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Li Y, Zhang Y, Gao L, Lyu M, Zheng B, Zhang F, Xu J. Risk prediction model of impacted supernumerary tooth-associated root resorption in children based on cone-beam computed tomography analysis: a case control study. BMC Oral Health 2024; 24:920. [PMID: 39123166 PMCID: PMC11312240 DOI: 10.1186/s12903-024-04493-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 06/17/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND External surface resorption is pressure-induced resorption and occurs on the external surface of the root, pressure exerted by impacted teeth, is common causes of external surface resorption. Predictive risk factors of impacted supernumerary tooth-associated root resorption (ISTARR) mentioned in this article include supernumerary teeth and patient factors. To investigate the risk factors of impacted supernumerary tooth-associated root resorption and predict the incidence of root resorption. METHODS This restrospective study enrolled 324 patients with impacted supernumerary tooth. All Cone-Beam Computed Tomography (CBCT) data and patient information were divided into two groups (without tooth root resorption and with root resorption). CBCT images and patient information (age and gender) of 133 patients had adjacent tooth root resorption and 191 did not. seven variables were analysed using binary logistic regression. RESULTS Individual analysis of potential risk factors showed that age, crown mesiodistal direction, root formation, and odontotheca of the impacted supernumerary tooth were associated significantly with ISTARR. Binary logistic regression showed that impacted supernumerary tooth with odontotheca (Odd Ratio = 2.926), the crown is in the middle (Odd Ratio = 1.446), located at the middle third of the adjacent tooth root (Odd Ratio = 1.614), complete root development (Odd Ratio = 1.334), and patient's age (Odd Ratio = 1.261) were significantly associated with ISTARR risk. CONCLUSIONS The risk factors of root resorption can be detected and predicted early according to the features of supernumerary tooth and patient's age. Still, more prospective studies with larger sample size are needed to validate the result.
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Affiliation(s)
- Yakang Li
- Department of Periodontics, School of Stomatology, Capital Medical University, Tian Tan Xi Li No.4, Beijing, 100050, China
| | - Yuanmin Zhang
- Department of Pediatric Dentistry, School of Stomatology, Capital Medical University, Beijing, China
| | - Linpei Gao
- Department of Periodontics, School of Stomatology, Capital Medical University, Tian Tan Xi Li No.4, Beijing, 100050, China
| | - Menghao Lyu
- Department of Periodontics, School of Stomatology, Capital Medical University, Tian Tan Xi Li No.4, Beijing, 100050, China
| | - Baozhu Zheng
- Department of Periodontics, School of Stomatology, Capital Medical University, Tian Tan Xi Li No.4, Beijing, 100050, China
| | - Fengqiu Zhang
- Department of Periodontics, School of Stomatology, Capital Medical University, Tian Tan Xi Li No.4, Beijing, 100050, China
| | - Junji Xu
- Department of Periodontics, School of Stomatology, Capital Medical University, Tian Tan Xi Li No.4, Beijing, 100050, China.
- Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China.
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing, China.
- College & Hospital of Stomatology, Key Lab. of Oral Diseases Research of Anhui Province, Anhui Medical University, Hefei, Anhui, China.
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Mukherjee T, Pattnaik A, Sahu SS. Analyzing VEGFA/VEGFR1 Interaction: Application of the Resonant Recognition Model-Stockwell Transform Method to Explore Potential Therapeutics for Angiogenesis-Related Diseases. Protein J 2024; 43:697-710. [PMID: 39014261 DOI: 10.1007/s10930-024-10219-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2024] [Indexed: 07/18/2024]
Abstract
The interaction between vascular endothelial growth factor A (VEGFA) and VEGF receptor 1(VEGFR1) is a central focus for drug development in pathological angiogenesis, where aberrant angiogenesis underlies various anomalies necessitating therapeutic intervention. Identifying hotspots of these proteins is crucial for developing new therapeutics. Although machine learning techniques have succeeded significantly in prediction tasks, they struggle to pinpoint hotspots linked to angiogenic activity accurately. This study involves the collection of diverse VEGFA and VEGFR1 protein sequences from various species via the UniProt database. Electron-ion interaction Potential (EIIP) values were assigned to individual amino acids and transformed into frequency-domain representations using discrete Fast Fourier Transform (FFT). A consensus spectrum emerged by consolidating FFT data from multiple sequences, unveiling specific characteristic frequencies. Subsequently, the Stockwell Transform (ST) was employed to yield the hotspots. The Resonant Recognition Model (RRM) identified a characteristic frequency of 0.128007 with an associated wavelength of 1570 nm and RRM-ST identified hotspots for VEGFA (Human 36, 46, 48, 67, 71, 74, 82, 86, 89, 93) and VEGFR1 (Human 224, 259, 263, 290, 807, 841, 877, 881, 885, 892, 894, 909, 913, 1018, 1022, 1026, 1043). These findings were cross-validated by Hotspots Wizard 3.0 webserver and Protein Data Bank (PDB). The study proposes using a 1570 nm wavelength for photo bio modulation to boost VEGFA/VEGFR1 interaction in the condition that is needed. It also aims to reduce VEGFA/VEGFR2 interaction, limiting harmful angiogenesis in conditions like diabetic retinopathy. Also, the identified hotspots assist in designing agonistic or antagonistic peptides tailored to specific medical requirements with abnormal angiogenesis.
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Affiliation(s)
- Tuhin Mukherjee
- Division of Pharmacology, Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Ashok Pattnaik
- Division of Pharmacology, Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
| | - Sitanshu Sekhar Sahu
- Department of Electronics and Communication Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
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Naveed M, Ali I, Aziz T, Javed K, Saleem A, Hanif N, Alharbi M. Investigating the anti-cancer compounds from Calliandra harrisii for precision medicine in pancreatic cancer via in-silico drug design and GC-MS analysis. Z NATURFORSCH C 2024; 79:209-220. [PMID: 38635803 DOI: 10.1515/znc-2024-0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/06/2024] [Indexed: 04/20/2024]
Abstract
Pancreatic cancer is a fatal illness caused by mutations in multiple genes. Pancreatic cancer damages the organ that helps in digestion, resulting in symptoms including fatigue, bloating, and nausea. The use of medicinal plants has been crucial in the treatment of numerous disorders. The medicinal plant Calliandra Harrisi has been widely exploited for its possibilities in biology and medicine. The current study aimed to assess the biopotential of biologically active substances against pancreatic cancer. The GC-MS data of these phytochemicals from Calliandra Harrisi were further subjected to computational approaches with pancreatic cancer genes to evaluate their potential as therapeutic candidates. Molecular docking analysis revealed that N-[Carboxymethyl] maleamic acid is the leading molecule responsible for protein denaturation inhibition, having the highest binding affinity of 6.8 kJ/mol among all other compounds with KRAS inflammatory proteins. Furthermore, ADMET analysis and Lipinski's rule validation were also performed revealing its higher absorption in the gastrointestinal tract. The results of the hepatotoxicity test demonstrated that phytochemicals are non-toxic, safe to use, and do not cause necrosis, fibrosis, or vacuolar degeneration even at excessive levels. Calliandra Harrisi has phytoconstituents that have a variety of pharmacological uses in consideration.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, 66901 University of Central Punjab , Lahore 54590, Pakistan
| | - Imran Ali
- Department of Biotechnology, Faculty of Science and Technology, 66901 University of Central Punjab , Lahore 54590, Pakistan
| | - Tariq Aziz
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, 37796 University of Ioannina , Arta 47132, Greece
| | - Khushbakht Javed
- Department of Biotechnology, Faculty of Science and Technology, 66901 University of Central Punjab , Lahore 54590, Pakistan
| | - Ayesha Saleem
- Department of Biotechnology, Faculty of Science and Technology, 66901 University of Central Punjab , Lahore 54590, Pakistan
| | - Nimra Hanif
- Department of Biotechnology, Faculty of Science and Technology, 66901 University of Central Punjab , Lahore 54590, Pakistan
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, 37850 King Saud University , P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Abuzaid O, Idris AB, Yılmaz S, Idris EB, Idris LB, Hassan MA. Prediction of the most deleterious non-synonymous SNPs in the human IL1B gene: evidence from bioinformatics analyses. BMC Genom Data 2024; 25:56. [PMID: 38858637 PMCID: PMC11163699 DOI: 10.1186/s12863-024-01233-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 05/22/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Polymorphisms in IL1B play a significant role in depression, multiple inflammatory-associated disorders, and susceptibility to infection. Functional non-synonymous SNPs (nsSNPs) result in changes in the encoded amino acids, potentially leading to structural and functional alterations in the mutant proteins. So far, most genetic studies have concentrated on SNPs located in the IL1B promoter region, without addressing nsSNPs and their association with multifactorial diseases. Therefore, this study aimed to explore the impact of deleterious nsSNPs retrieved from the dbSNP database on the structure and functions of the IL1B protein. RESULTS Six web servers (SIFT, PolyPhen-2, PROVEAN, SNPs&GO, PHD-SNP, PANTHER) were used to analyze the impact of 222 missense SNPs on the function and structure of IL1B protein. Five novel nsSNPs (E100K, T240I, S53Y, D128Y, and F228S) were found to be deleterious and had a mutational impact on the structure and function of the IL1B protein. The I-mutant v2.0 and MUPro servers predicted that these mutations decreased the stability of the IL1B protein. Additionally, these five mutations were found to be conserved, underscoring their significance in protein structure and function. Three of them (T240I, D128Y, and F228S) were predicted to be cancer-causing nsSNPs. To analyze the behavior of the mutant structures under physiological conditions, we conducted a 50 ns molecular dynamics simulation using the WebGro online tool. Our findings indicate that the mutant values differ from those of the IL1B wild type in terms of RMSD, RMSF, Rg, SASA, and the number of hydrogen bonds. CONCLUSIONS This study provides valuable insights into nsSNPs located in the coding regions of IL1B, which lead to direct deleterious effects on the functional and structural aspects of the IL1B protein. Thus, these nsSNPs could be considered significant candidates in the pathogenesis of disorders caused by IL1B dysfunction, contributing to effective drug discovery and the development of precision medications. Thorough research and wet lab experiments are required to verify our findings. Moreover, bioinformatic tools were found valuable in the prediction of deleterious nsSNPs.
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Affiliation(s)
- Ola Abuzaid
- Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Abeer Babiker Idris
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan.
| | - Semih Yılmaz
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
- Erciyes Teknopark, Promoseed Biotechnology A.Ş, Kayseri, Turkey
| | - Einass Babikir Idris
- Department of Medical Microbiology, Rashid Medical Complex, Riyadh, Saudi Arabia
| | | | - Mohamed A Hassan
- Department of Bioinformatics, Africa City of Technology, Khartoum, Sudan
- Sanimed International Lab and Management L.L.C, Abu Dhabi, UAE
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Banjan B, Raju R, Keshava Prasad TS, Abhinand CS. Computational identification of potential bioactive compounds from Triphala against alcoholic liver injury by targeting alcohol dehydrogenase. Mol Divers 2024:10.1007/s11030-024-10879-9. [PMID: 38743308 DOI: 10.1007/s11030-024-10879-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
Alcoholic liver injury resulting from excessive alcohol consumption is a significant social concern. Alcohol dehydrogenase (ADH) plays a critical role in the conversion of alcohol to acetaldehyde, leading to tissue damage. The management of alcoholic liver injury encompasses nutritional support and, in severe cases liver transplantation, but potential adverse effects exist, and effective medications are currently unavailable. Natural products with their potential benefits and historical use in traditional medicine emerge as promising alternatives. Triphala, a traditional polyherbal formula demonstrates beneficial effects in addressing diverse health concerns, with a notable impact on treating alcoholic liver damage through enhanced liver metabolism. The present study aims to identify potential active phytocompounds in Triphala targeting ADH to prevent alcoholic liver injury. Screening 119 phytocompounds from the Triphala formulation revealed 62 of them showing binding affinity to the active site of the ADH1B protein. Promising lipid-like molecule from Terminalia bellirica, (4aS, 6aR, 6aR, 6bR, 7R, 8aR, 9R, 10R, 11R, 12aR, 14bS)-7, 10, 11-trihydroxy-9-(hydroxymethyl)-2, 2, 6a, 6b, 9, 12a-hexamethyl-1, 3, 4, 5, 6, 6a, 7, 8, 8a, 10, 11, 12, 13, 14b-tetradecahydropicene-4a-carboxylic acid showed high binding efficiency to a competitive ADH inhibitor, 4-Methylpyrazole. Pharmacokinetic analysis further confirmed the drug-likeness and non-hepatotoxicity of the top-ranked compound. Molecular dynamics simulation and MM-PBSA studies revealed the stability of the docked complexes with minimal fluctuation and consistency of the hydrogen bonds throughout the simulation. Together, computational investigations suggest that (4aS, 6aR, 6aR, 6bR, 7R, 8aR, 9R, 10R, 11R, 12aR, 14bS)-7, 10, 11-trihydroxy-9-(hydroxymethyl)-2, 2, 6a, 6b, 9, 12a-hexamethyl-1, 3, 4, 5, 6, 6a, 7, 8, 8a, 10, 11, 12, 13, 14b-tetradecahydropicene-4a-carboxylic acid from the Triphala formulation holds promise as an ADH inhibitor, suggesting an alternative therapy for alcoholic liver injury.
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Affiliation(s)
- Bhavya Banjan
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, Karnataka, 575018, India
| | - Chandran S Abhinand
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, Karnataka, 575018, India.
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Nayak AK, Chakraborty A, Shukla S, Kumar N, Samanta S. An immunoinformatic approach for developing a multi-epitope subunit vaccine against Monkeypox virus. In Silico Pharmacol 2024; 12:42. [PMID: 38746047 PMCID: PMC11089034 DOI: 10.1007/s40203-024-00220-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
An in-silico approach was implemented to develop a multi-epitope subunit vaccine construct against the recent outbreak of the Monkeypox virus. The contribution of 10 different antigenic proteins based on their antigenicity led to the selection of 10 HTL, 9 CTL, and 6 BCL epitopes. The construct was further investigated for its allergenicity, antigenicity, and physio-chemical properties using servers such as AllerTOP and Allergen FP, VaxiJen and ANTIGENPro, and ProtParam respectively. The secondary structure of the vaccine was predicted using the SOPMA server followed by I-TASSER for the 3D structure. After refinement and validation of structural stability of the modelled vaccine, a molecular docking assay was implemented to study the interaction of the known TLR4 receptor with that of the constructed vaccine using the ClusPro server. The docked vaccine and TLR4 receptor were studied using the molecular dynamics (MD) simulation to validate the stability of the complex. After codon optimization the cDNA was constructed and in-silico cloning of the vaccine construct was carried out. The vaccine was also subjected to computational immune assay which predicted a powerful immune response against the Monkeypox virus validating that the developed multi-epitope vaccine construct can be a potent vaccine candidate. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00220-5.
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Affiliation(s)
- Ashmad Kumar Nayak
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Madhya Pradesh India
| | - Aritra Chakraborty
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Madhya Pradesh India
| | - Sakshi Shukla
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Madhya Pradesh India
| | - Nikhil Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Madhya Pradesh India
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Madhya Pradesh India
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Zhang Q, Fan S, Tang M, Wang C, Li X, Jin Y, Yang Z. Computation-Guided Rational Design of Cysteine-Less Protein Variants in Engineered hCGL. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9937-9946. [PMID: 38651303 DOI: 10.1021/acs.jafc.3c06821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The engineered human cystathionine-γ-lyase (hCGL) resulting in enhanced activity toward both cysteine and cystine unveils a potential robust antitumor activity. However, the presence of cysteine residues has the potential to induce oligomerization or incorrect disulfide bonding, which may decrease the bioavailability of biopharmaceuticals. Through a meticulous design process targeting the cysteine residues within engineered hCGL, a set of potential beneficial mutants were obtained by virtual screening employing Rosetta and ABACUS. Experimental measurements have revealed that most of the mutants showed increased activity toward both substrates l-Cys and CSSC. Furthermore, mutants C109V and C229D demonstrated Tm value increases of 8.2 and 1.8 °C, respectively. After an 80 min incubation at 60 °C, mutant C229D still maintained high residual activity. Unexpectedly, mutant C109V, displaying activity approximately 2-fold higher than the activity of wild type (WT) for both substrates, showed disappointing instability in plasma, which suggests that computational design still requires further consideration. Analysis of their structure and molecular dynamics (MD) simulation revealed the impact of hydrophobic interaction, hydrogen bonds, and near-attack conformation (NAC) stability on activity and stability. This study acquired information about mutants that exhibit enhanced activity or thermal resistance and serve as valuable guidance for subsequent specific cysteine modifications.
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Affiliation(s)
- Qian Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Shuai Fan
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mengjia Tang
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Chenyu Wang
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Xiaoxiao Li
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Yuanyuan Jin
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhaoyong Yang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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Gupta A, Choudhary P, Singh S. Identification and targeting of metastatic biomarkers for hepatocellular carcinoma therapeutics using small molecules library of curcumin analogues. Mol Divers 2024:10.1007/s11030-024-10871-3. [PMID: 38689175 DOI: 10.1007/s11030-024-10871-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
The understanding of the molecular basis of complex diseases like hepatocellular carcinoma (HCC) needs large datasets of multiple genes and proteins involved in different phenomenon of its development. This study focuses on the molecular basis of HCC and the development of therapeutic strategies. We analyzed a dataset of 5475 genes (Homo sapiens) involved in HCC hallmarks, involving comprehensive data on multiple genes and frequently mutated genes. As HCC is characterized by metastasis, angiogenesis, and oxidative stress, exploration of genes associated with them has been targeted. Through gene ontology, functional characterization, and pathway enrichment analysis, we identified target proteins such as Lysyl oxidase, Survivin, Cofilin, and Cathepsin B. A library of curcumin analogs was used to target these proteins. Tetrahrydrocurcumin showed promising binding affinities for all four proteins, suggesting its potential as an inhibitor against these proteins for HCC therapy.
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Affiliation(s)
- Ayushi Gupta
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, Devghat, Jhalwa, Prayagraj, 211015, Uttar Pradesh, India
| | - Princy Choudhary
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, Devghat, Jhalwa, Prayagraj, 211015, Uttar Pradesh, India
| | - Sangeeta Singh
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, Devghat, Jhalwa, Prayagraj, 211015, Uttar Pradesh, India.
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Yadalam PK, Arumuganainar D, Ronsivalle V, Di Blasio M, Badnjevic A, Marrapodi MM, Cervino G, Minervini G. Prediction of interactomic hub genes in PBMC cells in type 2 diabetes mellitus, dyslipidemia, and periodontitis. BMC Oral Health 2024; 24:385. [PMID: 38532421 DOI: 10.1186/s12903-024-04041-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/17/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND AND OBJECTIVE In recent years, the complex interplay between systemic health and oral well-being has emerged as a focal point for researchers and healthcare practitioners. Among the several important connections, the convergence of Type 2 Diabetes Mellitus (T2DM), dyslipidemia, chronic periodontitis, and peripheral blood mononuclear cells (PBMCs) is a remarkable example. These components collectively contribute to a network of interactions that extends beyond their domains, underscoring the intricate nature of human health. In the current study, bioinformatics analysis was utilized to predict the interactomic hub genes involved in type 2 diabetes mellitus (T2DM), dyslipidemia, and periodontitis and their relationships to peripheral blood mononuclear cells (PBMC) by machine learning algorithms. MATERIALS AND METHODS Gene Expression Omnibus datasets were utilized to identify the genes linked to type 2 diabetes mellitus(T2DM), dyslipidemia, and Periodontitis (GSE156993).Gene Ontology (G.O.) Enrichr, Genemania, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were used for analysis for identification and functionalities of hub genes. The expression of hub D.E.G.s was confirmed, and an orange machine learning tool was used to predict the hub genes. RESULT The decision tree, AdaBoost, and Random Forest had an A.U.C. of 0.982, 1.000, and 0.991 in the R.O.C. curve. The AdaBoost model showed an accuracy of (1.000). The findings imply that the AdaBoost model showed a good predictive value and may support the clinical evaluation and assist in accurately detecting periodontitis associated with T2DM and dyslipidemia. Moreover, the genes with p-value < 0.05 and A.U.C.>0.90, which showed excellent predictive value, were thus considered hub genes. CONCLUSION The hub genes and the D.E.G.s identified in the present study contribute immensely to the fundamentals of the molecular mechanisms occurring in the PBMC associated with the progression of periodontitis in the presence of T2DM and dyslipidemia. They may be considered potential biomarkers and offer novel therapeutic strategies for chronic inflammatory diseases.
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Affiliation(s)
- Pradeep Kumar Yadalam
- Department of periodontics, Saveetha Institute Of Medical And Technical Science (SIMATS), Saveetha Dental College and Hospital, Saveetha University, Chennai, India.
| | | | - Vincenzo Ronsivalle
- Department of Biomedical and Surgical and Biomedical Sciences, Catania University, Catania, 95123, Italy
| | - Marco Di Blasio
- Department of Medicine and Surgery, University Center of Dentistry, University of Parma, Parma, 43126, Italy.
| | - Almir Badnjevic
- Verlab Research Institute for Biomedical Engineering, Medical Devices, and Artificial Intelligence, Bosnia and Herzegovina, Sarajevo, 71000, Bosnia-Herzegovina
| | - Maria Maddalena Marrapodi
- Department of Woman, Child and General and Specialist Surgery, University of Campania "Luigi Vanvitelli", Naples, 80121, Italy
| | - Gabriele Cervino
- School of Dentistry, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, via Consolare Valeria, 1, Messina, 98125, Italy
| | - Giuseppe Minervini
- Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, India
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, University of Campania "Luigi Vanvitelli", Caserta, 80121, Italy
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Hashemi Sheikhshabani S, Ghafouri-Fard S, Amini-Farsani Z, Modarres P, Khazaei Feyzabad S, Amini-Farsani Z, Shaygan N, Omrani MD. In Silico Prediction of Functional SNPs Interrupting Antioxidant Defense Genes in Relation to COVID-19 Progression. Biochem Genet 2024:10.1007/s10528-024-10705-9. [PMID: 38460087 DOI: 10.1007/s10528-024-10705-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/16/2024] [Indexed: 03/11/2024]
Abstract
The excessive production of reactive oxygen species and weakening of antioxidant defense system play a pivotal role in the pathogenesis of different diseases. Extensive differences observed among individuals in terms of affliction with cancer, cardiovascular disorders, diabetes, bacterial, and viral infections, as well as response to treatments can be partly due to their genomic variations. In this work, we attempted to predict the effect of SNPs of the key genes of antioxidant defense system on their structure, function, and expression in relation to COVID-19 pathogenesis using in silico tools. In addition, the effect of SNPs on the target site binding efficiency of SNPs was investigated as a factor with potential to change drug response or susceptibility to COVID-19. According to the predicted results, only six missense SNPs with minor allele frequency (MAF) ≥ 0.1 in the coding region of genes GPX7, GPX8, TXNRD2, GLRX5, and GLRX were able to strongly affect their structure and function. Our results predicted that 39 SNPs with MAF ≥ 0.1 led to the generation or destruction of miRNA-binding sites on target antioxidant genes from GPX, PRDX, GLRX, TXN, and SOD families. The results obtained from comparing the expression profiles of mild vs. severe COVID-19 patients using GEO2R demonstrated a significant change in the expression of approximately 250 miRNAs. The binding efficiency of 21 of these miRNAs was changed due to the elimination or generation of target sites in these genes. Altogether, this study reveals the fundamental role of the SNPs of antioxidant defense genes in COVID-19 progression and susceptibility of individuals to this virus. In addition, different responses of COVID-19 patients to antioxidant defense system enhancement drugs may be due to presence of these SNPs in different individuals.
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Affiliation(s)
- Somayeh Hashemi Sheikhshabani
- Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Amini-Farsani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parastoo Modarres
- Department of Cell and Molecular Biology and Microbiology, University of Isfahan, Isfahan, Iran
| | - Sharareh Khazaei Feyzabad
- Department of Laboratory Sciences, School of Paramedical Sciences, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Zahra Amini-Farsani
- Bayesian Imaging and Spatial Statistics Group, Institute of Statistics, Ludwig-Maximilian-Universität München, Ludwigstraße 33, 80539, Munich, Germany
| | - Nasibeh Shaygan
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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11
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Nabi B, Kumawat M, Yadav PK, Ahlawat N, Mir MA, Kumar V, Kumar M, Ahlawat S. Molecular Prediction and Correlation of the Structure and Function of Universal Stress Protein A (UspA) from Salmonella Typhimurium. Biochem Genet 2024:10.1007/s10528-024-10699-4. [PMID: 38427123 DOI: 10.1007/s10528-024-10699-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/13/2024] [Indexed: 03/02/2024]
Abstract
Salmonella Typhimurium (ST) is a zoonotic pathogen that can cause gastroenteritis in humans when they consume contaminated food or water. When exposed to various stressors, both from living organisms (biotic) and the environment (abiotic), Salmonella Typhimurium produces Universal Stress Proteins (USPs). These proteins are gaining recognition for their crucial role in bacterial stress resistance and the ability to enter a prolonged state of growth arrest. Additionally, USPs exhibit diverse structures due to the fusion of the USP domain with different catalytic motifs, enabling them to participate in various reactions and cellular activities during stressful conditions. In this particular study, researchers cloned and analyzed the uspA gene obtained from poultry-derived strains of Salmonella Typhimurium. The gene comprises 435 base pairs, encoding a USP family protein consisting of 144 amino acids. Phylogenetic analysis demonstrated a close relationship between the uspA genes of Salmonella Typhimurium and those found in other bacterial species. We used molecular dynamics simulations and 3D structure prediction to ensure that the USPA protein was stable. Furthermore, we also carried out motif search and network analysis of protein-protein interactions. The findings from this study offer valuable insights for the development of inhibitors targeted against Salmonella Typhimurium.
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Affiliation(s)
- Bilkees Nabi
- Department of Biochemistry & Biochemical Engineering, SHUATS, Prayagraj, 211007, India
| | - Manoj Kumawat
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Pramod Kumar Yadav
- Department of Computational Biology & Bioinformatics, SHUATS, Prayagraj, 211007, India
| | - Neeraj Ahlawat
- Department of Animal Husbandry and Dairying, SHUATS, Prayagraj, 211007, India
| | - Manzoor Ahmad Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, 190006, India
| | - Vivek Kumar
- Department of Computational Biology & Bioinformatics, SHUATS, Prayagraj, 211007, India
| | - Manoj Kumar
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India.
| | - Sushma Ahlawat
- Department of Biochemistry & Biochemical Engineering, SHUATS, Prayagraj, 211007, India.
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12
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Haghir Ebrahim Abadi MH, Ghasemlou A, Bayani F, Sefidbakht Y, Vosough M, Mozaffari-Jovin S, Uversky VN. AI-driven covalent drug design strategies targeting main protease (m pro) against SARS-CoV-2: structural insights and molecular mechanisms. J Biomol Struct Dyn 2024:1-29. [PMID: 38287509 DOI: 10.1080/07391102.2024.2308769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024]
Abstract
The emergence of new SARS-CoV-2 variants has raised concerns about the effectiveness of COVID-19 vaccines. To address this challenge, small-molecule antivirals have been proposed as a crucial therapeutic option. Among potential targets for anti-COVID-19 therapy, the main protease (Mpro) of SARS-CoV-2 is important due to its essential role in the virus's life cycle and high conservation. The substrate-binding region of the core proteases of various coronaviruses, including SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), could be used for the generation of new protease inhibitors. Various drug discovery methods have employed a diverse range of strategies, targeting both monomeric and dimeric forms, including drug repurposing, integrating virtual screening with high-throughput screening (HTS), and structure-based drug design, each demonstrating varying levels of efficiency. Covalent inhibitors, such as Nirmatrelvir and MG-101, showcase robust and high-affinity binding to Mpro, exhibiting stable interactions confirmed by molecular docking studies. Development of effective antiviral drugs is imperative to address potential pandemic situations. This review explores recent advances in the search for Mpro inhibitors and the application of artificial intelligence (AI) in drug design. AI leverages vast datasets and advanced algorithms to streamline the design and identification of promising Mpro inhibitors. AI-driven drug discovery methods, including molecular docking, predictive modeling, and structure-based drug repurposing, are at the forefront of identifying potential candidates for effective antiviral therapy. In a time when COVID-19 potentially threat global health, the quest for potent antiviral solutions targeting Mpro could be critical for inhibiting the virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Fatemeh Bayani
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sina Mozaffari-Jovin
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
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13
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Selim MS, Mounier MM, Abdelhamid SA, Hamed AA, Abo Elsoud MM, Mohamed SS. Characterization, modeling, and anticancer activity of L.arginase production from marine Bacillus licheniformis OF2. BMC Biotechnol 2024; 24:6. [PMID: 38273334 PMCID: PMC10811824 DOI: 10.1186/s12896-024-00829-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND L-arginase, is a powerful anticancer that hydrolyzes L-arginine to L-ornithine and urea. This enzyme is widely distributed and expressed in organisms like plants, fungi, however very scarce from bacteria. Our study is based on isolating, purifying, and screening the marine bacteria that can produce arginase. RESULTS The highest arginase producing bacteria will be identified by using microbiological and molecular biology methods as Bacillus licheniformis OF2. Characterization of arginase is the objective of this study. The activity of enzyme was screened, and estimated beside partial sequencing of arginase gene was analyzed. In silico homology modeling was applied to generate the protein's 3D structure, and COACH and COFACTOR were applied to determine the protein's binding sites and biological annotations based on the I-TASSER structure prediction. The purified enzyme was undergone an in vitro anticancer test. CONCLUSIONS L-arginase demonstrated more strong anti-cancer cells with an IC50 of 21.4 ug/ml in a dose-dependent manner. L-arginase underwent another investigation for its impact on the caspase 7 and BCL2 family of proteins (BCL2, Bax, and Bax/Bcl2). Through cell arrest in the G1/S phase, L-arginase signals the apoptotic cascade, which is supported by a flow cytometry analysis of cell cycle phases.
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Affiliation(s)
- Manal S Selim
- Microbial Biotechnology Department, National Research Centre, Cairo, Egypt
| | - Marwa M Mounier
- Pharmacognosy Department, National Research Centre, Cairo, Egypt
| | | | | | | | - Sahar S Mohamed
- Microbial Biotechnology Department, National Research Centre, Cairo, Egypt
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14
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Das P, Majumder R, Sen N, Nandi SK, Ghosh A, Mandal M, Basak P. A computational analysis to evaluate deleterious SNPs of GSK3β, a multifunctional and regulatory protein, for metabolism, wound healing, and migratory processes. Int J Biol Macromol 2024; 256:128262. [PMID: 37989431 DOI: 10.1016/j.ijbiomac.2023.128262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/04/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023]
Abstract
This study focused on GSK-3β, a critical serine/threonine kinase with diverse cellular functions. However, there is limited understanding of the impact of non-synonymous single nucleotide polymorphisms (nsSNPs) on its structure and function. Through an exhaustive in-silico investigation 12 harmful nsSNPs were predicted from a pool of 172 acquired from the NCBI dbSNP database using 12 established tools that detects deleterious SNPs. Consistently, these nsSNPs were discovered in locations with high levels of conservation. Notably, the three harmful nsSNPs F67C, A83T, and T138I were situated in the active/binding site of GSK-3β, which may affect the protein's capacity to bind to substrates and other proteins. Molecular dynamics simulations revealed that the F67C and T138I mutants had stable structures, indicating rigidness, whereas the A83T mutant was unstable. Analysis of secondary structures revealed different modifications in all mutant forms, which may affect the stability, functioning, and interactions of the protein. These mutations appear to alter the structural dynamics of GSK-3β, which may have functional ramifications, such as the formation of novel secondary structures and variations in coil-to-helix transitions. In conclusion, this study illuminates the possible structural and functional ramifications of these GSK-3 nsSNPs, revealing how protein compactness, stiffness, and interactions may affect biological activities.
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Affiliation(s)
- Pratik Das
- School of Bioscience and Engineering, Jadavpur University, Kolkata, India
| | - Ranabir Majumder
- Cancer Biology Lab, School of Medical Science & Technology, Indian Institute of Technology Kharagpur, India
| | - Nandita Sen
- Molecular biology wing, Dept of Biotechnology, PES University, Bangalore, India
| | - Samit Kumar Nandi
- Department of Veterinary Surgery & Radiology, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Arabinda Ghosh
- Department of Computational Biology and Biotechnology, Mahapurusha Srimanta Sankaradeva Viswavidyalaya, Guwahati Unit, Guwahati, Assam, India
| | - Mahitosh Mandal
- Cancer Biology Lab, School of Medical Science & Technology, Indian Institute of Technology Kharagpur, India
| | - Piyali Basak
- School of Bioscience and Engineering, Jadavpur University, Kolkata, India.
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15
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Naveed M, Jabeen K, Aziz T, Mughual MS, Ul-Hassan J, Sheraz M, Rehman HM, Alharbi M, Albekairi TH, Alasmari AF. Whole proteome analysis of MDR Klebsiella pneumoniae to identify mRNA and multiple epitope based vaccine targets against emerging nosocomial and lungs associated infections. J Biomol Struct Dyn 2023:1-14. [PMID: 38141172 DOI: 10.1080/07391102.2023.2293266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/29/2023] [Indexed: 12/25/2023]
Abstract
Klebsiella pneumonia is a Gram negative facultative anaerobic bacterium involved in various community-acquired pneumonia, nosocomial and lungs associated infections. Frequent usage of several antibiotics and acquired resistance mechanisms has made this bacterium multi-drug resistance (MDR), complicating the treatment of patients. To avoid the spread of this bacterium, there is an urgent need to develop a vaccine based on immuno-informatics approaches that is more efficient than conventional method of vaccine prediction or development. Initially, the complete proteomic sequence of K. pneumonia was picked over for specific and prospective vaccine targets. From the annotation of the whole proteome, eight immunogenic proteins were selected, and these shortlisted proteins were interpreted for CTL, B-cells, and HTL epitopes prediction, to construct mRNA and multi-epitope vaccines. The Antigenicity, allergenicity and toxicity analysis validate the vaccine's design, and its molecular docking was done with immuno-receptor the TLR-3. The docking interaction showed a stronger binding affinity with a minimum energy of -1153.2 kcal/mol and established 23 hydrogen bonds, 3 salt bridges, 1 disulfide bond, and 340 non-binding contacts. Further validation was done using In-silico cloning which shows the highest CAI score of 0.98 with higher GC contents of 72.25% which represents a vaccine construct with a high value of expression in E. coli. Immune Simulation shows that the antibodies (IgM, IgG1, and IgG2) production exceeded 650,000 in 2 to 3 days but the response was completely neutralized in the 5th day. In conclusion, the study provides the effective, safe and stable vaccine construct against Klebsiella pneumonia, which further needs in vitro and in vivo validations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Khizra Jabeen
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Tariq Aziz
- Department of Agriculture, University of Ioannina, Arta, Greece
| | - Muhammad Saad Mughual
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Jawad Ul-Hassan
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Mohsin Sheraz
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | | | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Thamer H Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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16
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Dhawale SA, Bhosle P, Mahajan S, Patil G, Gawale S, Ghodke M, Tapadiya G, Ansari A. Dual targeting in prostate cancer with phytoconstituents as a potent lead: a computational approach for novel drug discovery. J Biomol Struct Dyn 2023:1-14. [PMID: 37649379 DOI: 10.1080/07391102.2023.2251059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023]
Abstract
Prostate Cancer (PCa) is an abnormal cell growth within the prostate. This condition is the second most widespread malignancy in elderly males and one of the most frequently diagnosed life-threatening conditions. The Androgen receptor signaling pathway played a crucial role in the initiation and spread to increase the risk of PCa. Hence, targeting the AR receptor signaling pathway is a key strategy for a therapeutic plan for PCa. Our study focuses on recognizing potential inhibitors for dual targeting in PCa by using the in-silico approach. In this study, we target the two enzymes that are CYP17A1 (3RUK) and 5α-reductase (3G1R) responsible for PCa, with the help of phytoconstituents. The natural plant contains various phytochemical types produced from secondary metabolites and used as a medical treatment. The in-silico investigation of phytoconstituents and enzymes was done by approaching molecular docking, ADMET analysis, and high-level molecular dynamic simulation used to assess the stability and binding affinities of the protein-ligand complex. Some phytoconstituents, such as Peonidin, Pelargonidin, Malvidin and Berberine show complex has good molecular interaction with protein. The reliability of the docking scores was examined using a molecular dynamic simulation, which revealed that the complex remained stable throughout the simulation, which ranged from 0 to 200 ns. The selected hits may be effective against CYP17A1 (3RUK) and 5α-reductase (3G1R) (PCa) using a computer-aided drug design (CADD) method, which further enables researchers for upcoming in-vivo and in-vitro research, according to our in-silico approach.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sachin A Dhawale
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, India
| | - Pallavi Bhosle
- Pharmacology, Shrinath College of Pharmacy, Aurangabad, India
| | | | - Geetanjali Patil
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, India
| | - Sachin Gawale
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, India
| | - Mangesh Ghodke
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, India
| | - Ganesh Tapadiya
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, India
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Lira SS, Ahammad I. A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy. Sci Rep 2021; 11:23212. [PMID: 34853389 PMCID: PMC8636637 DOI: 10.1038/s41598-021-02715-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/18/2021] [Indexed: 01/01/2023] Open
Abstract
DRD2 is a neuronal cell surface protein involved in brain development and function. Variations in the Drd2 gene have clinical significance since DRD2 is a pharmacotherapeutic target for treating psychiatric disorders like ADHD and schizophrenia. Despite numerous studies on the disease association of single nucleotide polymorphisms (SNPs) in the intronic regions, investigation into the coding regions is surprisingly limited. In this study, we aimed at identifying potential functionally and pharmaco-therapeutically deleterious non-synonymous SNPs of Drd2. A wide array of bioinformatics tools was used to evaluate the impact of nsSNPs on protein structure and functionality. Out of 260 nsSNPs retrieved from the dbSNP database, initially 9 were predicted as deleterious by 15 tools. Upon further assessment of their domain association, conservation profile, homology models and inter-atomic interaction, the mutant F389V was considered as the most impactful. In-depth analysis of F389V through Molecular Docking and Dynamics Simulation revealed a decline in affinity for its native agonist dopamine and an increase in affinity for the antipsychotic drug risperidone. Remarkable alterations in binding interactions and stability of the protein-ligand complex in simulated physiological conditions were also noted. These findings will improve our understanding of the consequence of nsSNPs in disease-susceptibility and therapeutic efficacy.
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Affiliation(s)
- Samia Sultana Lira
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh.
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18
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Computational analysis of missense variants in MMP2 gene linked with Winchester syndrome and Nodulosis-Arthropathy-Osteolysis reveals structural shift in protein-protein and protein-ligand complexes. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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19
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Naveed M, Bukhari B, Afzal N, Sadia H, Meer B, Riaz T, Ali U, Ahmed N. Geographical, Molecular, and Computational Analysis of Migraine-Causing Genes. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Migraine is a re-occurring type of headache and causes moderate-to-severe pain that is troubling or pulsing. The pain occurs in half of the head, and common symptoms are photophobia, phonophobia, nausea, depression, anxiety, vomiting, etc. This study evaluates the prevalence of migraine and responsible genes through molecular modeling in the region of Bahawalpur, Pakistan. This research was aimed to determine the prevalence of migraine-causing genes in the population of Bahawalpur and also to do molecular and in-silico analysis of migraine-causing gene as no similar research was conducted before. The disease was characterized and diagnosed under the criteria of the Second Edition of the International Classification of Headache Disorders and molecular identification of migraine-causing genes, i.e. GRIA1, GRIA3, and ESR1, by PCR amplification. The total number of samples collected for migraine patients was 230, out of which 30 were positive for PCR amplification of the genes GRIA1, GRIA3, and ESR1. Therapeutic potentials of commercial drugs, namely Cyclobenzaprine, Divalproex, Ergotamine, and Sumatriptan, were analyzed in silico through molecular docking. Ergotamine demonstrated the highest binding affinity of [Formula: see text]8.4 kcal/mol for the target molecule and, hence, the highest potential. The bivariate analysis showed that the prevalence of migraine concerning gender and age was significantly correlated ([Formula: see text], [Formula: see text]). It was observed that almost 31.4% of women suffered from headaches daily, 70% weekly, 28.1% monthly, and 23.5% rarely. Comparatively, only 8.3% of males suffered from daily headaches, 34% weekly, 12.8% monthly, and 14.9% rarely. The study shows promising results and encourages future researchers to conduct such a comprehensive epidemiological study on an even larger population to justify a more precise association of risk factors involved in migraine pathophysiology.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Bakhtawar Bukhari
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Nadia Afzal
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Haleema Sadia
- Department of Animal Sciences, Quaid-e-Azam University, Islamabad, Pakistan
| | - Bisma Meer
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Tanzeela Riaz
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Urooj Ali
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Naveed Ahmed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
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20
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Yazar M, Özbek P. In Silico Tools and Approaches for the Prediction of Functional and Structural Effects of Single-Nucleotide Polymorphisms on Proteins: An Expert Review. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 25:23-37. [PMID: 33058752 DOI: 10.1089/omi.2020.0141] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are single-base variants that contribute to human biological variation and pathogenesis of many human diseases. Among all SNP types, nonsynonymous single-nucleotide polymorphisms (nsSNPs) can alter many structural, biochemical, and functional features of a protein such as folding characteristics, charge distribution, stability, dynamics, and interactions with other proteins/nucleotides. These modifications in the protein structure can lead nsSNPs to be closely associated with many multifactorial diseases such as cancer, diabetes, and neurodegenerative diseases. Predicting structural and functional effects of nsSNPs with experimental approaches can be time-consuming and costly; hence, computational prediction tools and algorithms are being widely and increasingly utilized in biology and medical research. This expert review examines the in silico tools and algorithms for the prediction of functional or structural effects of SNP variants, in addition to the description of the phenotypic effects of nsSNPs on protein structure, association between pathogenicity of variants, and functional or structural features of disease-associated variants. Finally, case studies investigating the functional and structural effects of nsSNPs on selected protein structures are highlighted. We conclude that creating a consistent workflow with a combination of in silico approaches or tools should be considered to increase the performance, accuracy, and precision of the biological and clinical predictions made in silico.
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Affiliation(s)
- Metin Yazar
- Department of Bioengineering, Marmara University, Göztepe, İstanbul, Turkey.,Department of Genetics and Bioengineering, Istanbul Okan University, Tuzla, Istanbul, Turkey
| | - Pemra Özbek
- Department of Bioengineering, Marmara University, Göztepe, İstanbul, Turkey
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21
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Muthumanickam S, Indhumathi T, Boomi P, Balajee R, Jeyakanthan J, Anand K, Ravikumar S, Kumar P, Sudha A, Jiang Z. In silico approach of naringin as potent phosphatase and tensin homolog (PTEN) protein agonist against prostate cancer. J Biomol Struct Dyn 2020; 40:1629-1638. [PMID: 33034258 DOI: 10.1080/07391102.2020.1830855] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Prostate cancer (PC) is one of the major impediments affecting men, which leads approximately 31,620 deaths in both developing and developed countries. Although some chemotherapy drugs have been reported for prostate cancer, they are not effective due to the lack of safety, efficacy and low selectivity. Hence, the novel alternative anticancer agents with remarkable effect are highly appreciable. Natural plants contain several bio-active compounds which have been traditionally used for the various medical treatments. Particularly, naringin is a natural bio-active compound commonly found in the citrus fruits, which have shown numerous biological activities. Phosphatase and tensin homolog (PTEN) is a tumor suppressor gene, which activates both lipid phosphates and protein phosphates. The PTEN gene is negative regulator of PI3K/AKT/mTOR pathways, since, this signaling pathway play an essential role in the cell survival, proliferation and migration. In the present in silico investigation, structure based virtual screening, molecular docking, molecular dynamics simulation and Adsorption, Distribution, Metabolism, Excretion (ADME) prediction were employed to determine the binding affinity, stability and drug likeness properties of top ranked screened compounds and naringin, respectively. The results revealed that the complex has good molecular interactions, binding stability (peak between 0.3 and 0.4 nm) and no violations in the Lipinski Rule of 5 in naringin, but the screened compounds violated the drug likeness properties. From the in silico analyses, it is identified that naringin compound might assist in the development of novel therapeutic candidate against prostate cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Pandi Boomi
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | | | - Krishnan Anand
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences and National Health Laboratory Service, University of the Free State, Bloemfontein, South Africa
| | - Sundaram Ravikumar
- Department of Biomedical Science, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Ponnuchamy Kumar
- Department of Animal Health and Management, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Arumugam Sudha
- Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Karaikudi, Tamil Nadu, India
| | - Zhihui Jiang
- School of life Science, Department of Biotechnology, Anyang Institute of Technology, Henan, China
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22
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Akhtar M, Jamal T, Jamal H, Din JU, Jamal M, Arif M, Arshad M, Jalil F. Identification of most damaging nsSNPs in human CCR6 gene: In silico analyses. Int J Immunogenet 2019; 46:459-471. [PMID: 31364806 DOI: 10.1111/iji.12449] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/05/2019] [Accepted: 06/12/2019] [Indexed: 12/30/2022]
Abstract
Single nucleotide polymorphisms in CCR6 (C-C chemokine receptor type 6) gene have been found to be the possible cause of many diseases like rheumatoid arthritis, psoriasis, lupus nephritis and systemic sclerosis and other autoimmune diseases. Therefore, identification of structurally and functionally important polymorphisms in CCR6 is important in order to study its potential malfunctioning and discovering therapeutic targets. Several bioinformatics tools were used to identify most damaging nsSNPs that might be vital for CCR6 structure and function. The in silico tools included PROVEAN, SIFT, SNP&GO and PolyPhen2 followed by I-Mutant MutPred and ConSurf. Phyre2 and I-TASSER were used for protein 3-D Modelling while gene-gene interaction was predicted by STRING and GeneMANIA. Our study suggested that three nsSNPs rs1376162684, rs751102128 and rs1185426631 are the most damaging in CCR6 gene while 7 missense SNPs rs1438637216, rs139697820, rs768420505, rs1282264186, rs1394647982, rs769360638 and rs1263402382 are found to revert into stop codons. Prediction of post-transcriptional modifications highlighted the significance of rs1376162684 because it effected potential phosphorylation site. Gene-gene interactions showed relation of CCR6 with other genes depicting its importance in several pathways and co-expressions. In future, studying diseases related to CCR6 should include investigation of these 10 nsSNPs. Being the first of its type, this study also proposes future perspectives that will help in precision medicines. For such purposes, CCR6 proteins from patients of autoimmune diseases should be explored. Animal models can also be of significance find out the effects of CCR6 in diseases.
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Affiliation(s)
- Mehran Akhtar
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Tazkira Jamal
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | | | - Jalal Ud Din
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Arif
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Maria Arshad
- Attaur Rahman School of Applied Biosciences, NUST, Islamabad, Pakistan
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
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Mutation screening of the BRCA1 gene in sporadic breast cancer in the Central of Iran. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Computational analysis of deleterious SNPs of SLC45A2 involved in oculocutaneous albinism type 4. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Naveed M, Imran K, Mushtaq A, Mumtaz AS, Janjua HA, Khalid N. In silico functional and tumor suppressor role of hypothetical protein PCNXL2 with regulation of the Notch signaling pathway. RSC Adv 2018; 8:21414-21430. [PMID: 35539910 PMCID: PMC9080940 DOI: 10.1039/c8ra00589c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/31/2018] [Indexed: 12/21/2022] Open
Abstract
Since the last decade, various genome sequencing projects have led to the accumulation of an enormous set of genomic data; however, numerous protein-coding genes still need to be functionally characterized. These gene products are called "hypothetical proteins". The hypothetical protein pecanex-like protein 2 Homo sapiens (PCNXL2) is found to be mutated in colorectal carcinoma with microsatellite instability; therefore, annotation of the function of PCNXL2 in tumorigenesis is very important. In the present study, bioinformatics analysis of PCNXL2 was performed at the molecular level to assess its role in the progression of cancer for designing new anti-cancer drugs. The retrieved sequence of PCNXL2 was functionally and structurally characterized through the web tools Pfam, Batch CD (conserved domain) search, ExPASy, COACH and I-TASSER directed for pathway analysis and design to explore the intercellular interactions of PCNXL2 involved in cancer development. The present study has shown that PCNXL2 encodes multi-pass transmembrane proteins whose tumor suppressor function may involve regulating Notch signaling by transporting protons across the membrane to provide suitable membrane potential for γ secretase function, which may liberate the Notch intracellular domain NICD from the receptor to inside the cell. Furthermore, domain A of PCNXL2 may exhibit nuclear transport activity of NICD from the cytoplasm to the nucleus through interaction with a nuclear localization signal that may act as an activator for Notch signaling in the nucleus. Conclusively, the tumor suppressor role of PCNXL2 by regulation of the Notch signaling pathway and its functional and structural characteristics are important findings. However, further studies are required to validate the putative role of PCNXL2 as a cancer biomarker in cancer development.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab Lahore 5400 Pakistan +92 301 5524624
- Department of Biotechnology and Biochemistry, University of Gujrat Gujrat 50700 Pakistan
| | - Komal Imran
- Department of Biotechnology and Biochemistry, University of Gujrat Gujrat 50700 Pakistan
| | - Ayesha Mushtaq
- Department of Biotechnology and Biochemistry, University of Gujrat Gujrat 50700 Pakistan
| | - Abdul Samad Mumtaz
- Department of Plant Sciences, Quaid-i-Azam University Islamabad 44500 Pakistan
| | - Hussnain A Janjua
- Department of Industrial Biotechnology, Att-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology H-12 Islamabad Pakistan
| | - Nauman Khalid
- School of Food and Agricultural Sciences, University of Management and Technology Lahore 54000 Pakistan +92 42 3518478 +92 333 5278329
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Nailwal M, Chauhan JB. Computational Analysis of High-Risk SNPs in Human DBY Gene Responsible for Male Infertility: A Functional and Structural Impact. Interdiscip Sci 2018. [PMID: 29520635 DOI: 10.1007/s12539-018-0290-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND DEAD-box helicase 3, Y-linked (DBY) is a candidate gene of the AZF region which is involved in spermatogenesis process. Mutations in the DBY gene may disrupt the spermatogenesis and lead to infertility in men. Identification of functionally neutral mutation from the disease-causing mutation is the biggest challenge in human genetic variation analysis. Owing to the importance of DBY in male infertility, functional analysis was carried out to reveal the association between genetic mutation and phenotypic variation through various in silico approaches. METHODS The present study analyzed the functional consequences of the nsSNPs in human DBY gene using SIFT, PolyPhen 2, PROVEAN, SNAP2, PMut, nsSNPAnalyzer, PhD-SNP and SNPs&GO along with stability analysis through I-Mutant2.0, MuPro and iPTREE-STAB. The conservational analysis of amino acid residues, biophysical properties and conserved domains of the DBY protein was analyzed using various computational tools. The 3D structure of the protein was generated using SPARKS-X and validated using RAMPAGE. RESULTS Out of 1130 SNPs reported in dbSNP, only one nsSNP (G300D) was found to have a functional effect on stability as well as the function of the DBY protein. The results showed the presence of G300 in the putative structure of DBY domain. CONCLUSION To the best of our knowledge, this is the first study to detect pathologically significant nsSNPs (G300D) through a computational approach in the DBY which can be useful for development in potent drug discovery studies.
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Affiliation(s)
- Mili Nailwal
- P.G. Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), New Vallabh Vidyanagar, Dist-Anand, Gujarat, 388121, India
| | - Jenabhai B Chauhan
- P.G. Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), New Vallabh Vidyanagar, Dist-Anand, Gujarat, 388121, India.
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Arshad M, Bhatti A, John P. Identification and in silico analysis of functional SNPs of human TAGAP protein: A comprehensive study. PLoS One 2018; 13:e0188143. [PMID: 29329296 PMCID: PMC5766082 DOI: 10.1371/journal.pone.0188143] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/01/2017] [Indexed: 12/02/2022] Open
Abstract
Genetic polymorphisms in TAGAP gene have been associated with many diseases including rheumatoid arthritis, multiple sclerosis and other autoimmune disorders. Identifying functional SNPs in such disease associated genes is an uphill task hence before planning larger population study, it is better to scrutinize putative functional SNPs. In this study we used various computational approaches to identify nsSNPs which are deleterious to the structure and/or function of TAGAP protein that might be causing these diseases. Computational analysis was performed by five different in silico tools including SIFT, PROVEAN, PolyPhen-2, PhD-SNP and SNPs&GO. The study concludes that mutations of Glycine → Glutamic Acid at position 120, Glycine → Tryptophan at position 141 and Valine → Methionine at position 151 are major mutations in native TAGAP protein which might contribute to its malfunction and ultimately causing disease. The study also proposed 3D structures of native TAGAP protein and its three mutants. Future studies should consider these nsSNPs as main target mutations in various diseases involving TAGAP malfunction. This is the first comprehensive study, where TAGAP gene variants were analyzed using in silico tools hence will be of great help while considering large scale studies and also in developing precision medicines for cure of diseases related to these polymorphisms. Furthermore, animal models of various autoimmune diseases and having these mutations might be of help in exploring their precise roles.
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Affiliation(s)
- Maria Arshad
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Attya Bhatti
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Peter John
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
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Naveed M, Tehreem S, Usman M, Chaudhry Z, Abbas G. Structural and functional annotation of hypothetical proteins of human adenovirus: prioritizing the novel drug targets. BMC Res Notes 2017; 10:706. [PMID: 29212526 PMCID: PMC5719520 DOI: 10.1186/s13104-017-2992-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 11/25/2017] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE Human adenoviruses are small double stranded DNA viruses that provoke vast array of human diseases. Next generation sequencing techniques increase genomic data of HAdV rapidly, which increase their serotypes. The complete genome sequence of human adenovirus shows that it contains large amount of proteins with unknown cellular or biochemical function, known as hypothetical proteins. Hence, it is indispensable to functionally and structurally annotate these proteins to get better understanding of the novel drug targets. The purpose was the characterization of 38 randomly retrieved hypothetical proteins through determination of their physiochemical properties, subcellular localization, function, structure and ligand binding sites using various sequence and structure based bioinformatics tools. RESULTS Function of six hypothetical proteins P03269, P03261, P03263, Q83127, Q1L4D7 and I6LEV1 were predicted confidently and then used further for structure analysis. We found that these proteins may act as DNA terminal protein, DNA polymerase, DNA binding protein, adenovirus E3 region protein CR1 and adenoviral protein L1. Functional and structural annotation leading to detection of binding sites by means of docking analysis can indicate potential target for therapeutics to defeat adenoviral infection.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, 54000 Pakistan
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, 50700 Pakistan
| | - Sana Tehreem
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, 50700 Pakistan
| | - Muhammad Usman
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, 50700 Pakistan
| | - Zoma Chaudhry
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, 50700 Pakistan
| | - Ghulam Abbas
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, 50700 Pakistan
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