Khurshid Ahmad
@yu.ac.kr
Assistant Professor, Department of Medical Biotechnology
Yeungnam University
EDUCATION
Ph.D. (Bioinformatics)
RESEARCH INTERESTS
Bioinformatics, Skeletal muscle, extracellular matrix
Scopus Publications
Scholar Citations
Scholar h-index
Scholar i10-index
Scopus Publications
Yazdan Ahmad Qadri, Khurshid Ahmad, and Sung Won Kim
MDPI AG
Parkinson’s disease and Alzheimer’s disease are among the most common neurodegenerative disorders. These diseases are correlated with advancing age and are hence increasingly becoming prevalent in developed countries due to an increasingly aging demographic. Several tools are used to predict and diagnose these diseases, including pathological and genetic tests, radiological scans, and clinical examinations. Artificial intelligence is evolving to artificial general intelligence, which mimics the human learning process. Large language models can use an enormous volume of online and offline resources to gain knowledge and use it to perform different types of tasks. This work presents an understanding of two major neurodegenerative disorders, artificial general intelligence, and the efficacy of using artificial general intelligence in detecting and predicting these neurodegenerative disorders. A detailed discussion on detecting these neurodegenerative diseases using artificial general intelligence by analyzing diagnostic data is presented. An Internet of Things-based ubiquitous monitoring and treatment framework is presented. An outline for future research opportunities based on the challenges in this area is also presented.
Danishuddin, Md Azizul Haque, Shawez Khan, Jong-Joo Kim, and Khurshid Ahmad
MDPI AG
Bladder cancer is among the most prevalent tumors in the urinary system and is known for its high malignancy. Although traditional diagnostic and treatment methods are established, recent research has focused on understanding the molecular mechanisms underlying bladder cancer. The primary objective of this study is to identify novel diagnostic markers and discover more effective targeted therapies for bladder cancer. This study identified differentially expressed genes (DEGs) between bladder cancer tissues and adjacent normal tissues using data from The Cancer Genome Atlas (TCGA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to explore the functional roles of these genes. A protein–protein interaction (PPI) network was also constructed to identify and analyze hub genes within this network. Gene set variation analysis (GSVA) was conducted to investigate the involvement of these genes in various biological processes and pathways. Ten key genes were found to be significantly associated with bladder cancer: IL6, CCNA2, CCNB1, CDK1, PLK1, TOP2A, AURKA, AURKB, FOXM1, and CALML5. GSVA analyses revealed that these genes are involved in a variety of biological processes and signaling pathways, including coagulation, UV-response-down, apoptosis, Notch signaling, and Wnt/beta-catenin signaling. The diagnostic relevance of these genes was validated through ROC curve analysis. Additionally, potential therapeutic drug interactions with these key genes were identified. This study provides valuable insights into key genes and their roles in bladder cancer. The identified genes and their interactions with therapeutic drugs could serve as potential biomarkers, presenting new opportunities for enhancing the diagnosis and prognosis of bladder cancer.
Afsha Fatima Qadri, Sibhghatulla Shaikh, Ye Chan Hwang, Khurshid Ahmad, Inho Choi, and Eun Ju Lee
Elsevier BV
Syed Sayeed Ahmad, Khurshid Ahmad, Jeong Ho Lim, Sibhghatulla Shaikh, Eun Ju Lee, and Inho Choi
Elsevier BV
Khurshid Ahmad, Eun Ju Lee, Shahid Ali, Ki Soo Han, Sun Jin Hur, Jeong Ho Lim, and Inho Choi
Elsevier BV
Shahid Ali, Abdul Rahaman, Omnia Badra, Khurshid Ahmad, and Inho Choi
Frontiers Media SA
Sibhghatulla Shaikh, Eun Ju Lee, Khurshid Ahmad, and Inho Choi
Frontiers Media SA
Licochalcone B (LicB), a chalcone derived from Glycyrrhiza uralensis and Glycyrrhiza glabra, has received considerable attention due to its diverse pharmacological properties. Accumulated data indicates that LicB has pharmacological effects that include anti-cancer, hepatoprotective, anti-inflammatory, and neuroprotective properties. The action mechanism of LicB has been linked to several molecular targets, such as phosphoinositide 3-kinase/Akt/mammalian target of rapamycin, p53, nuclear factor-κB, and p38, and the involvements of caspases, apoptosis, mitogen-activated protein kinase-associated inflammatory pathways, and anti-inflammatory nuclear factor erythroid 2–related factor 2 signaling pathways highlight the multifaceted therapeutic potential of LicB. This review systematically updates recent findings regarding the pharmacological effects of LicB, and the mechanistic pathways involved, and highlights the potential use of LicB as a promising lead compound for drug discovery.
Khurshid Ahmad, Sibhghatulla Shaikh, Faez Iqbal Khan, and Mohammad Ehtisham Khan
Frontiers Media SA
Syed Sayeed Ahmad, Jeong Ho Lim, Khurshid Ahmad, Hee Jin Chun, Sun Jin Hur, Eun Ju Lee, and Inho Choi
Elsevier BV
Syed Sayeed Ahmad, Hee Jin Chun, Khurshid Ahmad, and Inho Choi
Elsevier BV
Shahid Ali, Khurshid Ahmad, Sibhghatulla Shaikh, Hee Jin Chun, Inho Choi, and Eun Ju Lee
Informa UK Limited
Myostatin is a widely recognized inhibitory factor of skeletal muscle growth and significantly influences muscle development and metabolism. In mice, myostatin inhibition improves insulin sensitivity, increases glucose uptake by skeletal muscle, and reduces body fat. Furthermore, Mss51 is downregulated in response to myostatin inhibition, and its deletion appears to improve the metabolic state of skeletal muscle and reduce adipose tissue, which makes Mss51 a potential target for the treatment of obesity and type 2 diabetes. Here, we report a computationally predicted and validated three-dimensional structure of Mss51. Computational screening was used to identify naturally occurring compounds from the Herbal and Specs chemical database that might inhibit Mss51, based on binding affinities and physiochemical and ADMET properties. ZINC00338371, ZINC95099599 and ZINC08214878 were found to bind to Mss51 with high binding affinity and specificity. In addition, 100 ns molecular dynamics simulations were conducted to assess the stabilities of the interactions between the three compounds and Mss51. MD simulation demonstrated that all three compounds bind to the active pocket site of Mss51 stably and cause conformation changes. ZINC00338371 was found to bind most stably with binding free energy -229.022 ± 13.776 kJ/mol to Mss51, suggesting that it has therapeutic potential as a treatment option for obesity and type 2 diabetes.Communicated by Ramaswamy H. Sarma.
Syed Sayeed Ahmad, Khurshid Ahmad, Ye Chan Hwang, Eun Ju Lee, and Inho Choi
MDPI AG
Ginseng is usually consumed as a daily food supplement to improve health and has been shown to benefit skeletal muscle, improve glucose metabolism, and ameliorate muscle-wasting conditions, cardiovascular diseases, stroke, and the effects of aging and cancers. Ginseng has also been reported to help maintain bone strength and liver (digestion, metabolism, detoxification, and protein synthesis) and kidney functions. In addition, ginseng is often used to treat age-associated neurodegenerative disorders, and ginseng and ginseng-derived natural products are popular natural remedies for diseases such as diabetes, obesity, oxidative stress, and inflammation, as well as fungal, bacterial, and viral infections. Ginseng is a well-known herbal medication, known to alleviate the actions of several cytokines. The article concludes with future directions and significant application of ginseng compounds for researchers in understanding the promising role of ginseng in the treatment of several diseases. Overall, this study was undertaken to highlight the broad-spectrum therapeutic applications of ginseng compounds for health management.
Khurshid Ahmad, Sibhghatulla Shaikh, Hee Jin Chun, Shahid Ali, Jeong Ho Lim, Syed Sayeed Ahmad, Eun Ju Lee, and Inho Choi
Springer Science and Business Media LLC
AbstractThe regenerative ability of skeletal muscle (SM) in response to damage, injury, or disease is a highly intricate process that involves the coordinated activities of multiple cell types and biomolecular factors. Of these, extracellular matrix (ECM) is considered a fundamental component of SM regenerative ability. This review briefly discusses SM myogenesis and regeneration, the roles played by muscle satellite cells (MSCs), other cells, and ECM components, and the effects of their dysregulations on these processes. In addition, we review the various types of ECM scaffolds and biomaterials used for SM regeneration, their applications, recent advances in ECM scaffold research, and their impacts on tissue engineering and SM regeneration, especially in the context of severe muscle injury, which frequently results in substantial muscle loss and impaired regenerative capacity. This review was undertaken to provide a comprehensive overview of SM myogenesis and regeneration, the stem cells used for muscle regeneration, the significance of ECM in SM regeneration, and to enhance understanding of the essential role of the ECM scaffold during SM regeneration.
Khurshid Ahmad, Sibhghatulla Shaikh, Jeong Ho Lim, Syed Sayeed Ahmad, Hee Jin Chun, Eun Ju Lee, and Inho Choi
Elsevier BV
Sibhghatulla Shaikh, Shahid Ali, Jeong Ho Lim, Khurshid Ahmad, Ki Soo Han, Eun Ju Lee, and Inho Choi
MDPI AG
Androgenic alopecia (AGA) is a dermatological disease with psychosocial consequences for those who experience hair loss. AGA is linked to an increase in androgen levels caused by an excess of dihydrotestosterone in blood capillaries produced from testosterone by 5α-reductase type II (5αR2), which is expressed in scalp hair follicles; 5αR2 activity and dihydrotestosterone levels are elevated in balding scalps. The diverse health benefits of flavonoids have been widely reported in epidemiological studies, and research interest continues to increase. In this study, a virtual screening approach was used to identify compounds that interact with active site residues of 5αR2 by screening a library containing 241 flavonoid compounds. Here, we report two potent flavonoid compounds, eriocitrin and silymarin, that interacted strongly with 5αR2, with binding energies of −12.1 and −11.7 kcal/mol, respectively, which were more significant than those of the control, finasteride (−11.2 kcal/mol). Molecular dynamic simulations (200 ns) were used to optimize the interactions between compounds and 5αR2 and revealed that the interaction of eriocitrin and silymarin with 5αR2 was stable. The study shows that eriocitrin and silymarin provide developmental bases for novel 5αR2 inhibitors for the management of AGA.
Alaa Eldin M. A. Morshdy, Karima M. E. Abdallah, Heba E. Abdallah, Fahad D. Algahtani, Mohamed Tharwat Elabbasy, Suleman Atique, Khursheed Ahmad, Mohammad A. A. Al-Najjar, Hossam M. Abdallah, and Abdallah Fikry A. Mahmoud
MDPI AG
Staphylococcus aureus is one of the most widespread foodborne bacteria that cause high morbidity, mortality, and economic loss, primarily if foodborne diseases are caused by pathogenic and multidrug-resistant (MDR) strains. This study aimed to determine the prevalence of S. aureus in chicken meat in Egyptian markets. Thus, this study might be the first to assess the efficiency of different natural phenolic compounds as novel antibacterial agents against MDR S. aureus pathogens isolated from raw chicken meat in the Egyptian market. The incidence and quantification of pathogenic S. aureus were detected in retail raw chicken meat parts (breast, thigh, fillet, and giblets). In total, 73 out of 80 (91.3%) of the chicken meat parts were contaminated, with S. aureus as the only species isolated. Of the 192 identified S. aureus isolates, 143 were coagulase-positive S. aureus and 117 isolates were MDR (81.8%, 117/143). Twenty-two antibiotic resistance profile patterns were detected. One strain was randomly selected from each pattern to further analyze virulence and resistance genes. Extracted DNA was assessed for the presence of antibiotic-resistance genes, i.e., vancomycin-resistance (vanA), aminoglycosides-resistance (aacA–aphD), apramycin-resistance (apmA), and methicillin-resistance (mecA), penicillin-resistance (blaZ), and virulence genes staphylococcal enterotoxins (sea and seb), Panton–Valentine leucocidin (pvl), clumping factor A (clfA), and toxic shock syndrome toxin (tst). Clustering analyses revealed that six S. aureus strains harbored the most virulence and resistance genes. The activity of hydroquinone was significantly higher than thymol, carvacrol, eugenol, and protocatechuic acid. Therefore, phenolic compounds, particularly hydroquinone, could potentially alternate with conventional antibiotics against the pathogenic MDR S. aureus inhabiting raw chicken meat. Hence, this study indicates that urgent interventions are necessary to improve hygiene for safer meat in Egyptian markets. Moreover, hydroquinone could be a natural phenolic compound for inhibiting foodborne pathogens.
Saheem Ahmad, Firoz Akhter, Khurshid Ahmad, and Saif Khan
Frontiers Media SA
Department of Medical Laboratory Sciences, College of Applied Medical Science, University of Hail, Hail, Saudi Arabia, Department of Biomedical Engineering, Stony Brook University, New York, NY, United States, Department of Medical Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea, Department of Basic Medical and Dental Sciences, College of Dentistry, University of Hail, Hail, Saudi Arabia
Sibhghatulla Shaikh, Khurshid Ahmad, Mohammad Ehtisham Khan, and Faez Iqbal Khan
Frontiers Media SA
Shahid Ali, Sibhghatulla Shaikh, Khurshid Ahmad, and Inho Choi
Informa UK Limited
The enzyme dipeptidyl peptidase 4 (DPP4) is a potential therapeutic target for type 2 diabetes (T2DM). Many synthetic anti-DPP4 medications are available to treat T2DM. The need for secure and efficient medicines has been unmet due to the adverse side effects of existing DPP4 medications. The present study implemented a combined approach to machine learning and structure-based virtual screening to identify DPP4 inhibitors. Two ML models were trained based on DPP4 IC50 datasets. The ML models random forest (RF) and multilayer perceptron (MLP) neural network showed good accuracy, with the area under the curve being 0.93 and 0.91, respectively. The natural compound library was screened through ML models, and 1% (217) of compounds were selected for further screening. Structure-based virtual screening was performed along with positive control sitagliptin to obtain more specific and selective leads for DPP4. Based on binding affinity, drug-likeness properties, and interaction with DPP4, Z-614 and Z-997 compounds showed high binding affinity and specificity in the catalytic pocket of DPP4. Finally, the stability conformation of the DPP4 enzyme complex was checked by a molecular dynamics (MD) simulation. The MD simulation showed that both compounds bind better in the catalytic pocket, but the Z-614 compound altered the DPP4 native conformation. Therefore, Z-614 showed a high deviation in the backbone. This combined approach (ML and structure-based) study reported that Z-997 binds most stably to DPP4 in their catalytic pocket with a binding free energy of -70.3 kJ/mol, suggesting its therapeutic potential as a treatment option for T2DM disease.Communicated by Ramaswamy H. Sarma.
Prachi Srivastava, Anshul Tiwari, Khurshid Ahmad, Neha Srivastava, and Prekshi Garg
Frontiers Media SA
Dementia is a debilitating and prevalent disorder affecting millions worldwide (Chern and Golub, 2019). The emergence of multi-omics analysis has led to a better understanding of the underlying disease mechanism and its effective treatment. This advanced approach combines data from multiple sources, such as genomics, transcriptomics, proteomics, and metabolomics, that helps understand the complex biological processes resulting in dementia. The potential benefits of multi-omics analysis in dementia research are significant. Researchers can develop more targeted and effective therapies by identifying key molecular pathways and biomarkers associated with these disorders. Multi-omics analysis may also help to identify subtypes of dementia disorders, allowing for more personalized treatment approaches. For a better understanding of the complex biological processes involved in dementia, the multi-omics analysis combines data from multiple resources leading to new insights and potential treatments for this devastating disorder (Mavrina et al., 2022). This Research Topic presents eight manuscripts, consisting of five original research papers, one case report, one review, and one mini-review. The manuscripts cover a diverse range of Research Topic related to recent advances and applications of multi-omics analysis in the field of dementia and neurodegenerative disorders. These expert-contributed manuscripts provide valuable insights into the underlying molecular mechanisms of dementia-related disorders as well as new diagnostic and treatment strategies. Wang et al., examined the upregulated expression of PLAGL2 in gliomas and identified a correlation with negative clinicopathological characteristics, including tumor grade. Moreover, the investigation revealed the role of PLAGL2 as an independent prognostic indicator, not for only progression-free survival (PFS) but also overall survival (OS) in clinical glioma specimens. Therefore, findings highlight the role of PLAGL2 expression in glioma progression and suggest its potential use as a prognostic marker for diagnosis and prognosis. The study’s results could have a significant impact on the diagnosis and treatment of patients with high-grade gliomas. Alqahtani et al., examined 47 genes associated with dementia and discovered that compositional, selectional, and mutational forces affect codon usage bias (CUB). The study suggested the positive association between high GC content and elevated gene expression OPEN ACCESS
Syed Sayeed Ahmad, Hee Jin Chun, Khurshid Ahmad, Sibhghatulla Shaikh, Jeong Ho Lim, Shahid Ali, Sung Soo Han, Sun Jin Hur, Jung Hoon Sohn, Eun Ju Lee,et al.
Korean Society of Animal Science and Technology
Abstract Cultured meat is a potential sustainable food generated by the in vitro myogenesis of muscle satellite (stem) cells (MSCs). The self-renewal and differentiation properties of MSCs are of primary interest for cultured meat production. MSC proliferation and differentiation are influenced by a variety of growth factors such as insulin-like growth factors (IGF-1 and IGF-2), transforming growth factor beta (TGF-β), fibroblast growth factors (FGF-2 and FGF-21), platelet-derived growth factor (PDGF) and hepatocyte growth factor (HGF) and by hormones like insulin, testosterone, glucocorticoids, and thyroid hormones. In this review, we investigated the roles of growth factors and hormones during cultured meat production because these factors provide signals for MSC growth and structural stability. The aim of this article is to provide the important idea about different growth factors such as FGF (enhance the cell proliferation and differentiation), IGF-1 (increase the number of myoblasts), PDGF (myoblast proliferation), TGF-β1 (muscle repair) and hormones such as insulin (cell survival and growth), testosterone (muscle fiber size), dexamethasone (myoblast proliferation and differentiation), and thyroid hormones (amount and diameter of muscle fibers and determine the usual pattern of fiber distributions) as media components during myogenesis for cultured meat production.
Jeong Ho Lim, Khurshid Ahmad, Hee Jin Chun, Ye Chan Hwang, Afsha Fatima Qadri, Shahid Ali, Syed Sayeed Ahmad, Sibhghatulla Shaikh, Jungseok Choi, Jihoe Kim,et al.
MDPI AG
Immunoglobulin-like cell adhesion molecule (IgLON4) is a glycosylphosphatidylinositol-anchored membrane protein that has been associated with neuronal growth and connectivity, and its deficiency has been linked to increased fat mass and low muscle mass. Adequate information on IgLON4 is lacking, especially in the context of skeletal muscle. In this study, we report that IgLON4 is profusely expressed in mouse muscles and is intensely localized on the cell membrane. IgLON4 expression was elevated in CTX-injected mouse muscles, which confirmed its role during muscle regeneration, and was abundantly expressed at high concentrations at cell-to-cell adhesion and interaction sites during muscle differentiation. IgLON4 inhibition profoundly affected myotube alignment, and directional analysis confirmed this effect. Additionally, results demonstrating a link between IgLON4 and lipid rafts during myogenic differentiation suggest that IgLON4 promotes differentiation by increasing lipid raft accumulation. These findings support the notion that a well-aligned environment promotes myoblast differentiation. Collectively, IgLON4 plays a novel role in myogenesis and regeneration, facilitates myotube orientation, and is involved in lipid raft accumulation.
Sibhghatulla Shaikh, Shahid Ali, Jeong Ho Lim, Hee Jin Chun, Khurshid Ahmad, Syed Sayeed Ahmad, Ye Chan Hwang, Ki Soo Han, Na Ri Kim, Eun Ju Lee,et al.
Frontiers Media SA
Type 2 diabetes mellitus (T2DM) is a growing global public health issue, and dipeptidyl peptidase-4 (DPP-4) is a potential therapeutic target in T2DM. Several synthetic anti-DPP-4 medications can be used to treat T2DM. However, because of adverse effects, there is an unmet demand for the development of safe and effective medications. Natural medicines are receiving greater interest due to the inherent safety of natural compounds. Glycyrrhiza uralensis (licorice) is widely consumed and used as medicine. In this study, we investigated the abilities of a crude water extract (CWE) of G. uralensis and two of its constituents (licochalcone A (LicA) and licochalcone B (LicB)) to inhibit the enzymatic activity of DPP-4 in silico and in vitro. In silico studies showed that LicA and LicB bind tightly to the catalytic site of DPP-4 and have 11 amino acid residue interactions in common with the control inhibitor sitagliptin. Protein-protein interactions studies of LicA-DPP4 and LicB-DPP4 complexes with GLP1 and GIP reduced the DPP-4 to GLP1 and GIP interactions, indicated that these constituents might reduce the degradations of GLP1 and GIP. In addition, molecular dynamics simulations revealed that LicA and LicB stably bound to DPP-4 enzyme. Furthermore, DPP-4 enzyme assay showed the CWE of G. uralensis, LicA, and LicB concentration-dependently inhibited DPP-4; LicA and LicB had an estimated IC50 values of 347.93 and 797.84 μM, respectively. LicA and LicB inhibited DPP-4 at high concentrations, suggesting that these compounds could be used as functional food ingredients to manage T2DM.
Arif Tasleem Jan, Safikur Rahman, Khurshid Ahmad, and Rinki Minakshi
Frontiers Media SA
COPYRIGHT © 2022 Jan, Rahman, Ahmad and Minakshi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: Unfolded protein response (UPR): An impending target for multiple neurological disorders
Shahid Ali, Khurshid Ahmad, Sibhghatulla Shaikh, Jeong Ho Lim, Hee Jin Chun, Syed Sayeed Ahmad, Eun Ju Lee, and Inho Choi
MDPI AG
Myostatin (MSTN), a negative regulator of muscle mass, is reported to be increased in conditions linked with muscle atrophy, sarcopenia, and other muscle-related diseases. Most pharmacologic approaches that treat muscle disorders are ineffective, emphasizing the emergence of MSTN inhibition. In this study, we used computational screening to uncover natural small bioactive inhibitors from the Traditional Chinese Medicine database (~38,000 compounds) for the MSTN protein. Potential ligands were screened, based on binding affinity (150), physicochemical (53) and ADMET properties (17). We found two hits (ZINC85592908 and ZINC85511481) with high binding affinity and specificity, and their binding patterns with MSTN protein. In addition, molecular dynamic simulations were run on each complex to better understand the interaction mechanism of MSTN with the control (curcumin) and the hit compounds (ZINC85592908 and ZINC85511481). We determined that the hits bind to the active pocket site (Helix region) and trigger conformational changes in the MSTN protein. Since the stability of the ZINC85592908 compound was greater than the MSTN control, we believe that ZINC85592908 has therapeutic potential against the MSTN protein and may hinder downstream singling by inhibiting the MSTN protein and increasing myogenesis in the skeletal muscle tissues.