Volume 24, Issue 3
Comparative Computational Studies on Selective CytochromeP450 1B1 Inhibitors213-224
Mohd Usman Mohd Siddique, Azim Ansari, Barij Nayan Sinha, Venkatesan Jayaprakash
doi: 10.7546/ijba.2020.24.3.000537
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Mohd Usman Mohd Siddique, Azim Ansari, Barij Nayan Sinha, Venkatesan Jayaprakash (2020) Comparative Computational Studies on Selective CytochromeP450 1B1 Inhibitors, Int J Bioautomation, 24 (3), 213-224, doi: 10.7546/ijba.2020.24.3.000537
Abstract: Selective inhibitors of CYP isoforms gaining importance in the treatment of cancers caused by hormonal imbalance. Metabolites of estradiol and polyaromatic hydrocarbons generated due to CYP1B1 activity were reported to be oncogenic. The selective CYP1B1 inhibitors could have the potential therapeutic utility in controlling the cancer due to these oncogens. Due to the CYP isoforms high sequence similarity the design of selective CYP inhibitor is difficult. Recently our group has reported two novel chemical classes (scaffolds) that are specific towards CYP1B1. The chemical architecture of these compounds should give valuable information for its selectivity and potency against CYP1B1. Overlay of our compounds and ANF by Shape and electrostatic based similarity and molecular docking displayed different orientations. Moreover the study has shown the overlay of three atom bridge of selective inhibitor superimposed on -O-CH- linking aryl groups rather than -CO-CH=CH- of ANF. Molecular docking simulation revealed that the selective inhibitors are either establishing H-bonding interaction with Asp333 or π-π staking interaction Phe231 and Phe268. Molecular docking simulation has provided much more information rather than simple shape and electrostatic based similarity study. Crucial H-bonding interactions and π-π staking interactions responsible for selectivity towards CYP1B1 were identified. Two atom linker between the aryl groups matter, cyclization simply ensures the planarity of ANF and quinazolines.

Keywords: CYP1B1, Selective inhibitors, Similarity search, Docking, Druggability, ADME
Comparative Analysis of Carbonic Anhydrase with Reference to Anopheles gambiae – A Vector of Malaria and its Homology Model Prediction225-234
Nathan Vinod Kumar
doi: 10.7546/ijba.2020.24.3.000605
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Nathan Vinod Kumar (2020) Comparative Analysis of Carbonic Anhydrase with Reference to Anopheles gambiae – A Vector of Malaria and its Homology Model Prediction, Int J Bioautomation, 24 (3), 225-234, doi: 10.7546/ijba.2020.24.3.000605
Abstract: Carbonic anhydrase (CA) is widely distributed enzyme which plays a crucial role in hydration of carbon dioxide. CA of Anopheles gambiae, a common vector that transmits the malaria disease in tropical countries is not well studies. CA is essential for the normal physiological function and inhibition of it can lead to lethal effect. Recently, CA was identified as a potential drug target for developing mosquito larvicidal drugs. CA of A. gambiae was characterized and compared with 12 other members of the class insecta. CA of A. gambiae comprised of 309 amino acid residues with 34.56 kDa and theoretical pI of 6.34. The Leu rich protein had more of negatively charged residues and was classified as a stable protein. Mitochondrial targeting peptide containing enzyme had about 46.28% random coils, 28.16% α-helix and 3.24% β-turns. The homology model for the CA of A. gambiae was predicted using template 4lu3.1.A and the model quality was validated by least RMSD score, Z-score and Ramachandran plot analysis. The present study is a preliminary report exploring proteomics aspects of CA of A. gambiae using in silico tools.

Keywords: Carbonic anhydrase, Homology model, Protein structure
Bioinformatics Analysis of the Melanocortin 1 Receptor Gene (MC1R) in the Southern Platyfish Xiphophorus maculatus (Günther, 1866)235-244
Abdul Khader Sultan Mohideen, Anbu Arun
doi: 10.7546/ijba.2020.24.3.000609
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Abdul Khader Sultan Mohideen, Anbu Arun (2020) Bioinformatics Analysis of the Melanocortin 1 Receptor Gene (MC1R) in the Southern Platyfish Xiphophorus maculatus (Günther, 1866), Int J Bioautomation, 24 (3), 235-244, doi: 10.7546/ijba.2020.24.3.000609
Abstract: The Southern platyfish Xiphophorus maculatus is one of the most popular ornamental fish used widely as a premier model system in understanding the genetic basis of color pattern polymorphism. Coloration in X. maculatus is found to be linked with melanin synthesis. Melanocortin genes are involved in the synthesis of melanin pigments. Bioinformatic analysis of the MC1R gene of X. maculatus revealed a 966 bp open reading frame encoding 322 amino acids. The deduced MC1R protein sequence was predicted to possess 7transmembrane G-protein-coupled receptor (7TM GPCR) domain from amino acids 59 to 299 (241 amino acids). The predicted three dimensional structure of the MC1R protein contains seven helices (α1 to α7) from amino acid residues 48-67, 80-102,122-144, 165-187, 197-219, 240-262 and 277-299 respectively within the transmembrane region. In the extracellular region, the presence of amino acid residues from N-terminal position 6-Serine, 8-Leucine, 17-Proline, 20-Glutamic acid, 25-Asparagine and 26-Glutamic acid were predicted to be the binding sites of the receptor. The intracellular region comprising of amino acids residues from 68-79, 145-164, 220-239 and 300-322 interacts with the G protein. The predicted model of the MC1R protein of X. maculatus provides a detailed view of the structure and shows tremendous scope in the field of aquaculture as a target protein/model especially in enhancing fish body coloration.

Keywords: Xiphophorus maculatus, MC1R, GPCR, Southern platyfish
Comprehensive Molecular Simulation of Triple-negative Breast Cancer Transcriptomics Features of miR-145 and the 3' UTR of ARF6 mRNA245-254
Jeremias Ivan, Rizky Nurdiansyah, Arli Aditya Parikesit
doi: 10.7546/ijba.2020.24.3.000616
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Jeremias Ivan, Rizky Nurdiansyah, Arli Aditya Parikesit (2020) Comprehensive Molecular Simulation of Triple-negative Breast Cancer Transcriptomics Features of miR-145 and the 3' UTR of ARF6 mRNA, Int J Bioautomation, 24 (3), 245-254, doi: 10.7546/ijba.2020.24.3.000616
Abstract: Triple-negative breast cancer is one of the deadliest diseases for women, according to the World Health Organization. The most common drugs used and in development for this disease are based upon the proteomics approach, but this so far has not accounted for the whole repertoire of human genome expression. However, a novel approach is currently under development to model the molecular interaction between miR-145 and the 3' untranslated region (UTR) of ARF6 mRNA. This approach should eventually be useful for transcriptomics-based drug development. The utilized methods are molecular-docking and dynamics based, using open-source software. It was found that there was a fine-grained molecular interaction between miR-145 and the 3' UTR of ARF6 mRNA. It is concluded that the information from the interaction could be utilized as the basis for drug development.

Keywords: Breast cancer, Human genomic, miR-145, 3' UTR of ARF6 mRNA, Molecular docking, Molecular dynamics
Protein Sequence Retrieval and Phylogenetic Analysis of Various α-amylase Producing Bacillus species255-264
Sonali Priyadarshini, Sukanta Kumar Pradhan, Pratima Ray
doi: 10.7546/ijba.2020.24.3.000640
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Sonali Priyadarshini, Sukanta Kumar Pradhan, Pratima Ray (2020) Protein Sequence Retrieval and Phylogenetic Analysis of Various α-amylase Producing Bacillus species, Int J Bioautomation, 24 (3), 255-264, doi: 10.7546/ijba.2020.24.3.000640
Abstract: Due to advancements made in biotechnology, genetic manipulation and medium optimization has been possible and that has led to high yield in enzyme especially α-amylase with improvised properties that find its application suitably in detergent, laundry and starch processing industries. Various species of the genus Bacillus produce α-amylases with varying properties. The amylases that find application miraculously in different fields can be easily obtained from plant, animal and microbial sources. Out of the three sources, microbial source especially the genus Bacillus is extensively studied for its ability to produce the enzyme. In the present study, protein sequences of primarily identified α-amylase producing Bacillus spp. were retrieved from protein database of National Center for Biotechnology Information. Multiple sequence alignment was performed and construction of Phylogenetic tree among these sequences was carried out using Neighbor-joining method; data sets based on 1000 re-samplings in molecular genetics evolutionary analysis.

Keywords: Alkaline α-amylase, Bacillus, Phylogenetic analysis, Protein sequence
A Computational Study to Predict Wound Healing Agents from the Peel of the Mangosteen (Garcinia mangostana L.) Extract265-276
Marisca Evalina Gondokesumo, Sutiman Bambang Sumitro, Kusworini Handono, Bambang Pardjianto, Wahyu Widowati, Didik Huswo Utomo
doi: 10.7546/ijba.2020.24.3.000607
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Marisca Evalina Gondokesumo, Sutiman Bambang Sumitro, Kusworini Handono, Bambang Pardjianto, Wahyu Widowati, Didik Huswo Utomo (2020) A Computational Study to Predict Wound Healing Agents from the Peel of the Mangosteen (Garcinia mangostana L.) Extract, Int J Bioautomation, 24 (3), 265-276, doi: 10.7546/ijba.2020.24.3.000607
Abstract: This study aimed to identify potentially active compounds from mangosteen peel extracts that heal skin burns and to evaluate their molecular mechanisms. There are about 120 compounds that have been identified in mangosteen peel by datamining, including 60 types of xanthones. The SMILE format of each compound was downloaded from the PubChem database. The compound data was then analyzed for potential anti-inflammatory, antioxidant, and antibacterial activities with PASS SERVER. To prediction mechanisms, firstly, target protein predictions were made with Swiss target prediction and HitPick. Target Protein data was then analyzed by interaction with STRING to determine its molecular mechanism. Further analysis of the shortest pathway was done with Cytoscape. The screening process of fifty compounds, which are predicted to have anti-inflammatory, antioxidant, and antibacterial activities by PASS SERVER. The four highest potency compounds were Smeaxanthone A, Garcinone E, γ-mangosteen, and Gartanin, which were types of xanthone. Based on the result of computational study these four compounds have potential targets prediction related to interleukin 6, epidermal growth factor, and transforming growth factor beta 1, that are involved in the regulation of epithelial cell proliferation which plays a role in the healing process of skin burns.

Keywords: Mangosteen peel, Skin burns, Wound healing, Xanthones, Molecular docking
Genetic Algorithm and Cuckoo Search Hybrid Technique for Parameter Identification of Fermentation Process Model277-288
Maria Angelova, Peter Vassilev, Tania Pencheva
doi: 10.7546/ijba.2020.24.3.000707
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Maria Angelova, Peter Vassilev, Tania Pencheva (2020) Genetic Algorithm and Cuckoo Search Hybrid Technique for Parameter Identification of Fermentation Process Model, Int J Bioautomation, 24 (3), 277-288, doi: 10.7546/ijba.2020.24.3.000707
Abstract: This paper presents a hybrid scheme based on two population-based metaheuristic techniques, namely genetic algorithm (GA) and cuckoo search (CS). In particular, the hybrid is formed by the application of standard simple genetic algorithms (SGA) and CS, specifically adapted and for first time applied by the authors for the purposes of parameter identification of yeast fed-batch fermentation process model. The parameters of the hybrid technique SGA-CS have been thoroughly explored and tuned to meet the specific peculiarities of the considered here optimization problem. A comparison of SGA, CS and developed hybrid SGA-CS has been performed, outlining the advantages and disadvantages of each algorithm. Additionally, a new modification of SGA-CS hybrid technique, inspired by proven as very effective modification of SGA, working with implementation of main genetic operators in order crossover, mutation and selection, has been here elaborated. Presented modified hybrid technique has been tested, aiming at verification of the obtained promising results of developed SGA-CS technique.

Keywords: Genetic algorithm, Cuckoo search, Hybrid technique, Parameter identification, Fed-batch fermentation process
Separation of the Electromyographic from the Electrocardiographic Signals and Vice Versa. A Topical Review of the Dynamic Procedure289-317
Ivaylo Christov, Atanas Gotchev, Giovanni Bortolan, Tatyana Neycheva, Rositsa Raikova, Ramun Schmid
doi: 10.7546/ijba.2020.24.3.000744
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Ivaylo Christov, Atanas Gotchev, Giovanni Bortolan, Tatyana Neycheva, Rositsa Raikova, Ramun Schmid (2020) Separation of the Electromyographic from the Electrocardiographic Signals and Vice Versa. A Topical Review of the Dynamic Procedure, Int J Bioautomation, 24 (3), 289-317, doi: 10.7546/ijba.2020.24.3.000744
Abstract: Electrocardiographic (ECG) and electromyographic (EMG) signals are inevitably and simultaneously recorded from the same electrodes and are respectively useful signal and noise in electrocardiography, and vice versa in electromyography. The frequency domains of the two signals overlap, making it difficult to filter the noise without distortion of the useful signal. An original ‘dynamic method’ for separation of the two signals was created. In a series of publications that began in 1999 with filtering of EMG noise from ECG signal, we have described the method and have made a number of improvements such as noise analysis and automatic on/off triggering in presence/absence of noise, online application, and tuning the parameters, to fulfill the last filtering recommendations of the American Heart Association. No matter if the Dynamic procedure is to be used in electrocardiography or in electromyography, the method contains the following: (i) Evaluation of the frequency bands of the ECG signal; (ii) filtering (suppression) of the EMG signal by dynamic change of the size of the filtering window for maximal preservation of the morphology of the ECG waves. The cutoff frequency is individual for any signal sample and varies from 13 Hz at the linear segments of the ECG signal, trough 25 Hz for the T-waves of high amplitude, and up to 400 Hz for the QRS-complexes; (iii) EMG signal separation by subtraction of the filtered ECG signal from ECG + EMG initial signal. With the current review, we are attempting to summarize all done over the years on the Dynamic procedure.

Keywords: Electrocardiography, Electromyography, Dynamic filtration, High frequency noise, Wings function

Sponsored by National Science Fund of Bulgaria, Grant No KP-06-NP/1/13, 2019

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