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Nasreen K, Parray ZA, Shamsi A, Ahmad F, Ahmed A, Malik A, Lakhrm NA, Hassan MI, Islam A. Crowding Milleu stabilizes apo-myoglobin against chemical-induced denaturation: Dominance of hardcore repulsions in the heme devoid protein. Int J Biol Macromol 2021; 181:552-560. [PMID: 33744250 DOI: 10.1016/j.ijbiomac.2021.03.089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/27/2022]
Abstract
Macromolecular crowding can have significant consequences on the structure and dynamics of a protein. The size and shape of a co-solute molecule and the nature of protein contribute significantly in macromolecular crowding, which results in different outcomes in similar conditions. The structure of apo-myoglobin (apo-Mb) both in the absence and presence of denaturants (GdmCl and urea) was investigated in crowded conditions at pH 7.0, with a comparable size of crowders (~70 kDa) but of different shapes (ficoll and dextran) at various concentrations using spectroscopic techniques like absorption and circular dichroism to monitor changes in secondary and tertiary structure, respectively. The crowders in the absence of denaturants showed structural stabilization of the tertiary structure while no significant change in the secondary structure was observed. The effect of crowders on the stability of the protein was also investigated using probes such as Δε291 and θ222 using chemical denaturants. The analysis of chemical-induced denaturation curves showed that both the crowders stabilize apo-Mb by increasing the values of the midpoint of transition (Cm) and change in free energy in the absence of denaturant (∆GD°), and it was observed that dextran 70 shows more stabilization than ficoll 70 under similar conditions. In this study apo-Mb showed stabilization under crowded conditions, which is a deviation from earlier work from our group where holo form of the same protein was destabilized. This study emphasizes that volume exclusion is a dominant force in a simple protein while soft interactions may play important role in the proteins that are possessing prosthetic group. Hence, the effect of crowders is protein-dependent, and excluded volume plays a great role in the stabilization of apo-Mb, which does not interact with the crowders.
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Affiliation(s)
- Khalida Nasreen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anas Shamsi
- 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
| | - Anwar Ahmed
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ajamaluddin Malik
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nasser Abobakr Lakhrm
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Md Imtaiyaz Hassan
- 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.
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102
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Ahanger IA, Bashir S, Parray ZA, Alajmi MF, Hussain A, Ahmad F, Hassan MI, Islam A, Sharma A. Rationalizing the Role of Monosodium Glutamate in the Protein Aggregation Through Biophysical Approaches: Potential Impact on Neurodegeneration. Front Neurosci 2021; 15:636454. [PMID: 33746704 PMCID: PMC7969894 DOI: 10.3389/fnins.2021.636454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/29/2021] [Indexed: 11/13/2022] Open
Abstract
Monosodium glutamate (MSG) is the world’s most extensively used food additive and is generally recognized as safe according to the FDA. However, it is well reported that MSG is associated with a number of neurological diseases, and in turn, neurological diseases are associated with protein aggregation. This study rationalized the role of MSG in protein aggregation using different biophysical techniques such as absorption, far-UV CD, DLS, and ITC. Kinetic measurements revealed that MSG causes significant enhancement of aggregation of BSA through a nucleation-dependent polymerization mechanism. Also, CTAB-BSA aggregation is enhanced by MSG significantly. MSG-induced BSA aggregation also exhibits the formation of irreversible aggregates, temperature dependence, non-Arrhenius behavior, and enhancement of hydrodynamic diameter. From the isothermal titration calorimetry measurement, the significant endothermic heat of the interaction of BSA-MSG indicates that protein aggregation may be due to the coupling of MSG with the protein. The determined enthalpy change (ΔH) is largely positive, also suggesting an endothermic nature, whereas entropy change (ΔS) is positive and Gibbs free energy change (ΔG) is largely negative, suggesting the spontaneous nature of the interaction. Furthermore, even a low concentration of MSG is involved in the unfolding of the secondary structure of protein with the disappearance of original peaks and the formation of a unique peak in the far-UV CD, which is an attention-grabbing observation. This is the first investigation which links the dietary MSG with protein aggregation and thus will be very instrumental in understanding the mechanism of various MSG-related human physiological as well as neurological diseases.
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Affiliation(s)
- Ishfaq Ahmad Ahanger
- Department of Chemistry, Biochemistry and Forensic Science, Amity School of Applied Sciences, Amity University Haryana, Gurgaon, India.,Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Sania Bashir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anurag Sharma
- Department of Chemistry, Biochemistry and Forensic Science, Amity School of Applied Sciences, Amity University Haryana, Gurgaon, India
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103
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Patel K, Gooley TA, Bailey N, Bailey M, Hegerova L, Batchelder A, Holdread H, Dunleavy V, Downey T, Frisvold J, Megrath S, Pagarigan K, Szeto J, Rueda J, Islam A, Maree C, Nyatsatsang S, Bork SE, Lipke A, O'Mahony DS, Wagner T, Pulido J, Mignone J, Youssef S, Hartman M, Goldman JD, Pagel JM. Use of the IL-6R antagonist tocilizumab in hospitalized COVID-19 patients. J Intern Med 2021; 289:430-433. [PMID: 32745348 PMCID: PMC7436582 DOI: 10.1111/joim.13163] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 01/10/2023]
Affiliation(s)
- K Patel
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - T A Gooley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - N Bailey
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - M Bailey
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - L Hegerova
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - A Batchelder
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - H Holdread
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - V Dunleavy
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - T Downey
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - J Frisvold
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - S Megrath
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - K Pagarigan
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - J Szeto
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
| | - J Rueda
- Infectious Disease, Swedish Medical Center, Seattle, WA, USA
| | - A Islam
- Infectious Disease, Swedish Medical Center, Seattle, WA, USA
| | - C Maree
- Infectious Disease, Swedish Medical Center, Seattle, WA, USA
| | - S Nyatsatsang
- Infectious Disease, Swedish Medical Center, Seattle, WA, USA
| | - S E Bork
- Hospital Medicine, Swedish Medical Center, Seattle, WA, USA
| | - A Lipke
- Pulmonary and Critical Care, Swedish Medical Center, Seattle, WA, USA
| | - D S O'Mahony
- Pulmonary and Critical Care, Swedish Medical Center, Seattle, WA, USA
| | - T Wagner
- Pulmonary and Critical Care, Swedish Medical Center, Seattle, WA, USA
| | - J Pulido
- US Anesthesia Partners, Seattle, WA, USA.,Swedish Heart and Vascular Institute, Swedish Medical Center, Seattle, WA, USA
| | - J Mignone
- Swedish Heart and Vascular Institute, Swedish Medical Center, Seattle, WA, USA
| | - S Youssef
- Swedish Heart and Vascular Institute, Swedish Medical Center, Seattle, WA, USA
| | - M Hartman
- Swedish Heart and Vascular Institute, Swedish Medical Center, Seattle, WA, USA
| | - J D Goldman
- Infectious Disease, Swedish Medical Center, Seattle, WA, USA
| | - J M Pagel
- From the Center for Blood Disorders and Stem Cell Transplantation, Swedish Cancer Institute, Swedish Medical Center, Seattle, WA, USA
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104
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Hejazi II, Beg MA, Imam MA, Athar F, Islam A. Glossary of phytoconstituents: Can these be repurposed against SARS CoV-2? A quick in silico screening of various phytoconstituents from plant Glycyrrhiza glabra with SARS CoV-2 main protease. Food Chem Toxicol 2021; 150:112057. [PMID: 33592201 PMCID: PMC7882218 DOI: 10.1016/j.fct.2021.112057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/01/2021] [Accepted: 02/06/2021] [Indexed: 12/23/2022]
Abstract
World is familiar with the viral pathogen Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2). The principle working enzymes of SARS CoV-2 have been identified as main proteases 3Cl pro which act as main regulators for SARS infection. The need for therapy is required immediately pertaining to the vulnerable conditions. Protein-ligand studies are imperative for understanding the functioning of biological interactions as they are crucial in providing a hypothetical origin for the design and unearthing of novel drug targets. Phytoconstituents from Glycyrrhiza glabra, earlier reported to be anticancerous in nature were used as repurposed drugs against SARS CoV-2 main protease 3Clpro. We analyzed the molecular interactions of protein-phytocompounds, by AutoDock Vina 4.2 tools. The best interactions of each algorithm were subjected to molecular dynamic (MD) simulations to have an insight of the molecular dynamic mechanisms involved. Selected phytoconstituents gave a good score for binding affinity with the main protease 6LU7 of SARS CoV-2 as compared to the antiviral drugs already being used in the disease therapy. DehydroglyasperinC(-8.7,-8.1,-6.7,-7.1)kcal/mol, Licochalcone D(-8.4,-8.2,-7.1,-7.9) kcal/mol, Liquiritin(-8.6,-9.0,-7.2,-7.8) kcal/mol have showed energy interactions with 3Clpro better than many FDA approved repurposed drugs; Remdesvir, Favipiravir, and Hydroxychloroquine. MD Simulation also corelates our findings for molecular docking studies.
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Affiliation(s)
- Iram Iqbal Hejazi
- Deen Dayal Upadhyaya Kaushal Kendra, Jamia Millia Islamia, New Delhi, 110025, India.
| | - Md Amjad Beg
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
| | - Md Ali Imam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
| | - Fareeda Athar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
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105
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Roy S, Khan S, Jairajpuri DS, Hussain A, Alajmi MF, Islam A, Luqman S, Parvez S, Hassan MI. Investigation of sphingosine kinase 1 inhibitory potential of cinchonine and colcemid targeting anticancer therapy. J Biomol Struct Dyn 2021; 40:6350-6362. [PMID: 33565370 DOI: 10.1080/07391102.2021.1882341] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sphingosine kinase 1 (SphK1) and sphingosine-1-phosphate (S1P) signaling regulates numerous diseases such as cancer, diabetes, and inflammation-related ailments, rheumatoid arthritis, atherosclerosis, and multiple sclerosis. The importance of SphK1 in chemo-resistance has been extensively explored in breast, lung, colon, and hepatocellular carcinomas. SphK1 is considered an attractive drug target for the development of anticancer therapy. New drug molecules targeting the S1P signaling are required owing to its pleiotropic nature and association with multiple downstream targets. Here, we have investigated the binding affinity and SphK1 inhibitory potential of cinchonine and colcemid using a combined molecular docking and simulation studies followed by experimental analysis. These compounds bind to SphK1 with a significantly high affinity and subsequently inhibit kinase activity (IC50 7-9 μM). Further, MD simulation studies revealed that both cinchonine and colcemid bind to the residues at the active site pocket of SphK1 with several non-covalent interactions, which may be responsible for inhibiting its kinase activity. Besides, the binding of cinchonine and colcemid causes substantial conformational changes in the structure of SphK1. Taken together, cinchonine and colcemid may be implicated in designing potential drug molecules with improved affinity and specificity for SphK1 targeting anticancer therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonam Roy
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Shama Khan
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa; Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Suaib Luqman
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Suhel Parvez
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
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106
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Shamsi A, Mohammad T, Anwar S, Amani S, Khan MS, Husain FM, Rehman MT, Islam A, Hassan MI. Potential drug targets of SARS-CoV-2: From genomics to therapeutics. Int J Biol Macromol 2021; 177:1-9. [PMID: 33577820 PMCID: PMC7871800 DOI: 10.1016/j.ijbiomac.2021.02.071] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 01/18/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from China has become a global threat due to the continuous rise in cases of Coronavirus disease 2019 (COVID-19). The problem with COVID-19 therapeutics is due to complexity of the mechanism of the pathogenesis of this virus. In this review, an extensive analysis of genome architecture and mode of pathogenesis of SARS-CoV-2 with an emphasis on therapeutic approaches is performed. SARS-CoV-2 genome consists of a single, ~29.9 kb long RNA having significant sequence similarity to BAT-CoV, SARS-CoV and MERS-CoV genome. Two-third part of SARS-Cov-2 genome comprises of ORF (ORF1ab) resulting in the formation of 2 polyproteins, pp1a and pp1ab, later processed into 16 smaller non-structural proteins (NSPs). The four major structural proteins of SARS-CoV-2 are the spike surface glycoprotein (S), a small envelope (E), membrane (M), and nucleocapsid (N) proteins. S protein helps in receptor binding and membrane fusion and hence plays the most important role in the transmission of CoVs. Priming of S protein is done by serine 2 transmembrane protease and thus plays a key role in virus and host cell fusion. This review highlights the possible mechanism of action of SARS-CoV-2 to search for possible therapeutic options.
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Affiliation(s)
- Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Samreen Amani
- Department of Biochemistry, F/O Life Science, Aligarh Muslim University, Aligarh, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asimul Islam
- 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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107
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Ahanger I, Parray ZA, Nasreen K, Ahmad F, Hassan MI, Islam A, Sharma A. Heparin Accelerates the Protein Aggregation via the Downhill Polymerization Mechanism: Multi-Spectroscopic Studies to Delineate the Implications on Proteinopathies. ACS Omega 2021; 6:2328-2339. [PMID: 33521471 PMCID: PMC7841943 DOI: 10.1021/acsomega.0c05638] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Heparin is one of the members of the glycosaminoglycan (GAG) family, which has been associated with protein aggregation diseases including Alzheimer's disease, Parkinson's disease, and prion diseases. Here, we investigate heparin-induced aggregation of bovine serum albumin (BSA) using different spectroscopic techniques [absorption, 8-anilino-1-naphthalene sulfonic acid (ANS) and thioflavin T (ThT) fluorescence binding, and far- and near-UV circular dichroism]. Kinetic measurements revealed that heparin is involved in the significant enhancement of aggregation of BSA. The outcomes showed dearth of the lag phase and a considerable change in rate constant, which provides conclusive evidence, that is, heparin-induced BSA aggregation involves the pathway of the downhill polymerization mechanism. Heparin also causes enhancement of fluorescence intensity of BSA significantly. Moreover, heparin was observed to form amyloids and amorphous aggregates of BSA which were confirmed by ThT and ANS fluorescence, respectively. Circular dichroism measurements exhibit a considerable change in the secondary and tertiary structure of the protein due to heparin. In addition, binding studies of heparin with BSA to know the cause of aggregation, isothermal titration calorimetry measurements were exploited, from which heparin was observed to promote the aggregation of BSA by virtue of electrostatic interactions between positively charged amino acid residues of protein and negatively charged groups of GAG. The nature of binding of heparin with BSA is very much apparent with an appreciable heat of interaction and is largely exothermic in nature. Moreover, the Gibbs free energy change (ΔG) is negative, which indicates spontaneous nature of binding, and the enthalpy change (ΔH) and entropy change (ΔS) are also largely negative, which suggest that the interaction is driven by hydrogen bonding.
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Affiliation(s)
- Ishfaq
Ahmad Ahanger
- Department
of Chemistry, Biochemistry and Forensic Science, Amity School of Applied
Sciences, Amity University Haryana, Gurugram 122 413, India
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Zahoor Ahmad Parray
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Khalida Nasreen
- 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
| | - Asimul Islam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anurag Sharma
- Department
of Chemistry, Biochemistry and Forensic Science, Amity School of Applied
Sciences, Amity University Haryana, Gurugram 122 413, India
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108
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Akter K, Khalilullah I, Saqueeb SN, Islam A, Zaman MS, Rahman M, Rokonujjaman M, Wadud MA, Aziz S, Rahman MA, Rahman SM, Jahan I. Level of Serum Vitamin D, To Which People Are at Risk of Developing Acute Myocardial Infarction in Bangladesh. Mymensingh Med J 2021; 30:176-181. [PMID: 33397871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Incidence of Myocardial Infarction is increasing day by day in developing countries. Most of the patients who sustain myocardial infarction have coronary atherosclerosis. There are several risk factors for the development of atherosclerosis. Among all the risk factors, vitamin D deficiency has been proposed to play an important role in the development of atherosclerosis. With this aim, a case-control study was carried out to explore the association of serum vitamin D with acute myocardial infarction. The enrolled study subjects were categorized into Group A which comprised of STEMI, Group B, comprised of NSTEMI and Group C comprised of age and sex matched individuals free from acute myocardial infarction. The mean values of serum vitamin D (in ng/ml) were 20.17, 20.8 and 24.77 respectively in STEMI, NSTEMI and control groups. It differed significantly among groups (p<0.001) and it was significantly low in STEMI and NSTEMI groups compared to control group (p<0.001 and p=0.004). From this study it can be concluded that low serum vitamin D is an independent risk factor for developing acute myocardial infarction. Individuals with serum vitamin D <20ng/ml have higher chance of developing acute myocardial infarction compared to those with serum vitamin D >20ng/ml.
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Affiliation(s)
- K Akter
- Dr Khaleda Akter, Specialist, Laboratory Diagnostic Services, Ibrahim Cardiac Hospital & Research Institute (ICH&RI), Dhaka, Bangladesh; E-mail:
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109
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Islam S, Rahman MK, Ferdous J, Rahman M, Akter S, Faraque MO, Chowdhury MNU, Hossain MA, Hassan MM, Islam A, Islam A. Hemoprotozoa and Anaplasma spp. in rodents and shrews of Bangladesh. Trop Biomed 2020; 37:842-851. [PMID: 33612737 DOI: 10.47665/tb.37.4.842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hemoprotozoans are important pathogens of animals and humans, among which some species have zoonotic significance. The prevalence of different hemoprotozoa and Anaplasma spp. in larger mammals have been reported from different regions of the world. But, very few studies have been conducted to estimate the prevalence of hemoprotozoa in rodents and shrews of South-East Asia. The study assessed the prevalence of hemoprotozoa and Anaplasma spp. in rodents and shrews of Bangladesh. Blood samples (n=451) were collected from rodents and shrews between June 2011 and June 2013 and July-December 2015 from 4 land gradients of Bangladesh. Giemsa-stained blood smears revealed that 13% of animals were harboring hemoprotozoa (4.7% Babesia spp., 0.67% Plasmodium spp.), and Anaplasma spp. (7.5%). The study may serve as a guide for future hemoparasitic research of rodents and shrews.
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Affiliation(s)
- S Islam
- Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka-1212, Bangladesh.,EcoHealth Alliance, New York, NY10001-2320, USA
| | - M K Rahman
- Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka-1212, Bangladesh.,EcoHealth Alliance, New York, NY10001-2320, USA
| | - J Ferdous
- Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka-1212, Bangladesh.,EcoHealth Alliance, New York, NY10001-2320, USA
| | - M Rahman
- Department of Parasitology and Pathology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram-4225, Bangladesh
| | - S Akter
- Department of Medicine and Surgery, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram-4225, Bangladesh
| | - M O Faraque
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram-4225, Bangladesh
| | - M N U Chowdhury
- Bangladesh Forest Department, Ministry of Environment and Forests, Government of the People's Republic of Bangladesh, Bangladesh
| | - M A Hossain
- Department of Parasitology and Pathology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram-4225, Bangladesh
| | - M M Hassan
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram-4225, Bangladesh
| | - A Islam
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka-1212, Bangladesh
| | - A Islam
- EcoHealth Alliance, New York, NY10001-2320, USA
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Waseem R, Shamsi A, Kazim S, Islam A. An Insight Into Mitochondrial Dysfunction and its Implications in Neurological Diseases. Curr Drug Targets 2020; 22:1585-1595. [PMID: 33390128 DOI: 10.2174/1389450121999201230204050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/01/2020] [Revised: 08/31/2020] [Accepted: 10/05/2020] [Indexed: 11/22/2022]
Abstract
In the last few years, a massive increase in the research has been observed that focusses on investigating the role of mitochondria in pathogenesis of several neurodegenerative disorders. Mitochondria are vital cell organelles having im-portant roles in different cellular processes including energy production, calcium signaling, ROS generation, apoptosis, etc. Therefore, healthy mitochondria are necessary for cell survival and functioning. It would seem feasible that mitochondrial dysfunction will have implications in various pathological conditions. A large body of evidence indicates the role of mito-chondrion as a potential key player in the loss or dysfunction of neurons in various neurodegenerative disorders. In this review, we provide an insight into the mitochondrial dysfunction and its involvement in the pathology of several neurolog-ical diseases such as Alzheimer’s disease, Parkinson’s disease, Amyotrophic Lateral Sclerosis, Hypoxic-Ischemic Brain Injury and many more.
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Affiliation(s)
- Rashid Waseem
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi.. India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi.. India
| | - Syed Kazim
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi.. India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi.. India
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111
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Shamsi A, Mohammad T, Anwar S, Nasreen K, Hassan MI, Ahmad F, Islam A. Insight into the binding of PEG-400 with eye protein alpha-crystallin: Multi spectroscopic and computational approach: possible therapeutics targeting eye diseases. J Biomol Struct Dyn 2020; 40:4496-4506. [DOI: 10.1080/07391102.2020.1858964] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Khalida Nasreen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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112
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Parray ZA, Ahmad F, Hassan MI, Islam A. Conformational changes in cytochrome c directed by ethylene glycol accompanying complex formation: Protein-solvent preferential interaction or/and kosmotropic effect. Spectrochim Acta A Mol Biomol Spectrosc 2020; 242:118788. [PMID: 32810818 DOI: 10.1016/j.saa.2020.118788] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/04/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
When proteins interact with solvent or co-solutes with a high specificity and affinity, protein-ligand complexes may be formed. Such phenomenon may involve the processes like intra- and intermolecular interactions, which result in interaction based protein folding. In this study, cytochrome c (cyt c) was treated with different concentrations of ethylene glycol (EG) in crowded and confined media to check its structural stability using various spectroscopic techniques at pH 7.0 and 25 °C. The various spectroscopic techniques including circular dichroism (Soret, far- and near-UV regions), Fourier transform infrared (FTIR), absorption (UV and visible) and Trp fluorescence shows both secondary and tertiary structure of cyt c increases when treated with EG. The investigations using dynamic light scattering (DLS), time resolved fluorescence and isothermal titration calorimetry (ITC) for binding studies shows weak interaction between EG and cyt c. Small increase in the structure of the protein and insignificant decrease in hydrodynamic radii of the protein was observed from the studies. Molecular docking studies showed that EG has binding site on the protein and interact with few amino acid residues by weak interactions such as van der Waals and hydrogen bonding. This study helps in understanding the protein-ligand interactions, provides facts and the mechanisms that mediates the recognition of binding site for specific ligand to the receptor protein, which make possible of the discovery, design, and development of drugs at molecular level without affecting proteins within an organism.
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Affiliation(s)
- Zahoor Ahmad Parray
- 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
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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113
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Naiyer A, Khan B, Islam A, Hassan MI, Sundd M, Ahmad F. Heme-iron ligand (M80-Fe) in cytochrome c is destabilizing: combined in vitro and in silico approaches to monitor changes in structure, stability and dynamics of the protein on mutation. J Biomol Struct Dyn 2020; 40:4122-4139. [PMID: 34043488 DOI: 10.1080/07391102.2020.1853607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Structure, stability and dynamics properties of horse cytochrome c (cyt c) and its genetically engineered M80G mutant have been investigated. The nature of the Met80 axial ligation to heme iron is believed to be the major determinant of the oxidation-reduction reactions inside and outside the cell of a particular cytochrome. This ligation has played an important role in the studies of protein structure, stability and protein folding/unfolding. To understand this ligation better, Met80 of horse cyt c has been mutated to Gly that is unable to bind to the heme iron. We have examined the effect of the M80G mutation on the structure and stability of the WT (wild type) protein by using absorbance spectroscopy, far-UV, near-UV and Soret circular dichroism, fluorescence spectroscopy and differential scanning calorimetry. We have observed that mutation caused a partial loss of secondary and tertiary structure with slightly increased overall stability of the protein. We have also measured the dynamic behavior of WT cyt c and its M80G mutant in the oxidized form (Fe3+) using the essential dynamics (ED) method. A 400 ns MD simulations were run for WT cyt c and its mutant M80G in water using GROMOS96 force field. MD results revealed that the stability and flexibility increased in mutant M80G (Fe…S (Met80) bond removed). Essential dynamics analysis revealed that the first five eigenvectors were mainly involved in overall motions of WT cyt c and its M80G mutant but the amplitude of concerted motions decreased in M80G mutant relative to WT cyt c.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullah Naiyer
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Bushra Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Monica Sundd
- NMR-II Lab, National Institute of Immunology, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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114
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Rahman M, Islam A, Samad M, Islam S, Uddin M, Rumi M, Rostal M, Hagan E, Epistein J, Flora M, Hassan M. Epidemiological assessment of antimicrobial resistance of Salmonella species from wildlife at human-animal interface in Bangladesh. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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115
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Islam A, Hossain M, Rostal M, Ferdous J, Miah M, Mukharjee S, Haider N, Hasan M, Rahman M, Daszak P, Rahman M, Epstein J. Epidemiology and molecular characterization of rotavirus A in bats and rhesus macaques at human-wildlife interfaces in Bangladesh. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.1377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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116
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Islam A, Hossain M, Islam S, Samad M, Rahman M, Chowdhury M, Hassan M, Alexandersen S, Rahman M, Flora M, Epstein J, Klaassen M. Detection and genetic characterization of avian influenza A (H5N6) virus clade 2.3.4.4 in isolates from house crow and poultry in Bangladesh, 2017. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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117
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Chowdhury M, Islam S, Hossain M, Rahman M, Zulkar Nine H, Sadik A, Kabir M, Doe M, Chowdhury M, Islam A. Detection of Influenza A and Adenovirus in captive wild birds in Bangladesh. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.11.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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118
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Dutta Choudhury S, Islam A, Abedin J, Hagan E, Shano S, Rahman N, Shermin R, Rahman Z, Shirin T, Daszak P, Sabrina Flora M, H Epstein J. Prevalence and genetic diversity of Coronavirus in human in Bangladesh. Int J Infect Dis 2020. [PMID: 33039608 PMCID: PMC7817406 DOI: 10.1016/j.ijid.2020.11.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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119
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Ferdous J, Islam A, Machalaba C, Feferholtz Y, Rahman M, Hagan E, Berthe F, Daszak P, Karesh W, Flora M. Economic burden of rabies and its impact in Bangladesh through a One Health approach. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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120
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Shamsi A, Anwar S, Shahbaaz M, Mohammad T, Alajmi MF, Hussain A, Hassan I, Ahmad F, Islam A. Evaluation of Binding of Rosmarinic Acid with Human Transferrin and Its Impact on the Protein Structure: Targeting Polyphenolic Acid-Induced Protection of Neurodegenerative Disorders. Oxid Med Cell Longev 2020; 2020:1245875. [PMID: 33204390 PMCID: PMC7661129 DOI: 10.1155/2020/1245875] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/30/2020] [Indexed: 12/15/2022]
Abstract
Rosmarinic acid (RA) is a natural compound that is gaining wide popularity owing to its broad-spectrum biological activities. RA is known for its wide range of medicinal properties and therapeutic applications in a vast range of neurodegenerative disorders thus making it a vital natural compound. Human transferrin (hTf) is a clinically significant protein that plays a pivotal role in maintaining iron homeostasis. The importance of studies pertaining to hTf is attributable to the pivotal role of iron deposition in CNS in neurodegenerative disorders. The study was intended to have an insight into the interaction between RA and hTf employing multispectroscopic approach, molecular docking, and molecular dynamic simulation studies. Fluorescence quenching studies revealed that RA shows an excellent binding affinity to hTf with a binding constant (K) of 107 M-1 and is guided by static mode of quenching. Isothermal titration calorimetry (ITC) further validated the spontaneous nature of binding. The estimation of enthalpy change (∆H) and entropy change (∆S) suggested that the RA-hTf complex formation is driven by hydrogen bonding, thereby making this process seemingly specific. Further, Fourier transform infrared (FTIR) and circular dichroism (CD) spectra suggested that RA induces conformational and structural changes in hTf. Additionally, molecular dynamics (MD) studies were carried out to investigate the stability of the hTf and hTf-RA system and suggested that binding of RA induces structural alteration in hTf with free hTf being more stable. This study provides a rationale to use RA in drug development against neurodegenerative disorders by designing novel functional foods containing RA.
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Affiliation(s)
- Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Mohd Shahbaaz
- South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
- Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin Prospekt, Chelyabinsk, 454080, Russia
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
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121
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Hellevik T, Berzaghi R, Islam A, Gorchs L, Pettersen I, Stuge T, Akhtar M, Martinez-Zubiaurre I. OC-0081: Immuno-regulatory properties of irradiated tumor fibroblasts. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)00107-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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122
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Yousuf M, Khan P, Shamsi A, Shahbaaz M, Hasan GM, Haque QMR, Christoffels A, Islam A, Hassan MI. Inhibiting CDK6 Activity by Quercetin Is an Attractive Strategy for Cancer Therapy. ACS Omega 2020; 5:27480-27491. [PMID: 33134711 PMCID: PMC7594119 DOI: 10.1021/acsomega.0c03975] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Cyclin-dependent kinase 6 (CDK6) is a potential drug target that plays an important role in the progression of different types of cancers. We performed in silico and in vitro screening of different natural compounds and found that quercetin has a high binding affinity for the CDK6 and inhibits its activity with an IC50 = 5.89 μM. Molecular docking and a 200 ns whole atom simulation of the CDK6-quercetin complex provide insights into the binding mechanism and stability of the complex. Binding parameters ascertained by fluorescence and isothermal titration calorimetry studies revealed a binding constant in the range of 107 M-1 of quercetin to the CDK6. Thermodynamic parameters associated with the formation of the CDK6-quercetin complex suggested an electrostatic interaction-driven process. The cell-based protein expression studies in the breast (MCF-7) and lung (A549) cancer cells revealed that the treatment of quercetin decreases the expression of CDK6. Quercetin also decreases the viability and colony formation potential of selected cancer cells. Moreover, quercetin induces apoptosis, by decreasing the production of reactive oxygen species and CDK6 expression. Both in silico and in vitro studies highlight the significance of quercetin for the development of anticancer leads in terms of CDK6 inhibitors.
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Affiliation(s)
- Mohd Yousuf
- Department
of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Parvez Khan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anas Shamsi
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Mohd Shahbaaz
- South
African Medical Research Council Bioinformatics Unit, South African
National Bioinformatics Institute, University
of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
- Laboratory
of Computational Modeling of Drugs, South
Ural State University, 76 Lenin Prospekt, Chelyabinsk 454080, Russia
| | - Gulam Mustafa Hasan
- Department
of Biochemistry, College of Medicine, Prince
Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | | | - Alan Christoffels
- South
African Medical Research Council Bioinformatics Unit, South African
National Bioinformatics Institute, University
of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Asimul Islam
- 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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123
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Bashir S, Shamsi A, Ahmad F, Hassan MI, Kamal MA, Islam A. Biophysical Elucidation of Fibrillation Inhibition by Sugar Osmolytes in α-Lactalbumin: Multispectroscopic and Molecular Docking Approaches. ACS Omega 2020; 5:26871-26882. [PMID: 33111013 PMCID: PMC7581248 DOI: 10.1021/acsomega.0c04062] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 09/25/2020] [Indexed: 05/02/2023]
Abstract
Protein aggregation is among the most challenging new frontiers in protein chemistry as well as in molecular medicine and has direct implications in protein misfolding. This study investigated the role of sugar molecules (glucose, fructose, sucrose, and the mixture of glucose and fructose) in protecting the structural integrity of α-lactalbumin (α-LA) against aggregation. The research focused here is the inhibitory capabilities of sugars against α-LA fibril formation investigated employing diverse multispectroscopic and microscopic techniques. The aggregation was induced in α-LA thermally with a change in concentration. UV-vis spectroscopy, ThT binding assay, Trp fluorescence, Rayleigh scattering, and turbidity assay depicted synchronized results. Further, transmission electron microscopy (TEM) complemented that a mixture of glucose and fructose was the best inhibitor of α-LA fibril formation. Inhibition of α-LA aggregation by sugar osmolytes is attributed to the formation of hydrogen bonds between these osmolytes, as evidenced by the molecular docking results. This hydrogen bonding is a key player that prevents aggregation in α-LA in the presence of sugar osmolytes. This study provides an insight into the ability of naturally occurring sugar osmolytes to inhibit fibril formation and can serve as a platform to treat protein misfolding and aggregation-oriented disorders.
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Affiliation(s)
- Sania Bashir
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anas Shamsi
- 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
| | - Mohammad Azhar Kamal
- Department
of Biochemistry, College of Science, University
of Jeddah, Jeddah 21589, Saudi Arabia
- University
of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University
of Jeddah, Jeddah 21589, Saudi Arabia
| | - Asimul Islam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Correspondence:
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124
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Mohammad T, Shamsi A, Anwar S, Umair M, Hussain A, Rehman MT, AlAjmi MF, Islam A, Hassan MI. Identification of high-affinity inhibitors of SARS-CoV-2 main protease: Towards the development of effective COVID-19 therapy. Virus Res 2020; 288:198102. [PMID: 32717346 PMCID: PMC7380256 DOI: 10.1016/j.virusres.2020.198102] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/17/2020] [Accepted: 07/19/2020] [Indexed: 01/08/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease, caused by a newly emerged highly pathogenic virus called novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Targeting the main protease (Mpro, 3CLpro) of SARS-CoV-2 is an appealing approach for drug development because this enzyme plays a significant role in the viral replication and transcription. The available crystal structures of SARS-CoV-2 Mpro determined in the presence of different ligands and inhibitor-like compounds provide a platform for the quick development of selective inhibitors of SARS-CoV-2 Mpro. In this study, we utilized the structural information of co-crystallized SARS-CoV-2 Mpro for the structure-guided drug discovery of high-affinity inhibitors from the PubChem database. The screened compounds were selected on the basis of their physicochemical properties, drug-likeliness, and strength of affinity to the SARS-CoV-2 Mpro. Finally, we have identified 6-Deaminosinefungin (PubChem ID: 10428963) and UNII-O9H5KY11SV (PubChem ID: 71481120) as potential inhibitors of SARS-CoV-2 Mpro which may be further exploited in drug development to address SARS-CoV-2 pathogenesis. Both compounds are structural analogs of known antivirals, having considerable protease inhibitory potential with improved pharmacological properties. All-atom molecular dynamics simulations suggested SARS-CoV-2 Mpro in complex with these compounds is stable during the simulation period with minimal structural changes. This work provides enough evidence for further implementation of the identified compounds in the development of effective therapeutics of COVID-19.
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Affiliation(s)
- Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohd Umair
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Asimul Islam
- 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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125
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Abedin S, Paul SK, Nasreen SA, Nessa A, Ahmed S, Haque N, Ahamed F, Islam A, Ifa IA, Debnath P, Ahmed MU, Nahar S. Molecular Detection of Human Coronavirus from North Central Part of Bangladesh Depending on ORF1ab and N Gene. Mymensingh Med J 2020; 29:865-870. [PMID: 33116089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Coronavirus disease 2019 (COVID-19) resulted severe respiratory illness such as pneumonia and lung dysfunctions that was first identified at Wuhan, the capital of Hubeiin China during the end of December 2019. The etiological cause of COVID-19 has been confirmed as a novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which was similar with the zoonotic virus SARS-CoV (2002). Now a days for early diagnosis of COVID-19 the nucleic acid based test like RT PCR (real time reverse transcription polymerase chain reaction) is most consistent and used all over the world. In this study among 11,280 cases 825(7.31%) were positive by molecular RT PCR method on June 2020 at Microbiology department of Mymensingh Medical College and the samples are collected from different areas of Northern part of Bangladesh. Among this positive cases 588(71%) N gene, 10 ORF1ab (2%) and 227(27%) both N and ORF gene showed significant curve which is specific for COVID-19 positive patients. Because N and ORF gene of this virus inhibit immune system of human body especially interferon. Out of SARS-CoV-2 positive cases maximum number of N gene were found in male patients and above 40 years old aged group. So, Molecular diagnosis of this pandemic virus especially by N and ORF gene might be helpful to reduce the spread of SARS-CoV-2 as well as early treatment for saving many lives.
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Affiliation(s)
- S Abedin
- Dr Sahida Abedin, Lecturer, Department of Virology, MMC, Mymensingh, Bangladesh; E-mail:
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126
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Khan SH, Prakash A, Pandey P, Islam A, Hassan MI, Lynn AM, Ahmad F. Effects of natural mutations (L94I and L94V) on the stability and mechanism of folding of horse cytochrome c: A combined in vitro and molecular dynamics simulations approach. Int J Biol Macromol 2020; 159:976-985. [PMID: 32439437 DOI: 10.1016/j.ijbiomac.2020.05.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 02/06/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 12/13/2022]
Abstract
Known crystal structures of 10 cytochromes (cyts) c from different sources led to the conclusion that natural mutations in these proteins does not affect their 3D structure, hence evolution preserved structure for function. A sequence alignment of horse cyt c with all other 284 cyts c led to two important conclusions: (i) Leu at position 94 is conserved in all 30 mammalian known sequences, and (ii) there are 14 other species which have either Val or Ile at 94th position. We asked a question: Is the avoidance of substitution by Val or Ile at position 94 in the mammalian cyts c by design or by chance? To answer this question, we introduced natural substitutes of Leu94 by Val and Ile in horse cyt c using site-directed mutagenesis. Here, from our in vitro and molecular dynamic simulation studies on L94V and L94I mutants, we concluded that (i) although the natural mutations destabilize the wild type cyt c, it does not significantly affect the mechanism of folding of the protein, (ii) urea-induced denaturation of WT cyt c and its mutants is a two-state process, and (iii) denaturation of WT cyt c and its mutants by guanidinium chloride is not a two-state process.
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Affiliation(s)
- Sabab Hasan Khan
- Centre for Interdisciplinary research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon 122413, India
| | - Preeti Pandey
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - 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
| | - Andrew M Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Faizan Ahmad
- Centre for Interdisciplinary research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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127
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Amir M, Alam A, Ishrat R, Alajmi MF, Hussain A, Rehman MT, Islam A, Ahmad F, Hassan MI, Dohare R. A Systems View of the Genome Guardians: Mapping the Signaling Circuitry Underlying Oligonucleotide/Oligosaccharide-Binding Fold Proteins. OMICS 2020; 24:518-530. [PMID: 32780668 DOI: 10.1089/omi.2020.0072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The oligonucleotide/oligosaccharide-binding (OB)-fold domain proteins are considered as genome guardians, whose functions are extending beyond genomic stability. The broad functional diversity of the OB-fold proteins is attributed to their protein-DNA, protein-RNA, and protein-protein interactions (PPI). To understand the connectivity of the human OB-fold proteins, we report here a systems-level approach. Specifically, we mapped all human OB-fold PPI networks and evaluated topological features such as network robustness and network hub, among others. We found that the OB-fold network comprised of 227 nodes forming 5523 interactions, and has a scale-free topology having UBA52, ATR, and TP53 as leading hub proteins that control efficient communication within the network. Furthermore, four different clusters and subclusters have been identified, which are implicated in diverse cellular processes, including DNA replication, repair, maintenance of genomic stability, RNA processing, spermatogenesis, complement system, and telomere maintenance. The importance of these clusters is further strengthened by knockout studies, which showed a significant decrease in topological properties. In summary, this study provides new insights on the role of OB-fold protein as genome guardians in regard to the underlying mechanism of signaling pathways, the roles of key regulators, and thus, offers new prospects as potential targets for diagnostics and therapeutics purposes.
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Affiliation(s)
- Mohd Amir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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128
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Shamsi A, Mohammad T, Anwar S, Hassan MI, Ahmad F, Hasan I, Islam A. Biophysical Insights into Implications of PEG-400 on the α-Crystallin Structure: Multispectroscopic and Microscopic Approach. ACS Omega 2020; 5:19210-19216. [PMID: 32775924 PMCID: PMC7409245 DOI: 10.1021/acsomega.0c02648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
Aggregation and precipitation of α-crystallin play a vital role in the cataract development. This study was targeted to delineate the effect of PEG-400 on the structural integrity of α-crystallin employing a multispectroscopic and microscopic approach. Intrinsic fluorescence and UV-vis spectroscopy suggested alterations in the tertiary structure of α-crystallin, namely global transition of native α-crystallin to a non-native form in the presence of PEG-400. Circular dichroism spectroscopy suggested secondary structural transition in a native conformation of α-crystallin in the presence of PEG-400. Loss in the native conformation of α-crystallin is implicated in cataract developments, thus highlighting the clinical significance of this work. Further, a significant increase in ANS fluorescence of PEG-400-incubated α-crystallin (7 days) suggested this non-native form to be molten globule (MG)-like state. Increased Thioflavin T fluorescence (ThT) and congo red (CR) absorbance along with transmission electron microscopy (TEM) confirmed the formation of the aggregates of α-crystallin after prolonged incubation with PEG-400. Insights into PEG-400-induced structural alterations can provide a platform to search for new therapeutic molecules that can combat α-crystallin-directed eye diseases.
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Affiliation(s)
- Anas Shamsi
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Taj Mohammad
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Saleha Anwar
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md. Imtaiyaz Hassan
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ikramul Hasan
- Department
of Basic Medical Science, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 65527, KSA
| | - Asimul Islam
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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129
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Raina N, Singh AK, Hassan MI, Ahmad F, Islam A. Concentration dependent effect of ethylene glycol on the structure and stability of holo α-lactalbumin: Characterization of intermediate state amidst soft interactions. Int J Biol Macromol 2020; 164:2151-2161. [PMID: 32735932 DOI: 10.1016/j.ijbiomac.2020.07.224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 03/19/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/16/2022]
Abstract
The interior of the cell is crowded with different kinds of biological molecules with varying sizes, shapes and compositions which may affect physiological processes especially protein folding, protein conformation and protein stability. To understand the consequences of such a crowded environment, pH-induced unfolding of holo alpha-lactalbumin (holo α-LA) was studied in the presence of ethylene glycol (EG). The effect of EG on the folding and stability of holo α-LA in aqueous solution was investigated using several spectroscopic techniques. The results indicate that stabilization/destabilization of holo α-LA by EG is concentration- and pH-dependent. Low concentration of EG stabilizes the protein at pH near its pI. From the results of far-UV CD, UV-visible and ANS fluorescence, intermediate state (MG state) was characterized in the presence of high concentration of ethylene glycol. The results invoke a new mechanism for the formation of MG state identical to active component of BAMLET. MG state of holo α-LA has a direct implication to cancer therapy. MG state of α-LA in complex with specific type of lipid is a novel class of protein-based anti-cancer complexes that incorporate oleic acid and deliver it to the cancer cells.
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Affiliation(s)
- Neha Raina
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh 201310, India; Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh 201310, 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
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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130
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Alamry KA, Srivastava S, Shahbaaz M, Khan P, Gupta P, Syed SB, Azum N, Asiri AM, Islam A, Ahmad F, Hassan MI. Unravelling the unfolding pathway of human Fas-activated serine/threonine kinase induced by urea. J Biomol Struct Dyn 2020; 39:5516-5525. [PMID: 32662329 DOI: 10.1080/07391102.2020.1790423] [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] [Indexed: 10/23/2022]
Abstract
Fas-activated serine/threonine kinase (FASTK) is a mitochondria-associated nuclear protein that inhibits Fas- and UV-induced apoptosis. This protein is generally activated during Fas-mediated apoptosis by phosphorylating a nuclear RNA-binding protein T-cell intracellular antigen-1 and thus considered as a modulator of apoptosis. In the present study, we have examined the equilibrium unfolding and conformational stability of the kinase domain of FASTK (FASTK353-444). The kinase domain of FASTK353-444 was cloned, expressed, and purified. The folding ↔ unfolding transitions of urea-induced denaturation was monitored with the help of circular dichroism, intrinsic fluorescence, and UV absorption spectroscopies. Analysis of transition curves obtained from different probes revealed a coincidence of denaturation curves, suggesting that folding/unfolding of FASTK follows a two-state process with the midpoint (Cm) value at 3.50 ± 0.1 M. Urea-induced denaturation curves were further analyzed to estimate change in the Gibbs free energy in the absence of urea (ΔGD0) associated with the equilibrium of denaturation. To get atomistic insights into the urea-induced denaturation of FASTK, we performed an all-atom molecular dynamics simulation for 100 ns. A close agreement was noticed between experimental and computational studies. This study will help to understand the unfolding mechanism and structural stability of the kinase domain of FASTK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khalid A Alamry
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Saurabha Srivastava
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, Cape Town, South Africa.,Laboratory of Computational Modeling of Drugs, South Ural State University, Chelyabinsk, Russia
| | - Parvez Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Sunayana Begum Syed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Naved Azum
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Abdullah M Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.,Center of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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131
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Rahman MO, Islam AS, Choudhury MS, Raihan AA, Alam MS, Chowdury M, Islam A. A Study of Association between H. Pylori Genotype and Chronic Gastritis. Mymensingh Med J 2020; 29:664-675. [PMID: 32844810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The prevalence of Helicobacter pylori (HP) infection is very high in Bangladesh. Chronic gastritis due to H. pylori is commonly associated with important gastric diseases such as peptic ulcer diseases or gastric carcinoma and MALT-oma. The natural course of chronic gastritis is HP-associated antral gastritis or pangastritis or rarely atrophies. This study was done to see the association of H. pylori genotypes with chronic gastritis. This observational cross sectional study was carried out at Bangabandhu Sheikh Mujib Medical University from July 2012 to April 2013 to find out the association of H. pylori genotypes with chronic gastritis in dyspeptic patients of Bangladesh. A total of 50 dyspeptic subjects were involved in the study whose upper GI endoscopies were carried out in presence of an experienced endoscopist. During the procedure four biopsies were taken, two from the antrum and two from body of the stomach. Endoscopic diagnosis was categorized into normal and erosive gastritis. Two (one from antrum and one from body) biopsy samples were collected in phosphate buffer saline and PCR analysis carried out by Multiplex PCR assay. Another two were collected in 10% formalin and histopathological examination was done according to updated Sydney system of classification. Among 50 patents only 34 were PCR positive. So, only 34 subjects were included in the study. Among them 21 patients (61.8%) were male and 13 patients (38.2%) were female, with the mean age of 29.91 years. Endoscopy revealed erosive gastritis in 5(14.7%) patients and normal findings in 29(86.3%) patients. Amongst the strains, cagA gene was detected in 58.8% and was not significantly associated with severity of any parameter of chronic gastritis such as H. pylori density, inflammation (mononuclear infiltration), activity (neutrophilic infiltration), atrophy and intestinal metaplasia. All the strains were positive for vacA allele. s1m1 (55.9%) genotype was most predominant. No vacA allele (s1m1, s1m2, s2m1 and s2m2) were significantly associated with severity of chronic gastritis. In this study, H. pylori genotype -cagA, vacA-s1, s2, m1, m2 allele and histological grading of chronic gastritis according to updated Sydney system of classification is identified. This study will identify the genotypes associated with severe gastritis in our country and thereby help us to take appropriate preventive measure. Further study with larger sample size may be carried out to establish proper association between different genotypes and parameters of chronic gastritis.
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Affiliation(s)
- M O Rahman
- Dr Muhammad Oliur Rahman, Associate Professor, Department of Gastroenterology, Sylhet MAG Osmani Medical College, Sylhet, Bangladesh
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132
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Haque N, Bari MS, Ahmed S, Paul SK, Nasreen SA, Ahamed F, Islam A, Roy S, Abedin S, Khan MK, Fariha RH, Debnath P. Detection of 2019-Novel Coronavirus (2019-nCoV) by rRT-PCR at Mymensingh Medical College, Mymensingh, Bangladesh. Mymensingh Med J 2020; 29:589-595. [PMID: 32844798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The coronavirus disease (COVID-19) is highly pathogenic viral infection caused by SARS-CoV-2. Currently, COVID-19 has caused global health concern. WHO has declared COVID-19 as a pandemic disease on March 11, 2020 and characterized by fever, dry cough, fatigue, myalgia and chest pain with pneumonia in severe cases. The virus has spread to at least 213 countries and more than 9093827 confirmed cases and 471490 deaths have been recorded. In the beginning, the world public health authorities tried to eradicate the disease in China through quarantine but are now transitioning to prevention strategies worldwide to delay its spread. There are some newly developed and promising methods for detection of SARS-CoV-2, in order to facilitate the development of novel approaches for early diagnosis. Nucleic acid based tests currently offer the most sensitive and early detection and confirmation for SARS-CoV-2 infection. Among them Real-time reverse transcription polymerase chain reaction (rRT-PCR) is the most popular and the "gold standard" testing method for the detection of SARS-CoV-2. The present study was carried out to detect 2019-Novel Coronavirus (2019-nCoV) by rRT-PCR method at Mymensingh Medical College, Mymensingh, Bangladesh from 1st April, 2020 to 31st May, 2020. A total of 14356 samples were tested from four districts of Mymensingh division namely, Mymensingh, Jamalpur, Sherpur, Netrokona and some parts of Sunamganj for rRT-PCR. Among them 1086 (7.5%) patients were positive for SARS-CoV-2. Out of 1086 positive cases 716(65.9%) were male and 370(34.1%) were female with a Mean±SD age 34.1±12 years. Maximum positivity was found in Mymensingh district followed by Netrokona, Jamalpur, Sherpur and Sunamganj respectively. This is the first base line study for genetic detection of 2019-nCoV in Mymensingh division which may reflect the total scenario of Bangladesh situation. We hope this paper will help the researcher to increase the availability, accuracy, and speed of widespread COVID-19 testing throughout the world in this crisis moment.
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Affiliation(s)
- N Haque
- Dr Nazia Haque, Assistant Professor, Department of Microbiology, Mymensingh Medical College (MMC), Mymensingh, Bangladesh; E-mail:
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Anwar S, Shamsi A, Shahbaaz M, Queen A, Khan P, Hasan GM, Islam A, Alajmi MF, Hussain A, Ahmad F, Hassan MI. Rosmarinic Acid Exhibits Anticancer Effects via MARK4 Inhibition. Sci Rep 2020; 10:10300. [PMID: 32587267 PMCID: PMC7316822 DOI: 10.1038/s41598-020-65648-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Abstract
Microtubule affinity regulating kinase (MARK4) is a potential drug target for different types of cancer as it controls the early step of cell division. In this study, we have screened a series of natural compounds and finally identified rosmarinic acid (RA) as a potential inhibitor of MARK4. Molecular docking and 500 ns all-atom simulation studies suggested that RA binds to the active site pocket of MARK4, forming enough number of non-covalent interactions with critical residues and MARK4-RA complex is stable throughout the simulation trajectory. RA shows an excellent binding affinity to the MARK4 with a binding constant (K) of 107 M-1. Furthermore, RA significantly inhibits MARK4 activity (IC50 = 6.204 µM). The evaluation of enthalpy change (∆H) and entropy change (∆S) suggested that the MARK4-RA complex formation is driven by hydrogen bonding and thus complexation process is seemingly specific. The consequence of MARK4 inhibition by RA was further evaluated by cell-based tau-phosphorylation studies, which suggested that RA inhibited the phosphorylation of tau. The treatment of cancer cells with RA significantly controls cell growth and subsequently induces apoptosis. Our study provides a rationale for the therapeutic evaluation of RA and RA-based inhibitors in MARK4 associated cancers and other diseases.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, Cape Town, 7535, South Africa
- Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin Prospekt, Chelyabinsk, 454080, Russia
| | - Aarfa Queen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
- Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Parvez Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, 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, Kingdom of Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - 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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134
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Parray Z, Ahmad F, Hassan MI, Hasan I, Islam A. Effects of Ethylene Glycol on the Structure and Stability of Myoglobin Using Spectroscopic, Interaction, and In Silico Approaches: Monomer Is Different from Those of Its Polymers. ACS Omega 2020; 5:13840-13850. [PMID: 32566850 PMCID: PMC7301589 DOI: 10.1021/acsomega.0c01185] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Investigation of changes in thermal stabilities and structures of proteins in the presence of different co-solutes (ligands) is an integral part in the basic research, discovery, and development of drugs. Ethylene glycol (EG) is known to be toxic and causes teratogenic, inducing primarily skeletal and external malformations and other diseases. The effect of EG on the structure and thermal stability of myoglobin (Mb) was studied using various spectroscopic techniques at pH 7.0 and two different temperatures. As revealed by circular dichroism, Trp fluorescence, nano-DSF, and absorption (UV and visible) measurements, EG (i) has no significant effect on secondary and tertiary structures of Mb at 25 °C, and (ii) it decreases the thermal stability of the protein, which increases with increasing concentration of EG. As revealed by ANS (8-anilino-1-naphthalene sulfonic acid) fluorescence measurements, heat-induced denatured protein has newly exposed hydrophobic patches that bind to ANS. Isothermal titration calorimetry revealed that the interaction between EG and Mb is temperature dependent; the preferential interaction of EG is entropy driven at low temperature, 298 K (25 °C), and it is enthalpy driven at higher temperature, 343 K (70 °C). Molecular docking study showed that EG interacts with side chains of amino acid residues of Mb through van der Waals interactions and hydrogen bonding.
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Affiliation(s)
- Zahoor
Ahmad Parray
- 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
| | - Ikramul Hasan
- Department
of Basic Medical Science, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 110025, KSA
| | - Asimul Islam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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135
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Anwar S, Shamsi A, Kar RK, Queen A, Islam A, Ahmad F, Hassan MI. Structural and biochemical investigation of MARK4 inhibitory potential of cholic acid: Towards therapeutic implications in neurodegenerative diseases. Int J Biol Macromol 2020; 161:596-604. [PMID: 32535203 DOI: 10.1016/j.ijbiomac.2020.06.078] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 03/12/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Microtubule affinity regulating kinase (MARK4) is considered as a potential drug target for diabetes, cancer, and neurodegenerative diseases. Since the role of MARK4 in the phosphorylation of tau protein and subsequently Alzheimer's disease has been established, therefore, we have investigated the binding affinity and MARK4 inhibitory potential of cholic acid (CHA) using both computational and spectroscopic methods. Molecular docking suggested a strong binding of CHA to the functionally important residues of MARK4. We further performed 500 ns molecular dynamics simulation which suggested the MARK4-CHA system was quite stable throughout the simulation trajectory. CHA potential binds to the MARK4 with a binding constant (K) of 107 M-1 at 288 K. Further, MARK4 activity was inhibited by CHA with an IC50 = 5.5 μM. Further insights into the thermodynamic parameters suggested that MARK4-CHA complex formation is driven by both electrostatic and van der Waals interactions. Overall study provides a rationale to use CHA in the drug development via MARK4 inhibition, towards possible therapeutic implications in neurodegenerative diseases.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamic Research, Hebrew University of Jerusalem, Israel
| | - Aarfa Queen
- Department of Chemistry, 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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136
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Zehra Z, Luthra M, Siddiqui SM, Shamsi A, Gaur NA, Islam A. Corona virus versus existence of human on the earth: A computational and biophysical approach. Int J Biol Macromol 2020; 161:271-281. [PMID: 32512089 PMCID: PMC7273167 DOI: 10.1016/j.ijbiomac.2020.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022]
Abstract
SARS-CoV-2 has a positive sense RNA genome of 29.9 kb in size, showing high sequence similarity to the BAT-CoV, SARS-CoV, MERS-CoV. SARS-CoV-2 is composed of 14 open reading frames (ORFs), which encodes for a total of 27 proteins divided into structural and non-structural proteins (NSPs). The fundamental structural protein-encoding genes are a spike protein (S) gene, envelope protein (E) gene, a membrane protein (M) gene, and a nucleocapsid protein (N) gene. They make about 33% of the entire genome and are vital for the viral life cycle. Rest 67% is distributed among different NSPs (such as Mpro, helicase, and RNA-dependent RNA polymerase) encoding genes across the ORFs, which are involved in virus-cell receptor interactions during viral entry. Researchers are trying to formulate vaccines, therapeutic antibodies or protein-targeted antiviral drugs to control the spread. This review proceeds stepwise through the COVID-19 outbreak, structural and genomic organization, entry mechanism, pathogenesis, and finally highlighting the essential proteins involved at each step that might be potential targets for drug discovery. Currently, approved treatment modalities consist of only supportive care and oxygen supplementation. This review is established on the current knowledge that has expanded on structural motifs and topology of proteins and their functions.
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Affiliation(s)
- Zainy Zehra
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Manav Luthra
- Department of Orthopedics, Medical College, Jalaun, UP, India.
| | - Sobia Manaal Siddiqui
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, UP, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Naseem A Gaur
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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137
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Yousuf M, Shamsi A, Khan P, Shahbaaz M, AlAjmi MF, Hussain A, Hassan GM, Islam A, Rizwanul Haque QM, Hassan MI. Ellagic Acid Controls Cell Proliferation and Induces Apoptosis in Breast Cancer Cells via Inhibition of Cyclin-Dependent Kinase 6. Int J Mol Sci 2020; 21:E3526. [PMID: 32429317 PMCID: PMC7278979 DOI: 10.3390/ijms21103526] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
Cyclin-Dependent Kinase 6 (CDK6) plays an important role in cancer progression, and thus, it is considered as an attractive drug target in anticancer therapeutics. This study presents an evaluation of dietary phytochemicals, capsaicin, tocopherol, rosmarinic acid, ursolic acid, ellagic acid (EA), limonene, caffeic acid, and ferulic acid for their potential to inhibit the activity of CDK6. Molecular docking and fluorescence binding studies revealed appreciable binding affinities of these compounds to the CDK6. Among them, EA shows the highest binding affinity for CDK6, and thus a molecular dynamics simulation study of 200 ns was performed to get deeper insights into the binding mechanism and stability of the CDK6-EA complex. Fluorescence binding studies revealed that EA binds to the CDK6 with a binding constant of K = 107 M-1 and subsequently inhibits its enzyme activity with an IC50 value of 3.053 µM. Analysis of thermodynamic parameters of CDK6-EA complex formation suggested a hydrophobic interaction driven process. The treatment of EA decreases the colonization of cancer cells and induces apoptosis. Moreover, the expression of CDK6 has been downregulated in EA-treated human breast cancer cell lines. In conclusion, this study establishes EA as a potent CDK6 inhibitor that can be further evaluated in CDK6 directed anticancer therapies.
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Affiliation(s)
- Mohd Yousuf
- Microbiology Research Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (M.Y.); (Q.M.R.H.)
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (A.S.); (P.K.); (A.I.)
| | - Parvez Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (A.S.); (P.K.); (A.I.)
| | - Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
- Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin Prospekt, 454080 Chelyabinsk, Russia
| | - Mohamed F. AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.)
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.)
| | - Gulam Mustafa Hassan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia;
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (A.S.); (P.K.); (A.I.)
| | - Qazi Mohd Rizwanul Haque
- Microbiology Research Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (M.Y.); (Q.M.R.H.)
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (A.S.); (P.K.); (A.I.)
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138
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Amir M, Mohammad T, Dohare R, Islam A, Ahmad F, Imtaiyaz Hassan M. Structure, function and therapeutic implications of OB-fold proteins: A lesson from past to present. Brief Funct Genomics 2020; 19:377-389. [PMID: 32393969 DOI: 10.1093/bfgp/elaa008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Oligonucleotide/oligosaccharide-binding (OB)-fold proteins play essential roles in the regulation of genome and its correct transformation to the subsequent generation. To maintain the genomic stability, OB-fold proteins are implicated in various cellular processes including DNA replication, DNA repair, cell cycle regulation and maintenance of telomere. The diverse functional spectrums of OB-fold proteins are mainly due to their involvement in protein-DNA and protein-protein complexes. Mutations and consequential structural alteration in the OB-fold proteins often lead to severe diseases. Here, we have investigated the structure, function and mode of action of OB-fold proteins (RPA, BRCA2, DNA ligases and SSBs1/2) in cellular pathways and their relationship with diseases and their possible use in therapeutic intervention. Due to the crucial role of OB-fold proteins in regulating the key physiological process, a detailed structural understanding in the context of underlying mechanism of action and cellular complexity offers a new avenue to target OB-proteins for therapeutic intervention.
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139
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Wahiduzzaman, Hassan MI, Islam A, Ahmad F. Urea Stress: Myo-inositol's efficacy to counteract destabilization of TIM-β-globin complex by urea is as good as that of the methylamine. Int J Biol Macromol 2020; 151:1108-1115. [DOI: 10.1016/j.ijbiomac.2019.10.153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 11/29/2022]
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140
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Mathur S, Ferreira M, Maia N, Martin C, Chowdhury N, Islam A, Singer L. Is Frailty Associated with Sarcopenia and Dynapenia in Lung Transplant Candidates? J Heart Lung Transplant 2020. [DOI: 10.1016/j.healun.2020.01.501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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141
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Naiyer A, Islam A, Hassan MI, Ahmad F, Sundd M. Backbone and side chain 1H, 15N and 13C chemical shift assignments of the molten globule state of L94G mutant of horse cytochrome-c. Biomol NMR Assign 2020; 14:37-44. [PMID: 31686356 DOI: 10.1007/s12104-019-09917-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
Proteins fold via a number of intermediates that help them to attain their unique native 3D structure. These intermediates can be trapped under extreme conditions of pH, temperature and chemical denaturants. Similar states can also be achieved by other processes like chemical modification, site directed mutagenesis (or point mutation) and cleavage of covalent bonds of natural proteins under physiological conditions usually taken as dilute buffer (near neutral pH) and 25 °C. Structural characterization of molten globules is hampered due to (i) their transient nature, (ii) very low population at equilibrium, and (iii) prone to aggregation at high concentration. Furthermore, the dynamic nature of these folding intermediates makes them unsuitable for X-ray diffraction. Hence, understanding their structures at the atomic level is often a challenge. However, characterization of these intermediates at the atomic level is possible by NMR, which could possibly unravel new details of the protein folding process. We have previously shown that the L94G mutant of horse cytochrome-c displays characteristics of the molten globule (MG) state at pH 6.0 and 25 °C. As a first step towards characterizing this MG state at the atomic level by NMR, we report its complete backbone, side chain and heme chemical shift assignments.
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Affiliation(s)
- Abdullah Naiyer
- 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
| | - Md Imtaiyaz Hassan
- 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.
| | - Monica Sundd
- NMR-II Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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142
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Shafat Z, Hamza A, Deeba F, Faizan MI, Khan N, Islam A, Ahmed A, Alamery SF, Parveen S. Optimization of parameters for expression and purification of G glycoprotein ectodomain of respiratory syncytial virus. Future Virol 2020. [DOI: 10.2217/fvl-2019-0157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: G glycoprotein ectodomain (Ge) of BA genotype of group B respiratory syncytial virus was expressed and purified to achieve maximum yield of the protein. Materials & methods: We optimized different parameters like strains, temperature, inducer concentration and post induction time period for efficient protein expression in Escherichia coli. The protein was purified using affinity chromatography and confirmed by western blotting. Results: It was concluded that a 5-h induction with 0.75 mM isopropyl β-D-1-thiogalactopyranoside at 37°C in BL21(DE3) cells was the most favorable condition for maximal protein expression. The far-UV circular dichroism spectroscopy suggested that it is an α-helical protein. Conclusion: The purified Ge protein can be characterized by antigenic and biophysical methods in future studies, which will probably assist in vaccine development.
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Affiliation(s)
- Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Abu Hamza
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Farah Deeba
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imam Faizan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Nazim Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Salman F Alamery
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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143
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Khan S, Kaushik R, Sharma M, Raina N, Ahmad F, Islam A. Molecular basis of pathogenic parasitic infections: insights from parasite kinome. Front Biosci (Landmark Ed) 2020; 25:1488-1509. [PMID: 32114442 DOI: 10.2741/4865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Infectious diseases caused by numerous parasitic pathogens represent a global health conundrum. Several animal and plant pathogens are responsible for causing acute illness in humans and deadly plant infections. These pathogens have evolved a diverse array of infection strategies and survival methods within the host organism. Recent research has highlighted the role of protein kinases in the overall virulence and pathogenicity of the pathogens. Protein kinases (Pks) are a group of enzymes known to catalyse the phosphorylation of a wide variety of cellular substrates involved in different signalling cascades. They are also involved in regulating pathogen life cycle and infectivity. In this review, we attempt to address the role of parasite kinome in host infection, pathogen survival within the host tissue and thereby disease manifestation. The understanding of the parasite kinome can be a potential target for robust diagnosis and effective therapeutics.
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Affiliation(s)
- Sheeza Khan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Vandalur, Chennai, Tamil Nadu-600048, India
| | - Rishah Kaushik
- Department of Environmental Studies, University of Delhi, Delhi-110 007, India
| | - Meesha Sharma
- Department of Environmental Studies, University of Delhi, Delhi-110 007, India
| | - Neha Raina
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi-110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi-110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India,
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144
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Mohammad T, Siddiqui S, Shamsi A, Alajmi MF, Hussain A, Islam A, Ahmad F, Hassan MI. Virtual Screening Approach to Identify High-Affinity Inhibitors of Serum and Glucocorticoid-Regulated Kinase 1 among Bioactive Natural Products: Combined Molecular Docking and Simulation Studies. Molecules 2020; 25:E823. [PMID: 32070031 PMCID: PMC7070812 DOI: 10.3390/molecules25040823] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 12/31/2022] Open
Abstract
Serum and glucocorticoid-regulated kinase 1 (SGK1) is a serine/threonine kinase that works under acute transcriptional control by several stimuli, including serum and glucocorticoids. It plays a significant role in the cancer progression and metastasis, as it regulates inflammation, apoptosis, hormone release, neuro-excitability, and cell proliferation. SGK1 has recently been considered as a potential drug target for cancer, diabetes, and neurodegenerative diseases. In the present study, we have performed structure-based virtual high-throughput screening of natural compounds from the ZINC database to find potential inhibitors of SGK1. Initially, hits were selected based on their physicochemical, absorption, distribution, metabolism, excretion, and toxicity (ADMET), and other drug-like properties. Afterwards, PAINS filter, binding affinities estimation, and interaction analysis were performed to find safe and effective hits. We found four compounds bearing appreciable binding affinity and specificity towards the binding pocket of SGK1. The docking results were complemented by all-atom molecular dynamics simulation for 100 ns, followed by MM/PBSA, and principal component analysis to investigate the conformational changes, stability, and interaction mechanism of SGK1 in-complex with the selected compound ZINC00319000. Molecular dynamics simulation results suggested that the binding of ZINC00319000 stabilizes the SGK1 structure, and it leads to fewer conformational changes. In conclusion, the identified compound ZINC00319000 might be further exploited as a scaffold to develop promising inhibitors of SGK1 for the therapeutic management of associated diseases, including cancer.
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Affiliation(s)
- Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (T.M.); (A.S.); (A.I.); (F.A.)
| | - Shiza Siddiqui
- Department of Biotechnology, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India;
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (T.M.); (A.S.); (A.I.); (F.A.)
| | - Mohamed F. Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.)
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.)
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (T.M.); (A.S.); (A.I.); (F.A.)
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (T.M.); (A.S.); (A.I.); (F.A.)
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (T.M.); (A.S.); (A.I.); (F.A.)
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145
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Anwar S, Kar RK, Haque MA, Dahiya R, Gupta P, Islam A, Ahmad F, Hassan MI. Effect of pH on the structure and function of pyruvate dehydrogenase kinase 3: Combined spectroscopic and MD simulation studies. Int J Biol Macromol 2020; 147:768-777. [PMID: 31982536 DOI: 10.1016/j.ijbiomac.2020.01.218] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 11/14/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/22/2022]
Abstract
Pyruvate dehydrogenase kinase-3 (PDK3) plays important role in the glucose metabolism and is associated with cancer progression, and thus being considered as an attractive target for cancer therapy. In this study, we employed spectroscopic techniques to study the structural and conformational changes in the PDK3 at varying pH conditions ranging from pH 2.0 to 12.0. UV/Vis, fluorescence and circular dichroism spectroscopic measurements revealed that PDK3 maintains its native-like structure (both secondary and tertiary) in the alkaline conditions (pH 7.0-12.0). However, a significant loss in the structure was observed under acidic conditions (pH 2.0-6.0). The propensity of aggregate formation at pH 4.0 was estimated by thioflavin T fluorescence measurements. To further complement structural data, kinase activity assay was performed, and maximum activity of PDK3 was observed at pH 7.0-8.0 range; whereas, its activity was lost under acidic pH. To further see conformational changes at atomistic level we have performed all-atom molecular dynamics at different pH conditions for 150 ns. A well defined correlation was observed between experimental and computational studies. This work highlights the significance of structural dependence of pH for wide implications in protein-protein interaction, biological function and drug design procedures.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamic Research, Hebrew University of Jerusalem, Israel
| | - Md Anzarul Haque
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rashmi Dahiya
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Preeti Gupta
- 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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146
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Shamsi A, Mohammad T, Anwar S, Alajmi MF, Hussain A, Hassan MI, Ahmad F, Islam A. Probing the interaction of Rivastigmine Tartrate, an important Alzheimer's drug, with serum albumin: Attempting treatment of Alzheimer's disease. Int J Biol Macromol 2020; 148:533-542. [PMID: 31954794 DOI: 10.1016/j.ijbiomac.2020.01.134] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [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: 10/27/2019] [Revised: 01/11/2020] [Accepted: 01/14/2020] [Indexed: 01/16/2023]
Abstract
The present study was aimed at investigating the binding between an important drug of Alzheimer's therapy, Rivastigmine tartrate (RT), with Bovine serum albumin (BSA). BSA is a model protein that is increasingly being used for studies related to drug-protein interaction owing to its structural similarity with human serum albumin (HSA) which is extremely abundant in the circulatory system comprising around 60% of the total plasma protein. Fluorescence spectroscopy implied that complex formation is taking place between BSA and RT; binding constant calculated was of the order of 104 M-1 implicative of the strength of this interaction. Fluorescence spectroscopy was carried out at three different temperatures in a bid to find out the operative mode of quenching; static quenching was taking place for RT-BSA interaction with a binding constant of 2.5 × 104 M-1 at 298 K. Further, changes in Far UV CD spectra clearly implied that RT induces structural transition in BSA suggestive of RT-BSA complex formation. The negative value of ∆G0 as obtained from fluorescence spectroscopy and isothermal titration calorimetry (ITC) suggests the reaction to be spontaneous and thermodynamically favorable. Additionally, molecular docking was employed to investigate different forces and critical residues involved in RT-BSA interaction. Furthermore, all-atom molecular dynamics simulation for 50 ns was performed on the BSA-RT complex to investigate its conformational behavior, stability and dynamics.
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Affiliation(s)
- Anas Shamsi
- Centre for Interdisciplinary Research in basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Saleha Anwar
- Centre for Interdisciplinary Research in basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in basic Sciences, Jamia Millia Islamia, New Delhi, India.
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147
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Mohammad T, Arif K, Alajmi MF, Hussain A, Islam A, Rehman MT, Hassan I. Identification of high-affinity inhibitors of pyruvate dehydrogenase kinase-3: towards therapeutic management of cancer. J Biomol Struct Dyn 2020; 39:586-594. [DOI: 10.1080/07391102.2020.1711810] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Kaynat Arif
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md. Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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148
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Kumar B, Mohammad T, Amaduddin, Hussain A, Islam A, Ahmad F, Alajmi MF, Singh S, Pandey KC, Hassan MI, Abid M. Targeting metacaspase-3 from Plasmodium falciparum towards antimalarial therapy: A combined approach of in-silico and in-vitro investigation. J Biomol Struct Dyn 2020; 39:421-430. [PMID: 31900062 DOI: 10.1080/07391102.2019.1711194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Malaria is a global challenge, and its infection is propagated through Plasmodium falciparum, an obligate human parasite. The genome of P. falciparum encodes many proteases that play significant roles in their survival and pathogenesis thus being considered as attractive drug targets. P. falciparum metacaspase-3 (PfMCA3) is one such protease and a validated drug target to control malarial infection. First, we modeled the three-dimensional structure of PfMCA3 and predicted its ligand-binding pocket. The structural features of PfMCA3 were used for virtual screening followed by docking and molecular dynamics (MD) simulation studies to identify potent inhibitors. We used an in-house library of 513 compounds for screening to identify lead molecule fits well in the active site pocket of PfMCA3. The binding affinity and mechanism were investigated by combined docking and MD simulation studies. Docking studies reveal that the selected compounds are forming enough number of non-covalent interactions to the PfMCA3. In the enzyme inhibition assay, one of the selected compounds, H6 was found with appreciable inhibitory potential. MD simulation studies further support the binding of compound H6 with PfMCA3 and formation of a stable complex throughout the simulation trajectory. Taken together, we proposed that compound H6 is a promising lead scaffold that can be further exploited as a potential inhibitor of PfMCA3 for therapeutic management of malarial infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bhumika Kumar
- Department of Bioscience, Jamia Millia Islamia, New Delhi, India.,Protein Biochemistry and Engineering Lab, ICMR-National Institute of Malaria Research, Indian Council of Medical Research, Dwarka, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Amaduddin
- Department of Bioscience, Jamia Millia Islamia, New Delhi, India.,Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Kailash C Pandey
- Protein Biochemistry and Engineering Lab, ICMR-National Institute of Malaria Research, Indian Council of Medical Research, Dwarka, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Abid
- Department of Bioscience, Jamia Millia Islamia, New Delhi, India
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149
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Parray ZA, Ahmad F, Alajmi MF, Hussain A, Hassan MI, Islam A. Formation of molten globule state in horse heart cytochrome c under physiological conditions: Importance of soft interactions and spectroscopic approach in crowded milieu. Int J Biol Macromol 2020; 148:192-200. [PMID: 31945437 DOI: 10.1016/j.ijbiomac.2020.01.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 11/20/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 11/17/2022]
Abstract
To understand protein folding problem under physiological condition, usually taken as dilute aqueous buffer at pH 7.0 and 25 °C, knowledge of properties of folding intermediates is important, such as molten globule (MG). We observed that polyethylene glycol 400 Da (PEG 400) induces molten globule state conformation in cytochrome c at pH 7.0 and 25 °C. This PEG-induced MG state has: (i) native tertiary structure partially perturbed, (ii) unperturbed native secondary structure, (iii) newly exposed hydrophobic patches, and (iv) has 1.58 times more hydrodynamic volume than that of the native protein. Isothermal titration calorimetry and docking studies showed specific binding between PEG 400 and cytochrome c. The study delineates that PEG-protein interactions are more complex than the excluded-volume. The soft interactions need to be seriously studied in crowding milieu that leads to destabilization of protein and overcome stabilizing exclusion volume effect. This study not only can help in unraveling the mystery of steps involved in the proper folding of proteins to solve the massively complicated problems of protein folding but also provides novel insights towards importance of structural change in proteins inside cell where intermediate states of protein import-export easily via membranes rather than native form of proteins.
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Affiliation(s)
- Zahoor Ahmad Parray
- 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
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Imtaiyaz Hassan
- 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.
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Gupta P, Khan FI, Ambreen D, Lai D, Alajmi MF, Hussain A, Islam A, Ahmad F, Hassan MI. Investigation of guanidinium chloride-induced unfolding pathway of sphingosine kinase 1. Int J Biol Macromol 2020; 147:177-186. [PMID: 31917989 DOI: 10.1016/j.ijbiomac.2020.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 09/24/2019] [Revised: 01/03/2020] [Accepted: 01/04/2020] [Indexed: 01/11/2023]
Abstract
Sphingosine kinase 1 (SphK1) is a lipid kinase which plays vital role in the regulation of varieties of biological processes including, cell growth, apoptosis and mitogenesis. In the present study, we investigated the guanidinium chloride (GdmCl)-induced denaturation of SphK1 at pH 8.0 and 25 °C using two different spectroscopic probes, i.e., mean residue ellipticity at 222 nm ([θ]222) and fluorescence emission maxima (λmax). A significant overlap between the transition curves obtained from both the spectral properties indicate that GdmCl-induced unfolding of SphK1 follows two-state process i.e., Native (N) ⇌ Denatured (D) state. Interestingly, a visible protein aggregation was observed at low concentrations of GdmCl ([GdmCl] ≤ 1.5 M). The analysis of transition curves was done to estimate the thermodynamic parameters associated with the stability of SphK1. To complement our experimental findings, 100 ns molecular dynamics (MD) simulations were performed. Spectroscopic studies together with MD simulations provided mechanistic insights of unfolding pathway of SphK1 along with its stability parameters.
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Affiliation(s)
- Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Dilkash Ambreen
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - 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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