Publications by authors named "Azhar Mehmood"

14 Publications

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In silico analysis of quranic and prophetic medicinals plants for the treatment of infectious viral diseases including corona virus.

Saudi J Biol Sci 2021 May 23;28(5):3137-3151. Epub 2021 Feb 23.

The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.

Coronavirus disease (COVID-19) is an infection of the respiratory system caused by single standard RNA viruses named as Severe Acute Respiratory Syndrome 2 (SARS-CoV-2). The disease appeared as a serious problem and the leading cause of death in human beings throughout the world. The main source of different phytochemicals are plants, which helps in the development of new drugs against various ailments. Islam is comprehensive religion and a complete code of life for Muslims. The teaching of Islam, according to the Holy Quran and Hadith are universal for the benefit of humanity. Islam believes that every ailment is from God and who made the disease definitely made its medication. There is a complete guideline with regard to taking measures against infectious diseases such as quarantine and seeking medicinal treatment. The research objective is to gather the knowledge of medicinal plants described in the Holy Quran or utilized by the Prophet (SAW) for the treatment of different ailments or advised to use them to boost immunity and strengthen the body. Scientists across the globe have found these plants beneficial for many diseases and have antiviral potential. In present study, the six plant species including and were selected which contain phytochemicals like Calcium Elenolate, Thymoquinone, S-Allylcysteine, Dipropyl Disulfide, Sesquiterpene, Monoterpene, Pelargonidin 3-Galactoside ion and Kaempferol. The phytochemicals monoterpene (from ) shows best interaction with target proteins RdRP, 3CLPro, ACE2. Calcium Elonate (from olive) bonds with 3CLPro, ACE2 and Kemoferol and Pelargomidine (from Senna Makki) bonds with RdRP, ACE2. The ligands show a unique set of intersections i.e. hydrogen bonding, and alkyl interaction. These medicinal plants can be utilized immediately for the treatment of COVID-19 as their safety is already established. This treatment can enhance recovery when combined with other treatments. Furthermore, the screening of bioactive compounds or phytochemicals found in these plants can be utilized to design new therapeutic drug to treat COVID-19 pandemic.
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http://dx.doi.org/10.1016/j.sjbs.2021.02.058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7899931PMC
May 2021

network-based analysis of drugs used against COVID-19: Human well-being study.

Saudi J Biol Sci 2021 Mar 21;28(3):2029-2039. Epub 2021 Jan 21.

Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.

Introduction: Researchers worldwide with great endeavor searching and repurpose drugs might be potentially useful in fighting newly emerged coronavirus. These drugs show inhibition but also show side effects and complications too. On December 27, 2020, 80,926,235 cases have been reported worldwide. Specifically, in Pakistan, 471,335 has been reported with inconsiderable deaths.

Problem Statement: Identification of COVID-19 drugs pathway through drug-gene and gene-gene interaction to find out the most important genes involved in the pathway to deal with the actual cause of side effects beyond the beneficent effects of the drugs.

Methodology: The medicines used to treat COVID-19 are retrieved from the Drug Bank. The drug-gene interaction was performed using the Drug Gene Interaction Database to check the relation between the genes and the drugs. The networks of genes are developed by Gene MANIA, while Cytoscape is used to check the active functional association of the targeted gene. The developed systems cross-validated using the EnrichNet tool and identify drug genes' concerned pathways using Reactome and STRING.

Results: Five drugs Azithromycin, Bevacizumab, CQ, HCQ, and Lopinavir, are retrieved. The drug-gene interaction shows several genes that are targeted by the drug. Gene MANIA interaction network shows the functional association of the genes like co-expression, physical interaction, predicted, genetic interaction, co-localization, and shared protein domains.

Conclusion: Our study suggests the pathways for each drug in which targeted genes and medicines play a crucial role, which will help experts o overcome and deal with the side effects of these drugs, as we find out the gene analysis for the COVID-19 drugs.
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http://dx.doi.org/10.1016/j.sjbs.2021.01.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7825994PMC
March 2021

Association between single nucleotide polymorphisms of DNA damage response pathway genes and increased risk in breast cancer.

Future Oncol 2020 Sep 27;16(26):1977-1995. Epub 2020 Jun 27.

Department of Biosciences, COMSATS University, Islamabad, Pakistan.

We aimed to evaluate the role of selected single nucleotide polymorphisms of DNA damage response pathway genes in breast cancer (BC). In present study, 500 BC patients and 500 controls was used to estimate the frequency of single nucleotide polymorphisms of DNA damage response pathway genes. Tetra-amplification refractory mutation system-PCR technique was used for screening of the six selected polymorphisms. Logistic regression analysis showed that heterozygous mutant genotype of rs1800057 (p < 0.0001) and homozygous mutant genotype of rs1801516 (p < 0.0001) was associated with significant increased risk of BC. In the gene, heterozygous mutant genotype of rs2227931 (p < 0.0001) was associated with significant increased risk of BC. However, significant decreased risk of BC was found associated with heterozygous mutant genotype of rs2227928 (p < 0.0002) and homozygous mutant genotype of rs2229032 (p < 0.0001) in patients compared with controls. The present results showed that alteration in DNA damage response pathway gene ( & ) results in increased BC risk.
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http://dx.doi.org/10.2217/fon-2020-0086DOI Listing
September 2020

nCOV-19 peptides mass fingerprinting identification, binding, and blocking of inhibitors flavonoids and anthraquinone of and hydroxychloroquine.

J Biomol Struct Dyn 2021 07 22;39(11):4089-4099. Epub 2020 Jun 22.

Department of Bioinformatics, Govt. Postgraduate College Mandian Abbottabad, Abbottabad, KPK, Pakistan.

An rare pandemic of viral pneumonia occurs in December 2019 in Wuhan, China, which is now recognized internationally as Corona Virus Disease 2019 (COVID-19), the etiological agent classified as Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). According to the World Health Organization (WHO), it has so far expanded to more than 213 countries/territories worldwide. Our study aims to find the viral peptides of SARS-COV-2 by peptide mass fingerprinting (PMF) in order to predict its novel structure and find an inhibitor for each viral peptide. For this reason, we calculated the mass of amino acid sequences translated from the SARS-CoV2 whole genome and identify the peptides that may be a target for inhibition. Molecular peptide docking with phytochemicals (aqueous and ethanolic) leaf extracts of flavonoids (3.56 ± 0.03), (3.83 ± 0.02), anthraquinone (11.68 ± 0.04), (10.86 ± 0.06) and hydroxychloroquine present therapy of COVID-19 in Pakistan for comparative study. Results indicate that 15 peptides of SARS-CoV2 have been identified from PMF, which is then used as a selective inhibitor. The maximum energy obtained from AutoDock Vina for hydroxychloroquine is -5.1 kcal/mol, kaempferol (flavonoid) is -6.2 kcal/mol, and for anthraquinone -6 kcal/mol. Visualization of docking complex, important effects are observed regarding the binding of peptides to drug compounds. In conclusion, it is proposed that these compounds are effective antiviral agents against COVID-19 and can be used in clinical trials.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1778534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7332867PMC
July 2021

Linkage disequilibrium and haplotype analysis of and genes in thyroid cancer.

Future Oncol 2020 Apr 7;16(12):779-792. Epub 2020 Apr 7.

Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan.

This study was planned to examine the effects of single nucleotide polymorphism (SNPs) on the risk of thyroid cancer in 499 patients and 500 controls. Three SNPs of gene and three SNPs of gene were analyzed using Tetra-primer ARMS-PCR followed by sequencing. rs121913314 of gene genotype TT showed 32-fold increased risk of thyroid cancer and rs2305994 of genotypes TT and CT showed 2.7-fold and 16-fold increased risk in thyroid cancer (p < 0.0001). Haplotype analysis revealed that CATGCC, CATGCT, CATGTC, CATGTT, TATGCC and TATGTTA haplotypes are associated with thyroid cancer risk. Results showed that genotypes and allele distribution of and genes are significantly linked with increased risk of thyroid cancer.
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http://dx.doi.org/10.2217/fon-2019-0690DOI Listing
April 2020

Proteomic Analysis of Medicinal Plant Calotropis Gigantea by In Silico Peptide Mass Fingerprinting.

Curr Comput Aided Drug Des 2021 ;17(2):254-265

Department of Bioinformatics, Govt. Post Graduate College Mandian Abbottabad, Abbottabad, Pakistan.

Medicinal plants are the basic source of medicinal compounds traditionally used for the treatment of human diseases. Calotropis gigantea is a medicinal plant belonging to the family of Apocynaceae in the plant kingdom and subfamily Asclepiadaceae usually bearing multiple medicinal properties to cure a variety of diseases.

Background: The Peptide Mass Fingerprinting (PMF) identifies the proteins from a reference protein database by comparing the amino acid sequence that is previously stored in the database and identified.

Objective: The purpose of the study is to identify the peptides having anti-cancerous properties by in silico peptide mass fingerprinting.

Methods: The calculation of in silico peptide masses is done through the ExPASy PeptideMass and these masses are used to identify the peptides from the MASCOT online server. Anticancer probability is calculated by iACP server, docking of active peptides is done by CABS-dock the server.

Results: The anti-cancer peptides are identified with the MASCOT peptide mass fingerprinting server, the identified peptides are screened and only the anti-cancer are selected. De-novo peptide structure prediction is used for 3D structure prediction by PEP-FOLD 3 server. The docking results confirm strong bonding with the interacting amino acids of the receptor protein of breast cancer BRCA1 which shows the best peptide binding to the active chain, the human leukemia protein docking with peptides shows the accurate binding.

Conclusion: These peptides are stable and functional and are the best way for the treatment of cancer and many other deadly diseases.
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http://dx.doi.org/10.2174/1573409916666200219114531DOI Listing
January 2021

Subtractive Proteome Mining Approach towards Unique Putative Drug Targets Identification for Salmonella typhimurium.

Infect Disord Drug Targets 2020 ;20(6):884-892

Department of Bioinformatics, Govt. Post Graduate College Mandian Abbottabad, KPK, Pakistan.

Background: Salmonella typhimurium is a rod-shaped bacteria with a Gram-negative genus, belonging to the Enterobacteriaceae family of microbes, which invades the intestinal lumen of Human. Salmonella typhimurium is a root source, accounting for gastroenteritis in humans as well as in other mammals. Gastroenteritisis associated with Salmonella Typhimurium interacts with the contaminated food and water and spreads to nearby people in the area. Small intestine is attacked by Salmonella, which then enter into the bloodstream momentarily, and are responsible for millions of mortalities and morbidities around the globe. Salmonella typhimurium toxins cause gastrointestiritis due to inflammation in the stomach and intestine in infants and young children. It accounts for millions of deaths with a higher incidence rate in developing countries.

Methods: In the current research, subtractive proteome mining has been done to recognize putative drug targets. The proteome was analyzed through blast in order to exclude homologous proteins. Bacterial essential proteins were predicted and the participation of the essential genes in the metabolic pathways has been analyzed.

Results: 36 essential genes and 15 unique pathways have been identified as potential drug targets among the total of 1934 proteins. The location of proteins is determined as an outer membrane. 3 proteins out of 36 essential proteins are recognized as putative drug targets.

Conclusion: In the future, virtual screening for the evaluation of novel clinical compounds for the identified proteins will be effective and valuable for Salmonella Typhimurium infection in Homo sapiens.
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http://dx.doi.org/10.2174/1871526519666191211142758DOI Listing
September 2021

Relationship of single nucleotide polymorphisms and haplotype interaction of mitochondrial unfolded protein response pathway genes with head and neck cancer.

Future Oncol 2019 Nov 25;15(33):3819-3829. Epub 2019 Oct 25.

Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad Pakistan.

In this study, we evaluated the effect of selected polymorphisms of mitochondrial unfolded protein response (UPR) pathway in 500 head and neck cancer (HNC) patients and 500 healthy controls from Pakistan. The experiments were conducted using tetra-ARMS PCR followed by DNA sequencing. Multivariate analysis showed that AA genotype of rs3782116 showed fivefold, GG genotype of rs6598072 approximately twofold and CC genotype of rs4946936 and TT genotype of rs12212067 showed twofold increased risk of HNC. Furthermore, haplotype analysis showed that certain haplotypes of UPR pathway single nucleotide polymorphisms have significant association with increased HNC risk. These results show that genetic aberrations in UPR pathway genes have association with increased HNC risk and can be an indicator of advance clinical outcome especially invasion and metastasis.
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http://dx.doi.org/10.2217/fon-2019-0365DOI Listing
November 2019

In silico T-cell and B-cell Epitope Based Vaccine Design Against Alphavirus Strain of Chikungunya.

Infect Disord Drug Targets 2020 ;20(4):523-530

Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan

Background: Chikungunya an arbovirus, is transmitted to humans by the bite of Aedes mosquito. The virus occurrences have been reported in Southeast Asian countries including Pakistan. Its symptoms include typical febrile illness and arthralgic syndrome. The virus has not decisively proved to be life-threatening.

Methods: The attempt was to design T-cell and B-cell epitope-based vaccine for Chikungunya. The proteome of chikungunya was retrieved, antigenic proteins were identified and T-cell epitopes and B-cell epitopes were predicted. Interacting HLA alleles were also identified. The final analysis was done to confirm that predicted T-cell epitopes and B-cell epitopes can be used as a vaccine.

Results: About 32 T-cell epitopes and a 10mer B-cell epitope were identified. Both T-cell and Bcell epitopes demonstrated strong interactions with HLA alleles. The predicted T-cell and B-cell epitopes were docked with respective HLA alleles. The docking analysis showed that the predicted respective epitopes best fit into the binding pockets of the alleles.

Conclusion: On the basis of this computational analysis, it is suggested that these predicted epitopes can be used as a remedy against Alphavirus strain of chikungunya. Further laboratory experiments can be conducted to determine the efficacy and stability of this work.
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http://dx.doi.org/10.2174/1871526519666190521100521DOI Listing
May 2021

Author Correction: Effect of Plant Density, Boron Nutrition and Growth Regulation on Seed Mass, Emergence and Offspring Growth Plasticity in Cotton.

Sci Rep 2018 Jul 6;8(1):10489. Epub 2018 Jul 6.

Department of Agronomy, University of Agriculture, Faisalabad, 38040, Pakistan.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
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http://dx.doi.org/10.1038/s41598-018-28825-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035241PMC
July 2018

Effect of Plant Density, Boron Nutrition and Growth Regulation on Seed Mass, Emergence and Offspring Growth Plasticity in Cotton.

Sci Rep 2018 05 21;8(1):7953. Epub 2018 May 21.

Department of Agronomy, University of Agriculture, Faisalabad, 38040, Pakistan.

Seed nutrients reserves have direct relationship with seed functional traits and influence offspring performance. Effects of plant density, foliage boron (B) nutrition and mepiquat chloride (MC) growth regulation on seed nutrients reserves, seed mass and production, and emergence and offspring growth traits of cotton were studied in two years field experiment. Seed nutrients reserves and seed mass were decreased at higher maternal plant density relative to lower plant density with concomitant decrease in emergence and offspring seedling growth. However, maternal foliage B nutrition and MC growth regulation enhanced seed nutrients reserves, seed mass, emergence and offspring seedling growth performance. There was a significant positive relationship between seed mass and seed nutrients reserves indicating that changes in nutrient availability/uptake in response to maternal ecological factors determine variation in seed functional traits. Nonetheless, seed mass was positively correlated with emergence percentage and negatively with emergence timing. Furthermore, variation in offspring seedling growth traits with seed mass indicated the significance of initial seed nutrients reserves for early seedling vigour and establishment. In conclusion, lower maternal plant density, B nutrition and MC growth regulation ensued in higher emergence and offspring seedling growth of cotton because of higher seed nutrient reserves and seed mass.
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http://dx.doi.org/10.1038/s41598-018-26308-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5962529PMC
May 2018

Identification of phytotoxins in different plant parts of Brassica napus and their influence on mung bean.

Environ Sci Pollut Res Int 2018 Jun 24;25(18):18071-18080. Epub 2018 Apr 24.

Department of Agronomy, College of Agriculture, University of Sargodha, Sargodha, Pakistan.

Plants in Brassica genus have been found to possess strong allelopathic potential. They may inhibit seed germination and emergence of subsequent crops following them in a rotation system. Series of laboratory and greenhouse experiments were conducted to determine the allelopathic impacts of Brassica napus L. against mung bean. We studied (1) the effects of aqueous extract (5%) of different plant parts (root, stem, leaf, flower, and whole plant) of B. napus, (2) the effects of leaf and flower extracts of B. napus at 0, 1, 2, 3, and 4% concentrations, and (3) the effect of residues of different B. napus plant parts and decomposition periods (0, 7, 14, and 21 days) on germination and seedling growth of mung bean. Various types of phenolics including quercitin, chlorogenic acid, p-coumeric acid, m-coumaric acid, benzoic acid, caffeic acid, syringic acid, vanillic acid, ferulic acid, cinamic acid, and gallic acid were identified in plant parts of B. napus. Among aqueous extracts of various plant parts, leaf and flower were found to have stronger inhibitory effects on germination and seedling growth traits of mung bean, higher concentrations were more toxic. The decomposition period changed the phtotoxic effect of residues, more inhibitory effect was shown at 14 days decomposition while decomposition for 21 days reduced inhibitory effect. The more total water-soluble phenolic was found in 5% (w/v) aqueous extract and 5% (w/w) residues of B. napus flowers at 14 days of decomposition (89.80 and 10.47 mg L), respectively. The strong inhibitory effects of B. napus should be managed when followed in rotation.
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http://dx.doi.org/10.1007/s11356-018-2043-xDOI Listing
June 2018

The Absence of HCV RNA and NS5A Protein in Peripheral Blood Mononuclear Cells Is a Prognostic Tool for Sustained Virological Response.

Viral Immunol 2017 10 5;30(8):568-575. Epub 2017 Sep 5.

1 Nuclear Medicine, Oncology, and Radiotherapy, Institute NORI, Islamabad, Pakistan .

Hepatitis C Virus (HCV) infection is a major health concern worldwide. The presence of both HCV viral RNA and NS5A proteins in peripheral blood mononuclear cells (PBMCs) indicate the efficacy of the treatment during sustained virological response (SVR) and end of treatment response (ETR). The main objective of this study was to detect the absence or presence of HCV RNA and NS5A proteins in PBMCs. Blood samples were taken from selected patients (Islamabad, Pakistan) before treatment, at ETR, and during SVR. Two hundred HCV responders to pegylated IFN-α-2a plus ribavirin were selected. HCV RNA was extracted from the patients to determine the viral load by reverse transcription (RT)-polymerase chain reaction before treatment. Out of 200 patients, 152 (76%) and 48 (24%) achieved positive and negative ETR, respectively. Among ETR patients, 134 (88.2%) showed SVR, whereas 18 (11.8%) displayed relapse. The male to female ratio was 92:108 with mean age of 37.4 years. Among 152 ETR-positive patients, 29 (19%) patients' PBMCs were positive for HCV RNA and 27 (17.8%) were positive for NS55A proteins. Patients having HCV RNA in PBMCs showed higher relapse frequency compared with patients lacking it. Similarly, patients having NS5A protein showed significantly higher relapse frequency compared with patients lacking it. All PBMC-positive samples were of genotype 3a. In addition, patients with positive NS5A in their PBMCs showed greater risk of relapse compared with patients having HCV RNA. We conclude that the absence of both viral HCV and proteins can be used as an indicator for diagnosis of SVR in the future.
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http://dx.doi.org/10.1089/vim.2017.0030DOI Listing
October 2017

Expression analysis of human epidermal growth factor receptor type 2 transcripts in breast cancer cohort and its association with clinical features.

J Cancer Res Ther 2016 Apr-Jun;12(2):1036-9

Department of Biosciences, COMSATS Institute of Information and Technology, Islamabad, Pakistan.

Aim Of Study: Increased expression of human epidermal growth factor receptor type 2 (HER2) is significantly associated with poor prognosis in breast cancer patients. However, data on HER2 at transcript levels in Pakistani mammary tumor affected females is still limited. In the current study, HER2 transcripts were explored in breast cancer cohort and correlated with various clinical parameters.

Materials And Methods: Freshly excised tumors along with adjacent normal background tissues of 94 patients were collected at the time of surgery and immediately stored in RNAlater ® solution. Clinical data for these samples (disease stage, grade, age, and menopausal status) was also retrieved after a subsequent follow-up. Isolation of RNA and cDNA synthesis was done using an already established protocol. HER2 expression was evaluated using the quantitative real-time polymerase chain reaction (qRT-PCR) technique while β-actin was used as an internal control.

Results: In the given cohort, 31 (33%) patients were found positive for HER2. These tumors showed a pronounced increase in HER2 as compared to controls (P = 0.0004). Interestingly, the significant relevance of high HER2 mRNA among moderately differentiated tumor tissues in comparison to controls was also observed (P = 0.02). A significant association of HER2 levels with premenopausal status was also reported.

Conclusion: Based on these findings, early screening of HER2 using qRT-PCR should be incorporated for breast cancer patients of Pakistani population diagnosis.
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http://dx.doi.org/10.4103/0973-1482.176179DOI Listing
March 2017
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