Forthcoming and Online First Articles

International Journal of Computational Biology and Drug Design

International Journal of Computational Biology and Drug Design (IJCBDD)

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International Journal of Computational Biology and Drug Design (8 papers in press)

Regular Issues

  • Importance of safety maintenance of the survived with recent former infection experience during a pandemic syndrome episode: A Study by Difference Equation Approach   Order a copy of this article
    by Subhasis Bhattacharya, Suman Paul, Sudip Mukherjee 
    Abstract: During the outbreak of a highly infectious disease conceded by a virus, handling of healthcare catastrophe is the most momentous part. Any type of known or unknown relaxation may generate enormous loss in terms of population. Present study consider the concern that survived one who has some fresh former infection history can be fingered with appropriate care throughout the syndrome period otherwise a huge harm can be advent by the state. The study follow difference equation modelling considering two aspects where the survived with former infection history handled with care and not reckoned as a part of sustained population and the other is they encompassed with the general population category. The study considers an example of a hypothetical state with some give infection rate, death rate and quarantine rate. By using R- programme language the study observes that proper care for such group of population is very significant to reduce the situation like human loss.
    Keywords: Infectious disease; SARS-CoV-2; 2019-nCov; Difference Equation; Survived from the infected; Quarantine rate; Death Rate.

  • A Model for the Roles of Actin and Myosin in Adjustable Preload Tension and Acute Length Adaption   Order a copy of this article
    by Omid Komari, Adam Klausner, Paul Ratz, John Speich 
    Abstract: Muscle mechanical behaviour potentially plays an important role in some of the most common bladder disorders. These include overactive bladder, which can involve involuntary contractions during bladder filling, and impaired contractility or underactive bladder, which may involve weak or incomplete contractions during voiding. Actin-myosin cross-bridges in detrusor smooth muscle (DSM) are responsible for contracting and emptying the bladder. The total tension produced by the muscle is the sum of its preload and active tensions. Studies suggest that actin-myosin cross-links are involved in adjustable preload stiffness (APS), which is characterized by a preload tension curve that can be shifted along the length axis as a function of strain history and activation history. DSM also exhibits length adaptation in which the active tension curve can exhibit a similar shift. Actin-myosin cross-bridges are also responsible for myogenic contractions in response to quick stretch of DSM strips and spontaneous rhythmic contractions (SRC) that may occur during bladder filling. Studies show that SRC may participate in the mechanical regulation of both APS and length adaptation. However, the mechanical mechanisms of these interrelated functions are unknown. This study focused on developing a conceptual model with actin-myosin cross-bridges and cross-links that produce the coupled mechanical behaviours of APS, SRC, and length adaptation in DSM.
    Keywords: Biomechanics; Tissue Biomechanics; Biomechanical Models; Detrusor Smooth Muscle; Urodynamic; Length-tension curve; Adjustable preload tension; Actin-Myosin; Spontaneous Rhythmic Contractions.
    DOI: 10.1504/IJECB.2023.10055952
     
  • Potential of the Flavonoid Compounds of Ageratum Conyzoides as Candidates for the Treatment of Foot-Mouth Diseases (FMD) in Livestock Animals: a Bioinformatics Approach   Order a copy of this article
    by Endik E.D.N. Nugroho, Ahmad Misbakhus Sururi, Reza R.A. Ardiansyah, Dwi D.A.R. Rahayu, Roisatul Ainiyah, Amang Fathurrohman, Zainul Ahwan, M. Dayat, Mulyono Wibisono, Fatit Rahmar Aji, Kasiman Kasiman 
    Abstract: Livestock ecology and economy are threatened by foot-and-mouth disease (FMD) caused by FMD-virus. Especially with natural herbal compounds, this difficulty remains. Overcoming this issue requires the discovery of herbal therapeutic ingredients, especially flavonoids. An herbaceous plant called Ageratum conyzoides may solve this problem. This work examines the in silico suppression of RdRp and 3Cpro FMDV by A. conyzoides flavonoid compounds as FMD antivirals. This study used precocene I, II, 5-methoxynobiletin, lycopsamine, sinensetin, eupalestin, quercetin, kaempferol, 5,6,7,8,3',5'-hexamethoxyflavone, and isoflavone glycosides. Potential compounds were then assessed for Lipinski druglikeness, ADME, and toxicity prediction. The results showed that six compounds could synergistically inhibit RdRp and 3Cpro, with binding values -6.9 to -7.5 kcal/mol lower than ribavirin, the control drug. Lipinski's druglikeness analysis implies oral drug potential for the six substances. As an FMD-antiviral candidate, ADMET (Absorption, Distribution, Metabolism, and Excretion) analysis is also positive. Further research is needed to determine the anti-FMD potential.
    Keywords: Ageratum conyzoides; Foot and Mouth Disease; Virus; inhibitor.
    DOI: 10.1504/IJCBDD.2024.10062280
     
  • Public Perception Analysis on COVID-19 Tweets using Hybridised Method   Order a copy of this article
    by Radhakrishna Jana, Dharmpal Singh, Saikat Maity, Hrithik Paul, Ankush Mallick, Sayani Ghatak, Saurav Mallik, Mingqiang Wang 
    Abstract: Social media is a platform where users can interact with others in the network of the social media platform, share their posts, images, and other content, and do a lot more. One of the most widely used social media sites, now a days, is Twitter. Most Twitter users will tweet and retweet a certain tweet. The sole explanation for the rise in social media usage during the COVID-19 pandemic is that people became more bored at that time, and there were no longer any newspapers available in homes. At that time, people used Twitter to see the daily news and tweet and retweet something on Twitter. This paper mainly focuses on sentiment analysis using tweets that have been performed during the COVID-19 pandemic. Based on Text (Tweets) and Sentiment (i.e., Positive and Negative), various computational models are used for this work, viz., LSTM (Long Short-Term Memory) and SimpleRNN. LSTM yields the best accuracy (92%). Based on the data, both these models provide meaningful forecasts, but in order to maintain confidence, XAI has been combined with both models.
    Keywords: Machine Learning; Sentiment Analysis; SimpleRNN; LSTM; COVID-19; Twitter; Tweets; Explainable artificial intelligence.
    DOI: 10.1504/IJCBDD.2024.10063893
     
  • Molecular dynamics simulation of the interactions of antimicrobial peptides with phospholipids of the inner membrane of gram-negative bacteria   Order a copy of this article
    by Yury Lisnyak, Artur Martynov, Boris Farber 
    Abstract: Antimicrobial peptides (AMP), positively charged polypeptides, are now extensively studied in the world to develop efficient drugs against extremely resistant bacterial strains. By molecular dynamics (MD) simulations, there were studied the ligand-receptor interactions of polymyxin B with two model systems in the water-salt solution: an anionic sodium dodecyl sulfate (SDS) micelle and explicit lipid bilayer of zwitterionic phosphatidylethanolamine (PEA), which mimics the gram-negative bacteria membrane. As a result, the polymyxin binding to PEA is stronger. The polymyxin B molecule interacts differently with these two types of membrane mimetics. The interaction of the peptide with SDS micelle occurs mainly due to electrostatic interactions and/or hydrogen bonding interactions of protonated Dab groups and polar groups of polymyxin with charged and polar groups of SDS micelles. The interaction of the peptide with the DPC micelle occurs mainly by the hydrophobic interactions of its Phe, Leu, and methyloctanoyl.
    Keywords: drug-target interactions; molecular dynamics simulations; polymyxin B; micelles.
    DOI: 10.1504/IJCBDD.2024.10064211
     
  • Herbal Bioactive Compounds as Promising Inhibitors of p37 in Monkeypox Virus: a Computational Approach   Order a copy of this article
    by Linh Thuy Hoang, Tuan Duc Nguyen, Hieu Trung Nguyen, Huong Thi Thu Phung, Dao Thanh Tran 
    Abstract: Monkeypox is a highly contagious disease caused by the monkeypox virus (MPXV) that has recently been deemed a Public Health Emergency of International Concern by the World Health Organization. Tecovirimat is a drug approved by the European Medicines Agency for treating monkeypox, which targets the poxvirus p37 enzyme required for virus replication. However, the structure and function of MPXV p37 are unclear. We predicted the MPXV p37 structure using prediction software, with the best results coming from AlphaFold. The binding affinity of p37 with tecovirimat and ten broad-spectrum bioactive molecules and potential antimicrobial agents from natural herbs was estimated via molecular docking simulations. Curry and olive compounds showed the best binding affinities with p37. Like tecovirimat, curry substances interacted with MPXV p37 mainly through hydrophobic interaction. The results reveal that curry leaves and olives could be promising inhibitors of MPXV p37, potentially serving as a natural drug to treat monkeypox.
    Keywords: Monkeypox; Monkeypox virus; P37; Tecovirimat; Herbal Substance; Virtual Screening; AlphaFold; Molecular docking; Natural herbs; Natural drug.
    DOI: 10.1504/IJCBDD.2024.10064328
     
  • Virtual Screening Integrating Ligand Based and Structure Based Models followed by Pharmacokinetic Study for the Identification of COX-2 Inhibitor Leads   Order a copy of this article
    by Divya V 
    Abstract: Cyclooxygenase-2 (COX-2) inhibitors prevent the cyclooxygenase pathways from producing the inflammatory mediators COX-2. Using Quantitative Structure Activity Relationship (QSAR) development, virtual screening, and molecular docking approaches, 10 intriguing COX-2 inhibitors were found in the current study from a series of 1023 compounds, comprising compound 50 analogues. One statistical model was adopted for COX-2 inhibition with R2 = 0.8382 and Q2 = 0.7998. Docking studies were performed to quantify the binding affinity of eligible query compounds towards COX-2 protein and to uncover the specific interactions that take place between ligands and the protein they are trying to bind to using Celecoxib as reference. There were found to be powerful hydrogen bonding interactions between the target molecule and ligand molecules. The pharmacokinetic features using ADMET investigation revealed that molecules VS309, VS313, VS315, VS316, VS317, VS325 and VS326 were said to be taken as best molecules without any hazardous impact.
    Keywords: COX-2 Inhibitors; QSAR; Virtual screening; molecular docking; pharmacokinetic analysis.
    DOI: 10.1504/IJCBDD.2024.10064371
     
  • Algorithms to Compare Pentagonal Pyramidal/ Bipyramidal Metal Complexes on Proteins Structure   Order a copy of this article
    by Swati Adhikari, Parthajit Roy 
    Abstract: The task of identifying the inherent features of a coordination complex by comparing two such complexes is not trivial as such complexes may have different geometries. For obtaining deviation statistics due to such comparison in which function of one complex is known and the other is unknown, on protein's structure, in this study one algorithm has been proposed that is capable of comparing two complexes in which pair of structure possesses pentagonal pyramidal/bipyramidal geometries. The proposed algorithm applies some mathematical transformations on both of the comparing structures so that minimum mean square error (MSE) will be produced due to their deviations and produces various statistical reports that will be beneficial for researchers from different fields of studies. To evaluate the performance of the proposed model, total 38 pentagonal pyramidal calcium binding sites and 254 pentagonal bipyramidal calcium and iron binding sites on protein's structure have been tested.
    Keywords: Algorithms for Bioinformatics; Coordination Complex; Shape of Coordination Complex; Metalloprotein; VSEPR Theory.
    DOI: 10.1504/IJCBDD.2024.10064948