1
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Gupta D, Kumari R, Kumar M, Singh M, Rawat S, Ethayathulla AS, Kaur P. Influence of different pH milieu on the structure and function of human Aurora kinase B protein (AURK-B): Amalgamation of both spectroscopic and computational approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 312:124047. [PMID: 38394881 DOI: 10.1016/j.saa.2024.124047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024]
Abstract
Aurora kinase B (AURK-B) is a serine/threonine kinase protein that plays an essential role in chromosomal separation during the cell cycle event. AURK-B is highly expressed in various types of cancer such as human seminoma, thyroid carcinoma, non-small cell lung carcinoma (NSCLC), oral carcinoma, and gastric cancer. Hence, it is a potential therapeutic target in the treatment of various cancers. The structure of AURK-B in complex with one of its substrate inner centromeric protein (INCENP) is present, but the structural and functional characterization of native AURK-B at different pH environment is still unexplored.This study determines the effect of different pH milieu on the structure and function of AURK-B protein wherein the influence of pH on the protein conformation was probed using Circular dichroism (CD) and fluorescence spectroscopy. The structural studies were further combined with functional activity assay to observe the change in kinase activity at various pH milieu (2.0-11.0). CD and fluorescence spectroscopy experiments dictate that at high acidic conditions (pH 2.0 - 5.0), the secondary and tertiary structures of AURK-B become distorted, leading to diminished activity. The protein, however, was observed to stabilize towards pH 7.0 - 8.0 with minimal structure alteration over the basic pH range (pH 9.0 -11.0). The measured spectroscopic structural features were found to be in-line with obtained experimental kinase activity assays. Further, in-vitro experiments indicate that the enzyme is maximally active at pH 8.0. More ordered conformation and compact structure was observed at this pH (pH 8.0) as compared to other pH values through molecular dynamics simulation studies (MDS). As AURK-B localizes itself in the intracellular compartment, this study may provide a clue about the role of different pH environments in enhancing cancer growth, proliferation, and invasion.
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Affiliation(s)
- Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India
| | - Renu Kumari
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India
| | - Shivani Rawat
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India.
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2
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Alotaibi BS, Hakami MA, Anwar S, Mawkili W, Albaqami A, Hassan MI. Structure-based investigation of pyruvate dehydrogenase kinase-3 inhibitory potential of thymoquinone, targeting lung cancer therapy. Int J Biol Macromol 2024; 265:131064. [PMID: 38518935 DOI: 10.1016/j.ijbiomac.2024.131064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/05/2024] [Accepted: 03/20/2024] [Indexed: 03/24/2024]
Abstract
Protein kinases are an attractive therapeutic target for cardiovascular, cancer and neurodegenerative diseases. Cancer cells demand energy generation through aerobic glycolysis, surpassing "oxidative phosphorylation" (OXPHOS) in mitochondria. The pyruvate dehydrogenase kinases (PDKs) have many regulatory roles in energy generation balance by controlling the pyruvate dehydrogenase complex. Overexpression of PDKs is associated with the overall survival of cancer. PDK3, an isoform of PDK is highly expressed in various cancer types, is targeted for inhibition in this study. PDK3 has been shown to binds strongly with a natural compound, thymoquinone (TQ), which is known to exhibit anti-cancer potential. Detailed interaction between the PDK3 and TQ was carried out using spectroscopic and docking methods. The overall changes in the protein's structures after TQ binding were estimated by UV-Vis spectroscopy, circular dichroism and fluorescence binding studies. The kinase activity assay was also carried out to see the kinase inhibitory potential of TQ. The enzyme inhibition assay suggested an excellent inhibitory potential of TQ towards PDK3 (IC50 = 5.49 μM). We observed that TQ forms a stable complex with PDK3 without altering its structure and can be a potent PDK3 inhibitor which may be implicated in cancer therapy after desired clinical validation.
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Affiliation(s)
- Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah, Riyadh, Saudi Arabia
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah, Riyadh, Saudi Arabia
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Wedad Mawkili
- Department of Pharmacology and Toxicology, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | - Amirah Albaqami
- Department of Clinical Laboratory Sciences, Turabah University College, Taif University, Taif 21944, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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3
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Jairajpuri DS, Khan S, Anwar S, Hussain A, Alajmi MF, Hassan I. Investigating the role of thymol as a promising inhibitor of pyruvate dehydrogenase kinase 3 for targeted cancer therapy. Int J Biol Macromol 2024; 259:129314. [PMID: 38211912 DOI: 10.1016/j.ijbiomac.2024.129314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/17/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Protein kinases have emerged as major contributors to various diseases. They are currently exploited as a potential target in drug discovery because they play crucial roles in cell signaling, growth, and regulation. Their dysregulation is associated with inflammatory disorders, cancer, and neurodegenerative diseases. Pyruvate dehydrogenase kinase 3 (PDK3) has become an attractive drug target in cancer therapeutics. In the present study, we investigated the effective role of thymol in PDK3 inhibition due to the high affinity predicted through molecular docking studies. Hence, to better understand this inhibition mechanism, we carried out a 100 ns molecular dynamics (MD) simulation to analyse the dynamics and stability of the PDK3-thymol complex. The PDK3-thymol complex was stable and energetically favourable, with many intramolecular hydrogen bond interactions in the PDK3-thymol complex. Enzyme inhibition assay showed significant inhibition of PDK3 by thymol, revealing potential inhibitory action of thymol towards PDK3 (IC50 = 2.66 μM). In summary, we established thymol as one of the potential inhibitors of PDK3, proposing promising therapeutic implications for severe diseases associated with PDK3 dysregulation. This study further advances our understanding of thymol's therapeutic capabilities and potential role in cancer treatment.
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Affiliation(s)
- Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Shama Khan
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - 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
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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4
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Voura M, Anwar S, Sigala I, Parasidou E, Fragoulidou S, Hassan MI, Sarli V. Synthesis, Structural Modification, and Bioactivity Evaluation of Substituted Acridones as Potent Microtubule Affinity-Regulating Kinase 4 Inhibitors. ACS Pharmacol Transl Sci 2023; 6:1052-1074. [PMID: 37470016 PMCID: PMC10353068 DOI: 10.1021/acsptsci.3c00084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 07/21/2023]
Abstract
Acridones present numerous pharmacological activities, including inhibition of microtubule affinity-regulating kinase 4 (MARK4) kinase activity. To investigate structure-activity relationships and develop potent MARK4 inhibitors, derivatives of 2-methylacridone were synthesized and tested for their activity against MARK4 kinase. Selective substitutions at the nitrogen atom were accomplished by treating 2-methylacridone with alkyl halides in the presence of K2CO3. In addition, amidation of acridone acetic acid 11 with piperazine or tryptophan methyl ester followed by derivatization with various amines gave a series of new acridone derivatives. Among the tested compounds, six were identified as possessing high inhibitory activity against MARK4. The molecular modeling studies showed that the derivatives bearing piperazine or tryptophan bind well to the ATP-binding site of MARK4. The antiproliferative activity of six active compounds was evaluated against HeLa and U87MG cancer cells. Tryptophan derivatives 23a, 23b, and 23c showed significant cytotoxicity against both cell lines with EC50 values ranging from 2.13 to 4.22 μM, while derivatives bearing piperazine were found to be not cytotoxic. Additionally, compound 23a decreased the proliferation of human MDA-MB-435 and U251 cancer cells in the low micromolar range; however, it also affects the non-cancerous HGF cells. Due to their high binding affinity against MARK4, the synthesized compounds could be potential agents to target MARK4 against cancer and tauopathies.
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Affiliation(s)
- Maria Voura
- Laboratory
of Organic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Saleha Anwar
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ioanna Sigala
- Laboratory
of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Eleftheria Parasidou
- Laboratory
of Organic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Souzanna Fragoulidou
- Laboratory
of Organic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Md. Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Vasiliki Sarli
- Laboratory
of Organic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
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5
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Wang Y, Liu T, Xie J, Cheng M, Sun L, Zhang S, Xin J, Zhang N. A review on application of molecular simulation technology in food molecules interaction. Curr Res Food Sci 2022; 5:1873-1881. [PMID: 36276243 PMCID: PMC9579209 DOI: 10.1016/j.crfs.2022.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022] Open
Abstract
Molecular simulation is a new technology to analyze the interaction between molecules. This review mainly summarizes the application of molecular simulation technology in the food industry. This technology has been employed to assess structural changes of biomolecules, the interaction between components, and the mechanism of physical and chemical property alterations. These conclusions provide a deeper understanding of the molecular interaction mechanism in foods, break through the limitations of scientific experiments and avoid blind and time-consuming scientific research. In this paper, the advantages and development trends of molecular simulation technology in the food research field are described. This methodology can be used to contribute to further studies of the mechanism of molecular interactions in food, confirm experimental results and provide new ideas for research in the field of food sciences.
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Affiliation(s)
- Yan Wang
- Key Laboratory for Food Science & Engineering, Harbin University of Commerce, Harbin, 150076, PR China
| | - Tianjiao Liu
- Key Laboratory for Food Science & Engineering, Harbin University of Commerce, Harbin, 150076, PR China
| | - Jinhui Xie
- Key Laboratory for Food Science & Engineering, Harbin University of Commerce, Harbin, 150076, PR China
| | - Meijia Cheng
- Key Laboratory for Food Science & Engineering, Harbin University of Commerce, Harbin, 150076, PR China
| | - Lirui Sun
- Key Laboratory for Food Science & Engineering, Harbin University of Commerce, Harbin, 150076, PR China
| | - Shuai Zhang
- Key Laboratory for Food Science & Engineering, Harbin University of Commerce, Harbin, 150076, PR China
| | - Jiaying Xin
- Key Laboratory for Food Science & Engineering, Harbin University of Commerce, Harbin, 150076, PR China,State Key Laboratory for Oxo Synthesis & Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, PR China
| | - Na Zhang
- Key Laboratory for Food Science & Engineering, Harbin University of Commerce, Harbin, 150076, PR China,Corresponding author.
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6
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Anwar S, DasGupta D, Shafie A, Alhumaydhi FA, Alsagaby SA, Shahwan M, Anjum F, Al Abdulmonem W, Sharaf SE, Imtaiyaz Hassan M. Implications of tempol in pyruvate dehydrogenase kinase 3 targeted anticancer therapeutics: Computational, spectroscopic, and calorimetric studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118581] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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7
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Yousuf M, Shamsi A, Anjum F, Shafie A, Islam A, Haque QMR, Elasbali AM, Yadav DK, Hassan MI. Effect of pH on the structure and function of cyclin-dependent kinase 6. PLoS One 2022; 17:e0263693. [PMID: 35148332 PMCID: PMC8836317 DOI: 10.1371/journal.pone.0263693] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
Cyclin-dependent kinase 6 (CDK6) is an important protein kinase that regulates cell growth, development, cell metabolism, inflammation, and apoptosis. Its overexpression is associated with reprogramming glucose metabolism through alternative pathways and apoptosis, which ultimately plays a significant role in cancer development. In the present study, we have investigated the structural and conformational changes in CDK6 at varying pH employing a multi-spectroscopic approach. Circular dichroism (CD) spectroscopy revealed at extremely acidic conditions (pH 2.0–4.0), the secondary structure of CDK6 got significantly disrupted, leading to aggregates formation. These aggregates were further characterized by employing Thioflavin T (ThT) fluorescence. No significant secondary structural changes were observed over the alkaline pH range (pH 7.0–11.0). Further, fluorescence and UV spectroscopy revealed that the tertiary structure of CDK6 was disrupted under extremely acidic conditions, with slight alteration occurring in mild acidic conditions. The tertiary structure remains intact over the entire alkaline range. Additionally, enzyme assay provided an insight into the functional aspect of CDK at varying pH; CDK6 activity was optimal in the pH range of 7.0–8.0. This study will provide a platform that provides newer insights into the pH-dependent dynamics and functional behavior of CDK6 in different CDK6 directed diseased conditions, viz. different types of cancers where changes in pH contribute to cancer development.
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Affiliation(s)
- Mohd Yousuf
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | | | - Abdelbaset Mohamed Elasbali
- Clinical Laboratory Science, College of Applied Medical Sciences-Qurayyat, Jouf University, Sakaka, Saudi Arabia
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Incheon City, South Korea
- * E-mail: (DKY); (MIH)
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- * E-mail: (DKY); (MIH)
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8
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An identification of MARK inhibitors using high throughput MALDI-TOF mass spectrometry. Biomed Pharmacother 2021; 146:112549. [PMID: 34923338 DOI: 10.1016/j.biopha.2021.112549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 01/06/2023] Open
Abstract
MAP/microtubule affinity-regulating kinases (MARKs) were recently identified as potential drug targets for Alzheimer's disease (AD) due to their role in pathological hyperphosphorylation of tau protein. Hyperphosphorylated tau has decreased affinity for microtubule binding, impairing their stability and associated functions. Destabilization of microtubules in neuronal cells leads to neurodegeneration, and microtubule-unbound tau forms neurofibrillary tangles, one of the primary hallmarks of AD. Many phosphorylation sites of tau protein have been identified, but phosphorylation at Ser262, which occurs in early stages of AD, plays a vital role in the pathological hyperphosphorylation of tau. It has been found that Ser262 is phosphorylated by MARK4, which is currently an intensively studied target for treating Alzheimer's disease and other neurodegenerative diseases. Our present study aimed to develop a high throughput compatible assay to directly detect MARK enzymatic activity using echoacoustic transfer and MALDI-TOF mass spectrometer. We optimized the assay for all four isoforms of MARK and validated its use for identifying potential inhibitors by the screening of 1280 compounds from the LOPAC®1280 International (Library Of Pharmacologically Active Compounds). Six MARK4 inhibitors with IC50 < 1 µM were identified. To demonstrate their therapeutic potential, active compounds were further tested for MARK4 selectivity and ability to cross the blood-brain barrier. Lastly, the molecular docking with the most active inhibitors to predict their interaction with MARK4 was performed.
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9
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Oyewusi HA, Huyop F, Wahab RA, Hamid AAA. In silico assessment of dehalogenase from Bacillus thuringiensis H2 in relation to its salinity-stability and pollutants degradation. J Biomol Struct Dyn 2021; 40:9332-9346. [PMID: 34014147 DOI: 10.1080/07391102.2021.1927846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Increased scientific interest has led to the rise in biotechnological uses of halophilic and halotolerant microbes for hypersaline wastewater bioremediation. Hence, this study performed molecular docking, molecular dynamic (MD) simulations, and validation by Molecular Mechanic Poisson-Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis H2. We aimed to identify the interactions of DehH2 with substrates haloacids, haloacetates, and chlorpyrifos under extreme salinity (35% NaCl). MD simulations revealed that DehH2 preferentially degraded haloacids and haloacetates (-6.3 to -4.7 kcal/mol) by forming three or four hydrogen bonds to the catalytic triad, Asp125, Arg201, and Lys202. Conversely, chlorpyrifos was the least preferred substrate in both MD simulations and MM-PBSA calculations. MD simulation results ranked the DehH2-L-2CP complex (RMSD □0.125-0.23 nm) as the most stable while the least was the DehH2-chlorpyrifos complex (RMSD 0.32 nm; RMSF 0.0 - 0.29). The order of stability was as follows: DehH2-L-2CP > DehH2-MCA > DehH2-D-2CP > DehH2-3CP > DehH2-2,2-DCP > DehH2-2,3-DCP > DehH2-TCA > DehH2-chlorpyrifos. The MM-PBSA calculations further affirmed the DehH2-L-2CP complex's highest stability with the lowest binding energy of -45.14 kcal/mol, followed closely by DehH2-MCA (-41.21 kcal/mol), DehH2-D-2CP (-31.59 kcal/mol), DehH2-3CP (-30.75 kcal/mol), DehH2-2,2- DCP (-29.72 kcal/mol), DehH2-2,3-DCP (-22.20 kcal/mol) and DehH2-TCA (-18.46 kcal/mol). The positive binding energy of the DehH2-chlorpyrifos complex (+180.57 kcal/mol) proved the enzyme's non-preference for the substrate. The results ultimately illustrated the unique specificity of the DehH2 to degrade the above-said pollutants under a hypersaline condition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan Pahang, Malaysia
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10
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Motiei M, Mirahmadi-Zare SZ, Nasr-Esfahani MH. Chemical stabilization of γ-polyglutamate by chitosan and the effect of co-solvents on the stability. Biophys Chem 2021; 275:106605. [PMID: 33964508 DOI: 10.1016/j.bpc.2021.106605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 12/23/2022]
Abstract
In protein-based formulations, conformational distortions and attractive interactions may cause insoluble and undesired aggregates. In the case of ionic peptides, including cationic or anionic, commonly electrostatic interactions are the main factors that control structure assembling. In this study, it was proposed that grafting of chitosan (CS) to γ-polyglutamic acid (γ-PGA) might exhibit much strong inhibiting effect on the formation of protein aggregates due to multiple amino groups and hydrophilic properties. To guarantee stable and safe biopharmaceutical formulation, the potency of a variety of stabilizers including sugars (glucose, sucrose), polyols (sorbitol, glycerol), surfactant (Tween 20), salting-out salt (PBS), and also different pH values have been evaluated on stabilizing or destabilizing the native state of CS-g-PGA copolymer using FTIR, CD, DLS, and SDS-PAGE. The comparable analysis revealed that the stability of CS-g-PGA was strongly dependent on pH owing to the polyelectrolyte characteristics of the polymers. Altogether these results implied that CS at optimized conditions might be an important precursor for the pharmaceutical industry and function as a new polymer for aggregation suppression and protein stabilization.
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Affiliation(s)
- Marjan Motiei
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, 8159358686 Isfahan, Iran; Centre of Polymer Systems, Tomas Bata University in Zlín, Třída Tomáše Bati 5678, 76001 Zlín, Czech Republic
| | - Seyede Zohreh Mirahmadi-Zare
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, 8159358686 Isfahan, Iran.
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, 8159358686 Isfahan, Iran
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11
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Li Y, Qiao B, Olvera de la Cruz M. Protein Surface Printer for Exploring Protein Domains. J Chem Inf Model 2020; 60:5255-5264. [PMID: 32846088 DOI: 10.1021/acs.jcim.0c00582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.
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Affiliation(s)
- Yang Li
- Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60201, United States
| | - Baofu Qiao
- Department of Material Science and Engineering, Northwestern University, Evanston, Illinois 60201, United States
| | - Monica Olvera de la Cruz
- Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60201, United States.,Department of Material Science and Engineering, Northwestern University, Evanston, Illinois 60201, United States.,Department of Chemistry, Northwestern University, Evanston, Illinois 60201, United States
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12
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Roy S, Mahapatra AD, Mohammad T, Gupta P, Alajmi MF, Hussain A, Rehman MT, Datta B, Hassan MI. Design and Development of Novel Urea, Sulfonyltriurea, and Sulfonamide Derivatives as Potential Inhibitors of Sphingosine Kinase 1. Pharmaceuticals (Basel) 2020; 13:E118. [PMID: 32526899 PMCID: PMC7346089 DOI: 10.3390/ph13060118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 12/17/2022] Open
Abstract
Sphingosine kinase 1 (SphK1) is one of the well-studied drug targets for cancer and inflammatory diseases. Recently discovered small-molecule inhibitors of SphK1 have been recommended in cancer therapeutics; however, selectivity and potency of first-generation inhibitors are great challenge. In search of effective SphK1 inhibitors, a set of small molecules have been designed and synthesized bearing urea, sulfonylurea, sulfonamide, and sulfonyltriurea groups. The binding affinity of these inhibitors was measured by fluorescence-binding assay and isothermal titration calorimetry. Compounds 1, 5, 6, and 7 showed an admirable binding affinity to the SphK1 in the sub-micromolar range and significantly inhibited SphK1 activity with admirable IC50 values. Molecular docking studies revealed that these compounds fit well into the sphingosine binding pocket of SphK1 and formed significant number of hydrogen bonds and van der Waals interactions. These molecules may be exploited as potent and selective inhibitors of SphK1 that could be implicated in cancer therapeutics after the required in vivo validation.
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Affiliation(s)
- Sonam Roy
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.R.); (T.M.); (P.G.)
| | - Amarjyoti Das Mahapatra
- Department of Chemistry, Indian Institute of Technology, Palaj, Gandhinagar, Gujarat 382355, India;
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.R.); (T.M.); (P.G.)
| | - Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.R.); (T.M.); (P.G.)
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.); (M.T.R.)
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.); (M.T.R.)
| | - Md. Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.); (M.T.R.)
| | - Bhaskar Datta
- Department of Chemistry, Indian Institute of Technology, Palaj, Gandhinagar, Gujarat 382355, India;
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.R.); (T.M.); (P.G.)
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MARK4 Inhibited by AChE Inhibitors, Donepezil and Rivastigmine Tartrate: Insights into Alzheimer's Disease Therapy. Biomolecules 2020; 10:biom10050789. [PMID: 32443670 PMCID: PMC7277793 DOI: 10.3390/biom10050789] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 12/26/2022] Open
Abstract
Microtubule affinity-regulating kinase (MARK4) plays a key role in Alzheimer’s disease (AD) development as its overexpression is directly linked to increased tau phosphorylation. MARK4 is a potential drug target of AD and is thus its structural features are employed in the development of new therapeutic molecules. Donepezil (DP) and rivastigmine tartrate (RT) are acetylcholinesterase (AChE) inhibitors and are used to treat symptomatic patients of mild to moderate AD. In keeping with the therapeutic implications of DP and RT in AD, we performed binding studies of these drugs with the MARK4. Both DP and RT bound to MARK4 with a binding constant (K) of 107 M−1. The temperature dependency of binding parameters revealed MARK−DP complex to be guided by static mode while MARK−RT complex to be guided by both static and dynamic quenching. Both drugs inhibited MARK4 with IC50 values of 5.3 μM (DP) and 6.74 μM (RT). The evaluation of associated enthalpy change (ΔH) and entropy change (ΔS) implied the complex formation to be driven by hydrogen bonding making it seemingly strong and specific. Isothermal titration calorimetry further advocated a spontaneous binding. In vitro observations were further complemented by the calculation of binding free energy by molecular docking and interactions with the functionally-important residues of the active site pocket of MARK4. This study signifies the implications of AChE inhibitors, RT, and DP in Alzheimer’s therapy targeting MARK4.
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Anwar S, Mohammad T, Shamsi A, Queen A, Parveen S, Luqman S, Hasan GM, Alamry KA, Azum N, Asiri AM, Hassan MI. Discovery of Hordenine as a Potential Inhibitor of Pyruvate Dehydrogenase Kinase 3: Implication in Lung Cancer Therapy. Biomedicines 2020; 8:E119. [PMID: 32422877 PMCID: PMC7277448 DOI: 10.3390/biomedicines8050119] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 11/16/2022] Open
Abstract
Design and development of potential pyruvate dehydrogenase kinase 3 (PDK3) inhibitors have gained attention because of their possible therapeutic uses in lung cancer therapy. In the present study, the binding affinity of naturally occurring alkaloids, hordenine, vincamine, tryptamine, cinchonine, and colcemid was measured with PDK3. The molecular docking and fluorescence binding studies suggested that all these compounds show a considerable binding affinity for PDK3. Among them, the affinity of hordenine to the PDK3 was excellent (K = 106 M-1) which was further complemented by isothermal titration calorimetric measurements. Hordenine binds in the active site pocket of PDK3 and forms a significant number of non-covalent interactions with functionally important residues. All-atom molecular dynamics (MD) simulation study suggested that the PDK3-hordenine complex is stabilized throughout the trajectory of 100ns and leads to fewer conformational changes. The enzyme inhibition studies showed that hordenine inhibits the activity of PDK3 with an IC50 value of 5.4 µM. Furthermore, hordenine showed a cytotoxic effect on human lung cancer cells (A549 and H1299) with an admirable IC50 value. However, it did not inhibit the growth of HEK293 cells up to 200 µM, indicating its non-toxicity to non-cancerous cell lines. In summary, our findings provide the basis for the therapeutic implication of hordenine and its derivatives in lung cancer and PDK3-related diseases after required in vivo validation.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
| | - Aarfa Queen
- Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India;
| | - Shahnaz Parveen
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.P.); (S.L.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suaib Luqman
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.P.); (S.L.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia;
| | - Khalid A. Alamry
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (K.A.A.); (N.A.); (A.M.A.)
| | - Naved Azum
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (K.A.A.); (N.A.); (A.M.A.)
| | - Abdullah M. Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (K.A.A.); (N.A.); (A.M.A.)
- Center of Excellence for Advanced Materials Research (CEAMR), King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
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