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Khalid Zia M, Siddiqui T, Ansari S, Muaz M, Ahsan H, Halim Khan F. Insight into the molecular interaction between the anticancer drug, enzalutamide and human alpha-2-macroglobulin: Biochemical and biophysical approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 311:123957. [PMID: 38310741 DOI: 10.1016/j.saa.2024.123957] [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: 10/19/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/06/2024]
Abstract
The drug pharmacokinetics is affected upon binding with proteins, thus making drug-protein interactions crucial. This study investigated the interaction between enzalutamide and human major antiproteinase alpha-2-macroglobulin (α2M) by using multi spectroscopic and calorimetric techniques. The spectroscopic techniques such as circular dichroism (CD), intrinsic fluorescence, and UV-visible absorption were used to determine the mechanism of enzalutamide-α2M interaction. Studies on the quenching of fluorescence at three different temperatures showed that the enzalutamide-α2M complex is formed through static quenching mechanism. The change in microenvironment around tyrosine residues in protein was detected through synchronised fluorescence. The secondary structure of α2M was slightly altered by enzalutamide according to far UV-CD spectral analysis. Changes in position of amide I band in FTIR spectra further confirm the secondary structural alteration in α2M. According to thermodynamic characteristics such as fluorescence quenching and isothermal titration calorimetry (ITC), hydrogen bonds and hydrophobic interactions were involved in the interaction machanism. The ITC reiterated the exothermic and spontaneous nature of the interaction. The lower proteinase inhibitory activity of the α2M-enzalutamide conjugate as reflects the disruption of the native α2M structure upon interaction with enzalutamide.
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Affiliation(s)
- Mohammad Khalid Zia
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Tooba Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Sana Ansari
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Muaz
- Interdisciplinary Nanotechnology Centre, Aligarh Muslim University, Aligarh 202002, India
| | - Haseeb Ahsan
- Department of Biochemistry, Faculty of Dentistry, Jamia Millia Islamia, New Delhi 110025, India
| | - Fahim Halim Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
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Siddique F, Anwaar A, Bashir M, Nadeem S, Rawat R, Eyupoglu V, Afzal S, Bibi M, Bin Jardan YA, Bourhia M. Revisiting methotrexate and phototrexate Zinc15 library-based derivatives using deep learning in-silico drug design approach. Front Chem 2024; 12:1380266. [PMID: 38576849 PMCID: PMC10991842 DOI: 10.3389/fchem.2024.1380266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/05/2024] [Indexed: 04/06/2024] Open
Abstract
Introduction: Cancer is the second most prevalent cause of mortality in the world, despite the availability of several medications for cancer treatment. Therefore, the cancer research community emphasized on computational techniques to speed up the discovery of novel anticancer drugs. Methods: In the current study, QSAR-based virtual screening was performed on the Zinc15 compound library (271 derivatives of methotrexate (MTX) and phototrexate (PTX)) to predict their inhibitory activity against dihydrofolate reductase (DHFR), a potential anticancer drug target. The deep learning-based ADMET parameters were employed to generate a 2D QSAR model using the multiple linear regression (MPL) methods with Leave-one-out cross-validated (LOO-CV) Q2 and correlation coefficient R2 values as high as 0.77 and 0.81, respectively. Results: From the QSAR model and virtual screening analysis, the top hits (09, 27, 41, 68, 74, 85, 99, 180) exhibited pIC50 ranging from 5.85 to 7.20 with a minimum binding score of -11.6 to -11.0 kcal/mol and were subjected to further investigation. The ADMET attributes using the message-passing neural network (MPNN) model demonstrated the potential of selected hits as an oral medication based on lipophilic profile Log P (0.19-2.69) and bioavailability (76.30% to 78.46%). The clinical toxicity score was 31.24% to 35.30%, with the least toxicity score (8.30%) observed with compound 180. The DFT calculations were carried out to determine the stability, physicochemical parameters and chemical reactivity of selected compounds. The docking results were further validated by 100 ns molecular dynamic simulation analysis. Conclusion: The promising lead compounds found endorsed compared to standard reference drugs MTX and PTX that are best for anticancer activity and can lead to novel therapies after experimental validations. Furthermore, it is suggested to unveil the inhibitory potential of identified hits via in-vitro and in-vivo approaches.
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Affiliation(s)
- Farhan Siddique
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Ahmar Anwaar
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Maryam Bashir
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
- Southern Punjab Institute of Health Sciences, Multan, Pakistan
| | - Sumaira Nadeem
- Department of Pharmacy, The Women University, Multan, Pakistan
| | - Ravi Rawat
- School of Health Sciences & Technology, UPES University, Dehradun, India
| | - Volkan Eyupoglu
- Department of Chemistry, Cankırı Karatekin University, Cankırı, Türkiye
| | - Samina Afzal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Mehvish Bibi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
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Xie J, Kim HM, Kamada K, Oh JM. Blood Compatibility of Drug-Inorganic Hybrid in Human Blood: Red Blood Cell Hitchhiking and Soft Protein Corona. MATERIALS (BASEL, SWITZERLAND) 2023; 16:6523. [PMID: 37834660 PMCID: PMC10573551 DOI: 10.3390/ma16196523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/16/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
A drug-delivery system consisting of an inorganic host-layered double hydroxide (LDH)-and an anticancer drug-methotrexate (MTX)-was prepared via the intercalation route (MTX-LDH), and its hematocompatibility was investigated. Hemolysis, a red blood cell counting assay, and optical microscopy revealed that the MTX-LDH had no harmful toxic effect on blood cells. Both scanning electron microscopy and atomic force microscopy exhibited that the MTX-LDH particles softly landed on the concave part inred blood cells without serious morphological changes of the cells. The time-dependent change in the surface charge and hydrodynamic radius of MTX-LDH in the plasma condition demonstrated that the proteins can be gently adsorbed on the MTX-LDH particles, possibly through protein corona, giving rise to good colloidal stability. The fluorescence quenching assay was carried out to monitor the interaction between MTX-LDH and plasma protein, and the result showed that the MTX-LDH had less dynamic interaction with protein compared with MTX alone, due to the capsule moiety of the LDH host. It was verified by a quartz crystal microbalance assay that the surface interaction between MTX-LDH and protein was reversible and reproducible, and the type of protein corona was a soft one, having flexibility toward the biological environment.
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Affiliation(s)
- Jing Xie
- Department of Energy and Materials Engineering, Dongguk University-Seoul, Seoul 04620, Republic of Korea;
| | - Hyoung-Mi Kim
- Biomedical Manufacturing Technology Center, Daegyeong Division, Korea Institute of Industrial Technology (KITECH), Yeongcheon-si 38822, Republic of Korea;
| | - Kai Kamada
- Department of Materials Science and Engineering, Faculty of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Jae-Min Oh
- Department of Energy and Materials Engineering, Dongguk University-Seoul, Seoul 04620, Republic of Korea;
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Zia MK, Siddiqui T, Ahsan H, Khan FH. Comprehensive insight into the molecular interaction of an anticancer drug-ifosfamide with human alpha-2-macroglobulin: biophysical and in silico studies. J Biomol Struct Dyn 2022; 40:3907-3916. [PMID: 33267704 DOI: 10.1080/07391102.2020.1852115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Ifosfamide is an active alkylating chemotherapeutic drug chemically related to nitrogen mustard. The pharmacokinetics of drugs is affected upon binding with protein, making the studies on drug-protein interaction promising. The present study investigates the interaction between ifosfamide and human antiproteinase-alpha-2-macroglobulin (α2M) by using multi-spectroscopic and in silico techniques. The UV-visible absorption, intrinsic fluorescence and circular dichroism (CD) spectroscopic methods were employed to unveil the mode and mechanism of ifosfamide-α2M interaction. Fluorescence quenching studies performed at three different temperatures indicated that ifosfamide-α2M complex formation involves static quenching. Far UV-CD spectra revealed a minor alteration in the secondary structure of α2M instigated by ifosfamide. The thermodynamic parameters determined by fluorescence quenching experiment and isothermal titration calorimetry (ITC) suggested that the complex between ifosfamide and α2M involves hydrogen bonding and hydrophobic interactions. Molecular docking illustrates that ifosfamide binds with moderate affinity to Lys1240, Asn173, Ser957, Leu955, Asp953, Lys1216 and Thr1236 residues during the interaction. Molecular dynamic (MD) simulation suggested that the ifosfamide forms a stable complex with α2M. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Khalid Zia
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Tooba Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Haseeb Ahsan
- Faculty of Dentistry, Department of Biochemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Fahim Halim Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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Calapoglu F, Sahin S, Ozmen I, Ozbek Yazici S. Investigation of interaction between dexamethasone/pheniramine and trypsin by fluorescence, UV-vis, CD, and molecular docking. J Biomol Struct Dyn 2022; 41:2202-2210. [PMID: 35098895 DOI: 10.1080/07391102.2022.2029565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Antihistamines and glucocorticoids are commonly used to treat allergy symptoms and the inflammatory conditions. In present study, the in-vitro binding interactions a glucocortikoid, dexamethasone/an antihistamine, pheniramine with TSN (TSN) secreted from pancreas to small intestine for protein digestion were investigated by fluorescence emission spectroscopy (FES), UV-Vis spectroscopy, synchronous fluorescence spectroscopy (SFS), CD spectroscopy, FT-IR and molecular modeling methods. Also, the effect of these drugs on the catalytic activity of trypsin (TSN) was determined. The fluorescence quenching experiments indicated that each drugs quenched the intrinsic fluorescence of TSN with their increased concentrations. The results of SFS and UV-Vis spectra proved the interaction of dexamethasone and pheniramine with TSN. CD spectra showed that the secondary structure of enzyme was altered in the presence of the drugs. All these spectroscopy results were validated and explained by molecular docking and molecular dynamic simulation (MD) studies. The IC50 values were determined as 0.0049 mM and 0.0038 mM for dexamethasone and pheniramine, respectively. So, both drugs have inhibition effect on the catalytic activity of TSN. The results of this study can provide valuable information in the field of pharmacokinetics and pharmacodynamics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Furkan Calapoglu
- Faculty of Arts and Sciences, Department of Chemistry, Suleyman Demirel University, Cunur, Isparta, Turkey
| | - Selmihan Sahin
- Faculty of Arts and Sciences, Department of Chemistry, Suleyman Demirel University, Cunur, Isparta, Turkey
| | - Ismail Ozmen
- Faculty of Arts and Sciences, Department of Chemistry, Suleyman Demirel University, Cunur, Isparta, Turkey
| | - Sercan Ozbek Yazici
- Faculty of Health Sciences, Department of Nutrition and Dietetics, Burdur Mehmet Akif Ersoy University, Istiklal Yerleskesi, Burdur, Turkey
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Jourdi G, Abdoul J, Siguret V, Decleves X, Frezza E, Pailleret C, Gouin-Thibault I, Gandrille S, Neveux N, Samama CM, Pasquali S, Gaussem P. Induced forms of α 2-macroglobulin neutralize heparin and direct oral anticoagulant effects. Int J Biol Macromol 2021; 184:209-217. [PMID: 34126147 DOI: 10.1016/j.ijbiomac.2021.06.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
Alpha2-macroglobulin (α2M) is a physiological macromolecule that facilitates the clearance of many proteinases, cytokines and growth factors in human. Here, we explored the effect of induced forms of α2M on anticoagulant drugs. Gla-domainless factor Xa (GDFXa) and methylamine (MA)-induced α2M were prepared and characterized by electrophoresis, immunonephelometry, chromogenic, clot waveform and rotational thromboelastometry assays. Samples from healthy volunteers and anticoagulated patients were included. In vivo neutralization of anticoagulants was evaluated in C57Bl/6JRj mouse bleeding-model. Anticoagulant binding sites on induced α2M were depicted by computer-aided energy minimization modeling. GDFXa-induced α2M neutralized dabigatran and heparins in plasma and whole blood. In mice, a single IV dose of GDFXa-induced α2M following anticoagulant administration significantly reduced blood loss and bleeding time. Being far easier to prepare, we investigated the efficacy of MA-induced α2M. It neutralized rivaroxaban, apixaban, dabigatran and heparins in spiked samples in a concentration-dependent manner and in samples from treated patients. Molecular docking analysis evidenced the ability of MA-induced α2M to bind non-covalently these compounds via some deeply buried binding sites. Induced forms of α2M have the potential to neutralize direct oral anticoagulants and heparins, and might be developed as a universal antidote in case of major bleeding or urgent surgery.
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Affiliation(s)
- Georges Jourdi
- Université de Paris, Innovative Therapies in Haemostasis, INSERM UMR_S1140, F-75006, Paris, France; AP-HP. Centre-Université de Paris, Hôpital Cochin, F-75014, Paris, France; Research Centre, Montreal Heart Institute, University of Montreal, Faculty of Pharmacy, Montreal, Canada.
| | - Johan Abdoul
- Université de Paris, Innovative Therapies in Haemostasis, INSERM UMR_S1140, F-75006, Paris, France
| | - Virginie Siguret
- Université de Paris, Innovative Therapies in Haemostasis, INSERM UMR_S1140, F-75006, Paris, France; AP-HP. Nord-Université de Paris, Hôpital Lariboisière, F-75010 Paris, France
| | - Xavier Decleves
- AP-HP. Centre-Université de Paris, Hôpital Cochin, F-75014, Paris, France; Université de Paris, Variabilité de réponse aux psychotropes, INSERM UMR_S1144, F-75006 Paris, France
| | - Elisa Frezza
- Laboratoire CiTCoM, Université de Paris, CNRS, F-75006 Paris, France
| | - Claire Pailleret
- Université de Paris, Innovative Therapies in Haemostasis, INSERM UMR_S1140, F-75006, Paris, France; Clinique du Mont Louis, F-75011 Paris, France
| | - Isabelle Gouin-Thibault
- Laboratoire d'hématologie, CHU Pontchaillou, Université de Rennes 1, CIC-Inserm1414, F-35000 Rennes, France
| | - Sophie Gandrille
- Université de Paris, Innovative Therapies in Haemostasis, INSERM UMR_S1140, F-75006, Paris, France; AP-HP. Centre-Université de Paris, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - Nathalie Neveux
- AP-HP. Centre-Université de Paris, Hôpital Cochin, F-75014, Paris, France
| | - Charles Marc Samama
- Université de Paris, Innovative Therapies in Haemostasis, INSERM UMR_S1140, F-75006, Paris, France; AP-HP. Centre-Université de Paris, Hôpital Cochin, F-75014, Paris, France
| | - Samuela Pasquali
- Laboratoire CiTCoM, Université de Paris, CNRS, F-75006 Paris, France
| | - Pascale Gaussem
- Université de Paris, Innovative Therapies in Haemostasis, INSERM UMR_S1140, F-75006, Paris, France; AP-HP. Centre-Université de Paris, Hôpital Européen Georges Pompidou, F-75015 Paris, France.
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Antipsychotic clozapine binding to alpha-2-macroglobulin protects interacting partners against oxidation and preserves the anti-proteinase activity of the protein. Int J Biol Macromol 2021; 183:502-512. [PMID: 33930446 DOI: 10.1016/j.ijbiomac.2021.04.155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 12/20/2022]
Abstract
In this study, the interaction between clozapine, an atypical antipsychotic drug, and alpha-2-macroglobulin (α2M), a multipurpose anti-proteinase, was investigated under simulated (patho) physiological conditions using multiple spectroscopic techniques and molecular modeling. It was found that α2M binds clozapine with a moderate affinity (the binding constant of 0.9 × 105 M-1 at 37 °C). The preferable binding site for both clozapine's atropisomers was revealed to be a large pocket at the interface of C and D monomer subunits of the protein. Hydrogen bonds and the hydrophobic effect were proposed as dominant forces in complex formation. The binding of clozapine did not induce significant conformational change of the protein, as confirmed by virtually unaltered α2M secondary structure and anti-proteinase activity. However, both clozapine and α2M shielded each other from the deleterious influence of strong oxidants: sodium hypochlorite and 2,2'-azobis-2-methyl-propanimidamide dihydrochloride (AAPH). Moreover, clozapine in a concentration range that is usually targeted in the plasma during patients' treatment effectively protected the anti-proteinase activity of α2M under AAPH-induced free radical overproduction. Our results suggest that the cooperation between α2M and clozapine may be a path by which these two molecules synergistically protect neural tissue against injury caused by disturbed proteostasis or oxidative stress.
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Zia MK, Siddiqui T, Ahsan H, Khan FH. Characterization of the binding between anti-tumor drug 5-fluorouracil and human alpha-2-macroglobulin: spectroscopic and molecular docking analyses. J Biomol Struct Dyn 2021; 40:7949-7959. [PMID: 33798029 DOI: 10.1080/07391102.2021.1905550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
5-Fluorouracil (5-FU) is a well-recognized anticancer drug used in the treatment of tumors of head, neck and breast. Drug pharmacokinetics is affected upon binding with protein, thus, making drug-protein interactions imperative to study. Present work investigates the interaction between 5-FU and human major antiproteinase-alpha-2-macroglobulin (α2M) by multi-spectroscopic, calorimetric and molecular docking techniques. UV/Visible absorption, intrinsic fluorescence and circular dichroism (CD) spectroscopic methods have been employed to unveil the mode and mechanism of 5-FU-α2M interaction. Synchronous fluorescence showed alteration in the microenvironment of tryptophan and tyrosine residues of protein. Far UV-CD spectra suggest slight alterations in the secondary structure of α2M by 5-FU. Thermodynamic parameters determined by fluorescence quenching experiments and isothermal titration calorimetry (ITC) suggested the involvement of hydrogen bonds and hydrophobic interactions. Moreover, ITC corroborate the spontaneous and exothermic nature of the interaction process. Molecular docking illustrates that 5-FU binds with moderate affinity and Asp953, Tyr1264, Lys1236, Thr1232, Tyr1323 and Leu951 were the main residues involved. Molecular dynamics simulation studies suggested that 5-FU was stabilizing the α2M structure and forming a stable complex. It was concluded that 5-FU lower the antiproteolytic activity of α2M significantly and causes disruption in the native structure and conformation of α2M.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Khalid Zia
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Tooba Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Haseeb Ahsan
- Department of Biochemistry, Faculty of Dentistry, Jamia Millia Islamia, New Delhi, India
| | - Fahim Halim Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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