Interaction of fumigaclavine C with High Mobility Group Box 1 protein (HMGB1) and its DNA complex: A computational approach.
Abstract The fumigaclavines represent a small group of clavine-type alkaloids produced by the pathogenic fungus Aspergillus fumigatus. The leading compound in the family is fumigaclavine C (Fm-C) endowed with potent anti-inflammatory properties. Fm-C represses the production of several inflammatory cytokines in cells via a mechanism implicating a reduced nucleo-cytoplasmic transport and extracellular export of the alarmin protein HMGB1, through a direct drug-protein interaction, and a down-regulation of HMGB1 expression. We have investigated the interaction of Fm-C with HMGB1 using two complementary forms of the H...
Source: Computational Biology and Chemistry - October 31, 2020 Category: Bioinformatics Authors: Bailly C, Vergoten G Tags: Comput Biol Chem Source Type: research

Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay.
Abstract Caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 pandemic is ongoing, with no proven safe and effective vaccine to date. Further, effective therapeutic agents for COVID-19 are limited, and as a result, the identification of potential small molecule antiviral drugs is of particular importance. A critical antiviral target is the SARS-CoV-2 main protease (Mpro), and our aim was to identify lead compounds with potential inhibitory effects. We performed an initial molecular docking screen of 300 small molecules, which included phenolic compounds and fatty acids from our ...
Source: Computational Biology and Chemistry - October 23, 2020 Category: Bioinformatics Authors: Pitsillou E, Liang J, Karagiannis C, Ververis K, Darmawan KK, Ng K, Hung A, Karagiannis TC Tags: Comput Biol Chem Source Type: research

LMI-DForest: A deep forest model towards the prediction of lncRNA-miRNA interactions.
Abstract The interactions between miRNAs and long non-coding RNAs (lncRNAs) are subject to intensive recent studies due to its critical role in gene regulations. Computational prediction of lncRNA-miRNA interactions has become a popular alternative strategy to the experimental methods for identification of underlying interactions. It is desirable to develop the machine learning-based models for prediction of lncRNA-miRNA based on the experimentally validated interactions between lncRNAs and miRNAs. The accuracy and robustness of existing models based on machine learning techniques are subject to further improvemen...
Source: Computational Biology and Chemistry - October 20, 2020 Category: Bioinformatics Authors: Wang W, Guan X, Khan MT, Xiong Y, Wei DQ Tags: Comput Biol Chem Source Type: research

Computational analysis of TP53 vs. CTNNB1 mutations in hepatocellular carcinoma suggests distinct cancer subtypes with differential gene expression profiles and chromatin states.
In conclusion, our results strongly imply differential chromatin states and transcriptional regulation in relation to the mutational status of TP53 vs. CTNNB1, suggesting that these genes might be inducing different cellular pathways involving distinct chromatin environments during the course of carcinogenesis. PMID: 33096424 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - October 16, 2020 Category: Bioinformatics Authors: Biterge Süt B Tags: Comput Biol Chem Source Type: research

Transboundary Pathogenic microRNA Analysis Framework for Crop Fungi Driven by Biological Big Data and Artificial Intelligence Model.
Abstract Plant fungal diseases have been affecting the world's agricultural production and economic levels for a long time, such as rice blast, gray tomato mold, potato late blight etc. Recent studies have shown that fungal pathogens transmit microRNA as an effector to host plants for infection. However, bioassay-based verification analysis is time-consuming and challenging, and it is difficult to analyze from a global perspective. With the accumulation of fungal and plant-related data, data analysis methods can be used to analyze pathogenic fungal microRNA further. Based on the microRNA expression data of fungal ...
Source: Computational Biology and Chemistry - October 9, 2020 Category: Bioinformatics Authors: Zhang T, Chang H, Zhang B, Liu S, Zhao T, Zhao E, Zhao H, Zhang H Tags: Comput Biol Chem Source Type: research

Alkylated benzimidazoles: Design, synthesis, docking, DFT analysis, ADMET property, molecular dynamics and activity against HIV and YFV.
Abstract A series of alkylated benzimidazole derivatives was synthesized and screened for their anti-HIV, anti-YFV, and broad-spectrum antiviral properties. The physicochemical parameters and drug-like properties of the compounds were assessed first, and then docking studies and MD simulations on HIV-RT allosteric sites were conducted to find the possible mode of their action. DFT analysis was also performed to confirm the nature of the hydrogen bonding interaction of active compounds. The in silico studies indicated that the molecules behaved like possible NNRTIs. The nature - polar or non-polar and position of t...
Source: Computational Biology and Chemistry - October 6, 2020 Category: Bioinformatics Authors: Srivastava R, Gupta SK, Naaz F, Sen Gupta PS, Yadav M, Singh VK, Singh A, Rana MK, Gupta SK, Schols D, Singh RK Tags: Comput Biol Chem Source Type: research

Clinical significance of transcription factor RUNX2 in lung adenocarcinoma and its latent transcriptional regulating mechanism.
This study aims to thoroughly analysis the expression level and potential mechanisms of RUNX2 mRNA in LUAD. We applied in-house immunohistochemistry, high-throughput RNA-sequencing, and gene microarrays to comprehensively investigate the expression level of RUNX2 in LUAD. A pool standard mean difference (SMD) and summary receiver operating characteristic curves (SROC) were calculated to assess the integrated expression value of RUNX2 in LUAD. The hazard ratios (HRs) were integrated to evaluate the overall prognostic effect of RUNX2 on the LUAD patients. The differentially expressed genes (DEGs) of LUAD, the potential targe...
Source: Computational Biology and Chemistry - October 5, 2020 Category: Bioinformatics Authors: Yang DP, Huang WY, Chen G, Chen SW, Yang J, He RQ, Huang SN, Gan TQ, Ma J, Yang LJ, Song JH, Mo JX, Tang ZQ, Li CB, Zhou HF, Kong JL Tags: Comput Biol Chem Source Type: research

Editorial.
PMID: 33032890 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - October 5, 2020 Category: Bioinformatics Authors: Li W, Hamelberg D Tags: Comput Biol Chem Source Type: research

Improved pharmacological properties of nitrotyrosine drug via fluorination: A theoretical study.
In this study, the fluorination of 3-nitrotyrosine as an anti-Parkinson and anti-Alzheimer drug was explored using density functional theory calculations. We have investigated the most important chemical properties of 3-nitrotyrosine that affect the pharmacological activity of the drug. We found that the intramolecular hydrogen bonding and intramolecular charge of the drug were influenced by fluorine substitution. Our results also reveal that the fluorination altered the stability, solubility, and molecular polarity of the 3-nitrotyrosine drug. The density of state analysis also determines sharp resonance states of fluorin...
Source: Computational Biology and Chemistry - October 1, 2020 Category: Bioinformatics Authors: Zhang Y, Dong Z, Han J, Wei Z Tags: Comput Biol Chem Source Type: research

Homotherapy for heteropathy active components and mechanisms of Qiang-Huo-Sheng-Shi decoction for treatment of rheumatoid arthritis and osteoarthritis.
This study provides new insight into the molecular mechanisms behind how QHSSD presents homotherapy-for-heteropathy therapeutic efficacy in both OA and RA. For the first time, a two-disease model was linked with a TCM formula using network pharmacology to identify the key active components and understand the common mechanisms of its multi-pathway regulation. This study will inspire more innovative and important studies on the modern research of TCM formulas. PMID: 33035753 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - October 1, 2020 Category: Bioinformatics Authors: Shi YY, Li YQ, Xie X, Zhou YT, Zhang Q, Yu JL, Li P, Mi N, Li F Tags: Comput Biol Chem Source Type: research

Uncovering the pharmacological mechanism of motherwort (Leonurus japonicus Houtt.) for treating menstrual disorders: A systems pharmacology approach.
In this study, a network pharmacology-based approach was used that integrated drug-likeness evaluation, oral bioavailability prediction, target exploration, network construction, bioinformatic annotation and molecular docking to investigate the mechanisms that underlie motherwort treatment for MDs. In total, 29 bioactive compounds were collected from 51 compounds in motherwort, which shared 17 common MDs-related targets. Network analysis indicated that motherwort played a therapeutic role in MDs treatment through multiple components that acted on multiple targets. Pathway enrichment analysis showed that the putative target...
Source: Computational Biology and Chemistry - September 28, 2020 Category: Bioinformatics Authors: Wang C, Lv X, Liu W, Liu S, Sun Z Tags: Comput Biol Chem Source Type: research

A Recurrent Neural Network model to predict blood-brain barrier permeability.
Abstract The rapid development of computational methods and the increasing volume of chemical and biological data have contributed to an immense growth in chemical research. This field of study is known as "chemoinformatics," which is a discipline that uses machine-learning techniques to extract, process, and extrapolate data from chemical structures. One of the significant lines of research in chemoinformatics is the study of blood-brain barrier (BBB) permeability, which aims to identify drug penetration into the central nervous system (CNS). In this research, we attempt to solve the problem of BBB perm...
Source: Computational Biology and Chemistry - September 23, 2020 Category: Bioinformatics Authors: Alsenan S, Al-Turaiki I, Hafez A Tags: Comput Biol Chem Source Type: research

Structural and functional annotation of PR/SET Domain (PRDM) protein family: In-silico study elaborating role of PRDM12 mutation in congenital insensitivity to pain.
Abstract Congenital insensitivity to pain (CIP), classified as a type of hereditary sensory and autonomic neuropathies, is a rare disease in which the affected individuals fail to perceive sensation of pain. One of the PR/SET Domain Proteins, PRDM12, has been identified in recent past as a candidate gene for congenital insensitivity to pain. In the present study, we performed whole exome sequencing in a Pakistani family with CIP phenotype to ascertain the causative mutation. We identified a previously described alanine repeat duplication in PRDM12 (Ala353_Ala359dup) in this family. After this, we performed structu...
Source: Computational Biology and Chemistry - September 23, 2020 Category: Bioinformatics Authors: Mehmood S, Dad R, Ahmad A, Ullah MI, John P, Ali A, Hubner CA, Mohyuddin A, Hassan MJ Tags: Comput Biol Chem Source Type: research

Analysis of CRISPR-Cas systems in Gardnerella suggests its potential role in the mechanisms of bacterial vaginosis.
In this study, we analyzed CRISPR-Cas systems among the 13 Gardnerella species recently classified, considering that these systems act as prokaryotic immune systems against phages, plasmids, and other mobile genetic elements. In silico analyses for CRISPR-Cas systems mining over the 81 Gardnerella spp., strains genomes analyzed led to the identification of subtypes I-E and II-C. Spacers analyses showed a hypervariable region across species, providing a high resolution level in order to distinguish clonality in strains, which was supported with phylogenomic analyses based on Virtual Genomic Fingerprinting. Moreover, most of...
Source: Computational Biology and Chemistry - September 21, 2020 Category: Bioinformatics Authors: Ruiz-Hernández UE, Pelcastre-Rodriguez LI, Cabrero-Martínez OA, Hernández-Cortez C, Castro-Escarpulli G Tags: Comput Biol Chem Source Type: research

Identification of novel vaccine candidates against carbapenem resistant Klebsiella pneumoniae: A systematic reverse proteomic approach.
Abstract Klebsiella pneumoniae is declared as antibiotic resistant by WHO, with the critical urgency of developing novel antimicrobial therapeutics as drug resistance is the second most dangerous threat after terrorism. Besides many attempts still, there is no effective vaccine available against K. pneumoniae. By utilizing all the available proteomic data we prioritized the novel proteins ideal for vaccine development using bioinformatics tools and techniques. Among the huge data, eight proteins passed all the barriers and were considered ideal candidates for vaccine development. These include: copper silver efflu...
Source: Computational Biology and Chemistry - September 20, 2020 Category: Bioinformatics Authors: Mehmood A, Naseer S, Ali A, Fatimah H, Rehman S, Kiani A Tags: Comput Biol Chem Source Type: research

Identification of novel human USP2 inhibitor and its putative role in treatment of COVID-19 by inhibiting SARS-CoV-2 papain-like (PLpro) protease.
Abstract Human ubiquitin carboxyl-terminal hydrolase-2 (USP2) inhibitors, such as thiopurine analogs, have been reported to inhibit SARS-CoV papain-like proteases (PLpro). The PLpro have significant functional implications in the innate immune response during SARS-CoV-2 infection and considered an important antiviral target. Both proteases share strikingly similar USP fold with right-handed thumb-palm-fingers structural scaffold and conserved catalytic triad Cys-His-Asp/Asn. In this urgency situation of COVID-19 outbreak, there is a lack of in-vitro facilities readily available to test SARS-CoV-2 inhibitors in who...
Source: Computational Biology and Chemistry - September 12, 2020 Category: Bioinformatics Authors: Mirza MU, Ahmad S, Abdullah I, Froeyen M Tags: Comput Biol Chem Source Type: research

ICTC-RAAC: An improved web predictor for identifying the types of ion channel-targeted conotoxins by using reduced amino acid cluster descriptors.
Abstract Conotoxins are small peptide toxins which are rich in disulfide and have the unique diversity of sequences. It is significant to correctly identify the types of ion channel-targeted conotoxins because that they are considered as the optimal pharmacological candidate medicine in drug design owing to their ability specifically binding to ion channels and interfering with neural transmission. Comparing with other feature extracting methods, the reduced amino acid cluster (RAAC) better resolved in simplifying protein complexity and identifying functional conserved regions. Thus, in our study, 673 RAACs genera...
Source: Computational Biology and Chemistry - September 6, 2020 Category: Bioinformatics Authors: Sun Z, Huang S, Zheng L, Liang P, Yang W, Zuo Y Tags: Comput Biol Chem Source Type: research

lncRNA-miRNA-mRNA interaction network for colorectal cancer; An in silico analysis.
CONCLUSIONS: We introduced a set of lncRNAs, mRNAs and miRNAs differentially expressed in CRC which might be considered for further experimental research as potential biomarkers of CRC development. PMID: 32932199 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - September 6, 2020 Category: Bioinformatics Authors: Ghasemi T, Khalaj-Kondori M, Hosseinpour Feizi MA, Asadi P Tags: Comput Biol Chem Source Type: research

Site mapping and small molecule blind docking reveal a possible target site on the SARS-CoV-2 main protease dimer interface.
Abstract The SARS-CoV-2 virus is causing COVID-19 resulting in an ongoing pandemic with serious health, social, and economic implications. Much research is focused in repurposing or identifying new small molecules which may interact with viral or host-cell molecular targets. An important SARS-CoV-2 target is the main protease (Mpro), and the peptidomimetic α-ketoamides represent prototypical experimental inhibitors. The protease is characterised by the dimerization of two monomers each which contains the catalytic dyad defined by Cys145 and His41 residues (active site). Dimerization yields the functional hom...
Source: Computational Biology and Chemistry - September 4, 2020 Category: Bioinformatics Authors: Liang J, Karagiannis C, Pitsillou E, Darmawan KK, Ng K, Hung A, Karagiannis TC Tags: Comput Biol Chem Source Type: research

iPiDA-sHN: Identification of Piwi-interacting RNA-disease associations by selecting high quality negative samples.
In this study, we proposed a new computational predictor named iPiDA-sHN to predict potential piRNA-disease associations. iPiDA-sHN presented the piRNA-disease pairs by incorporating piRNA sequence information, the known piRNA-disease association network, and the disease semantic graph. High-level features of piRNA-disease associations were extracted by the Convolutional Neural Network (CNN). Two-step positive-unlabeled learning strategy based on Support Vector Machine (SVM) was employed to select the high quality negative samples from the unknown piRNA-disease pairs. Finally, the SVM predictor trained with the known piRNA...
Source: Computational Biology and Chemistry - August 28, 2020 Category: Bioinformatics Authors: Wei H, Ding Y, Liu B Tags: Comput Biol Chem Source Type: research

A review of Cloud computing technologies for comprehensive microRNA analyses.
Abstract Cloud computing revolutionized many fields that require ample computational power. Cloud platforms may also provide huge support for microRNA analysis mainly through disclosing scalable resources of different types. In Clouds, these resources are available as services, which simplifies their allocation and releasing. This feature is especially useful during the analysis of large volumes of data, like the one produced by next generation sequencing experiments, which require not only extended storage space but also a distributed computing environment. In this paper, we show which of the Cloud properties and...
Source: Computational Biology and Chemistry - August 28, 2020 Category: Bioinformatics Authors: Mrozek D Tags: Comput Biol Chem Source Type: research

ncRDeep: Non-coding RNA classification with convolutional neural network.
Abstract A non-coding RNA (ncRNA) is a kind of RNA that is not converted into protein, however, it is involved in many biological processes, diseases, and cancers. Numerous ncRNAs have been identified and classified with high throughput sequencing technology. Hence, accurate ncRNAs class prediction is important and necessary for further study of their functions. Several computation techniques have been employed to predict the class of ncRNAs. Recent classification methods used the secondary structure as their primary input. However, the computational tools of RNA secondary structure are not accurate enough which a...
Source: Computational Biology and Chemistry - August 26, 2020 Category: Bioinformatics Authors: Chantsalnyam T, Lim DY, Tayara H, Chong KT Tags: Comput Biol Chem Source Type: research

Computational prediction of miRNA/mRNA duplexomes at the whole human genome scale reveals functional subnetworks of interacting genes with embedded miRNA annealing motifs.
Abstract Perfect annealing between microRNAs (miRNAs) and messenger RNAs (mRNAs) was computationally searched at a broad scale in the human genome to determine whether theoretical pairing is restrictively represented in functional subnetworks or is randomly distributed. Massive RNA interference (RNAi) pairing motifs in genes constitute a remarkable subnetwork that displays highly genetically and biochemically interconnected genes. These analyses show unexpected repertoires of genes defined by their congruence in comatching with miRNAs at numerous sites and by their interconnection based on protein/protein interact...
Source: Computational Biology and Chemistry - August 21, 2020 Category: Bioinformatics Authors: Pasquier C, Robichon A Tags: Comput Biol Chem Source Type: research

FWAVina: A novel optimization algorithm for protein-ligand docking based on the fireworks algorithm.
Abstract Protein-ligand docking is an essential process that has accelerated drug discovery. How to accurately and effectively optimize the predominant position and orientation of ligands in the binding pocket of a target protein is a major challenge. This paper proposed a novel ligand binding pose search method called FWAVina based on the fireworks algorithm, which combined the fireworks algorithm with the efficient Broyden-Fletcher-Goldfarb-Shannon local search method adopted in AutoDock Vina to address the pose search problem in docking. The FWA was used as a global optimizer to rapidly search promising poses, ...
Source: Computational Biology and Chemistry - August 19, 2020 Category: Bioinformatics Authors: Li J, Song Y, Li F, Zhang H, Liu W Tags: Comput Biol Chem Source Type: research

Gastric cancer in proximal site exerts poorer survival outcome with divergent genetic features than distal site.
CONCLUSION: The current study first demonstrated that PGC exerts poorer survival outcome than DGC based on the SEER database. Further bioinformatic investigation depicts the specific genetic features for PGC and DGC, which may generate differences in tumor malignancy. Our findings provide promising genetic targets for future specific and individualized gastric cancer therapy. PMID: 32841839 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - August 17, 2020 Category: Bioinformatics Authors: Zhao Q, Chen K, Tong W, Ge C, Zhao D Tags: Comput Biol Chem Source Type: research

Data fusion-based algorithm for predicting miRNA-Disease associations.
In this study, we constructed a novel miRNA-gene-disease fusion (MGDF) algorithm by integrating three genome-wide networks, namely microRNA (miRNA), gene function, and disease similarity networks. The data fusion method was applied to construct a miRNA-gene-disease association network model from these networks to explore miRNA-disease associations mediated by genes with similar functions. mmiRNAs bind to their target genes and regulate their expression, so the miRNA-gene and gene-disease regulatory relationships were included in the network model to more accurately predict miRNA-disease associations. The proposed MGDF was ...
Source: Computational Biology and Chemistry - August 11, 2020 Category: Bioinformatics Authors: Wang C, Sun K, Wang J, Guo M Tags: Comput Biol Chem Source Type: research

Transient pockets as mediators of gas molecules routes inside proteins: The case study of dioxygen pathway in homogentisate 1,2-dioxygenase and its implication in Alkaptonuria development.
Abstract Alkaptonuria (AKU) is an ultra-rare disease caused by mutations in homogentisate 1,2-dioxygenase (HGD) enzyme, characterized by the loss of enzymatic activity and the accumulation of its substrate, homogentisic acid (HGA) in different tissues, leading to ochronosis and organ degeneration. Although the pathological effects of HGD mutations are largely studied, less is known about the structure of the enzyme, in particular the pathways for dioxygen diffusion to the active site, required for the enzymatic reaction, are still uninvestigated. In the present project, the combination of two in silico techniques,...
Source: Computational Biology and Chemistry - August 5, 2020 Category: Bioinformatics Authors: Bernini A, Galderisi S, Spiga O, Amarabom CO, Santucci A Tags: Comput Biol Chem Source Type: research

In silico modeling for dual inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzymes in Alzheimer's disease.
Abstract In this research, we have implemented two-dimensional quantitative structure-activity relationship (2D-QSAR) modeling using two different datasets, namely, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzyme inhibitors. A third dataset has been derived based on their selectivity and used for the development of partial least squares (PLS) based regression models. The developed models were extensively validated using various internal and external validation parameters. The features appearing in the model against AChE enzyme suggest that a small ring size, higher number of -CH2- groups, high...
Source: Computational Biology and Chemistry - August 4, 2020 Category: Bioinformatics Authors: Kumar V, Saha A, Roy K Tags: Comput Biol Chem Source Type: research

Identification of key pathways and genes responsible for aggressive behavior.
Abstract Aggression is a complex behavior, underpinned by cross talk between several biomolecules. To date a composite molecular network of the behavioral disorder has not been constructed. The present study aims to develop the same from the system network analyses recruiting genes with empirical evidence demonstrating their role in the incidence and progression of aggression. In short, 327 genes were recruited in the study after extensive literature survey and subsequent shortlisting by sieving out the comorbidities like cancer and other pathological and physiological ailments, other languages and repeated citati...
Source: Computational Biology and Chemistry - August 3, 2020 Category: Bioinformatics Authors: Uddin N, Hussain M, Rauf I, Zaidi SF Tags: Comput Biol Chem Source Type: research

Deciphering potential inhibitors targeting THI4 of Fusarium solani sp. to combat fungal keratitis: An integrative computational approach.
Abstract Mycotic keratitis is a fungal infection of corneal epithelium. It is more common in tropical and subtropical countries and is one of the leading causes of blindness. Many of the antifungal drugs have been less effective in treating this condition and certain drugs which are efficient and yet limited in use due to its extreme side effects. Hence, in this study an attempt is made to identify potential and least toxic antifungal inhibitors that targets thiamine thiazole synthase, a novel target for suppressing Fusarium solani subsp.pisi (Nectria haematococca MPVI) infections, to combat mycotic keratitis. Int...
Source: Computational Biology and Chemistry - August 1, 2020 Category: Bioinformatics Authors: Nagarajan H, Deepika Lakshmi P, Vetrivel U Tags: Comput Biol Chem Source Type: research

An in-silico approach to study the possible interactions of miRNA between human and SARS-CoV2.
CONCLUSION: Our analysis concludes that the genes identified in this study can be effective in analyzing the virus-host interaction. It also provides a new direction to understand viral pathogenesis with a probable new way to link, that can be used to understand and relate the miRNAs of the virus to the host conditions. PMID: 32771962 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - July 31, 2020 Category: Bioinformatics Authors: Sarma A, Phukan H, Halder N, Madanan MG Tags: Comput Biol Chem Source Type: research

Insight into the structures of Interleukin-18 systems.
Abstract Structure-based molecular designs play a critical role in the context of next generation drug development. Besides their fundamental scientific aspects, the findings established in this approach have significant implications in the expansions of target-based therapies and vaccines. Interleukin-18 (IL-18), also known as interferon gamma (IFN-γ) inducing factor, is a pro-inflammatory cytokine. The IL-18 binds first to the IL-18α receptor and forms a lower affinity complex. Upon binding with IL-18β a hetero-trimeric complex with higher affinity is formed that initiates the signal transductio...
Source: Computational Biology and Chemistry - July 30, 2020 Category: Bioinformatics Authors: Roy U Tags: Comput Biol Chem Source Type: research

Repurposing approved drugs as potential inhibitors of 3CL-protease of SARS-CoV-2: Virtual screening and structure based drug design.
Abstract 3CL proteases (3CLpro) are only found in RNA viruses and have a central role in polyprotein processing during replication. Therefore, 3CLpro has emerged as promising drug target for therapeutic treatment of infections caused by Coronaviruses. In the light of the recent major outbreak of the SARS-CoV-2 virus and the continuously rising numbers of infections and casualties, there is an urgent need for quickly available drugs or vaccines to stop the current COVID-19 pandemic. Repurposing of approved drugs as 3CLpro inhibitors could dramatically shorten the period up to approval as therapeutic against SARS-Co...
Source: Computational Biology and Chemistry - July 30, 2020 Category: Bioinformatics Authors: Meyer-Almes FJ Tags: Comput Biol Chem Source Type: research

Design, molecular docking analysis of an anti-inflammatory drug, computational analysis and intermolecular interactions energy studies of 1-benzothiophene-2-carboxylic acid.
Abstract In this paper, theoretical study on molecular geometry, vibrational, pharmaceutical and electronic properties of the monomeric and dimeric structures of 1-benzothiophene-2-carboxylic acid (2BT) were carried out using B3LYP hybrid functional with 6-311++G(d,p) as basis set. The structural study show that the stability of 2BT crystalline structure arising from O-H…O, C-H…O as well as S-H…O hydrogen bonding interactions. Vibrational analysis, for monomer and dimer species, show a good compatibility between experimental and theoretical frequencies. Then, the 1H and 13C NMR chemical shifts...
Source: Computational Biology and Chemistry - July 26, 2020 Category: Bioinformatics Authors: Sagaama A, Issaoui N Tags: Comput Biol Chem Source Type: research

In silico analysis of proteins and microRNAs related to human African trypanosomiasis in tsetse fly.
In conclusion, our work helps to elucidate the function of miRNAs in tsetse fly and establishes a foundation for further investigations into the molecular regulatory mechanisms of HAT disease. PMID: 32745971 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - July 23, 2020 Category: Bioinformatics Authors: Yang Z, Wang M, Zeng X, Wan AT, Tsui SK Tags: Comput Biol Chem Source Type: research

Computational-based identification and analysis of globally expressed differential genes in high-grade serous ovarian carcinoma cell lines.
This study is directed to investigate the global gene expression profiling, and to perform the analyses of identified global Differently Expressed Genes (DEGs) of OVCA. The microarray dataset (GSE71524) is comprised of tumor and cell line samples of OVCA and it was used for the identification of DEGs in the current study. The STRING database was used to construct Protein-Protein Interaction (PPI) network of DEGs, and hub genes were identified by the CytoHubba. In addition, a functional enrichment analysis of up- and down-regulated DEGs was performed by a bioinformatics database called as DAVID. The microRNAs (miRNAs) and t...
Source: Computational Biology and Chemistry - July 21, 2020 Category: Bioinformatics Authors: Masood F, Khan W, Uddin R Tags: Comput Biol Chem Source Type: research

Structural and functional insights of STAT2-NS5 interaction for the identification of NS5 antagonist - An approach for restoring interferon signaling.
This study also provides an insight on the mechanism of immunological processes involved in alleviating the antiviral immune response and computational identification of potent inhibitors for viral NS5 protein. PMID: 32721859 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - July 17, 2020 Category: Bioinformatics Authors: Choubey SK, Nachiappan M, Richard M, Chitra JP, Jeyakanthan J Tags: Comput Biol Chem Source Type: research

Adaptive weighted sum tests via LASSO method in multi-locus family-based association analysis.
Abstract Family based multi-locus tests integrate information from individual loci by weighted averaging of the marginal statistics, and have been proven to be more efficient and robust than the single-locus tests in genetic association studies. The power depends on how much information the weights can extract from data. The currently published weighted sum methods are only applicable to either common or rare variants and may suffer from substantial power loss especially for rare variants. In this paper, we propose a novel data-driven weight to improve the power under both common and rare variant circumstances. We...
Source: Computational Biology and Chemistry - July 13, 2020 Category: Bioinformatics Authors: Liu R, Yuan M, Xu H, Chen P, Xu XS, Yang Y Tags: Comput Biol Chem Source Type: research

Spectroscopic elucidation (FT-IR, FT-Raman and UV-visible) with NBO, NLO, ELF, LOL, drug likeness and molecular docking analysis on 1-(2-ethylsulfonylethyl)-2-methyl-5-nitro-imidazole: An antiprotozoal agent.
Abstract 1-(2-ethylsulfonylethyl)-2-methyl-5-nitro-imidazole (1EMI) C8H13N3O4S also known as Tinidazole, selected for its antiprotozoal property is extensively used for spectroscopic elucidations and computational aspects using density functional methods. Along with spectral conclusions, further investigations on fundamental reactive properties such as electrical, optical, nonlinear combined with DFT simulations were performed. Molecular docking procedure supports the results of chosen appropriate antiprotozoal agent based on ligand-protein interactions. Experimental and simulated (B3LYP/6-311++G (d,p)) IR and Ram...
Source: Computational Biology and Chemistry - July 9, 2020 Category: Bioinformatics Authors: Manjusha P, Prasana JC, Muthu S, Rizwana BF Tags: Comput Biol Chem Source Type: research

A deep learning approach based on convolutional LSTM for detecting diabetes.
In this study, we developed a novel diabetes classifying model based on Convolutional Long Short-term Memory (Conv-LSTM) that was not applied yet in this regard. We applied another three popular models such as Convolutional Neural Network (CNN), Traditional LSTM (T-LSTM), and CNN-LSTM and compared the performance with our developed model over the Pima Indians Diabetes Database (PIDD). Significant features were extracted from the dataset using Boruta algorithm that returned glucose, BMI, insulin, blood pressure, and age as important features for classifying diabetes patients more accurately. We performed hyperparameter opti...
Source: Computational Biology and Chemistry - July 9, 2020 Category: Bioinformatics Authors: Rahman M, Islam D, Mukti RJ, Saha I Tags: Comput Biol Chem Source Type: research

In silico design novel (5-imidazol-2-yl-4-phenylpyrimidin-2-yl)[2-(2-pyridylamino)ethyl]amine derivatives as inhibitors for glycogen synthase kinase 3 based on 3D-QSAR, molecular docking and molecular dynamics simulation.
Abstract Glycogen Synthase Kinase 3 (GSK-3) is a member of cellular kinase with various functions, such as glucose regulation, cellular differentiation, neuronal function and cell apoptosis. It has been proved as an important therapeutic target in type 2 diabetes mellitus and Alzheimer's disease. To better understand their structure-activity relationships and mechanism of action, an integrated computational study, including three dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, and molecular dynamics (MD), was performed on 79 (5-Imidazol-2-yl-4-phenylpyrimidin-2-yl)[2-(2-pyrid...
Source: Computational Biology and Chemistry - July 3, 2020 Category: Bioinformatics Authors: He Q, Han C, Li G, Guo H, Wang Y, Hu Y, Lin Z, Wang Y Tags: Comput Biol Chem Source Type: research

An improved chemical reaction optimization algorithm for solving the shortest common supersequence problem.
Abstract The shortest common supersequence (SCS) problem is a classical NP-hard problem, which is normally solved by heuristic algorithms. One important heuristic that is inspired by the process of chemical reactions in nature is the chemical reaction optimization (CRO) and its algorithm known as CRO_SCS. In this paper we propose a novel CRO algorithm, dubbed IMCRO, to solve the SCS problem efficiently. Two new operators are introduced in two of the four reactions of the CRO: a new circular shift operator is added to the decomposition reaction, and a new two-step crossover operator is included in the inter-molecul...
Source: Computational Biology and Chemistry - July 2, 2020 Category: Bioinformatics Authors: Luo F, Chen C, Fuentes J Tags: Comput Biol Chem Source Type: research

Improved neural networks based on genetic algorithm for pulse recognition.
Abstract Pulse diagnosis is an important part of Chinese medicine and has played an important role in the development of Chinese medical science. However, the pulse is traditionally determined by cutting it off, which leads to a lack of objective standard pulse identification methods and affects their accuracy and feasibility. This research has studied and discussed the processing and identification of four kinds of pulse: normal pulse, wiry pulse, smooth pulse, and thready pulse. Four frequency-domain characteristics of the pulse wave and six kinds of wavelet scale energy characteristic information were extracted...
Source: Computational Biology and Chemistry - June 25, 2020 Category: Bioinformatics Authors: Chen Z, Huang A, Qiang X Tags: Comput Biol Chem Source Type: research

Identifying essential proteins using modified-monkey algorithm (MMA).
Abstract Proteins are the most essential macromolecules needed for the normal flow of life. Essential proteins play a key role to control other proteins in an interaction network for the growth and understanding of the molecular mechanism of cellular life. Though there are many computational algorithms for essential drug discovery depending on nature of essential proteins, but still lots of improvements and optimizations are required. In this work, modified-Monkey algorithm (MMA) is proposed for the identification of essential proteins in protein-protein interaction network (PPIN). Nature of a monkey can be distin...
Source: Computational Biology and Chemistry - June 25, 2020 Category: Bioinformatics Authors: Payra AK, Ghosh A Tags: Comput Biol Chem Source Type: research

New acridine derivatives as promising agents against methicillin-resistant staphylococci - From tests to in silico analysis.
ski P Abstract The present study describes the antibacterial activity of several new derivatives of tacrine or cyclopentaquinoline bound to either 6-hydrazinenicotinic acid or 4-fluorobenzoic acid through an aliphatic chain against methicillin-resistant staphylococcal strains. All derivatives showed antibacterial activity against all tested methicillin-resistant staphylococci. Of these, compounds 6, 18, 23 and 24 exhibited the highest activity, ranging from 4.87 to 19.5 μg/mL MBC (Minimum Bactericidal Concentration) depending on the bacterial strain. These values were not much greater than that for vancomycin...
Source: Computational Biology and Chemistry - June 24, 2020 Category: Bioinformatics Authors: Czarnecka K, Lisiecki P, Szewczyk E, Chufarova N, Wójtowicz P, Kręcisz P, Szymański P Tags: Comput Biol Chem Source Type: research

In silico development of anesthetics based on barbiturate and thiobarbiturate inhibition of GABAA.
In this study, obtained results indicate that there is a very good correlation between all developed models. Molecular fragments that account for the increase/decrease of a studied activity were defined and further used for the computer-aided design of new compounds as potential anesthetics. PMID: 32622179 [PubMed - as supplied by publisher] (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - June 24, 2020 Category: Bioinformatics Authors: Stošić B, Janković R, Stošić M, Marković D, Stanković D, Sokolović D, Veselinović AM Tags: Comput Biol Chem Source Type: research

Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors.
e;n-Vega JA Abstract The global emergency caused by COVID-19 makes the discovery of drugs capable of inhibiting SARS-CoV-2 a priority, to reduce the mortality and morbidity of this disease. Repurposing approved drugs can provide therapeutic alternatives that promise rapid and ample coverage because they have a documented safety record, as well as infrastructure for large-scale production. The main protease of SARS-CoV-2 (Mpro) is an excellent therapeutic target because it is critical for viral replication; however, Mpro has a highly flexible active site that must be considered when performing computer-assisted dru...
Source: Computational Biology and Chemistry - June 24, 2020 Category: Bioinformatics Authors: Jiménez-Alberto A, Ribas-Aparicio RM, Aparicio-Ozores G, Castelán-Vega JA Tags: Comput Biol Chem Source Type: research

Prognostic prediction of carcinoma by a differential-regulatory-network-embedded deep neural network.
Abstract The accurate prognostic prediction is essential for precise diagnosis and treatment of carcinoma. In addition to clinical survival prediction method, many computational methods based on transcriptomic data have been proposed to build the prediction models and study the prognosis of cancer patients. We propose a differential-regulatory-network-embedded deep neural network (DRE-DNN) method by integrating differential regulatory analysis based on gene co-expression network and deep neural network (DNN) method. From three public hepatocellular carcinoma (HCC) datasets, we derive differential regulatory networ...
Source: Computational Biology and Chemistry - June 23, 2020 Category: Bioinformatics Authors: Li J, Ping Y, Li H, Li H, Liu Y, Liu B, Wang Y Tags: Comput Biol Chem Source Type: research

Geo-Measures: A PyMOL plugin for protein structure ensembles analysis.
Abstract Although molecular dynamics encompasses several applications, studies focusing on biomolecular systems are central issues of this research area. Such simulations require the generation of trajectory files, which provide a path for the analysis and interpretation of results with biological significance. However, although several programs have been developed in Python language for the analyses of molecular dynamics (MD) trajectories, they usually require some knowledge of programming languages in order to write or run the scripts using command lines, which certainly hinders the access of MD simulations to m...
Source: Computational Biology and Chemistry - June 23, 2020 Category: Bioinformatics Authors: Kagami LP, das Neves GM, Timmers LFSM, Caceres RA, Eifler-Lima VL Tags: Comput Biol Chem Source Type: research

Molecular docking studies, structural and spectroscopic properties of monomeric and dimeric species of benzofuran-carboxylic acids derivatives: DFT calculations and biological activities.
oui N Abstract Structural optimization, molecular docking analysis, electronic and vibrational properties have been investigated for the 1-benzofuran-2-carboxylic acid (2BF) and 1-benzofuran-3-carboxylic acid (3BF) using DFT/B3LYP/6-311++G(d,p) level of theory. The theoretical parameters have a very good consistency with the experimental ones. The weak intermolecular interactions were analyzed by different tool such as: Hirshfeld surfaces, topological analysis and natural bond orbital studies. The nonlinear optical properties have been investigated. Molecular electrostatic potential and frontier molecular orbitals...
Source: Computational Biology and Chemistry - June 19, 2020 Category: Bioinformatics Authors: Sagaama A, Noureddine O, Brandán SA, Jędryka AJ, Flakus HT, Ghalla H, Issaoui N Tags: Comput Biol Chem Source Type: research