MUNEEBA MALIK¹, MAMOONA MAQBOOL², TOOBA NISAR³, TAZEEM AKHTER⁴, JAVED AHMED UJAN^5,6, ALANOOD S. ALGARNI⁷, FAKHRIA A. AL JOUFI⁸, SULTAN SHAFI K. ALANAZI⁹, MOHAMMAD HADI ALMOTARED¹⁰, MOUNIR M. SALEM BEKHIT¹¹, MUHAMMAD JAMIL^12,*

Oncology Research, Vol.31, No.6, pp. 899-916, 2023, DOI:10.32604/or.2023.030760

Abstract The low survival rate of Kidney renal clear cell carcinoma (KIRC) patients is largely attributed to cisplatin resistance. Rather than focusing solely on individual proteins, exploring protein-protein interactions could offer greater insight into drug resistance. To this end, a series of in silico and in vitro experiments were conducted to identify hub genes in the intricate network of cisplatin resistance-related genes in KIRC chemotherapy. The genes involved in cisplatin resistance across KIRC were retrieved from the National Center for Biotechnology Information (NCBI) database using search terms as “Kidney renal clear cell carcinoma” and “Cisplatin resistance”. The genes retrieved were analyzed… More >

Mehdi Hassan^1,2, Safdar Ali³, Jin Young Kim^2,*, Muhammad Sanaullah⁴, Hani Alquhayz⁵, Khushbakht Safdar⁶

CMC-Computers, Materials & Continua, Vol.76, No.2, pp. 1643-1663, 2023, DOI:10.32604/cmc.2023.038578

Abstract Breast cancer resistance protein (BCRP) is an important resistance protein that significantly impacts anticancer drug discovery, treatment, and rehabilitation. Early identification of BCRP substrates is quite a challenging task. This study aims to predict early substrate structure, which can help to optimize anticancer drug development and clinical diagnosis. For this study, a novel intelligent approach-based methodology is developed by modifying the ResNet101 model using transfer learning (TL) for automatic deep feature (DF) extraction followed by classification with linear discriminant analysis algorithm (TLRNDF-LDA). This study utilized structural fingerprints, which are exploited by DF contrary to conventional molecular descriptors. The proposed in… More >

Hafiza Arooj Razzaq¹, Siddra Ijaz^1,*, Imran Ul Haq², Faisal Saeed Awan¹

Phyton-International Journal of Experimental Botany, Vol.92, No.8, pp. 2451-2460, 2023, DOI:10.32604/phyton.2023.030501

Abstract The imperative aspect of the CRISPR/Cas9 system is a short stretch of 20 nucleotides of gRNA that control the overall specificity. Due to the small size, the chance of its multiple occurrences in the genome increases; however, a few mismatches are tolerated by the Cas9 endonuclease activity. An accurate and careful in silico-based off-target prediction while target selection is preferred to address the issue. These predictions are based on a comprehensive set of selectable parameters. Therefore, we investigated the possible off-target prediction and their screening in StERF3 gene-edited potato plants while developing StERF3-loss-of-function mutants using CRISPR/Cas9 approach. The 201 off-targets… More >

SEUNGHYUN AHN¹, JUNG-YEON LEE¹, JIHA SUNG^1,2, HYUN JOO KIM³, SEYEON PARK^1,2,*

BIOCELL, Vol.47, No.7, pp. 1661-1673, 2023, DOI:10.32604/biocell.2023.027984

Abstract Background: Although the GABAA receptor (GABAAR) has been proposed as the main action site for sevoflurane, isoflurane, halothane, enflurane, propofol, and benzodiazepines (BZDs), binding of these anesthetics with high-resolution structures of the GABAAR have been rarely examined by comparative docking analyses. Moreover, various combinations of ligands on more GABAARs with various subtypes need to be analyzed to understand the elaborate action mechanism of GABAARs better because some GABAA ligands showed specificity toward the distinct subtypes of the GABAAR. Methods: We performed in silico docking analysis to compare the binding modes of sevoflurane, isoflurane, halothane, enflurane, propofol, and BZDs to the… More >

Oliver Tusevski^1,*, Marija Todorovska¹, Jasmina Petreska Stanoeva², Marina Stefova², Sonja Gadzovska Simic¹

Phyton-International Journal of Experimental Botany, Vol.92, No.3, pp. 921-941, 2023, DOI:10.32604/phyton.2023.024995

Abstract Three Hypericum perforatum hairy root lines (HR B, HR F and HR H) along with non-transformed roots were analyzed for phenolic compounds composition and in vitro enzyme inhibitory properties. In silico molecular modeling was performed to predict the interactions of the most representative phenolic compounds in HR clones with enzymes related to depression, neurodegeneration and diabetes. Chromatographic analyses revealed that HR clones represent an efficient source of quinic acid and hydroxybenzoic acids, epicatechin and procyanidin derivatives, quercetin and kaempferol glycosides, as well numerous xanthones. In vitro antidepressant activity of HR extracts through monoamine oxidase A (MAO-A) inhibition was attributed to… More >

Rachele Allena^1,*, Denis Aubry²

Molecular & Cellular Biomechanics, Vol.19, No.1, pp. 1-16, 2022, DOI:10.32604/mcb.2022.018958

Abstract Cells adapt to their environment and stimuli of different origin. During confined migration through sub-cellular and sub-nuclear pores, they can undergo large strains and the nucleus, the most voluminous and the stiffest organelle, plays a critical role. Recently, patterned microfluidic devices have been employed to analyze the cell mechanical behavior and the nucleus self-deformations. In this paper, we present an in silico model to simulate the interactions between the cell and the underneath microstructured substrate under the effect of the sole gravity. The model lays on mechanical features only and it has the potential to assess the contribution of the… More >

KATARINA BARALIć^1,*, KATARINA ŽIVANčEVIć¹, DRAGICA BoŽIĆ¹, DANYEL JENNEN², ALEKSANDRA BUHA DJORDJEVIC¹, EVICA ANTONIJEVIć MILJAKOVIć¹, DANIJELA ĐUKIć-ĆOSIć¹

BIOCELL, Vol.46, No.2, pp. 519-533, 2022, DOI:10.32604/biocell.2022.018271

Abstract This in silico toxicogenomic study aims to explore the relationship between phthalates and bisphenol A (BPA) co-exposure and obesity, as well as its comorbid conditions, in order to construct a possible set of genomic biomarkers. The Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org) was used as the main data mining tool, along with GeneMania (https://genemania.org), ToppGene Suite (https://toppgene.cchmc.org) and DisGeNET (http://www.disgenet.org). Among the phthalates, bis(2-ethylhexyl) phthalate (DEHP) and dibutyl phthalate (DBP) were chosen as the most frequently curated phthalates in CTD, which also share similar mechanisms of toxicity. DEHP, DBP and BPA interacted with 84, 90 and 194 obesity-related genes/proteins, involved in… More >

JIAYU ZHANG^1,2,3,#, RUOYAN CAO^1,2,3,#, JIANMIN PENG^1,2,3, QINCHAO HU^1,2,3, JUAN XIA^1,2,3,*, BIN CHENG^1,2,3,*

BIOCELL, Vol.46, No.1, pp. 111-125, 2022, DOI:10.32604/biocell.2022.016612

Abstract Metabolic reprogramming and immunologic suppression are two critical characteristics promoting the progression of head and neck squamous cell carcinoma (HNSCC). The integrative analysis of all the metabolism-related genes (MRGs) in HNSCC is lacking and the interaction between the metabolism and the immune characteristics also requires more exploration to uncover the potential mechanisms. Therefore, this study was designed to establish a prognostic signature based on all the MRGs in HNSCC. Genes of HNSCC samples were available from the TCGA and GEO databases while the MRGs were retrieved from a previous study. Ultimately 4 prognostic MRGs were selected to construct a model… More >

Bahram Barati¹, Fatemeh Fazeli Zafar¹, Shuanhu Hu¹, Najmeh Fani², Sajjad Eshtiaghi³, Shuang Wang^1,*

Journal of Renewable Materials, Vol.9, No.11, pp. 1843-1857, 2021, DOI:10.32604/jrm.2021.016301

Abstract Enhancing the stability of biomolecules is one of the hot topics in industry. In this study, we enhanced the stability of an important protein called LEPTIN. LEPTIN is a hormone secreted by fat cells playing an essential role in body weight and composition, and its deficiency can result in several disorders. The treatment of related LEPTIN dysfunctions is often available in the form of injection. To decrease the cost and the frequency of its applications can be achieved by increasing its lifetime through engineering LEPTIN. In this study, to engineer LEPTIN, we have introduced disulfide bonds. Disulfide By Design server… More > Graphic Abstract

JIA-FONG HONG¹, BAGHDAD OUDDANE², JIANG-SHIOU HWANG^3,4,5, HANS-UWE DAHMS^1,6,7,*

BIOCELL, Vol.45, No.1, pp. 65-77, 2021, DOI:10.32604/biocell.2021.014154

Abstract Harmful algal blooms (HABs) that are formed by cyanobacteria have become a serious issue worldwide in recent years. Cyanobacteria can release a type of secondary metabolites called cyanotoxins into aquatic systems which may indirectly or directly provide health risks to the environment and humans. Cyanotoxins provide some of the most powerful natural poisons including potent neurotoxins, hepatotoxins, cytotoxins, and endotoxins that may result in environmental health risks, and long-term morbidity and mortality to animals and humans. In this research, we used the chemcomputational tool Molinspiration for molecular property predictions, Pred-hERG 4.2 web software for cardiac toxicity prediction, and Pred-Skin 2.0… More >