from Moringa oleifera seeds; however, its specific milk-clotting properties have remained unclear. Here, we used various biophysical and molecular simulation approaches for characterizing the structure and function of the aspartic-type endopeptidase. The endopeptidase was preferentially active toward κ-casein (CN) and hydrolyzed it more than calf rennet; however, its ability to hydrolyze α-CN and β-CN was weaker than that of calf rennet. The endopeptidase cleaved κ-CN at Gln135-Asp136 and generated a 15 588.18 Da peptide with 135 amino acids. We further simulated the docking complex of the endopeptidase and κ-CN and found out that they possibly combined with each other via hydrogen bonds. The flocculation reaction between the endopeptidase and κ-CN indicated that milk coagulation occurred within 60 min. Overall, our observations suggest that the aspartic-type endopeptidase can be a potential rennet alternative for cheese making.

Identification of Naturally Occurring Antiviral Molecules for SARS-CoV-2 Mitigation

Aim: This study aimed to virtually screen the naturally occurring antiviral molecules for SARS-CoV-2 mitigation based on multiple molecular targets using docking and molecular dynamics simulations. Background: The coronavirus catastrophe (COVID-19) caused by a novel strain of coronavirus (SARS-CoV-2) has turned the world upside down at an unprecedented level and has been declared a pandemic by the World Health Organization. It has resulted in a huge number of infections as well as fatalities due to severe lower respiratory tract sickness. Objective: The objective of this study was the identification of inhibitors against the crucial molecular targets linked with viral infection caused by SARS-CoV-2. Materials and Methods: In silico screening of twenty naturally occurring antiviral molecules was performed using the Autodock docking tool. Further, molecular dynamics (MD) simulations were performed on the most stable docked complex between cysteine-like protease or 3CL protease (3CLpro) and the best-identified inhibitor (bilobetin). Results: 3CLpros is one of the very important molecular targets as it is involved in the replication process of the virus. In the present study, we have initially investigated the inhibitory potential of naturally occurring antiviral molecules against the activity of main viral protease (3CLpro) to put a halt to viral replication. The investigation had been carried out through docking of the molecules with 3CLpro. Based on the results, the three most potential molecules (bilobetin, ginkgetin and sciadopitysin) have been screened. Further, these molecules were subjected to checking their activity on other molecular targets like papain-like protease (PLpro), spike protein S1, RNA dependent RNA polymerase (RdRp), and Angiotensin-Converting Enzyme 2 (ACE2) receptor. In addition to 3CLpro inhibition, ginkgetin was also predicted as an inhibitor of PLpro. However, none of these three compounds was found to be effective on the rest of the molecular targets. Molecular Dynamics (MD) simulations of the most stable docked complex between 3CLpro and its best inhibitor (bilobetin) confirmed notable conformational stability of the docked complex under a dynamic state. Conclusion: Bilobetin alone or a combination of bilobetin and ginkgetin may be used to impede viral replication. These observations are solely based on the results from blind docking with protein molecules and need to be further corroborated with experimental results.