Biology subjects

abdelmoneim, a. h.

Publications and source records attributed to abdelmoneim, a. h..

4 recordsLinked to original sources

bioRxiv2020

In Silico Analysis of B3GALTL Gene Reveling 13 Novel Mutations Associated with Peters'-plus syndrome

BackgroundPeters-plus syndrome is a rare autosomal recessive disorder, which is characterized by a specific malformation of the eye that includes corneal opaqueness and iridocorneal adhesions (Peters anomaly) along with other systemic manifestations. Furthermore, various researches report the association between B3GALTL gene and Peters-plus syndrome. In the current work we aim to analyze the deleterious SNPs in B3GALTL gene that predispose to Peters-plus syndrome. Methodthe associated SNPs of the coding region of the B3GALTL gene was acquired from National Center for Biotechnology Information and then analyzed by eight softwares (SIFT, Polyphen2, Proven, SNAP2, SNP@GO, PMut, Imutant and Mupro). The physiochemical properties of the resulted SNPs were then analyzed by Hope project website and visualized by chimera software. ResultThirteen novel mutations (Y172C, A222V, C260R, C260Y, D349G, I354K, R377C, G379C, G393R, G393E, G395E, G425E, R445W) are discovered in B3GALTL gene to cause deleterious effects leading to the development of Peters-plus syndrome. ConclusionThirteen novel mutations in B3GALTL gene are predicted to cause Peters-plus syndrome.

bioinformatics↗

bioRxiv2020

Immunoinformatic design of multi epitopes peptide-based universal cancer vaccine using matrix metalloproteinase-9 protein as a target

BackgroundCancer remains a major public health hazard despite the extensive research over the years on cancer diagnostic and treatment, this is mainly due to the complex pathophysiology and genetic makeup of cancer. A new approach toward cancer treatment is the use of cancer vaccine, yet the different molecular bases of cancers reduce the effectiveness of this approach. In this work we aim to use matrix metalloproteinase-9 protein (MMP9) which is essential molecule in the survival and metastasis of all type of cancer as a target for universal cancer vaccine design. Methodreference sequence of matrix metalloproteinase-9 protein was obtained from NCBI databases along with the related sequence, which is then checked for conservation using BioEdit, furthermore the B cell and T cell related peptide were analyzed using IEDB website. The best candidate peptide were then visualized using chimera software. ResultThree Peptides found to be good candidate for interactions with B cells (SLPE, RLYT, and PALPR), while ten peptides found as a good target for interactions with MHC1 (YRYGYTRVA, YGYTRVAEM, YLYRYGYTR, WRFDVKAQM, ALWSAVTPL, LLLQKQLSL, LIADKWPAL, KLFGFCPTR, MYPMYRFTE, FLIADKWPA) with world combined coverage of 94.77%. In addition, ten peptides were also found as a good candidates for interactions with MHC2 (KMLLFSGRRLWRFDV, GRGKMLLFSGRRLWR, RGKMLLFSGRRLWRF, GKMLLFSGRRLWRFD, TFTRVYSRDADIVIQ, AVIDDAFARAFALWS, FARAFALWSAVTPLT, MLLFSGRRLWRFDVK, GNQLYLFKDGKYWRF, NQLYLFKDGKYWRFS), with world combined coverage of 90.67%. CONCLUSION23 peptide-based vaccine was designed for use as a universal cancer vaccine which has a high world population coverage for MHC1(94.77%) and MHC2 (90.67%) related alleles.

immunology↗

bioRxiv2019

Multi-epitope Peptide Vaccine Prediction for Candida albicans targeting Pyruvate Kinase Protein; an Immunoinformatics Approach

The fungus Candida albicans is an opportunistic pathogen that causes a wide range of infections. Its the primary cause of candidiasis and the fourth most common cause of nosocomial infection. In addition, disseminated invasive candidiasis which is a major complication of the disease has an estimated mortality rate of 40%-60% even with the use of antifungal drugs. Over the last decades, several different anti-Candida vaccines have been suggested with different strategies for immunization against candidiasis such as, live-attenuated fungi, recombinant proteins, and glycoconjugates but none has been approved by the FDA, yet. This study aims to introduce a new possible vaccine for C. albicans through analyzing peptides of its pyruvate kinase (PK) protein as an immunogenic stimulant computationally.\n\nA total number of 28 C. albicans, pyruvate kinase proteins were obtained from NCBI on the 9th of February 2019 and were subjected to multiple sequence alignment using Bioedit for conservancy. The main analytical tool was IEDB, Chimera for homology modelling, and MOE for docking.\n\nAmong the tested peptides, fifteen promising T-cell peptides were predicted. Five peptides were more important than the others (HMIFASFIR, YRGVYPFIY, AVAAVSAAY, LRWAVSEAV, and IFASFIRTA) They show high Binding Affinity to MHC molecules, low binding energy required indicating more stable bonds, and their ideal length of nine peptides. (PTRAEVSDV) peptide is the most promising linear B-cell peptide due to its physiochemical parameters and optimal length (nine amino acids). Its highly recommended to have these five strong candidates in future in vivo and in vitro analysis studies.

bioinformatics↗

bioRxiv2019

In silico analysis of coding SNPs and 3′-UTR associated miRNAs in DCAF17 gene that may affect the regulation and pathogenesis of Woodhouse-Sakati Syndrome

BackgroundWoodhouse-Sakati Syndrome refers to a group of inherited disorders characterized by alopecia, hypogonadism, diabetes mellitus, hypothyroidism and progressive extrapyramidal signs. The aim of this study is to identify the pathogenic SNPs in the DCAF17 gene with their related mciroRNAs and their effect on the structure and function of the protein.\n\nMaterial and MethodsWe used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein. After that we defined the miRNAs founded in the 3'-UTR region on the DCAF17 gene and studied the annotations relative to it.\n\nResultsTen deleterious SNPs out of 339 were found to have a damaging effect on the protein structure and function, with one significant micoRNA in the 3'-UTR region.\n\nConclusionThis was the first in silico analysis of DCAF17 gene, in which 10 novel mutations were found using different bioinformatics tools that could be used as a diagnostic markers for Woodhouse-Sakati syndrome, with one relevant microRNA that can regulate the function of the protein.

bioinformatics↗