Muhammad Shahid Nadeem

Synthesis, in vitro potential and computational studies on 2-amino-1,4-dihydropyrimidines as multitarget antibacterial ligands

In this study, we have investigated small multitargeted molecules containing 2-aminopyrimidine scaffold that may further act as precursor for developing more potent antibacterials. An efficient route to 2-amino-1,4-dihydropyrimidines by using ultrasound irradiation as the energy source was developed. In silico density functional theory calculations illustrated that tin chloride-mediated Biginelli reaction to produce 2-amino-1,4-dihydropyrimidines has energetics quite accessible under the reaction conditions. Calculated minimum inhibitory concentrations against the various bacterial strains showed that compounds 3 and 11 displayed comparable in vitro activity to ciprofloxacin in Staphylococcus aureus strains and reduced potency in Escherichia coli strains. Further, we investigated in silico ADMET profiling of synthesized compounds in order to understand the mechanism of action that help in explaining in vitro results. Lead compounds 3, 6, and 11 are predicted to have acceptable pharmacokinetic/drug-like properties. Data mining and computational analysis were employed to derive compound promiscuity phenomenon. All the compounds were found nonsubstrate towards various aminergic G-protein coupled receptors, ion-channels, kinase inhibitor, nuclear receptor ligand, protease inhibitor, and enzyme inhibitor. Compound 3 was further investigated by in silico binding to different antibacterial targets. Binding energy data revealed that that these compounds have the ability to bind with other bacterial targets. Hence, combined in silico and in vitro studies shed insights into the mechanism of synthesis and antibacterial activity of 2-amino-1,4-dihydropyrimidines. Results of this study are promising and can be used for further investigation by medicinal chemists to explore their chemical functionalization and in vivo studies.

High Y‐chromosomal Differentiation Among Ethnic Groups of Dir and Swat Districts, Pakistan

The ethnic groups that inhabit the mountainous Dir and Swat districts of northern Pakistan are marked by high levels of cultural and phenotypic diversity. To obtain knowledge of the extent of genetic diversity in this region, we investigated Y‐chromosomal diversity in five population samples representing the three main ethnic groups residing within these districts, including Gujars, Pashtuns and Kohistanis. A total of 27 Y‐chromosomal short tandem repeats (Y‐STRs) and 331 Y‐chromosomal single nucleotide polymorphisms (Y‐SNPs) were investigated. In the Y‐STRs, we observed very high and significant levels of genetic differentiation in nine of the 10 pairwise between‐group comparisons (RST 0.179–0.746), and the differences were mirrored in the Y‐SNP haplogroup frequency distribution. No genetic differences were found between the two Pashtun subethnic groups Tarklanis and Yusafzais (RST = 0.000). Utmankhels, also considered Pashtuns culturally, were not closely related to any of the other population samples (RST 0.451–0.746). Thus, our findings provide examples of both associations and dissociations between cultural and genetic legacies. When analyzed within a larger continental‐scale context, these five ethnic groups fall mostly outside the previously characterized Y‐chromosomal gene pools of the Indo‐Pakistani subcontinent. Male founder effects, coupled with culturally and topographically based constraints upon marriage and movement, are likely responsible for the high degree of genetic structure in this region.

Seroprevalence and Risk Factors of Toxoplasma gondii in Wild Birds of Punjab Province, Pakistan

Abstract Toxoplasma gondii is a protozoan parasite of veterinary and human public health importance for which birds act as an intermediate host. No information is available about the epidemiology of T. gondii in wild birds of Pakistan. The present study was designed to determine the seroprevalence and risk factors associated with T. gondii antibodies in wild birds of District Kasur, Punjab Province, Pakistan. A total of 200 wild birds of 28 species were captured from four tehsils (administrative subdistricts of districts) of the district Kasur and their serum samples screened for the presence of T. gondii antibodies using a latex agglutination test (cut-off value: 1:64). Twenty-five (13%) individual birds and 13 (46%) of the bird species were seropositive for T. gondii antibodies. There were statistical differences in T. gondii prevalence between adults and young (15% and 7%, respectively, P=0.001) and healthy and sick (11% and 50%, respectively, P=0.000) while there were not differences between genders, sites, urbanicity, and tehsils. The present study provides evidence of T. gondii antibodies in wild birds of Pakistan.

Identification of variants in the mitochondrial lysine-tRNA (MT-TK) gene in myoclonic epilepsy-pathogenicity evaluation and structural characterization by in silico approach

Variations in mitochondrial genes have an established link with myoclonic epilepsy. In the present study we evaluated the nucleotide sequence of MT‐TK gene of 52 individuals from 12 unrelated families and reported three variations in 2 of the 13 epileptic patients. The DNA sequences coding for MT‐TK gene were sequenced and mutations were detected in all participants. The mutations were further analyzed by the in silico analysis and their structural and pathogenic effects were determined. All the investigated patients had symptoms of myoclonus, 61.5% were positive for ataxia, 23.07% were suffering from hearing loss, 15.38% were having mild to severe dementia, 69.23% were males, and 61.53% had cousin marriage in their family history. DNA extracted from saliva was used for the PCR amplification of a 440 bp DNA fragment encompassing complete MT‐TK gene. The nucleotide sequence analysis revealed three mutations, m.8306T>C, m.8313G>C, and m.8362T>G that are divergent from available reports. The identified mutations designate the heteroplasmic condition. Furthermore, pathogenicity of the identified variants was predicted by in silico tools viz., PON‐mt‐tRNA and MitoTIP. Secondary structure of altered MT‐TK was predicted by RNAStructure web server. Studies by MitoTIP and PON‐mt‐tRNA tools have provided strong evidences of pathogenic effects of these mutations. Single nucleotide variations resulted in disruptive secondary structure of mutant MT‐TK models, as predicted by RNAStructure. In vivo confirmation of structural and pathogenic effects of identified mutations in the animal models can be prolonged on the basis of these findings.

A Crosstalk Between K ras (Kirsten Rat Sarcoma Viral Oncogene Homologue) and Adherence Molecular Complex Leads to Disassociation of Cells-A Possible Contribution Towards Metastasis in Colorectal Cancer

Constitutive activation of mutant K ras (Kirsten rat sarcoma viral oncogene homologue) and disassembly of E‐cadherin–catenin complex (E‐cadherin, α‐catenin, β‐catenin, and γ‐catenin) play an important role in apoptosis, differentiation, and cell proliferation. In this study, the expression pattern of K ras and E‐cadherin–catenin complex has been evaluated in normal and mutant colorectal cancer cell lines with an object to determine its impact on disassociation of cells from one another. We addressed the expression analysis of K ras with reference to its association with adherence molecules in two colorectal cancer cell lines, that is, Caco‐2 (wild type K ras served as a control) and DLD1 (heterozygous mutation at codon 13) at message level by qRT‐PCR and translational level by western blotting. Compared to the control Caco‐2 cell lines, the K ras in DLD1 cell lines showed slightly higher values while α‐catenin showed a slight lower (1.3‐folds), β‐catenin and E‐cadherin showed significantly lower expression (4.2‐fold decrease). It can be inferred that a possible cross talk exists between K ras and adherent junction mediated signalling. Mutation at codon 13 (G to D) leads to the overexpression of K ras and reduced expression of adherent junction complex resulting in metastasis. J. Cell. Biochem. 117: 2340–2345, 2016.