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Ahmed S, Nadeem M, Hussain I, Fatima S, Anwar S, Rizvi MA, Hassan MI, Tabish M. Preparation of nanoformulation of 5-fluorouracil to improve anticancer efficacy: integrated spectroscopic, docking, and MD simulation approaches. J Biomol Struct Dyn 2023:1-14. [PMID: 37850451 DOI: 10.1080/07391102.2023.2270704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/08/2023] [Indexed: 10/19/2023]
Abstract
Nanoformulations (NFs) can be used as a novel drug delivery system to treat all cancer types. One of the major drawbacks of conventional anticancer drugs is that they have poor specificity and higher toxicity towards normal cells. 5-fluorouracil (5-FU) is a well-studied anticancer drug that has a significant role in various cancers, specifically colorectal cancer therapy. This study was performed to determine the functional groups, particle size, surface charge, heterogeneity, and stability of the NF. The NFs of 5-FU were prepared through the ultrasonication technique by increasing the surfactant (Tween-80) concentrations. Among all three NFs, nanoformulated 5-FU (n5-FU) showed the most effective particle size (10.72 nm) with a zeta potential of (-4.57 mV). The cytotoxicity and apoptosis profiles confirmed that n5-FU enhanced the anticancer effect of the pure drug in HCT-116 cells, as evident from MTT assay, fluorescence microscopy, and FACS analysis. In HCT-116 cells, the IC50 values of pure and n5-FU were obtained as 41.3 μM and 18.8 μM, respectively, indicating that n5-FU was more effective against the cancer cell line. The cellular uptake study was performed to check the intake of NF in cancer cells. However, the microtubule-affinity regulating kinase-4 (MARK-4), a cancer-target protein, was purified to study the inhibition and interaction studies. The inhibition assay confirmed the inhibitory potential of 5-FU against MARK-4 protein. the multi-spectroscopic, molecular docking and MD simulation studies were performed to analyse the conformational changes, binding studies, intermolecular interactions, and stability of MARK-4 protein upon binding 5-FU. This demonstrates that NF can enhance the effectiveness of anticancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shahbaz Ahmed
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, UP, India
| | - Masood Nadeem
- Department of Biosciences, Jamia Milia Islamia, New Delhi, India
| | - Irfan Hussain
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, UP, India
| | - Sana Fatima
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, UP, India
| | - Saleha Anwar
- Center for Interdisciplinary Research in Basic Sciences, Jamia Milia Islamia, New Delhi, India
| | | | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Milia Islamia, New Delhi, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, UP, India
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Microtubule-affinity regulating kinase 4: A potential drug target for cancer therapy. Cell Signal 2022; 99:110434. [PMID: 35961526 DOI: 10.1016/j.cellsig.2022.110434] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 12/29/2022]
Abstract
The human genome encodes more than 500 protein kinases that work by transferring the γ-phosphate group from ATP to serine, threonine, or tyrosine (Ser/Thr/Tyr) residues. Various kinases are associated with the onset of cancer and its further progression. The recent advancements in developing small-molecule kinase inhibitors to treat different cancer types have shown noticeable results in clinical therapies. Microtubule-affinity regulating kinase 4 (MARK-4) is a Ser/Thr protein kinase that relates structurally to AMPK/Snf1 subfamily of the CaMK kinases. The protein kinase modulates major signalling pathways such as NF-κB, mTOR and the Hippo-signalling pathway. MARK4 is associated with various cancer types due to its important role in regulating microtubule dynamics and subsequent cell division. Aberrant expression of MARK4 is linked with several pathologies such as cancer, Alzheimer's disease, obesity, etc. This review provides detailed information on structural aspects of MARK4 and its role in various signalling pathways related to cancer. Several therapeutic molecules were designed to inhibit the MARK4 activity from controlling associated diseases. The review further highlights kinase-targeted drug discovery and development in oncology and cancer therapies. Finally, we summarize the latest findings regarding the role of MARK4 in cancer, diabetes, and neurodegenerative disease path to provide a solid rationale for future investigation and therapeutic intervention.
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Yousuf M, Shamsi A, Anjum F, Shafie A, Islam A, Haque QMR, Elasbali AM, Yadav DK, Hassan MI. Effect of pH on the structure and function of cyclin-dependent kinase 6. PLoS One 2022; 17:e0263693. [PMID: 35148332 PMCID: PMC8836317 DOI: 10.1371/journal.pone.0263693] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
Cyclin-dependent kinase 6 (CDK6) is an important protein kinase that regulates cell growth, development, cell metabolism, inflammation, and apoptosis. Its overexpression is associated with reprogramming glucose metabolism through alternative pathways and apoptosis, which ultimately plays a significant role in cancer development. In the present study, we have investigated the structural and conformational changes in CDK6 at varying pH employing a multi-spectroscopic approach. Circular dichroism (CD) spectroscopy revealed at extremely acidic conditions (pH 2.0–4.0), the secondary structure of CDK6 got significantly disrupted, leading to aggregates formation. These aggregates were further characterized by employing Thioflavin T (ThT) fluorescence. No significant secondary structural changes were observed over the alkaline pH range (pH 7.0–11.0). Further, fluorescence and UV spectroscopy revealed that the tertiary structure of CDK6 was disrupted under extremely acidic conditions, with slight alteration occurring in mild acidic conditions. The tertiary structure remains intact over the entire alkaline range. Additionally, enzyme assay provided an insight into the functional aspect of CDK at varying pH; CDK6 activity was optimal in the pH range of 7.0–8.0. This study will provide a platform that provides newer insights into the pH-dependent dynamics and functional behavior of CDK6 in different CDK6 directed diseased conditions, viz. different types of cancers where changes in pH contribute to cancer development.
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Affiliation(s)
- Mohd Yousuf
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | | | - Abdelbaset Mohamed Elasbali
- Clinical Laboratory Science, College of Applied Medical Sciences-Qurayyat, Jouf University, Sakaka, Saudi Arabia
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Incheon City, South Korea
- * E-mail: (DKY); (MIH)
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- * E-mail: (DKY); (MIH)
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Syed SB, Khan FI, Khan SH, Srivastava S, Hasan GM, Lobb KA, Islam A, Hassan MI, Ahmad F. Unravelling the unfolding mechanism of human integrin linked kinase by GdmCl-induced denaturation. Int J Biol Macromol 2018; 117:1252-1263. [PMID: 29885398 DOI: 10.1016/j.ijbiomac.2018.06.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/26/2018] [Accepted: 06/06/2018] [Indexed: 12/14/2022]
Abstract
Integrin-linked kinase (ILK) is a ubiquitously expressed Ser/Thr kinase which plays significant role in the cell-matrix interactions and growth factor signalling. In this study, guanidinium chloride (GdmCl)-induced unfolding of kinase domain of ILK (ILK193-446) was carried out at pH 7.5 and 25 °C. Eventually, denaturation curves of mean residue ellipticity at 222 nm ([θ]222) and fluorescence emission spectrum were analysed to estimate stability parameters. The optical properties maximum emission (λmax) and difference absorption coefficient at 292 nm (Δε292) were analysed. The denaturation curve was measured only in the GdmCl molar concentration ranging 3.0-4.2 M because protein was aggregating below 3.0 M of GdmCl concentrations. The denaturation process of ILK193-446 was found as reversible at [GdmCl] ≥ 3.0 M. Moreover, a coincidence of normalized denaturation curves of optical properties ([θ]222, Δε292 and λmax) suggesting that GdmCl-induced denaturation of ILK193-446 is a two-state process. In addition, 100 ns molecular dynamics simulations were performed to see the effects of GdmCl on the structure and stability of ILK193-446. Both the spectroscopic and molecular dynamics approaches provided clear insights into the stability and conformational properties of ILK193-446.
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Affiliation(s)
- Sunayana Begum Syed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faez Iqbal Khan
- Computational Mechanistic Chemistry and Drug Discovery, Rhodes University, South Africa
| | - Sabab Hasan Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Saurabha Srivastava
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Kevin A Lobb
- Computational Mechanistic Chemistry and Drug Discovery, Rhodes University, South Africa
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
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Idrees D, Rahman S, Shahbaaz M, Haque MA, Islam A, Ahmad F, Hassan MI. Estimation of thermodynamic stability of human carbonic anhydrase IX from urea-induced denaturation and MD simulation studies. Int J Biol Macromol 2017; 105:183-189. [DOI: 10.1016/j.ijbiomac.2017.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/01/2017] [Accepted: 07/03/2017] [Indexed: 12/20/2022]
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Shahbaaz M, Amir M, Rahman S, Mustafa Hasan G, Dohare R, Bisetty K, Ahmad F, Kim J, Hassan MI. Structural insights into Rab21 GTPase activation mechanism by molecular dynamics simulations. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1357813] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mohd. Shahbaaz
- Department of Chemistry, Durban University of Technology, Durban, South Africa
| | - Mohd. Amir
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Ravins Dohare
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, Durban, South Africa
| | - Faizan Ahmad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Jihoe Kim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Md. Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Naz H, Khan P, Tarique M, Rahman S, Meena A, Ahamad S, Luqman S, Islam A, Ahmad F, Hassan MI. Binding studies and biological evaluation of β-carotene as a potential inhibitor of human calcium/calmodulin-dependent protein kinase IV. Int J Biol Macromol 2016; 96:161-170. [PMID: 27956097 DOI: 10.1016/j.ijbiomac.2016.12.024] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/02/2016] [Accepted: 12/04/2016] [Indexed: 12/27/2022]
Abstract
Human calcium/calmodulin-dependent protein kinase IV (CAMKIV), a member of Ser/Thr kinase family, is associated with cancer, cerebral hypoxia and neurodegenerative diseases. β-carotene is a colored organic compound, abundant in plants and fruits and is used in cancer prevention. Here, we report a strong binding affinity of β-carotene with CAMKIV using molecular docking, fluorescence binding and isothermal titration calorimetry methods. Furthermore, β-carotene also reduces the enzyme activity of CAMKIV moderately as observed during ATPase assay. To see the role of β-carotene on cell proliferation and apoptosis, cancerous cells (HeLa, HuH7and MCF-7) and normal (HEK-293-T) cell lines were used. Admirable anticancer activity of β-carotene was observed. We further performed propidium iodide and DAPI (4',6-diamidino-2-phenylindole) assays to understand the mechanism of anticancer activity of β-carotene at molecular level. Our findings provide a newer insight into the use of β-carotene in cancer prevention and protection via inhibition of CAMKIV by regulating the signaling pathways.
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Affiliation(s)
- Huma Naz
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Parvez Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Mohd Tarique
- Department of Biochemistry, All India Institute of Medical Sciences, AIIMS, New Delhi, 110029, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Abha Meena
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Shahzaib Ahamad
- Department of Biotechnology, College of Engineering & Technology, IFTM University, Lodhipur-Rajput, Delhi Road, Moradabad, India
| | - Suaib Luqman
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
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8
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Naz F, Sami N, Islam A, Ahmad F, Hassan MI. Ubiquitin-associated domain of MARK4 provides stability at physiological pH. Int J Biol Macromol 2016; 93:1147-1154. [DOI: 10.1016/j.ijbiomac.2016.09.087] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 01/08/2023]
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9
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Naz F, Sami N, Naqvi AT, Islam A, Ahmad F, Imtaiyaz Hassan M. Evaluation of human microtubule affinity-regulating kinase 4 inhibitors: fluorescence binding studies, enzyme, and cell assays. J Biomol Struct Dyn 2016; 35:3194-3203. [PMID: 27748164 DOI: 10.1080/07391102.2016.1249958] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Human microtubule affinity-regulating kinase 4 (MARK4) is considered as an encouraging drug target for the design and development of inhibitors to cure several life-threatening diseases such as Alzheimer disease, cancer, obesity, and type-II diabetes. Recently, we have reported four ligands namely, BX-912, BX-795, PKR-inhibitor, and OTSSP167 (hydrochloride) which bind preferentially to the two different constructs of human MARK4 containing kinase domain. To ensure the role of ubiquitin-associated (UBA) domain in the ligand binding, we made a newer construct of MARK4 which contains both kinase and UBA domains, named as MARK4-F3. We observed that OTSSP167 (hydrochloride) binds to the MARK4-F3 with a binding constant (K) of 3.16 × 106, M-1 (±.21). However, UBA-domain of MARK4-F3 doesn't show any interaction with ligands directly as predicted by the molecular docking. To validate further, ATPase inhibition assays of all three constructs of MARK4 in the presence of mentioned ligands were carried out. An appreciable correlation between the binding experiments and ATPase inhibition assays of MARK4 was observed. In addition, cell-proliferation inhibition activity for all four ligands on the Human embryonic kidney (HEK-293) and breast cancer cell lines (MCF-7) was performed using MTT assay. IC50 values of OTSSP167 for HEK-293 and MCF-7 were found to be 58.88 (±1.5), and 48.2 (±1.6), respectively. OTSSP167 among all four inhibitors, showed very good enzyme inhibition activity against three constructs of MARK4. Moreover, all four inhibitors showed anti-neuroblastoma activity and anticancer properties. In conclusion, OTSSP167 may be considered as a promising scaffold to discover novel inhibitors of MARK4.
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Affiliation(s)
- Farha Naz
- a Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Neha Sami
- a Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Abu Turab Naqvi
- a Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Asimul Islam
- a Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Faizan Ahmad
- a Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Md Imtaiyaz Hassan
- a Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
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Naz F, Shahbaaz M, Bisetty K, Islam A, Ahmad F, Hassan MI. Designing New Kinase Inhibitor Derivatives as Therapeutics Against Common Complex Diseases: Structural Basis of Microtubule Affinity-Regulating Kinase 4 (MARK4) Inhibition. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:700-11. [PMID: 26565604 DOI: 10.1089/omi.2015.0111] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Drug development for common complex diseases is in need of new molecular entities and actionable drug targets. MAP/microtubule affinity-regulating kinase 4 (MARK4) is associated with numerous diseases such as neurodegenerative disorders, obesity, cancer, and type 2 diabetes. Understanding the structural basis of ligands' (inhibitors) and substrates' binding to MARK4 is crucial to design new kinase inhibitors for therapeutic purposes. This study reports new observations on docking three well-known kinase inhibitors in the kinase domain of MARK4 variants and the calculated binding affinity. These variants of MARK4 are named as MARK4-F1 (59 N-terminal residues along with kinase domain) and MARK4-F2 (kinase domain of MARK4). We additionally performed molecular dynamics (MD) simulation and fluorescence binding studies to calculate the actual binding affinity of kinase inhibitors, BX-912, BX-795, and OTSSP167 (hydrochloride) for the MARK4. Docking analyses revealed that ligands bind in the large hydrophobic cavity of the kinase domain of MARK4 through several hydrophobic and hydrogen-bonded interactions. Simulations suggested that OTSSP167 (hydrochloride) is forming a stable complex, and hence the best inhibitor of MARK4. Intrinsic fluorescence of MARK4 was significantly quenched by addition of ligands, indicating their potential binding to MARK4. A lower KD value of MARK4 with OTSSP167 (hydrochloride) suggested that it is a better interacting partner than BX-912 and BX-795. These data form a basis for designing novel and potent OTSSP167 (hydrochloride) derivatives as therapeutic candidates against common complex diseases. The inhibitors designed as such might possibly suppress the growth of tumor-forming cells and be potentially applied for treatment of a wide range of human cancers as well.
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Affiliation(s)
- Farha Naz
- 1 Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Mohd Shahbaaz
- 2 Department of Chemistry, Durban University of Technology , Durban, South Africa
| | - Krishna Bisetty
- 2 Department of Chemistry, Durban University of Technology , Durban, South Africa
| | - Asimul Islam
- 1 Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Faizan Ahmad
- 1 Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Md Imtaiyaz Hassan
- 1 Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia, Jamia Nagar, New Delhi, India
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Khan FI, Bisetty K, Singh S, Permaul K, Hassan MI. Chitinase from Thermomyces lanuginosus SSBP and its biotechnological applications. Extremophiles 2016; 19:1055-66. [PMID: 26462798 DOI: 10.1007/s00792-015-0792-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/03/2015] [Indexed: 12/30/2022]
Abstract
Chitinases are ubiquitous class of extracellular enzymes, which have gained attention in the past few years due to their wide biotechnological applications. The effectiveness of conventional insecticides is increasingly compromised by the occurrence of resistance; thus, chitinase offers a potential alternative to the use of chemical fungicides. The thermostable enzymes from thermophilic microorganisms have numerous industrial, medical, environmental and biotechnological applications due to their high stability for temperature and pH. Thermomyces lanuginosus produced a large number of chitinases, of which chitinase I and II are successfully cloned and purified recently. Molecular dynamic simulations revealed that the stability of these enzymes are maintained even at higher temperature. In this review article we have focused on chitinases from different sources, mainly fungal chitinase of T. lanuginosus and its industrial application.
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Prakash A, Idrees D, Haque MA, Islam A, Ahmad F, Hassan MI. GdmCl-induced unfolding studies of human carbonic anhydrase IX: a combined spectroscopic and MD simulation approach. J Biomol Struct Dyn 2016; 35:1295-1306. [PMID: 27092977 DOI: 10.1080/07391102.2016.1179596] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Carbonic anhydrase IX (CAIX) is a transmembrane glycoprotein, associated with tumor, acidification which leads to the cancer, and is considered as a potential biomarker for hypoxia-induced cancers. The overexpression of CAIX is linked with hypoxia condition which is mediated by the transcription of hypoxia-induced factor (HIF-1). To understand the biophysical properties of CAIX, we have carried out a reversible isothermal denaturation of CAIX-induced by GdmCl at pH 8.0 and 25°C. Three different spectroscopic probes, the far-UV CD at 222 nm ([θ]222), Trp fluorescence emission at 342 nm (F342) and difference molar absorption coefficient at 287 nm (Δε287) were used to estimate stability parameters, [Formula: see text] (Gibbs free energy change in the absence of GdmCl; Cm (midpoint of the denaturation curve), i.e. molar GdmCl concentration ([GdmCl]) at which ΔGD = 0; and m, the slope (=∂ΔGD/∂[GdmCl])). GdmCl induces a reversible denaturation of CAIX. Coincidence of the normalized transition curves of all optical properties suggests that unfolding/refolding of CAIX is a two-state process. We further performed molecular dynamics simulation of CAIX for 40 ns to see the dynamics of protein structure in different GdmCl concentrations. An excellent agreement was observed between in silico and in vitro studies.
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Affiliation(s)
- Amresh Prakash
- a Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Danish Idrees
- a Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Md Anzarul Haque
- a Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Asimul Islam
- a Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Faizan Ahmad
- a Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Md Imtaiyaz Hassan
- a Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
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Khan FI, Aamir M, Wei DQ, Ahmad F, Hassan MI. Molecular mechanism of Ras-related protein Rab-5A and effect of mutations in the catalytically active phosphate-binding loop. J Biomol Struct Dyn 2016; 35:105-118. [PMID: 26727234 DOI: 10.1080/07391102.2015.1134346] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Ras-related protein (Rab-5a) is primarily involved in the regulation of early endosome fusion during endocytosis and takes part in the budding process. During GTP hydrolysis, Rab5a was spotted in the cytoplasmic side of early endosomes in association with the GTP. Previous study suggested that the substitution of alanine with proline at position 30 of Rab5a reduces the GTPase activity around 12-fold, while, with arginine substitution stimulates the intrinsic GTP hydrolysis by 5-fold. Most of the other substitutions at this position show a little or no effect on the GTPase activity. In this paper, structure analysis and molecular dynamics (MD) simulation studies of human Rab5a and its mutants have been extensively carried out. The effect of binding of a non-hydrolyzable GTP analog guanosine-5'-(β, γ)-imidotriphosphate (GppNHp) with Rab5a and its mutants are described. The objective of the current study is to perform a detailed examination of structural flexibility of Rab5a and its mutants p.Ala30Pro and p.Ala30Arg using MD simulations. Our observations suggest that mutant p.Ala30Arg stabilize the protein molecule when bound to GppNHp which offers additional contacts. Despite an in silico approach, this study provides a deep insight into the impact of mutation on the structure, function, stability, and mechanism of binding of GppNHp to the Rab5a at molecular level.
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Affiliation(s)
- Faez Iqbal Khan
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Henan 450001 , China
| | - Mohd Aamir
- b Centre for Interdisciplinary Research in Basic Science , Jamia Millia Islamia , New Delhi 110025 , India
| | - Dong-Qing Wei
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Henan 450001 , China
| | - Faizan Ahmad
- b Centre for Interdisciplinary Research in Basic Science , Jamia Millia Islamia , New Delhi 110025 , India
| | - Md Imtaiyaz Hassan
- b Centre for Interdisciplinary Research in Basic Science , Jamia Millia Islamia , New Delhi 110025 , India
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14
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Idrees D, Shahbaaz M, Bisetty K, Islam A, Ahmad F, Hassan MI. Effect of pH on structure, function, and stability of mitochondrial carbonic anhydrase VA. J Biomol Struct Dyn 2016; 35:449-461. [PMID: 26828699 DOI: 10.1080/07391102.2016.1149097] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Mitochondrial carbonic anhydrase VA (CAVA) catalyzes the hydration of carbon dioxide to produce proton and bicarbonate which is primarily expressed in the mitochondrial matrix of liver, and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis, and neuronal transmission. To understand the effect of pH on the structure, function, and stability of CAVA, we employed spectroscopic techniques such as circular dichroism, fluorescence, and absorbance measurements in wide range of pH (from pH 2.0 to pH 11.5). CAVA showed an aggregation at acidic pH range from pH 2.0 to pH 5.0. However, it remains stable and maintains its secondary structure in the pH range, pH 7.0-pH 11.5. Furthermore, this enzyme has an appreciable activity at more than pH 7.0 (7.0 < pH ≤ 11.5) with maximum activity at pH 9.0. The maximal values of kcat and kcat/Km at pH 9.0 are 3.7 × 106 s-1 and 5.5 × 107 M-1 s-1, respectively. However, this enzyme loses its activity in the acidic pH range. We further performed 20-ns molecular dynamics simulation of CAVA to see the dynamics at different pH values. An excellent agreement was observed between in silico and in vitro studies. This study provides an insight into the activity of CAVA in the pH range of subcellular environment.
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Affiliation(s)
- Danish Idrees
- a Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia, Jamia Nagar, New Delhi 110025 , India
| | - Mohd Shahbaaz
- b Department of Chemistry , Durban University of Technology , Durban 4000 , South Africa
| | - Krishna Bisetty
- b Department of Chemistry , Durban University of Technology , Durban 4000 , South Africa
| | - Asimul Islam
- a Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia, Jamia Nagar, New Delhi 110025 , India
| | - Faizan Ahmad
- a Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia, Jamia Nagar, New Delhi 110025 , India
| | - Md Imtaiyaz Hassan
- a Center for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia, Jamia Nagar, New Delhi 110025 , India
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15
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Idrees D, Prakash A, Haque MA, Islam A, Ahmad F, Hassan MI. Spectroscopic and MD simulation studies on unfolding processes of mitochondrial carbonic anhydrase VA induced by urea. J Biomol Struct Dyn 2016; 34:1987-97. [PMID: 26421381 DOI: 10.1080/07391102.2015.1100552] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Carbonic anhydrase VA (CAVA) is primarily expressed in the mitochondria and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis and neuronal transmission. To understand the biophysical properties of CAVA, we carried out a reversible urea-induced isothermal denaturation at pH 7.0 and 25°C. Spectroscopic probes, [θ]222 (mean residue ellipticity at 222 nm), F344 (Trp-fluorescence emission intensity at 344 nm) and Δε280 (difference absorption at 280 nm) were used to monitor the effect of urea on the structure and stability of CAVA. The urea-induced reversible denaturation curves were used to estimate [Formula: see text], Gibbs free energy in the absence of urea; Cm, the mid-point of the denaturation curve, i.e. molar urea concentration ([urea]) at which ΔGD = 0; and m, the slope (=∂ΔGD/∂[urea]). Coincidence of normalized transition curves of all optical properties suggests that unfolding/refolding of CAVA is a two-state process. We further performed 40 ns molecular dynamics simulation of CAVA to see the dynamics at different urea concentrations. An excellent agreement was observed between in silico and in vitro studies.
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Affiliation(s)
- Danish Idrees
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Amresh Prakash
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Md Anzarul Haque
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Asimul Islam
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Faizan Ahmad
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Md Imtaiyaz Hassan
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
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Naz F, Islam A, Ahmad F, Hassan MI. Atypical PKC phosphorylates microtubule affinity-regulating kinase 4 in vitro. Mol Cell Biochem 2015; 410:223-8. [PMID: 26346160 DOI: 10.1007/s11010-015-2555-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/03/2015] [Indexed: 01/28/2023]
Abstract
MAP/Microtubule affinity-regulating kinase 4 (MARK4), a Ser/Thr protein kinases, is related to the Par-1 (partitioning-defective) gene products, and is the human ortholog of Par-1. MARK4 shows its role in the cell polarity at the time of embryonic development. It is mostly located at the basal region of cells, providing apico-basal polarity. Here, we made two variants of human Par-1d (MARK4), kinase domain (MARK4-F2), and kinase domain along with 59 N-terminal residues (MARK4-F1) and saw their ATPase hydrolysis in the presence of each other. We observed that the activity of one variant was increased in the presence of other. We also demonstrated that both variants were phosphorylated by atypical PKC and their activities were increased in the presence of increasing concentration of atypical protein kinase c (aPKC). The phosphorylation was observed at the serine and threonine residues of MARK4. The interaction of MARK2 and MARK3 with aPKC and their negative regulation by aPKC is already known. This study confirms a functional link between aPKC and MARK4, two central determinants of cell polarity, and it suggests that aPKC may regulate all four members of Par-1 through phosphorylating them in polarized cells.
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Affiliation(s)
- Farha Naz
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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