Muhammad Umer Khan

Dr. Muhammad Umer Khan

orcid

Research Focus & Metrics

Academic Career Length

8Years (2019-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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28 November 2023 in AMB Express
Verified
Journal Article
Open access
PDF file
ASAzra Sakhawat
Azra Sakhawat
MKMuhammad Umer Khan
Muhammad Umer Khan
RRRaima Rehman
Raima Rehman
SKSamiullah Khan
Samiullah Khan
MSMuhammad Adnan Shan
Muhammad Adnan Shan
QAQurban Ali
Qurban Ali
Brain-Derived Neurotrophic Factor (BDNF) is a neurotrophin gene family gene that encodes proteins vital for the growth, maintenance, and survival of neurons in the nervous system. The study aimed to screen natural compounds against BDNF variant (V66M), which affects memory, cognition, and mood regulation. BDNF variant (V66M) as a target structure was selected, and Vitamin D, Curcumin, Vitamin C, and Quercetin as ligands structures were taken from PubChem database. Multiple tools like AUTODOCK VINA, BIOVIA discovery studio, PyMOL, CB-dock, IMOD server, Swiss ADEMT, and Swiss predict ligands target were used to analyze binding energy, interaction, stability, toxicity, and visualize BDNF-ligand complexes. Compounds Vitamin D3, Curcumin, Vitamin C, and Quercetin with binding energies values of − 5.5, − 6.1, − 4.5, and − 6.7 kj/mol, respectively, were selected. The ligands bind to the active sites of the BDNF variant (V66M) via hydrophobic bonds, hydrogen bonds, and electrostatic interactions. Furthermore, ADMET analysis of the ligands revealed they exhibited sound pharmacokinetic and toxicity profiles. In addition, an MD simulation study showed that the most active ligand bound favorably and dynamically to the target protein, and protein–ligand complex stability was determined. The finding of this research could provide an excellent platform for discovering and rationalizing novel drugs against stress related to BDNF (V66M). Docking, preclinical drug testing and MD simulation results suggest Quercetin as a more potent BDNF variant (V66M) inhibitor and forming a more structurally stable complex.

10 February 2024 in Molecular Biology Reports
Verified
Journal Article
Closed access
PDF file
ASAyman Saleem
Ayman Saleem
MKMuhammad Umer Khan
Muhammad Umer Khan
TATAZEEN ZAHID ASGHAR
TAZEEN ZAHID ASGHAR
IKIqra Khurram
Iqra Khurram
Muhammad Usman GhaniMuhammad Usman Ghani
Muhammad Usman Ghani
Javad Sharifi-RadJavad Sharifi-Rad
Javad Sharifi-Rad

15 September 2023 in Scientific Reports
Verified
Journal Article
Open access
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IKIqra Khurram
Iqra Khurram
MKMuhammad Umer Khan
Muhammad Umer Khan
SISaooda Ibrahim
Saooda Ibrahim
ASAyman Saleem
Ayman Saleem
ZKZaman Khan
Zaman Khan
QAQurban Ali
Qurban Ali
Breast cancer is the most prevalent and leading cause of mortality worldwide among women. Cell-free DNA (cfDNA) analysis is an alternative quantitative approach to conventional methods for cancer diagnosis. The current research project aimed to determine the efficacy of cfDNA as a diagnostic biomarker in breast cancer patients in Pakistan. Eighty-four female breast cancer patients were selected as cases, and 152 healthy females as controls. Immunohistochemistry was performed to identify tumor biomarkers along with clinical profiling. cfDNA was extracted from serum using the phenol–chloroform method. The cfDNA level in the serum was estimated using Agarose Gel Electrophoresis and Nanodrop. SPPS version 25.0 was used to perform statistical analyses. The results showed that the cancer biomarkers were significantly associated with breast cancer. The changes in hematological parameters were insignificant, whereas the biochemical parameter variations between the cases and controls were statistically significant. A significant association of cfDNA level with breast cancer was observed. Further cfDNA levels and cancer biomarkers were not statistically significant. A significant correlation was observed between cfDNA and biochemical parameters, except for creatinine, whereas hematological parameters showed no significant correlation.ROC analysis declared cfDNA as an authentic diagnostic marker for breast cancer. It was concluded that the level of cfDNA is significantly increased in breast cancer patients and can be utilized as a diagnostic biomarker.

1 February 2025 in Food Science & Nutrition
Verified
Journal Article
Open access
SISaooda Ibrahim
Saooda Ibrahim
MKMuhammad Umer Khan
Muhammad Umer Khan
IKIqra Khurram
Iqra Khurram
RRRaima Rehman
Raima Rehman
ARAbdur Rauf
Abdur Rauf
MQMohammed Mansour Quradha
Mohammed Mansour Quradha
Proteolysis Targeting Chimeras (PROTACs) have revolutionized cancer therapy by offering a selective and innovative approach to degrade key oncogenic proteins associated with various malignancies. These hybrid molecules exploit the ubiquitin‐proteasome system, facilitating the degradation of target proteins through an event‐driven mechanism, thereby overcoming drug resistance and enhancing selectivity. With diverse targets including androgen receptors, BTK, estrogen receptors, BET proteins, and BRAF, PROTACs offer a versatile strategy for personalized cancer treatment. Advantages of PROTACs over traditional small molecule inhibitors include their ability to operate at lower concentrations, catalyzing the degradation of multiple proteins of interest with reduced cytotoxicity. Notably, PROTACs address challenges associated with traditionally “undruggable” targets, expanding the therapeutic landscape of cancer therapy. Ongoing preclinical and clinical studies highlight the transformative potential of PROTACs, with promising results in prostate, breast, lung, melanoma, and colorectal cancers. Despite their potential, challenges persist in optimizing physicochemical properties and enhancing bioavailability. Further research is needed to refine PROTAC design and address complexities in molecule development. Nevertheless, the development of oral androgen receptor PROTACs represents a significant milestone, demonstrating the feasibility and efficacy of this innovative therapeutic approach. This review provides a comprehensive overview of PROTACs in cancer therapy, emphasizing their mechanism of action, advantages, and challenges. As PROTAC research progresses, continued exploration in both preclinical and clinical settings will be crucial to unlocking their full therapeutic potential and shaping the future of personalized cancer treatment.

9 September 2024 in AMB Express
Verified
Journal Article
Open access
PDF file
MKMuhammad Umer Khan
Muhammad Umer Khan
ASAzra Sakhawat
Azra Sakhawat
RRRaima Rehman
Raima Rehman
AWAbbas Haider Wali
Abbas Haider Wali
MGMuhammad Usman Ghani
Muhammad Usman Ghani
DADaoud Ali
Daoud Ali
Cystic fibrosis transmembrane conductance regulator (CFTR) protein is an ion channel found in numerous epithelia and controls the flow of water and salt across the epithelium. The aim of our study to find natural compounds that can improve lung function for people with cystic fibrosis (CF) caused by the p.Gly628Arg (rs397508316) mutation of CFTR protein. The sequence of CFTR protein as a target structure was retrieved from UniProt and PDB database. The ligands that included Armepavine, Osthole, Curcumin, Plumbagine, Quercetin, and one Trikafta (R*) reference drug were screened out from PubChem database. Autodock vina software carried out docking, and binding energies between the drug and the target were included using docking-score. The following tools examined binding energy, interaction, stability, toxicity, and visualize protein-ligand complexes. The compounds having binding energies of −6.4, −5.1, −6.6, −5.1, and − 6.5 kcal/mol for Armepavine, Osthole, Curcumin, Plumbagine, Quercetin, and R*-drug, respectively with mutated CFTR (Gly628Arg) structure were chosen as the most promising ligands. The ligands bind to the mutated CFTR protein structure active sites in hydrophobic bonds, hydrogen bonds, and electrostatic interactions. According to ADMET analyses, the ligands Armepavine and Quercetin also displayed good pharmacokinetic and toxicity characteristics. An MD simulation for 200 ns was also established to ensure that Armepavine and Quercetin ligands attached to the target protein favorably and dynamically, and that protein-ligand complex stability was maintained. It is concluded that Armepavine and Quercetin have stronger capacity to inhibit the effect of mutated CFTR protein through improved trafficking and restoration of original function.

19 November 2024 in Medical Oncology
Verified
Journal Article
Closed access
PDF file
IKIqra Khurram
Iqra Khurram
MKMuhammad Umer Khan
Muhammad Umer Khan
SISaooda Ibrahim
Saooda Ibrahim
Muhammad Usman GhaniMuhammad Usman Ghani
Muhammad Usman Ghani
IAIram Amin
Iram Amin
Daniela CalinaDaniela Calina
Daniela Calina