Review
Biotechnology & Applied Microbiology
Dongdong Zhao, Xinna Zhu, Hang Zhou, Naxin Sun, Ting Wang, Changhao Bi, Xueli Zhang
Summary: Effective metabolic pathways are crucial for efficient cell factories, and utilizing CRISPR technology in pathway engineering can enhance efficiency, reduce costs, and simplify target customization. This technology has been proven to be robust and effective in various organisms.
METABOLIC ENGINEERING
(2021)
Review
Oncology
Wei Sun, Erhu Zhao, Hongjuan Cui
Summary: Cancer cells selectively utilize serine or synthesize serine for nucleotide biosynthesis. The serine-glycine-one-carbon metabolism (SGOC) pathway plays a crucial role in tumorigenesis. Accumulating evidence shows that metabolic enzymes in the SGOC pathway are involved in tumor development and drug resistance. This review focuses on the involvement of serine and glycine in the folate-mediated one-carbon pathway, as well as the effects of SGOC metabolic enzymes on tumor occurrence and drug resistance.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Microbiology
Yajie Gao, Qianqian Yuan, Zhitao Mao, Hao Liu, Hongwu Ma
Summary: A new method utilizing flux balance analysis (FBA) to calculate biologically relevant pathways in metabolic networks has been developed to improve the classification of metabolites in the bow-tie connectivity structure, providing insights into how system-level structures impact biological functions.
Article
Immunology
Federico Serral, Agustin M. Pardo, Ezequiel Sosa, Maria Mercedes Palomino, Marisa F. Nicolas, Adrian G. Turjanski, Pablo Ivan P. Ramos, Dario Fernandez Do Porto
Summary: Carbapenem-resistant Klebsiella pneumoniae (CR-KP) is an emerging threat to public health, and the development of novel antimicrobials is urgently needed. This study used genome-wide interrogation and metabolic data integration to identify potential targets for drug development. Pathways involved in lipopolysaccharide and peptidoglycan synthesis were confirmed as suitable targets, while other cellular functions, such as energy metabolism pathways, were also suggested for further investigation.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Feifei Guo, Chunhong Jiang, Yujie Xi, Dan Wang, Yi Zhang, Ning Xie, Yi Guan, Fangbo Zhang, Hongjun Yang
Summary: The study found that pathway fingerprint similarity based on drug-target-pathway heterogeneous network can reveal the pharmacological mechanism of natural products, providing a new method for drug similarity evaluation.
JOURNAL OF CHEMINFORMATICS
(2021)
Review
Oncology
Borja Guerra, Carlota Recio, Haidee Aranda-Tavio, Miguel Guerra-Rodriguez, Jose M. Garcia-Castellano, Leandro Fernandez-Perez
Summary: Cancer cells exhibit metabolic reprogramming for energy and signaling, with lipid metabolism playing a key role in cancer progression and drug resistance. Targeting the mevalonate (MVA) biosynthetic pathway may offer a potential strategy to improve therapeutic window in cancer treatment.
FRONTIERS IN ONCOLOGY
(2021)
Review
Pharmacology & Pharmacy
Richa Garg, Sanjana Kumariya, Roshan Katekar, Saurabh Verma, Umesh K. Goand, Jiaur R. Gayen
Summary: Metabolic Syndrome is a multifactorial disease associated with increased risk of cardiovascular disorders, type 2 diabetes mellitus, fatty liver disease, etc., with stress kinase activation potentially playing a crucial role in regulating whole-body metabolism.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Jingjing Li, Yifei Gou, Jiarui Yang, Lingxuan Zhao, Bin Wang, Tong Hao, Jinsheng Sun
Summary: In this study, a genome-scale metabolic network model of Eriocheir sinensis was reconstructed, and its optimal nutrient requirements were predicted. Suggestions for feed improvement were provided based on the simulation results. This study is of great importance in improving the yield and economic value of E. sinensis.
Article
Biochemical Research Methods
Abdur Rahman M. A. Basher, Steven J. Hallam
Summary: The pathway2vec software package automatically generates features for pathway inference by building a three-layered network consisting of compounds, enzymes, and pathways. The benchmark results show improved prediction outcomes in metabolic pathway prediction tasks by leveraging embeddings.
Review
Pharmacology & Pharmacy
Felix F. Lillich, John D. Imig, Ewgenij Proschak
Summary: Metabolic syndrome requires polypharmacological treatment, however, complex treatment regimens often lead to drug-drug interactions and poor patient adherence. Multi-target approaches aim at reducing polypharmacology and improving efficacy.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sofia Tsouka, Mojgan Masoodi
Summary: Pathway analysis is commonly used for functional interpretation of metabolomics data, but lacks standardization and understanding of its impact on functional outcome. In this study, we investigated the consideration of non-human native enzymatic reactions and interconnectivity of pathways in pathway analysis. Exclusion of non-human reactions resulted in loss of information, while considering pathway connectivity provided better emphasis on certain metabolites but occasionally overemphasized central compounds. We proposed a penalization scheme to mitigate the effect of such compounds. We also performed over-representation analysis to compare and assess different methodologies. Our findings raise awareness on the capabilities and shortcomings of current pathway analysis practices in metabolomics.
Article
Biology
Yinchun Su, Jiashuo Wu, Xiangmei Li, Ji Li, Xilong Zhao, Bingyue Pan, Junling Huang, Qingfei Kong, Junwei Han
Summary: In order to identify potential drugs against COVID-19, researchers have developed a computational approach called DTSEA. This method effectively ranks genes and performs enrichment analysis on drug target sets to predict candidate drugs. The DTSEA method has shown high accuracy and reliability in predicting potential drugs for COVID-19.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemical Research Methods
Yang Li, Guanyu Qiao, Keqi Wang, Guohua Wang
Summary: This paper proposes a new model DTI-MGNN based on multi-channel graph convolutional network and graph attention for predicting drug-target interaction. The model combines topological structure and semantic features to improve the representation learning ability of drug-target interactions, and achieves state-of-the-art results on public datasets.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Vidya Niranjan, Akshay Uttarkar, Keerthana Murali, Swarna Niranjan, Jayalatha Gopal, Jitendra Kumar
Summary: This study conducted a timeline genomic analysis of Mycobacterium tuberculosis and identified proteins with fewer mutations as high-confidence drug targets. Through target screening and molecular simulation studies, naloxone was identified as a potential drug candidate for the treatment of tuberculosis.
Article
Biochemical Research Methods
Minwoo Pak, Sangseon Lee, Inyoung Sung, Bonil Koo, Sun Kim
Summary: Drug response prediction (DRP) is crucial for precision medicine to anticipate patient reactions to drugs. While most studies use cell line transcriptome data and drug chemical structures to predict drug response, this study proposes a framework that leverages drug target interaction (DTI) information to improve deep learning-based DRP models. By computing gene perturbation scores through network propagation techniques, the framework integrates this DTI information with existing DRP models. The results show significant performance boosts, especially when dealing with unknown drugs.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biology
Mohammad Uzzal Hossain, Arafat Rahman Oany, Shah Adil Ishtiyaq Ahmad, Md. Anayet Hasan, Md. Arif Khan, Md Al Ahad Siddikey
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2016)
Article
Genetics & Heredity
Md. Amran Gazi, Mohammad Golam Kibria, Mustafa Mahfuz, Md. Rezaul Islam, Prakash Ghosh, Md. Nure Alam Afsar, Md. Arif Khan, Tahmeed Ahmed
Article
Chemistry, Multidisciplinary
Mohammad Uzzal Hossein, Chaman Ara Keya, Keshob Chandra Das, Abu Hashem, Taimur Md Omar, Md Arif Khan, S. M. Rakib-Uz-Zaman, Md Salimullah
FRONTIERS IN CHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Syed Shahariar Bappy, Sorna Sultana, Juthi Adhikari, Shafi Mahmud, Md. Arif Khan, K. M. Kaderi Kibria, Md. Masuder Rahman, Abu Zaffar Shibly
Summary: This study focused on designing a peptide-based epitope vaccine against CHIKV using immunoinformatics and docking tools. Two potential immunogenic envelope glycoprotein sequences were identified, interacting with HLA molecules with low IC50 scores and showing high conservancy in endemic countries. The identified peptides have great potential for vaccine development and further validation through antigen testing, production, and clinical trials is needed.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Md Arif Khan, Shafi Mahmud, A. S. M. Rubayet Ul Alam, Md Ekhtiar Rahman, Firoz Ahmed, Mohammed Rahmatullah
Summary: This study identified 23 potential drug candidates, among which Epirubicin, Vapreotida, and Saquinavir showed better binding affinity against SARS-CoV-2 Main Protease. Molecular dynamics simulation suggested the stability of the docked complex with these drugs. These findings suggest a potential inhibitory effect of these drugs on COVID-19 through synergistic interactions in the active cavity, paving the way for drug discovery with further in-vitro and in-vivo validations needed.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Shafi Mahmud, Md. Jahirul Islam, Md. Rimon Parves, Md. Arif Khan, Lamiya Tabussum, Sinthyia Ahmed, Md. Ackas Ali, Sayo O. Fakayode, Mohammad A. Halim
Summary: This study aimed to identify potent inhibitors of P-glycoprotein using computational approaches. Two compounds showed promising anti-tumor activity with acceptable pharmacokinetic properties, and molecular docking and dynamics simulations verified their stable binding with P-glycoprotein. Principal component analysis and QSAR modeling provided insights into the interactions and predictive capabilities of the drug candidates.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Multidisciplinary
Shafi Mahmud, Suvro Biswas, Gobindo Kumar Paul, Mohasana Akter Mita, Shamima Afrose, Md Robiul Hasan, Mst Sharmin Sultana Shimu, Mohammad Abu Raihan Uddin, Md Salah Uddin, Shahriar Zaman, K. M. Kaderi Kibria, Md Arif Khan, Talha Bin Emran, Md Abu Saleh
Summary: This study explored the potential of antiviral peptides in inhibiting the main protease of SARS-CoV-2, showing promising results in binding energy and stability of peptide-main protease complexes. Further wet-lab experiments are needed to confirm these findings.
ARABIAN JOURNAL OF CHEMISTRY
(2021)
Article
Pharmacology & Pharmacy
Trina Ekawati Tallei, Fatimawali, Afriza Yelnetty, Rinaldi Idroes, Diah Kusumawaty, Talha Bin Emran, Talha Zahid Yesiloglu, Wolfgang Sippl, Shafi Mahmud, Taha Alqahtani, Ali M. Alqahtani, Saeed Asiri, Mohammed Rahmatullah, Rownak Jahan, Md Arif Khan, Ismail Celik
Summary: The article explores the potential of bromelain to counteract various SARS-CoV-2 variants by targeting its binding site with human ACE2. The research suggests that bromelain could serve as a promising inhibitor against different strains of the virus, although more studies are needed to verify its efficacy.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Infectious Diseases
A. M. U. B. Mahfuz, Md Arif Khan, Emran Hossain Sajib, Anamika Deb, Shafi Mahmud, Mahmudul Hasan, Otun Saha, Ariful Islam, Md Mizanur Rahaman
Summary: Nipah virus (NiV) is a zoonotic virus that causes severe infections in humans and animals. This study designed potential small interfering RNA (siRNA) molecules to silence the gene encoding the nucleocapsid protein of NiV, offering a promising molecular therapeutic approach against this dangerous virus.
INFECTION GENETICS AND EVOLUTION
(2022)
Article
Immunology
M. Nazmul Hoque, Md. Murshed Hasan Sarkar, Md. Arif Khan, Md. Arju Hossain, Md. Imran Hasan, Md. Habibur Rahman, Md. Ahashan Habib, Shahina Akter, Tanjina Akhtar Banu, Barna Goswami, Iffat Jahan, Tasnim Nafisa, Md. Maruf Ahmed Molla, Mahmoud E. Soliman, Yusha Araf, M. Salim Khan, Chunfu Zheng, Tofazzal Islam
Summary: This study utilized machine learning approaches to analyze RNA-seq data from COVID-19 patients, recovered individuals, and healthy individuals, finding disease-related differentially expressed genes. It provides insights into the role of SARS-CoV-2 infection in the pathophysiology and comorbidity of COVID-19.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Md. Arju Hossain, Sheikh Abdullah Al Ashik, Moshiur Rahman Mahin, Md. Al Amin, Md Habibur Rahman, Md. Arif Khan, Abdullah Al Emran
Summary: The study identified shared molecular etiology between PCOS and metabolic diseases through in-silico research, suggesting new therapeutic targets. Ten potential hub proteins were identified from protein-protein interaction analysis, with one significant hub protein, IGF2R, showing promising results in molecular docking studies.
Article
Multidisciplinary Sciences
Md Abdullah Al Mamun Khan, Asif Ahsan, Md Arif Khan, Jannatul Maowa Sanjana, Suvro Biswas, Md Abu Saleh, Dipali Rani Gupta, M. Nazmul Hoque, Tahsin Islam Sakif, Md Masuder Rahman, Tofazzal Islam
Summary: Magnaporthe oryzae causes destructive blast disease in major cereal crops and poses a threat to global food security. This study focused on discovering naturally occurring biofungicides as alternatives to synthetic chemical fungicides for controlling M. oryzae. Through molecular docking and simulation analysis, two alkaloidal metabolites, camptothecin and GKK1032A2, were identified as potential fungicides with excellent binding energy and bioactivity scores. These compounds showed superior efficacy compared to commercial fungicides. In particular, GKK1032A2 exhibited multi-site mode of action against M. oryzae. These findings suggest that camptothecin and GKK1032A2 could serve as lead compounds for developing novel fungicides against blast fungus.
Article
Chemistry, Multidisciplinary
A. M. U. B. Mahfuz, Md Arif Khan, Suvro Biswas, Shamima Afrose, Shafi Mahmud, Newaz Mohammed Bahadur, Firoz Ahmed
Summary: This study identified a potential pan-FGFR inhibitor from the PubChem database using a pharmacophore model generated from the structure of FGFR4 inhibited by LY2874455. Molecular docking and dynamics studies confirmed the initial finding, and ADMET analysis revealed similar properties between the identified compound and LY2874455. The compound has the potential to be used in the treatment of various cancers and can serve as a lead compound for the synthesis of more effective anticancer drugs.
ARABIAN JOURNAL OF CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
A. M. U. B. Mahfuz, Md Arif Khan, Promita Deb, Sharmin Jahan Ansary, Rownak Jahan
Summary: TBX5 gene encodes the transcription factor TBX5, crucial for heart and limb development. This study identified 5 most damaging SNPs through in silico analyses, predicting their structural and functional consequences using various tools and predictors. Wet-lab experiments can further validate these findings regarding their potential role in causing Holt-Oram Syndrome.
BIOCHEMISTRY AND BIOPHYSICS REPORTS
(2021)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.