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MERS-CoV, a zoonotic virus, poses a serious threat to public health globally. Thus, it is imperative to develop an effective vaccination strategy for protection against MERS-CoV. Immunoinformatics and computational biology tools provide a faster and more cost-effective strategy to design potential vaccine candidates. In this work, the spike proteins from different strains of MERS-CoV were selected to predict HTL-epitopes that show affinity for T-helper MHC-class II HTL allelic determinant (HLA-DRB1:0101). The antigenicity and conservation of these epitopes among the selected spike protein variants in different MERS-CoV strains were analyzed. The analysis identified five epitopes with high antigenicity: QSIFYRLNGVGITQQ, DTIKYYSIIPHSIRS, PEPITSLNTKYVAPQ, INGRLTTLNAFVAQQ and GDMYVYSAGHATGTT. Then, a multi-epitope vaccine candidate was designed using linkers and adjuvant molecules. Finally, the vaccine construct was subjected to molecular docking with TLR5 (Toll-like receptor-5). The proposed vaccine construct had strong binding energy of −32.3 kcal/mol when interacting with TLR5.Molecular dynamics simulation analysis showed that the complex of the vaccine construct and TLR5 is stable. Analysis using in silico immune simulation also showed that the prospective multi-epitope vaccine design had the potential to elicit a response within 70 days, with the immune system producing cytokines and immunoglobulins. Finally, codon adaptation and in silico cloning analysis showed that the candidate vaccine could be expressed in the Escherichia coli K12 strain. Here we also designed support vaccine construct MEV-2 by using B-cell and CD8+ CTL epitopes to generate the complete immunogenic effect. This study opens new avenues for the extension of research on MERS vaccine development. Communicated by Ramaswamy H. Sarma

Background: The screening, design, and synthesis of various dimerization inhibitors have been an active area of interest for structure-based drug design efforts. Functionally important dimers, such as human immunodeficiency virus (HIV) protease and surviving, are being targeted for such studies over time. Computational repurposing of potential drug candidates provides a cost and time-efficient way in the drug discovery life cycle. Objective: Concerning the current coronavirus disease (COVID-19) scenario, the functionally active dimer of SARS-CoV-2 (severe acute respiratory syndrome) main protease (Mpro) is used as a target to screen possible dimerization inhibitors. Methods: A database of small molecule protein-protein interaction inhibitors was screened for the study. This study used molecular docking, followed by molecular dynamics (MD) simulation and post-simulation binding energy predictions. Results: From the selected 183 compounds, a diazene-based compound and a salicylic-type compound were identified as possible dimerization inhibitors in this study. These two compounds formed stable complexes with the Mpro during the MD simulations. The complexes formed by these two compounds were also unable to form important salt bridge interactions required for the dimerization of the protomers. Conclusion: Experimental studies on both compounds were previously conducted as dimerization inhibitors in HIV. The data led to the possibility of exploring the identified compounds as dimerization inhibitors, which could be important for SARS-CoV-2 therapeutics.

In recent years, the pharmaceutical business has seen a considerable increase in data digitization. With digitization, however, comes the challenge of obtaining, analyzing, and applying knowledge to solve complex clinical problems. Artificial intelligence (AI), which entails a variety of advanced tools and networks that can mimic human intellect, can overcome such challenges with traditional pharmaceutical development. Artificial intelligence and machine learning have a vast role in therapeutic development, including the prediction of drug target and properties of small molecules. By predicting the 3D protein structure, AI techniques, such as Alpha Fold, can help with structure-based drug development. Machine learning algorithms have been utilized to anticipate the properties of small molecules based on their chemical structure. Many researches have shown the importance of using in silico predictive ADMET (absorption, distribution, metabolism, excretion, and toxicity) models to speed up the discovery of small compounds with enhanced efficacy, safety, and dosage. This chapter discusses various roles of these methods in the development of effective therapeutics.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme-2 (ACE2) receptor, a critical component of the renin-angiotensin system (RAS) that initiates viral transmission. Most of the critical mutations found in SARS CoV-2 are associated with the RBD of the spike protein. The mutations have the potential to reduce the efficacy of vaccines and neutralizing antibodies. Preventing the interaction between Spike RBD and ACE2 is considered a viable therapeutic strategy since ACE2 binding by RBD is the first step in virus infection. Because the interactions between the two entities are critical for both viral transmission and therapeutic development, it is essential to understand their interactions in detail. In this review, the structural details of ACE2, RBD and their interactions are discussed. In addition, some critical mutations of RBD and their impact on ACE2-RBD interactions are also discussed.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme-2 (ACE2) receptor, a critical component of the renin-angiotensin system (RAS) that initiates the viral transmission. Most of the critical mutations found in SARS-CoV-2 are associated with the RBD of the spike protein. These mutations have the potential to reduce the efficacy of vaccines and neutralizing antibodies.In this review, the structural details of ACE2, RBD and their interactions are discussed. In addition, some critical mutations of RBD and their impact on ACE2-RBD interactions are also discussed.Preventing the interaction between Spike RBD and ACE2 is considered a viable therapeutic strategy since ACE2 binding by RBD is the first step in virus infection. Because the interactions between the two entities are critical for both viral transmission and therapeutic development, it is essential to understand their interactions in detail.

Viruses are a class of complex and dynamic macromolecular machines that can virtually infect all known life forms in the biosphere. This remarkable complexity results from a unique organization involving protein (capsid) and nucleic acid (DNA/RNA). A virus structure is metastable and highly responsive to environmental changes. Although major events of a virus life cycle are well characterized, several important questions with respect to how the nucleocapsid assemble/disassemble remain to be explored. In recent years due to enhanced computational power, molecular dynamics (MD) simulations have become an attractive alternative for addressing these questions since it is challenging to probe dynamic behavior with in vitro experimentation. The ability to simulate a complete virus particle provides an unprecedented atomic level resolution which can be used to understand its behavior under specific conditions. The current review outlines contributions made by all-atom and coarse-grained MD simulations towards understanding the mechanics and dynamics of virus structure and function. Databases and programs which facilitate such in silico investigations have also been discussed.

The rapid global spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has created an unprecedented healthcare crisis. The treatment for the severe respiratory illness caused by this virus is primarily symptomatic at this point, although the usage of a broad antiviral drug Remdesivir has been allowed on emergency basis by the Food and Drug Administration (FDA). The ever-increasing death toll highlights an urgent need for development of specific antivirals. In this work, we have utilized docking and simulation methods to identify small molecule inhibitors of SARS-CoV-2 Membrane (M) and Envelope (E) proteins, which are essential for virus assembly and budding. A total of 70 compounds from an Indian medicinal plant source (Azadirachta indica or Neem) were virtually screened against these two proteins and further analyzed with molecular dynamics simulations, which resulted in the identification of a few common compounds with strong binding to both structural proteins. The compounds bind to biologically critical regions of M and E, indicating their potential to inhibit the functionality of these components. We hope that our computational approach may result in the identification of effective inhibitors of SARS-CoV-2 assembly. Communicated by Ramaswamy H. Sarma

Pseudomonas aeruginosa is one of the most common pathogens associated with nosocomial infections and a great concern to immunocompromised individuals especially in the cases of cystic fibrosis, AIDS and burn wounds. The pathogenicity of P. aeruginosa is largely directed by the quorum sensing (QS) system. Hence, QS may be considered an important therapeutic target to combat P. aeruginosa infections. The anti-quorum sensing and anti-biofilm efficacy of aromatic aldehyde, 5-hydroxymethylfurfural (5-HMF) against P. aeruginosa PAO1 were assessed. At the sub-inhibitory concentration, 5-HMF suppressed the production of QS-controlled virulence phenotypes and biofilm formation in P. aeruginosa. It was also able to significantly enhance the survival rate of C. elegans infected with P. aeruginosa. The in silico studies revealed that 5-HMF could serve as a competitive inhibitor for the auto-inducer molecules as it exhibited a strong affinity for the regulatory proteins of the QS-circuits i.e. LasR and RhlR. In addition, a significant down-regulation in the expression of QS-related genes was observed suggesting the ability of 5-HMF in mitigating the pathogenicity of P. aeruginosa.

Viroporins are oligomeric, pore forming, viral proteins that play critical roles in the life cycle of pathogenic viruses. Viroporins like HIV-1 Vpu, Alphavirus 6 K, Influenza M2, HCV p7, and Picornavirus 2B, form discrete aqueous passageways which mediate ion and small molecule transport in infected cells. The alterations in host membrane structures induced by viroporins is essential for key steps in the virus life cycle like entry, replication and egress. Any disruption in viroporin functionality severely compromises viral pathogenesis. The envelope (E) protein encoded by coronaviruses is a viroporin with ion channel activity and has been shown to be crucial for the assembly and pathophysiology of coronaviruses. We used a combination of virtual database screening, molecular docking, all-atom molecular dynamics simulation and MM-PBSA analysis to test four FDA approved drugs - Tretinoin, Mefenamic Acid, Ondansetron and Artemether - as potential inhibitors of ion channels formed by SARS-CoV-2 E protein. Interaction and binding energy analysis showed that electrostatic interactions and polar solvation energy were the major driving forces for binding of the drugs, with Tretinoin being the most promising inhibitor. Tretinoin bound within the lumen of the channel formed by E protein, which is lined by hydrophobic residues like Phe, Val and Ala, indicating its potential for blocking the channel and inhibiting the viroporin functionality of E. In control simulations, tretinoin demonstrated a lower binding energy with a known target as compared to SARS-CoV-2 E protein. This work thus highlights the possibility of exploring Tretinoin as a potential SARS-CoV-2 E protein ion channel blocker and virus assembly inhibitor, which could be an important therapeutic strategy in the treatment for coronaviruses., Highlights • Screened a database of 1806 small molecule compounds from DrugBank for potential SARS CoV-2 E protein inhibitors. • Tested four FDA-approved drugs Tetinoin, Mefenamic acid, Ondansetron and Artemether as SARS CoV-2 E protein inhibitors. • Used a combination of molecular docking, MD simulations and MM-PBSA analysis to propose Tretinoin as a promising inhibitor.

The multidrug-resistant opportunistic pathogen, Pseudomonas aeruginosa is recognized to causes severe chronic infection in immune-compromised individuals. The production of numerous virulence factors and biofilm formation in P. aeruginosa is regulated by cell-to-cell communication system known as Quorum sensing (QS). The anti-QS property of the ethanolic leaf extract of Syzygium jambos in inhibiting the QS-regulated virulence traits was studied. At sub-MIC concentration, the test extract strongly attenuated the QS signaling circuit of P. aeruginosa resulting in significant decrease in the production of virulence determinants and biofilm formation. The ethanolic leaf extract was fractionated and separated using HPLC based activity profiling. The bioactive components contributing to the anti-QS efficacy of S. jambos were identified. Molecular docking of the active compounds revealed relatively strong binding affinity of the phytoconstituents for the transcriptional activators of the QS circuit in P. aeruginosa, i.e., LasR and RhlR, as compared to the natural ligands, 3-oxo-C12-HSL and C4-HSL. The findings indicated the potential of S. jambos and its bioactive components as QS antagonist in the treatment of chronic infections caused by P. aeruginosa.

The production of virulence determinants and biofilm formation in numerous pathogens is regulated by the cell-density-dependent phenomenon, Quorum sensing (QS). The QS system in multidrug resistant opportunistic pathogen, P. aeruginosa constitutes of three main regulatory circuits namely Las, Rhl, and Pqs which are closely linked to its pathogenicity and establishment of chronic infections. In spite intensive antibiotic therapy, P. aeruginosa continue to be an important cause of nosocomial infections and also the major cause of mortality in Cystic Fibrosis patients with 80% of the adults suffering from chronic P. aeruginosa infection. Hence, targeting QS circuit offers an effective intervention to the ever increasing problem of drug resistant pathogens. In the present study, the pentacyclic triterpenes i.e. Betulin (BT) and Betulinic acid (BA) exhibited significant attenuation in production of QS-regulated virulence factors and biofilm formation in P. aeruginosa, at the sub-lethal concentration. The test compound remarkably interfered in initial stages of biofilm development by decreasing the exopolysaccharide production and cell surface hydrophobicity. Based on the in vivo studies, the test compounds notably enhanced the survival of Caenorhabditis elegans infected with P. aeruginosa. Furthermore, molecular docking analysis revealed that BT and BA can act as a strong competitive inhibitor for QS receptors, LasR and RhlR. The findings suggest that BT and BA can serve as potential anti-infectives in the controlling chronic infection of P. aeruginosa.

Anti-quorum sensing and anti-biofilm efficacy of Cinnamic acid against Pseudomonas aeruginosa was comparatively assessed with respect to potent quorum sensing inhibitor, Baicalein. At sub-lethal concentration, Cinnamic acid effectively inhibited both the production of the QS-dependent virulence factors and biofilm formation in P. aeruginosa without affecting the viability of the bacterium. The phytocompound interfered with the initial attachment of planktonic cells to the substratum thereby causing reduction in biofilm development. In addition, the in vivo study indicated that the test compound protected Caenorhabditis elegans from the virulence factors of P. aeruginosa leading to reduced mortality. The in silico analysis revealed that Cinnamic acid can act as a competitive inhibitor for the natural ligands towards the ligand binding domain of the transcriptional activators of the quorum sensing circuit in P. aeruginosa, LasR and RhlR. The findings suggest that Cinnamic acid may serve as a novel quorum sensing based anti-infective in controlling P. aeruginosa infections.

Graphical abstract, SARS-CoV-2 has posed global challenge for healthcare due to COVID-19. The main protease (Mpro) of this virus is considered as a major target for drug development efforts. In this work, we have used virtual screening approach with molecular dynamics simulations to identify high affinity and low molecular weight alternatives of boceprevir, a repurposed drug currently being evaluated against Mpro. Out of 180 compounds screened, two boceprevir analogs (PubChem ID: 57841991 and 58606278) were reported as potential alternatives with comparable predicted protease inhibitor potential and pharmacological properties. Further experimental validation of the reported compounds may contribute to the ongoing investigation of boceprevir.

Viruses are parasite by nature and they are responsible for many diseases. Inhibitor development is very difficult for viruses due to their rapid mutative nature. A common approach for treating virus infection is targeting them at the genomic level and an encapsulation mechanism can be one of the targets. Sesbania mosaic virus (SeMV) is a spherical virus and its capsid is formed by a coat protein, which contains the Arginine Rich Motif (ARM). This ARM interacts with RNA operator loops present in their genome and starts encapsulation. Though the structure of SeMV was already solved by crystallography, it lacks the critical ARM domain. We predicted the full-length three-dimensional structure of this protein by using crystal structure (lacking ARM) as a template along with tertiary structure of RNA operator loops. Docking studies were performed to discover the interacting residues of protein and RNA which are driving protein and RNA to interact with each other. We observed that these interactions lead to conformation changes in the coat protein structure, which starts genome encapsulation process. The ARM region is found to be crucial for these interactions. Molecular dynamics simulation studies were performed to check the conformational changes and free energy landscapes were generated to check the viability of these changes in terms of energy. In this work we proposed one RNA operator loop that is responsible for noticeable conformational changes in the SeMV structure and might be involved in the activation of the viral protein. The results of this in silico study can be tested further through in vitro studies and can be used to stop encapsulation.

LGP2, a member of retinoic acid inducible gene-I like receptors (RLR), encoded by the gene DHX58 in human induces antiviral response against many RNA viruses. The LGP2 shares a considerable similarity to the amino acid sequence of Hef Helicase Domain, the helicase domain of RIG-I-like protein helicase-associated endonuclease (Hef), which is involved in RNA binding. Earlier studies suggest that RLR contains a conserved C-terminal domain (CTD), which is responsible for the binding specificity to the viral RNAs and C-terminal domain of LGP2 also takes part in RNA binding. The present study is aimed to explore the interactions of LGP2 and RNA, thereby finding the crucial residues for the interaction, with the help of in-silico tools. The predicted crucial residues were validated by docking and molecular dynamics simulation studies as well as by fitting the model on a LGP2 density map. Our results in this study suggest that the residues in the helicase domain of LGP2 are crucial for RNA binding and it is positioned around the groove region of LGP2. Though earlier experimental studies identified the RNA binding residues, but our in silico binding studies with the full length LGP2 predicted some additional residues that can be valuable

The gadolinium doped CaAl12O19 phosphor has been prepared by a low temperature solution combustion method in a short time and characterized using powder X-ray diffraction, energy dispersive analysis of X-ray mapping, electron paramagnetic resonance (EPR) and photoluminescence spectroscopic techniques. EPR and optical analysis of the sample confirm the presence of Gd(3+) in the CaAl12O19 matrix.

The capability of performing an array of functions with its single subunit structure makes T7 RNA polymerase (T7RNAP) as one of the simplest yet attractive target for various investigations ranging from structure determinations to several biological tests. In this study, with the help of molecular dynamics (MD) calculations and molecular docking, we investigated the effect of varying pH conditions on conformational flexibility of T7RNAP. We also studied its effect on the interactions with a well established inhibitor (heparin), substrate GTP and T7 promoter of T7RNAP. The simulation studies were validated with the help of three dimensional reconstructions of the polymerase at different pH environments using transmission electron microscopy and single particle analysis. On comparing the simulated structures, it was observed that the structure of T7RNAP changes considerably and interactions with its binding partners also changes as the pH shifts from basic to acidic. Further, it was observed that the C-terminal end plays a vital role in the inefficiency of the polymerase at low pH. Thus, this in-silico study may provide a significant insight into the structural investigations on T7RNAP as well as in designing potent inhibitors against it in varying pH environments.

Non-enveloped viruses require membrane-penetrating peptides for gaining entry inside the cytoplasm of host cells during the early stages of infection. Although several such peptides have been identified as essential components for non-enveloped virus entry, the molecular mechanism of membrane destabilization by these peptides is not well established. Here, we investigate the putative membrane penetrating peptide VP4 of Hepatitis A Virus (HAV) using a combination of molecular dynamics simulation and mutational studies. Using all-atom molecular dynamics simulation, we show that effective membrane disruption requires specific oligomeric forms (pentameric or hexameric) of VP4, while the monomeric form cannot cause similar disruption in target membranes. Reduction in hydrophobicity of VP4 significantly affects membrane penetration properties in silico, with even the oligomeric associations showing decreased membrane penetration efficiency. A synthetic peptide with a concurrent reduction in hydrophobicity is unable to disrupt liposomes in vitro, while the introduction of these mutations in the context of the viral genome adversely affects the propagation of HAV in cell culture. Taken together, our studies highlight hydrophobicity and oligomerization as some of the crucial mechanistic aspects of membrane penetration by capsid components of non-enveloped viruses.

Background T7 lysozyme (T7L), also known as N-acetylmuramoyl-L-alanine amidase, is a T7 bacteriophage gene product. It involves two functions: It can cut amide bonds in the bacterial cell wall and interacts with T7 RNA polymerase (T7RNAP) as a part of transcription inhibition. In this study, with the help of molecular dynamics (MD) calculations and computational interaction studies, we investigated the effect of varying pH conditions on conformational flexibilities of T7L and their influence on T7RNAP -T7L interactions. Results From the MD studies of the T7L at three different pH strengths viz. 5, neutral and 7.9 it was observed that T7L structure at pH 5 exhibited less stable nature with more residue level fluctuations, decrease of secondary structural elements and less compactness as compared to its counterparts: neutral pH and pH 7.9. The T-pad analysis of the MD trajectories identified local fluctuations in few residues that influenced the conformational differences in three pH strengths. From the docking of the minimum energy representative structures of T7L at different pH strengths (obtained from the free energy landscape analysis) with T7RNAP structures at same pH strengths, we saw strong interaction patterns at pH 7.9 and pH 5. The MD analysis of these complexes also confirmed the observations of docking study. From the combined in silico studies, it was observed that there are conformational changes in N-terminal and near helix 1 of T7L at different pH strengths, which are involved in the T7RNAP interaction, thereby varying the interaction pattern. Conclusion Since T7L has been used for developing novel therapeutics and T7RNAP one of the most biologically useful protein in both in-vitro and in vivo experiments, this in silico study of pH dependent conformational differences in T7L and the differential interaction with T7RNAP at different pH can provide a significant insight into the structural investigations on T7L and T7RNAP in varying pH environments. Electronic supplementary material The online version of this article (doi:10.1186/s12900-017-0077-9) contains supplementary material, which is available to authorized users.

RMSD matrices of the trajectories at a) pH 5, b) pH 7 and c) pH 7.9; Distribution of cluster ids were represented along the trajectories at d) pH 5, e) pH 7 and f) pH 7.9 at a function of time. (DOCX 1258 kb)

HADDOCK docking results of T7RNAP and Lysozyme (at pHÂ 7.9). A surface representation of the docked complex is shown. (DOCX 331Â kb)

Hydrophobic interactions within 5 angstroms for T7L representative structures at individual pH: a) pH 7, b) pH 7.9 and c) pH 5. The interactions were calculated by Protein Interactions Calculator (PIC) server ( http://pic.mbu.iisc.ernet.in ). (DOCX 979 kb)

HADDOCK docking results of T7RNAP and Lysozyme (at neutral pH). A surface representation of the docked complex is shown. (DOCX 274Â kb)

Plants in nature may face a wide range of favorable or unfavorable biotic and abiotic factors during their life cycle. Any of these factors may cause stress in plants; therefore, they have to be more adaptable to stressful environments and must acquire greater response to different stresses. The objective of this study is to retrieve and arrange data from the literature in a standardized electronic format for the development of information resources on potential stress responsive genes in Arabidopsis thaliana. This provides a powerful mean for manipulation, comparison, search, and retrieval of records describing the nature of various stress responsive genes in Arabidopsis thaliana. The database is based exclusively on published stress tolerance genes associated with plants.

HIV integrase is a 32 kDa protein produced from the C-terminal portion of the Pol gene product, and is an attractive target for new anti-HIV drugs. Integrase is an enzyme produced by a retrovirus (such as HIV) that enables its genetic material to be integrated into the DNA of the infected cell. Raltegravir and Elvitegravir are two important drugs against integrase., Comment: 9 pages, 6 tables