1
|
Rabbani G, Ahmad A, Zamzami MA, Baothman OA, Hosawi SA, Altayeb H, Shahid Nadeem M, Ahmad V. Fabrication of an affordable and sensitive corticosteroid-binding globulin immunosensor based on electrodeposited gold nanoparticles modified glassy carbon electrode. Bioelectrochemistry 2024; 157:108671. [PMID: 38401223 DOI: 10.1016/j.bioelechem.2024.108671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/09/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
Herein, we fabricated an ultrasensitive electrochemical immunosensor for the quantitative detection of corticosteroid-binding globulin (CBG). CBG is a protein that regulates glucocorticoid levels and is an important biomarker for inflammation. A decrease in CBG levels is a key biomarker for inflammatory diseases, such as septic shock. To enhance the electrochemical performance and provide a large surface area for anti-CBG immobilization, we functionalized the glassy carbon electrode surface with AuNPs. Electrochemical characterization methods including cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were used to examine the construction of the fabricated immunosensor. The electrochemical signal demonstrated a remarkable sensitivity to the CBG antigen, with a detection range from 0.01 to 100 μg/mL and a limit of detection of 0.012 μg/mL, making it suitable for both clinical and research applications. This label-free immunosensor offers significant advantages, including high sensitivity, low detection limits and excellent selectivity, making it a promising tool for detecting CBG in complex biological samples. Its potential applications include early disease diagnosis, treatment monitoring and studying CBG-related physiological processes.
Collapse
Affiliation(s)
- Gulam Rabbani
- IT-medical Fusion Center, 350-27 Gumidae-ro, Gumi-si, Gyeongbuk 39253, Republic of Korea.
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21452, Saudi Arabia.
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21452, Saudi Arabia
| | - Othman A Baothman
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21452, Saudi Arabia
| | - Salman A Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21452, Saudi Arabia
| | - Hisham Altayeb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21452, Saudi Arabia
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21452, Saudi Arabia
| | - Varish Ahmad
- Department of Health Information Technology, Faculty of Applied Studies, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| |
Collapse
|
2
|
Ahmad I, Singh AK, Mohd S, Katari SK, Nalamolu RM, Ahmad A, Baothman OA, Hosawi SA, Altayeb H, Nadeem MS, Ahmad V. In Silico Insights into the Arsenic Binding Mechanism Deploying Application of Computational Biology-Based Toolsets. ACS Omega 2024; 9:7529-7544. [PMID: 38405466 PMCID: PMC10882604 DOI: 10.1021/acsomega.3c06313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/27/2024]
Abstract
An assortment of environmental matrices includes arsenic (As) in its different oxidation states, which is often linked to concerns that pose a threat to public health worldwide. The current difficulty lies in addressing toxicological concerns and achieving sustained detoxification of As. Multiple conventional degradation methods are accessible; however, they are indeed labor-intensive, expensive, and reliant on prolonged laboratory evaluations. Molecular interaction and atomic level degradation mechanisms for enzyme-As exploration are, however, underexplored in those approaches. A feasible approach in this case for tackling this accompanying concern of As might be to cope with undertaking multivalent computational methodologies and tools. This work aimed to provide molecular-level insight into the enzyme-aided As degradation mechanism. AutoDock Vina, CABS-flex 2.0, and Desmond high-performance molecular dynamics simulation (MDS) were utilized in the current investigation to simulate multivalent molecular processes on two protein sets: arsenate reductase (ArsC) and laccase (LAC) corresponding arsenate (ART) and arsenite (AST), which served as model ligands to comprehend binding, conformational, and energy attributes. The structural configurations of both proteins exhibited variability in flexibility and structure framework within the range of 3.5-4.5 Å. The LAC-ART complex exhibited the lowest calculated binding affinity, measuring -5.82 ± 0.01 kcal/mol. Meanwhile, active site residues ILE-200 and HIS-206 were demonstrated to engage in H-bonding with the ART ligand. In contrast to ArsC, the ligand binding affinity of this bound complex was considerably greater. Additional validation of docked complexes was carried out by deploying Desmond MDS of 100 ns to capture protein and ligand conformation behavior. The system achieved stability during the 100 ns simulation run, as confirmed by the average P-L RMSD, which was ∼1 Å. As a preliminary test of the enzyme's ability to catalyze As species, corresponding computational insights might be advantageous for bridging gaps and regulatory consideration.
Collapse
Affiliation(s)
- Imran Ahmad
- Department
of Biochemistry, King George’s Medical
University, Lucknow, Uttar Pradesh 226003, India
- Environmental
Toxicology Group, CSIR-Indian Institute
of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anil Kumar Singh
- Environmental
Toxicology Group, CSIR-Indian Institute
of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shayan Mohd
- Department
of Bioengineering, Faculty of Engineering, Integral University, Dasauli, Kursi Road, Lucknow 226026, India
| | - Sudheer Kumar Katari
- Department
of Biotechnology, Vignan’s Foundation
for Science, Technology & Research, Vadlamudi, Andhra Pradesh 522213, India
| | - Ravina Madhulitha Nalamolu
- Department
of Biotechnology, Vignan’s Foundation
for Science, Technology & Research, Vadlamudi, Andhra Pradesh 522213, India
| | - Abrar Ahmad
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Othman A. Baothman
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Salman A. Hosawi
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Hisham Altayeb
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Muhammad Shahid Nadeem
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Varish Ahmad
- Department
of Health Information Technology, Faculty of Applied Studies, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
| |
Collapse
|
3
|
Alam MM, Alsenani NI, Abdelhamid AA, Ahmad A, Baothman OA, Hosawi SA, Altayeb H, Nadeem MS, Ahmad V, Nazreen S, Elhenawy AA. New paracetamol hybrids as anticancer and COX-2 inhibitors: Synthesis, biological evaluation and docking studies. Arch Pharm (Weinheim) 2024; 357:e2300340. [PMID: 37880869 DOI: 10.1002/ardp.202300340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/31/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023]
Abstract
Drug repurposing is an emerging field in drug development that has provided many successful drugs. In the current study, paracetamol, a known antipyretic and analgesic agent, was chemically modified to generate paracetamol derivatives as anticancer and anticyclooxygenase-2 (COX-2) agents. Compound 11 bearing a fluoro group was the best cytotoxic candidate with half-maximal inhibitory concentration (IC50 ) values ranging from 1.51 to 6.31 μM and anti-COX-2 activity with IC50 = 0.29 μM, compared to the standard drugs, doxorubicin and celecoxib. The cell cycle and apoptosis studies revealed that compound 11 possesses the ability to induce cell cycle arrest in the S phase and apoptosis in colon Huh-7 cells. These results were strongly supported by docking studies, which showed strong interactions with the amino acids of the COX-2 protein, and in silico pharmacokinetic predictions were found to be favorable for these newly synthesized paracetamol derivatives. It can be concluded that compound 11 could block cell growth and proliferation by inhibiting the COX-2 enzyme in cancer therapy.
Collapse
Affiliation(s)
- Mohammad Mahboob Alam
- Department of Chemistry, Faculty of Science, Al-Baha University, Al-Baha, Kingdom of Saudi Arabia
| | - Nawaf I Alsenani
- Department of Chemistry, Faculty of Science, Al-Baha University, Al-Baha, Kingdom of Saudi Arabia
| | - Antar A Abdelhamid
- Department of Chemistry, Faculty of Science, Al-Baha University, Al-Baha, Kingdom of Saudi Arabia
- Department of Chemistry, Faculty of Science, Sohag University, Sohag, Egypt
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Othman A Baothman
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Salman A Hosawi
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hisham Altayeb
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohammad Shahid Nadeem
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Varish Ahmad
- Department of Health Information Technology, Faculty of Applied Studies, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Syed Nazreen
- Department of Chemistry, Faculty of Science, Al-Baha University, Al-Baha, Kingdom of Saudi Arabia
| | - Ahmed A Elhenawy
- Department of Chemistry, Faculty of Science, Al-Baha University, Al-Baha, Kingdom of Saudi Arabia
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| |
Collapse
|
4
|
Kashif M, Kumar B, Bharati AP, Altayeb H, Asalam M, Akhtar MS, Khan MI, Ahmad A, Chaudhary H, Hosawi SB, Zamzami MA, Baothman OA. Association of peptidyl prolyl cis/trans isomerase Rrd1 with C terminal domain of RNA polymerase II. Int J Biol Macromol 2023; 242:124653. [PMID: 37141964 DOI: 10.1016/j.ijbiomac.2023.124653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 04/16/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023]
Abstract
The largest subunit of RNAPII extends as the conserved unstructured heptapeptide consensus repeats Y1S2P3T4S5P6S7 and their posttranslational modification, especially the phosphorylation state at Ser2, Ser5 and Ser7 of CTD recruits different transcription factors involved in transcription. In the current study, fluorescence anisotropy, pull down assay and molecular dynamics simulation studies employed to conclude that peptidyl-prolyl cis/trans-isomerase Rrd1 has strong affinity for unphosphorylated CTD rather than phosphorylated CTD for mRNA transcription. Rrd1 preferentially interacts with unphosphorylated GST-CTD in comparison to hyperphosphorylated GST-CTD in vitro. Fluorescence anisotropy revealed that recombinant Rrd1 prefers to bind unphosphorylated CTD peptide in comparison to phosphorylated CTD peptide. In computational studies, the RMSD of Rrd1-unphosphorylated CTD complex was greater than the RMSD of Rrd1-pCTD complex. During 50 ns MD simulation run Rrd1-pCTD complex get dissociated twice viz. 20 ns to 30 ns and 40 ns to 50 ns, while Rrd1-unpCTD complex remain stable throughout the process. Additionally, the Rrd1-unphosphorylated CTD complexes acquire comparatively higher number of H-bonds, water bridges and hydrophobic interactions occupancy than Rrd1-pCTD complex, concludes that the Rrd1 interacts more strongly with the unphosphorylated CTD than the pCTD.
Collapse
Affiliation(s)
- Mohd Kashif
- Department of Biotech, Babasaheb Bhimrao Ambedkar University, Lucknow, India.
| | - Bhupendra Kumar
- Center for Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, U.P., India
| | - Akhilendra Pratap Bharati
- Department Of Life Sciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, India.
| | - Hisham Altayeb
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Mohd Asalam
- CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Mohd Sohail Akhtar
- CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India.
| | - Mohammad Imran Khan
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Hani Chaudhary
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Salman Bakr Hosawi
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Othman A Baothman
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| |
Collapse
|
5
|
Anwar F, Altayeb H, Alhayyani S, Kumar V, Al-Abbasi FA, Ashraf GM. Analysis of Interaction Between Odorant Receptors and Flexible Spike of SARS CoV-2- Key to Loss of Smell. Curr Neuropharmacol 2023; 21:151-159. [PMID: 35761501 PMCID: PMC10193757 DOI: 10.2174/1570159x20666220627165846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/06/2022] [Accepted: 06/13/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The development of a vaccine for SARS-CoV-2 is primarily focused on the structure of the spike (S) protein. The heavy glycosylation of S with flexible hinges at the stalk shields from antibody attachment. OBJECTIVE This study deciphers the flexible nature of hinges responsible for binding the odorant receptor on neurons responsible for the loss of smell in COVID-19 patients. METHODS The 3D structure via EPIK in Maestro, protein docking with ligands via Maestro protein analysis tool, and molecular dynamic simulation at 30 ns run using DESMOND was prepared. RESULTS The data of the study strongly suggest that strong and stable bond formation results from the reaction between R:14: Trp and Phe at the residue, targeting the flexible hinges of SARS-CoV-2. The difference in the conformational structure of the S protein and its binding with the odorant receptor in COVID-19 is the prime factor for the loss of smell and taste in patients, as supported by the concept of Antigen (epitope) Antibody interaction by the stable formation of a hydrogen bond among odorant receptor and the S protein. The flexibility of structural proteins determines the binding potential of antibodies or other defense proteins produced to participate in the antigen-antibody reaction. CONCLUSION Molecular and atomic details potentiate the design and screening of small molecules that can inhibit the fusion at entry level or odorant receptors and potentially be used in the prevention and treatment of infection, particularly when formulated as nasal drops, paving a new approach for pharmacologists in the treatment of COVID-19 infection.
Collapse
Affiliation(s)
- Firoz Anwar
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hisham Altayeb
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Sultan Alhayyani
- Department of Chemistry, College of Sciences & Arts, King Abdulaziz University, Rabigh King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Vikas Kumar
- Department of Pharmaceutical Sciences, Natural Product Discovery Laboratory, Shalom Institute of Health and Allied Sciences. SHUATS, Naini, Prayagraj, India
| | - Fahad A Al-Abbasi
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| |
Collapse
|