Design of novel JAK3 Inhibitors towards Rheumatoid Arthritis using molecular docking analysis.
Abstract Multiple cytokines play a pivotal role in the pathogenesis of Rheumatoid Arthritis by inducing intracellular signaling and it is known that the members of the Janus kinase (JAK) family are essential for such signal transduction. Janus kinase 3 is a tyrosine kinase that belongs to the Janus family of kinases. Drugs targeting JAK3 in the treatment of Rheumatoid arthritis is relevant. Therefore, it is of interest to design suitable inhibitors for JAK3 dimer using molecular docking with Molegro Virtual Docker. The compound possessing the highest affinity score is subjected to virtual screening to retrieve inh...
Source: Bioinformation - August 24, 2019 Category: Bioinformatics Authors: Jain D, Udhwani T, Sharma S, Gandhe A, Reddy PB, Nayarisseri A, Singh SK Tags: Bioinformation Source Type: research
Structural insights from water-ferredoxin interaction in mesophilic algae and halophilic archaea.
Abstract We analyzed the water-ferredoxin interaction in mesophilic (moderate temperature) algae (PDB ID: 1AWD) and halophilic (salt-tolerant) archaea (PDB ID: 1DOI) using POWAIND version 2.0 (a protein-water interactions calculation program). It is found that the shell water (SW) is 2.5 fold greater in halophilic ferredoxin than mesophilic ferredoxin. Water-ferredoxin interactions in the core and cavity are the signature of stability. The normalized frequency of such interactions is less in halophilic relative to mesophilic ferredoxin and the halophilic signature for stability by such interactions is negligible. ...
Source: Bioinformation - August 24, 2019 Category: Bioinformatics Authors: Bandyopadhyay AK, Islam RNU, Mitra D, Banerjee S, Goswami A Tags: Bioinformation Source Type: research
A Comparison on Some Interval Mapping Approaches for QTL Detection.
Abstract Quantitative trait locus (QTL) analysis is a statistical method that links two types of information such as phenotypic data (trait measurements) and genotypic data (usually molecular markers). There a number of QTL tools have been developed for gene linkage mapping. Standard Interval Mapping (SIM) or Simple Interval Mapping or Interval Mapping (IM), Haley Knott, Extended Haley Knott and Multiple Imputation (IMP) method when the single-QTL is unlinked and Composite Interval Mapping (CIM) is designed to map the genetic linkage for both linked and unlinked genes in the chromosome. Performance of these method...
Source: Bioinformation - August 24, 2019 Category: Bioinformatics Authors: Akond Z, Alam MJ, Hasan MN, Uddin MS, Alam M, Mollah MNH Tags: Bioinformation Source Type: research
Insights from the salt bridge analysis of malate dehydrogenase from H. salinarum and E.coli.
Abstract Halophilic proteins have greater abundance of acidic over basic residues in sequence. In structure, the surface is decorated by negative charges, with lower content of Lysine. Using sequence BLOCKs and 3D model of malate dehydrogenase from halophilic archaea (Halobacterium salinarum; hsMDH) and X-ray structure from mesophilic bacteria (E. coli; ecMDH), we show that not only acidic and basic residues have higher mean relative abundance (MRA) and thus, impart higher polarity to the sequences, but also show their presence in the surface of the structure of hsMDH relative to its mesophilic counterpart. These ...
Source: Bioinformation - August 24, 2019 Category: Bioinformatics Authors: Bandyopadhyay AK, Islam RNU, Mitra D, Banerjee S, Yasmeen S, Goswami A Tags: Bioinformation Source Type: research
FLT3 inhibitor design using molecular docking based virtual screening for acute myeloid leukemia.
Abstract Acute Myeloid Leukaemia (AML) is a blood cancer, which affects the red blood cells in the bone marrow. Of the possible proteins that are affected in AML, fms-like tyrosine kinase 3 (FLT3) has long been recognized as a potential therapeutic target as it affects the other signaling pathways and leads to a cascade of events. First-generation inhibitors sorafenib and midostaurin, as well as secondgeneration agents such as quizartinib and crenolanib are known. It is of interest to identify new compounds against FLT3 with improved activity using molecular docking and virtual screening. Molecular docking of exis...
Source: Bioinformation - August 24, 2019 Category: Bioinformatics Authors: Gokhale P, Chauhan APS, Arora A, Khandekar N, Nayarisseri A, Singh SK Tags: Bioinformation Source Type: research
Re-positioning of known drugs for Pim-1 kinase target using molecular docking analysis.
Abstract The Concept of reusing existing drugs for new targets is gaining momentum in recent years because of cost-effectiveness as safety and toxicology data are already available. Therefore, it is of interest to re-profile known drugs against the Pim-1 kinase target using molecular docking analysis. Results show that known drugs such as nilotinib, vemurafenib, Idelalisib, and other small kinases inhibitors have high binding ability with Pim-1 kinase for consideration as potential inhibitors. PMID: 31435157 [PubMed] (Source: Bioinformation)
Source: Bioinformation - August 24, 2019 Category: Bioinformatics Authors: Arrouchi H, Lakhlili W, Ibrahimi A Tags: Bioinformation Source Type: research
Virtual Screening of IL-6 Inhibitors for Idiopathic Arthritis.
Abstract Juvenile idiopathic arthritis (JIA) is a heterogeneous disease characterized by the arthritis of unknown origin and IL6 is a known target for JIA. 20 known inhibitors towards IL-6 were screened and Methotrexate (MTX) having PubChem ID: 126941 showed high binding capacity with the receptor IL-6. The similarity searching with this compound gave 269 virtual screened compounds. The said screening presented 269 possible drugs having structural similarity to Methotrexate. The docking studies of the screened drugs separated the compound having PubChem CID: 122677576 (re-rank value of -140.262). Toxicity and inte...
Source: Bioinformation - August 24, 2019 Category: Bioinformatics Authors: Shukla P, Khandelwal R, Sharma D, Dhar A, Nayarisseri A, Singh SK Tags: Bioinformation Source Type: research
Insights from the molecular docking analysis of phytohormone reveal brassinolide interaction with HSC70 from Pennisetum glaucum.
Abstract The prevailing abiotic stresses, especially heat stress is of great significance on the growth of plants, yield and distribution. In the conditions of heat stress, plants modulate protein processes leading to development of heat tolerance. Of such proteins, the molecular chaperone functions of HSP70/HSC70 proteins are important where their enhanced expression positively correlates with the acquisition of heat tolerance. The key players in the regulation of such tailored protein responses of plants to heat stress are the phytohormones. In the present study, phytohormone mediated interaction of Pennisetum g...
Source: Bioinformation - August 24, 2019 Category: Bioinformatics Authors: Baloji G, Pasham S, Mahankali V, Garladinne M, Ankanagari S Tags: Bioinformation Source Type: research
Design of PD-L1 inhibitors for lung cancer.
Abstract The progression of lung cancer is associated with inactivation of programmed cell death protein 1, abbreviated as PD- 1 which regulates the suppression of the body's immune system by suppressing T- cell inflammatory activity and is responsible for preventing cancer cell growth. It is of interest to identify inhibitors for PD-L1 dimeric structure through molecular docking and virtual screening. The virtual screened compound XGIQBUNWFCCMAS-UHFFFAOYSA-N (PubChem CID: 127263272) displays a high affinity with the target protein. ADMET analysis and cytotoxicity studies further add weight to this compound as a p...
Source: Bioinformation - August 24, 2019 Category: Bioinformatics Authors: Udhwani T, Mukherjee S, Sharma K, Sweta J, Khandekar N, Nayarisseri A, Singh SK Tags: Bioinformation Source Type: research
Computational classification of MocR transcriptional regulators into subgroups as a support for experimental and functional characterization.
Abstract MocR bacterial transcriptional regulators are a subfamily within the GntR family. The MocR proteins possess an N-terminal domain containing the winged Helix-Turn-Helix (wHTH) motif and a C-terminal domain whose architecture is homologous to the fold type-I pyridoxal 5'-phosphate (PLP) dependent enzymes and whose archetypical protein is aspartate aminotransferase (AAT). The ancestor of the fold type-I PLP dependent super-family is considered one of the earliest enzymes. The members of this super-family are the product of evolution which resulted in a diversified protein population able to catalyze a set of...
Source: Bioinformation - August 24, 2019 Category: Bioinformatics Authors: Pascarella S Tags: Bioinformation Source Type: research
Tracking iron oxide labelled mesenchymal stem cells(MSCs) using magnetic resonance imaging (MRI) in a rat model of hepatic cirrhosis.
Abstract Homing and tumor attenuation potential of BM-MSCs labelled with superparamagnetic iron-oxide nanoparticles (SPIONs) in a rat model of hepatic cirrhosis was evaluated. Rat BM-MSCs were derived, characterized and labelled with SPIONs (200 nm; 25 mg Fe/ml). Hepatic cirrhosis was induced in Wistar rats (n=30; 10/group) with carbon tetrachloride (CCl4; 0.3 mL/kg body weight) injected twice a week for 12 weeks. Group-I was administered vehicle (castor-oil) alone; Group-II received two doses of unlabelled BM-MSCs (3x106 cells) and Group-III received two doses of SPIONs labelled BM-MSCs (3x106 cells) via tail vei...
Source: Bioinformation - August 1, 2019 Category: Bioinformatics Authors: Noorwali A, Faidah M, Ahmed N, Bima A Tags: Bioinformation Source Type: research
Molecular docking analysis of nuclear factor- κB and genistein interaction in the context of breast cancer.
Molecular docking analysis of nuclear factor-κB and genistein interaction in the context of breast cancer. Bioinformation. 2019;15(1):11-17 Authors: Mukund V, Behera SK, Alam A, Nagaraju GP Abstract Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is a transcription factor and it contributes to breast cancer growth and metastasis. Hence, NF-κB is considered as a target for anti-breast cancer drugs. NF-κB was retrieved from the UniProtKB Data Base with UniProt ID P19838, its energy was minimized and subjected to molecular dynamic simulations using Gromacs v...
Source: Bioinformation - August 1, 2019 Category: Bioinformatics Authors: Mukund V, Behera SK, Alam A, Nagaraju GP Tags: Bioinformation Source Type: research
Identification of potential drug targets and vaccine candidates in Clostridium botulinum using subtractive genomics approach.
Abstract A subtractive genomic approach has been utilized for the identification of potential drug targets and vaccine candidates in Clostridium botulinum, the causative agent of flaccid paralysis in humans. The emergence of drug-resistant pathogenic strains has become a significant global public health threat. Treatment with antitoxin can target the neurotoxin at the extracellular level, however, can't converse the paralysis caused by botulism. Therefore, identification of drug targets and vaccine candidates in C. botulinum would be crucial to overcome drug resistance to existing antibiotic therapy. A total of 17...
Source: Bioinformation - August 1, 2019 Category: Bioinformatics Authors: Sudha R, Katiyar A, Katiyar P, Singh H, Prasad P Tags: Bioinformation Source Type: research
Classification of Functional Metagenomes Recovered from Different Environmental Samples.
Abstract Classification of functional metagenomes from the microbial community plays the vital role in the metagenomics research. In this paper, an investigation was made to study the performance of beta-t random forest classifier for classification of metagenomics data. Nine key functional meta-genomic variables were selected using the beta-t test statistic from the 10 different microbial community using p-value at 5% level of significance. Then beta-t random forest classifier showed the higher accuracy (96%), true positive rate (96%) and lower false positive rate (5%), false discovery rate (5%) and misclassifica...
Source: Bioinformation - August 1, 2019 Category: Bioinformatics Authors: Akond Z, Hasan MN, Alam MJ, Alam M, Mollah MNH Tags: Bioinformation Source Type: research
Phytochemicals as alternatives to antibiotics against major pathogens involved in bovine respiratory disease(BRD)and bovine mastitis(BM).
Abstract Bovine respiratory disease (BRD) and bovine mastitis (BM) are the most common and costly infectious diseases in beef cattle and dairy cattle, respectively. In the current study, we evaluated the antimicrobial activity of seven phytochemicals against twelve BRD- and/or BMcausing bacterial pathogens. Our results show that allyl isothiocyanate, benzyl isothiocynate, cinnamaldehyde and eugenol are effective against most of the BRD- and/or BM-causing bacterial pathogens and could be repurposed as alternatives to antibiotics for the prevention/elimination of BRD and BM in feedlots. PMID: 31359996 [PubMed] ...
Source: Bioinformation - August 1, 2019 Category: Bioinformatics Authors: Rajamanickam K, Yang J, Sakharkar MK Tags: Bioinformation Source Type: research
Polyhydroxyalkanoates (PHA) genes Database.
Abstract Polyhydroxyalkanoates (PHA) are polyesters of various hydroxyl alkanoates that are synthesized by many gram-positive and gramnegative bacteria from about 75 different genera. PHA genes database is a repository of genes and its genomic information related to PHA.It contains data on the genomic characterization of intermediates of PHA. These include CAB genes, responsible for biodegradable plastic synthesis. The genomic database provides data on PHA genes from archaeal, bacterial and eukaryotic genomes. PMID: 31359997 [PubMed] (Source: Bioinformation)
Source: Bioinformation - August 1, 2019 Category: Bioinformatics Authors: Alamgeer M Tags: Bioinformation Source Type: research
A review on PIM kinases in tumors.
Abstract The Proviral Integration site for Moloney murine leukemia virus (PIM) kinases is serine/threonine kinases that promote growth and survival in multiple cell types, implicated in the pathogenesis of various diseases. Over expression of Pim-1 experimentally leads to tumor formation in mice, whereas there is no observable phenotype concerning the complete knockout of the protein. When it is over expressed it may lead to cancer development by three major ways; by inhibiting apoptosis, by promoting cell proliferation and also through promoting genomic instability. Expression in normal tissues is nearly undetect...
Source: Bioinformation - August 1, 2019 Category: Bioinformatics Authors: Arrouchi H, Lakhlili W, Ibrahimi A Tags: Bioinformation Source Type: research
Molecular characterization of leaf spot fungi using internal transcribed spacer (ITS) based phylogenetic inference.
We report nineteen positive isolates identified with species-level characterization using ITS sequence supported with a phylogenetic tree and corresponding secondary structure analysis. PMID: 31359999 [PubMed] (Source: Bioinformation)
Source: Bioinformation - August 1, 2019 Category: Bioinformatics Authors: Chitrakani B, Sureshkumar S, Rajapriya P, Pandi M Tags: Bioinformation Source Type: research
Oncogenic Human Papillomavirus involvement in epithelial ovarian carcinoma among women in Morocco.
Abstract Epithelial Ovarian cancer (EOC) although rare is the most lethal gynecological cancer in women worldwide. Despite its high prevalence few studies have been performed to evaluate the prevalence and determinants of HPV infection worldwide. The aim of the present study was to investigate the presence of HPV-DNA in Moroccan patients with EOC using PCR among women in Casablanca, and to examine the prevalence of some HPV genotypes in Moroccan population. We performed a study of HPV detection on Fresh biopsies of 70 epithelial ovarian cancer patients. PCR was realized using the MY09/11 and GP5+/6+ primers. Genot...
Source: Bioinformation - August 1, 2019 Category: Bioinformatics Authors: Hammou RA, Benhessou M, Bouziyane A, Hassou N, Benhchekroun MN, Bessi H, Ennaji MM Tags: Bioinformation Source Type: research
Stability of buried and networked salt-bridges (BNSB)in thermophilic proteins.
Abstract Thermophilic proteins function at high temperature, unlike mesophilic proteins. Thermo-stability of these proteins is due to the unique buried and networked salt-bridge (BNSB). However, it is known that the desolvation cost of BNSB is too high compared to other favorable energy terms. Nonetheless, it is known that stability is provided generally by hydrophobic isosteres without the need for BNSB. We show in this analysis that the BNSB is the optimal evolutionary design of salt-bridge to offset desolvation cost efficiently. Hence, thermophilic proteins with a high level of BNSB provide thermo-stability. ...
Source: Bioinformation - August 1, 2019 Category: Bioinformatics Authors: Bandyopadhyay AK, Islam RNU, Mitra D, Banerjee S, Goswami A Tags: Bioinformation Source Type: research
Re-annotation for hypothetical protein CA803_03125 of Methicillin-Resistant Staphylococcus aureus strain SO-1977 isolated from Sudan.
This study aims to describe the global detection and functional inference of hypothetical protein CA803_03125 from Staphylococcus aureus SO-1977. Computational methods were utilized to study this protein based on sequence similarity and presence of known protein domains. The BLASTp result revealed a significant similarity between the hypothetical protein (CA803_03125) and ADP-ribose hydrolase protein from four S. aureus strains (MW2, MRSA252, COL, and N315). Evolutionary tree diagram revealed a close relationship between the hypothetical protein and proteins of MW2 and COL strains. The physicochemical characterization reve...
Source: Bioinformation - July 30, 2019 Category: Bioinformatics Authors: Mohamed SB, Hassan MM, Munir KA, Abdalla NI, Adlan TA, Babiker AK Tags: Bioinformation Source Type: research
Genome-wide identification of the SPL gene family in Dichanthelium oligosanthes.
In this study, 14 SPL genes were identified in the genome of D. oligosanthes. Gene structure analysis of the identified DoSPLs revealed the similarity and redundancy in their exon/intron organizations. Sequence comparisons within the DoSPLs and along with rice SPLs revealed the putative paralogs and orthologs in D. oligosanthes SPL genes. Phylogenetic analysis clustered the DoSPLs into eight groups along with other plant SPLs. Identification of the conserved SBP motifs in all 14 DoSPLs suggested them to be putative SPLs. In addition, the prediction of sub-cellular localization and associated functions for DoSPLs further su...
Source: Bioinformation - July 30, 2019 Category: Bioinformatics Authors: Nanda S, Hussain S Tags: Bioinformation Source Type: research
Effect of Salvia Officinalis L. and Rosmarinus Officinalis L. leaves extracts on anxiety and neural activity.
Abstract Anxiety, the illness of our time, is one of the most prevalent and co-morbid psychiatric disorder that represents a significant socioeconomic burden. Conventional treatment is associated with a number of side effects and there is a need to develop new therapeutic strategies. Therefore, it is of interest to investigate the modulating effects of Salvia Officinalis L. and Rosmarinus Officinalis L. leaves extracts on anxiety using different behavioral tests, and on neural activity using the Multi-electrode array technique. Data shows the decrease of the time of the immobility associated with a significant inc...
Source: Bioinformation - July 30, 2019 Category: Bioinformatics Authors: Choukairi Z, Hazzaz T, Lkhider M, Ferrandez JM, Fechtali T Tags: Bioinformation Source Type: research
Molecular docking analysis of candidate compoundsderived from medicinal plants with type 2 diabetes mellitus targets.
This study aimed to evaluate molecular interactions of selected diabetes mellitus (DM) targets with bioactive compounds isolated from Ficus benghelensis, Ficus racemosa, Ficus religiosa, Thespesia populena and Ficus lacur bouch. In this article, screening of the best substances as bioactive compounds is achieved by molecular docking analysis with 3 best selected DM target proteins i.e., aldose reductase (AR), Insulin Receptor (IR) and Mono-ADP ribosyltransferase-sirtuin-6 (SIRT6). In this analysis six potential bioactive compounds (gossypetin, herbacetin, kaempferol, leucoperalgonidin, leucodelphinidin and sorbifolin) were...
Source: Bioinformation - July 30, 2019 Category: Bioinformatics Authors: Singh P, Singh VK, Singh AK Tags: Bioinformation Source Type: research
Impact of omega-3 fatty acids on calorie intake and certain anthropometric measurements in children with sickle cell disease in Saudi Arabia.
Abstract The nutritional status and growth in children with sickle cell disease is compromised due to intake of diet that is low in calories as well as deficient in nutrients. Growth stunting and a low body mass index have been observed in these children. Some children exhibit pica, which is an abnormal eating pattern by ingesting things other than food, like paper, wood etc. This also was found to correlate to lower hemoglobin values. Interventions with certain essential nutrients such as omega-3 fatty acids are known to benefit these children in terms of lowering their complications due to the disease. We theref...
Source: Bioinformation - July 30, 2019 Category: Bioinformatics Authors: Khan S, Damanhouri G, Jameel T, Ali A, Makki A, Khan S, AlAnsari I, Halawani S, Zahrani F, AlKazmi M, Ghita I Tags: Bioinformation Source Type: research
Impact of rotavirus and hepatitis A virus by worldwide climatic changes during the period between 2000 and 2013.
Abstract Enteric viruses are present in the environment as a result of the discharge of poorly or untreated wastewater. The spread of enteric viruses in the environment depend to human activities like stools of infected individuals ejected in the external environment can be transmitted by water sources and back to susceptible individuals for other cycles of illness. Among the enteric viruses Rotaviruses (RV) and Hepatitis A viruses (HAV) is the most detected in wastewater causing gastroenteritis and acute hepatitis. Therefore, it is of interest to climate change, mainly temperature and carbon Dioxide (CO2) variati...
Source: Bioinformation - July 30, 2019 Category: Bioinformatics Authors: Tarek F, Hassou N, Benchekroun MN, Boughribil S, Hafid J, Ennaji MM Tags: Bioinformation Source Type: research
Molecular docking based screening analysis of GSK3B.
In this study we report the contribution and prognostic significance of GSK3B to two breast cancer subtypes; ductal carcinoma in-situ (DCIS) and invasive ductal carcinoma (IDC) using the Oncomine platform. We performed high throughput screening using molecular docking. We identified BT-000775, a compound that was subjected to further computational hit optimization protocols. Through computational predictions, BT-000775 is a highly selective GSK3B inhibitor, with superior binding affinity and robust ADME profiles suitable for the patho-physiological presentations. PMID: 31354196 [PubMed] (Source: Bioinformation)
Source: Bioinformation - July 30, 2019 Category: Bioinformatics Authors: Ogunleye AJ, Olanrewaju AJ, Arowosegbe M, Omotuyi OI Tags: Bioinformation Source Type: research
Dtar-Finder: program for drug target identification and characterization in bacteria.
Abstract The drug target identification is the primary step for drug discovery. Recent development of computational techniques and availability of sequencing data has provided numerous opportunities for target identification but very few of them are fully automated. Here, we have developed a Perl program named Dtar-Finder for drug target identification and its characterization. Dtar-Finder predicts the drug targets which are essential to pathogen and non homologous to human, essential human anti-targets and gut microflora. This program is divided in 6 modules where modules 1-4 extract drug targets while module 5-6...
Source: Bioinformation - July 30, 2019 Category: Bioinformatics Authors: Prasad P, Sudha R Tags: Bioinformation Source Type: research
Analysis of salt-bridges in prolyl oligopeptidase from Pyrococcus furiosus and Homo sapiens.
We present comparative analyses of sequences, structures and salt-bridges of prolyl-oligopeptidase from Pyrococcus furiosus (pfPOP - PDB ID: 5T88) and human (huPOP - PDB ID: 3DDU). A similar level of hydrophobic and hydrophilic residues in pfPOP and huPOP is observed. A low level of interactions between shell-waters and atom-types in pfPOP indicated hyper thermophilic features are negligible. Salt-bridge-forming-residues (sbfrs) are high in pfPOP's core and surface (pfPOP). Increased sbfrs largely indicate specific-electrostatic is important for thermo stability in pfPOP. Four classes of sbfrs are found namely positionally...
Source: Bioinformation - July 30, 2019 Category: Bioinformatics Authors: Bandyopadhyay AK, Islam RNU, Mitra D, Banerjee S, Goswami A Tags: Bioinformation Source Type: research
Phytochemical screening, antioxidant activity and inhibitory potential of Ficus carica and Olea europaea leaves.
Abstract It is our interest to screen Oela europaea L and Ficus carica L leaf extract for total phenolic, flavonoid contents and to evaluate their free radical scavenging and Ferric reducing power (FRAP) using 1,1-diphenyl-2-picrylhydrazyl (DPPH). Data shows that Olea europaea and Ficus carica have strong antioxidant potency to scavenge free radical at an optimal phenolic and flavonoid concentration. Results further suggest a strong correlation between antioxidant activities, phenolic and flavonoid contents. Thus, the screening of Ficus carica and Olea europaea leaf extracts for potential antioxidants as source of...
Source: Bioinformation - July 30, 2019 Category: Bioinformatics Authors: Ayoub L, Hassan F, Hamid S, Abdelhamid Z, Souad A Tags: Bioinformation Source Type: research
Data mining analysis of human gut microbiota links Fusobacterium spp. with colorectal cancer onset.
Abstract Gut microbiota and their metabolites play a vital role in colon health and disease. Accumulating evidence suggests that the gut microbiota contributes to the risk of colorectal cancer (CRC). However, the role of a specific microbial community together with their metabolites contributing to the risk, initiation and progression of CRC is still unknown. Hence, we used a Bayesian Networks in combination with the IDA (Intervention calculus when the DAG is absent) to generate a graphical model that allows causal relationships to be inferred from observational data. Results from the analysis of publically availa...
Source: Bioinformation - July 19, 2019 Category: Bioinformatics Authors: Kharrat N, Assidi M, Abu-Elmagd M, Pushparaj PN, Alkhaldy A, Arfaoui L, Naseer MI, El Omri A, Messaoudi S, Buhmeida A, Rebai A Tags: Bioinformation Source Type: research
Molecular docking and ADMET analysis of hydroxamic acids as HDAC2 inhibitors.
We reported 96 hydroxamic compounds optimized using hydrogen-donors, hydrophobic and electron withdrawing groups followed by molecular docking studies. The optimized compounds show good LibDock score and H-bond interaction in the active site of HDAC2. We selected 20 compounds as the best HDAC2 inhibitors based on the LibDock score, binding energy and hydrogen bonding. ADMET predictions on these compounds show good absorption, BBB penetration and no liver toxicity. We subsequently report four compounds selected as best HDAC2 inhibitors based on the LibDock, binding energy, H-bonding and ADMET properties. PMID: 31312074...
Source: Bioinformation - July 19, 2019 Category: Bioinformatics Authors: Alsawalha M, Rao Bolla S, Kandakatla N, Srinivasadesikan V, Veeraraghavan VP, Surapaneni KM Tags: Bioinformation Source Type: research
Prediction of normalized signal strength on DNA sequencing microarrays by n-grams within a neural network model.
Abstract We have shown previously that a feed-forward, back propagation neural network model based on composite n-grams can predict normalized signal strengths of a microarray based DNA sequencing experiment. The microarray comprises a 4xN set of 25-base single-stranded DNA molecule ('oligos'), specific for each of the four possible bases (A, C, G, or T) for Adenine, Cytosine, Guanine and Thymine respectively at each of N positions in the experimental DNA. Strength of binding between reference oligos and experimental DNA varies according to base complementarity and the strongest signal in any quartet should `call ...
Source: Bioinformation - July 19, 2019 Category: Bioinformatics Authors: Chilaka C, Carr S, Shalaby N, Banzhaf W Tags: Bioinformation Source Type: research
Molecular docking based design of Dengue NS5 methyltransferase inhibitors.
Abstract Dengue is a viral infection caused by RNA infection of the family Flaviviridae and spread by the Aedes mosquitoes. Dengue NS5 methyltransferase is a known drug target for the disease. Therefore, it is of interest to design potential inhibitors for the target using molecular docking analysis. Our analysis shows the binding of compounds STOCK1N-98943, STOCK1N-98872, STOCK1N-98956, STOCK1N-98865, and STOCK1N-98950 with the protein drug target with optimal binding features for further in vitro and in vivo evaluations. PMID: 31312076 [PubMed] (Source: Bioinformation)
Source: Bioinformation - July 19, 2019 Category: Bioinformatics Authors: Kausar MA, Ali A, Qiblawi S, Shahid S, Izhari MA, Saral A Tags: Bioinformation Source Type: research
Putative role of conserved water molecules in the hydration and inter-domain recognition of mono nuclear copper centers in O2-bound human ceruloplasmin: A comparative study between X-ray and MD simulated structures.
Abstract Human Ceruloplasmin (hCP) is an unique multicopper oxidase which involves in different biological functions e.g., iron metabolism, copper transportation, biogenic amine oxidation ,and its malfunction causes Wilson's and Menkes diseases. MD- simulation studies of O2- bound solvated structure have revealed the role of several conserved/ semi-conserved water molecules in the hydration of type-I copper centers and their involvement to recognition dynamics of these metal centers. In O2- bound structure, hydration potentiality of CuRS (Cu1106) type-I copper center is observed to be unique, where two water molec...
Source: Bioinformation - July 19, 2019 Category: Bioinformatics Authors: Mukhopadhyay BP Tags: Bioinformation Source Type: research
Phylogenetic insight of Nonribosomal peptide synthetases (NRPS) Adenylate domain in Antibacterial potential Streptomyces BDUSMP 02 isolated from Pitchavaram Mangrove.
Abstract Identification of gene clusters in Streptomyces holds promise for the discovery of regulatory pathways linked to bioactive metabolites. We isolated a broad-spectrum antibacterial potential Streptomyces sp BDUSMP 02 from mangrove sediment. We further found a distinct of phylogeny pattern for NRPS A-domain in the Streptomyces sp BDUSMP 02. The result suggests that Streptomyces sp BDUSMP 02 has the potential to produce a new type of antibacterial compounds belonging to NRPS type. PMID: 31312078 [PubMed] (Source: Bioinformation)
Source: Bioinformation - July 19, 2019 Category: Bioinformatics Authors: Sivalingam P, Muthuselvam M, Pote J, Prabakar K Tags: Bioinformation Source Type: research
Identification of novel inhibitor targeting Fyn kinase using molecular docking analysis.
Abstract Identification of tyrosine Fyn kinase inhibitor is recognized as an effective and feasible therapeutic measure in reducing consequences of memory loss disorder Alzheimer's. The present investigation has been attempted with an objective to find out a novel potent inhibitor with similar homological structure to Fyn kinase using structure based in silico screening measure. Such derived structure was compared with natural data base pool and were systematically analyzed. Ligand based interaction was also tested and evaluated. We applied a molecular dynamic simulation technique to validate the stability of the ...
Source: Bioinformation - July 19, 2019 Category: Bioinformatics Authors: Nedunchezhian D, Langeswaran K, Santhoshkumar S Tags: Bioinformation Source Type: research
Screening and GC-MS profiling of ethanolic extract of Tylophora pauciflora.
Abstract Medicinal plants are boundless source of raw materials for the pharmaceutical. Identification of natural compounds from medicinal plant is helpful in the discovery of novel therapeutic agents. Tylophora pauciflora is a medicinal plant, which possess many biological activities such as antioxidant activity, anti-inflammatory activity and anti cancer activity. There is no GC-MS analysis reported on this plant. Thus, the present study is aimed to identify the present of phyto-chemical compounds from ethanolic extract of Tylophora pauciflora using GC-MS analysis. Results, the extract possess totally 14 bioacti...
Source: Bioinformation - July 19, 2019 Category: Bioinformatics Authors: Starlin T, Prabha PS, Thayakumar BKA, Gopalakrishnan VK Tags: Bioinformation Source Type: research
Genomics of the OLIG family of a bHLH transcription factor associated with oligo dendrogenesis.
Abstract The glial cell neoplasms are not fully classified by using cellular morphology. However, this is possible using known molecular markers in glial development. Oligo-dendrocyte lineage gene induces differentiation of neural progenitors and putative immature progenitor cells of the adult central nervous system. These oligo-dendrocyte lineage genes OLIG1 and OLIG2 encode basic helix-loop-helix transcription factors. The murine bHLH transcription factors found in chromosome 21 are essential for oligo-dendrocyte development. Moreover, OLIG3 of the OLIG family is known to be linked with the brain and spinal cord...
Source: Bioinformation - July 19, 2019 Category: Bioinformatics Authors: Choudhury S Tags: Bioinformation Source Type: research
Virtual screening of inhibitors against Envelope glycoprotein of Chikungunya Virus: a drug repositioning approach.
Abstract Chikungunya virus (CHIKV) a re-emerging mosquito-borne alpha virus causes significant distress which is further accentuated in the lack of specific therapeutics or a preventive vaccine, mandating accelerated research for anti-CHIKV therapeutics. In recent years, drug repositioning has gained recognition for the curative interventions for its cost and time efficacy. CHIKV envelope proteins are considered to be the promising targets for drug discovery because of their essential role in viral attachment and entry in the host cells. In the current study, we propose structure-based virtual screening of drug mo...
Source: Bioinformation - July 19, 2019 Category: Bioinformatics Authors: Agarwal G, Gupta S, Gabrani R, Gupta A, Chaudhary VK, Gupta V Tags: Bioinformation Source Type: research
Molecular docking analysis of netropsin and novobiocin with the viral protein targets HABD, MTD and RCD.
Abstract Dengue, West Nile and Zika virus belongs to the family flaviviridae and genus flavivirus. It is of interest to design and develop inhibitors with improved activity against these diseases. We used the helicases target to screen for potential inhibitors against these viruses using molecular docking analysis. NS3 helicases of flavivirus family of viruses such as Dengue, West Nile and Zika are prime targets for drug development. The computer aided molecular docking analysis of netropsin and novobiocin with the viral protein targets HABD, MTD and RCD is reported for further consideration. PMID: 31285639 [...
Source: Bioinformation - July 10, 2019 Category: Bioinformatics Authors: Alwabli AS, Alattas SG, Alhebshi AM, Zabermawi NM, Alkenani N, Ghmady KA, Qadri I Tags: Bioinformation Source Type: research
Screening of caspase-3 inhibitors from natural molecule database using e-pharmacophore and docking studies.
Abstract Caspase a protease family member, have a vital role in cell death and inflammation process. Caspase-3, an effector caspase controls the regulation of apoptosis and has an anti apoptotic function. The mechanical significance of restoring apoptosis signaling to selectively target malignant cells is utilized to develop strong therapeutic strategies by the caspase family of mortality - induction molecules. Caspase-3 has currently no clear role in treatment for tumor progression and tumor sensitivity. The present study was aimed to screen caspase for potential inhibitors using computer aided docking methodolog...
Source: Bioinformation - July 10, 2019 Category: Bioinformatics Authors: Eda SR, Veeramachaneni GK, Bondili JS, Jinka R Tags: Bioinformation Source Type: research
Insights into Molecular Interactions of human Wnt5b and Frizzled proteins for their role in teratogenicity.
Abstract Wnt-Fzd signalling plays vital role in different physiological pathways including embryonic development and supposed to be probable target of many teratogens. The present study was done to investigate the role of human Wnt5b interaction with different isoforms of human Fzds and also the molecular interactions of their complexes with selected known teratogens [Carbamazepine (CBZ), Retinoic acid (RA), Valproic acid (VPA), Aminopterin (AMP) and Phenytoin (PHY)] using Niclosamide (NLM) as standard. The models of hWnt5b and hFzd isoforms, whose solved crystal structures were unavailable, were generated using h...
Source: Bioinformation - July 10, 2019 Category: Bioinformatics Authors: Dahiya S, Saini V, Kumar P, Kumar A Tags: Bioinformation Source Type: research
Phenylhydrazine hydrochloride induced dosedependent embryo cytotoxicity in zebrafish.
Abstract Phenylhydrazine hydrochloride (PHZ) is a chemical compound. PHZ and its derivatives were used firstly as antipyretics, treatment of blood disorders such as polycythaemia Vera. For many years phenyl hydrazine was used for experimental induction of anaemia in animal models. However, this compound is reported to cause damage to red blood cells, potentially resulting in anaemia and consequential secondary involvement of other tissues, such as the spleen and liver. Recent studies suggest that PHZ cause genotoxicity in mice models. The aim of our study is to study the effect of PHZ in embryonic and larval stage...
Source: Bioinformation - July 10, 2019 Category: Bioinformatics Authors: Rajagopal RE, Balasubramanian M, Kalyanaraman S Tags: Bioinformation Source Type: research
Classification of Mycobacterium tuberculosis DR, MDR,XDR Isolates and Identification of Signature MutationPattern of Drug Resistance.
This study focuses on development of an effective pipeline to identify drug resistance mutations in whole genome data of Mycobacterium tuberculosis utilizing the Next Generation Sequencing approach and classification of drug resistance strains based on genetic markers obtained from TGS-TB, tbvar and TBDReamDB. 74 isolates are characterized into 20 DR-TB, 16 MDR-TB, 16 XDR-TB and 6 nonresistant strains based on known drug resistance genetic markers. Results provide mutation pattern for each of the classified strains and profiling of drug resistance to the group of anti-TB drugs. The presence of specific mutation causing res...
Source: Bioinformation - July 10, 2019 Category: Bioinformatics Authors: Prasanna A, Niranjan V Tags: Bioinformation Source Type: research
Gene mapping and molecular analysis of hereditarynon-polyposis colorectal cancer (Lynch Syndrome)using systems biological approaches.
Abstract Hereditary non-polyposis colorectal cancer (HNPCC) also known as Lynch Syndrome (LS), is a hereditary form of colorectal cancer (CRC). LSis caused by mutations in the mismatch repair (MMR) genes, mostly in MLH1, MSH2, MSH6 and PMS2. Identification of these gene mutations is essential to diagnose CRC, especially at a young age to increase the survival rate. Using open target platform, we have performed genetic association studies to analyze the different genes involved in the LS and to obtain target for disease evidence. We have also analyzed upstream regulators as target molecules in the data sets. We dis...
Source: Bioinformation - July 10, 2019 Category: Bioinformatics Authors: Rasool M, Karim S, Naseer MI, Pushparaj PN, Abuzenadah A, Al-Qahtani MH Tags: Bioinformation Source Type: research
Molecular docking and pharmacokinetic evaluation of natural compounds as targeted inhibitors against Crz1 protein in Rhizoctonia solani.
This study Comprises of quantitative structure-toxicity relationship (QSTR) and quantitative structure-activity relationship (QSAR). All compounds showed high binding energy for Crz1 protein through molecular docking. Further, a pharmacokinetic study revealed that these compounds had minimal side effects. Biological activity spectrum prediction of these compounds showed potential antifungal properties by showing significant interaction with Crz1. Hence, these compounds can be used for the prevention and treatment of wet root rot in Chickpea. PMID: 31285645 [PubMed] (Source: Bioinformation)
Source: Bioinformation - July 10, 2019 Category: Bioinformatics Authors: Malik A, Afaq S, Gamal BE, Ellatif MA, Hassan WN, Dera A, Noor R, Tarique M Tags: Bioinformation Source Type: research
Structure-based virtual screening and molecular docking for the identification of potential novel EGFRkinase inhibitors against ovarian cancer.
Abstract Epidermal Growth Factor Receptor (EGFR) is, for the most part, deregulated and over-communicated in ovarian disease, which is legitimately connected with STAT3 enactment that prompts the collection of hostile to apoptotic occasions and along these lines, docetaxel medicate obstruction happens. As to, expanding of docetaxel medicate affectability by focusing on EGFR receptor alongside docetaxel drugs is one of the real techniques in ovarian disease treatment. In this specific circumstance, utilizing atomic recreation considers, the present examination depicted the auxiliary and pragmatic properties of IBS ...
Source: Bioinformation - July 10, 2019 Category: Bioinformatics Authors: Sait KHW, Alam Q, Anfinan N, Al-Ghamdi O, Malik A, Noor R, Jahan F, Tarique M Tags: Bioinformation Source Type: research
PocketPipe: A computational pipeline for integratedPocketome prediction and comparison.
Abstract Functional characterisation of proteins often depends on specific interactions with other molecules. In the drug discovery scenario, the ability of a protein to bind with drug-like molecule with a high affinity is referred as druggability. Deciphering such druggable binding pockets on proteins plays an important role in structure-based drug designing studies. Moreover, availability of plethora of structural data poses a need automated pipelines which can efficiently integrate robust algorithms towards large-scale pocket identification and comparison. These pipelines have direct applicability on off-target...
Source: Bioinformation - July 10, 2019 Category: Bioinformatics Authors: Ansar S, Sadhasivam A, Vetrivel U Tags: Bioinformation Source Type: research
A comparative analysis of BCL-2 family.
Abstract The BCL-2 family is conserved in evolution and shares a BCL-2 homology domain. It promotes and inhibits apoptosis. It is also known that apoptosis has a major role in effective cancer treatment. Therefore, it is of interest to document information related to the BCL-2 family of proteins for analysis by prediction tools. Hence, insights from a prediction based comparative functional analysis of 108 genes in this family are documented. PMID: 31285648 [PubMed] (Source: Bioinformation)
Source: Bioinformation - July 10, 2019 Category: Bioinformatics Authors: Choudhury S Tags: Bioinformation Source Type: research