A new insight into protein-protein interactions and the effect of conformational alterations in PCNA

Analysis of cholesterol-recognition motifs of the plasma membrane Ca2+-ATPase

The plasma membrane Ca2+-ATPase (PMCA) is crucial for the fine tuning of intracellular calcium levels in eukaryotic cells. In this study, we show the presence of CARC sequences in all human and rat PMCA isoforms and we performed further analysis by molecular dynamics simulations. This analysis focuses on PMCA1, containing three CARC motifs, and PMCA4, with four CARC domains. In PMCA1, two CARC motifs reside within transmembrane domains, while the third is situated at the intracellular interface. The simulations depict more stable RMSD values and lower RMSF fluctuations in the presence of cholesterol, emphasizing its potential stabilizing effect. In PMCA4, a distinct dynamic was found. Notably, the total energy differences between simulations with cholesterol and phospholipids are pronounced in PMCA4 compared to PMCA1. RMSD values for PMCA4 indicate a more energetically favorable conformation in the presence of cholesterol, suggesting a robust interaction between CARCs and this lipid in the membranes. Furthermore, RMSF analysis for CARCs in both PMCA isoforms exhibit lower values in the presence of cholesterol compared to POPC alone. The analysis of H-bond occupancy and total energy values strongly suggests the potential interaction of CARCs with cholesterol. Given the crucial role of PMCAs in physiological calcium regulation and their involvement in diverse pathological processes, this study underscores the significance of CARC motifs and their interaction with cholesterol in elucidating PMCA function. These insights into the energetic preferences associated with CARC-cholesterol interactions offer valuable implications for understanding PMCA function in maintaining calcium homeostasis and addressing potential associated pathologies.

Binding patterns of inhibitors to different pockets of kinesin Eg5

The kinesin-5 family member, Eg5, plays very important role in the mitosis. As a mitotic protein, Eg5 is the target of various mitotic inhibitors. There are two targeting pockets in the motor domain of Eg5, which locates in the α2/L5/α3 region and the α4/α6 region respectively. We investigated the interactions between the different inhibitors and the two binding pockets of Eg5 by using all-atom molecular dynamics method. Combined the conformational analysis with the free-energy calculation, the binding patterns of inhibitors to the two binding pockets are shown. The α2/L5/α3 pocket can be divided into 4 regions. The structures and binding conformations of inhibitors in region 1 and 2 are highly conserved. The shape of α4/α6 pocket is alterable. The space of this pocket in ADP-binding state of Eg5 is larger than that in ADP·Pi-binding state due to the limitation of a hydrogen bond formed in the ADP·Pi-binding state. The results of this investigation provide the structural basis of the inhibitor-Eg5 interaction and offer a reference for the Eg5-targeted drug design.

Pre-eclampsia: Re-visiting pathophysiology, role of immune cells, biomarker identification and recent advances in its management

Pre-eclampsia (PE) is a hypertension condition that occurs exclusively during pregnancy and has the potential to impact nearly all organ systems. It is estimated to complicate approximately 2-8% of pregnancies worldwide. PE is a prominent medical disorder that poses a significant risk to pregnant mothers and their infants. This review commences by giving the most up-to- date concepts about the pathophysiology of PE. The condition involves atypical infiltration of trophoblast cells into the spiral arteries of the decidua and myometrium, resulting in an insufficient establishment of proper blood flow between the uterus and placenta. The aberrant activation of natural killer (NK) cells in both the peripheral blood and the decidua has been identified as one of the contributing factors to the development of PE. The strong evidence for the genetic etiology of PE is provided by the association between maternal killer cell immunoglobulin-like receptor (KIR) and Human Leukocyte Antigen (HLA-C) in trophoblast cells. Recent observations provide evidence that changes in the expression of anti-angiogenic factors in the placenta are the underlying cause of the clinical symptoms associated with the condition. This review also provides a comprehensive overview of the latest advancements in understanding the underlying causes of PE. It specifically highlights the emergence of new diagnostic biomarkers and their potential implications for therapeutic interventions in managing this medical condition.

Screening approach by a combination of computational and in vitro experiments: identification of fluvastatin sodium as a potential SIRT2 inhibitor

BACKGROUND

Sirtuins (SIRTs) are NAD+-dependent deacetylases that play various roles in numerous pathophysiological processes, holding promise as therapeutic targets worthy of further investigation. Among them, the SIRT2 subtype is closely associated with tumorigenesis and malignancies. Dysregulation of SIRT2 activation can regulate the expression levels of related genes in cancer cells, leading to tumor occurrence and metastasis.

METHODS

In this study, we used computer simulations to screen for novel SIRT2 inhibitors from the FDA database, based on which 10 compounds with high docking scores and good interactions were selected for in vitro anti-pancreatic cancer metastasis testing and enzyme binding inhibition experiments. The results showed that fluvastatin sodium may possess inhibitory activity against SIRT2. Subsequently, fluvastatin sodium was subjected to molecular docking experiments with various SIRT isoforms, and the combined results from Western blotting experiments indicated its potential as a SIRT2 inhibitor. Next, molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations were performed, revealing the binding mode of fluvastatin sodium at the SIRT2 active site, further validating the stability and interaction of the ligand-protein complex under physiological conditions.

RESULTS

Overall, this study provides a systematic virtual screening workflow for the discovery of SIRT2 activity inhibitors, identifies the potential inhibitory effect of fluvastatin sodium as a lead compound on SIRT2, and opens up a new direction for developing highly active and selectively targeted SIRT2 inhibitors.

Systematic exploration of network pharmacology, in silico modeling and pharmacokinetic profiling for vitamin E in polycystic ovarian syndrome

Aim: This study seeks to explore the possibility of using vitamin E to alleviate the symptoms of polycystic ovarian syndrome (PCOS). Methods: Various computational methods were employed, including network pharmacology utilizing a compound-target-pathway approach, Swiss ADME, OSIRIS® property explorer, pkCSM, PASS online web resource and MOLINSPIRATION® software. In addition, in silico analysis of vitamin E was performed with ten receptors. Results & discussion: Our findings highlight the diverse potential of vitamin E in alleviating PCOS. The observed influence on hormones is in line with existing PCOS theories regarding cyst development, further enhancing the therapeutic promise of vitamin E. Conclusion: In conclusion, our computational analysis indicates that vitamin E shows potential as a therapeutic agent for alleviating PCOS in adolescents.

Molecular dynamics simulation of the effect of temperature on the conformation of ubiquitin protein

CONTENT

Ubiquitin, a ubiquitous small protein found in all living organisms, is crucial for tagging proteins earmarked for degradation and holds pivotal importance in biomedicine. Protein functionality is intricately linked to its structure. To comprehend the impact of diverse temperatures on ubiquitin protein structure, our study delved into the energy landscape, hydrogen bonding, and overall structural stability of ubiquitin protein at varying temperatures. Through meticulous analysis of root mean square deviation and root mean square fluctuation, we validated the robustness of the simulation conditions employed. Within our simulated system, the bonding energy and electrostatic potential energy exhibited linear augmentation, while the van der Waals energy demonstrated a linear decline. Additionally, our findings highlighted that the α-Helix secondary structure of the ubiquitin protein gradually transitions toward helix destabilization under high-temperature conditions. The secondary structure of ubiquitin protein experiences distinct changes under varying temperatures. The outcomes of our molecular simulations offer a theoretical framework that enhances our comprehension of how temperature impacts the structural stability of ubiquitin protein. These insights contribute not only to a deeper understanding of iniquity's behavior but also hold broader implications in the realm of biomedicine and beyond.

METHODS

All the MD simulations were performed using the GROMACS software with GROMOS96 force field and SPC for water. The ubiquitin protein was put in the center of a cubic box with a length of 8 nm, a setting that allowed > 0.8 nm in the minimal distance between the protein surface and the box wall. To remove the possible coordinate collision of the configurations, in the beginning, the steepest descent method was used until the maximum force between atoms was under 100 kJ/mol·nm with a 0.01 nm step size. Minimization was followed by 30 ps of position-restrained MD simulation. The protein was restrained to its initial position, and the solvent was freely equilibrated. The product phase was obtained with the whole system simulated for 10 ns without any restraint using an integral time step of 1 fs with different temperatures. The cutoff for short-range electronic interaction was set to 1.5 nm. The long-range interactions were treated with a particle-mesh Ewald (PME) method with a grid width of 1.2 nm.

Discovery of a novel SHP2 allosteric inhibitor using virtual screening, FMO calculation, and molecular dynamic simulation

CONTEXT

SHP2 is a non-receptor protein tyrosine phosphatase to remove tyrosine phosphorylation. Functionally, SHP2 is an essential bridge to connect numerous oncogenic cell-signaling cascades including RAS-ERK, PI3K-AKT, JAK-STAT, and PD-1/PD-L1 pathways. This study aims to discover novel and potent SHP2 inhibitors using a hierarchical structure-based virtual screening strategy that combines molecular docking and the fragment molecular orbital method (FMO) for calculating binding affinity (referred to as the Dock-FMO protocol). For the SHP2 target, the FMO method prediction has a high correlation between the binding affinity of the protein-ligand interaction and experimental values (R2 = 0.55), demonstrating a significant advantage over the MM/PBSA (R2 = 0.02) and MM/GBSA (R2 = 0.15) methods. Therefore, we employed Dock-FMO virtual screening of ChemDiv database of ∼2,990,000 compounds to identify a novel SHP2 allosteric inhibitor bearing hydroxyimino acetamide scaffold. Experimental validation demonstrated that the new compound (E)-2-(hydroxyimino)-2-phenyl-N-(piperidin-4-ylmethyl)acetamide (7188-0011) effectively inhibited SHP2 in a dose-dependent manner. Molecular dynamics (MD) simulation analysis revealed the binding stability of compound 7188-0011 and the SHP2 protein, along with the key interacting residues in the allosteric binding site. Overall, our work has identified a novel and promising allosteric inhibitor that targets SHP2, providing a new starting point for further optimization to develop more potent inhibitors.

METHODS

All the molecular docking studies were employed to identify potential leads with Maestro v10.1. The protein-ligand binding affinities of potential leads were further predicted by FMO calculations at MP2/6-31G* level using GAMESS v2020 system. MD simulations were carried out with AmberTools18 by applying the FF14SB force field. MD trajectories were analyzed using VMD v1.9.3. MM/GB(PB)SA binding free energy analysis was carried out with the mmpbsa.py tool of AmberTools18. The docking and MD simulation results were visualized through PyMOL v2.5.0.

Gallic Acid-Modified Polyethylenimine-Polypropylene Carbonate-Polyethylenimine Nanoparticles: Synthesis, Characterization, and Anti-Periodontitis Evaluation

The aim of the research was to develop novel gallic acid (GA)-modified amphiphilic nanoparticles of polyethylenimine (PEI)-polypropylene carbonate (PPC)-PEI (PEPE) and comprehensively assess its properties as an antiperiodontitis nanoparticle targeting the Toll-like receptor (TLR). The first step is to evaluate the binding potential of GA to the core trigger receptors TLR2 and TLR4/MD2 for periodontitis using molecular docking techniques. Following this, we conducted NMR, transmission electron microscopy, and dynamic light scattering analyses on the synthesized PEPE nanoparticles. As the final step, we investigated the synthetic results and in vitro antiperiodontitis properties of GA-PEPE nanoparticles. The investigation revealed that GA exhibits potential for targeted binding to TLR2 and the TLR4/MD2 complex. Furthermore, we successfully developed 91.19 nm positively charged PEPE nanoparticles. Spectroscopic analysis indicated the successful synthesis of GA-modified PEPE. Additionally, CCK8 results demonstrated that GA modification significantly reduced the biotoxicity of PEPE. The in vitro antiperiodontitis properties assessment illustrated that 6.25 μM of GA-PEPE nanoparticles significantly reduced the expression of pro-inflammatory factors TNF-α, IL-1β, and IL-6. The GA-PEPE nanoparticles, with their targeted TLR binding capabilities, were found to possess excellent biocompatibility and antiperiodontitis properties. GA-PEPE nanoparticles will provide highly innovative input into the development of anti- periodontitis nanoparticles.

MVNMDA: A Multi-View Network Combing Semantic and Global Features for Predicting miRNA-Disease Association

A growing body of experimental evidence suggests that microRNAs (miRNAs) are closely associated with specific human diseases and play critical roles in their development and progression. Therefore, identifying miRNA related to specific diseases is of great significance for disease screening and treatment. In the early stages, the identification of associations between miRNAs and diseases demanded laborious and time-consuming biological experiments that often carried a substantial risk of failure. With the exponential growth in the number of potential miRNA-disease association combinations, traditional biological experimental methods face difficulties in processing massive amounts of data. Hence, developing more efficient computational methods to predict possible miRNA-disease associations and prioritize them is particularly necessary. In recent years, numerous deep learning-based computational methods have been developed and have demonstrated excellent performance. However, most of these methods rely on external databases or tools to compute various auxiliary information. Unfortunately, these external databases or tools often cover only a limited portion of miRNAs and diseases, resulting in many miRNAs and diseases being unable to match with these computational methods. Therefore, there are certain limitations associated with the practical application of these methods. To overcome the above limitations, this study proposes a multi-view computational model called MVNMDA, which predicts potential miRNA-disease associations by integrating features of miRNA and diseases from local views, global views, and semantic views. Specifically, MVNMDA utilizes known association information to construct node initial features. Then, multiple networks are constructed based on known association to extract low-dimensional feature embedding of all nodes. Finally, a cascaded attention classifier is proposed to fuse features from coarse to fine, suppressing noise within the features and making precise predictions. To validate the effectiveness of the proposed method, extensive experiments were conducted on the HMDD v2.0 and HMDD v3.2 datasets. The experimental results demonstrate that MVNMDA achieves better performance compared to other computational methods. Additionally, the case study results further demonstrate the reliable predictive performance of MVNMDA.

PCNA promotes PRRSV replication by increasing the synthesis of viral genome

Porcine reproductive and respiratory syndrome virus (PRRSV) is an RNA virus belonging to the Arteriviridae family. Currently, the strain has undergone numerous mutations, bringing massive losses to the swine industry worldwide. Despite several studies had been conducted on PRRSV, the molecular mechanisms by which it causes infection remain unclear. Proliferating cell nuclear antigen (PCNA) is a sign of DNA damage and it participates in DNA replication and repair. Therefore, in this study, we investigated the potential role of PCNA in PRRSV infection. We observed that PCNA expression was stable after PRRSV infection in vitro; however, PCNA was translocated from the nucleus to the cytoplasm. Notably, we found the redistribution of PCNA from the nucleus to the cytoplasm in cells transfected with the N protein. PCNA silencing inhibited PRRSV replication and the synthesis of PRRSV shorter subgenomic RNA (sgmRNA) and genomic RNA (gRNA), while PCNA overexpression promoted virus replication and PRRSV shorter sgmRNA and gRNA synthesis. By performing immunoprecipitation and immunofluorescence colocalization, we confirmed that PCNA interacted with replication-related proteins, namely NSP9, NSP12, and N, but not with NSP10 and NSP11. Domain III of the N protein (41-72 aa) interacted with the IDCL domain of PCNA (118-135 aa). Therefore, we propose cytoplasmic transport of PCNA and its subsequent influence on PRRSV RNA synthesis could be a viral strategy for manipulating cell function, thus PCNA is a potential target to prevent and control PRRSV infection.

Genetic Dissection of Budding Yeast PCNA Mutations Responsible for the Regulated Recruitment of Srs2 Helicase

DNA-damage tolerance (DDT) is a mechanism by which eukaryotes bypass replication-blocking lesions to resume DNA synthesis and maintain cell viability. In Saccharomyces cerevisiae, DDT is mediated by sequential ubiquitination and sumoylation of proliferating cell nuclear antigen (PCNA, encoded by POL30) at the K164 residue. Deletion of RAD5 or RAD18, encoding two ubiquitin ligases required for PCNA ubiquitination, results in severe DNA-damage sensitivity, which can be rescued by inactivation of SRS2 encoding a DNA helicase that inhibits undesired homologous recombination. In this study, we isolated DNA-damage resistant mutants from rad5Δ cells and found that one of them contained a pol30-A171D mutation, which could rescue both rad5Δ and rad18Δ DNA-damage sensitivity in a srs2-dependent and PCNA sumoylation-independent manner. Pol30-A171D abolished physical interaction with Srs2 but not another PCNA-interacting protein Rad30; however, Pol30-A171 is not located in the PCNA-Srs2 interface. The PCNA-Srs2 structure was analyzed to design and create mutations in the complex interface, one of which, pol30-I128A, resulted in phenotypes reminiscent of pol30-A171D. This study allows us to conclude that, unlike other PCNA-binding proteins, Srs2 interacts with PCNA through a partially conserved motif, and the interaction can be strengthened by PCNA sumoylation, which turns Srs2 recruitment into a regulated process. IMPORTANCE It is known that budding yeast PCNA sumoylation serves as a ligand to recruit a DNA helicase Srs2 through its tandem receptor motifs that prevent unwanted homologous recombination (HR) at replication forks, a process known as salvage HR. This study reveals detailed molecular mechanisms, in which constitutive PCNA-PIP interaction has been adapted to a regulatory event. Since both PCNA and Srs2 are highly conserved in eukaryotes, from yeast to human, this study may shed light to investigation of similar regulatory mechanisms.

Structure restoration and aggregate inhibition of V30M mutant transthyretin protein by potential quinoline molecules

Transthyretin (TTR) is a tetrameric protein found in human plasma and cerebrospinal fluid that functions as a transporter of thyroxine (T4) and retinol. A mutation resulting in the substitution of valine to methionine at position 30 (V30M) is the most common mutation that destabilizes the tetramer structure of TTR protein resulting in a fatal neuropathy known as TTR amyloidosis. The V30M TTR-induced neuropathy can be inhibited through stabilization of the TTR tetramer by the binding of small molecules. We accessed the potential of in-house synthesized quinoline molecules to stabilize the V30M TTR structure and analyzed the impact of protein-ligand interactions through molecular docking, molecular dynamics (MD) simulations, steered MD, and umbrella sampling simulations. This study revealed that the binding of quinoline molecules reverted back the structural changes including the residual flexibility, changes in secondary structural elements, and also restored the alterations in the electrostatic surface potential induced by the V30M mutation. Further, the top-most 4G and 4R molecules were compared with an FDA-approved drug (Tafamidis) and a reference quinoline molecule 14C. Here, we intend to suggest that the quinoline molecules could revert the structural changes, cease tetramer dissociation, prevent abnormal oligomerization and therefore could be developed as an effective therapeutics against TTR amyloidosis.

Molecular Dynamic Simulations Unravel the Underlying Impact of Missense Mutation in Autoimmunity Gene PTPN22 on Predisposition to Rheumatoid Arthritis

Genetic mutations in various proteins have been implicated with increased risk or severity of rheumatoid arthritis (RA) in different population groups. In the present case-control study, we have investigated the risk association of single nucleotide mutations present in some of the highly reported anti-inflammatory proteins and/or cytokines, with RA susceptibility in the Pakistani subjects. The study involves 310 ethnically and demographically similar participants from whom blood samples were taken and processed for DNA extraction. Through extensive data mining, 5 hotspot mutations reported in 4 genes, that is, interleukin (IL)-4 (-590; rs2243250), IL-10 (-592; rs1800872), IL-10 (-1082; rs1800896), PTPN22 (C1858T; rs2476601), and TNFAIP3 (T380G; rs2230926), were selected for RA susceptibility analyses using genotyping assays. The results demonstrated the association of only 2 DNA variants [rs2243250 (odds ratio, OR = 2.025, 95% confidence interval, CI = 1.357-3.002, P = 0.0005 Allelic) and rs2476601 (OR = 4.25, 95% CI = 1.569-11.55, P = 0.004 Allelic)] with RA susceptibility in the local population. The former single nucleotide mutation was nonfunctional, whereas the latter, residing in the exonic region of a linkage-proven autoimmunity gene PTPN22, was involved in R620→W620 substitution. Comparative molecular dynamic simulations and free-energy calculations revealed a radical impact on the geometry/confirmation of key functional moieties in the mutant protein leading to a rather weak binding of W620 variant with the interacting receptor (SRC kinase). The interaction imbalance and binding instabilities provide convincing clues about the insufficient inhibition of T cell activation and/or ineffective clearance of autoimmune clones-a hallmark of several autoimmune disorders. In conclusion, the present research describes the association of 2 hotspot mutations in IL-4 promoter and PTPN22 gene with RA susceptibility in the Pakistani study cohort. It also details how a functional mutation in PTPN22 impacts the overall protein geometry, charge, and/or receptor interactions to contribute to RA susceptibility.

Screening of phytochemicals as potential anti-breast cancer agents targeting HER2: an in-silico approach

Breast cancer is the most common cancer among women around the world. Human Epidermal growth factor Receptor-2 (HER2) is a membrane tyrosine kinase overexpressed in 30% of human breast cancers; thus, it serves as an important drug target. Currently available HER2 inhibitor lapatinib targets the ATP binding site of the cytoplasmic kinase domain, blocking autophosphorylation and activation of HER-2. However, it causes side effects like diarrhea, nausea, rash and possible liver toxicity. As phytochemicals have fewer side effects and are relatively affordable, they offer an effective alternative. Hence, we aimed to identify potential phytochemicals that could act as HER2 inhibitors employing computational methods such as molecular docking, molecular dynamic simulation, and ADMET prediction. Out of 1500 phytochemicals docked to the ATP binding site of the HER2 kinase domain, luxenchalcone, rhinacanthin Q, subtrifloralacton D, and 7,7″-dimethyllanaraflavone exhibited higher binding affinity than the reference inhibitor and satisfied the Lipinski's rule of five. Analysis of molecular dynamics simulation trajectory showed that Rhinacanthin Q, subtrifloralacton D, and 7,7″-dimethyllanaraflavone formed a stable and compact complex without vast conformational fluctuations. MM/PBSA binding free energy analysis revealed that Rhinacanthin Q, subtrifloralacton D, and 7,7″-dimethyllanaraflavone have high binding affinity to HER2. Therefore, Rhinacanthin Q, subtrifloralacton D, and 7,7″-dimethyllanaraflavone could be potential bioactive molecules to act as inhibitor of HER2 protein. Eventually, experimental studies are needed to evaluate the potentials of these phytochemicals further. The development of drug for HER2 positive breast cancer could be accelerated with the findings of our research. Communicated by Ramaswamy H. Sarma.

Deleterious single nucleotide polymorphisms (SNPs) of human IFNAR2 gene facilitate COVID-19 severity in patients: a comprehensive in silico approach

In humans, the dimeric receptor complex IFNAR2-IFNAR1 accelerates cellular response triggered by type I interferon (IFN) family proteins in response to viral infection including Coronavirus infection. Studies have revealed the association of the IFNAR2 gene with severe illness in Coronavirus infection and indicated the association of genomic variants, i.e. single nucleotide polymorphisms (SNPs). However, comprehensive analysis of SNPs of the IFNAR2 gene has not been performed in both coding and non-coding region to find the causes of loss of function of IFNAR2 in COVID-19 patients. In this study, we have characterized coding SNPs (nsSNPs) of IFNAR2 gene using different bioinformatics tools and identified deleterious SNPs. We found 9 nsSNPs as pathogenic and disease-causing along with a decrease in protein stability. We employed molecular docking analysis that showed 5 nsSNPs to decrease binding affinity to IFN. Later, MD simulations showed that P136R mutant may destabilize crucial binding with the IFN molecule in response to COVID-19. Thus, P136R is likely to have a high impact on disrupting the structure of the IFNAR2 protein. GTEx portal analysis predicted 14 sQTLs and 5 eQTLs SNPs in lung tissues hampering the post-transcriptional modification (splicing) and altering the expression of the IFNAR2 gene. sQTLs and eQTLs SNPs potentially explain the reduced IFNAR2 production leading to severe diseases. These mutants in the coding and non-coding region of the IFNAR2 gene can help to recognize severe illness due to COVID 19 and consequently assist to develop an effective drug against the infection.Communicated by Ramaswamy H. Sarma.

Identification of potential ZIKV NS2B-NS3 protease inhibitors from Andrographis paniculata: An insilico approach

Andrographis paniculata is a widely used medicinal plant for treating a variety of human infections. The plant's bioactives have been shown to have a variety of biological activities in various studies, including potential antiviral, anticancer, and anti-inflammatory effects in a variety of experimental models. The present investigation identifies a potent antiviral compound from the phytochemicals of Andrographis paniculata against Zika virus using computational docking simulation. The ZIKV NS2B-NS3 protease, which is involved in viral replication, has been considered as a promising target for Zika virus drug development. The bioactives from Andrographis paniculata, along with standard drugs as control were screened for their binding energy using AutoDock 4.2 against the viral protein. Based on the higher binding affinity the phytocompounds Bisandrographolide A (-11.7), Andrographolide (-10.2) and Andrographiside (-9.7) have convenient interactions at the binding site of target protein (ZIKV NS2B-NS3 protease) in comparison with the control drug. In addition, using insilico tools, the selected high-scoring molecules were analysed for pharmacological properties such as ADME (Absorption, Distribution, Metabolism, and Excretion profile) and toxicity. Andrographolide was reported to have strong pharmacodynamics properties and target accuracy based on the Lipinski rule and lower binding energy. The selected bioactives showed lower AMES toxicity and has potent antiviral activity against zika virus targets. Further, MD simulation studies validated Bisandrographolide A & Andrographolide as a potential hit compound by exhibiting good binding with the target protein. The compounds exhibited good hydrogen bonds with ZIKV NS2B-NS3 protease. As a result, bioactives from the medicinal plant Andrographis paniculata can be studied in vitro and in vivo to develop an antiviral phytopharmaceutical for the successful treatment of zika virus.Communicated by Ramaswamy H. Sarma.

A ricin-based peptide BRIP from Hordeum vulgare inhibits Mpro of SARS-CoV-2

COVID-19 pandemic caused by SARS-CoV-2 led to the research aiming to find the inhibitors of this virus. Towards this world problem, an attempt was made to identify SARS-CoV-2 main protease (M^pro) inhibitory peptides from ricin domains. The ricin-based peptide from barley (BRIP) was able to inhibit M^pro in vitro with an IC₅₀ of 0.52 nM. Its low and no cytotoxicity upto 50 µM suggested its therapeutic potential against SARS-CoV-2. The most favorable binding site on M^pro was identified by molecular docking and steered molecular dynamics (MD) simulations. The M^pro-BRIP interactions were further investigated by evaluating the trajectories for microsecond timescale MD simulations. The structural parameters of M^pro-BRIP complex were stable, and the presence of oppositely charged surfaces on the binding interface of BRIP and M^pro complex further contributed to the overall stability of the protein-peptide complex. Among the components of thermodynamic binding free energy, Van der Waals and electrostatic contributions were most favorable for complex formation. Our findings provide novel insight into the area of inhibitor development against COVID-19.

Virus-host interaction network analysis in Colorectal cancer identifies core virus network signature and small molecules

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Systematic analysis of virus-host networks identified key pathways in CRC.

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Core virus-CRC network revealed the growth pathway regulated by viruses.

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Short linear motif analysis identified druggable regions in virus proteins.

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Virtual screening revealed key anti-viral molecules against viral proteins.

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Molecular dynamics simulations showed the effect of anti-viral molecules.

Colorectal cancer (CRC) is a significant contributor to cancer-related deaths caused by an unhealthy lifestyle. Multiple studies reveal that viruses are involved in colorectal tumorigenesis. The viruses such as Human Cytomegalovirus (HCMV), Human papillomaviruses (HPV16 & HPV18), and John Cunningham virus (JCV) are known to cause colorectal cancer. The molecular mechanisms of cancer genesis and maintenance shared by these viruses remain unclear. We analysed the virus-host networks and connected them with colorectal cancer proteome datasets and extracted the core shared interactions in the virus-host CRC network. Our network topology analysis identified prominent virus proteins RL6 (HCMV), VE6 (HPV16 and HPV18), and Large T antigen (JCV). Sequence analysis uncovered short linear motifs (SLiMs) in each viral target. We used these targets to identify the antiviral drugs through a structure-based virtual screening approach. This analysis highlighted that temsavir, pimodivir, famotine, and bictegravir bind to each virus protein target, respectively. We also assessed the effect of drug binding using molecular dynamic simulations, which shed light on the modulatory effect of drug molecules on SLiM regions in viral targets. Hence, our systematic screening of virus-host networks revealed viral targets, which could be crucial for cancer therapy.

Antiviral Effect of Polyphenolic Substances in Geranium wilfordii Maxim against HSV-2 Infection Using in vitro and in silico Approaches

Background

Herpes simplex virus type 2 (HSV-2) infestation was the most widespread STD (sexually transmitted diseases) among humans and was the leading cause of infectious recurrent genital herpes. Existing therapies against HSV-2 did incompletely restrain the comeback of activated HSV-2 infestation. Geranium wilfordii Maxim had long been used as traditional Chinese medicine for treating the diseases owing to its anti-inflammatory and antiviral effects. Herein, the study was designed to investigate the antiviral activity of G.wilfordii and its potential effect in regulating the host's immune response.

Methods

To identify the stage of infection at which the compounds inhibited HSV-2, we performed virucidal, therapeutic, and prophylactic assays. The antiviral efficacy was evaluated by the analysis of viral components HSV-2 gD and VP16. The antiviral activities of these compounds were also evaluated by phenotypic analysis, such as cell proliferation and apoptosis. Molecular docking studies on candidate compounds were done to indicate binding interactions between the compounds and adopted compound targets.

Results

Quercetin, corilagin, and geraniin inhibited the replication of HSV-2, with geraniin showing greater TI. The obtained IC₅₀ value of quercetin was 204.7 μM and TI (IC₅₀/EC₅₀) was 5.1, whereas the obtained IC₅₀ value of corilagin was 118.0 μg/ml and TI was 4.05. Geraniin exhibited prominent antiviral activity with an IC₅₀ of 212.4 μM and an EC₅₀ of 18.37 μM, resulting in a therapeutic index (TI) of 11.56. Geraniin showed important in vitro virucidal activity through blocking viral attachment. Compared with the virus group, the apoptosis rates in quercetin-, corilagin-, and geraniin-treated groups were significantly decreased (p < 0.001).The expressions at the transcription genes of virus own replication key factors (including HSV-2 gD and VP16) and cytokines (including TBK1) of infected cells treated with quercetin, corilagin, and geraniin were inhibited. The in silico approaches demonstrated a high number of potential strong intermolecular interactions as hydrogen bonds between geraniin, corilagin, and the activity site of HSV-2 gD. Molecular docking studies demonstrated the effects of corilagin by targeting TBK1.

Conclusions

Together, these results highlighted the importance of G.wilfordii treatment in HSV-2 infection and underscored its therapeutic potential. However, additional in vitro and in vivo research was required to validate our findings.

Plant‐Based Natural Bioactive Compounds 2,4‐Ditert‐Butylphenolas: A Potential Candidates Against SARS‐Cov‐2019

The novel coronavirus 2019 is spreading around the world and causing serious concern. However, there is limited information about novel coronavirus that hinders the design of effective drug. Bioactive compounds are rich source of chemo preventive ingredients. In our present research focuses on identifying and recognizing bioactive chemicals in Lantana camara, by evaluating their potential toward new coronaviruses and confirming the findings using molecular docking, ADMET, network analysis and dynamics investigations.. The spike protein receptor binding domain were docked with 25 identified compounds and 2,4-Ditertbutyl-phenol (-6.3kcal/mol) shows highest docking score, its interactions enhances the increase in binding and helps to identify the biological activity. The ADME/toxicity result shows that all the tested compounds can serve as inhibitors of the enzymes CYP1A2 and CYP2D6. In addition, Molecular dynamics simulations studies with reference inhibitors were carried out to test the stability. This study identifies the possible active molecules against the receptor binding domain of spike protein, which can be further exploited for the treatment of novel coronavirus 2019. The results of the toxicity risk for phytocompounds and their active derivatives showed a moderate to good drug score.

In-silico validation of novel therapeutic activities of withaferin a using molecular docking and dynamics studies

Withaferin A is a bioactive molecule of W. somnifera. We access its efficacy against various target proteins associated with Cancer, Type-II Diabetes and hypercholesterolemia using molecular docking. Although it's efficacy against some of these targets have been reported earlier, we validate each mechanism in order to report the most appropriate mechanism of action. We explain the anti-cancer activity of Withaferin A by inhibition of Mortalin (mtHsp70) and Nrf2 protein with binding energies -8.85 kcal/mol and -12.59 kcal/mol respectively. Similarly, the anti-diabetic activity could be explained by inhibition of alpha and betα-glucosidase with binding energies -6.44 and -4.43 kcal/mol respectively and the cholesterol reduction could be explained by its ability to inhibition of NPC1 and SRB1 with binding energies -5.73 and -7.16 kcal/mol respectively. The molecular dynamics of the apoprotein and the protein-ligand complex simulated for the best targets of each activity namely Nrf2 protein for anti-cancer, α-glucosidase for anti-diabetic and SR-B1 for anti-hypercholesterolemia activity indicated the formation of stable complexes due to low RMSD deviations, low RMSF fluctuations and low RG values after the docking simulation. Finally, an ADME + T (Adsorption, distribution, metabolism, excretion and toxicity) prediction on Withaferin A showed that it obeyed all the Lipinsky's rules and qualified the drug-like criteria. All these results validate that Withaferin A possess potential anti-cancer, anti-diabetic and cholesterol reducing properties. This is the first report that indicates the possibility of Withaferin A binding and inhibiting SR-B1 as a mechanism of its anti-hypercholesterolemia activity.

A lesson for the maestro of the replication fork: Targeting the protein-binding interface of proliferating cell nuclear antigen for anticancer therapy

The proliferating cell nuclear antigen (PCNA) has emerged as a promising candidate for the development of novel cancer therapeutics. PCNA is a nononcogenic mediator of DNA replication that regulates a diverse range of cellular functions and pathways through a comprehensive list of protein-protein interactions. The hydrophobic binding pocket on PCNA offers an opportunity for the development of inhibitors to target various types of cancers and modulate protein-protein interactions. In the present study, we explored the binding modes and affinity of molecule I1 (standard molecule) with the previously suggested dimer interface pocket and the hydrophobic pocket present on the frontal side of the PCNA monomer. We also identified potential lead molecules from the library of in-house synthesized 3-methylenisoindolin-1-one based molecules to inhibit the protein-protein interactions of PCNA. Our results were based on robust computational methods, including molecular docking, conventional, steered, and umbrella sampling molecular dynamics simulations. Our results suggested that the standard inhibitor I1 interacts with the hydrophobic pocket of PCNA with a higher affinity than the previously suggested binding site. Also, the proposed molecules showed better or comparable binding free energies as calculated by the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach and further validated by enhanced umbrella sampling simulations. In vitro and in vivo methods could test the computationally suggested molecules for advancement in the drug discovery pipeline.

Identification of acridinedione scaffolds as potential inhibitor of DENV-2 C protein: An in silico strategy to combat dengue

Dengue is a prominent viral disease transmitted by mosquitoes to humans that affects mainly tropical and subtropical countries worldwide. The global spread of dengue virus (DENV) is mainly occurred by Aedes aegypti and Aedes albopictus mosquitoes. The dengue virus serotypes-2 (DENV-2) is a widely prevalent serotype of DENV, that causes the hemorrhagic fever and bleeding in the mucosa, which can be fatal. In the life cycle of DENV-2, a structural capsid (DENV-2 C) protein forms the nucleocapsid assembly and bind to the viral progeny RNA. For DENV-2 maturation, the nucleocapsid is a vital component. We used virtual ligand screening to filter out the best in-house synthesized acridinedione analogs (DSPD molecules) that could efficiently bind to DENV-2 C protein. The molecular docking and dynamics simulations studies were performed to analyze the effect of DSPD molecules on DENV-2 C protein after binding. Our findings showed that DSPD molecules strongly interacted with DENV-2 C protein, as evident from molecular interactions and several time-dependent molecular dynamics-driven analyses. Moreover, this study was also supported by the thermodynamic binding free energy and steered molecular dynamics simulations. Therefore, we intend to suggest that the DSPD3 molecule could be used as a potential therapeutic molecule against dengue complications as compared to the cocrystallized inhibitor ST-148. However, further studies are required to demonstrate the ability of DSPD3 to induce DENV-2 C tetramer formation.

Mechanistic behavior and subtle key events during DNA clamp opening and closing in T4 bacteriophage

Clamp loaders ensure processive DNA replication by loading the toroidal shaped sliding clamps onto the DNA. The sliding clamps serve as a platform for the attachment of polymerases and several other proteins associated with the regulation of various cellular processes. Clamp loaders are fascinating as nanomachines that engage in protein-protein and protein-DNA interactions. The loading mechanism of the clamp around dsDNA at the atomic level has not yet been fully explored. We performed microsecond timescale molecular dynamics simulations to reveal the dynamics of two different intermediate complexes involved in loading of the clamps around DNA. We conducted various time-dependent MD-driven analyses including the highly robust Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations to observe changes in the structural elements of the clamp loader-clamp-DNA complexes in open and closed states. Our studies revealed the structural consequences of ATP hydrolysis events at different subunits of the clamp loader. This study would help in a better understanding of the clamp loading mechanism and would allow tackling various complications that might arise due to irregularities in this process.

Identification of polypharmacological anticancerous molecules against Aurora kinase family of proteins

The Human Aurora Kinase (AURK) protein family is the key player of cell cycle events including spindle assembly, kinetochore formation, chromosomal segregation, centrosome separation, microtubule dynamics, and cytokinesis. Their aberrant expression has been extensively linked with chromosomal instability in addition to derangement of multiple tumor suppressors and oncoprotein regulated pathways. Therefore, the AURK family of kinases is a promising target for the treatment of various types of cancer. Over the past few decades, several potential inhibitors of AURK proteins have been identified and have reached various phases of clinical trials. But very few molecules have currently crossed the safety criteria due to their various toxic side effects. In the present study, we have adopted a computational polypharmacological strategy and identified four novel molecules that can target all three AURKs. These molecules were further investigated for their binding stabilities at the ATP binding pocket using molecular dynamics based simulation studies. The molecules selected adopting a multipronged computational approach can be considered as potential AURKs inhibitors for cancer therapeutics.

Comprehensive Characterization of the Coding and Non-Coding Single Nucleotide Polymorphisms in the Tumor Protein p63 (TP63) Gene Using In Silico Tools

Single nucleotide polymorphisms (SNPs) help to understand the phenotypic variations in humans. Genome-wide association studies (GWAS) have identified SNPs located in the tumor protein 63 (TP63) locus to be associated with the genetic susceptibility of cancers. However, there is a lack of in-depth characterization of the structural and functional impacts of the SNPs located at the TP63 gene. The current study was designed for the comprehensive characterization of the coding and non-coding SNPs in the human TP63 gene for their functional and structural significance. The functional and structural effects of the SNPs were investigated using a wide variety of computational tools and approaches, including molecular dynamics (MD) simulation. The deleterious impact of eight nonsynonymous SNPs (nsSNPs) affecting protein stability, structure, and functions was measured by using 13 bioinformatics tools. These eight nsSNPs are in highly conserved positions in protein and were predicted to decrease protein stability and have a deleterious impact on the TP63 protein function. Molecular docking analysis showed five nsSNPs to reduce the binding affinity of TP63 protein to DNA with significant results for three SNPs (R319H, G349E, and C347F). Further, MD simulations revealed the possible disruption of TP63 and DNA binding, hampering the essential protein function. PolymiRTS study found five non-coding SNPs in miRNA binding sites, and the GTEx portal recognized five eQTLs SNPs in single tissue of the lung, heart (LV), and cerebral hemisphere (brain). Characterized nsSNPs and non-coding SNPs will help researchers to focus on TP63 gene loci and ascertain their association with certain diseases.

Pathogenic genetic variants from highly connected cancer susceptibility genes confer the loss of structural stability

Genetic polymorphisms in DNA damage repair and tumor suppressor genes have been associated with increasing the risk of several types of cancer. Analyses of putative functional single nucleotide polymorphisms (SNP) in such genes can greatly improve human health by guiding choice of therapeutics. In this study, we selected nine genes responsible for various cancer types for gene enrichment analysis and found that BRCA1, ATM, and TP53 were more enriched in connectivity. Therefore, we used different computational algorithms to classify the nonsynonymous SNPs which are deleterious to the structure and/or function of these three proteins. The present study showed that the major pathogenic variants (V1687G and V1736G of BRCA1, I2865T and V2906A of ATM, V216G and L194H of TP53) might have a greater impact on the destabilization of the proteins. To stabilize the high-risk SNPs, we performed mutation site-specific molecular docking analysis and validated using molecular dynamics (MD) simulation and molecular mechanics/Poisson Boltzmann surface area (MM/PBSA) studies. Additionally, SNPs of untranslated regions of these genes affecting miRNA binding were characterized. Hence, this study will assist in developing precision medicines for cancer types related to these polymorphisms.

Universal two-point interaction of mediator KIX with 9aaTAD activation domains

The nine-amino-acid activation domain (9aaTAD) is defined by a short amino acid pattern including two hydrophobic regions (positions p3-4 and p6-7). The KIX domain of mediator transcription CBP interacts with the 9aaTAD domains of transcription factors MLL, E2A, NF-kB, and p53. In this study, we analyzed the 9aaTADs-KIX interactions by nuclear magnetic resonance. The positions of three KIX helixes α1-α2-α3 are influenced by sterically-associated hydrophobic I611, L628, and I660 residues that are exposed to solvent. The positions of two rigid KIX helixes α1 and α2 generate conditions for structural folding in the flexible KIX-L12-G2 regions localized between them. The three KIX I611, L628, and I660 residues interact with two 9aaTAD hydrophobic residues in positions p3 and p4 and together build a hydrophobic core of five residues (5R). Numerous residues in 9aaTAD position p3 and p4 could provide this interaction. Following binding of the 9aaTAD to KIX, the hydrophobic I611, L628, and I660 residues are no longer exposed to solvent and their position changes inside the hydrophobic core together with position of KIX α1-α2-α3 helixes. The new positions of the KIX helixes α1 and α2 allow the KIX-L12-G2 enhanced formation. The second hydrophobic region of the 9aaTAD (positions p6 and p7) provides strong binding with the KIX-L12-G2 region. Similarly, multiple residues in 9aaTAD position p6 and p7 could provide this interaction. In conclusion, both 9aaTAD regions p3, p4 and p6, p7 provide co-operative and highly universal binding to mediator KIX. The hydrophobic core 5R formation allows new positions of the rigid KIX α-helixes and enables the enhanced formation of the KIX-L12-G2 region. This contributes to free energy and is the key for the KIX-9aaTAD binding. Therefore, the 9aaTAD-KIX interactions do not operate under the rigid key-and-lock mechanism what explains the 9aaTAD natural variability.

In-silico evaluation of bioactive compounds from tea as potential SARS-CoV-2 nonstructural protein 16 inhibitors

Background and aim

A novel coronavirus, called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been found to cause COVID-19 in humans and some other mammals. The nonstructural protein 16 (NSP16) of SARS-CoV-2 plays a significant part in the replication of viruses and suppresses the ability of innate immune system to detect the virus. Therefore, inhibiting NSP16 can be a secure path towards identifying a potent medication against SARS-CoV-2. Tea (Camellia sinensis) polyphenols have been reported to exhibit potential treatment options against various viral diseases.

Methods

We conducted molecular docking and structural dynamics studies with a set of 65 Tea bioactive compounds to illustrate their ability to inhibit NSP16 of SARS-CoV-2. Moreover, post-simulations end state thermodynamic free energy calculations were estimated to strengthen our results.

Results and conclusion

Six bioactive tea molecules showed better docking scores than the standard molecule sinefungin. These results were further validated by MD simulations, where Theaflavin compound demonstrated lower binding free energy in comparison to the standard molecule sinefungin. The compound theaflavin could be considered as a novel lead compound for further evaluation by in-vitro and in-vivo studies.

Bioactive Molecules of Tea as Potential Inhibitors for RNA-Dependent RNA Polymerase of SARS-CoV-2

The coronavirus disease (COVID-19), a worldwide pandemic, is caused by the severe acute respiratory syndrome-corona virus-2 (SARS-CoV-2). At this moment in time, there are no specific therapeutics available to combat COVID-19. Drug repurposing and identification of naturally available bioactive molecules to target SARS-CoV-2 are among the key strategies to tackle the notorious virus. The enzyme RNA-dependent RNA polymerase (RdRp) performs a pivotal role in replicating the virus. RdRp is a prime target for Remdesivir and other nucleotides analog-based antiviral drugs. In this study, we showed three bioactive molecules from tea (epicatechin-3,5-di-O-gallate, epigallocatechin-3,5-di-O-gallate, and epigallocatechin-3,4-di-O-gallate) that showed better interaction with critical residues present at the catalytic center and the NTP entry channel of RdRp than antiviral drugs Remdesivir and Favipiravir. Our computational approach to identify these molecules included molecular docking studies, followed by robust molecular dynamics simulations. All the three molecules are readily available in tea and could be made accessible along with other medications to treat COVID-19 patients. However, these results require validation by further in vitro and in vivo studies.

An in-silico approach to identify the potential hot spots in SARS-CoV-2 spike RBD to block the interaction with ACE2 receptor

A novel acute viral pneumonia induced by SARS-CoV-2 exploded at the end of 2019, causing a severe medical and economic crisis. For developing specific pharmacotherapy against SARS-CoV-2, an in silico virtual screening was developed for the available in-house molecules. The conserved domain analysis was performed to identify the highly conserved and exposed amino acid regions in the SARS-CoV-2-S RBD sites. The Protein-Protein interaction analyses demonstrated the higher affinity between the SARS-CoV-2-S and ACE2 due to varieties of significant interactions between them. The computational alanine scanning mutation study has recognized the highly stabilized amino acids in the SARS-CoV-2-S RBD/ACE2 complex. The cumulative sequence investigations have inferred that Lys417, Phe486, Asn487, Tyr489, and Gln493 are perhaps the iconic target amino acids to develop a drug molecule or vaccine against SARS-CoV-2 infection. Most of the selected compounds include luteolin, zhebeirine, 3-dehydroverticine, embelin, andrographolide, ophiopogonin D, crocin-1, sprengerinin A, B, C, peimine, etc. were exhibited distinguish drug actions through the strong hydrogen bonding with the hot spots of the RBD. Besides, the 100 ns molecular dynamics simulation and free energy binding analysis showed the significant efficacy of luteolin to inhibit the infection of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Investigation of Cyc1 protein structure stability after H53I mutation using computational approaches to improve redox potential

Acidithiobacillus ferrooxidans (Af) is an acidophilic bacterium that grows in rigid surroundings and gets its own energy from the oxidation of Fe²⁺ to Fe³⁺. These bacteria are involved in the bioleaching process. Cyc₁ is a periplasmic protein with a crucial role in electron transportation in the respiratory chain. His53 of the Cyc₁ protein, involved in electron transfer to CoxB, was selected for mutation and bioinformatics studies. His53 was substituted by Ile using PyMol software. Molecular dynamics simulations were performed for wild and mutant types of Cyc₁ protein. The conformational changes of mutated protein were studied by analyzing RMSD, RMSF, SASA, Rg, H Bond, and DSSP. The results of the RMSF analysis indicated an increase in the flexibility of the ligand in the mutant. Finally, active site instability leads to an increase in the value of E₀ at the mutation point and improving electron transfer. On the other, His53 in Cyc₁ is interconnected to Glu126 in CoxB through the water molecule (W76) and hydrogen bonding. In the H53I mutation, there was a decrease in the distance between H2O 2030, 2033, and isoleucine 53, and subsequently, the distance to the water molecule 76 between the two proteins was reduced and strengthens the hydrogen bond between Cyc₁ and CoxB, finally improves electron transfer and the bioleaching process.

In silico drug repositioning based on the integration of chemical, genomic and pharmacological spaces

BACKGROUND

Drug repositioning refers to the identification of new indications for existing drugs. Drug-based inference methods for drug repositioning apply some unique features of drugs for new indication prediction. Complementary information is provided by these different features. It is therefore necessary to integrate these features for more accurate in silico drug repositioning.

RESULTS

In this study, we collect 3 different types of drug features (i.e., chemical, genomic and pharmacological spaces) from public databases. Similarities between drugs are separately calculated based on each of the features. We further develop a fusion method to combine the 3 similarity measurements. We test the inference abilities of the 4 similarity datasets in drug repositioning under the guilt-by-association principle. Leave-one-out cross-validations show the integrated similarity measurement IntegratedSim receives the best prediction performance, with the highest AUC value of 0.8451 and the highest AUPR value of 0.2201. Case studies demonstrate IntegratedSim produces the largest numbers of confirmed predictions in most cases. Moreover, we compare our integration method with 3 other similarity-fusion methods using the datasets in our study. Cross-validation results suggest our method improves the prediction accuracy in terms of AUC and AUPR values.

CONCLUSIONS

Our study suggests that the 3 drug features used in our manuscript are valuable information for drug repositioning. The comparative results indicate that integration of the 3 drug features would improve drug-disease association prediction. Our study provides a strategy for the fusion of different drug features for in silico drug repositioning.

Bioinformatics analysis of DNMT1 expression and its role in head and neck squamous cell carcinoma prognosis

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common type of malignancy in the world. DNA cytosine-5-methyltransferase 1 (DNMT1) play key roles in carcinogenesis and regulation of the immune micro-environment, but the gene expression and the role of DNMT1 in HNSCC is unknown. In this study, we utilized online tools and databases for pan-cancer and HNSCC analysis of DNMT1 expression and its association with clinical cancer characteristics. We also identified genes that positively and negatively correlated with DNMT1 expression and identified eight hub genes based on protein–protein interaction (PPI) network analysis. Enrichment analyses were performed to explore the biological functions related with of DNMT1. The Tumor Immune Estimation Resource (TIMER) database was performed to explore the relationship between DNMT1 expression and immune-cell infiltration. We demonstrated that DNMT1 gene expression was upregulated in HNSCC and associated with poor prognosis. Based on analysis of the eight hub genes, we determined that DNMT1 may be involved in cell cycle, proliferation and metabolic related pathways. We also found that significant difference of B cells infiltration based on TP 53 mutation. These findings suggest that DNMT1 related epigenetic alterations have close relationship with HNSCC progression, and DNMT1 could be a novel diagnostic biomarker and a promising therapeutic target for HNSCC.

Could Dermaseptin Analogue be a Competitive Inhibitor for ACE2 Towards Binding with Viral Spike Protein Causing COVID19?: Computational Investigation

Initial phase of COVID-19 infection is associated with the binding of viral spike protein S1 receptor binding domain (RBD) with the host cell surface receptor, ACE2. Peptide inhibitors typically interact with spike proteins in order to block its interaction with ACE2, and this knowledge would promote the use of such peptides as therapeutic scaffolds. The present study examined the competitive inhibitor activity of a broad spectrum antimicrobial peptide, Dermaseptin-S4 (S4) and its analogues. Three structural S4 analogues viz., S4 (K₄), S4 (K₂₀) and S4 (K₄K₂₀) were modelled by substituting charged lysine for non-polar residues in S4 and subsequently, docked with S1. Further, the comparative analysis of inter-residue contacts and non-covalent intermolecular interactions among S1–S4 (K₄), S1–S4 (K₄K₂₀) and S1–ACE2 complexes were carried out to explore their mode of binding with S1. Interestingly, S1–S4 (K₄) established more inter-molecular interactions compared to S4 (K₄K₂₀) and S1–ACE2. In order to substantiate this study, the normal mode analysis (NMA) was conducted to show how the structural stability of the flexible loop region in S1 is affected by atomic displacements in unbound S1 and docked complexes. Markedly, the strong interactions consistently maintained by S1–S4 (K₄) complex revealed their conformational transition over the harmonic motion period. Moreover, S1–S4 (K₄) peptide complex showed a higher energy deformation profile compared to S1–S4 (K₄K₂₀), where the higher energy deformation suggests the rigidity of the docked complex and thus it’s harder deformability, which is also substantiated by molecular dynamics simulation. In conclusion, S1–S4 (K₄) complex has definitely exhibited a functionally significant dynamics compared to S1–ACE2 complex; this peptide inhibitor, S4 (K₄) will need to be considered as the best therapeutic scaffold to block SARS-CoV-2 infection.

Himalayan bioactive molecules as potential entry inhibitors for the human immunodeficiency virus

The human immunodeficiency virus interacts with the cluster of differentiation 4 receptors and one of the two chemokine receptors (CCR5 and CXCR4) to gain entry in human cells. Both the co-receptors are essential for viral entry, replication, and are considered critical targets for antiviral drugs. In this study, bioactive molecules from different Himalayan plants were screened considering their potential to bind with the CCR5 and CXCR4 co-receptors. We utilized computational and thermodynamic parameters to validate the binding of the selected biomolecules to the active site of the co-receptors. The molecules Butyl 2-ethylhexyl phthalate and Dactylorhin-A showed a higher binding affinity with CCR5 co-receptor than the standard antagonist Maraviroc. Moreover, Pseudohypericin, Amarogentin, and Dactylorhin-E exhibited stronger interactions with CXCR4 than the co-crystallized inhibitor Isothiourea-1 t. Hence, we suggest that these molecules could be developed as potential inhibitors of the CCR5 and CXCR4 co-receptors. However, this require further in-vitro and in-vivo validation.

Prediction of potential inhibitors against SARS-CoV-2 endoribonuclease: RNA immunity sensing

The World Health Organization has classified the COVID-19 outbreak a pandemic which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and declared it a global health emergency. Repurposing drugs with minimum side effects are one approach to quickly respond in attempt to prevent the spread of COVID-19. SARS-CoV-2 encodes several RNA processing enzymes that are unusual and unique for single-stranded RNA viruses, including Nsp15, a hexameric endoribonuclease that discriminatory cleaves immediately 3′ of uridines. The structure of SARS-CoV-2 Nsp15 is reported to be homologous to that of the Nsp15 endoribonucleases of SARS-CoV and MERS-CoV, but it exhibits differences that may contribute to the greater virulence of SARS-CoV-2. This study aimed to identify drugs that targeted SARS-COV-2 Nsp15 using a molecular docking-based virtual screening of a library containing 10,000 approved and experimental drugs. The molecular docking results revealed 19 medications that demonstrated a good ability to inhibit Nsp15. Among all the candidated 19 drugs only five FDA approved drugs were used for further investigation by molecular dynamics simulation, the stability of Nsp15-ligand system was evaluated by calculating the RMSD, RMSF, radius of gyration and hydrogen bond profile. Furthermore, MM-PBSA method was employed to validate the binding affinity. According to the obtained results of MD, the complex of Olaparib was showed more stability and lower binding free energy than the control inhibitor during MD simulation time. Finally, we suggest that Olaparib is a potential drug for treating patients infected with SARS-CoV-2 and provide insight into the host immune response to viral RNA.

Communicated by Ramaswamy H. Sarma

Enhancing the catalytic activity of a GH5 processive endoglucanase from Bacillus subtilis BS-5 by site-directed mutagenesis

Processive endoglucanases possess both endo- and exoglucanase activity, making them attractive discovery and engineering targets. Here, a processive endoglucanase EG5C-1 from Bacillus subtilis was employed as the starting point for enzyme engineering. Referring to the complex structure information of EG5C-1 and cellohexaose, the amino acid residues in the active site architecture were identified and subjected to alanine scanning mutagenesis. The residues were chosen for a saturation mutagenesis since their variants showed similar activities to EG5C-1. Variants D70Q and S235W showed increased activity towards the substrates CMC and Avicel, an increase was further enhanced in D70Q/S235W double mutant, which displayed a 2.1- and 1.7-fold improvement in the hydrolytic activity towards CMC and Avicel, respectively. In addition, kinetic measurements showed that double mutant had higher substrate affinity (K_m) and a significantly higher catalytic efficiency (k_cat/K_m). The binding isotherms of wild-type EG5C-1 and double mutant D70Q/S235W suggested that the binding capability of EG5C-1 for the insoluble substrate was weaker than that of D70Q/S235W. Molecular dynamics simulations suggested that the collaborative substitutions of D70Q and S235W altered the hydrogen bonding network within the active site architecture and introduced new hydrogen bonds between the enzyme and cellohexaose, thus enhancing both substrate affinity and catalytic efficiency.

Antimicrobial, cytotoxicity, molecular modeling and DNA cleavage/binding studies of zinc-naproxen complex: switching DNA binding mode of naproxen by coordination to zinc ion

The intercalation DNA binding mode of the naproxen, a non-steroidal anti-inflammatory drug, has been reported previously. In this study, calf thymus deoxyribonucleic acid (CT-DNA) binding of zinc-naproxen complex, [Zn(naproxen)₂(MeOH)₂], at physiological pH has been investigated by multi-spectroscopic techniques and molecular docking. Zinc-naproxen complex displays significant binding property to the CT-DNA (K_b = 0.2 × 10⁵ L.mol^-1). All of the experimental results; relative increasing in viscosity of CT-DNA and fluorimetric studies using ethidium bromide (EB) and Hoechst 33258 probes, are indicative of groove binding mode of zinc-naproxen complex to CT-DNA. These results show that the coordination of naproxen to zinc metal switches the mode of binding from intercalation to groove. The molecular modeling also shows that the complex binds to the AT-rich region of minor groove of DNA. Structural and topography changes of DNA in interaction with the complex by atomic force microscopy (AFM) indicated that CT-DNA becomes swollen after interaction. The pUC18 plasmid DNA cleavage ability of zinc-naproxen complex by gel electrophoresis experiments revealed that zinc-naproxen complex cleaved supercoiled pUC18 plasmid DNA to nicked DNA. The cytotoxicity of the zinc complex performed by MTT method on HT29 and MCF7 cancer cell lines and on HEK 293 normal cell lines indicates that zinc complex has no cytotoxic effect on both HT29 and MCF7 cell lines but has better cytotoxicity effect on HEK 293 cell lines compared to cisplatin standard drug. The antimicrobial activity of the complex against Staphylococcus aureus and Escherichia coli bacteria revealed the high antimicrobial activity of the complex.Communicated by Ramaswamy H. Sarma.

RAB5A is associated with genes involved in exosome secretion: Integration of bioinformatics analysis and experimental validation

Exosomes, as cell-cell communicators with an endosomal origin, are involved in the progression of various diseases. RAB5A, a member of the small Rab GTPases family, which is well known as a key regulator of cellular endocytosis, is expected to be involved in exosome secretion. Here, we found the impact of RAB5A on exosome secretion from human hepatocellular carcinoma cell line using a rapid yet reliable bioinformatics approach followed by experimental analysis. Initially, RAB5A and exosome secretion-related genes were gathered from bioinformatics tools, namely, CTD, COREMINE, and GeneMANIA; and published papers. Protein-protein interaction (PPI) was then constructed by the Search Tool for Retrieval of Interacting Genes (STRING) database. Among them, several genes with different combined scores were validated by the real-time quantitative polymerase chain reaction (RT-qPCR) in stable RAB5A knockdown cells. Thereafter, to validate the bioinformatics results functionally, the impact of RAB5A knockdown on exosome secretion was evaluated. Bioinformatics analysis showed that RAB5A interacts with 37 genes involved in exosome secretion regulatory pathways. Validation by RT-qPCR confirmed the association of RAB5A with candidate interacted genes and interestingly showed that even medium to low combined scores of the STRING database could be experimentally valid. Moreover, the functional analysis demonstrated that the stable silencing of RAB5A could experimentally decrease exosome secretion. In conclusion, we suggest RAB5A as a regulator of exosome secretion based on our bioinformatics approach and experimental analysis. Also, we propose the usage of PPI-derived from the STRING database regardless of their combined scores in advanced bioinformatics analysis.

Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs

Background

The main protease (Mpro) of SARS-CoV-2 is involved in the processing of vital polypeptides required for viral genome replication and transcription and is one of the best-characterized targets to inhibit the progression of SARS-CoV-2 in infected individuals.

Methods

We screened a set of novel classes of acridinediones molecules to efficiently bind and inhibit the activity of the SARS-CoV-2 by targeting the Mpro. The repurposed FDA-approved antivirals were taken as standard molecules for this study. Long term (1.1 μs) MD simulations were performed to analyze the conformational space of the binding pocket of Mpro bound to the selected molecules.

Results

The molecules DSPD-2 and DSPD-6 showed more favorable MM-PBSA interaction energies and were seated more deeply inside the binding pocket of Mpro than the topmost antiviral drug (Saquinavir). Moreover, DSPD-5 also exhibited comparable binding energy to Saquinavir. The analysis of per residue contribution energy and SASA studies indicated that the molecules showed efficient binding by targeting the S1 subsite of the Mpro binding pocket.

Conclusion

The DSPD-2, DSPD-6, and DSPD-5 could be developed as potential inhibitors of SARS-CoV-2. Moreover, we suggest that targeting molecules to bind effectively to the S1 subsite could potentially increase the binding of molecules to the SARS-CoV-2 Mpro.

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A robust computational strategy applied to identify the potential lead for COVID-19.

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Repurposed FDA approved antiviral drugs were compared with a set of acridinedione analogs against Mpro of SARS-CoV-2.

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The acridinedione analogs have acceptable ADMET values and low toxicity profile.

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In-house synthesized acridinedione analogs showed good amount of interaction with Mpro of SARS-CoV-2.

Transcriptomic analysis of glioblastoma multiforme providing new insights into GPR17 signaling communication

Glioblastoma Multiforme (GBM) is one of the most aggressive malignant tumors in the central nervous system, which arises due to the failure or crosstalk in the signaling networks. GPR17, an orphan G protein-coupled receptor is anticipated to be associated with the biology of the GBM disease progression. In the present study, we have identified the differential expressions of around 170 genes along with GPR17 through the RNA-Seq analysis of 169 GBM samples. Coordinated expression patterns of all other gene products with this receptor were analysed using gene ontology and protein-protein interaction data. Several crucial signaling components and genes that play a significant role in tumor progression have been identified among which GPR17 was found to be significantly interacting with about 30 different pathways. High-throughput molecular docking of GPR17 by homology-based model against differentially expressed proteins, showed effective recognition and binding of PX, SH3, and Ig-like domains besides Gi protein. Pathways of PI3, Src, Ptdn, Ras, cytoplasmic tyrosine kinases, phospholipases, nexins and other proteins possessing these structural domains are identified as critical signaling components of the complex GBM signaling network. Our findings also provide a mechanistic insight of GPR17-T0510-3657 interaction, which potentially regulates the interaction of PX domain and helical mPTS recognition domain-containing proteins. Overall, our results demonstrate that GPR17 mediated signaling networks could be used as a therapeutic target for GBM.Communicated by Ramaswamy H. Sarma.

Discovery and in silico evaluation of aminoarylbenzosuberene molecules as novel checkpoint kinase 1 inhibitor determinants

Checkpoint kinase 1 (CHK1) is an essential kinase with a critical function in cell cycle arrest. Several potent inhibitors targeting CHK1 have been published, but most of them have failed in clinical trials. Acknowledging the emerging consequence of CHK1 inhibitors in medication of cancer, there is a demand for widening the chemical range of CHK1 inhibitors. In this research, we considered a set of in-house plant based semi-synthetic aminoarylbenzosuberene molecules as potential CHK1 inhibitors. Based on a combined computational research that consolidates molecular docking and binding free energy computations we recognized the crucial determinants for their receptor binding. The drug likeness of these molecules were also scrutinized based on their toxicity and bioavailibilty profile. The computational strategy indicates that the Bch10 could be regarded as a potential CHK1 inhibitor in comparison with top five co-crystallize molecules. Bch10 signifies a promising outlet for the development of potent inhibitors for CHK1.

Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus

SARS-CoV-2, an emerging coronavirus, has spread rapidly around the world, resulting in over ten million cases and more than half a million deaths as of July 1, 2020. Effective treatments and vaccines for SARS-CoV-2 infection do not currently exist. Previous studies demonstrated that nonstructural protein 16 (nsp16) of coronavirus is an S-adenosyl methionine (SAM)-dependent 2'-O-methyltransferase (2'-O-MTase) that has an important role in viral replication and prevents recognition by the host innate immune system. In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify clinically investigated and approved drugs which can act as promising inhibitors against nsp16 2'-O-MTase of SARS-CoV-2. Comparative analysis of primary amino acid sequences and crystal structures of seven human CoVs defined the key residues for nsp16 2-O'-MTase functions. Virtual screening and docking analysis ranked the potential inhibitors of nsp16 from more than 4,500 clinically investigated and approved drugs. Furthermore, molecular dynamics simulations were carried out on eight top candidates, including Hesperidin, Rimegepant, Gs-9667, and Sonedenoson, to calculate various structural parameters and understand the dynamic behavior of the drug-protein complexes. Our studies provided the foundation to further test and repurpose these candidate drugs experimentally and/or clinically for COVID-19 treatment.Communicated by Ramaswamy H. Sarma.

Structural based study to identify new potential inhibitors for dual specificity tyrosine-phosphorylation- regulated kinase

Background and Objectives The Dual-specificity tyrosine-phosphorylation regulated kinase-1A (DYRK1A) a serine/threonine kinase that has freshly gained recognition as an essential drug target due to the discovery of its involvement in pathological diseases. The development of new potent inhibitors of DYRK1A would contribute to clarify the molecular mechanisms of associated diseases. It would administer a new lead compound for molecular-targeted protein, which was the primary focus of our study. Methods The library of in-house synthesized pyrrolone-fused benzosuberene (PBS) compounds was docked with DYRK1A receptor. Further, molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) estimations were conducted to confirm our docking outcomes and compared the stability of chosen complexes with the 2C3 (standard molecule) complex. Results This study reports Ligand15, Ligand14, and Ligand11 as potent inhibitors which showed higher ligand efficiency, binding affinity, lipophilic ligand efficiency, and favorable torsion values as compared to 2C3. Conclusion The stated methodologies revealed a unique mechanism of active site binding. The binding interactions within the active site showed that the chosen molecules had notable interactions than the standard molecule, which led to the generation of potential compounds to inhibit DYRK1A.

Identification of novel and selective agonists for ABA receptor PYL3

Abscisic acid (ABA) although complicated and expensive to produce, plays an important role in signalling responsible for regulation of developmental manifestations such as seed maturation and surviving through stress conditions. Hence, development of cost effective molecules with minimal side effects that mimic the functions of ABA is the need of the hour. In this agreement, we screened a series of 27 in-house synthesized 3-methyleneisoindolin-1-one molecules over three ABA receptors (PYR1, PYL1, and PYL3). The commercial ABA agonist Pyrabactin was taken as a standard ligand in this study. The top three molecules for each receptor were selected and further evaluated to estimate the dynamical contribution and complex stability via Molecular Mechanics-Poisson Boltzmann surface area calculations. Two molecules (Mol26 and Mol25) showed higher binding free energy and stable complex conformation for PYL3 in comparison to Pyrabactin. This study revealed the structural basis of the binding mechanism of 3-methyleneisoindolin-1-one molecules with ABA receptors. Mol26 and Mol25 were identified for the development of specific PYL3 agonists with a vast potential in agriculture to accentuate the ABA like action in plants.

Identification of polyphenols from Broussonetia papyrifera as SARS CoV-2 main protease inhibitors using in silico docking and molecular dynamics simulation approaches

The current COVID-19 pandemic is caused by SARS CoV-2. To date, ∼463,000 people died worldwide due to this disease. Several attempts have been taken in search of effective drugs to control the spread of SARS CoV-2 infection. The main protease (Mpro) from SARS CoV-2 plays a vital role in viral replication and thus serves as an important drug target. This Mpro shares a high degree of sequence similarity (>96%) with the same protease from SARS CoV-1 and MERS. It was already reported that Broussonetia papyrifera polyphenols efficiently inhibit the catalytic activity of SARS CoV-1 and MERS Mpro. But whether these polyphenols exhibit any inhibitory effect on SARS CoV-2 Mpro is far from clear. To understand this fact, here we have adopted computational approaches. Polyphenols having proper drug-likeness properties and two repurposed drugs (lopinavir and darunavir; having binding affinity −7.3 to −7.4 kcal/mol) were docked against SARS CoV-2 Mpro to study their binding properties. Only six polyphenols (broussochalcone A, papyriflavonol A, 3'-(3-methylbut-2-enyl)-3',4',7-trihydroxyflavane, broussoflavan A, kazinol F and kazinol J) had interaction with both the catalytic residues (His41 and Cys145) of Mpro and exhibited good binding affinity (−7.6 to −8.2 kcal/mol). Molecular dynamic simulations (100 ns) revealed that all Mpro-polyphenol complexes are more stable, conformationally less fluctuated; slightly less compact and marginally expanded than Mpro-darunavir/lopinavir complex. Even the number of intermolecular H-bond and MM-GBSA analysis suggested that these six polyphenols are more potent Mpro inhibitors than the two repurposed drugs (lopinavir and darunavir) and may serve as promising anti-COVID-19 drugs.

Communicated by Ramaswamy H. Sarma