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Computational Biology and Chemistry

Joana M S Cardoso, Luís Fonseca, Conceição Egas, Isabel Abrantes
The pinewood nematode, Bursaphelenchus xylophilus, is an important plant-parasitic nematode responsible for the development of the pine wilt disease and recognised as a major forest pest. Previous studies on the comparison of B. xylophilus and B. mucronatus secretomes obtained under maritime pine, Pinus pinaster, wood extract stimulus revealed that several cysteine proteases were increased in B. xylophilus secretome. In nematodes, proteases are known to play critical roles in parasitic processes like tissue penetration, digestion of host tissues for nutrition and evasion of host immune response...
October 26, 2018: Computational Biology and Chemistry
Andrey Kechin, Evgeniy Khrapov, Uljana Boyarskikh, Alexander Kel, Maxim Filipenko
The use of targeted next-generation sequencing (NGS) provides great new opportunities for molecular and medical genetics. However, in order to take advantage of these opportunities, we need to have reliable tools for extracting the necessary information from the huge amount of data generated by NGS. Here we present our automatic multithreaded workflow for processing NGS data of BRCA1 and BRCA2 genes obtained with NGS technology named BRCA-analyzer. Optimizing it on the sequencing data of 899 samples from 693 patients, we were able to find the most reliable tools and adjust their parameters in such a way that all pathogenic variants found were confirmed by Sanger's sequencing...
October 23, 2018: Computational Biology and Chemistry
Nguyen Quoc Khanh Le, Green Arther Sandag, Yu-Yen Ou
Transporters involved in the cellular entry and exit of ions or molecules throughout the membrane proteins and thereby play an essential role in recognizing the immune system and energy transducers. According to their relevance in proteomics, numerous studies have been conducted to analyze the transporters; especially the discrimination of their classes and subfamilies. We realized that post translational modification information had a critical role in the process of transport proteins. Therefore, in this study, we aim to incorporate post translational information with radial basis function networks to improve the predictive performance of transport proteins in major classes (channels/pores, electrochemical transporters, and active transporters) and six different families (α-type channels, β-barrel porins, pore-forming toxins, porters, PP bond hydrolysis-driven transporters, and oxidoreduction-driven transporters)...
October 18, 2018: Computational Biology and Chemistry
Madhu Yadav, Ritika Srivastava, Farha Naaz, Ramendra K Singh
A series of molecules bearing oxathiadiazole, a five membered heterocyclic ring has been designed, synthesized and screened for antimicrobial activity. Molecules, 1a, 1b, 1d, 3a-b and 4a-b were found to be highly active (MIC value upto 1.5 μg/mL) against different human pathogens, namely S. aureus, B. cerus, P. aeruginosa and E. coli. Some of the compounds, 1a, 1b and 1d have also shown the antifungal activity (MIC value upto 6.2 μg/mL) against Candida albicans, Candida glubrate and Candida crusei. During in vitro cytotoxicity study, the oxathiadiazole derivatives showed less toxicity than the reference used against PBM, CEM and Vero (African green monkey kidney) cell lines...
October 16, 2018: Computational Biology and Chemistry
Mingxing Wang, Ying Wang, Dejiang Kong, Hailun Jiang, Jian Wang, Maosheng Cheng
It has been demonstrated by human genetics that the voltage-gated sodium channel Nav1.7 is currently a promising target for the treatment of pain. In this research, we performed molecular simulation works on a series of classic aryl sulfonamide Nav1.7 inhibitors using three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking and molecular dynamics (MD) simulations for the first time to explore the correlation between their structures and activities. The results of the relevant statistical parameters of comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analyses (CoMSIA) had been verified to be reasonable, and the deep relationship between the structures and activities of these inhibitors was obtained by analyzing the contour maps...
October 13, 2018: Computational Biology and Chemistry
Thitima Panyayai, Papungkorn Sangsawad, Eakasit Pacharawongsakda, Orathai Sawatdichaikul, Sissades Tongsima, Kiattawee Choowongkomon
Peptides derived from food proteins are promising bioactive source for inhibiting Angiotensin-I converting enzyme (ACE) activity. Bioactive peptides (BP) have received much attention, particularly from the pharmaceutical industry. As they not only own potent properties but also possess less side-effects than synthetic drugs. In this work, an 8000 possible tripeptides library was constructed to predict the potential ACE inhibitory peptides by using in silico tools. GOLD molecular docking was then applied to determine the binding mode of action between ACE and each of tripeptide from this in-house library...
October 12, 2018: Computational Biology and Chemistry
Fayaz Ali Larik, Aamer Saeed, Muahmmad Faisal, Pervaiz Ali Channar, Syed Sikandar Azam, Hammad Ismail, Erum Dilshad, Bushra Mirza
Thioureas are exquisite building blocks for the construction of five and six membered heterocyclic units, and also display an extensive range of biological activities. 4-Nitro-2-cyano aniline was reacted with the various acid chlorides which were freshly prepared from carboxylic acids to afford the desired products in good yield. All the newly synthesized compounds were evaluated antibacterial, antifungal, antioxidant and α-amylase activity. The compounds showed significant activity against bacteria and fungi...
October 10, 2018: Computational Biology and Chemistry
Naghmeh Poorinmohammad, Javad Hamedi, Mohammad Hossein Abbaspour Motlagh Moghaddam
Lantibiotics, an important group of ribosomally synthesized peptides, represent an important arsenal of novel promising antimicrobials showing high potency in fighting against the prevalence of antibiotic resistance among microbial pathogens. However, due to the lack of high throughput strategies for the isolation and identification of these compounds, our information regarding their structure and especially sequence-based properties is far from complete. Therefore, in the present study, a comprehensive sequence-based analysis of these peptides was performed with the help of machine learning approach together with a feature selection technique...
October 9, 2018: Computational Biology and Chemistry
Md Humayun Kabir, Djordje Djordjevic, Michael D O'Connor, Joshua W K Ho
Cell type identification from an unknown sample can often be done by comparing its gene expression profile against a gene expression database containing profiles of a large number of cell-types. This type of compendium-based cell-type identification strategy is particularly successful for human and mouse samples because a large volume of data exists for these organisms. However, such rich data repositories often do not exist for most non-model organisms. This makes transcriptome-based sample classification in these species challenging...
October 9, 2018: Computational Biology and Chemistry
Gokhan Zengin, Maria João Rodrigues, Hassan H Abdallah, Luisa Custodio, Azzurra Stefanucci, Muhammad Zakariyyah Aumeeruddy, Adriano Mollica, Kannan R R Rengasamy, Mohamad Fawzi Mahomoodally
The genus Silene is renowned in Turkey for its traditional use as food and medicine. Currently, there are 138 species of Silene in Turkey, amongst which have been several studies for possible pharmacological potential and application in food industry. However, there is currently a paucity of data on Silene salsuginea Hub.-Mor. This study endeavours to access its antioxidant, enzyme inhibitory, and anti-inflammatory properties. Besides, reversed-phase high-performance liquid chromatography-diode array detector (RP-HPLC-DAD) was used to detect phenolic compounds, and molecular docking was performed to provide new insights for tested enzymes and phenolics...
October 9, 2018: Computational Biology and Chemistry
Mueed Ur Rahman, Ashfaq Ur Rehman, Hao Liu, Hai-Feng Chen
Hepatitis C virus, Nonstructural 3 helicase (NS3h) protein is a well-studied segment of Non-structural 3/4 A helicase-protease protein that is crucial for the RNA duplex unwinding and RNA translocation during the process of HCV replication. Similar to other HCV nonstructural proteins, helicase is a potential target for antiviral drugs and several antiviral molecules have been used to target the RNA-binding cleft, despite the fact that none of those helicase antivirals have advanced the clinical trials. Compound 2t9 (5-bromo-1H-indol-3-yl acetic acid) has been identified through the integrated strategies and considered as a potential lead compound for the inactivation of HCV helicase...
October 9, 2018: Computational Biology and Chemistry
T K Shameera Ahamed, Vijisha K Rajan, K Sabira, K Muraleedharan
Developments of novel inhibitors to prevent the function of 5-lipoxygenase (5-LOX) proteins that are responsible for a variety of inflammatory and allergic disease are a major challenge in the scientific community. In this study, robust QSAR classification models for predicting 5-LOX activity were developed using machine learning algorithms. The Support Vector Machines (SVM), Logistic Regression, k-Nearest Neighbour (NN) and Decision Trees were adopted to improve the prediction ability of the classification models...
October 5, 2018: Computational Biology and Chemistry
Alagu Sankareswaran S, Arun Goutham R N, Suma Mohan S
SWI/SNF (SWItch/Sucrose Non-Fermentable) complexes regulate the gene expression programs by remodeling the nucleosome architecture of the chromatin functional elements. These large multi-component complexes comprise eight or more subunits and are conserved from yeast to human. Noticeably, nuclear actin and actin-related proteins (Arps) are an integral part of these complexes and are known to directly interact with the helicase-SANT-associated (HSA) domain of ATPase subunit. Recently, SWI/SNF subunits are gaining importance because of the prevalence of cancer-causing mutations associated with them...
October 1, 2018: Computational Biology and Chemistry
Nikhil Agrawal, Md Summon Hossain, Adam A Skelton, Kambadur Muralidhar, Sandeep Kaushik
l-Gulonate dehydrogenase (GuDH) is a crucial enzyme in the non-phosphorylated sugar metabolism or glucuronate-xylulose (GX) pathway. Some naturally occurring compounds inhibit GuDH. Ascorbic acid is one of such inhibitors for GuDH. However, the exact mechanism by which ascorbic acid inhibits GuDH is still unknown. In this study, we try to investigate GuDH inhibition using computational approaches by generating a model for buffalo GuDH. We used this model to perform blind dockings of ascorbic acid to GuDH. Some docked conformations of ascorbic acid bind near Asp39 and have steric clashes with crystal structure conformation of NADH...
September 27, 2018: Computational Biology and Chemistry
R Cataldo, F Ciriaco, E Alfinito
The selection of high-affinity aptamers is of paramount interest for clinical and technological applications. A novel strategy is proposed to validate the reliability of the 3D structures of a group of anti- Angiopoietin-2 aptamers, produced in silico by using free software. In a previous literature these aptamers were processed both in vitro and in silico, by using an approach different from that here presented, and finally tested with a SPS experiment. Computational expectations and experimental outcomes did not agree...
September 27, 2018: Computational Biology and Chemistry
Muhammet Uslupehlivan, Ecem Şener, Remziye Deveci
Pax6 is a transcription factor that involves in the formation of the eye, brain, and central nervous system in vertebrates. Due to various roles in the eye morphogenesis, Pax6 interacts with DNA and various transcription factors via post-translational modifications. Post-translational modifications of Pax6 have been studied extensively but there is a paucity of information about the glycosylation. Here, we focused on predicting the glycosylation positions of Pax6 protein in vertebrates. Also, 3D protein and glycoprotein models were generated using I-TASSER and GLYCAM servers in order to understand the effect of glycosylation on the Pax6 protein structure...
September 27, 2018: Computational Biology and Chemistry
Richa Bhatnager, Maheshwar Bhasin, Amita S Dang
Extracellular matrix is a dynamic meshwork of macromolecules that plays an important role in biological processes such as tissue remodeling and various developmental processes. Collagen is the chief component of ECM. Upon hydrolysis, it forms an irreversible left-handed helical structure which is further hydrolyzed by a specialized group of MMP family i.e. Gelatinases (MMP2 and MMP9). Present study was carried to figure out deleterious SNPs associated with MMP9 gene. Our results showed that two nsSNP (rs8125581 and rs41529445) that are present in catalytic domain are highly conserved and affect the protein structure and function...
September 14, 2018: Computational Biology and Chemistry
Junning Chen, Hailun Jiang, Fangfei Li, Baichun Hu, Ying Wang, MingXing Wang, Jian Wang, Maosheng Cheng
The NS2B-NS3 protease is essential for the replication process of Dengue Virus, which make it an attractive target for anti-virus drugs. Since a considerable number of NS2B-NS3 protease inhibitors have been reported so far, it is significant for the discovery of more effective antivirus compounds with the essential structure-activity relationship extracted from known inhibitors. In this perspective, the relationship between the chemical features of inhibitors and their biological activities was investigated with a combined ligand- and structure-based approach...
September 13, 2018: Computational Biology and Chemistry
Lalehan Ozalp, Safiye Sağ Erdem, Başak Yüce-Dursun, Özal Mutlu, Mehmet Özbil
Phthalocyanines are considered as good DNA binders, which makes them promising anti-tumor drug leads. The purpose of this study is to investigate the interactions between DNA and quaternary metallophthalocyanine derivatives (Q-MPc) possessing varying metals (M = Zn, Ni, Cu, Fe, Mg and Ca) by molecular docking since there seems to be a lack of information in the literature regarding this issue. In this direction, Autodock Vina and Molegro Virtual Docker programs were employed. Autodock Vina results reveal that each Q-MPc derivative binds to DNA strongly with similar binding energies and almost identical binding modes...
September 13, 2018: Computational Biology and Chemistry
Muhammad Athar Abbasi, Mubashir Hassan, Aziz Ur-Rehman, Sabahat Zahra Siddiqui, Ghulam Hussain, Syed Adnan Ali Shah, Muhammad Ashraf, Muhammad Shahid, Sung Yum Seo
The heterocyclic compounds have been extensively reported for their bioactivity potential. The current research work reports the synthesis of some new multi-functional derivatives of 2-furoic piperazide (1; 1-(2-furoyl)piperazine). The synthesis was initiated by reacting the starting compound 1 with 3,5-dichloro-2-hydroxybenzenesulfonyl chloride (2) in a basic, polar and protic medium to obtain the parent sulfonamide 3 which was then treated with different electrophiles, 4a-g, in a polar and aprotic medium to acquire the designed molecules, 5a-g...
September 10, 2018: Computational Biology and Chemistry
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