Publications by authors named "Muhammad Muzammal Adeel"

11 Publications

  • Page 1 of 1

Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data.

Genes (Basel) 2022 Jun 29;13(7). Epub 2022 Jun 29.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.

Complex chromosomal rearrangements such as translocations play a critical role in oncogenesis. Translocation detection is vital to decipher their biological role in activating cancer-associated mechanisms. High-throughput chromosomal conformations capture (Hi-C) data have shown promising progress in unveiling the genome variations in a disease condition. Until now, multiple structural data (Hi-C)-based methods are available that can detect translocations in cancer genomes. However, the consistency and specificity of Hi-C-based translocation results still need to be validated with conventional methods. This study used Hi-C data of cancerous cell lines, namely lung cancer (A549), Chronic Myelogenous Leukemia (K562), and Acute Monocytic Leukemia (THP-1), to detect the translocations. The results were cross-validated through whole-genome sequencing (WGS) and paired-read analysis. Moreover, PCR amplification validated the presence of translocated reads in different chromosomes. By integrating different data types, we showed that the results of Hi-C data are as reliable as WGS and can be utilized as an assistive method for detecting translocations in the diseased genome. Our findings support the utility of Hi-C technology to detect the translocations and study their effects on the three-dimensional architecture of the genome in cancer condition.
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http://dx.doi.org/10.3390/genes13071170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9319866PMC
June 2022

Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors.

Pharmaceuticals (Basel) 2022 May 25;15(6). Epub 2022 May 25.

Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia.

Rift valley fever virus (RVFV) is the causative agent of a viral zoonosis that causes a significant clinical burden in domestic and wild ruminants. Major outbreaks of the virus occur in livestock, and contaminated animal products or arthropod vectors can transmit the virus to humans. The viral RNA-dependent RNA polymerase (RdRp; L protein) of the RVFV is responsible for viral replication and is thus an appealing drug target because no effective and specific vaccine against this virus is available. The current study reported the structural elucidation of the RVFV-L protein by in-depth homology modeling since no crystal structure is available yet. The inhibitory binding modes of known potent L protein inhibitors were analyzed. Based on the results, further molecular docking-based virtual screening of Selleckchem Nucleoside Analogue Library (156 compounds) was performed to find potential new inhibitors against the RVFV L protein. ADME (Absorption, Distribution, Metabolism, and Excretion) and toxicity analysis of these compounds was also performed. Besides, the binding mechanism and stability of identified compounds were confirmed by a 50 ns molecular dynamic (MD) simulation followed by MM/PBSA binding free energy calculations. Homology modeling determined a stable multi-domain structure of L protein. An analysis of known L protein inhibitors, including Monensin, Mycophenolic acid, and Ribavirin, provide insights into the binding mechanism and reveals key residues of the L protein binding pocket. The screening results revealed that the top three compounds, A-317491, Khasianine, and VER155008, exhibited a high affinity at the L protein binding pocket. ADME analysis revealed good pharmacodynamics and pharmacokinetic profiles of these compounds. Furthermore, MD simulation and binding free energy analysis endorsed the binding stability of potential compounds with L protein. In a nutshell, the present study determined potential compounds that may aid in the rational design of novel inhibitors of the RVFV L protein as anti-RVFV drugs.
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http://dx.doi.org/10.3390/ph15060659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9228520PMC
May 2022

In Silico Analysis and Functional Characterization of Antimicrobial and Insecticidal Vicilin from Moth Bean ( (Jacq.) Marechal) Seeds.

Molecules 2022 May 19;27(10). Epub 2022 May 19.

Botany Division, Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan 60800, Pakistan.

Vicilin has nutraceutical potential and different noteworthy medicative health-promoting biotic diversions, and it is remarkable against pathogenic microorganisms and insects. In this study, vicilin (V) has been identified and characterized from the seed of (Jacq.) Marechal (Moth beans). LC-MS/MS analysis of V provided seven random fragmented sequences comprising 238 residues, showing significant homology with already reported vicilin (V). V was purified using ammonium sulfate precipitation (60%) followed by size exclusion chromatography on Hi-Load 16/60 Superdex 200 pg column and anion-exchange chromatography (Hi trap Q FF column). Purified V showed a major ~50 kDa band and multiple lower bands on 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) under both reduced and non-reduced conditions. After all, a three-dimensional molecular structure of V was predicted, which showed β-sheeted molecular conformation similar to crystallographic structure of V. All Vicilins from . and other plants were divided into six sub-groups by phylogenetic analysis, and V shared a high degree of similarity with vicilins of , , , and . Additionally, V (20 μg) has significant growth inhibition against different pathogenic bacteria along strong antifungal activity (50 μg). Likewise, V (3.0 mg) produced significant growth reduction in Rice Weevil larvae after 9 days compared with control. Furthermore, by using MMT assay, the cytotoxicity effect of V on the growth of HepG2 liver cancerous cells was tested. V showed cytotoxicity against the HepG-2 line and the acquired value was 180 µg after 48 h. Finally, we performed molecular docking against caspase-3 protein (PDB ID: 3DEI) for V bioactive receptor interface residues. Hence, our results reveal that V, has nutraceutical potential and moth beans can be used as a rich resource of functional foods.
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http://dx.doi.org/10.3390/molecules27103251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9145308PMC
May 2022

Structural Variations of the 3D Genome Architecture in Cervical Cancer Development.

Front Cell Dev Biol 2021 23;9:706375. Epub 2021 Jul 23.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.

Human papillomavirus (HPV) integration is the major contributor to cervical cancer (CC) development by inducing structural variations (SVs) in the human genome. SVs are directly associated with the three-dimensional (3D) genome structure leading to cancer development. The detection of SVs is not a trivial task, and several genome-wide techniques have greatly helped in the identification of SVs in the cancerous genome. However, in cervical cancer, precise prediction of SVs mainly translocations and their effects on 3D-genome and gene expression still need to be explored. Here, we have used high-throughput chromosome conformation capture (Hi-C) data of cervical cancer to detect the SVs, especially the translocations, and validated it through whole-genome sequencing (WGS) data. We found that the cervical cancer 3D-genome architecture rearranges itself as compared to that in the normal tissue, and 24% of the total genome switches their A/B compartments. Moreover, translocation detection from Hi-C data showed the presence of high-resolution (4;7) (q13.1; q31.32) and (1;16) (q21.2; q22.1) translocations, which disrupted the expression of the genes located at and nearby positions. Enrichment analysis suggested that the disrupted genes were mainly involved in controlling cervical cancer-related pathways. In summary, we detect the novel SVs through Hi-C data and unfold the association among genome-reorganization, translocations, and gene expression regulation. The results help understand the underlying pathogenicity mechanism of SVs in cervical cancer development and identify the targeted therapeutics against cervical cancer.
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http://dx.doi.org/10.3389/fcell.2021.706375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8344058PMC
July 2021

Identification and analysis of olfactory genes in Dioryctria abietella based on the antennal transcriptome.

Comp Biochem Physiol Part D Genomics Proteomics 2021 06 15;38:100814. Epub 2021 Feb 15.

Key Laboratory for Sustainable Forest Ecosysttem Management of Ministry of Education, College of Forestry, Northeast Forestry University, Harbin 150040, Heilongjiang, People's Republic of China. Electronic address:

The coneworm Dioryctria abietella (Lepidoptera: Pyralidae) is an economy devastating pest that infests many valuable conifer species in the Holarctic regions, such as Pinus koraiensis Siebold and Zucc. The chemosensory system plays a crucial role in the mating, foraging, and ovipositing of this pest, and therefore it is desirable to identify chemosensory molecules for pest control. However, little is known at molecular level about the olfactory mechanisms in D. abietella. In the present study, we first established antennal transcriptomes of D. abietella and identified 132 putative chemosensory genes, including 15 odorant-binding proteins, 18 chemosensory proteins, 65 odorant receptors, 5 sensory neuron membrane proteins, 24 ionotropic receptors, and 5 gustatory receptors. In addition, phylogenetic trees were constructed for chemosensory genes to investigate the orthologs between D. abietella and other species of insects. Furthermore, we also compared the patterns of motifs between OBPs and CSPs using MEME. Additionally, we observed that most of DabiOBPs and DabiCSPs had the antenna-biased expression by quantitative real-time PCR (RT-qPCR), and there was a higher expression of DabiPBP1 and DabiPBP2 in male antennae than in female antennae. The binding sites of DabiPBPs (DabiPBP1, DabiPBP2) and DabiPRs (DabiOR19, DabiOR31) to the sex pheromone were predicted well by three-dimensional docking structure modelling and molecular docking. Our finding supplied a foundation for further research on the binding process of OBPs or CSPs and sensing process of ORs, SNMPs, IRs or GRs in D. abietella.
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http://dx.doi.org/10.1016/j.cbd.2021.100814DOI Listing
June 2021

An Odorant Binding Protein (SaveOBP9) Involved in Chemoreception of the Wheat Aphid .

Int J Mol Sci 2020 Nov 6;21(21). Epub 2020 Nov 6.

Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.

Odorant binding proteins play a key role in the olfactory system and are involved in the odor perception and discrimination of insects. To investigate the potential physiological functions of SaveOBP9 in , fluorescence ligand binding experiments, molecular docking, RNA interference, and behavioral tests were performed. Fluorescence binding assay results showed that SaveOBP9 had broad and high (Ki < 10 μM) binding abilities with most of the wheat volatiles, but was more obvious at pH 7.4 than pH 5.0. The binding sites of SaveOBP9 to the volatiles were predicted well by three-dimensional docking structure modeling and molecular docking. Moreover, showed a strong behavioral response with the four compounds of wheat. The reduction in mRNA transcript levels after the RNA interference significantly reduced the expression level of SaveOBP9 and induced the non-significant response of to the tetradecane, octanal, decanal, and hexadecane. This study provides evidence that SaveOBP9 might be involved in the chemoreception of wheat volatile organic compounds and can successfully contribute in the integrated management programs of .
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http://dx.doi.org/10.3390/ijms21218331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7664216PMC
November 2020

Evolutionary Analysis of Makorin Ring Finger Protein 3 Reveals Positive Selection in Mammals.

Evol Bioinform Online 2019 17;15:1176934319834612. Epub 2019 Apr 17.

Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.

Makorin ring finger proteins (MKRNs) are part the of ubiquitin-proteasome system; a complex system important for cell functions. Ubiquitin fate through proteolytic, non-proteolytic pathways varies, depending on covalent linkage between ubiquitin and protein substrates. Makorin ring finger protein 3 is an integral part of covalent linkage of ubiquitin to protein substrates. Similar to others imprinted genes, MKRN3 also evolve under positive selection; however, which codons are specifically selected in MKRN3 during evolution are needed to be explored. Different maximum-likelihood (ML) codon-based methodologies were used to ascertain positive selection signatures in 22 mammalian sequences of MKRN3 to probe an individual codon for positive selection signatures. By applying the HyPhy software package implemented in the Data Monkey Web Server and CODEML implemented in PAML, evolutionary analysis based on two Ml frameworks were conducted. The analysis was executed by comparing M1a against M2a, M7 against M8, and PAML models and () was resulted by likelihood logs. M1a contributed ω1 () with value () 12.01, and positive selection was found in M2a with ω3 = 2.23603. To further improve selection test, M8 was compared to M7 with 2∆ () 30.17, and M8 showed positive selection with ω = 1.55759. The data were fit to M8 than M7, which suggests that M8 was the most significant model of selection. M8 was judged encouraging for this analysis and used to establish a positive selection of MKRN3 proteins. We found Gly312 as a positively selected amino acid in a zinc finger motif/Really Interesting New Gene (RING) finger motif; the former ones' region is involved in RNA binding and the later ones in ubiquitin ligase activity of the protein, vital for protein function. Selection analyses of MKRNs might advance the developments in unique approaches that could lead to genetic progress over the selection of superior individuals with the breeding values higher for certain traits as ancestries to get the next generation.
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http://dx.doi.org/10.1177/1176934319834612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472170PMC
April 2019

The role of chemosensory protein 10 in the detection of behaviorally active compounds in brown planthopper, Nilaparvata lugens.

Insect Sci 2020 Jun 31;27(3):531-544. Epub 2019 Jan 31.

Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.

Chemosensory proteins (CSPs) play important roles in insects' chemoreception, although their specific functional roles have not been fully elucidated. In this study, we conducted the developmental expression patterns and competitive binding assay as well as knock-down assay by RNA interference both in vitro and in vivo to reveal the function of NlugCSP10 from the brown planthopper (BPH), Nilaparvata lugens (Stål), a major pest in rice plants. The results showed that NlugCSP10 messenger RNA was significantly higher in males than in females and correlated to gender, development and wing forms. The fluorescence binding assays revealed that NlugCSP10 exhibited the highest binding affinity with cis-3-hexenyl acetate, eicosane, and (+)-β-pinene. Behavioral assay revealed that eicosane displayed attractant activity, while cis-3-hexenyl acetate, similar to (+)-β-pinene significantly repelled N. lugens adults. Silencing of NlugCSP10, which is responsible for cis-3-hexenyl acetate binding, significantly disrupted cis-3-hexenyl acetate communication. Overall, findings of the present study showed that NlugCSP10 could selectively interrelate with numerous volatiles emitted from host plants and these ligands could be designated to develop slow-release mediators that attract/repel N. lugens and subsequently improve the exploration of plans to control this insect pest.
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http://dx.doi.org/10.1111/1744-7917.12659DOI Listing
June 2020

Peptide vaccine against chikungunya virus: immuno-informatics combined with molecular docking approach.

J Transl Med 2018 10 27;16(1):298. Epub 2018 Oct 27.

Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University (HZAU), Wuhan, People's Republic of China.

Background: Chikungunya virus (CHIKV), causes massive outbreaks of chikungunya infection in several regions of Asia, Africa and Central/South America. Being positive sense RNA virus, CHIKV replication within the host resulting in its genome mutation and led to difficulties in creation of vaccine, drugs and treatment strategies. Vector control strategy has been a gold standard to combat spreading of CHIKV infection, but to eradicate a species from the face of earth is not an easy task. Therefore, alongside vector control, there is a dire need to prevent the infection through vaccine as well as through antiviral strategies.

Methods: This study was designed to find out conserved B cell and T cell epitopes of CHIKV structural proteins through immuno-informatics and computational approaches, which may play an important role in evoking the immune responses against CHIKV.

Results: Several conserved cytotoxic T-lymphocyte epitopes, linear and conformational B cell epitopes were predicted for CHIKV structural polyprotein and their antigenicity was calculated. Among B-cell epitopes "PPFGAGRPGQFGDI" showed a high antigenicity score and it may be highly immunogenic. In case of T cell epitopes, MHC class I peptides 'TAECKDKNL' and MHC class II peptides 'VRYKCNCGG' were found extremely antigenic.

Conclusion: The study led to the discovery of various epitopes, conserved among various strains belonging to different countries. The potential antigenic epitopes can be successfully utilized in designing novel vaccines for combating and eradication of CHIKV disease.
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http://dx.doi.org/10.1186/s12967-018-1672-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6204282PMC
October 2018

Positive selection drives the evolution of endocrine regulatory bone morphogenetic protein system in mammals.

Oncotarget 2018 Apr 13;9(26):18435-18445. Epub 2018 Jan 13.

Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China.

The rapid evolution of reproductive proteins might be driven by positive Darwinian selection. The bone morphogenetic protein family is the largest within the transforming growth factor (TGF) superfamily. A little have been known about the molecular evolution of bone morphogenetic proteins exhibiting potential role in mammalian reproduction. In this study we investigated mammalian bone morphogenetic proteins using maximum likelihood approaches of codon substitutions to identify positive Darwinian selection in various species. The proportion of positively selected sites was tested by different likelihood models for individual codon, and M8 were found to be the best model. The percentage of positively elected sites under M8 are 2.20% with ω = 1.089 for BMP2, 1.6% with ω = 1.61 for BMP 4 0.53% for BMP15 with ω = 1.56 and 0.78% for GDF9 with ω = 1.93. The percentage of estimated selection sites under M8 is strong statistical confirmation that divergence of bone morphogenetic proteins is driven by Darwinian selection. For the proteins, model M8 was found significant for all proteins with ω > 1. To further test positive selection on particular amino acids, the evolutionary conservation of amino acid were measured based on phylogenetic linkage among sequences. For exploring the impact of these somatic substitution mutations in the selection region on human cancer, we identified one pathogenic mutation in human BMP4 and one in BMP15, possibly causing prostate cancer and six neutral mutations in BMPs. The comprehensive map of selection results allows the researchers to perform systematic approaches to detect the evolutionary footprints of selection on specific gene in specific species.
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http://dx.doi.org/10.18632/oncotarget.24240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5915083PMC
April 2018

Modelling and simulation of mutant alleles of breast cancer metastasis suppressor 1 (BRMS1) gene.

Bioinformation 2014 22;10(7):454-9. Epub 2014 Jul 22.

Department of Bioinformatics and Biotechnology, Government College University (GCUF), 38000, Faisalabad, Punjab, Pakistan.

Computational tools occupy the prime position in the analysis of large volume of post-genomic data. These tools have advantage over the wet lab experiments in terms of high coverage, cost and time. Breast cancer is the most common cancer in females worldwide. It is a genetically heterogeneous disorder and many genes are involved in the pathway of the disease. Mutations in metastasis suppressor gene are the major cause of the disease. In this study, the effects of mutations in breast cancer metastasis suppressor 1gene upon protein structure and function were examined by means of computational tools and information from databases.This study can be useful to predict the potential effect of every allelic variant, devise new biological experiments and to interpret and predict the patho-physiological impact of new mutations or non-synonymous polymorphisms.
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http://dx.doi.org/10.6026/97320630010454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4135295PMC
September 2014
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